ch5m3d-1.2.5+dfsg/0000755000175000017500000000000012234705413013720 5ustar georgeskgeorgeskch5m3d-1.2.5+dfsg/CHANGELOG.txt0000644000175000017500000000211012230555426015745 0ustar georgeskgeorgeskCH5M3D 1.2.2, 2013-06-27 ------------------------ - Added ability to include more than one gallery on a single web page. - Fixed bug with deleting attached hydrogen atoms. - Removed "view-only" javascript library. All files in variations folder now call main library. (It was not documented which functions were missing from this library, and the size reduction was minimal). CH5M3D 1.2.1, 2013-06-24 ------------------------ - Added a number of web pages to the variations folder to provide more examples illustrating ways this library can be used to create web pages. Most notable addition was a gallery page showing multiple floating boxes and a sample script that creates mirror images of 2-butanol. - Updated sections of the documentation to better describe some user-accessible functions. CH5M3D 1.2, 2013-06-10 ----------------------- - Fixed a number of bugs. Most notable changes in routine to calculate charges. CH5M3D 1.1, 2013-04-10 ---------------------- - Development version. Never released. CH5M3D 1.0, 2013-03-13 ---------------------- - Initial release ch5m3d-1.2.5+dfsg/ch5m3d.css0000644000175000017500000000565312230555424015527 0ustar georgeskgeorgesk.QCHeader { margin: 0; color: navy; /* #FFB800 */ font-size: 24px; font-weight: bold; text-align: center; } .SFHeader { color: navy; /* #FFB800 */ font-size: 24px; font-weight: bold; text-align: left; } .SFHeader a { padding-right: 100px; } #Toolbar { width: 95%; height: 1em; padding: 10px 5px; list-style: none; font-size: 16px; font-weight: normal; background-color: navy; } #Toolbar ul { height: 0.5em; } #Toolbar li { float: left; width: 10em; height: 1.5em; padding: 0 20px; list-style: none; background-color: navy; color: yellow; } #Toolbar li ul { position: absolute; width: 10em; padding: 0; left: -999em; } #Toolbar li:hover ul { left: auto; } #Toolbar a { display: block; margin: 0; text-align: left; text-decoration: none; font-weight: normal; color: white; } #Toolbar a:hover { font-weight: normal; color: navy; background-color: lightsteelblue; } div.BrowserTest { width: 40%; margin: 0 auto; padding: 3px; border: 3px solid black; text-align: center; background-color: red; } div.Footer { width: 98%; padding: 5px; margin: 30px auto 0 auto; border-top: 3px solid #1729B0; text-align: center; color: navy; font-size: 12px; font-weight: bold; text-align: center; } textarea { resize:both; /* none|horizontal|vertical|both */ } br { clear: left; } P.clear { clear: both; float: none; height: 1px; } P.indent { text-indent: 3em; } div.viewDiv { visibility: visible; display: inline; } div.drawDiv { visibility: visible; display: none; } .drawWin { /* width: 510px; */ clear: both; float: left; padding: 5px; } P.fleft { padding: 0px 40px 0px 0px; float: left; } P.center { text-align: center; font-size: 16px; font-family: Times-Roman,Bookman,serif; font-weight: normal; font-variant: small-caps; padding: 0px; color: navy; } P.center a { text-decoration: none; color: navy; } td { text-align: center; } .modeTab { background-color: silver; } .Button { background-color: silver; } .plabel { background-color: antiquewhite; display: table-cell; color: navy; } .MOff { background-color: antiquewhite; display: table-cell; color: antiquewhite; } .MOn { background-color: antiquewhite; display: table-cell; color: navy; } .Row { background-color: antiquewhite; display: none; } .main { background-color: silver; } .metl { background-color: silver; display: none; } table.center { text-align: center; margin-left: auto; margin-right: auto; } div.gallery { clear: both; } div.galleryframe { float:left; width:300px; padding:10px; border:2px solid navy; margin: 5px; background: #eee; } div.screenshot { padding:5px 5px; width: 210px; float: left; text-align: center; } div.logo { padding: 0px 10px; float: left; text-align: center; } P.author { clear: both; margin-left: 3em; } ch5m3d-1.2.5+dfsg/molecules/0000755000175000017500000000000012230555426015713 5ustar georgeskgeorgeskch5m3d-1.2.5+dfsg/molecules/adamantane.xyz0000755000175000017500000000221412230555426020562 0ustar georgeskgeorgesk26 Molecular coordinates generated by CH5M3D. C -0.9076 1.2422 -0.8447 C -1.3788 0.5020 0.3965 C 0.4712 0.7402 -1.2412 H -0.8595 2.2913 -0.6377 H -1.5950 1.0679 -1.6466 H -2.3495 0.8554 0.6755 C -1.4472 -0.9877 0.1026 C -0.4028 0.7495 1.5351 H 0.8029 1.2612 -2.1149 C 1.4472 0.9877 -0.1026 C 0.4028 -0.7496 -1.5351 H 2.4179 0.6343 -0.3816 H 1.4954 2.0364 0.1043 H -0.7345 0.2285 2.4088 C 0.9760 0.2475 1.1387 H -0.3547 1.7983 1.7420 H 1.6631 0.4218 1.9402 C 0.9077 -1.2422 0.8448 H -1.7789 -1.5088 0.9763 H -2.1343 -1.1620 -0.6990 H 1.8783 -1.5956 0.5657 H 0.5760 -1.7633 1.7185 H 1.3735 -1.1030 -1.8142 C -0.0683 -1.4898 -0.2939 H -0.2843 -0.9238 -2.3366 H -0.1165 -2.5385 -0.5008 ch5m3d-1.2.5+dfsg/molecules/cyclohexane.xyz0000755000175000017500000000150612230555426020776 0ustar georgeskgeorgesk18 C6 H12 (xyz format) generated by CH5M3D. C -1.5341 -0.2896 0.0621 C -0.6932 0.0388 1.2850 C -0.9657 0.4281 -1.1513 H -2.5424 0.0304 0.2260 H -1.5183 -1.3462 -0.1085 H -1.0934 -0.4664 2.1391 C 0.7385 -0.4155 1.0523 H -0.7090 1.0950 1.4555 H -1.5577 0.1969 -2.0121 H -0.9815 1.4843 -0.9807 C 0.4660 -0.0262 -1.3840 H 1.3304 -0.1843 1.9131 H 0.7543 -1.4717 0.8817 H 0.8661 0.4790 -2.2381 C 1.3069 0.3022 -0.1611 H 0.4818 -1.0824 -1.5545 H 2.3148 -0.0176 -0.3250 H 1.2911 1.3584 0.0094 ch5m3d-1.2.5+dfsg/molecules/ruphen3.xyz0000755000175000017500000000567012230555426020066 0ustar georgeskgeorgesk67 C36 H24 RuN6 (xyz format) generated by CH5M3D. Ru 0.0219 -0.2280 0.1868 N -1.3342 -1.4092 -0.8990 N -1.0614 1.5137 0.7874 N 1.2569 -1.9246 -0.2434 N 1.7308 0.9694 0.5423 N -0.7394 -0.7600 2.1597 N 0.2044 0.8467 -1.6621 C 2.5732 -2.0980 0.1555 C -0.7955 -2.6049 -1.3892 C 0.5842 -2.9042 -1.0376 C -2.6473 -1.0080 -1.1753 C -1.5673 -3.5122 -2.2000 C -3.5060 -1.8803 -2.0097 H -3.0055 -0.0910 -0.7929 C 1.2209 -4.1134 -1.4723 C 3.2781 -3.3332 -0.2526 H 3.0675 -1.3615 0.7333 C -0.9270 -4.7653 -2.6813 H -4.4960 -1.6006 -2.2367 C -2.9539 -3.1456 -2.5344 H -3.5417 -3.7739 -3.1387 H 4.2820 -3.4849 0.0356 C 0.4813 -5.0712 -2.3072 C 2.5923 -4.3465 -1.0752 H 3.1022 -5.2234 -1.3716 C -1.6449 1.4725 2.0645 C -1.4740 0.2629 2.8040 C 2.0489 1.8353 -0.5104 C 1.2329 1.7708 -1.6852 C 1.5027 2.5899 -2.8211 C 3.1467 2.7267 -0.4359 C -0.6356 0.6567 -2.7881 C 2.4930 0.9395 1.7053 C -0.4062 1.4526 -3.9845 H -1.4114 -0.0490 -2.7705 C 3.6308 1.8265 1.8387 H 2.2620 0.2668 2.4786 H 4.2357 1.8012 2.6958 C 3.4382 3.6014 -1.5851 C 3.9514 2.7376 0.7606 H 4.7832 3.3833 0.8325 C 2.6022 3.5286 -2.7864 C 0.6824 2.4345 -3.9986 H -1.0098 1.3188 -4.8355 H 0.8717 3.0219 -4.8660 C -1.1729 2.6588 -0.0475 C -0.5258 -1.9901 2.7938 C -1.0786 -2.2259 4.1460 H 0.0315 -2.7405 2.3088 C -2.0374 0.1091 4.1270 H -0.9142 -3.1584 4.6308 C -2.7808 1.2589 4.7124 C -1.8347 -1.1698 4.8257 C -1.9035 3.8220 0.4391 H -0.7173 2.6655 -1.0038 C -2.3767 2.5905 2.5873 H -1.9828 4.6907 -0.1683 C -2.9414 2.5252 3.8935 C -2.5156 3.7940 1.7704 H -3.0437 4.6375 2.1386 H -2.2235 -1.3277 5.7913 H 4.2615 4.2742 -1.5540 H 2.8187 4.1447 -3.6311 H -1.4686 -5.4350 -3.2892 H 0.9417 -5.9679 -2.6452 H -3.1892 1.1958 5.6760 H -3.4669 3.3796 4.2644 ch5m3d-1.2.5+dfsg/molecules/trialanine.xyz0000755000175000017500000000267212230555426020627 0ustar georgeskgeorgesk33 Molecular coordinates generated by CH5M3D. C -2.9679 -2.7673 -0.3150 H -2.3386 -3.1054 0.4804 N -4.3901 -2.8145 0.1166 C -2.7685 -3.6495 -1.5455 C -2.6151 -1.3786 -0.6741 H -4.9704 -2.4797 -0.6545 H -4.6478 -3.7701 0.3566 H -4.5127 -2.2064 0.9310 H -3.3929 -3.2952 -2.3402 H -1.7378 -3.5949 -1.8606 H -3.0227 -4.6528 -1.3141 O -3.2358 -0.7867 -1.6765 N -1.6590 -0.6963 0.0265 C -1.3580 0.6448 -0.3381 H -1.9697 0.9475 -1.1922 C -1.6699 1.5809 0.8404 C 0.0454 0.7168 -0.7264 H -1.4397 2.6002 0.5615 H -2.7161 1.5001 1.0851 H -1.1036 1.3119 1.6913 N 0.5909 1.9130 -1.1249 O 0.7616 -0.3718 -0.7356 H -1.1964 -1.1163 0.7685 C 1.9317 1.9406 -1.5605 H 2.3275 0.9738 -1.5180 C 1.9647 2.4460 -2.9979 C 2.7155 2.8471 -0.6975 H 2.9764 2.4738 -3.3511 H 1.3718 1.7997 -3.6366 H 1.5465 3.4363 -3.0211 O 3.8889 3.2698 -1.1169 O 2.0918 3.5171 0.2510 H 0.0507 2.7273 -1.1355 ch5m3d-1.2.5+dfsg/molecules/s-2-butanol.xyz0000644000175000017500000000124412230555426020533 0ustar georgeskgeorgesk15 S-2-butanol C -0.5294 -0.3155 0.1496 C 0.6016 0.5705 -0.4385 C -1.6544 0.5913 0.6912 O 0.0029 -1.1177 1.2300 H -0.9320 -0.9746 -0.6299 H -0.7296 -1.6685 1.6320 H -2.4593 -0.0280 1.1085 H -1.2470 1.2484 1.4835 H -2.0460 1.2141 -0.1252 C 1.7416 -0.3268 -0.9583 H 0.2026 1.1804 -1.2637 H 0.9981 1.2363 0.3564 H 2.5358 0.3013 -1.3767 H 2.1536 -0.9196 -0.1212 H 1.3614 -0.9916 -1.7375 ch5m3d-1.2.5+dfsg/molecules/glucopyranose.xyz0000755000175000017500000000206712230555426021371 0ustar georgeskgeorgesk24 Molecular coordinates generated by CH5M3D. C 0.2311 -0.3186 1.2152 O 1.5565 -0.2137 0.6064 C -0.8347 -0.5756 0.1243 H 0.0010 0.6032 1.7339 C 0.1999 -1.4913 2.2030 C 1.5914 0.8918 -0.3561 O -2.1184 -0.6717 0.7190 C -0.8242 0.5634 -0.8531 H -0.6050 -1.4761 -0.3811 O -1.7994 0.3405 -1.8582 H -1.0454 1.4853 -0.3374 H 2.5722 0.9570 -0.7907 C 0.5633 0.6554 -1.4730 O 1.2932 2.1046 0.3328 O 0.5939 1.7322 -2.3856 H 0.7981 -0.2576 -1.9807 H -0.7660 -1.5627 2.6517 O 0.4898 -2.7002 1.5257 H 0.9344 -1.3197 2.9644 H 0.4702 -3.4281 2.1573 H -2.7762 -0.8231 0.0321 H -1.7843 1.0756 -2.4879 H -0.0606 1.5812 -3.0765 H 1.3192 2.8482 -0.2856 ch5m3d-1.2.5+dfsg/ch5m3d.js.license_header0000644000175000017500000000214012234705413020267 0ustar georgeskgeorgesk// --------------------------------------------------------------------------- // // CH5M3D // Version 1.2.5 // Written by Clarke Earley // // --------------------------------------------------------------------------- // // License Information // // This program is free software: you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation, either version 3 of the License, or // (at your option) any later version. // // This program is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // // You should have received a copy of the GNU General Public License // along with this program. If not, see . // // --------------------------------------------------------------------------- ch5m3d-1.2.5+dfsg/qchem/0000755000175000017500000000000012234705413015015 5ustar georgeskgeorgeskch5m3d-1.2.5+dfsg/qchem/ch5m3dq.js.license_header0000644000175000017500000000214412234705413021551 0ustar georgeskgeorgesk// --------------------------------------------------------------------------- // // CH5M3D // Version @VERNUM@ // Written by Clarke Earley // // --------------------------------------------------------------------------- // // License Information // // This program is free software: you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation, either version 3 of the License, or // (at your option) any later version. // // This program is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // // You should have received a copy of the GNU General Public License // along with this program. If not, see . // // --------------------------------------------------------------------------- ch5m3d-1.2.5+dfsg/qchem/data/0000755000175000017500000000000012230555426015731 5ustar georgeskgeorgeskch5m3d-1.2.5+dfsg/qchem/data/admin/0000755000175000017500000000000012230555426017021 5ustar georgeskgeorgeskch5m3d-1.2.5+dfsg/qchem/data/admin/butadiene/0000755000175000017500000000000012230555426020761 5ustar georgeskgeorgeskch5m3d-1.2.5+dfsg/qchem/data/admin/butadiene/butadiene.sum0000755000175000017500000000167612230555426023464 0ustar georgeskgeorgesk----- Summary for /home/scratch/www-data/butadieneDFT/butadieneDFT.out ----- 1,3-butadiene in s-cis conformation with DFT Functional ***** EQUILIBRIUM GEOMETRY LOCATED ***** NSERCH= 25 ENERGY= -155.8262337 THE POINT GROUP OF THE MOLECULE IS C1 THE ORDER OF THE PRINCIPAL AXIS IS 0 --- For stationary point, modes 1-6 are rotations and translations. --- MODES 1 TO 6 ARE TAKEN AS ROTATIONS AND TRANSLATIONS. FREQUENCY: 2.69 2.14 0.10 0.07 0.02 FREQUENCY: 3.33 170.40 271.93 469.52 621.14 FREQUENCY: 761.75 894.04 946.61 947.84 1019.87 FREQUENCY: 1036.18 1069.18 1101.40 1307.37 1339.56 FREQUENCY: 1427.82 1459.08 1700.30 1710.79 3144.92 FREQUENCY: 3151.73 3155.11 3164.11 3245.34 3246.72 ch5m3d-1.2.5+dfsg/qchem/data/admin/butadiene/butadiene.mol0000755000175000017500000000135512230555426023441 0ustar georgeskgeorgeskbutadieneDFT.out OpenBabel01231321203D 10 9 0 0 0 0 0 0 0 0999 V2000 0.4200 -0.4276 0.7412 C 0 0 0 0 0 1.2114 -0.5268 1.4828 H 0 0 0 0 0 0.7652 0.3224 -0.4681 C 0 0 0 0 0 1.8043 0.2590 -0.7881 H 0 0 0 0 0 -0.0759 1.0807 -1.1710 C 0 0 0 0 0 0.2457 1.5948 -2.0702 H 0 0 0 0 0 -1.1068 1.2221 -0.8598 H 0 0 0 0 0 -0.7566 -1.0067 0.9792 C 0 0 0 0 0 -1.5575 -0.9854 0.2459 H 0 0 0 0 0 -0.9488 -1.5324 1.9082 H 0 0 0 0 0 3 1 1 0 0 0 1 8 2 0 0 0 1 2 1 0 0 0 5 3 2 0 0 0 4 3 1 0 0 0 6 5 1 0 0 0 5 7 1 0 0 0 9 8 1 0 0 0 8 10 1 0 0 0 M END ch5m3d-1.2.5+dfsg/qchem/data/admin/butadiene/butadiene.out0000755000175000017500000332762512230555426023477 0ustar georgeskgeorgesk----- GAMESS execution script 'rungms' ----- This job is running on host thebrain under operating system Linux at Wed Jan 23 21:04:17 EST 2013 Available scratch disk space (Kbyte units) at beginning of the job is Filesystem 1K-blocks Used Available Use% Mounted on /dev/sda4 2048545652 283909360 1660576148 15% /home GAMESS temporary binary files will be written to /home/www-data/scr GAMESS supplementary output files will be written to /home/scratch/www-data Copying input file /home/scratch/www-data/butadieneDFT/butadieneDFT.inp to your run's scratch directory... Job requested to use 1 nodes with 6 nodes/cpu 1 nodes in generated host list = (thebrain:cpus=6) Distributed Data Interface kickoff program. Initiating 6 compute processes on 1 nodes to run the following command: /usr/local/gamess/gamess.00.x butadieneDFT ****************************************************** * GAMESS VERSION = 1 MAY 2012 (R1) * * FROM IOWA STATE UNIVERSITY * * M.W.SCHMIDT, K.K.BALDRIDGE, J.A.BOATZ, S.T.ELBERT, * * M.S.GORDON, J.H.JENSEN, S.KOSEKI, N.MATSUNAGA, * * K.A.NGUYEN, S.J.SU, T.L.WINDUS, * * TOGETHER WITH M.DUPUIS, J.A.MONTGOMERY * * J.COMPUT.CHEM. 14, 1347-1363(1993) * **************** 64 BIT LINUX VERSION **************** SINCE 1993, STUDENTS AND POSTDOCS WORKING AT IOWA STATE UNIVERSITY AND ALSO IN THEIR VARIOUS JOBS AFTER LEAVING ISU HAVE MADE IMPORTANT CONTRIBUTIONS TO THE CODE: IVANA ADAMOVIC, CHRISTINE AIKENS, YURI ALEXEEV, POOJA ARORA, ANDREY ASADCHEV, ROB BELL, PRADIPTA BANDYOPADHYAY, JONATHAN BENTZ, BRETT BODE, GALINA CHABAN, WEI CHEN, CHEOL HO CHOI, PAUL DAY, ALBERT DEFUSCO, TIM DUDLEY, DMITRI FEDOROV, GRAHAM FLETCHER, MARK FREITAG, KURT GLAESEMANN, DAN KEMP, GRANT MERRILL, NORIYUKI MINEZAWA, JONATHAN MULLIN, TAKESHI NAGATA, SEAN NEDD, HEATHER NETZLOFF, BOSILJKA NJEGIC, RYAN OLSON, MIKE PAK, JIM SHOEMAKER, LYUDMILA SLIPCHENKO, SAROM SOK, JIE SONG, TETSUYA TAKETSUGU, SIMON WEBB, SOOHAENG YOO, FEDERICO ZAHARIEV ADDITIONAL CODE HAS BEEN PROVIDED BY COLLABORATORS IN OTHER GROUPS: IOWA STATE UNIVERSITY: JOE IVANIC, LAIMUTIS BYTAUTAS, KLAUS RUEDENBERG UNIVERSITY OF TOKYO: KIMIHIKO HIRAO, TAKAHITO NAKAJIMA, TAKAO TSUNEDA, MUNEAKI KAMIYA, SUSUMU YANAGISAWA, KIYOSHI YAGI, MAHITO CHIBA, SEIKEN TOKURA, NAOAKI KAWAKAMI UNIVERSITY OF AARHUS: FRANK JENSEN UNIVERSITY OF IOWA: VISVALDAS KAIRYS, HUI LI NATIONAL INST. OF STANDARDS AND TECHNOLOGY: WALT STEVENS, DAVID GARMER UNIVERSITY OF PISA: BENEDETTA MENNUCCI, JACOPO TOMASI UNIVERSITY OF MEMPHIS: HENRY KURTZ, PRAKASHAN KORAMBATH UNIVERSITY OF ALBERTA: TOBY ZENG, MARIUSZ KLOBUKOWSKI UNIVERSITY OF NEW ENGLAND: MARK SPACKMAN MIE UNIVERSITY: HIROAKI UMEDA MICHIGAN STATE UNIVERSITY: KAROL KOWALSKI, MARTA WLOCH, JEFFREY GOUR, JESSE LUTZ, PIOTR PIECUCH UNIVERSITY OF SILESIA: MONIKA MUSIAL, STANISLAW KUCHARSKI FACULTES UNIVERSITAIRES NOTRE-DAME DE LA PAIX: OLIVIER QUINET, BENOIT CHAMPAGNE UNIVERSITY OF CALIFORNIA - SANTA BARBARA: BERNARD KIRTMAN INSTITUTE FOR MOLECULAR SCIENCE: KAZUYA ISHIMURA, MICHIO KATOUDA, AND SHIGERU NAGASE UNIVERSITY OF NOTRE DAME: DAN CHIPMAN KYUSHU UNIVERSITY: HARUYUKI NAKANO, FENG LONG GU, JACEK KORCHOWIEC, MARCIN MAKOWSKI, AND YURIKO AOKI, HIROTOSHI MORI AND EISAKU MIYOSHI PENNSYLVANIA STATE UNIVERSITY: TZVETELIN IORDANOV, CHET SWALINA, JONATHAN SKONE, SHARON HAMMES-SCHIFFER WASEDA UNIVERSITY: MASATO KOBAYASHI, TOMOKO AKAMA, TSUGUKI TOUMA, TAKESHI YOSHIKAWA, YASUHIRO IKABATA, HIROMI NAKAI UNIVERSITY OF NEBRASKA: PEIFENG SU, DEJUN SI, NANDUN THELLAMUREGE, YALI WANG, HUI LI UNIVERSITY OF ZURICH: ROBERTO PEVERATI, KIM BALDRIDGE N. COPERNICUS UNIVERSITY AND JACKSON STATE UNIVERSITY: MARIA BARYSZ PARALLEL VERSION RUNNING ON 6 PROCESSORS IN 1 NODES. EXECUTION OF GAMESS BEGUN Wed Jan 23 21:04:17 2013 ECHO OF THE FIRST FEW INPUT CARDS - INPUT CARD>! INPUT CARD>! GAMESS Calculation input file INPUT CARD>! 1,3-butadiene in s-cis conformation with DFT Functional INPUT CARD>! INPUT CARD> $CONTRL SCFTYP=RHF MAXIT=50 RUNTYP=OPTIMIZE INPUT CARD> COORD=UNIQUE MULT=1 INPUT CARD> DFTTYP=PBE0 INPUT CARD> ICHARG=0 INPUT CARD> MOLPLT=.FALSE. PLTORB=.FALSE. $END INPUT CARD> $SYSTEM TIMLIM=480 MWORDS=6 $END INPUT CARD> INPUT CARD> $STATPT OPTTOL=0.00005 NSTEP=30 HSSEND=.TRUE. $END INPUT CARD> INPUT CARD> $DFT METHOD=GRID NLEB=590 $END INPUT CARD> INPUT CARD> $BASIS GBASIS=N311 NGAUSS=6 INPUT CARD> NDFUNC=1 NPFUNC=1 $END INPUT CARD> INPUT CARD> $SCF DIRSCF=.T. $END INPUT CARD> $GUESS GUESS=HUCKEL $END INPUT CARD> INPUT CARD> $DATA INPUT CARD> 1,3-butadiene in s-cis conformation with DFT Functional INPUT CARD> C1 INPUT CARD> C 6 0.406 -0.421 0.749 INPUT CARD> H 1 1.178 -0.471 1.500 INPUT CARD> C 6 0.755 0.318 -0.482 INPUT CARD> H 1 1.773 0.209 -0.820 INPUT CARD> C 6 -0.066 1.097 -1.164 INPUT CARD> H 1 0.252 1.595 -2.062 INPUT CARD> H 1 -1.077 1.275 -0.843 INPUT CARD> C 6 -0.747 -1.025 0.976 INPUT CARD> H 1 -1.533 -1.043 0.242 INPUT CARD> H 1 -0.940 -1.534 1.904 INPUT CARD> $END 6000000 WORDS OF MEMORY AVAILABLE BASIS OPTIONS ------------- GBASIS=N311 IGAUSS= 6 POLAR=POPN311 NDFUNC= 1 NFFUNC= 0 DIFFSP= F NPFUNC= 1 DIFFS= F BASNAM= RUN TITLE --------- 1,3-butadiene in s-cis conformation with DFT Functional THE POINT GROUP OF THE MOLECULE IS C1 THE ORDER OF THE PRINCIPAL AXIS IS 0 ATOM ATOMIC COORDINATES (BOHR) CHARGE X Y Z C 6.0 0.7672287510 -0.7955746408 1.4154047648 H 1.0 2.2260972135 -0.8900609402 2.8345889816 C 6.0 1.4267431207 0.6009328641 -0.9108479261 H 1.0 3.3504841762 0.3949527314 -1.5495753099 C 6.0 -0.1247219152 2.0730294085 -2.1996410497 H 1.0 0.4762109489 3.0141129504 -3.8966149867 H 1.0 -2.0352348888 2.4094006343 -1.5930390076 C 6.0 -1.4116253128 -1.9369691374 1.8443725640 H 1.0 -2.8969499392 -1.9709842052 0.4573136890 H 1.0 -1.7763424285 -2.8988396652 3.5980382806 INTERNUCLEAR DISTANCES (ANGS.) ------------------------------ 1 C 2 H 3 C 4 H 5 C 1 C 0.0000000 1.0781860 * 1.4775937 * 2.1742470 * 2.4873032 * 2 H 1.0781860 * 0.0000000 2.1748044 * 2.4897440 * 3.3321248 3 C 1.4775937 * 2.1748044 * 0.0000000 1.0781693 * 1.3213652 * 4 H 2.1742470 * 2.4897440 * 1.0781693 * 0.0000000 2.0709421 * 5 C 2.4873032 * 3.3321248 1.3213652 * 2.0709421 * 0.0000000 6 H 3.4626136 4.2206251 2.0928779 * 2.4035393 * 1.0749567 * 7 H 2.7586535 * 3.6909606 2.0981883 * 3.0429238 1.0755678 * 8 C 1.3212698 * 2.0705354 * 2.4870499 * 3.3314820 3.0896998 9 H 2.0984885 * 3.0429047 2.7588840 * 3.6912036 2.9510210 * 10 H 2.0939222 * 2.4039777 * 3.4635134 4.2212076 4.1350527 6 H 7 H 8 C 9 H 10 H 1 C 3.4626136 2.7586535 * 1.3212698 * 2.0984885 * 2.0939222 * 2 H 4.2206251 3.6909606 2.0705354 * 3.0429047 2.4039777 * 3 C 2.0928779 * 2.0981883 * 2.4870499 * 2.7588840 * 3.4635134 4 H 2.4035393 * 3.0429238 3.3314820 3.6912036 4.2212076 5 C 1.0749567 * 1.0755678 * 3.0896998 2.9510210 * 4.1350527 6 H 0.0000000 1.8315573 * 4.1342285 3.9311175 5.1904394 7 H 1.8315573 * 0.0000000 2.9508746 * 2.5996702 * 3.9313177 8 C 4.1342285 2.9508746 * 0.0000000 1.0755817 * 1.0758782 * 9 H 3.9311175 2.5996702 * 1.0755817 * 0.0000000 1.8316588 * 10 H 5.1904394 3.9313177 1.0758782 * 1.8316588 * 0.0000000 * ... LESS THAN 3.000 ATOMIC BASIS SET ---------------- THE CONTRACTED PRIMITIVE FUNCTIONS HAVE BEEN UNNORMALIZED THE CONTRACTED BASIS FUNCTIONS ARE NOW NORMALIZED TO UNITY SHELL TYPE PRIMITIVE EXPONENT CONTRACTION COEFFICIENT(S) C 1 S 1 4563.2400000 0.001966650249 1 S 2 682.0240000 0.015230601932 1 S 3 154.9730000 0.076126909656 1 S 4 44.4553000 0.260801033080 1 S 5 13.0290000 0.616462078191 1 S 6 1.8277300 0.221006028032 2 L 7 20.9642000 0.114660080729 0.040248692673 2 L 8 4.8033100 0.919999647749 0.237593956746 2 L 9 1.4593300 -0.003030682134 0.815853851473 3 L 10 0.4834560 1.000000000000 1.000000000000 4 L 11 0.1455850 1.000000000000 1.000000000000 5 D 12 0.6260000 1.000000000000 H 6 S 13 33.8650000 0.025493814541 6 S 14 5.0947900 0.190373108582 6 S 15 1.1587900 0.852161486043 7 S 16 0.3258400 1.000000000000 8 S 17 0.1027410 1.000000000000 9 P 18 0.7500000 1.000000000000 C 10 S 19 4563.2400000 0.001966650249 10 S 20 682.0240000 0.015230601932 10 S 21 154.9730000 0.076126909656 10 S 22 44.4553000 0.260801033080 10 S 23 13.0290000 0.616462078191 10 S 24 1.8277300 0.221006028032 11 L 25 20.9642000 0.114660080729 0.040248692673 11 L 26 4.8033100 0.919999647749 0.237593956746 11 L 27 1.4593300 -0.003030682134 0.815853851473 12 L 28 0.4834560 1.000000000000 1.000000000000 13 L 29 0.1455850 1.000000000000 1.000000000000 14 D 30 0.6260000 1.000000000000 H 15 S 31 33.8650000 0.025493814541 15 S 32 5.0947900 0.190373108582 15 S 33 1.1587900 0.852161486043 16 S 34 0.3258400 1.000000000000 17 S 35 0.1027410 1.000000000000 18 P 36 0.7500000 1.000000000000 C 19 S 37 4563.2400000 0.001966650249 19 S 38 682.0240000 0.015230601932 19 S 39 154.9730000 0.076126909656 19 S 40 44.4553000 0.260801033080 19 S 41 13.0290000 0.616462078191 19 S 42 1.8277300 0.221006028032 20 L 43 20.9642000 0.114660080729 0.040248692673 20 L 44 4.8033100 0.919999647749 0.237593956746 20 L 45 1.4593300 -0.003030682134 0.815853851473 21 L 46 0.4834560 1.000000000000 1.000000000000 22 L 47 0.1455850 1.000000000000 1.000000000000 23 D 48 0.6260000 1.000000000000 H 24 S 49 33.8650000 0.025493814541 24 S 50 5.0947900 0.190373108582 24 S 51 1.1587900 0.852161486043 25 S 52 0.3258400 1.000000000000 26 S 53 0.1027410 1.000000000000 27 P 54 0.7500000 1.000000000000 H 28 S 55 33.8650000 0.025493814541 28 S 56 5.0947900 0.190373108582 28 S 57 1.1587900 0.852161486043 29 S 58 0.3258400 1.000000000000 30 S 59 0.1027410 1.000000000000 31 P 60 0.7500000 1.000000000000 C 32 S 61 4563.2400000 0.001966650249 32 S 62 682.0240000 0.015230601932 32 S 63 154.9730000 0.076126909656 32 S 64 44.4553000 0.260801033080 32 S 65 13.0290000 0.616462078191 32 S 66 1.8277300 0.221006028032 33 L 67 20.9642000 0.114660080729 0.040248692673 33 L 68 4.8033100 0.919999647749 0.237593956746 33 L 69 1.4593300 -0.003030682134 0.815853851473 34 L 70 0.4834560 1.000000000000 1.000000000000 35 L 71 0.1455850 1.000000000000 1.000000000000 36 D 72 0.6260000 1.000000000000 H 37 S 73 33.8650000 0.025493814541 37 S 74 5.0947900 0.190373108582 37 S 75 1.1587900 0.852161486043 38 S 76 0.3258400 1.000000000000 39 S 77 0.1027410 1.000000000000 40 P 78 0.7500000 1.000000000000 H 41 S 79 33.8650000 0.025493814541 41 S 80 5.0947900 0.190373108582 41 S 81 1.1587900 0.852161486043 42 S 82 0.3258400 1.000000000000 43 S 83 0.1027410 1.000000000000 44 P 84 0.7500000 1.000000000000 TOTAL NUMBER OF BASIS SET SHELLS = 44 NUMBER OF CARTESIAN GAUSSIAN BASIS FUNCTIONS = 112 NUMBER OF ELECTRONS = 30 CHARGE OF MOLECULE = 0 SPIN MULTIPLICITY = 1 NUMBER OF OCCUPIED ORBITALS (ALPHA) = 15 NUMBER OF OCCUPIED ORBITALS (BETA ) = 15 TOTAL NUMBER OF ATOMS = 10 THE NUCLEAR REPULSION ENERGY IS 105.3776403532 LEBEDEV GRID-BASED DFT OPTIONS ------------------------------ DFTTYP=PBE0 NRAD = 96 NLEB = 590 NRAD0 = 24 NLEB0 = 110 SWOFF = 5.00E-03 (PURE SCF -> DFT) SWITCH= 3.00E-04 (COARSE -> TIGHT GRID) THRESH= 0.00E+00 GTHRE= 1.00E+00 GRIMME'S EMPIRICAL DISPERSION CORRECTION= F $CONTRL OPTIONS --------------- SCFTYP=RHF RUNTYP=OPTIMIZE EXETYP=RUN MPLEVL= 0 CITYP =NONE CCTYP =NONE VBTYP =NONE DFTTYP=PBE0 TDDFT =NONE MULT = 1 ICHARG= 0 NZVAR = 0 COORD =UNIQUE PP =NONE RELWFN=NONE LOCAL =NONE NUMGRD= F ISPHER= -1 NOSYM = 0 MAXIT = 50 UNITS =ANGS PLTORB= F MOLPLT= F AIMPAC= F FRIEND= NPRINT= 7 IREST = 0 GEOM =INPUT NORMF = 0 NORMP = 0 ITOL = 20 ICUT = 9 INTTYP=BEST GRDTYP=BEST QMTTOL= 1.0E-06 $SYSTEM OPTIONS --------------- REPLICATED MEMORY= 6000000 WORDS (ON EVERY NODE). DISTRIBUTED MEMDDI= 0 MILLION WORDS IN AGGREGATE, MEMDDI DISTRIBUTED OVER 6 PROCESSORS IS 0 WORDS/PROCESSOR. TOTAL MEMORY REQUESTED ON EACH PROCESSOR= 6000000 WORDS. TIMLIM= 480.00 MINUTES, OR 0.3 DAYS. PARALL= T BALTYP= DLB KDIAG= 0 COREFL= F MXSEQ2= 300 MXSEQ3= 150 ---------------- PROPERTIES INPUT ---------------- MOMENTS FIELD POTENTIAL DENSITY IEMOM = 1 IEFLD = 0 IEPOT = 0 IEDEN = 0 WHERE =COMASS WHERE =NUCLEI WHERE =NUCLEI WHERE =NUCLEI OUTPUT=BOTH OUTPUT=BOTH OUTPUT=BOTH OUTPUT=BOTH IEMINT= 0 IEFINT= 0 IEDINT= 0 MORB = 0 EXTRAPOLATION IN EFFECT DIIS IN EFFECT ORBITAL PRINTING OPTION: NPREO= 1 112 2 1 ------------------------------- INTEGRAL TRANSFORMATION OPTIONS ------------------------------- NWORD = 0 CUTOFF = 1.0E-09 MPTRAN = 0 DIRTRF = T AOINTS =DUP ---------------------- INTEGRAL INPUT OPTIONS ---------------------- NOPK = 1 NORDER= 0 SCHWRZ= T ------------------------------------------ THE POINT GROUP IS C1 , NAXIS= 0, ORDER= 1 ------------------------------------------ DIMENSIONS OF THE SYMMETRY SUBSPACES ARE A = 112 ..... DONE SETTING UP THE RUN ..... CPU 0: STEP CPU TIME= 0.02 TOTAL CPU TIME= 0.0 ( 0.0 MIN) TOTAL WALL CLOCK TIME= 0.1 SECONDS, CPU UTILIZATION IS 28.57% ----------------------------- STATIONARY POINT LOCATION RUN ----------------------------- OBTAINING INITIAL HESSIAN, HESS=GUESS CARTESIAN COORDINATE OPTIMIZATION USING BADGER'S RULE FORCE CONSTANT GUESS PARAMETERS CONTROLLING GEOMETRY SEARCH ARE METHOD =QA UPHESS =BFGS NNEG = 0 NFRZ = 0 NSTEP = 30 IFOLOW = 1 HESS =GUESS RESTAR = F IHREP = 0 HSSEND = T NPRT = 0 NPUN = 0 OPTTOL = 5.000E-05 RMIN = 1.500E-03 RMAX = 1.000E-01 RLIM = 7.000E-02 DXMAX = 3.000E-01 PURIFY = F MOVIE = F TRUPD = T TRMAX = 5.000E-01 TRMIN = 5.000E-02 ITBMAT = 5 STPT = F STSTEP = 1.000E-02 PROJCT= T BEGINNING GEOMETRY SEARCH POINT NSERCH= 0 ... COORDINATES OF ALL ATOMS ARE (ANGS) ATOM CHARGE X Y Z ------------------------------------------------------------ C 6.0 0.4060000000 -0.4210000000 0.7490000000 H 1.0 1.1780000000 -0.4710000000 1.5000000000 C 6.0 0.7550000000 0.3180000000 -0.4820000000 H 1.0 1.7730000000 0.2090000000 -0.8200000000 C 6.0 -0.0660000000 1.0970000000 -1.1640000000 H 1.0 0.2520000000 1.5950000000 -2.0620000000 H 1.0 -1.0770000000 1.2750000000 -0.8430000000 C 6.0 -0.7470000000 -1.0250000000 0.9760000000 H 1.0 -1.5330000000 -1.0430000000 0.2420000000 H 1.0 -0.9400000000 -1.5340000000 1.9040000000 ******************** 1 ELECTRON INTEGRALS ******************** ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 0.0 ( 0.0 MIN) TOTAL WALL CLOCK TIME= 0.1 SECONDS, CPU UTILIZATION IS 25.00% ------------- GUESS OPTIONS ------------- GUESS =HUCKEL NORB = 0 NORDER= 0 MIX = F PRTMO = F PUNMO = F TOLZ = 1.0E-08 TOLE = 1.0E-05 SYMDEN= F PURIFY= F INITIAL GUESS ORBITALS GENERATED BY HUCKEL ROUTINE. HUCKEL GUESS REQUIRES 100788 WORDS. SYMMETRIES FOR INITIAL GUESS ORBITALS FOLLOW. BOTH SET(S). 15 ORBITALS ARE OCCUPIED ( 4 CORE ORBITALS). 5=A 6=A 7=A 8=A 9=A 10=A 11=A 12=A 13=A 14=A 15=A 16=A 17=A 18=A 19=A 20=A 21=A 22=A 23=A 24=A 25=A ...... END OF INITIAL ORBITAL SELECTION ...... CPU 0: STEP CPU TIME= 0.08 TOTAL CPU TIME= 0.1 ( 0.0 MIN) TOTAL WALL CLOCK TIME= 0.2 SECONDS, CPU UTILIZATION IS 62.50% ---------------------- AO INTEGRAL TECHNOLOGY ---------------------- S,P,L SHELL ROTATED AXIS INTEGRALS, REPROGRAMMED BY KAZUYA ISHIMURA (IMS) AND JOSE SIERRA (SYNSTAR). S,P,D,L SHELL ROTATED AXIS INTEGRALS PROGRAMMED BY KAZUYA ISHIMURA (INSTITUTE FOR MOLECULAR SCIENCE). S,P,D,F,G SHELL TO TOTAL QUARTET ANGULAR MOMENTUM SUM 5, ERIC PROGRAM BY GRAHAM FLETCHER (ELORET AND NASA ADVANCED SUPERCOMPUTING DIVISION, AMES RESEARCH CENTER). S,P,D,F,G,L SHELL GENERAL RYS QUADRATURE PROGRAMMED BY MICHEL DUPUIS (PACIFIC NORTHWEST NATIONAL LABORATORY). -------------------- 2 ELECTRON INTEGRALS -------------------- DIRECT SCF METHOD SKIPS INTEGRAL STORAGE ON DISK. DIRECT TRANSFORMATION SKIPS AO INTEGRAL STORAGE ON DISK. ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.02 TOTAL CPU TIME= 0.1 ( 0.0 MIN) TOTAL WALL CLOCK TIME= 0.2 SECONDS, CPU UTILIZATION IS 66.67% -------------------------- R-PBE0 SCF CALCULATION -------------------------- NUCLEAR ENERGY = 105.3776403532 MAXIT = 50 NPUNCH= 2 EXTRAP=T DAMP=F SHIFT=F RSTRCT=F DIIS=T DEM=F SOSCF=F DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) MEMORY REQUIRED FOR RHF ITERS= 781406 WORDS. DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 SCHWARZ INEQUALITY OVERHEAD: 6311 INTEGRALS, T= 0.01 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 EXCHANGE FUNCTIONAL =PBE&HFX CORRELATION FUNCTIONAL=PBE DFT THRESHOLD =.706E-08 GRID CHANGE THRESHOLD =.300E-03 FOR AN EULER-MACLAURIN QUADRATURE USING 96 RADIAL POINTS: SMALLEST GAUSSIAN PRIMITIVE EXPONENT= 0.1027410000 OF TYPE -S- ON ATOM NUMBER 2 HAS RADIAL NORMALIZATION= 1.000000 LARGEST GAUSSIAN PRIMITIVE EXPONENT= 4563.2400000000 OF TYPE -S- ON ATOM NUMBER 1 HAS RADIAL NORMALIZATION= 1.000000 DFT IS SWITCHED OFF, PERFORMING PURE SCF UNTIL SWOFF THRESHOLD IS REACHED. NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED 1 0 0 -154.5251924478 -154.5251924478 0.150617033 0.522010028 17630886 81261 * * * INITIATING DIIS PROCEDURE * * * 2 1 0 -154.9300293246 -0.4048368768 0.034577147 0.086554040 17647708 84064 3 2 0 -154.9510920467 -0.0210627221 0.025265321 0.022648672 17382429 96479 4 3 0 -154.9546488550 -0.0035568083 0.007566938 0.008827006 17090982 108855 5 4 0 -154.9551653505 -0.0005164954 0.001686109 0.002521297 16867188 116038 CONVERGED TO SWOFF, SO DFT CALCULATION IS NOW SWITCHED ON. * * * INITIATING DIIS PROCEDURE * * * 6 5 0 -155.8060785654 -0.8509132149 0.033653074 0.079416470 17689796 80128 7 6 0 -155.8226345799 -0.0165560145 0.019742957 0.016901863 17412974 95643 8 7 0 -155.8230555445 -0.0004209646 0.009876849 0.013471951 17126959 104551 9 8 0 -155.8243647550 -0.0013092105 0.001497601 0.003884093 16916749 112613 10 9 0 -155.8244113721 -0.0000466171 0.000409320 0.000922232 16353523 134238 11 10 0 -155.8244153647 -0.0000039925 0.000060392 0.000103174 15899316 148864 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 12 11 0 -155.8253645970 -0.0009492324 0.000983649 0.001390095 17696638 79434 13 12 0 -155.8253697981 -0.0000052010 0.000395582 0.000320883 16426001 131089 14 13 0 -155.8253700707 -0.0000002727 0.000192083 0.000210899 15650730 153029 15 14 0 -155.8253703259 -0.0000002551 0.000017673 0.000019733 15189659 166429 16 15 0 -155.8253703296 -0.0000000037 0.000010865 0.000013071 14300884 195775 17 16 0 -155.8253703302 -0.0000000005 0.000002804 0.000005568 13314197 221223 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 9.6 SECONDS ( 0.6 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.4, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.2 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8253703302 AFTER 17 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -18.0151740342 TOTAL ELECTRON NUMBER = 30.0000064336 ------------ EIGENVECTORS ------------ 1 2 3 4 5 -10.2296 -10.2293 -10.2164 -10.2164 -0.8330 A A A A A 1 C 1 S 0.390850 0.405760 -0.022776 0.000044 -0.073264 2 C 1 S 0.318869 0.331016 -0.018567 0.000026 -0.113407 3 C 1 X 0.000075 0.000114 -0.000051 -0.000006 -0.019405 4 C 1 Y 0.000040 0.000100 -0.000028 0.000019 -0.000086 5 C 1 Z -0.000066 -0.000155 0.000015 -0.000020 -0.015208 6 C 1 S 0.014167 0.014322 -0.000088 0.000133 0.294072 7 C 1 X 0.000205 -0.000209 -0.001154 -0.000034 -0.025045 8 C 1 Y 0.000344 -0.000441 -0.000622 -0.000062 0.004639 9 C 1 Z -0.000501 0.000750 0.000261 0.000058 -0.027881 10 C 1 S 0.004165 0.007686 -0.002463 -0.000179 0.139794 11 C 1 X -0.001005 -0.001240 0.001021 0.000048 -0.009893 12 C 1 Y -0.000508 0.000660 0.000594 -0.000050 -0.001259 13 C 1 Z -0.000475 -0.001847 -0.000238 0.000173 -0.013192 14 C 1 XX -0.005245 -0.005600 0.001007 0.000008 0.005410 15 C 1 YY -0.005008 -0.005488 0.000518 0.000004 -0.001371 16 C 1 ZZ -0.004925 -0.006043 0.000476 -0.000046 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-0.000435 -0.000887 30 C 3 Z 0.418877 -0.246673 -0.695381 0.005695 0.000118 31 C 3 S 0.054868 -0.607666 -0.561071 0.468700 -0.541497 32 C 3 X 2.192842 2.336794 1.217886 -0.025458 0.040451 33 C 3 Y -0.181061 -1.751383 -2.356279 0.064937 -0.030394 34 C 3 Z -0.838252 1.264828 2.752068 -0.084510 0.016407 35 C 3 S 0.487097 0.184133 -0.348258 0.394945 -0.197751 36 C 3 X -0.638125 -0.357805 -0.087409 -0.116383 0.041816 37 C 3 Y -0.034785 0.176100 0.483834 -0.045125 -0.014389 38 C 3 Z 0.286239 -0.016719 -0.690830 0.074679 -0.038122 39 C 3 XX -0.174961 -0.340215 -0.498982 -0.263000 0.268930 40 C 3 YY -0.952980 -0.830499 -0.184981 -0.265978 0.266102 41 C 3 ZZ -1.377179 -0.542598 0.531074 -0.301286 0.252580 42 C 3 XY 0.209120 0.771699 0.894565 0.002463 0.006816 43 C 3 XZ -0.350456 -0.875347 -1.080467 0.004029 -0.009768 44 C 3 YZ 1.004684 0.667436 -0.051508 0.026499 0.007547 45 H 4 S -0.515167 -0.375475 -0.051779 -0.000441 -0.005261 46 H 4 S -0.215854 -0.253675 -0.076917 0.068125 -0.055072 47 H 4 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0.373782 65 C 5 YY 0.443852 0.698921 0.633357 -0.360149 0.356276 66 C 5 ZZ 0.208351 0.327100 0.217648 -0.367192 0.365435 67 C 5 XY -0.560838 -0.837031 -0.676343 0.012741 -0.023645 68 C 5 XZ 0.436738 0.985217 0.937341 0.000245 0.006222 69 C 5 YZ -0.232737 -0.484285 -0.463183 0.016568 -0.028038 70 H 6 S 0.242258 0.311012 0.218486 0.008727 -0.019675 71 H 6 S 0.167114 0.221034 0.212966 0.062408 -0.006134 72 H 6 S -0.129769 -0.156417 -0.086885 -0.072817 0.105240 73 H 6 X -0.087808 -0.090254 -0.042853 -0.016478 0.015513 74 H 6 Y -0.113413 -0.142169 -0.117149 -0.009566 0.002484 75 H 6 Z 0.212837 0.262537 0.187271 0.020397 -0.014617 76 H 7 S -0.044261 0.237148 0.335061 0.011229 -0.011398 77 H 7 S -0.124824 0.211273 0.364757 0.055521 -0.074839 78 H 7 S 0.067089 -0.059500 -0.201663 -0.080740 0.072616 79 H 7 X -0.144935 0.212856 0.387703 0.026082 -0.021812 80 H 7 Y 0.028757 -0.047151 -0.085305 0.001155 -0.000961 81 H 7 Z 0.043347 -0.057925 -0.103891 -0.018151 0.013525 82 C 8 S -0.016510 0.007734 0.007086 -1.223552 -1.161327 83 C 8 S -0.084485 0.071322 -0.016486 1.485270 1.409956 84 C 8 X 0.302808 -0.610443 0.487628 -0.008559 -0.009124 85 C 8 Y 0.249026 -0.323264 0.237260 -0.004211 -0.007353 86 C 8 Z -0.251789 0.160376 -0.004915 0.004225 0.002656 87 C 8 S -0.113271 0.428070 -0.571722 -0.648085 -0.632990 88 C 8 X -1.384670 2.868950 -2.617771 -0.020130 -0.009568 89 C 8 Y -0.973942 1.517119 -1.322144 -0.008740 0.003278 90 C 8 Z 0.804690 -0.673526 0.276400 -0.010061 -0.001741 91 C 8 S 0.243741 -0.166522 0.307033 -0.280030 -0.282804 92 C 8 X 0.104226 -0.275192 0.397937 0.000841 0.018400 93 C 8 Y 0.196776 -0.194597 0.164835 0.015907 0.030689 94 C 8 Z -0.289095 0.195364 0.070286 0.002999 -0.089422 95 C 8 XX -1.076707 1.462590 -1.019382 0.386053 0.375626 96 C 8 YY -0.282370 0.436489 -0.405924 0.364488 0.338912 97 C 8 ZZ -0.010261 -0.296266 0.438250 0.376802 0.352146 98 C 8 XY -0.485692 0.834442 -0.758227 0.016227 0.027532 99 C 8 XZ 0.012935 -0.462701 0.591607 0.001505 -0.001437 100 C 8 YZ -0.055166 0.048317 -0.023560 -0.010546 -0.014986 101 H 9 S 0.043201 0.238395 -0.334900 -0.011504 -0.011094 102 H 9 S 0.123875 0.212926 -0.365036 -0.057499 -0.073481 103 H 9 S -0.066675 -0.060481 0.201858 0.082546 0.070383 104 H 9 X 0.113566 0.172762 -0.312826 -0.015357 -0.012922 105 H 9 Y 0.005656 0.012933 -0.022938 0.004954 0.003988 106 H 9 Z 0.102163 0.147425 -0.264800 -0.028177 -0.020901 107 H 10 S -0.241627 0.308618 -0.216775 -0.009245 -0.019460 108 H 10 S -0.166419 0.219435 -0.211848 -0.062527 -0.004553 109 H 10 S 0.129671 -0.155398 0.086302 0.075287 0.103115 110 H 10 X -0.034164 0.058264 -0.063085 0.004290 0.006833 111 H 10 Y -0.118047 0.144021 -0.114554 -0.011543 -0.004233 112 H 10 Z 0.224978 -0.268246 0.181612 0.025780 0.019283 111 112 26.6632 26.7625 A A 1 C 1 S -1.178772 -1.213654 2 C 1 S 1.438894 1.488728 3 C 1 X 0.011546 0.007845 4 C 1 Y 0.008429 -0.006852 5 C 1 Z -0.004075 0.017941 6 C 1 S -0.558353 -0.569165 7 C 1 X -0.132408 -0.092638 8 C 1 Y -0.095763 -0.007530 9 C 1 Z 0.073796 -0.061750 10 C 1 S -0.564851 -0.887830 11 C 1 X 0.156074 0.181587 12 C 1 Y 0.074703 -0.029295 13 C 1 Z 0.052608 0.157475 14 C 1 XX 0.457120 0.511329 15 C 1 YY 0.381884 0.428053 16 C 1 ZZ 0.379235 0.500509 17 C 1 XY 0.058076 0.067028 18 C 1 XZ 0.007749 -0.018006 19 C 1 YZ -0.008340 -0.083823 20 H 2 S -0.010800 -0.006629 21 H 2 S -0.106851 -0.123664 22 H 2 S 0.060119 0.056635 23 H 2 X 0.040359 0.044549 24 H 2 Y 0.000253 0.001226 25 H 2 Z 0.024941 0.042570 26 C 3 S -1.180201 1.212880 27 C 3 S 1.440644 -1.487783 28 C 3 X 0.007061 -0.015873 29 C 3 Y -0.010077 -0.004767 30 C 3 Z 0.008345 0.012489 31 C 3 S -0.559120 0.568881 32 C 3 X -0.069212 0.107371 33 C 3 Y 0.113600 -0.025058 34 C 3 Z -0.120158 -0.015818 35 C 3 S -0.565426 0.887549 36 C 3 X 0.148667 -0.233998 37 C 3 Y -0.101816 0.007605 38 C 3 Z 0.017741 0.061742 39 C 3 XX 0.432168 -0.488053 40 C 3 YY 0.400577 -0.443614 41 C 3 ZZ 0.387070 -0.507357 42 C 3 XY -0.059202 0.034900 43 C 3 XZ 0.022649 0.003131 44 C 3 YZ -0.037372 0.109126 45 H 4 S -0.010782 0.006613 46 H 4 S -0.106941 0.123667 47 H 4 S 0.060252 -0.056593 48 H 4 X 0.046522 -0.057698 49 H 4 Y -0.007949 0.010249 50 H 4 Z -0.004942 0.019029 51 C 5 S 0.920171 -0.878536 52 C 5 S -1.122820 1.075859 53 C 5 X 0.009367 -0.005424 54 C 5 Y -0.002275 0.007766 55 C 5 Z 0.001978 -0.006056 56 C 5 S 0.396493 -0.395146 57 C 5 X -0.107668 0.088177 58 C 5 Y 0.076129 -0.086766 59 C 5 Z -0.065509 0.069746 60 C 5 S 0.617160 -0.605766 61 C 5 X 0.023583 -0.028051 62 C 5 Y -0.089369 0.092073 63 C 5 Z 0.144609 -0.096232 64 C 5 XX -0.357661 0.360651 65 C 5 YY -0.322624 0.314346 66 C 5 ZZ -0.332118 0.335771 67 C 5 XY 0.049053 -0.052979 68 C 5 XZ -0.021340 0.009299 69 C 5 YZ 0.051927 -0.068411 70 H 6 S 0.008843 -0.016550 71 H 6 S 0.081937 -0.065416 72 H 6 S -0.040917 0.056176 73 H 6 X -0.006786 0.008782 74 H 6 Y -0.023203 0.022135 75 H 6 Z 0.035333 -0.038984 76 H 7 S 0.018090 -0.019477 77 H 7 S 0.000069 -0.034317 78 H 7 S -0.074428 0.080575 79 H 7 X 0.027830 -0.041614 80 H 7 Y -0.005550 0.010354 81 H 7 Z -0.008985 0.007704 82 C 8 S 0.919907 0.879679 83 C 8 S -1.122500 -1.077260 84 C 8 X 0.009502 0.008731 85 C 8 Y 0.000599 0.006530 86 C 8 Z 0.002407 -0.002770 87 C 8 S 0.396507 0.395768 88 C 8 X -0.136285 -0.122970 89 C 8 Y -0.054519 -0.068288 90 C 8 Z 0.009205 0.021143 91 C 8 S 0.616730 0.606060 92 C 8 X 0.098522 0.082018 93 C 8 Y 0.078564 0.082408 94 C 8 Z -0.116406 -0.070774 95 C 8 XX -0.385052 -0.383598 96 C 8 YY -0.306328 -0.296531 97 C 8 ZZ -0.320593 -0.331870 98 C 8 XY -0.054823 -0.064340 99 C 8 XZ 0.003464 -0.001693 100 C 8 YZ 0.025078 0.040206 101 H 9 S 0.018063 0.019473 102 H 9 S 0.000071 0.034404 103 H 9 S -0.074431 -0.080621 104 H 9 X 0.021600 0.035250 105 H 9 Y 0.001107 0.003480 106 H 9 Z 0.020387 0.025416 107 H 10 S 0.008778 0.016483 108 H 10 S 0.081792 0.065339 109 H 10 S -0.040789 -0.056164 110 H 10 X 0.013197 0.012878 111 H 10 Y 0.022578 0.021738 112 H 10 Z -0.033877 -0.038108 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 9.97 TOTAL CPU TIME= 10.1 ( 0.2 MIN) TOTAL WALL CLOCK TIME= 10.3 SECONDS, CPU UTILIZATION IS 98.06% --------------------------------------------------------------------- PROPERTIES FOR THE PBE0 DFT FUNCTIONAL (RHF TYPE) DENSITY MATRIX --------------------------------------------------------------------- ----------------- ENERGY COMPONENTS ----------------- WAVEFUNCTION NORMALIZATION = 1.0000000000 ONE ELECTRON ENERGY = -416.7423621134 TWO ELECTRON ENERGY = 155.5393514301 NUCLEAR REPULSION ENERGY = 105.3776403532 ------------------ TOTAL ENERGY = -155.8253703302 ELECTRON-ELECTRON POTENTIAL ENERGY = 155.5393514301 NUCLEUS-ELECTRON POTENTIAL ENERGY = -571.8747405826 NUCLEUS-NUCLEUS POTENTIAL ENERGY = 105.3776403532 ------------------ TOTAL POTENTIAL ENERGY = -310.9577487993 TOTAL KINETIC ENERGY = 155.1323784691 VIRIAL RATIO (V/T) = 2.0044671001 --------------------------------------- MULLIKEN AND LOWDIN POPULATION ANALYSES --------------------------------------- ATOMIC MULLIKEN POPULATION IN EACH MOLECULAR ORBITAL 1 2 3 4 5 2.000000 2.000000 2.000000 2.000000 2.000000 1 0.961408 1.035633 0.003025 -0.000010 0.601715 2 0.000079 0.000163 0.000001 -0.000000 0.045927 3 1.036053 0.961032 -0.000006 0.002977 0.602058 4 0.000088 0.000154 -0.000000 0.000001 0.045989 5 0.001237 0.001443 0.000435 1.996443 0.311938 6 -0.000019 -0.000003 0.000001 0.000086 0.015093 7 0.000009 0.000005 0.000001 0.000063 0.025085 8 0.001155 0.001570 1.996394 0.000440 0.312108 9 0.000008 0.000005 0.000064 -0.000000 0.025056 10 -0.000018 -0.000003 0.000087 -0.000001 0.015030 6 7 8 9 10 2.000000 2.000000 2.000000 2.000000 2.000000 1 0.356724 0.389354 0.287776 0.390260 0.368805 2 0.034639 0.069354 0.164310 0.133817 0.024751 3 0.356481 0.389744 0.287074 0.391377 0.368346 4 0.034547 0.069669 0.163784 0.134277 0.024581 5 0.503039 0.352247 0.345533 0.296090 0.419797 6 0.059789 0.097739 0.059781 0.129071 0.025001 7 0.046278 0.090929 0.142498 0.051419 0.162074 8 0.502750 0.352394 0.346413 0.294452 0.419710 9 0.046240 0.091045 0.143143 0.050761 0.161674 10 0.059512 0.097526 0.059688 0.128476 0.025260 11 12 13 14 15 2.000000 2.000000 2.000000 2.000000 2.000000 1 0.210906 0.248132 0.352044 0.586203 0.350839 2 0.054590 0.177128 0.139023 0.029469 0.009060 3 0.210442 0.248447 0.352047 0.586199 0.350960 4 0.054060 0.178051 0.138541 0.029520 0.009094 5 0.445461 0.319115 0.223332 0.372725 0.628740 6 0.261273 0.049230 0.169244 0.006439 0.005335 7 0.028419 0.206425 0.114548 0.005093 0.005992 8 0.445169 0.318717 0.225096 0.372796 0.628665 9 0.028540 0.205771 0.115472 0.005083 0.005983 10 0.261141 0.048985 0.170654 0.006473 0.005330 ----- POPULATIONS IN EACH AO ----- MULLIKEN LOWDIN 1 C 1 S 1.10490 1.04585 2 C 1 S 0.87920 0.90903 3 C 1 X 0.23439 0.22393 4 C 1 Y 0.18826 0.18438 5 C 1 Z 0.20886 0.20121 6 C 1 S 0.76352 0.40092 7 C 1 X 0.52463 0.49232 8 C 1 Y 0.45780 0.43040 9 C 1 Z 0.50165 0.46596 10 C 1 S 0.42629 0.23451 11 C 1 X 0.22908 0.29881 12 C 1 Y 0.31889 0.34532 13 C 1 Z 0.23640 0.30614 14 C 1 XX 0.01871 0.16920 15 C 1 YY 0.00017 0.13042 16 C 1 ZZ 0.01213 0.15477 17 C 1 XY 0.00866 0.01751 18 C 1 XZ 0.02117 0.04291 19 C 1 YZ 0.00810 0.01508 20 H 2 S 0.27363 0.27012 21 H 2 S 0.49041 0.42351 22 H 2 S 0.09278 0.17742 23 H 2 X 0.00998 0.02158 24 H 2 Y 0.00567 0.01539 25 H 2 Z 0.00984 0.02254 26 C 3 S 1.10490 1.04581 27 C 3 S 0.87920 0.90895 28 C 3 X 0.22892 0.21906 29 C 3 Y 0.19630 0.19095 30 C 3 Z 0.20626 0.19914 31 C 3 S 0.76352 0.40004 32 C 3 X 0.52466 0.48956 33 C 3 Y 0.46905 0.44045 34 C 3 Z 0.49029 0.45893 35 C 3 S 0.42663 0.23446 36 C 3 X 0.25879 0.31347 37 C 3 Y 0.29712 0.33599 38 C 3 Z 0.22864 0.30147 39 C 3 XX 0.01877 0.16867 40 C 3 YY 0.00451 0.13880 41 C 3 ZZ 0.01473 0.15754 42 C 3 XY 0.00725 0.01479 43 C 3 XZ 0.01286 0.02576 44 C 3 YZ 0.01081 0.02034 45 H 4 S 0.27364 0.27174 46 H 4 S 0.49042 0.42499 47 H 4 S 0.09280 0.17751 48 H 4 X 0.01399 0.02910 49 H 4 Y 0.00563 0.01519 50 H 4 Z 0.00588 0.01568 51 C 5 S 1.10484 1.04573 52 C 5 S 0.87924 0.90883 53 C 5 X 0.22565 0.21475 54 C 5 Y 0.19839 0.19205 55 C 5 Z 0.21349 0.20472 56 C 5 S 0.76052 0.39791 57 C 5 X 0.51349 0.48220 58 C 5 Y 0.46239 0.44069 59 C 5 Z 0.49305 0.46398 60 C 5 S 0.45610 0.25125 61 C 5 X 0.25483 0.32849 62 C 5 Y 0.32919 0.36032 63 C 5 Z 0.28010 0.34195 64 C 5 XX 0.01669 0.16854 65 C 5 YY -0.00052 0.13319 66 C 5 ZZ 0.00811 0.15180 67 C 5 XY 0.00624 0.01355 68 C 5 XZ 0.00830 0.01724 69 C 5 YZ 0.00746 0.01585 70 H 6 S 0.27315 0.26797 71 H 6 S 0.48565 0.42209 72 H 6 S 0.09312 0.18095 73 H 6 X 0.00594 0.01525 74 H 6 Y 0.00796 0.01862 75 H 6 Z 0.01224 0.02652 76 H 7 S 0.27270 0.26851 77 H 7 S 0.48141 0.42144 78 H 7 S 0.09860 0.18576 79 H 7 X 0.01389 0.02991 80 H 7 Y 0.00610 0.01556 81 H 7 Z 0.00614 0.01549 82 C 8 S 1.10485 1.04578 83 C 8 S 0.87924 0.90891 84 C 8 X 0.23020 0.21893 85 C 8 Y 0.18990 0.18508 86 C 8 Z 0.21730 0.20768 87 C 8 S 0.76054 0.39880 88 C 8 X 0.51369 0.48538 89 C 8 Y 0.44942 0.42954 90 C 8 Z 0.50567 0.47107 91 C 8 S 0.45630 0.25132 92 C 8 X 0.22198 0.30508 93 C 8 Y 0.35386 0.37464 94 C 8 Z 0.28857 0.35028 95 C 8 XX 0.01580 0.16940 96 C 8 YY -0.00446 0.12496 97 C 8 ZZ 0.00768 0.15121 98 C 8 XY 0.00653 0.01401 99 C 8 XZ 0.01505 0.03218 100 C 8 YZ 0.00573 0.01209 101 H 9 S 0.27270 0.26702 102 H 9 S 0.48141 0.42016 103 H 9 S 0.09861 0.18570 104 H 9 X 0.01029 0.02241 105 H 9 Y 0.00599 0.01574 106 H 9 Z 0.00985 0.02234 107 H 10 S 0.27288 0.26781 108 H 10 S 0.48574 0.42223 109 H 10 S 0.09343 0.18113 110 H 10 X 0.00545 0.01369 111 H 10 Y 0.00814 0.01924 112 H 10 Z 0.01250 0.02748 ----- MULLIKEN ATOMIC OVERLAP POPULATIONS ----- (OFF-DIAGONAL ELEMENTS NEED TO BE MULTIPLIED BY 2) 1 2 3 4 5 1 4.9003137 2 0.4143950 0.5509662 3 0.3811759 -0.0443241 4.9008118 4 -0.0443642 -0.0029933 0.4144048 0.5510020 5 -0.0741530 0.0051454 0.6436627 -0.0376019 4.8584964 6 0.0081805 -0.0003723 -0.0334848 -0.0112125 0.4083352 7 -0.0111668 0.0002439 -0.0419396 0.0080934 0.4158464 8 0.6437957 -0.0376217 -0.0740797 0.0051540 -0.0070257 9 -0.0419211 0.0080944 -0.0111808 0.0002453 0.0050466 10 -0.0334418 -0.0112222 0.0081857 -0.0003727 -0.0001770 6 7 8 9 10 6 0.5450935 7 -0.0380903 0.5393979 8 -0.0001771 0.0050491 4.8587331 9 -0.0002449 0.0016489 0.4158414 0.5394688 10 0.0000328 -0.0002454 0.4081613 -0.0381531 0.5453723 TOTAL MULLIKEN AND LOWDIN ATOMIC POPULATIONS ATOM MULL.POP. CHARGE LOW.POP. CHARGE 1 C 6.142814 -0.142814 6.068668 -0.068668 2 H 0.882311 0.117689 0.930562 0.069438 3 C 6.143232 -0.143232 6.064166 -0.064166 4 H 0.882355 0.117645 0.934209 0.065791 5 C 6.217575 -0.217575 6.133036 -0.133036 6 H 0.878060 0.121940 0.931404 0.068596 7 H 0.878837 0.121163 0.936676 0.063324 8 C 6.217830 -0.217830 6.136336 -0.136336 9 H 0.878846 0.121154 0.933366 0.066634 10 H 0.878140 0.121860 0.931576 0.068424 ------------------------------- BOND ORDER AND VALENCE ANALYSIS BOND ORDER THRESHOLD=0.050 ------------------------------- BOND BOND BOND ATOM PAIR DIST ORDER ATOM PAIR DIST ORDER ATOM PAIR DIST ORDER 1 2 1.078 0.961 1 3 1.478 1.055 1 8 1.321 1.905 3 4 1.078 0.961 3 5 1.321 1.905 5 6 1.075 0.964 5 7 1.076 0.966 5 8 3.090 0.069 8 9 1.076 0.966 8 10 1.076 0.964 TOTAL BONDED FREE ATOM VALENCE VALENCE VALENCE 1 C 3.899 3.899 -0.000 2 H 0.970 0.970 -0.000 3 C 3.899 3.899 -0.000 4 H 0.970 0.970 -0.000 5 C 3.897 3.897 -0.000 6 H 0.967 0.967 -0.000 7 H 0.976 0.976 0.000 8 C 3.897 3.897 -0.000 9 H 0.976 0.976 0.000 10 H 0.967 0.967 -0.000 --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.133784 -0.011914 0.030363 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.114827 -0.008795 0.027042 0.118296 ...... END OF PROPERTY EVALUATION ...... CPU 0: STEP CPU TIME= 0.02 TOTAL CPU TIME= 10.1 ( 0.2 MIN) TOTAL WALL CLOCK TIME= 10.3 SECONDS, CPU UTILIZATION IS 98.06% BEGINNING ONE ELECTRON GRADIENT... ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 10.1 ( 0.2 MIN) TOTAL WALL CLOCK TIME= 10.3 SECONDS, CPU UTILIZATION IS 98.06% ---------------------- GRADIENT OF THE ENERGY ---------------------- MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700735 WORDS. CPU 0: STEP CPU TIME= 2.31 TOTAL CPU TIME= 12.4 ( 0.2 MIN) TOTAL WALL CLOCK TIME= 12.6 SECONDS, CPU UTILIZATION IS 98.34% THE MINIMUM MEMORY REQUIRED FOR THIS RUN IS 131649 WORDS. USING 1107169 WORDS FOR 2E- DERIVATIVE INTEGRAL CONTRIBUTIONS. THE COARSE/FINE SCHWARZ SCREENINGS SKIPPED 78290/ 86346 BLOCKS. THE NUMBER OF GRADIENT INTEGRAL BLOCKS COMPUTED WAS 322896 ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.37 TOTAL CPU TIME= 12.8 ( 0.2 MIN) TOTAL WALL CLOCK TIME= 13.0 SECONDS, CPU UTILIZATION IS 98.38% NSERCH= 0 ENERGY= -155.8253703 ----------------------- GRADIENT (HARTREE/BOHR) ----------------------- ATOM ZNUC DE/DX DE/DY DE/DZ -------------------------------------------------------------- 1 C 6.0 -0.0070228 -0.0096898 0.0124279 2 H 1.0 -0.0058383 0.0007542 -0.0049317 3 C 6.0 0.0007755 0.0102530 -0.0139087 4 H 1.0 -0.0074319 0.0003938 0.0019556 5 C 6.0 0.0035713 -0.0030923 0.0032913 6 H 1.0 -0.0023475 -0.0030814 0.0059735 7 H 1.0 0.0069693 -0.0008933 -0.0028691 8 C 6.0 0.0054929 0.0026049 -0.0019230 9 H 1.0 0.0050126 -0.0001571 0.0057118 10 H 1.0 0.0008190 0.0029081 -0.0057276 MAXIMUM GRADIENT = 0.0139087 RMS GRADIENT = 0.0057643 NSERCH: 0 E= -155.8253703302 GRAD. MAX= 0.0139087 R.M.S.= 0.0057643 FORCE CONSTANT MATRIX NOT UPDATED --- TAKING FIRST STEP MIN SEARCH, CORRECT HESSIAN, TRYING PURE NR STEP NR STEP HAS LENGTH = 1.276844 TRIM/QA LAMBDA FOR NON-TS MODES = -0.00231301 TRIM/QA STEP HAS LENGTH = 0.300000 RADIUS OF STEP TAKEN= 0.30000 CURRENT TRUST RADIUS= 0.30000 BEGINNING GEOMETRY SEARCH POINT NSERCH= 1 ... COORDINATES OF ALL ATOMS ARE (ANGS) ATOM CHARGE X Y Z ------------------------------------------------------------ C 6.0 0.3965562389 -0.3999591213 0.7538924806 H 1.0 1.2111165897 -0.5546770468 1.4675563350 C 6.0 0.7457063024 0.3008464175 -0.4885539413 H 1.0 1.8001830111 0.2824183699 -0.7756840608 C 6.0 -0.0806609827 1.0745716005 -1.1897571992 H 1.0 0.2557546298 1.5798053966 -2.0857673874 H 1.0 -1.0821380336 1.2890800142 -0.8307699898 C 6.0 -0.7752799569 -0.9825662683 1.0023143529 H 1.0 -1.5296767345 -1.0617043109 0.2233997026 H 1.0 -0.9405610643 -1.5278150514 1.9233697073 INTERNUCLEAR DISTANCES (ANGS.) ------------------------------ 1 C 2 H 3 C 4 H 5 C 1 C 0.0000000 1.0939663 * 1.4685732 * 2.1852715 * 2.4859105 * 2 H 1.0939663 * 0.0000000 2.1851532 * 2.4657363 * 3.3740859 3 C 1.4685732 * 2.1851532 * 0.0000000 1.0930254 * 1.3316229 * 4 H 2.1852715 * 2.4657363 * 1.0930254 * 0.0000000 2.0824355 * 5 C 2.4859105 * 3.3740859 1.3316229 * 2.0824355 * 0.0000000 6 H 3.4645289 4.2538032 2.1040151 * 2.4051591 * 1.0822527 * 7 H 2.7478255 * 3.7337328 2.1058804 * 3.0535515 1.0852843 * 8 C 1.3320453 * 2.0845408 * 2.4866113 * 3.3755702 3.0853670 9 H 2.1046859 * 3.0523680 2.7460500 * 3.7273047 2.9428445 * 10 H 2.1041907 * 2.4050946 * 3.4648053 4.2512956 4.1476986 6 H 7 H 8 C 9 H 10 H 1 C 3.4645289 2.7478255 * 1.3320453 * 2.1046859 * 2.1041907 * 2 H 4.2538032 3.7337328 2.0845408 * 3.0523680 2.4050946 * 3 C 2.1040151 * 2.1058804 * 2.4866113 * 2.7460500 * 3.4648053 4 H 2.4051591 * 3.0535515 3.3755702 3.7273047 4.2512956 5 C 1.0822527 * 1.0852843 * 3.0853670 2.9428445 * 4.1476986 6 H 0.0000000 1.8572820 * 4.1430701 3.9366980 5.2116846 7 H 1.8572820 * 0.0000000 2.9350872 * 2.6149095 * 3.9421095 8 C 4.1430701 2.9350872 * 0.0000000 1.0872375 * 1.0830314 * 9 H 3.9366980 2.6149095 * 1.0872375 * 0.0000000 1.8585517 * 10 H 5.2116846 3.9421095 1.0830314 * 1.8585517 * 0.0000000 * ... LESS THAN 3.000 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 12.8 ( 0.2 MIN) TOTAL WALL CLOCK TIME= 13.0 SECONDS, CPU UTILIZATION IS 98.31% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 12.8 ( 0.2 MIN) TOTAL WALL CLOCK TIME= 13.0 SECONDS, CPU UTILIZATION IS 98.31% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 1.00E-04 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 1.50E-03 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8207450733 -155.8207450733 0.009758205 0.017904121 17674232 80326 2 1 0 -155.8235131593 -0.0027680859 0.005127011 0.003153497 17122688 107618 3 2 0 -155.8235448573 -0.0000316980 0.002868282 0.003075112 16718102 120186 4 3 0 -155.8236137699 -0.0000689126 0.000676687 0.001474964 16397332 131095 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 5 4 0 -155.8241718573 -0.0005580874 0.001254282 0.001458545 17674117 80335 6 5 0 -155.8241766143 -0.0000047570 0.000864409 0.000671146 16408237 131773 7 6 0 -155.8241767513 -0.0000001370 0.000379797 0.000806634 15951127 144722 8 7 0 -155.8241791122 -0.0000023610 0.000112468 0.000157280 15664070 155804 9 8 0 -155.8241792304 -0.0000001182 0.000008513 0.000013417 14828399 178624 10 9 0 -155.8241792316 -0.0000000012 0.000001961 0.000002622 13889540 205943 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 7.9 SECONDS ( 0.8 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8241792316 AFTER 10 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9893062930 TOTAL ELECTRON NUMBER = 30.0000110329 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.19 TOTAL CPU TIME= 21.0 ( 0.3 MIN) TOTAL WALL CLOCK TIME= 21.3 SECONDS, CPU UTILIZATION IS 98.64% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 21.0 ( 0.3 MIN) TOTAL WALL CLOCK TIME= 21.3 SECONDS, CPU UTILIZATION IS 98.64% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700735 WORDS. CPU 0: STEP CPU TIME= 2.28 TOTAL CPU TIME= 23.3 ( 0.4 MIN) TOTAL WALL CLOCK TIME= 23.6 SECONDS, CPU UTILIZATION IS 98.73% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 23.6 ( 0.4 MIN) TOTAL WALL CLOCK TIME= 23.9 SECONDS, CPU UTILIZATION IS 98.75% NSERCH= 1 ENERGY= -155.8241792 ----------------------- GRADIENT (HARTREE/BOHR) ----------------------- ATOM ZNUC DE/DX DE/DY DE/DZ -------------------------------------------------------------- 1 C 6.0 -0.0074050 0.0047463 0.0048351 2 H 1.0 0.0031742 -0.0059139 -0.0000750 3 C 6.0 -0.0049289 -0.0044619 -0.0086016 4 H 1.0 0.0031888 0.0052058 0.0015726 5 C 6.0 0.0004473 -0.0024580 -0.0027646 6 H 1.0 0.0005371 -0.0008104 0.0015438 7 H 1.0 0.0020970 0.0024878 0.0028617 8 C 6.0 -0.0016675 0.0064852 0.0052624 9 H 1.0 0.0027617 -0.0044354 -0.0033447 10 H 1.0 0.0017952 -0.0008455 -0.0012898 MAXIMUM GRADIENT = 0.0086016 RMS GRADIENT = 0.0039001 NSERCH: 1 E= -155.8241792316 GRAD. MAX= 0.0086016 R.M.S.= 0.0039001 HESSIAN UPDATED USING THE BFGS FORMULA ACTUAL ENERGY CHANGE WAS 0.0011910985 PREDICTED ENERGY CHANGE WAS -0.0009377068 RATIO= -1.270 MIN SEARCH, CORRECT HESSIAN, TRYING PURE NR STEP NR STEP HAS LENGTH = 4.332086 TRIM/QA LAMBDA FOR NON-TS MODES = -0.08243982 TRIM/QA STEP HAS LENGTH = 0.150000 RADIUS OF STEP TAKEN= 0.15000 CURRENT TRUST RADIUS= 0.15000 BEGINNING GEOMETRY SEARCH POINT NSERCH= 2 ... COORDINATES OF ALL ATOMS ARE (ANGS) ATOM CHARGE X Y Z ------------------------------------------------------------ C 6.0 0.4126391422 -0.4225504244 0.7368388294 H 1.0 1.2086596541 -0.5341382680 1.4828869372 C 6.0 0.7569651326 0.3243650722 -0.4625262285 H 1.0 1.8014952134 0.2628756112 -0.7904765569 C 6.0 -0.0806511035 1.0858221267 -1.1824478407 H 1.0 0.2572191985 1.5818879851 -2.0927755262 H 1.0 -1.0976070522 1.2764402978 -0.8350223414 C 6.0 -0.7667024639 -1.0109968636 0.9869939577 H 1.0 -1.5463087302 -1.0401471281 0.2247799198 H 1.0 -0.9447089910 -1.5235584089 1.9317488496 INTERNUCLEAR DISTANCES (ANGS.) ------------------------------ 1 C 2 H 3 C 4 H 5 C 1 C 0.0000000 1.0966715 * 1.4542763 * 2.1751833 * 2.4904185 * 2 H 1.0966715 * 0.0000000 2.1738648 * 2.4809004 * 3.3749968 3 C 1.4542763 * 2.1738648 * 0.0000000 1.0965288 * 1.3415308 * 4 H 2.1751833 * 2.4809004 * 1.0965288 * 0.0000000 2.0912573 * 5 C 2.4904185 * 3.3749968 1.3415308 * 2.0912573 * 0.0000000 6 H 3.4711160 4.2624134 2.1186842 * 2.4125846 * 1.0903826 * 7 H 2.7637222 * 3.7376148 2.1176965 * 3.0714966 1.0914390 * 8 C 1.3415265 * 2.0917360 * 2.4911570 * 3.3730983 3.0941548 9 H 2.1168625 * 3.0706236 2.7639381 * 3.7331495 2.9407801 * 10 H 2.1171732 * 2.4119340 * 3.4703125 4.2595182 4.1537554 6 H 7 H 8 C 9 H 10 H 1 C 3.4711160 2.7637222 * 1.3415265 * 2.1168625 * 2.1171732 * 2 H 4.2624134 3.7376148 2.0917360 * 3.0706236 2.4119340 * 3 C 2.1186842 * 2.1176965 * 2.4911570 * 2.7639381 * 3.4703125 4 H 2.4125846 * 3.0714966 3.3730983 3.7331495 4.2595182 5 C 1.0903826 * 1.0914390 * 3.0941548 2.9407801 * 4.1537554 6 H 0.0000000 1.8737117 * 4.1540880 3.9368572 5.2235261 7 H 1.8737117 * 0.0000000 2.9430613 * 2.5867144 * 3.9393392 8 C 4.1540880 2.9430613 * 0.0000000 1.0906906 * 1.0894804 * 9 H 3.9368572 2.5867144 * 1.0906906 * 0.0000000 1.8733264 * 10 H 5.2235261 3.9393392 1.0894804 * 1.8733264 * 0.0000000 * ... LESS THAN 3.000 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 23.6 ( 0.4 MIN) TOTAL WALL CLOCK TIME= 23.9 SECONDS, CPU UTILIZATION IS 98.75% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 23.7 ( 0.4 MIN) TOTAL WALL CLOCK TIME= 24.0 SECONDS, CPU UTILIZATION IS 98.71% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8237881915 -155.8237881915 0.006391147 0.010767246 17654923 80971 2 1 0 -155.8250606283 -0.0012724368 0.004255536 0.002070844 17020232 111608 3 2 0 -155.8250459391 0.0000146892 0.002229687 0.003639057 16528427 127020 4 3 0 -155.8251034541 -0.0000575150 0.000533403 0.001058678 16286244 135969 5 4 0 -155.8251072363 -0.0000037821 0.000082789 0.000123020 15800492 150776 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 6 5 0 -155.8254460613 -0.0003388250 0.000849559 0.001409506 17654801 80969 7 6 0 -155.8254522508 -0.0000061895 0.000459275 0.000354301 16375190 133014 8 7 0 -155.8254525537 -0.0000003029 0.000245264 0.000232195 15621984 154163 9 8 0 -155.8254528413 -0.0000002876 0.000041401 0.000042376 15138724 168270 10 9 0 -155.8254528500 -0.0000000087 0.000015206 0.000025903 14412434 193584 11 10 0 -155.8254528534 -0.0000000034 0.000002014 0.000002599 13702737 209212 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 8.2 SECONDS ( 0.7 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8254528534 AFTER 11 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9760227192 TOTAL ELECTRON NUMBER = 30.0000079741 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.41 TOTAL CPU TIME= 32.1 ( 0.5 MIN) TOTAL WALL CLOCK TIME= 32.4 SECONDS, CPU UTILIZATION IS 98.83% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 32.1 ( 0.5 MIN) TOTAL WALL CLOCK TIME= 32.4 SECONDS, CPU UTILIZATION IS 98.83% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700735 WORDS. CPU 0: STEP CPU TIME= 2.32 TOTAL CPU TIME= 34.4 ( 0.6 MIN) TOTAL WALL CLOCK TIME= 34.8 SECONDS, CPU UTILIZATION IS 98.91% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.35 TOTAL CPU TIME= 34.7 ( 0.6 MIN) TOTAL WALL CLOCK TIME= 35.1 SECONDS, CPU UTILIZATION IS 98.86% NSERCH= 2 ENERGY= -155.8254529 ----------------------- GRADIENT (HARTREE/BOHR) ----------------------- ATOM ZNUC DE/DX DE/DY DE/DZ -------------------------------------------------------------- 1 C 6.0 0.0038494 0.0054398 -0.0103819 2 H 1.0 0.0034713 -0.0024238 0.0027385 3 C 6.0 -0.0010237 -0.0047682 0.0118125 4 H 1.0 0.0044287 0.0012720 -0.0014404 5 C 6.0 -0.0039069 0.0011290 -0.0063982 6 H 1.0 0.0023062 0.0011720 -0.0036767 7 H 1.0 -0.0023611 0.0018426 0.0037540 8 C 6.0 -0.0068388 -0.0011247 0.0039902 9 H 1.0 -0.0003362 -0.0015550 -0.0042398 10 H 1.0 0.0004110 -0.0009836 0.0038418 MAXIMUM GRADIENT = 0.0118125 RMS GRADIENT = 0.0043411 NSERCH: 2 E= -155.8254528534 GRAD. MAX= 0.0118125 R.M.S.= 0.0043411 HESSIAN UPDATED USING THE BFGS FORMULA ACTUAL ENERGY CHANGE WAS -0.0012736218 PREDICTED ENERGY CHANGE WAS -0.0023705001 RATIO= 0.537 MIN SEARCH, CORRECT HESSIAN, TRYING PURE NR STEP NR STEP HAS LENGTH = 8.197144 TRIM/QA LAMBDA FOR NON-TS MODES = -0.04218051 TRIM/QA STEP HAS LENGTH = 0.150000 RADIUS OF STEP TAKEN= 0.15000 CURRENT TRUST RADIUS= 0.15000 BEGINNING GEOMETRY SEARCH POINT NSERCH= 3 ... COORDINATES OF ALL ATOMS ARE (ANGS) ATOM CHARGE X Y Z ------------------------------------------------------------ C 6.0 0.4148863322 -0.4195092368 0.7443963181 H 1.0 1.2043222108 -0.5108976412 1.4825304854 C 6.0 0.7584256155 0.3119505449 -0.4760606147 H 1.0 1.7960687978 0.2459353917 -0.7891757224 C 6.0 -0.0659106781 1.1074240146 -1.1549359889 H 1.0 0.2451115730 1.5824300662 -2.0807162040 H 1.0 -1.0986574990 1.2599647414 -0.8606354528 C 6.0 -0.7469705927 -1.0300501284 0.9702135531 H 1.0 -1.5561570223 -1.0226803875 0.2493681367 H 1.0 -0.9501187374 -1.5245673651 1.9150154896 INTERNUCLEAR DISTANCES (ANGS.) ------------------------------ 1 C 2 H 3 C 4 H 5 C 1 C 0.0000000 1.0846211 * 1.4637513 * 2.1684844 * 2.4839795 * 2 H 1.0846211 * 0.0000000 2.1707100 * 2.4664974 * 3.3449493 3 C 1.4637513 * 2.1707100 * 0.0000000 1.0858648 * 1.3316081 * 4 H 2.1684844 * 2.4664974 * 1.0858648 * 0.0000000 2.0839652 * 5 C 2.4839795 * 3.3449493 1.3316081 * 2.0839652 * 0.0000000 6 H 3.4666764 4.2425031 2.1101017 * 2.4206948 * 1.0860178 * 7 H 2.7726476 * 3.7323043 2.1202326 * 3.0680291 1.0846416 * 8 C 1.3317902 * 2.0831542 * 2.4817116 * 3.3452412 3.0901293 9 H 2.1198774 * 3.0664078 2.7685338 * 3.7316722 2.9546995 * 10 H 2.1106259 * 2.4199557 * 3.4654245 4.2413295 4.1393000 6 H 7 H 8 C 9 H 10 H 1 C 3.4666764 2.7726476 * 1.3317902 * 2.1198774 * 2.1106259 * 2 H 4.2425031 3.7323043 2.0831542 * 3.0664078 2.4199557 * 3 C 2.1101017 * 2.1202326 * 2.4817116 * 2.7685338 * 3.4654245 4 H 2.4206948 * 3.0680291 3.3452412 3.7316722 4.2413295 5 C 1.0860178 * 1.0846416 * 3.0901293 2.9546995 * 4.1393000 6 H 0.0000000 1.8434468 * 4.1373243 3.9319794 5.2007577 7 H 1.8434468 * 0.0000000 2.9529409 * 2.5791244 * 3.9344531 8 C 4.1373243 2.9529409 * 0.0000000 1.0837228 * 1.0855723 * 9 H 3.9319794 2.5791244 * 1.0837228 * 0.0000000 1.8421602 * 10 H 5.2007577 3.9344531 1.0855723 * 1.8421602 * 0.0000000 * ... LESS THAN 3.000 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 34.8 ( 0.6 MIN) TOTAL WALL CLOCK TIME= 35.1 SECONDS, CPU UTILIZATION IS 98.89% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 34.8 ( 0.6 MIN) TOTAL WALL CLOCK TIME= 35.1 SECONDS, CPU UTILIZATION IS 98.86% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8236318071 -155.8236318071 0.008505729 0.010701397 17678032 80286 2 1 0 -155.8250980570 -0.0014662499 0.002827674 0.001631027 17064716 109725 3 2 0 -155.8251104229 -0.0000123659 0.001698878 0.001633021 16537531 126977 4 3 0 -155.8251312953 -0.0000208723 0.000406889 0.000834017 16177741 138716 5 4 0 -155.8251330128 -0.0000017175 0.000116490 0.000199809 15686829 155575 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 6 5 0 -155.8257268503 -0.0005938375 0.000875264 0.001467973 17678673 80269 7 6 0 -155.8257324748 -0.0000056245 0.000405120 0.000346723 16398748 132466 8 7 0 -155.8257327864 -0.0000003116 0.000190588 0.000225122 15648541 153222 9 8 0 -155.8257330829 -0.0000002965 0.000015335 0.000026456 15210451 166314 10 9 0 -155.8257330867 -0.0000000038 0.000009499 0.000008259 14286654 196044 11 10 0 -155.8257330869 -0.0000000003 0.000003283 0.000005124 13153778 225680 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 8.2 SECONDS ( 0.7 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8257330869 AFTER 11 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9948289845 TOTAL ELECTRON NUMBER = 30.0000037282 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.42 TOTAL CPU TIME= 43.2 ( 0.7 MIN) TOTAL WALL CLOCK TIME= 43.6 SECONDS, CPU UTILIZATION IS 98.92% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 43.2 ( 0.7 MIN) TOTAL WALL CLOCK TIME= 43.6 SECONDS, CPU UTILIZATION IS 98.92% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700735 WORDS. CPU 0: STEP CPU TIME= 2.31 TOTAL CPU TIME= 45.5 ( 0.8 MIN) TOTAL WALL CLOCK TIME= 46.0 SECONDS, CPU UTILIZATION IS 98.93% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 45.9 ( 0.8 MIN) TOTAL WALL CLOCK TIME= 46.3 SECONDS, CPU UTILIZATION IS 98.94% NSERCH= 3 ENERGY= -155.8257331 ----------------------- GRADIENT (HARTREE/BOHR) ----------------------- ATOM ZNUC DE/DX DE/DY DE/DZ -------------------------------------------------------------- 1 C 6.0 0.0011060 0.0030426 0.0046171 2 H 1.0 -0.0017646 -0.0005930 -0.0026010 3 C 6.0 0.0000991 -0.0041282 -0.0048605 4 H 1.0 -0.0016977 0.0012332 0.0020276 5 C 6.0 0.0018545 0.0033462 0.0069183 6 H 1.0 -0.0012589 -0.0014477 -0.0018455 7 H 1.0 0.0004280 -0.0001367 -0.0024527 8 C 6.0 0.0027616 -0.0023468 -0.0051129 9 H 1.0 -0.0001298 -0.0001494 0.0026749 10 H 1.0 -0.0013982 0.0011797 0.0006347 MAXIMUM GRADIENT = 0.0069183 RMS GRADIENT = 0.0026910 NSERCH: 3 E= -155.8257330869 GRAD. MAX= 0.0069183 R.M.S.= 0.0026910 HESSIAN UPDATED USING THE BFGS FORMULA ACTUAL ENERGY CHANGE WAS -0.0002802335 PREDICTED ENERGY CHANGE WAS -0.0014706325 RATIO= 0.191 MIN SEARCH, CORRECT HESSIAN, TRYING PURE NR STEP NR STEP HAS LENGTH = 17.179628 TRIM/QA LAMBDA FOR NON-TS MODES = -0.03495455 TRIM/QA STEP HAS LENGTH = 0.150000 RADIUS OF STEP TAKEN= 0.15000 CURRENT TRUST RADIUS= 0.15000 BEGINNING GEOMETRY SEARCH POINT NSERCH= 4 ... COORDINATES OF ALL ATOMS ARE (ANGS) ATOM CHARGE X Y Z ------------------------------------------------------------ C 6.0 0.4191149622 -0.4372215040 0.7412309180 H 1.0 1.1969708131 -0.4970538899 1.4840456063 C 6.0 0.7651296288 0.3332062579 -0.4681581794 H 1.0 1.7866225952 0.2315604893 -0.7955270572 C 6.0 -0.0754784856 1.0700761069 -1.1770174651 H 1.0 0.2470048221 1.6010158198 -2.0592207578 H 1.0 -1.0893088270 1.2604563487 -0.8630209173 C 6.0 -0.7547786555 -0.9977886006 0.9838266431 H 1.0 -1.5498354471 -1.0238213515 0.2557041561 H 1.0 -0.9444414063 -1.5404296768 1.8981370533 INTERNUCLEAR DISTANCES (ANGS.) ------------------------------ 1 C 2 H 3 C 4 H 5 C 1 C 0.0000000 1.0772248 * 1.4750956 * 2.1630931 * 2.4892259 * 2 H 1.0772248 * 0.0000000 2.1649292 * 2.4647555 * 3.3401018 3 C 1.4750956 * 2.1649292 * 0.0000000 1.0774740 * 1.3236618 * 4 H 2.1630931 * 2.4647555 * 1.0774740 * 0.0000000 2.0775139 * 5 C 2.4892259 * 3.3401018 1.3236618 * 2.0775139 * 0.0000000 6 H 3.4679335 4.2259991 2.0993510 * 2.4171786 * 1.0789695 * 7 H 2.7804813 * 3.7181498 2.1106045 * 3.0551864 1.0782812 * 8 C 1.3232968 * 2.0761214 * 2.4879567 * 3.3370824 3.0670442 9 H 2.1110664 * 3.0547097 2.7793100 * 3.7165875 2.9344209 * 10 H 2.1011392 * 2.4177988 * 3.4687891 4.2254569 4.1263073 6 H 7 H 8 C 9 H 10 H 1 C 3.4679335 2.7804813 * 1.3232968 * 2.1110664 * 2.1011392 * 2 H 4.2259991 3.7181498 2.0761214 * 3.0547097 2.4177988 * 3 C 2.0993510 * 2.1106045 * 2.4879567 * 2.7793100 * 3.4687891 4 H 2.4171786 * 3.0551864 3.3370824 3.7165875 4.2254569 5 C 1.0789695 * 1.0782812 * 3.0670442 2.9344209 * 4.1263073 6 H 0.0000000 1.8255435 * 4.1252263 3.9341178 5.1912335 7 H 1.8255435 * 0.0000000 2.9363969 * 2.5848704 * 3.9357264 8 C 4.1252263 2.9363969 * 0.0000000 1.0784041 * 1.0799976 * 9 H 3.9341178 2.5848704 * 1.0784041 * 0.0000000 1.8250950 * 10 H 5.1912335 3.9357264 1.0799976 * 1.8250950 * 0.0000000 * ... LESS THAN 3.000 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 45.9 ( 0.8 MIN) TOTAL WALL CLOCK TIME= 46.3 SECONDS, CPU UTILIZATION IS 98.94% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 45.9 ( 0.8 MIN) TOTAL WALL CLOCK TIME= 46.4 SECONDS, CPU UTILIZATION IS 98.92% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8219550861 -155.8219550861 0.009449002 0.014130796 17702833 79697 2 1 0 -155.8241382571 -0.0021831709 0.003316286 0.002069452 17145429 107937 3 2 0 -155.8241468503 -0.0000085932 0.001927977 0.002455808 16566052 126370 4 3 0 -155.8241772200 -0.0000303698 0.000455703 0.000917996 16244272 137329 5 4 0 -155.8241796855 -0.0000024655 0.000122400 0.000182145 15788255 151629 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 6 5 0 -155.8250451224 -0.0008654368 0.001139071 0.001440430 17702295 79727 7 6 0 -155.8250508910 -0.0000057687 0.000405657 0.000353456 16440119 130673 8 7 0 -155.8250511946 -0.0000003035 0.000182985 0.000225438 15674292 152741 9 8 0 -155.8250514759 -0.0000002814 0.000017559 0.000023955 15206509 166209 10 9 0 -155.8250514798 -0.0000000038 0.000009535 0.000016144 14320534 195663 11 10 0 -155.8250514804 -0.0000000006 0.000002594 0.000006817 13462400 217062 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 8.2 SECONDS ( 0.7 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8250514804 AFTER 11 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -18.0104232071 TOTAL ELECTRON NUMBER = 30.0000081334 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.45 TOTAL CPU TIME= 54.3 ( 0.9 MIN) TOTAL WALL CLOCK TIME= 54.9 SECONDS, CPU UTILIZATION IS 98.98% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 54.3 ( 0.9 MIN) TOTAL WALL CLOCK TIME= 54.9 SECONDS, CPU UTILIZATION IS 99.00% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700735 WORDS. CPU 0: STEP CPU TIME= 2.30 TOTAL CPU TIME= 56.6 ( 0.9 MIN) TOTAL WALL CLOCK TIME= 57.2 SECONDS, CPU UTILIZATION IS 99.00% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.37 TOTAL CPU TIME= 57.0 ( 0.9 MIN) TOTAL WALL CLOCK TIME= 57.6 SECONDS, CPU UTILIZATION IS 99.01% NSERCH= 4 ENERGY= -155.8250515 ----------------------- GRADIENT (HARTREE/BOHR) ----------------------- ATOM ZNUC DE/DX DE/DY DE/DZ -------------------------------------------------------------- 1 C 6.0 -0.0025929 -0.0146474 0.0094243 2 H 1.0 -0.0058276 0.0024664 -0.0056154 3 C 6.0 0.0039982 0.0146632 -0.0089789 4 H 1.0 -0.0078302 -0.0014221 0.0025979 5 C 6.0 0.0012390 -0.0096306 0.0020843 6 H 1.0 -0.0021717 -0.0003532 0.0044881 7 H 1.0 0.0055570 0.0021704 -0.0025199 8 C 6.0 0.0046917 0.0092938 -0.0018473 9 H 1.0 0.0032386 -0.0028401 0.0047383 10 H 1.0 -0.0003022 0.0002998 -0.0043714 MAXIMUM GRADIENT = 0.0146632 RMS GRADIENT = 0.0060581 NSERCH: 4 E= -155.8250514804 GRAD. MAX= 0.0146632 R.M.S.= 0.0060581 HESSIAN UPDATED USING THE BFGS FORMULA ACTUAL ENERGY CHANGE WAS 0.0006816066 PREDICTED ENERGY CHANGE WAS -0.0010977941 RATIO= -0.621 MIN SEARCH, CORRECT HESSIAN, TRYING PURE NR STEP NR STEP HAS LENGTH = 4.967209 TRIM/QA LAMBDA FOR NON-TS MODES = -0.12893621 TRIM/QA STEP HAS LENGTH = 0.075000 RADIUS OF STEP TAKEN= 0.07500 CURRENT TRUST RADIUS= 0.07500 BEGINNING GEOMETRY SEARCH POINT NSERCH= 5 ... COORDINATES OF ALL ATOMS ARE (ANGS) ATOM CHARGE X Y Z ------------------------------------------------------------ C 6.0 0.4157475836 -0.4250591140 0.7385584272 H 1.0 1.2035854184 -0.5003359093 1.4921636492 C 6.0 0.7611694300 0.3221362890 -0.4665904133 H 1.0 1.7967801289 0.2338261421 -0.8011623471 C 6.0 -0.0764570573 1.0795316272 -1.1804212856 H 1.0 0.2554809373 1.6045072325 -2.0680756438 H 1.0 -1.0996458868 1.2539261932 -0.8552890910 C 6.0 -0.7598274263 -1.0078654779 0.9868483044 H 1.0 -1.5549074438 -1.0160507345 0.2438989361 H 1.0 -0.9409256840 -1.5446162483 1.9100694640 INTERNUCLEAR DISTANCES (ANGS.) ------------------------------ 1 C 2 H 3 C 4 H 5 C 1 C 0.0000000 1.0928293 * 1.4594523 * 2.1707420 * 2.4876780 * 2 H 1.0928293 * 0.0000000 2.1700023 * 2.4799633 * 3.3581543 3 C 1.4594523 * 2.1700023 * 0.0000000 1.0918913 * 1.3359717 * 4 H 2.1707420 * 2.4799633 * 1.0918913 * 0.0000000 2.0899935 * 5 C 2.4876780 * 3.3581543 1.3359717 * 2.0899935 * 0.0000000 6 H 3.4672784 4.2431793 2.1130431 * 2.4206278 * 1.0833801 * 7 H 2.7669042 * 3.7273106 2.1170623 * 3.0712892 1.0876763 * 8 C 1.3353980 * 2.0899569 * 2.4889396 * 3.3578300 3.0856570 9 H 2.1159963 * 3.0713856 2.7676256 * 3.7266815 2.9335932 * 10 H 2.1133880 * 2.4215893 * 3.4684874 4.2436621 4.1454302 6 H 7 H 8 C 9 H 10 H 1 C 3.4672784 2.7669042 * 1.3353980 * 2.1159963 * 2.1133880 * 2 H 4.2431793 3.7273106 2.0899569 * 3.0713856 2.4215893 * 3 C 2.1130431 * 2.1170623 * 2.4889396 * 2.7676256 * 3.4684874 4 H 2.4206278 * 3.0712892 3.3578300 3.7266815 4.2436621 5 C 1.0833801 * 1.0876763 * 3.0856570 2.9335932 * 4.1454302 6 H 0.0000000 1.8520602 * 4.1458295 3.9357409 5.2128693 7 H 1.8520602 * 0.0000000 2.9367752 * 2.5628642 * 3.9375424 8 C 4.1458295 2.9367752 * 0.0000000 1.0882063 * 1.0831599 * 9 H 3.9357409 2.5628642 * 1.0882063 * 0.0000000 1.8526952 * 10 H 5.2128693 3.9375424 1.0831599 * 1.8526952 * 0.0000000 * ... LESS THAN 3.000 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 57.0 ( 0.9 MIN) TOTAL WALL CLOCK TIME= 57.6 SECONDS, CPU UTILIZATION IS 99.01% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 57.0 ( 0.9 MIN) TOTAL WALL CLOCK TIME= 57.6 SECONDS, CPU UTILIZATION IS 98.99% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 1.00E-04 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 1.50E-03 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8249645282 -155.8249645282 0.004502616 0.006772810 17674846 80394 2 1 0 -155.8254181531 -0.0004536249 0.003850444 0.002121776 16920419 114071 3 2 0 -155.8254334972 -0.0000153441 0.001807009 0.001817793 16445244 128535 4 3 0 -155.8254557464 -0.0000222492 0.000435007 0.000947492 16174410 138370 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 5 4 0 -155.8260007678 -0.0005450214 0.001125195 0.001480363 17673856 80424 6 5 0 -155.8260066134 -0.0000058456 0.000627886 0.000408370 16410613 131633 7 6 0 -155.8260066716 -0.0000000582 0.000306051 0.000525865 15825053 148232 8 7 0 -155.8260078296 -0.0000011580 0.000092052 0.000159499 15532461 158795 9 8 0 -155.8260079277 -0.0000000981 0.000011064 0.000014405 14770240 181745 10 9 0 -155.8260079294 -0.0000000017 0.000001934 0.000001981 13868972 206199 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 8.0 SECONDS ( 0.8 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8260079294 AFTER 10 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9878053630 TOTAL ELECTRON NUMBER = 30.0000060534 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.24 TOTAL CPU TIME= 65.2 ( 1.1 MIN) TOTAL WALL CLOCK TIME= 65.9 SECONDS, CPU UTILIZATION IS 99.04% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 65.3 ( 1.1 MIN) TOTAL WALL CLOCK TIME= 65.9 SECONDS, CPU UTILIZATION IS 99.04% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700735 WORDS. CPU 0: STEP CPU TIME= 2.31 TOTAL CPU TIME= 67.6 ( 1.1 MIN) TOTAL WALL CLOCK TIME= 68.2 SECONDS, CPU UTILIZATION IS 99.06% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 67.9 ( 1.1 MIN) TOTAL WALL CLOCK TIME= 68.6 SECONDS, CPU UTILIZATION IS 99.05% NSERCH= 5 ENERGY= -155.8260079 ----------------------- GRADIENT (HARTREE/BOHR) ----------------------- ATOM ZNUC DE/DX DE/DY DE/DZ -------------------------------------------------------------- 1 C 6.0 0.0015625 0.0000981 -0.0062936 2 H 1.0 0.0013501 0.0006586 0.0018725 3 C 6.0 0.0005741 -0.0000593 0.0067288 4 H 1.0 0.0013422 -0.0009528 -0.0011426 5 C 6.0 -0.0014119 -0.0011214 -0.0052579 6 H 1.0 -0.0000621 0.0007964 0.0013722 7 H 1.0 -0.0006785 0.0011908 0.0007735 8 C 6.0 -0.0022415 0.0007796 0.0044918 9 H 1.0 -0.0007121 -0.0007617 -0.0012295 10 H 1.0 0.0002771 -0.0006282 -0.0013153 MAXIMUM GRADIENT = 0.0067288 RMS GRADIENT = 0.0023377 NSERCH: 5 E= -155.8260079294 GRAD. MAX= 0.0067288 R.M.S.= 0.0023377 HESSIAN UPDATED USING THE BFGS FORMULA ACTUAL ENERGY CHANGE WAS -0.0009564490 PREDICTED ENERGY CHANGE WAS -0.0014002316 RATIO= 0.683 MIN SEARCH, CORRECT HESSIAN, TRYING PURE NR STEP NR STEP HAS LENGTH = 3.366079 TRIM/QA LAMBDA FOR NON-TS MODES = -0.01958742 TRIM/QA STEP HAS LENGTH = 0.075000 RADIUS OF STEP TAKEN= 0.07500 CURRENT TRUST RADIUS= 0.07500 BEGINNING GEOMETRY SEARCH POINT NSERCH= 6 ... COORDINATES OF ALL ATOMS ARE (ANGS) ATOM CHARGE X Y Z ------------------------------------------------------------ C 6.0 0.4137813837 -0.4150538196 0.7465684348 H 1.0 1.2061112559 -0.5085616162 1.4868556598 C 6.0 0.7584011526 0.3163240455 -0.4718813070 H 1.0 1.7945113584 0.2371432443 -0.7955038976 C 6.0 -0.0724642954 1.0915251183 -1.1681805888 H 1.0 0.2506948194 1.5958157436 -2.0715281935 H 1.0 -1.0992807513 1.2537514856 -0.8579249755 C 6.0 -0.7502794617 -1.0233992114 0.9738279820 H 1.0 -1.5539711584 -1.0176385387 0.2458322344 H 1.0 -0.9465043032 -1.5299064515 1.9119346515 INTERNUCLEAR DISTANCES (ANGS.) ------------------------------ 1 C 2 H 3 C 4 H 5 C 1 C 0.0000000 1.0883729 * 1.4622914 * 2.1701989 * 2.4844474 * 2 H 1.0883729 * 0.0000000 2.1719878 * 2.4721358 * 3.3532448 3 C 1.4622914 * 2.1719878 * 0.0000000 1.0883591 * 1.3327066 * 4 H 2.1701989 * 2.4721358 * 1.0883591 * 0.0000000 2.0867329 * 5 C 2.4844474 * 3.3532448 1.3327066 * 2.0867329 * 0.0000000 6 H 3.4658134 4.2430320 2.1103874 * 2.4202476 * 1.0838716 * 7 H 2.7656224 * 3.7307608 2.1163133 * 3.0678040 1.0848631 * 8 C 1.3329549 * 2.0870361 * 2.4821464 * 3.3459622 3.0855371 9 H 2.1179932 * 3.0687707 2.7643507 * 3.7244051 2.9398752 * 10 H 2.1098227 * 2.4202461 * 3.4637910 4.2386147 4.1379898 6 H 7 H 8 C 9 H 10 H 1 C 3.4658134 2.7656224 * 1.3329549 * 2.1179932 * 2.1098227 * 2 H 4.2430320 3.7307608 2.0870361 * 3.0687707 2.4202461 * 3 C 2.1103874 * 2.1163133 * 2.4821464 * 2.7643507 * 3.4637910 4 H 2.4202476 * 3.0678040 3.3459622 3.7244051 4.2386147 5 C 1.0838716 * 1.0848631 * 3.0855371 2.9398752 * 4.1379898 6 H 0.0000000 1.8472344 * 4.1396172 3.9315546 5.2030185 7 H 1.8472344 * 0.0000000 2.9432187 * 2.5659766 * 3.9299128 8 C 4.1396172 2.9432187 * 0.0000000 1.0844037 * 1.0840193 * 9 H 3.9315546 2.5659766 * 1.0844037 * 0.0000000 1.8458959 * 10 H 5.2030185 3.9299128 1.0840193 * 1.8458959 * 0.0000000 * ... LESS THAN 3.000 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 67.9 ( 1.1 MIN) TOTAL WALL CLOCK TIME= 68.6 SECONDS, CPU UTILIZATION IS 99.05% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 67.9 ( 1.1 MIN) TOTAL WALL CLOCK TIME= 68.6 SECONDS, CPU UTILIZATION IS 99.05% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8249776796 -155.8249776796 0.005235846 0.006945215 17684294 80154 2 1 0 -155.8255229281 -0.0005452485 0.001027112 0.000736365 16947905 114752 3 2 0 -155.8255291223 -0.0000061942 0.000457070 0.000276425 16217920 139125 4 3 0 -155.8255296541 -0.0000005318 0.000188865 0.000206701 15604901 157766 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 5 4 0 -155.8261017093 -0.0005720552 0.000830071 0.001424866 17685078 80137 6 5 0 -155.8261076345 -0.0000059253 0.000513612 0.000280809 16412115 131891 7 6 0 -155.8261078212 -0.0000001867 0.000277023 0.000209516 15643609 154043 8 7 0 -155.8261081858 -0.0000003646 0.000060735 0.000097155 15203973 167428 9 8 0 -155.8261082220 -0.0000000362 0.000014976 0.000028965 14649949 185858 10 9 0 -155.8261082255 -0.0000000035 0.000003350 0.000003360 13901204 203794 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 8.0 SECONDS ( 0.8 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8261082255 AFTER 10 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9933849837 TOTAL ELECTRON NUMBER = 30.0000052914 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.22 TOTAL CPU TIME= 76.1 ( 1.3 MIN) TOTAL WALL CLOCK TIME= 76.9 SECONDS, CPU UTILIZATION IS 99.06% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 76.2 ( 1.3 MIN) TOTAL WALL CLOCK TIME= 76.9 SECONDS, CPU UTILIZATION IS 99.06% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700735 WORDS. CPU 0: STEP CPU TIME= 2.31 TOTAL CPU TIME= 78.5 ( 1.3 MIN) TOTAL WALL CLOCK TIME= 79.2 SECONDS, CPU UTILIZATION IS 99.08% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 78.8 ( 1.3 MIN) TOTAL WALL CLOCK TIME= 79.6 SECONDS, CPU UTILIZATION IS 99.07% NSERCH= 6 ENERGY= -155.8261082 ----------------------- GRADIENT (HARTREE/BOHR) ----------------------- ATOM ZNUC DE/DX DE/DY DE/DZ -------------------------------------------------------------- 1 C 6.0 0.0003776 0.0037759 0.0018202 2 H 1.0 0.0000656 -0.0007827 -0.0008747 3 C 6.0 -0.0001295 -0.0022975 -0.0005126 4 H 1.0 -0.0004635 0.0000546 0.0004935 5 C 6.0 -0.0000722 0.0006849 0.0010086 6 H 1.0 -0.0005427 -0.0001577 0.0004539 7 H 1.0 0.0006290 0.0001965 -0.0010444 8 C 6.0 0.0007400 -0.0024039 -0.0027867 9 H 1.0 -0.0000124 -0.0001178 0.0017212 10 H 1.0 -0.0005920 0.0010477 -0.0002790 MAXIMUM GRADIENT = 0.0037759 RMS GRADIENT = 0.0012550 NSERCH: 6 E= -155.8261082255 GRAD. MAX= 0.0037759 R.M.S.= 0.0012550 HESSIAN UPDATED USING THE BFGS FORMULA ACTUAL ENERGY CHANGE WAS -0.0001002961 PREDICTED ENERGY CHANGE WAS -0.0003558793 RATIO= 0.282 MIN SEARCH, CORRECT HESSIAN, TRYING PURE NR STEP NR STEP HAS LENGTH = 4.345372 TRIM/QA LAMBDA FOR NON-TS MODES = -0.02387427 TRIM/QA STEP HAS LENGTH = 0.075000 RADIUS OF STEP TAKEN= 0.07500 CURRENT TRUST RADIUS= 0.07500 BEGINNING GEOMETRY SEARCH POINT NSERCH= 7 ... COORDINATES OF ALL ATOMS ARE (ANGS) ATOM CHARGE X Y Z ------------------------------------------------------------ C 6.0 0.4173245838 -0.4338849445 0.7363839665 H 1.0 1.2014105712 -0.5044913685 1.4876278340 C 6.0 0.7579951760 0.3139952267 -0.4756184236 H 1.0 1.7972672279 0.2447714572 -0.7945535172 C 6.0 -0.0682343151 1.1048206892 -1.1586410761 H 1.0 0.2500003789 1.5864928032 -2.0773638237 H 1.0 -1.1008855675 1.2475229678 -0.8543349044 C 6.0 -0.7604014958 -1.0078314953 0.9830744792 H 1.0 -1.5511304701 -1.0168121435 0.2398050808 H 1.0 -0.9423460893 -1.5345831923 1.9136203846 INTERNUCLEAR DISTANCES (ANGS.) ------------------------------ 1 C 2 H 3 C 4 H 5 C 1 C 0.0000000 1.0881836 * 1.4643534 * 2.1699276 * 2.4888757 * 2 H 1.0881836 * 0.0000000 2.1727571 * 2.4748316 * 3.3473307 3 C 1.4643534 * 2.1727571 * 0.0000000 1.0893108 * 1.3321336 * 4 H 2.1699276 * 2.4748316 * 1.0893108 * 0.0000000 2.0862264 * 5 C 2.4888757 * 3.3473307 1.3321336 * 2.0862264 * 0.0000000 6 H 3.4680110 4.2410567 2.1078181 * 2.4165788 * 1.0850497 * 7 H 2.7681187 * 3.7222186 2.1143173 * 3.0673073 1.0859718 * 8 C 1.3331577 * 2.0872546 * 2.4860690 * 3.3571781 3.0869629 9 H 2.1121577 * 3.0652922 2.7595181 * 3.7246823 2.9421010 * 10 H 2.1085840 * 2.4162474 * 3.4665350 4.2433230 4.1435872 6 H 7 H 8 C 9 H 10 H 1 C 3.4680110 2.7681187 * 1.3331577 * 2.1121577 * 2.1085840 * 2 H 4.2410567 3.7222186 2.0872546 * 3.0652922 2.4162474 * 3 C 2.1078181 * 2.1143173 * 2.4860690 * 2.7595181 * 3.4665350 4 H 2.4165788 * 3.0673073 3.3571781 3.7246823 4.2433230 5 C 1.0850497 * 1.0859718 * 3.0869629 2.9421010 * 4.1435872 6 H 0.0000000 1.8535353 * 4.1373558 3.9230780 5.2048785 7 H 1.8535353 * 0.0000000 2.9289292 * 2.5548143 * 3.9276998 8 C 4.1373558 2.9289292 * 0.0000000 1.0852568 * 1.0846598 * 9 H 3.9230780 2.5548143 * 1.0852568 * 0.0000000 1.8548215 * 10 H 5.2048785 3.9276998 1.0846598 * 1.8548215 * 0.0000000 * ... LESS THAN 3.000 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 78.8 ( 1.3 MIN) TOTAL WALL CLOCK TIME= 79.6 SECONDS, CPU UTILIZATION IS 99.08% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 78.8 ( 1.3 MIN) TOTAL WALL CLOCK TIME= 79.6 SECONDS, CPU UTILIZATION IS 99.08% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8248058132 -155.8248058132 0.005862175 0.006897055 17684682 80126 2 1 0 -155.8254015614 -0.0005957483 0.001003678 0.000807773 16941164 114997 3 2 0 -155.8254086346 -0.0000070731 0.000443129 0.000449276 16249742 136957 4 3 0 -155.8254102587 -0.0000016241 0.000208541 0.000276269 15810488 150556 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 5 4 0 -155.8259720044 -0.0005617457 0.000928755 0.001450014 17685003 80114 6 5 0 -155.8259779605 -0.0000059561 0.000617320 0.000421667 16414707 131631 7 6 0 -155.8259782301 -0.0000002696 0.000323957 0.000277896 15692117 152131 8 7 0 -155.8259787813 -0.0000005512 0.000070200 0.000120579 15320369 164361 9 8 0 -155.8259788334 -0.0000000521 0.000013954 0.000030400 14754732 182814 10 9 0 -155.8259788372 -0.0000000038 0.000003682 0.000003793 13940178 202912 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 8.0 SECONDS ( 0.8 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8259788372 AFTER 10 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9916484894 TOTAL ELECTRON NUMBER = 30.0000046362 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.22 TOTAL CPU TIME= 87.1 ( 1.5 MIN) TOTAL WALL CLOCK TIME= 87.9 SECONDS, CPU UTILIZATION IS 99.09% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 87.1 ( 1.5 MIN) TOTAL WALL CLOCK TIME= 87.9 SECONDS, CPU UTILIZATION IS 99.09% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700735 WORDS. CPU 0: STEP CPU TIME= 2.30 TOTAL CPU TIME= 89.4 ( 1.5 MIN) TOTAL WALL CLOCK TIME= 90.2 SECONDS, CPU UTILIZATION IS 99.09% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 89.7 ( 1.5 MIN) TOTAL WALL CLOCK TIME= 90.6 SECONDS, CPU UTILIZATION IS 99.08% NSERCH= 7 ENERGY= -155.8259788 ----------------------- GRADIENT (HARTREE/BOHR) ----------------------- ATOM ZNUC DE/DX DE/DY DE/DZ -------------------------------------------------------------- 1 C 6.0 0.0024092 -0.0029765 -0.0007273 2 H 1.0 -0.0008279 0.0009570 -0.0000156 3 C 6.0 -0.0023914 -0.0011796 -0.0023543 4 H 1.0 0.0002557 0.0006159 0.0009720 5 C 6.0 0.0018492 0.0040263 0.0035407 6 H 1.0 -0.0003517 -0.0017167 -0.0013010 7 H 1.0 -0.0002351 -0.0008245 -0.0008469 8 C 6.0 -0.0023114 0.0024790 0.0010435 9 H 1.0 0.0008656 -0.0007432 -0.0001767 10 H 1.0 0.0007378 -0.0006377 -0.0001344 MAXIMUM GRADIENT = 0.0040263 RMS GRADIENT = 0.0016743 NSERCH: 7 E= -155.8259788372 GRAD. MAX= 0.0040263 R.M.S.= 0.0016743 HESSIAN UPDATED USING THE BFGS FORMULA ACTUAL ENERGY CHANGE WAS 0.0001293883 PREDICTED ENERGY CHANGE WAS -0.0002210917 RATIO= -0.585 MIN SEARCH, CORRECT HESSIAN, TRYING PURE NR STEP NR STEP HAS LENGTH = 3.324171 TRIM/QA LAMBDA FOR NON-TS MODES = -0.09084346 TRIM/QA STEP HAS LENGTH = 0.050000 RADIUS OF STEP TAKEN= 0.05000 CURRENT TRUST RADIUS= 0.05000 BEGINNING GEOMETRY SEARCH POINT NSERCH= 8 ... COORDINATES OF ALL ATOMS ARE (ANGS) ATOM CHARGE X Y Z ------------------------------------------------------------ C 6.0 0.4138517241 -0.4300258572 0.7382371066 H 1.0 1.2023646410 -0.5069105045 1.4876598444 C 6.0 0.7613401590 0.3231228327 -0.4700063243 H 1.0 1.7972520570 0.2428785522 -0.7977199476 C 6.0 -0.0739072212 1.0897633917 -1.1707418207 H 1.0 0.2529469907 1.5924434032 -2.0742067331 H 1.0 -1.0998108764 1.2490013092 -0.8495933399 C 6.0 -0.7588101955 -1.0122452492 0.9831063018 H 1.0 -1.5511354013 -1.0136492999 0.2380710646 H 1.0 -0.9430918775 -1.5343785782 1.9151938482 INTERNUCLEAR DISTANCES (ANGS.) ------------------------------ 1 C 2 H 3 C 4 H 5 C 1 C 0.0000000 1.0905495 * 1.4655488 * 2.1738815 * 2.4883466 * 2 H 1.0905495 * 0.0000000 2.1716157 * 2.4777077 * 3.3534067 3 C 1.4655488 * 2.1716157 * 0.0000000 1.0894718 * 1.3328189 * 4 H 2.1738815 * 2.4777077 * 1.0894718 * 0.0000000 2.0874856 * 5 C 2.4883466 * 3.3534067 1.3328189 * 2.0874856 * 0.0000000 6 H 3.4678686 4.2421191 2.1078656 * 2.4157032 * 1.0843292 * 7 H 2.7625192 * 3.7210201 2.1131068 * 3.0672378 1.0867251 * 8 C 1.3319446 * 2.0871378 * 2.4911044 * 3.3585908 3.0865181 9 H 2.1099661 * 3.0659450 2.7633090 * 3.7233619 2.9310923 * 10 H 2.1085820 * 2.4169112 * 3.4705302 4.2459427 4.1430185 6 H 7 H 8 C 9 H 10 H 1 C 3.4678686 2.7625192 * 1.3319446 * 2.1099661 * 2.1085820 * 2 H 4.2421191 3.7210201 2.0871378 * 3.0659450 2.4169112 * 3 C 2.1078656 * 2.1131068 * 2.4911044 * 2.7633090 * 3.4705302 4 H 2.4157032 * 3.0672378 3.3585908 3.7233619 4.2459427 5 C 1.0843292 * 1.0867251 * 3.0865181 2.9310923 * 4.1430185 6 H 0.0000000 1.8567672 * 4.1418859 3.9233992 5.2079595 7 H 1.8567672 * 0.0000000 2.9305811 * 2.5507441 * 3.9262976 8 C 4.1418859 2.9305811 * 0.0000000 1.0875931 * 1.0841449 * 9 H 3.9233992 2.5507441 * 1.0875931 * 0.0000000 1.8583909 * 10 H 5.2079595 3.9262976 1.0841449 * 1.8583909 * 0.0000000 * ... LESS THAN 3.000 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 89.7 ( 1.5 MIN) TOTAL WALL CLOCK TIME= 90.6 SECONDS, CPU UTILIZATION IS 99.08% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 89.8 ( 1.5 MIN) TOTAL WALL CLOCK TIME= 90.6 SECONDS, CPU UTILIZATION IS 99.08% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8252793067 -155.8252793067 0.004564081 0.004437787 17681690 80180 2 1 0 -155.8255689016 -0.0002895949 0.000821673 0.000564200 16818563 118662 3 2 0 -155.8255722142 -0.0000033126 0.000422423 0.000352071 16097552 141131 4 3 0 -155.8255732122 -0.0000009980 0.000126524 0.000240963 15666289 154190 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 5 4 0 -155.8261543275 -0.0005811153 0.000862024 0.001438692 17680347 80206 6 5 0 -155.8261604401 -0.0000061125 0.000541764 0.000382013 16416730 131439 7 6 0 -155.8261607120 -0.0000002719 0.000269110 0.000249714 15684577 152344 8 7 0 -155.8261612085 -0.0000004965 0.000061474 0.000122807 15303217 164581 9 8 0 -155.8261612561 -0.0000000476 0.000015923 0.000031898 14740606 183583 10 9 0 -155.8261612600 -0.0000000040 0.000001410 0.000001779 13935802 202904 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 8.0 SECONDS ( 0.8 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8261612600 AFTER 10 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9902809442 TOTAL ELECTRON NUMBER = 30.0000059461 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.23 TOTAL CPU TIME= 98.0 ( 1.6 MIN) TOTAL WALL CLOCK TIME= 98.9 SECONDS, CPU UTILIZATION IS 99.10% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 98.0 ( 1.6 MIN) TOTAL WALL CLOCK TIME= 98.9 SECONDS, CPU UTILIZATION IS 99.10% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700735 WORDS. CPU 0: STEP CPU TIME= 2.30 TOTAL CPU TIME= 100.3 ( 1.7 MIN) TOTAL WALL CLOCK TIME= 101.2 SECONDS, CPU UTILIZATION IS 99.10% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 100.7 ( 1.7 MIN) TOTAL WALL CLOCK TIME= 101.6 SECONDS, CPU UTILIZATION IS 99.10% NSERCH= 8 ENERGY= -155.8261613 ----------------------- GRADIENT (HARTREE/BOHR) ----------------------- ATOM ZNUC DE/DX DE/DY DE/DZ -------------------------------------------------------------- 1 C 6.0 -0.0021444 -0.0032126 -0.0017192 2 H 1.0 0.0004812 0.0005383 0.0005642 3 C 6.0 0.0005099 0.0022263 0.0003400 4 H 1.0 0.0001372 -0.0001570 -0.0001214 5 C 6.0 0.0000531 0.0002282 -0.0008589 6 H 1.0 0.0003753 -0.0005803 -0.0000209 7 H 1.0 -0.0003004 0.0002097 0.0006024 8 C 6.0 0.0003409 0.0010283 0.0026977 9 H 1.0 -0.0000195 -0.0002315 -0.0014120 10 H 1.0 0.0005667 -0.0000494 -0.0000719 MAXIMUM GRADIENT = 0.0032126 RMS GRADIENT = 0.0011060 NSERCH: 8 E= -155.8261612600 GRAD. MAX= 0.0032126 R.M.S.= 0.0011060 HESSIAN UPDATED USING THE BFGS FORMULA ACTUAL ENERGY CHANGE WAS -0.0001824228 PREDICTED ENERGY CHANGE WAS -0.0003146846 RATIO= 0.580 MIN SEARCH, CORRECT HESSIAN, TRYING PURE NR STEP NR STEP HAS LENGTH = 3.302533 TRIM/QA LAMBDA FOR NON-TS MODES = -0.04689256 TRIM/QA STEP HAS LENGTH = 0.050000 RADIUS OF STEP TAKEN= 0.05000 CURRENT TRUST RADIUS= 0.05000 BEGINNING GEOMETRY SEARCH POINT NSERCH= 9 ... COORDINATES OF ALL ATOMS ARE (ANGS) ATOM CHARGE X Y Z ------------------------------------------------------------ C 6.0 0.4150232718 -0.4171893099 0.7449856896 H 1.0 1.2043378742 -0.5069105228 1.4895183130 C 6.0 0.7626326754 0.3153667940 -0.4716656616 H 1.0 1.7982333407 0.2409861197 -0.7983590810 C 6.0 -0.0727357759 1.0865859776 -1.1692351655 H 1.0 0.2484698989 1.5964409080 -2.0709946166 H 1.0 -1.0992340323 1.2498470126 -0.8548166726 C 6.0 -0.7517738569 -1.0193259019 0.9744690327 H 1.0 -1.5569852260 -1.0122997986 0.2463063394 H 1.0 -0.9469681697 -1.5335012785 1.9097918226 INTERNUCLEAR DISTANCES (ANGS.) ------------------------------ 1 C 2 H 3 C 4 H 5 C 1 C 0.0000000 1.0887590 * 1.4620914 * 2.1744834 * 2.4826378 * 2 H 1.0887590 * 0.0000000 2.1719775 * 2.4792023 * 3.3524794 3 C 1.4620914 * 2.1719775 * 0.0000000 1.0884529 * 1.3338751 * 4 H 2.1744834 * 2.4792023 * 1.0884529 * 0.0000000 2.0864117 * 5 C 2.4826378 * 3.3524794 1.3338751 * 2.0864117 * 0.0000000 6 H 3.4658609 4.2444108 2.1126683 * 2.4204598 * 1.0845715 * 7 H 2.7624903 * 3.7267341 2.1181609 * 3.0685998 1.0859152 * 8 C 1.3329091 * 2.0866764 * 2.4831708 * 3.3516925 3.0808157 9 H 2.1193525 * 3.0701628 2.7674554 * 3.7308904 2.9346338 * 10 H 2.1113850 * 2.4204620 * 3.4658892 4.2448814 4.1363688 6 H 7 H 8 C 9 H 10 H 1 C 3.4658609 2.7624903 * 1.3329091 * 2.1193525 * 2.1113850 * 2 H 4.2444108 3.7267341 2.0866764 * 3.0701628 2.4204620 * 3 C 2.1126683 * 2.1181609 * 2.4831708 * 2.7674554 * 3.4658892 4 H 2.4204598 * 3.0685998 3.3516925 3.7308904 4.2448814 5 C 1.0845715 * 1.0859152 * 3.0808157 2.9346338 * 4.1363688 6 H 0.0000000 1.8481131 * 4.1373388 3.9287504 5.2031020 7 H 1.8481131 * 0.0000000 2.9353297 * 2.5572087 * 3.9259741 8 C 4.1373388 2.9353297 * 0.0000000 1.0856499 * 1.0850373 * 9 H 3.9287504 2.5572087 * 1.0856499 * 0.0000000 1.8468773 * 10 H 5.2031020 3.9259741 1.0850373 * 1.8468773 * 0.0000000 * ... LESS THAN 3.000 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 100.7 ( 1.7 MIN) TOTAL WALL CLOCK TIME= 101.6 SECONDS, CPU UTILIZATION IS 99.10% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 100.7 ( 1.7 MIN) TOTAL WALL CLOCK TIME= 101.6 SECONDS, CPU UTILIZATION IS 99.09% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8253659199 -155.8253659199 0.003348656 0.004955614 17687903 80103 2 1 0 -155.8255889351 -0.0002230151 0.001126417 0.000572241 16812512 119477 3 2 0 -155.8255878733 0.0000010618 0.000653108 0.001157683 16144090 141556 4 3 0 -155.8255934540 -0.0000055807 0.000131375 0.000254115 15835724 151049 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 5 4 0 -155.8261485576 -0.0005551036 0.000918801 0.001463117 17687860 80107 6 5 0 -155.8261547129 -0.0000061553 0.000457153 0.000355210 16421583 131505 7 6 0 -155.8261550960 -0.0000003832 0.000211254 0.000235190 15702857 151776 8 7 0 -155.8261554565 -0.0000003605 0.000030894 0.000033078 15286972 164536 9 8 0 -155.8261554628 -0.0000000063 0.000018434 0.000022658 14441575 192150 10 9 0 -155.8261554657 -0.0000000029 0.000002325 0.000004776 13574868 215595 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 8.0 SECONDS ( 0.8 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8261554657 AFTER 10 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9916872882 TOTAL ELECTRON NUMBER = 30.0000055333 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.22 TOTAL CPU TIME= 108.9 ( 1.8 MIN) TOTAL WALL CLOCK TIME= 109.9 SECONDS, CPU UTILIZATION IS 99.11% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 108.9 ( 1.8 MIN) TOTAL WALL CLOCK TIME= 109.9 SECONDS, CPU UTILIZATION IS 99.11% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700735 WORDS. CPU 0: STEP CPU TIME= 2.31 TOTAL CPU TIME= 111.2 ( 1.9 MIN) TOTAL WALL CLOCK TIME= 112.2 SECONDS, CPU UTILIZATION IS 99.12% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 111.6 ( 1.9 MIN) TOTAL WALL CLOCK TIME= 112.5 SECONDS, CPU UTILIZATION IS 99.12% NSERCH= 9 ENERGY= -155.8261555 ----------------------- GRADIENT (HARTREE/BOHR) ----------------------- ATOM ZNUC DE/DX DE/DY DE/DZ -------------------------------------------------------------- 1 C 6.0 -0.0001363 0.0030896 0.0007804 2 H 1.0 0.0000391 -0.0003211 -0.0004571 3 C 6.0 0.0014948 -0.0030036 0.0008196 4 H 1.0 -0.0003994 0.0003432 0.0000186 5 C 6.0 -0.0005237 0.0002097 0.0002681 6 H 1.0 -0.0004346 0.0002736 0.0001665 7 H 1.0 0.0000174 0.0005825 -0.0006833 8 C 6.0 0.0012940 -0.0012541 -0.0022234 9 H 1.0 -0.0006864 -0.0001070 0.0012217 10 H 1.0 -0.0006649 0.0001873 0.0000888 MAXIMUM GRADIENT = 0.0030896 RMS GRADIENT = 0.0010775 NSERCH: 9 E= -155.8261554657 GRAD. MAX= 0.0030896 R.M.S.= 0.0010775 HESSIAN UPDATED USING THE BFGS FORMULA ACTUAL ENERGY CHANGE WAS 0.0000057943 PREDICTED ENERGY CHANGE WAS -0.0001729859 RATIO= -0.033 MIN SEARCH, CORRECT HESSIAN, TRYING PURE NR STEP NR STEP HAS LENGTH = 1.054036 TRIM/QA LAMBDA FOR NON-TS MODES = -0.00555913 TRIM/QA STEP HAS LENGTH = 0.050000 RADIUS OF STEP TAKEN= 0.05000 CURRENT TRUST RADIUS= 0.05000 BEGINNING GEOMETRY SEARCH POINT NSERCH= 10 ... COORDINATES OF ALL ATOMS ARE (ANGS) ATOM CHARGE X Y Z ------------------------------------------------------------ C 6.0 0.4165508238 -0.4230344737 0.7434042701 H 1.0 1.2045591364 -0.5089984716 1.4895393211 C 6.0 0.7596865597 0.3181157057 -0.4722830897 H 1.0 1.7951296280 0.2374064466 -0.7997615295 C 6.0 -0.0738346689 1.0872775636 -1.1717514546 H 1.0 0.2553708064 1.6062924571 -2.0658606099 H 1.0 -1.1039613171 1.2367018546 -0.8603683547 C 6.0 -0.7563542304 -1.0103410759 0.9812006030 H 1.0 -1.5533392038 -1.0082491701 0.2435735342 H 1.0 -0.9428075341 -1.5351708363 1.9123073099 INTERNUCLEAR DISTANCES (ANGS.) ------------------------------ 1 C 2 H 3 C 4 H 5 C 1 C 0.0000000 1.0886066 * 1.4645619 * 2.1721009 * 2.4878388 * 2 H 1.0886066 * 0.0000000 2.1750349 * 2.4792725 * 3.3563159 3 C 1.4645619 * 2.1750349 * 0.0000000 1.0889897 * 1.3325253 * 4 H 2.1721009 * 2.4792725 * 1.0889897 * 0.0000000 2.0865486 * 5 C 2.4878388 * 3.3563159 1.3325253 * 2.0865486 * 0.0000000 6 H 3.4693106 4.2445592 2.1102661 * 2.4182045 * 1.0849811 * 7 H 2.7638322 * 3.7281098 2.1136684 * 3.0670821 1.0864842 * 8 C 1.3331101 * 2.0868478 * 2.4851141 * 3.3524275 3.0823756 9 H 2.1148933 * 3.0671950 2.7607576 * 3.7218879 2.9297288 * 10 H 2.1097480 * 2.4172187 * 3.4669047 4.2418920 4.1405033 6 H 7 H 8 C 9 H 10 H 1 C 3.4693106 2.7638322 * 1.3331101 * 2.1148933 * 2.1097480 * 2 H 4.2445592 3.7281098 2.0868478 * 3.0671950 2.4172187 * 3 C 2.1102661 * 2.1136684 * 2.4851141 * 2.7607576 * 3.4669047 4 H 2.4182045 * 3.0670821 3.3524275 3.7218879 4.2418920 5 C 1.0849811 * 1.0864842 * 3.0823756 2.9297288 * 4.1405033 6 H 0.0000000 1.8540746 * 4.1418523 3.9294715 5.2086700 7 H 1.8540746 * 0.0000000 2.9259885 * 2.5417382 * 3.9238985 8 C 4.1418523 2.9259885 * 0.0000000 1.0859480 * 1.0849750 * 9 H 3.9294715 2.5417382 * 1.0859480 * 0.0000000 1.8533936 * 10 H 5.2086700 3.9238985 1.0849750 * 1.8533936 * 0.0000000 * ... LESS THAN 3.000 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 111.6 ( 1.9 MIN) TOTAL WALL CLOCK TIME= 112.6 SECONDS, CPU UTILIZATION IS 99.11% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.02 TOTAL CPU TIME= 111.6 ( 1.9 MIN) TOTAL WALL CLOCK TIME= 112.6 SECONDS, CPU UTILIZATION IS 99.12% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8254920975 -155.8254920975 0.002637310 0.002749581 17687136 80111 2 1 0 -155.8256188453 -0.0001267478 0.000692365 0.000426199 16728700 121357 3 2 0 -155.8256202344 -0.0000013891 0.000416273 0.000539213 16023171 143744 4 3 0 -155.8256214549 -0.0000012205 0.000124762 0.000268337 15654135 155172 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 5 4 0 -155.8261932769 -0.0005718220 0.000874757 0.001439883 17687169 80116 6 5 0 -155.8261995595 -0.0000062826 0.000531108 0.000358672 16425511 131196 7 6 0 -155.8261999078 -0.0000003483 0.000272379 0.000240115 15691790 152168 8 7 0 -155.8262003016 -0.0000003938 0.000044162 0.000078724 15254547 165553 9 8 0 -155.8262003228 -0.0000000212 0.000017691 0.000037102 14617994 187962 10 9 0 -155.8262003278 -0.0000000050 0.000002235 0.000002025 13938119 203104 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 8.0 SECONDS ( 0.8 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262003278 AFTER 10 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9910810574 TOTAL ELECTRON NUMBER = 30.0000053041 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.23 TOTAL CPU TIME= 119.8 ( 2.0 MIN) TOTAL WALL CLOCK TIME= 120.8 SECONDS, CPU UTILIZATION IS 99.14% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 119.8 ( 2.0 MIN) TOTAL WALL CLOCK TIME= 120.9 SECONDS, CPU UTILIZATION IS 99.13% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700735 WORDS. CPU 0: STEP CPU TIME= 2.31 TOTAL CPU TIME= 122.1 ( 2.0 MIN) TOTAL WALL CLOCK TIME= 123.2 SECONDS, CPU UTILIZATION IS 99.13% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.35 TOTAL CPU TIME= 122.5 ( 2.0 MIN) TOTAL WALL CLOCK TIME= 123.5 SECONDS, CPU UTILIZATION IS 99.13% NSERCH= 10 ENERGY= -155.8262003 ----------------------- GRADIENT (HARTREE/BOHR) ----------------------- ATOM ZNUC DE/DX DE/DY DE/DZ -------------------------------------------------------------- 1 C 6.0 0.0014286 0.0003144 0.0008700 2 H 1.0 -0.0003525 -0.0000327 -0.0000432 3 C 6.0 -0.0007506 0.0001265 -0.0003513 4 H 1.0 -0.0002918 -0.0005534 -0.0001779 5 C 6.0 0.0003804 -0.0001774 -0.0000894 6 H 1.0 0.0003654 0.0006606 0.0001476 7 H 1.0 -0.0003733 -0.0003157 -0.0001636 8 C 6.0 -0.0007338 0.0006614 -0.0003057 9 H 1.0 0.0000462 -0.0003274 -0.0000026 10 H 1.0 0.0002814 -0.0003562 0.0001162 MAXIMUM GRADIENT = 0.0014286 RMS GRADIENT = 0.0004687 NSERCH: 10 E= -155.8262003278 GRAD. MAX= 0.0014286 R.M.S.= 0.0004687 HESSIAN UPDATED USING THE BFGS FORMULA ACTUAL ENERGY CHANGE WAS -0.0000448621 PREDICTED ENERGY CHANGE WAS -0.0000793777 RATIO= 0.565 MIN SEARCH, CORRECT HESSIAN, TRYING PURE NR STEP NR STEP HAS LENGTH = 2.629101 TRIM/QA LAMBDA FOR NON-TS MODES = -0.02161035 TRIM/QA STEP HAS LENGTH = 0.050000 RADIUS OF STEP TAKEN= 0.05000 CURRENT TRUST RADIUS= 0.05000 BEGINNING GEOMETRY SEARCH POINT NSERCH= 11 ... COORDINATES OF ALL ATOMS ARE (ANGS) ATOM CHARGE X Y Z ------------------------------------------------------------ C 6.0 0.4165162796 -0.4304147181 0.7383986388 H 1.0 1.2039096666 -0.5110877411 1.4873100801 C 6.0 0.7611718252 0.3198572362 -0.4721406886 H 1.0 1.8002021918 0.2494167334 -0.7936123188 C 6.0 -0.0744352081 1.0861653350 -1.1717892364 H 1.0 0.2498851417 1.5945740165 -2.0728690796 H 1.0 -1.1002533178 1.2425391631 -0.8515969957 C 6.0 -0.7565178648 -1.0143196468 0.9805902177 H 1.0 -1.5533224784 -1.0046337217 0.2419276641 H 1.0 -0.9461562358 -1.5320966565 1.9137817184 INTERNUCLEAR DISTANCES (ANGS.) ------------------------------ 1 C 2 H 3 C 4 H 5 C 1 C 0.0000000 1.0896627 * 1.4652989 * 2.1734339 * 2.4879442 * 2 H 1.0896627 * 0.0000000 2.1739213 * 2.4772038 * 3.3550249 3 C 1.4652989 * 2.1739213 * 0.0000000 1.0899037 * 1.3322820 * 4 H 2.1734339 * 2.4772038 * 1.0899037 * 0.0000000 2.0874461 * 5 C 2.4879442 * 3.3550249 1.3322820 * 2.0874461 * 0.0000000 6 H 3.4686556 4.2448616 2.1091819 * 2.4185593 * 1.0842546 * 7 H 2.7617840 * 3.7222118 2.1119263 * 3.0663164 1.0859460 * 8 C 1.3325205 * 2.0864524 * 2.4887421 * 3.3588155 3.0838306 9 H 2.1110366 * 3.0654354 2.7606256 * 3.7270784 2.9252596 * 10 H 2.1100012 * 2.4180820 * 3.4694853 4.2480886 4.1395581 6 H 7 H 8 C 9 H 10 H 1 C 3.4686556 2.7617840 * 1.3325205 * 2.1110366 * 2.1100012 * 2 H 4.2448616 3.7222118 2.0864524 * 3.0654354 2.4180820 * 3 C 2.1091819 * 2.1119263 * 2.4887421 * 2.7606256 * 3.4694853 4 H 2.4185593 * 3.0663164 3.3588155 3.7270784 4.2480886 5 C 1.0842546 * 1.0859460 * 3.0838306 2.9252596 * 4.1395581 6 H 0.0000000 1.8542675 * 4.1403849 3.9199136 5.2057631 7 H 1.8542675 * 0.0000000 2.9271959 * 2.5398531 * 3.9204170 8 C 4.1403849 2.9271959 * 0.0000000 1.0865605 * 1.0839290 * 9 H 3.9199136 2.5398531 * 1.0865605 * 0.0000000 1.8552531 * 10 H 5.2057631 3.9204170 1.0839290 * 1.8552531 * 0.0000000 * ... LESS THAN 3.000 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 122.5 ( 2.0 MIN) TOTAL WALL CLOCK TIME= 123.5 SECONDS, CPU UTILIZATION IS 99.13% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 122.5 ( 2.0 MIN) TOTAL WALL CLOCK TIME= 123.6 SECONDS, CPU UTILIZATION IS 99.13% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8255729972 -155.8255729972 0.001167597 0.002394905 17687477 80086 2 1 0 -155.8256340975 -0.0000611002 0.000601223 0.000425970 16617021 124871 3 2 0 -155.8256344634 -0.0000003660 0.000346731 0.000571910 15940370 145994 4 3 0 -155.8256355950 -0.0000011316 0.000105602 0.000215257 15603198 156558 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 5 4 0 -155.8261979734 -0.0005623784 0.000864851 0.001445338 17687328 80089 6 5 0 -155.8262042879 -0.0000063145 0.000504644 0.000375239 16427040 131063 7 6 0 -155.8262046480 -0.0000003600 0.000256160 0.000245514 15684604 152167 8 7 0 -155.8262050133 -0.0000003654 0.000035200 0.000062520 15238795 165685 9 8 0 -155.8262050256 -0.0000000123 0.000016918 0.000038126 14537641 190390 10 9 0 -155.8262050304 -0.0000000048 0.000002125 0.000002148 13894042 204478 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 8.0 SECONDS ( 0.8 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262050304 AFTER 10 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9911039183 TOTAL ELECTRON NUMBER = 30.0000054081 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.22 TOTAL CPU TIME= 130.7 ( 2.2 MIN) TOTAL WALL CLOCK TIME= 131.8 SECONDS, CPU UTILIZATION IS 99.14% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 130.7 ( 2.2 MIN) TOTAL WALL CLOCK TIME= 131.8 SECONDS, CPU UTILIZATION IS 99.14% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700735 WORDS. CPU 0: STEP CPU TIME= 2.31 TOTAL CPU TIME= 133.0 ( 2.2 MIN) TOTAL WALL CLOCK TIME= 134.2 SECONDS, CPU UTILIZATION IS 99.15% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 133.4 ( 2.2 MIN) TOTAL WALL CLOCK TIME= 134.5 SECONDS, CPU UTILIZATION IS 99.15% NSERCH= 11 ENERGY= -155.8262050 ----------------------- GRADIENT (HARTREE/BOHR) ----------------------- ATOM ZNUC DE/DX DE/DY DE/DZ -------------------------------------------------------------- 1 C 6.0 -0.0005229 -0.0017943 -0.0008709 2 H 1.0 -0.0000409 0.0003809 0.0004495 3 C 6.0 -0.0010543 0.0012809 -0.0005928 4 H 1.0 0.0005198 0.0001579 0.0001558 5 C 6.0 0.0003135 -0.0000884 -0.0004051 6 H 1.0 0.0000926 -0.0003552 0.0000528 7 H 1.0 0.0002641 0.0002626 0.0003958 8 C 6.0 0.0001273 -0.0002631 0.0015041 9 H 1.0 0.0000784 0.0001586 -0.0004841 10 H 1.0 0.0002224 0.0002598 -0.0002051 MAXIMUM GRADIENT = 0.0017943 RMS GRADIENT = 0.0006191 NSERCH: 11 E= -155.8262050304 GRAD. MAX= 0.0017943 R.M.S.= 0.0006191 HESSIAN UPDATED USING THE BFGS FORMULA ACTUAL ENERGY CHANGE WAS -0.0000047026 PREDICTED ENERGY CHANGE WAS -0.0000622900 RATIO= 0.075 MIN SEARCH, CORRECT HESSIAN, TRYING PURE NR STEP NR STEP HAS LENGTH = 0.838491 TRIM/QA LAMBDA FOR NON-TS MODES = -0.00838899 TRIM/QA STEP HAS LENGTH = 0.050000 RADIUS OF STEP TAKEN= 0.05000 CURRENT TRUST RADIUS= 0.05000 BEGINNING GEOMETRY SEARCH POINT NSERCH= 12 ... COORDINATES OF ALL ATOMS ARE (ANGS) ATOM CHARGE X Y Z ------------------------------------------------------------ C 6.0 0.4121230302 -0.4201416598 0.7428033981 H 1.0 1.2089311430 -0.5192419532 1.4822139468 C 6.0 0.7667791583 0.3279609217 -0.4643496700 H 1.0 1.7998149992 0.2441486319 -0.7973548184 C 6.0 -0.0717981090 1.0921790973 -1.1648813629 H 1.0 0.2461310031 1.5897116678 -2.0740207665 H 1.0 -1.1033384240 1.2386837023 -0.8594269861 C 6.0 -0.7559807927 -1.0132626611 0.9810506777 H 1.0 -1.5523154227 -1.0068440507 0.2421565804 H 1.0 -0.9493465855 -1.5331936962 1.9118090008 INTERNUCLEAR DISTANCES (ANGS.) ------------------------------ 1 C 2 H 3 C 4 H 5 C 1 C 0.0000000 1.0915365 * 1.4637817 * 2.1769377 * 2.4820465 * 2 H 1.0915365 * 0.0000000 2.1684928 * 2.4755490 * 3.3532162 3 C 1.4637817 * 2.1684928 * 0.0000000 1.0886138 * 1.3334114 * 4 H 2.1769377 * 2.4755490 * 1.0886138 * 0.0000000 2.0873828 * 5 C 2.4820465 * 3.3532162 1.3334114 * 2.0873828 * 0.0000000 6 H 3.4643271 4.2451708 2.1104811 * 2.4195764 * 1.0840443 * 7 H 2.7596136 * 3.7309751 2.1172723 * 3.0694059 1.0857446 * 8 C 1.3315483 * 2.0871272 * 2.4913572 * 3.3579609 3.0831827 9 H 2.1104230 * 3.0659388 2.7674998 * 3.7259019 2.9287515 * 10 H 2.1116483 * 2.4229760 * 3.4720475 4.2492827 4.1386830 6 H 7 H 8 C 9 H 10 H 1 C 3.4643271 2.7596136 * 1.3315483 * 2.1104230 * 2.1116483 * 2 H 4.2451708 3.7309751 2.0871272 * 3.0659388 2.4229760 * 3 C 2.1104811 * 2.1172723 * 2.4913572 * 2.7674998 * 3.4720475 4 H 2.4195764 * 3.0694059 3.3579609 3.7259019 4.2492827 5 C 1.0840443 * 1.0857446 * 3.0831827 2.9287515 * 4.1386830 6 H 0.0000000 1.8491962 * 4.1368061 3.9167829 5.2027438 7 H 1.8491962 * 0.0000000 2.9290404 * 2.5411536 * 3.9225969 8 C 4.1368061 2.9290404 * 0.0000000 1.0863492 * 1.0835265 * 9 H 3.9167829 2.5411536 * 1.0863492 * 0.0000000 1.8515816 * 10 H 5.2027438 3.9225969 1.0835265 * 1.8515816 * 0.0000000 * ... LESS THAN 3.000 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 133.4 ( 2.2 MIN) TOTAL WALL CLOCK TIME= 134.5 SECONDS, CPU UTILIZATION IS 99.15% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 133.4 ( 2.2 MIN) TOTAL WALL CLOCK TIME= 134.5 SECONDS, CPU UTILIZATION IS 99.15% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8254754620 -155.8254754620 0.001938966 0.003398697 17687745 80109 2 1 0 -155.8255922375 -0.0001167755 0.000944187 0.000451470 16725273 121654 3 2 0 -155.8255932130 -0.0000009755 0.000610582 0.000618016 16103162 142183 4 3 0 -155.8255949152 -0.0000017022 0.000111983 0.000226547 15659011 156453 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 5 4 0 -155.8261327581 -0.0005378429 0.000904817 0.001465584 17687626 80107 6 5 0 -155.8261390559 -0.0000062978 0.000476277 0.000361834 16426340 131132 7 6 0 -155.8261394177 -0.0000003618 0.000225830 0.000242914 15705562 151663 8 7 0 -155.8261397833 -0.0000003656 0.000045657 0.000053664 15292863 164435 9 8 0 -155.8261397945 -0.0000000111 0.000021076 0.000024717 14477572 190783 10 9 0 -155.8261397982 -0.0000000037 0.000002317 0.000004431 13674246 212629 11 10 0 -155.8261397983 -0.0000000002 0.000001379 0.000002057 12815543 236386 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 9.1 SECONDS ( 0.8 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8261397983 AFTER 11 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9916068510 TOTAL ELECTRON NUMBER = 30.0000057606 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 9.38 TOTAL CPU TIME= 142.8 ( 2.4 MIN) TOTAL WALL CLOCK TIME= 144.0 SECONDS, CPU UTILIZATION IS 99.15% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 142.8 ( 2.4 MIN) TOTAL WALL CLOCK TIME= 144.0 SECONDS, CPU UTILIZATION IS 99.15% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700735 WORDS. CPU 0: STEP CPU TIME= 2.31 TOTAL CPU TIME= 145.1 ( 2.4 MIN) TOTAL WALL CLOCK TIME= 146.3 SECONDS, CPU UTILIZATION IS 99.15% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 145.5 ( 2.4 MIN) TOTAL WALL CLOCK TIME= 146.7 SECONDS, CPU UTILIZATION IS 99.15% NSERCH= 12 ENERGY= -155.8261398 ----------------------- GRADIENT (HARTREE/BOHR) ----------------------- ATOM ZNUC DE/DX DE/DY DE/DZ -------------------------------------------------------------- 1 C 6.0 -0.0051973 0.0006651 -0.0019390 2 H 1.0 0.0015343 -0.0005146 0.0000788 3 C 6.0 0.0033896 0.0005155 0.0014805 4 H 1.0 -0.0004344 -0.0004015 -0.0007566 5 C 6.0 -0.0002965 0.0011192 0.0010709 6 H 1.0 -0.0004983 -0.0007243 0.0000455 7 H 1.0 -0.0000868 -0.0001368 -0.0009739 8 C 6.0 0.0017427 -0.0007251 0.0017459 9 H 1.0 0.0002518 -0.0003281 -0.0002705 10 H 1.0 -0.0004050 0.0005307 -0.0004816 MAXIMUM GRADIENT = 0.0051973 RMS GRADIENT = 0.0014198 NSERCH: 12 E= -155.8261397983 GRAD. MAX= 0.0051973 R.M.S.= 0.0014198 HESSIAN UPDATED USING THE BFGS FORMULA ACTUAL ENERGY CHANGE WAS 0.0000652321 PREDICTED ENERGY CHANGE WAS -0.0000425556 RATIO= -1.533 MIN SEARCH, CORRECT HESSIAN, TRYING PURE NR STEP NR STEP HAS LENGTH = 0.389741 TRIM/QA LAMBDA FOR NON-TS MODES = -0.01529483 TRIM/QA STEP HAS LENGTH = 0.050000 RADIUS OF STEP TAKEN= 0.05000 CURRENT TRUST RADIUS= 0.05000 BEGINNING GEOMETRY SEARCH POINT NSERCH= 13 ... COORDINATES OF ALL ATOMS ARE (ANGS) ATOM CHARGE X Y Z ------------------------------------------------------------ C 6.0 0.4199859975 -0.4176314214 0.7486075658 H 1.0 1.2094848602 -0.5192643483 1.4892018865 C 6.0 0.7624911682 0.3180018534 -0.4689867261 H 1.0 1.7982619563 0.2461679656 -0.7954939201 C 6.0 -0.0751830473 1.0832008752 -1.1706001161 H 1.0 0.2483561282 1.5970960049 -2.0703443960 H 1.0 -1.1041926912 1.2349731136 -0.8563166557 C 6.0 -0.7559170406 -1.0071988664 0.9741517685 H 1.0 -1.5572274913 -1.0021865389 0.2432913328 H 1.0 -0.9450598400 -1.5331586377 1.9064892604 INTERNUCLEAR DISTANCES (ANGS.) ------------------------------ 1 C 2 H 3 C 4 H 5 C 1 C 0.0000000 1.0872523 * 1.4632163 * 2.1735969 * 2.4861714 * 2 H 1.0872523 * 0.0000000 2.1760792 * 2.4803992 * 3.3604781 3 C 1.4632163 * 2.1760792 * 0.0000000 1.0883879 * 1.3339749 * 4 H 2.1735969 * 2.4803992 * 1.0883879 * 0.0000000 2.0859350 * 5 C 2.4861714 * 3.3604781 1.3339749 * 2.0859350 * 0.0000000 6 H 3.4691604 4.2512491 2.1129986 * 2.4191855 * 1.0854978 * 7 H 2.7622462 * 3.7325474 2.1155069 * 3.0668678 1.0865863 * 8 C 1.3346190 * 2.0895362 * 2.4787838 * 3.3505827 3.0713402 9 H 2.1228336 * 3.0724915 2.7624866 * 3.7278376 2.9230781 * 10 H 2.1091328 * 2.4174725 * 3.4619953 4.2417603 4.1316464 6 H 7 H 8 C 9 H 10 H 1 C 3.4691604 2.7622462 * 1.3346190 * 2.1228336 * 2.1091328 * 2 H 4.2512491 3.7325474 2.0895362 * 3.0724915 2.4174725 * 3 C 2.1129986 * 2.1155069 * 2.4787838 * 2.7624866 * 3.4619953 4 H 2.4191855 * 3.0668678 3.3505827 3.7278376 4.2417603 5 C 1.0854978 * 1.0865863 * 3.0713402 2.9230781 * 4.1316464 6 H 0.0000000 1.8532093 * 4.1303599 3.9203714 5.1998021 7 H 1.8532093 * 0.0000000 2.9153466 * 2.5336262 * 3.9142015 8 C 4.1303599 2.9153466 * 0.0000000 1.0845647 * 1.0870427 * 9 H 3.9203714 2.5336262 * 1.0845647 * 0.0000000 1.8501103 * 10 H 5.1998021 3.9142015 1.0870427 * 1.8501103 * 0.0000000 * ... LESS THAN 3.000 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 145.5 ( 2.4 MIN) TOTAL WALL CLOCK TIME= 146.7 SECONDS, CPU UTILIZATION IS 99.15% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 145.5 ( 2.4 MIN) TOTAL WALL CLOCK TIME= 146.7 SECONDS, CPU UTILIZATION IS 99.14% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8255165173 -155.8255165173 0.002005569 0.002614287 17700713 79863 2 1 0 -155.8256407811 -0.0001242638 0.001767921 0.000658352 16806019 118572 3 2 0 -155.8256383535 0.0000024276 0.001003551 0.001051158 16200879 138675 4 3 0 -155.8256457033 -0.0000073498 0.000174973 0.000261304 15868494 150216 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 5 4 0 -155.8261453416 -0.0004996384 0.000916407 0.001444626 17700361 79880 6 5 0 -155.8261519525 -0.0000066109 0.000467546 0.000358428 16445764 130569 7 6 0 -155.8261523310 -0.0000003785 0.000216194 0.000238012 15732992 151085 8 7 0 -155.8261527113 -0.0000003803 0.000044677 0.000049082 15323233 163784 9 8 0 -155.8261527228 -0.0000000115 0.000021000 0.000026772 14510826 190271 10 9 0 -155.8261527269 -0.0000000041 0.000002215 0.000004428 13751041 210797 11 10 0 -155.8261527270 -0.0000000001 0.000001412 0.000002166 12835358 236017 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 9.2 SECONDS ( 0.8 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8261527270 AFTER 11 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9903944359 TOTAL ELECTRON NUMBER = 30.0000060499 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 9.40 TOTAL CPU TIME= 154.9 ( 2.6 MIN) TOTAL WALL CLOCK TIME= 156.2 SECONDS, CPU UTILIZATION IS 99.15% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 154.9 ( 2.6 MIN) TOTAL WALL CLOCK TIME= 156.2 SECONDS, CPU UTILIZATION IS 99.15% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700735 WORDS. CPU 0: STEP CPU TIME= 2.32 TOTAL CPU TIME= 157.2 ( 2.6 MIN) TOTAL WALL CLOCK TIME= 158.5 SECONDS, CPU UTILIZATION IS 99.17% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 157.6 ( 2.6 MIN) TOTAL WALL CLOCK TIME= 158.9 SECONDS, CPU UTILIZATION IS 99.16% NSERCH= 13 ENERGY= -155.8261527 ----------------------- GRADIENT (HARTREE/BOHR) ----------------------- ATOM ZNUC DE/DX DE/DY DE/DZ -------------------------------------------------------------- 1 C 6.0 0.0037947 0.0026116 0.0033099 2 H 1.0 -0.0004341 -0.0004980 -0.0009412 3 C 6.0 0.0000348 -0.0024867 0.0004459 4 H 1.0 -0.0005818 0.0000204 0.0000133 5 C 6.0 -0.0004120 0.0002784 -0.0003322 6 H 1.0 0.0001939 0.0007648 -0.0002829 7 H 1.0 -0.0003881 -0.0000024 -0.0001372 8 C 6.0 -0.0021131 0.0007824 -0.0045430 9 H 1.0 -0.0001393 -0.0007948 0.0012688 10 H 1.0 0.0000450 -0.0006757 0.0011986 MAXIMUM GRADIENT = 0.0045430 RMS GRADIENT = 0.0015419 NSERCH: 13 E= -155.8261527270 GRAD. MAX= 0.0045430 R.M.S.= 0.0015419 HESSIAN UPDATED USING THE BFGS FORMULA ACTUAL ENERGY CHANGE WAS -0.0000129287 PREDICTED ENERGY CHANGE WAS -0.0001321063 RATIO= 0.098 MIN SEARCH, CORRECT HESSIAN, TRYING PURE NR STEP NR STEP HAS LENGTH = 0.412767 TRIM/QA LAMBDA FOR NON-TS MODES = -0.00490833 TRIM/QA STEP HAS LENGTH = 0.050000 RADIUS OF STEP TAKEN= 0.05000 CURRENT TRUST RADIUS= 0.05000 BEGINNING GEOMETRY SEARCH POINT NSERCH= 14 ... COORDINATES OF ALL ATOMS ARE (ANGS) ATOM CHARGE X Y Z ------------------------------------------------------------ C 6.0 0.4177480582 -0.4291047052 0.7388603227 H 1.0 1.2034105645 -0.5088447448 1.4883699086 C 6.0 0.7619770988 0.3179318202 -0.4733936078 H 1.0 1.8016055050 0.2499304726 -0.7923487275 C 6.0 -0.0748849673 1.0825159906 -1.1733112101 H 1.0 0.2501721213 1.5972500463 -2.0710520005 H 1.0 -1.1017610328 1.2375456311 -0.8556847248 C 6.0 -0.7553789563 -1.0126562160 0.9816284501 H 1.0 -1.5569500965 -0.9937439408 0.2475770296 H 1.0 -0.9449382949 -1.5408243539 1.9093545598 INTERNUCLEAR DISTANCES (ANGS.) ------------------------------ 1 C 2 H 3 C 4 H 5 C 1 C 0.0000000 1.0887556 * 1.4649631 * 2.1727290 * 2.4867819 * 2 H 1.0887556 * 0.0000000 2.1741525 * 2.4769446 * 3.3542532 3 C 1.4649631 * 2.1741525 * 0.0000000 1.0895796 * 1.3322206 * 4 H 2.1727290 * 2.4769446 * 1.0895796 * 0.0000000 2.0879530 * 5 C 2.4867819 * 3.3542532 1.3322206 * 2.0879530 * 0.0000000 6 H 3.4684006 4.2442647 2.1097658 * 2.4201855 * 1.0846897 * 7 H 2.7621016 * 3.7226721 2.1131389 * 3.0673983 1.0859996 * 8 C 1.3325523 * 2.0850586 * 2.4879556 * 3.3584654 3.0816527 9 H 2.1117788 * 3.0650098 2.7600209 * 3.7293521 2.9199821 * 10 H 2.1125557 * 2.4202506 * 3.4707382 4.2484711 4.1402579 6 H 7 H 8 C 9 H 10 H 1 C 3.4684006 2.7621016 * 1.3325523 * 2.1117788 * 2.1125557 * 2 H 4.2442647 3.7226721 2.0850586 * 3.0650098 2.4202506 * 3 C 2.1097658 * 2.1131389 * 2.4879556 * 2.7600209 * 3.4707382 4 H 2.4201855 * 3.0673983 3.3584654 3.7293521 4.2484711 5 C 1.0846897 * 1.0859996 * 3.0816527 2.9199821 * 4.1402579 6 H 0.0000000 1.8531671 * 4.1402417 3.9185432 5.2076325 7 H 1.8531671 * 0.0000000 2.9255954 * 2.5304222 * 3.9229294 8 C 4.1402417 2.9255954 * 0.0000000 1.0870628 * 1.0842371 * 9 H 3.9185432 2.5304222 * 1.0870628 * 0.0000000 1.8534724 * 10 H 5.2076325 3.9229294 1.0842371 * 1.8534724 * 0.0000000 * ... LESS THAN 3.000 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 157.6 ( 2.6 MIN) TOTAL WALL CLOCK TIME= 158.9 SECONDS, CPU UTILIZATION IS 99.16% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 157.6 ( 2.6 MIN) TOTAL WALL CLOCK TIME= 158.9 SECONDS, CPU UTILIZATION IS 99.16% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8255077616 -155.8255077616 0.001997082 0.002389726 17689005 80061 2 1 0 -155.8256324848 -0.0001247232 0.000703489 0.000437458 16725776 121933 3 2 0 -155.8256324457 0.0000000391 0.000426323 0.000866585 16048103 144895 4 3 0 -155.8256349226 -0.0000024768 0.000094953 0.000244090 15727168 154289 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 5 4 0 -155.8261920406 -0.0005571181 0.000878347 0.001466422 17688763 80064 6 5 0 -155.8261985393 -0.0000064986 0.000461286 0.000349132 16432970 130770 7 6 0 -155.8261988869 -0.0000003476 0.000229923 0.000226103 15682054 152396 8 7 0 -155.8261992067 -0.0000003199 0.000030725 0.000043272 15211929 166130 9 8 0 -155.8261992129 -0.0000000061 0.000013845 0.000031021 14451832 192676 10 9 0 -155.8261992160 -0.0000000031 0.000001890 0.000003149 13734471 208624 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 8.0 SECONDS ( 0.8 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8261992160 AFTER 10 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9912730390 TOTAL ELECTRON NUMBER = 30.0000047704 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.22 TOTAL CPU TIME= 165.8 ( 2.8 MIN) TOTAL WALL CLOCK TIME= 167.2 SECONDS, CPU UTILIZATION IS 99.16% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 165.8 ( 2.8 MIN) TOTAL WALL CLOCK TIME= 167.2 SECONDS, CPU UTILIZATION IS 99.16% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700735 WORDS. CPU 0: STEP CPU TIME= 2.31 TOTAL CPU TIME= 168.1 ( 2.8 MIN) TOTAL WALL CLOCK TIME= 169.5 SECONDS, CPU UTILIZATION IS 99.17% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 168.5 ( 2.8 MIN) TOTAL WALL CLOCK TIME= 169.9 SECONDS, CPU UTILIZATION IS 99.17% NSERCH= 14 ENERGY= -155.8261992 ----------------------- GRADIENT (HARTREE/BOHR) ----------------------- ATOM ZNUC DE/DX DE/DY DE/DZ -------------------------------------------------------------- 1 C 6.0 0.0002477 -0.0010895 -0.0008239 2 H 1.0 -0.0007167 0.0007237 0.0003684 3 C 6.0 -0.0006898 0.0004549 -0.0010227 4 H 1.0 0.0003931 0.0001259 0.0002772 5 C 6.0 0.0000766 -0.0007208 0.0000457 6 H 1.0 0.0001518 0.0001075 0.0000243 7 H 1.0 0.0001694 0.0003769 0.0002195 8 C 6.0 0.0008065 -0.0001026 0.0016311 9 H 1.0 -0.0004208 0.0005129 -0.0003391 10 H 1.0 -0.0000178 -0.0003888 -0.0003805 MAXIMUM GRADIENT = 0.0016311 RMS GRADIENT = 0.0005782 NSERCH: 14 E= -155.8261992160 GRAD. MAX= 0.0016311 R.M.S.= 0.0005782 HESSIAN UPDATED USING THE BFGS FORMULA ACTUAL ENERGY CHANGE WAS -0.0000464890 PREDICTED ENERGY CHANGE WAS -0.0001081483 RATIO= 0.430 MIN SEARCH, CORRECT HESSIAN, TRYING PURE NR STEP NR STEP HAS LENGTH = 1.609695 TRIM/QA LAMBDA FOR NON-TS MODES = -0.01227626 TRIM/QA STEP HAS LENGTH = 0.050000 RADIUS OF STEP TAKEN= 0.05000 CURRENT TRUST RADIUS= 0.05000 BEGINNING GEOMETRY SEARCH POINT NSERCH= 15 ... COORDINATES OF ALL ATOMS ARE (ANGS) ATOM CHARGE X Y Z ------------------------------------------------------------ C 6.0 0.4187014674 -0.4282555228 0.7413425276 H 1.0 1.2088147288 -0.5230990422 1.4852716584 C 6.0 0.7616165973 0.3243062342 -0.4679980323 H 1.0 1.8000153607 0.2527236480 -0.7911747723 C 6.0 -0.0747506618 1.0865513036 -1.1710076240 H 1.0 0.2470733420 1.5922158249 -2.0743289574 H 1.0 -1.1032707927 1.2346510390 -0.8544310312 C 6.0 -0.7568682665 -1.0100143727 0.9798001055 H 1.0 -1.5520962278 -1.0000938759 0.2402742008 H 1.0 -0.9482355475 -1.5289852361 1.9122519249 INTERNUCLEAR DISTANCES (ANGS.) ------------------------------ 1 C 2 H 3 C 4 H 5 C 1 C 0.0000000 1.0893598 * 1.4650749 * 2.1726412 * 2.4890195 * 2 H 1.0893598 * 0.0000000 2.1756250 * 2.4766161 * 3.3607044 3 C 1.4650749 * 2.1756250 * 0.0000000 1.0898804 * 1.3321975 * 4 H 2.1726412 * 2.4766161 * 1.0898804 * 0.0000000 2.0866934 * 5 C 2.4890195 * 3.3607044 1.3321975 * 2.0866934 * 0.0000000 6 H 3.4698367 4.2509128 2.1101300 * 2.4191637 * 1.0840926 * 7 H 2.7619108 * 3.7295621 2.1108915 * 3.0654940 1.0862817 * 8 C 1.3331427 * 2.0872225 * 2.4864286 * 3.3568606 3.0800724 9 H 2.1123712 * 3.0659700 2.7584329 * 3.7242571 2.9203346 * 10 H 2.1097752 * 2.4180540 * 3.4675457 4.2468677 4.1364836 6 H 7 H 8 C 9 H 10 H 1 C 3.4698367 2.7619108 * 1.3331427 * 2.1123712 * 2.1097752 * 2 H 4.2509128 3.7295621 2.0872225 * 3.0659700 2.4180540 * 3 C 2.1101300 * 2.1108915 * 2.4864286 * 2.7584329 * 3.4675457 4 H 2.4191637 * 3.0654940 3.3568606 3.7242571 4.2468677 5 C 1.0840926 * 1.0862817 * 3.0800724 2.9203346 * 4.1364836 6 H 0.0000000 1.8545708 * 4.1360857 3.9133705 5.2022578 7 H 1.8545708 * 0.0000000 2.9194043 * 2.5286179 * 3.9135989 8 C 4.1360857 2.9194043 * 0.0000000 1.0859947 * 1.0841672 * 9 H 3.9133705 2.5286179 * 1.0859947 * 0.0000000 1.8546922 * 10 H 5.2022578 3.9135989 1.0841672 * 1.8546922 * 0.0000000 * ... LESS THAN 3.000 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 168.5 ( 2.8 MIN) TOTAL WALL CLOCK TIME= 169.9 SECONDS, CPU UTILIZATION IS 99.18% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 168.5 ( 2.8 MIN) TOTAL WALL CLOCK TIME= 169.9 SECONDS, CPU UTILIZATION IS 99.17% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8256231027 -155.8256231027 0.001763328 0.001871716 17693465 79959 2 1 0 -155.8256804210 -0.0000573184 0.000559619 0.000390537 16631865 124343 3 2 0 -155.8256812821 -0.0000008611 0.000326871 0.000305245 15960560 145111 4 3 0 -155.8256819867 -0.0000007045 0.000069069 0.000156722 15555446 157350 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 5 4 0 -155.8262040372 -0.0005220505 0.000849508 0.001428420 17693241 79961 6 5 0 -155.8262105663 -0.0000065292 0.000534914 0.000367848 16438115 130626 7 6 0 -155.8262108730 -0.0000003066 0.000274412 0.000241909 15697633 152064 8 7 0 -155.8262112969 -0.0000004240 0.000054194 0.000106106 15281870 165015 9 8 0 -155.8262113320 -0.0000000351 0.000016902 0.000036007 14705895 185162 10 9 0 -155.8262113367 -0.0000000047 0.000001580 0.000001963 13962567 202104 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 8.3 SECONDS ( 0.8 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262113367 AFTER 10 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9911164592 TOTAL ELECTRON NUMBER = 30.0000058554 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.54 TOTAL CPU TIME= 177.0 ( 3.0 MIN) TOTAL WALL CLOCK TIME= 178.6 SECONDS, CPU UTILIZATION IS 99.11% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 177.0 ( 3.0 MIN) TOTAL WALL CLOCK TIME= 178.6 SECONDS, CPU UTILIZATION IS 99.11% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700735 WORDS. CPU 0: STEP CPU TIME= 2.31 TOTAL CPU TIME= 179.4 ( 3.0 MIN) TOTAL WALL CLOCK TIME= 180.9 SECONDS, CPU UTILIZATION IS 99.12% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 179.7 ( 3.0 MIN) TOTAL WALL CLOCK TIME= 181.3 SECONDS, CPU UTILIZATION IS 99.12% NSERCH= 15 ENERGY= -155.8262113 ----------------------- GRADIENT (HARTREE/BOHR) ----------------------- ATOM ZNUC DE/DX DE/DY DE/DZ -------------------------------------------------------------- 1 C 6.0 0.0005369 -0.0010480 -0.0000678 2 H 1.0 0.0000745 -0.0002558 0.0001519 3 C 6.0 -0.0018462 0.0016188 -0.0001460 4 H 1.0 0.0003673 -0.0001244 -0.0000186 5 C 6.0 0.0010698 0.0003226 -0.0006207 6 H 1.0 -0.0000577 -0.0004154 0.0000177 7 H 1.0 0.0000216 -0.0001101 0.0003735 8 C 6.0 -0.0007329 -0.0001378 0.0006425 9 H 1.0 0.0003661 -0.0002853 -0.0003412 10 H 1.0 0.0002006 0.0004355 0.0000088 MAXIMUM GRADIENT = 0.0018462 RMS GRADIENT = 0.0006105 NSERCH: 15 E= -155.8262113367 GRAD. MAX= 0.0018462 R.M.S.= 0.0006105 HESSIAN UPDATED USING THE BFGS FORMULA ACTUAL ENERGY CHANGE WAS -0.0000121207 PREDICTED ENERGY CHANGE WAS -0.0000514988 RATIO= 0.235 MIN SEARCH, CORRECT HESSIAN, TRYING PURE NR STEP NR STEP HAS LENGTH = 0.415798 TRIM/QA LAMBDA FOR NON-TS MODES = -0.02115196 TRIM/QA STEP HAS LENGTH = 0.050000 RADIUS OF STEP TAKEN= 0.05000 CURRENT TRUST RADIUS= 0.05000 BEGINNING GEOMETRY SEARCH POINT NSERCH= 16 ... COORDINATES OF ALL ATOMS ARE (ANGS) ATOM CHARGE X Y Z ------------------------------------------------------------ C 6.0 0.4135413884 -0.4168611043 0.7465875680 H 1.0 1.2112894617 -0.5183715806 1.4826567231 C 6.0 0.7672082105 0.3200141082 -0.4663710037 H 1.0 1.8004810682 0.2463076580 -0.7970399537 C 6.0 -0.0732998869 1.0849820824 -1.1666715501 H 1.0 0.2486285808 1.5978839613 -2.0666928360 H 1.0 -1.1055997750 1.2287442519 -0.8620543264 C 6.0 -0.7569502798 -1.0109950328 0.9751599138 H 1.0 -1.5591570203 -0.9992719884 0.2457917035 H 1.0 -0.9451417476 -1.5324323557 1.9086337615 INTERNUCLEAR DISTANCES (ANGS.) ------------------------------ 1 C 2 H 3 C 4 H 5 C 1 C 0.0000000 1.0901854 * 1.4626462 * 2.1785730 * 2.4805459 * 2 H 1.0901854 * 0.0000000 2.1676734 * 2.4756611 * 3.3525890 3 C 1.4626462 * 2.1676734 * 0.0000000 1.0873948 * 1.3349347 * 4 H 2.1785730 * 2.4756611 * 1.0873948 * 0.0000000 2.0859188 * 5 C 2.4805459 * 3.3525890 1.3349347 * 2.0859188 * 0.0000000 6 H 3.4642374 4.2430102 2.1125591 * 2.4180618 * 1.0847786 * 7 H 2.7574509 * 3.7306915 2.1189067 * 3.0683407 1.0858648 * 8 C 1.3324005 * 2.0914585 * 2.4844830 * 3.3558840 3.0737501 9 H 2.1169643 * 3.0718844 2.7676103 * 3.7317737 2.9235148 * 10 H 2.1073373 * 2.4207377 * 3.4647291 4.2453540 4.1314004 6 H 7 H 8 C 9 H 10 H 1 C 3.4642374 2.7574509 * 1.3324005 * 2.1169643 * 2.1073373 * 2 H 4.2430102 3.7306915 2.0914585 * 3.0718844 2.4207377 * 3 C 2.1125591 * 2.1189067 * 2.4844830 * 2.7676103 * 3.4647291 4 H 2.4180618 * 3.0683407 3.3558840 3.7317737 4.2453540 5 C 1.0847786 * 1.0858648 * 3.0737501 2.9235148 * 4.1314004 6 H 0.0000000 1.8496898 * 4.1316228 3.9192975 5.1987681 7 H 1.8496898 * 0.0000000 2.9177636 * 2.5292476 * 3.9149145 8 C 4.1316228 2.9177636 * 0.0000000 1.0842744 * 1.0856732 * 9 H 3.9192975 2.5292476 * 1.0842744 * 0.0000000 1.8510317 * 10 H 5.1987681 3.9149145 1.0856732 * 1.8510317 * 0.0000000 * ... LESS THAN 3.000 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 179.7 ( 3.0 MIN) TOTAL WALL CLOCK TIME= 181.3 SECONDS, CPU UTILIZATION IS 99.11% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 179.7 ( 3.0 MIN) TOTAL WALL CLOCK TIME= 181.3 SECONDS, CPU UTILIZATION IS 99.11% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8254894564 -155.8254894564 0.002618351 0.003983877 17700536 79865 2 1 0 -155.8256167712 -0.0001273148 0.001493781 0.000570536 16769120 120441 3 2 0 -155.8256156384 0.0000011328 0.000859609 0.000837931 16098761 142463 4 3 0 -155.8256203552 -0.0000047168 0.000159611 0.000209757 15765929 153806 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 5 4 0 -155.8261257329 -0.0005053777 0.000919301 0.001469431 17700514 79868 6 5 0 -155.8261323143 -0.0000065814 0.000408017 0.000346095 16445097 130576 7 6 0 -155.8261326984 -0.0000003841 0.000165258 0.000240378 15728054 151136 8 7 0 -155.8261330591 -0.0000003607 0.000030296 0.000052169 15316911 163632 9 8 0 -155.8261330675 -0.0000000083 0.000014358 0.000032400 14506008 190092 10 9 0 -155.8261330716 -0.0000000041 0.000001812 0.000004714 13775687 209796 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 8.0 SECONDS ( 0.8 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8261330716 AFTER 10 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9915460008 TOTAL ELECTRON NUMBER = 30.0000055433 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.23 TOTAL CPU TIME= 187.9 ( 3.1 MIN) TOTAL WALL CLOCK TIME= 189.6 SECONDS, CPU UTILIZATION IS 99.12% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 187.9 ( 3.1 MIN) TOTAL WALL CLOCK TIME= 189.6 SECONDS, CPU UTILIZATION IS 99.12% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700735 WORDS. CPU 0: STEP CPU TIME= 2.30 TOTAL CPU TIME= 190.3 ( 3.2 MIN) TOTAL WALL CLOCK TIME= 191.9 SECONDS, CPU UTILIZATION IS 99.12% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 190.6 ( 3.2 MIN) TOTAL WALL CLOCK TIME= 192.3 SECONDS, CPU UTILIZATION IS 99.12% NSERCH= 16 ENERGY= -155.8261331 ----------------------- GRADIENT (HARTREE/BOHR) ----------------------- ATOM ZNUC DE/DX DE/DY DE/DZ -------------------------------------------------------------- 1 C 6.0 -0.0030063 0.0027180 0.0013526 2 H 1.0 0.0014529 -0.0002772 -0.0006403 3 C 6.0 0.0045045 -0.0031275 0.0018816 4 H 1.0 -0.0011856 0.0000056 -0.0006705 5 C 6.0 -0.0016264 0.0011236 0.0004436 6 H 1.0 -0.0001235 0.0002821 0.0001205 7 H 1.0 -0.0002080 -0.0001584 -0.0009796 8 C 6.0 -0.0002392 -0.0002570 -0.0034266 9 H 1.0 0.0003365 -0.0002334 0.0012439 10 H 1.0 0.0000951 -0.0000758 0.0006749 MAXIMUM GRADIENT = 0.0045045 RMS GRADIENT = 0.0015876 NSERCH: 16 E= -155.8261330716 GRAD. MAX= 0.0045045 R.M.S.= 0.0015876 HESSIAN UPDATED USING THE BFGS FORMULA ACTUAL ENERGY CHANGE WAS 0.0000782651 PREDICTED ENERGY CHANGE WAS -0.0000713435 RATIO= -1.097 MIN SEARCH, CORRECT HESSIAN, TRYING PURE NR STEP NR STEP HAS LENGTH = 0.177631 TRIM/QA LAMBDA FOR NON-TS MODES = -0.00225111 TRIM/QA STEP HAS LENGTH = 0.050000 RADIUS OF STEP TAKEN= 0.05000 CURRENT TRUST RADIUS= 0.05000 BEGINNING GEOMETRY SEARCH POINT NSERCH= 17 ... COORDINATES OF ALL ATOMS ARE (ANGS) ATOM CHARGE X Y Z ------------------------------------------------------------ C 6.0 0.4209446869 -0.4278828770 0.7397695268 H 1.0 1.2082894776 -0.5204477245 1.4862240512 C 6.0 0.7655940705 0.3173526741 -0.4721654066 H 1.0 1.8045399816 0.2560527351 -0.7920815850 C 6.0 -0.0769093077 1.0801312466 -1.1699930521 H 1.0 0.2451701694 1.5965907301 -2.0686942827 H 1.0 -1.1051321020 1.2314635154 -0.8552214203 C 6.0 -0.7545680306 -1.0093953221 0.9787026127 H 1.0 -1.5538891380 -0.9954881691 0.2430401319 H 1.0 -0.9530398077 -1.5283768086 1.9104194241 INTERNUCLEAR DISTANCES (ANGS.) ------------------------------ 1 C 2 H 3 C 4 H 5 C 1 C 0.0000000 1.0888868 * 1.4638803 * 2.1745509 * 2.4837790 * 2 H 1.0888868 * 0.0000000 2.1755868 * 2.4797468 * 3.3569448 3 C 1.4638803 * 2.1755868 * 0.0000000 1.0888125 * 1.3336441 * 4 H 2.1745509 * 2.4797468 * 1.0888125 * 0.0000000 2.0884860 * 5 C 2.4837790 * 3.3569448 1.3336441 * 2.0884860 * 0.0000000 6 H 3.4665342 4.2481637 2.1109703 * 2.4204166 * 1.0854167 * 7 H 2.7615823 * 3.7287370 2.1170609 * 3.0694632 1.0859212 * 8 C 1.3330701 * 2.0855353 * 2.4851903 * 3.3594746 3.0728221 9 H 2.1139736 * 3.0660725 2.7595421 * 3.7305332 2.9131303 * 10 H 2.1140817 * 2.4222318 * 3.4694568 4.2534629 4.1304794 6 H 7 H 8 C 9 H 10 H 1 C 3.4665342 2.7615823 * 1.3330701 * 2.1139736 * 2.1140817 * 2 H 4.2481637 3.7287370 2.0855353 * 3.0660725 2.4222318 * 3 C 2.1109703 * 2.1170609 * 2.4851903 * 2.7595421 * 3.4694568 4 H 2.4204166 * 3.0694632 3.3594746 3.7305332 4.2534629 5 C 1.0854167 * 1.0859212 * 3.0728221 2.9131303 * 4.1304794 6 H 0.0000000 1.8517966 * 4.1324651 3.9114707 5.1994687 7 H 1.8517966 * 0.0000000 2.9167826 * 2.5232668 * 3.9100665 8 C 4.1324651 2.9167826 * 0.0000000 1.0864193 * 1.0848175 * 9 H 3.9114707 2.5232668 * 1.0864193 * 0.0000000 1.8507144 * 10 H 5.1994687 3.9100665 1.0848175 * 1.8507144 * 0.0000000 * ... LESS THAN 3.000 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 190.6 ( 3.2 MIN) TOTAL WALL CLOCK TIME= 192.3 SECONDS, CPU UTILIZATION IS 99.12% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 190.6 ( 3.2 MIN) TOTAL WALL CLOCK TIME= 192.3 SECONDS, CPU UTILIZATION IS 99.12% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8255771040 -155.8255771040 0.002901620 0.002590936 17700713 79871 2 1 0 -155.8257082657 -0.0001311617 0.000966094 0.000483895 16739143 120940 3 2 0 -155.8257094553 -0.0000011895 0.000605906 0.000715397 16091047 142493 4 3 0 -155.8257112375 -0.0000017822 0.000143497 0.000260869 15711394 154671 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 5 4 0 -155.8262107347 -0.0004994972 0.000918706 0.001465609 17700677 79881 6 5 0 -155.8262174827 -0.0000067481 0.000488976 0.000346507 16449135 130321 7 6 0 -155.8262178782 -0.0000003954 0.000232093 0.000238938 15717268 151436 8 7 0 -155.8262182419 -0.0000003638 0.000033425 0.000031416 15270229 164832 9 8 0 -155.8262182479 -0.0000000060 0.000013931 0.000023398 14423846 193357 10 9 0 -155.8262182504 -0.0000000025 0.000002556 0.000003835 13665267 210588 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 8.2 SECONDS ( 0.8 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262182504 AFTER 10 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9907669150 TOTAL ELECTRON NUMBER = 30.0000056454 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.47 TOTAL CPU TIME= 199.1 ( 3.3 MIN) TOTAL WALL CLOCK TIME= 200.8 SECONDS, CPU UTILIZATION IS 99.12% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 199.1 ( 3.3 MIN) TOTAL WALL CLOCK TIME= 200.9 SECONDS, CPU UTILIZATION IS 99.12% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700735 WORDS. CPU 0: STEP CPU TIME= 2.30 TOTAL CPU TIME= 201.4 ( 3.4 MIN) TOTAL WALL CLOCK TIME= 203.2 SECONDS, CPU UTILIZATION IS 99.12% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.37 TOTAL CPU TIME= 201.8 ( 3.4 MIN) TOTAL WALL CLOCK TIME= 203.5 SECONDS, CPU UTILIZATION IS 99.13% NSERCH= 17 ENERGY= -155.8262183 ----------------------- GRADIENT (HARTREE/BOHR) ----------------------- ATOM ZNUC DE/DX DE/DY DE/DZ -------------------------------------------------------------- 1 C 6.0 0.0004889 0.0005595 -0.0005612 2 H 1.0 -0.0003623 -0.0001021 0.0001280 3 C 6.0 0.0009850 -0.0009752 -0.0003520 4 H 1.0 0.0000131 0.0002778 0.0003237 5 C 6.0 -0.0012149 -0.0003471 0.0005549 6 H 1.0 0.0001657 0.0003321 -0.0003364 7 H 1.0 0.0000377 0.0005471 -0.0002143 8 C 6.0 0.0006710 -0.0001008 0.0003541 9 H 1.0 -0.0002339 -0.0001022 0.0000601 10 H 1.0 -0.0005501 -0.0000892 0.0000432 MAXIMUM GRADIENT = 0.0012149 RMS GRADIENT = 0.0004733 NSERCH: 17 E= -155.8262182504 GRAD. MAX= 0.0012149 R.M.S.= 0.0004733 HESSIAN UPDATED USING THE BFGS FORMULA ACTUAL ENERGY CHANGE WAS -0.0000851788 PREDICTED ENERGY CHANGE WAS -0.0001061784 RATIO= 0.802 MIN SEARCH, CORRECT HESSIAN, TRYING PURE NR STEP NR STEP HAS LENGTH = 1.688638 TRIM/QA LAMBDA FOR NON-TS MODES = -0.00525617 TRIM/QA STEP HAS LENGTH = 0.070711 RADIUS OF STEP TAKEN= 0.07071 CURRENT TRUST RADIUS= 0.07071 BEGINNING GEOMETRY SEARCH POINT NSERCH= 18 ... COORDINATES OF ALL ATOMS ARE (ANGS) ATOM CHARGE X Y Z ------------------------------------------------------------ C 6.0 0.4170857288 -0.4248064507 0.7451875317 H 1.0 1.2085840132 -0.5216537702 1.4867300377 C 6.0 0.7611818416 0.3292467668 -0.4639542626 H 1.0 1.7987043540 0.2512520587 -0.7887672682 C 6.0 -0.0728572945 1.0863493047 -1.1734488582 H 1.0 0.2470190493 1.5865689059 -2.0796690586 H 1.0 -1.1022793833 1.2309870045 -0.8564427940 C 6.0 -0.7590496964 -1.0058389067 0.9809752731 H 1.0 -1.5584399760 -0.9853707817 0.2455985198 H 1.0 -0.9389486367 -1.5467341314 1.9037908794 INTERNUCLEAR DISTANCES (ANGS.) ------------------------------ 1 C 2 H 3 C 4 H 5 C 1 C 0.0000000 1.0889142 * 1.4659544 * 2.1723127 * 2.4909439 * 2 H 1.0889142 * 0.0000000 2.1747114 * 2.4745734 * 3.3621894 3 C 1.4659544 * 2.1747114 * 0.0000000 1.0899723 * 1.3312431 * 4 H 2.1723127 * 2.4745734 * 1.0899723 * 0.0000000 2.0852123 * 5 C 2.4909439 * 3.3621894 1.3312431 * 2.0852123 * 0.0000000 6 H 3.4719401 4.2530474 2.1108663 * 2.4201706 * 1.0834092 * 7 H 2.7595909 * 3.7285786 2.1070525 * 3.0627059 1.0867947 * 8 C 1.3328500 * 2.0884936 * 2.4862379 * 3.3547537 3.0805283 9 H 2.1134151 * 3.0678759 2.7590451 * 3.7241867 2.9176490 * 10 H 2.1071100 * 2.4159110 * 3.4664052 4.2399726 4.1415754 6 H 7 H 8 C 9 H 10 H 1 C 3.4719401 2.7595909 * 1.3328500 * 2.1134151 * 2.1071100 * 2 H 4.2530474 3.7285786 2.0884936 * 3.0678759 2.4159110 * 3 C 2.1108663 * 2.1070525 * 2.4862379 * 2.7590451 * 3.4664052 4 H 2.4201706 * 3.0627059 3.3547537 3.7241867 4.2399726 5 C 1.0834092 * 1.0867947 * 3.0805283 2.9176490 * 4.1415754 6 H 0.0000000 1.8556204 * 4.1352505 3.9091464 5.2050034 7 H 1.8556204 * 0.0000000 2.9150132 * 2.5169067 * 3.9193496 8 C 4.1352505 2.9150132 * 0.0000000 1.0863806 * 1.0846750 * 9 H 3.9091464 2.5169067 * 1.0863806 * 0.0000000 1.8570138 * 10 H 5.2050034 3.9193496 1.0846750 * 1.8570138 * 0.0000000 * ... LESS THAN 3.000 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 201.8 ( 3.4 MIN) TOTAL WALL CLOCK TIME= 203.5 SECONDS, CPU UTILIZATION IS 99.13% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 201.8 ( 3.4 MIN) TOTAL WALL CLOCK TIME= 203.6 SECONDS, CPU UTILIZATION IS 99.13% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8254689357 -155.8254689357 0.002197234 0.003704530 17692999 79939 2 1 0 -155.8256392282 -0.0001702924 0.000710967 0.000736645 16771236 119963 3 2 0 -155.8256406645 -0.0000014363 0.000482864 0.000840618 16171289 140166 4 3 0 -155.8256440956 -0.0000034311 0.000140054 0.000298060 15800935 151080 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 5 4 0 -155.8261717211 -0.0005276255 0.000889890 0.001446773 17693310 79956 6 5 0 -155.8261784720 -0.0000067509 0.000584824 0.000383334 16442826 130216 7 6 0 -155.8261788222 -0.0000003503 0.000311033 0.000256522 15711363 151595 8 7 0 -155.8261792406 -0.0000004184 0.000050124 0.000077135 15276761 165112 9 8 0 -155.8261792662 -0.0000000255 0.000019417 0.000034927 14637152 186685 10 9 0 -155.8261792711 -0.0000000049 0.000004068 0.000002988 13949101 202654 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 8.0 SECONDS ( 0.8 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8261792711 AFTER 10 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9914289310 TOTAL ELECTRON NUMBER = 30.0000053248 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.22 TOTAL CPU TIME= 210.0 ( 3.5 MIN) TOTAL WALL CLOCK TIME= 211.8 SECONDS, CPU UTILIZATION IS 99.13% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.02 TOTAL CPU TIME= 210.0 ( 3.5 MIN) TOTAL WALL CLOCK TIME= 211.9 SECONDS, CPU UTILIZATION IS 99.13% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700735 WORDS. CPU 0: STEP CPU TIME= 2.30 TOTAL CPU TIME= 212.3 ( 3.5 MIN) TOTAL WALL CLOCK TIME= 214.2 SECONDS, CPU UTILIZATION IS 99.13% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 212.7 ( 3.5 MIN) TOTAL WALL CLOCK TIME= 214.5 SECONDS, CPU UTILIZATION IS 99.13% NSERCH= 18 ENERGY= -155.8261793 ----------------------- GRADIENT (HARTREE/BOHR) ----------------------- ATOM ZNUC DE/DX DE/DY DE/DZ -------------------------------------------------------------- 1 C 6.0 0.0004343 -0.0019599 0.0009383 2 H 1.0 -0.0000399 0.0003340 0.0000423 3 C 6.0 -0.0026080 0.0023953 -0.0001604 4 H 1.0 0.0002323 -0.0003331 -0.0003413 5 C 6.0 0.0025686 0.0002139 -0.0012802 6 H 1.0 -0.0002613 -0.0006078 0.0002662 7 H 1.0 -0.0001565 -0.0004913 0.0007709 8 C 6.0 -0.0010759 0.0008660 0.0002636 9 H 1.0 0.0000125 0.0000225 -0.0005152 10 H 1.0 0.0008939 -0.0004396 0.0000158 MAXIMUM GRADIENT = 0.0026080 RMS GRADIENT = 0.0010126 NSERCH: 18 E= -155.8261792711 GRAD. MAX= 0.0026080 R.M.S.= 0.0010126 HESSIAN UPDATED USING THE BFGS FORMULA ACTUAL ENERGY CHANGE WAS 0.0000389793 PREDICTED ENERGY CHANGE WAS -0.0000502683 RATIO= -0.775 MIN SEARCH, CORRECT HESSIAN, TRYING PURE NR STEP NR STEP HAS LENGTH = 0.442464 TRIM/QA LAMBDA FOR NON-TS MODES = -0.00411752 TRIM/QA STEP HAS LENGTH = 0.050000 RADIUS OF STEP TAKEN= 0.05000 CURRENT TRUST RADIUS= 0.05000 BEGINNING GEOMETRY SEARCH POINT NSERCH= 19 ... COORDINATES OF ALL ATOMS ARE (ANGS) ATOM CHARGE X Y Z ------------------------------------------------------------ C 6.0 0.4184752985 -0.4268268659 0.7415314790 H 1.0 1.2099923014 -0.5231719520 1.4836233721 C 6.0 0.7635743641 0.3224880790 -0.4683974213 H 1.0 1.8021225027 0.2546817226 -0.7900005940 C 6.0 -0.0749780948 1.0832305434 -1.1711467680 H 1.0 0.2478399360 1.5957450385 -2.0705210478 H 1.0 -1.1056259175 1.2266382984 -0.8597912747 C 6.0 -0.7564926741 -1.0091035338 0.9795002747 H 1.0 -1.5569135669 -0.9908040311 0.2456435404 H 1.0 -0.9469941493 -1.5328772990 1.9095584397 INTERNUCLEAR DISTANCES (ANGS.) ------------------------------ 1 C 2 H 3 C 4 H 5 C 1 C 0.0000000 1.0892575 * 1.4644092 * 2.1735970 * 2.4863845 * 2 H 1.0892575 * 0.0000000 2.1736640 * 2.4748819 * 3.3584941 3 C 1.4644092 * 2.1736640 * 0.0000000 1.0893156 * 1.3325749 * 4 H 2.1735970 * 2.4748819 * 1.0893156 * 0.0000000 2.0869289 * 5 C 2.4863845 * 3.3584941 1.3325749 * 2.0869289 * 0.0000000 6 H 3.4680763 4.2482336 2.1104420 * 2.4194995 * 1.0843231 * 7 H 2.7606279 * 3.7303506 2.1129568 * 3.0666873 1.0861597 * 8 C 1.3327509 * 2.0874225 * 2.4859903 * 3.3577966 3.0769476 9 H 2.1133235 * 3.0670901 2.7602998 * 3.7291979 2.9163414 * 10 H 2.1100098 * 2.4194041 * 3.4674341 4.2474261 4.1346314 6 H 7 H 8 C 9 H 10 H 1 C 3.4680763 2.7606279 * 1.3327509 * 2.1133235 * 2.1100098 * 2 H 4.2482336 3.7303506 2.0874225 * 3.0670901 2.4194041 * 3 C 2.1104420 * 2.1129568 * 2.4859903 * 2.7602998 * 3.4674341 4 H 2.4194995 * 3.0666873 3.3577966 3.7291979 4.2474261 5 C 1.0843231 * 1.0861597 * 3.0769476 2.9163414 * 4.1346314 6 H 0.0000000 1.8530991 * 4.1347975 3.9130538 5.2016285 7 H 1.8530991 * 0.0000000 2.9160640 * 2.5184712 * 3.9127213 8 C 4.1347975 2.9160640 * 0.0000000 1.0860728 * 1.0842684 * 9 H 3.9130538 2.5184712 * 1.0860728 * 0.0000000 1.8532291 * 10 H 5.2016285 3.9127213 1.0842684 * 1.8532291 * 0.0000000 * ... LESS THAN 3.000 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 212.7 ( 3.5 MIN) TOTAL WALL CLOCK TIME= 214.6 SECONDS, CPU UTILIZATION IS 99.12% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.02 TOTAL CPU TIME= 212.7 ( 3.5 MIN) TOTAL WALL CLOCK TIME= 214.6 SECONDS, CPU UTILIZATION IS 99.13% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8256321504 -155.8256321504 0.002117855 0.002487727 17697580 79911 2 1 0 -155.8257133586 -0.0000812082 0.000990345 0.000538584 16677718 123321 3 2 0 -155.8257146008 -0.0000012422 0.000592077 0.000397422 16023247 143775 4 3 0 -155.8257161212 -0.0000015204 0.000128711 0.000213872 15582110 157548 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 5 4 0 -155.8262243937 -0.0005082724 0.000927754 0.001468735 17697001 79911 6 5 0 -155.8262311100 -0.0000067163 0.000442224 0.000365817 16446554 130307 7 6 0 -155.8262314840 -0.0000003740 0.000186267 0.000238793 15738143 150741 8 7 0 -155.8262318798 -0.0000003958 0.000049334 0.000076813 15342364 163051 9 8 0 -155.8262318997 -0.0000000199 0.000018945 0.000031177 14568265 188370 10 9 0 -155.8262319041 -0.0000000044 0.000002472 0.000004208 13859236 207232 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 8.0 SECONDS ( 0.8 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262319041 AFTER 10 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9915552716 TOTAL ELECTRON NUMBER = 30.0000053055 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.22 TOTAL CPU TIME= 220.9 ( 3.7 MIN) TOTAL WALL CLOCK TIME= 222.8 SECONDS, CPU UTILIZATION IS 99.13% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 220.9 ( 3.7 MIN) TOTAL WALL CLOCK TIME= 222.9 SECONDS, CPU UTILIZATION IS 99.13% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700735 WORDS. CPU 0: STEP CPU TIME= 2.30 TOTAL CPU TIME= 223.2 ( 3.7 MIN) TOTAL WALL CLOCK TIME= 225.2 SECONDS, CPU UTILIZATION IS 99.13% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 223.6 ( 3.7 MIN) TOTAL WALL CLOCK TIME= 225.5 SECONDS, CPU UTILIZATION IS 99.13% NSERCH= 19 ENERGY= -155.8262319 ----------------------- GRADIENT (HARTREE/BOHR) ----------------------- ATOM ZNUC DE/DX DE/DY DE/DZ -------------------------------------------------------------- 1 C 6.0 -0.0002137 -0.0001204 0.0001003 2 H 1.0 0.0001124 -0.0000090 0.0000350 3 C 6.0 -0.0004619 0.0003527 -0.0000479 4 H 1.0 0.0000870 -0.0001064 -0.0000927 5 C 6.0 0.0004005 0.0001050 -0.0001121 6 H 1.0 -0.0000103 -0.0000821 0.0001142 7 H 1.0 -0.0000429 -0.0000969 0.0000179 8 C 6.0 -0.0000168 -0.0002303 0.0001210 9 H 1.0 0.0000309 0.0000177 -0.0000339 10 H 1.0 0.0001147 0.0001699 -0.0001017 MAXIMUM GRADIENT = 0.0004619 RMS GRADIENT = 0.0001623 NSERCH: 19 E= -155.8262319041 GRAD. MAX= 0.0004619 R.M.S.= 0.0001623 HESSIAN UPDATED USING THE BFGS FORMULA ACTUAL ENERGY CHANGE WAS -0.0000526330 PREDICTED ENERGY CHANGE WAS -0.0000550641 RATIO= 0.956 MIN SEARCH, CORRECT HESSIAN, TRYING PURE NR STEP NR STEP HAS LENGTH = 0.305837 TRIM/QA LAMBDA FOR NON-TS MODES = -0.00117407 TRIM/QA STEP HAS LENGTH = 0.100000 RADIUS OF STEP TAKEN= 0.10000 CURRENT TRUST RADIUS= 0.10000 BEGINNING GEOMETRY SEARCH POINT NSERCH= 20 ... COORDINATES OF ALL ATOMS ARE (ANGS) ATOM CHARGE X Y Z ------------------------------------------------------------ C 6.0 0.4221593205 -0.4164903086 0.7473854105 H 1.0 1.2081504538 -0.5258044035 1.4927307213 C 6.0 0.7689159288 0.3244454431 -0.4660131579 H 1.0 1.8058278917 0.2596772752 -0.7862241194 C 6.0 -0.0802558400 1.0770752043 -1.1700110763 H 1.0 0.2376282019 1.5706657213 -2.0851383812 H 1.0 -1.1036458380 1.2438549755 -0.8498403711 C 6.0 -0.7537379098 -1.0022445039 0.9775696367 H 1.0 -1.5572475974 -0.9759810598 0.2464428733 H 1.0 -0.9467946115 -1.5551983436 1.8930984641 INTERNUCLEAR DISTANCES (ANGS.) ------------------------------ 1 C 2 H 3 C 4 H 5 C 1 C 0.0000000 1.0887016 * 1.4634077 * 2.1734073 * 2.4818477 * 2 H 1.0887016 * 0.0000000 2.1800297 * 2.4835126 * 3.3644327 3 C 1.4634077 * 2.1800297 * 0.0000000 1.0871598 * 1.3353491 * 4 H 2.1734073 * 2.4835126 * 1.0871598 * 0.0000000 2.0911106 * 5 C 2.4818477 * 3.3644327 1.3353491 * 2.0911106 * 0.0000000 6 H 3.4649721 4.2589022 2.1111367 * 2.4218008 * 1.0872625 * 7 H 2.7633237 * 3.7368082 2.1211140 * 3.0720824 1.0851967 * 8 C 1.3337268 * 2.0836007 * 2.4824408 * 3.3548163 3.0641885 9 H 2.1170794 * 3.0664831 2.7585756 * 3.7287437 2.8987733 * 10 H 2.1173921 * 2.4215149 * 3.4701774 4.2484672 4.1306650 6 H 7 H 8 C 9 H 10 H 1 C 3.4649721 2.7633237 * 1.3337268 * 2.1170794 * 2.1173921 * 2 H 4.2589022 3.7368082 2.0836007 * 3.0664831 2.4215149 * 3 C 2.1111367 * 2.1211140 * 2.4824408 * 2.7585756 * 3.4701774 4 H 2.4218008 * 3.0720824 3.3548163 3.7287437 4.2484672 5 C 1.0872625 * 1.0851967 * 3.0641885 2.8987733 * 4.1306650 6 H 0.0000000 1.8525071 * 4.1210259 3.8914342 5.1961767 7 H 1.8525071 * 0.0000000 2.9166463 * 2.5169949 * 3.9221187 8 C 4.1210259 2.9166463 * 0.0000000 1.0866756 * 1.0868403 * 9 H 3.8914342 2.5169949 * 1.0866756 * 0.0000000 1.8492215 * 10 H 5.1961767 3.9221187 1.0868403 * 1.8492215 * 0.0000000 * ... LESS THAN 3.000 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 223.6 ( 3.7 MIN) TOTAL WALL CLOCK TIME= 225.5 SECONDS, CPU UTILIZATION IS 99.13% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 223.6 ( 3.7 MIN) TOTAL WALL CLOCK TIME= 225.6 SECONDS, CPU UTILIZATION IS 99.13% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8254131072 -155.8254131072 0.002600880 0.004328096 17708728 79724 2 1 0 -155.8256627845 -0.0002496773 0.001591699 0.000909338 16823579 118800 3 2 0 -155.8256649018 -0.0000021173 0.000889094 0.001153442 16243716 137192 4 3 0 -155.8256715508 -0.0000066490 0.000214091 0.000383038 15937478 147524 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 5 4 0 -155.8260908805 -0.0004193297 0.000968010 0.001501523 17708114 79742 6 5 0 -155.8260980549 -0.0000071744 0.000442340 0.000388867 16471064 129648 7 6 0 -155.8260984784 -0.0000004235 0.000201043 0.000258189 15779790 149702 8 7 0 -155.8260989400 -0.0000004616 0.000052322 0.000096458 15409059 161696 9 8 0 -155.8260989684 -0.0000000284 0.000017820 0.000033480 14661339 186774 10 9 0 -155.8260989731 -0.0000000047 0.000002196 0.000003707 13948114 205172 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 8.0 SECONDS ( 0.8 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8260989731 AFTER 10 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9894393012 TOTAL ELECTRON NUMBER = 30.0000047710 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.25 TOTAL CPU TIME= 231.8 ( 3.9 MIN) TOTAL WALL CLOCK TIME= 233.9 SECONDS, CPU UTILIZATION IS 99.14% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 231.9 ( 3.9 MIN) TOTAL WALL CLOCK TIME= 233.9 SECONDS, CPU UTILIZATION IS 99.14% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700735 WORDS. CPU 0: STEP CPU TIME= 2.30 TOTAL CPU TIME= 234.2 ( 3.9 MIN) TOTAL WALL CLOCK TIME= 236.2 SECONDS, CPU UTILIZATION IS 99.14% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 234.5 ( 3.9 MIN) TOTAL WALL CLOCK TIME= 236.6 SECONDS, CPU UTILIZATION IS 99.13% NSERCH= 20 ENERGY= -155.8260990 ----------------------- GRADIENT (HARTREE/BOHR) ----------------------- ATOM ZNUC DE/DX DE/DY DE/DZ -------------------------------------------------------------- 1 C 6.0 0.0007943 0.0020842 -0.0007211 2 H 1.0 -0.0006834 -0.0003155 0.0003683 3 C 6.0 0.0044402 -0.0025320 -0.0005392 4 H 1.0 -0.0007475 0.0005445 0.0009814 5 C 6.0 -0.0042059 -0.0004450 0.0015876 6 H 1.0 0.0005536 0.0001884 -0.0016489 7 H 1.0 0.0004917 0.0012322 -0.0002739 8 C 6.0 0.0008252 0.0012103 -0.0005695 9 H 1.0 -0.0007591 -0.0000607 0.0003617 10 H 1.0 -0.0007092 -0.0019063 0.0004535 MAXIMUM GRADIENT = 0.0044402 RMS GRADIENT = 0.0014973 NSERCH: 20 E= -155.8260989731 GRAD. MAX= 0.0044402 R.M.S.= 0.0014973 HESSIAN UPDATED USING THE BFGS FORMULA ACTUAL ENERGY CHANGE WAS 0.0001329310 PREDICTED ENERGY CHANGE WAS -0.0000166949 RATIO= -7.962 MIN SEARCH, CORRECT HESSIAN, TRYING PURE NR STEP NR STEP HAS LENGTH = 0.100995 TRIM/QA LAMBDA FOR NON-TS MODES = -0.01555745 TRIM/QA STEP HAS LENGTH = 0.050000 RADIUS OF STEP TAKEN= 0.05000 CURRENT TRUST RADIUS= 0.05000 BEGINNING GEOMETRY SEARCH POINT NSERCH= 21 ... COORDINATES OF ALL ATOMS ARE (ANGS) ATOM CHARGE X Y Z ------------------------------------------------------------ C 6.0 0.4198559927 -0.4224565320 0.7457033844 H 1.0 1.2100871466 -0.5244192321 1.4881388501 C 6.0 0.7646884973 0.3255095460 -0.4651044422 H 1.0 1.8024600742 0.2561160174 -0.7883484711 C 6.0 -0.0761553145 1.0815307170 -1.1708063184 H 1.0 0.2415981716 1.5818035618 -2.0790269828 H 1.0 -1.1037893623 1.2344477894 -0.8542541945 C 6.0 -0.7553209694 -1.0069895842 0.9783339598 H 1.0 -1.5558968345 -0.9818267646 0.2444410814 H 1.0 -0.9465274017 -1.5437155185 1.9009231333 INTERNUCLEAR DISTANCES (ANGS.) ------------------------------ 1 C 2 H 3 C 4 H 5 C 1 C 0.0000000 1.0890694 * 1.4643833 * 2.1737916 * 2.4861646 * 2 H 1.0890694 * 0.0000000 2.1762165 * 2.4784139 * 3.3620655 3 C 1.4643833 * 2.1762165 * 0.0000000 1.0891611 * 1.3328921 * 4 H 2.1737916 * 2.4784139 * 1.0891611 * 0.0000000 2.0872899 * 5 C 2.4861646 * 3.3620655 1.3328921 * 2.0872899 * 0.0000000 6 H 3.4681315 4.2542705 2.1110765 * 2.4206587 * 1.0844837 * 7 H 2.7616465 * 3.7328867 2.1139574 * 3.0672076 1.0861034 * 8 C 1.3329804 * 2.0870084 * 2.4838472 * 3.3554205 3.0727816 9 H 2.1137072 * 3.0670300 2.7563925 * 3.7252809 2.9068891 * 10 H 2.1115771 * 2.4208143 * 3.4670375 4.2459990 4.1333990 6 H 7 H 8 C 9 H 10 H 1 C 3.4681315 2.7616465 * 1.3329804 * 2.1137072 * 2.1115771 * 2 H 4.2542705 3.7328867 2.0870084 * 3.0670300 2.4208143 * 3 C 2.1110765 * 2.1139574 * 2.4838472 * 2.7563925 * 3.4670375 4 H 2.4206587 * 3.0672076 3.3554205 3.7252809 4.2459990 5 C 1.0844837 * 1.0861034 * 3.0727816 2.9068891 * 4.1333990 6 H 0.0000000 1.8522397 * 4.1283355 3.8989348 5.1981261 7 H 1.8522397 * 0.0000000 2.9161363 * 2.5146382 * 3.9158556 8 C 4.1283355 2.9161363 * 0.0000000 1.0863488 * 1.0843456 * 9 H 3.8989348 2.5146382 * 1.0863488 * 0.0000000 1.8522912 * 10 H 5.1981261 3.9158556 1.0843456 * 1.8522912 * 0.0000000 * ... LESS THAN 3.000 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 234.5 ( 3.9 MIN) TOTAL WALL CLOCK TIME= 236.6 SECONDS, CPU UTILIZATION IS 99.13% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 234.5 ( 3.9 MIN) TOTAL WALL CLOCK TIME= 236.6 SECONDS, CPU UTILIZATION IS 99.13% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8256508962 -155.8256508962 0.001705380 0.002121247 17701843 79797 2 1 0 -155.8257276965 -0.0000768003 0.000650930 0.000489745 16692903 122130 3 2 0 -155.8257268331 0.0000008634 0.000400840 0.001001128 16059184 144314 4 3 0 -155.8257301072 -0.0000032741 0.000075217 0.000174888 15757707 153603 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 5 4 0 -155.8262078786 -0.0004777715 0.000881988 0.001460237 17702247 79798 6 5 0 -155.8262148487 -0.0000069701 0.000490840 0.000350897 16458424 129903 7 6 0 -155.8262152047 -0.0000003560 0.000252496 0.000232272 15709682 151810 8 7 0 -155.8262155323 -0.0000003276 0.000040811 0.000039927 15245466 165551 9 8 0 -155.8262155402 -0.0000000079 0.000015012 0.000025674 14491911 191770 10 9 0 -155.8262155434 -0.0000000032 0.000002236 0.000003296 13760827 207708 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 8.0 SECONDS ( 0.8 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262155434 AFTER 10 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9912832917 TOTAL ELECTRON NUMBER = 30.0000052750 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.23 TOTAL CPU TIME= 242.8 ( 4.0 MIN) TOTAL WALL CLOCK TIME= 244.9 SECONDS, CPU UTILIZATION IS 99.14% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 242.8 ( 4.0 MIN) TOTAL WALL CLOCK TIME= 244.9 SECONDS, CPU UTILIZATION IS 99.13% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700735 WORDS. CPU 0: STEP CPU TIME= 2.30 TOTAL CPU TIME= 245.1 ( 4.1 MIN) TOTAL WALL CLOCK TIME= 247.2 SECONDS, CPU UTILIZATION IS 99.13% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.37 TOTAL CPU TIME= 245.4 ( 4.1 MIN) TOTAL WALL CLOCK TIME= 247.6 SECONDS, CPU UTILIZATION IS 99.14% NSERCH= 21 ENERGY= -155.8262155 ----------------------- GRADIENT (HARTREE/BOHR) ----------------------- ATOM ZNUC DE/DX DE/DY DE/DZ -------------------------------------------------------------- 1 C 6.0 0.0000522 0.0002234 0.0001049 2 H 1.0 -0.0000886 -0.0000681 0.0001374 3 C 6.0 0.0000551 0.0000086 -0.0000400 4 H 1.0 0.0000624 0.0001273 0.0000721 5 C 6.0 0.0000532 -0.0000706 -0.0000952 6 H 1.0 -0.0001947 -0.0003354 -0.0001940 7 H 1.0 0.0000852 0.0003378 0.0001076 8 C 6.0 0.0001629 -0.0000911 0.0002432 9 H 1.0 -0.0002325 0.0001389 -0.0000067 10 H 1.0 0.0000448 -0.0002709 -0.0003293 MAXIMUM GRADIENT = 0.0003378 RMS GRADIENT = 0.0001647 NSERCH: 21 E= -155.8262155434 GRAD. MAX= 0.0003378 R.M.S.= 0.0001647 HESSIAN UPDATED USING THE BFGS FORMULA ACTUAL ENERGY CHANGE WAS -0.0001165703 PREDICTED ENERGY CHANGE WAS -0.0001178071 RATIO= 0.990 MIN SEARCH, CORRECT HESSIAN, TRYING PURE NR STEP NR STEP HAS LENGTH = 0.068819 RADIUS OF STEP TAKEN= 0.06882 CURRENT TRUST RADIUS= 0.10000 BEGINNING GEOMETRY SEARCH POINT NSERCH= 22 ... COORDINATES OF ALL ATOMS ARE (ANGS) ATOM CHARGE X Y Z ------------------------------------------------------------ C 6.0 0.4209205486 -0.4300454623 0.7399326436 H 1.0 1.2125132890 -0.5282144566 1.4814800610 C 6.0 0.7660657484 0.3209368829 -0.4689066218 H 1.0 1.8057495082 0.2616028984 -0.7885553957 C 6.0 -0.0764758800 1.0792423993 -1.1706441662 H 1.0 0.2464743650 1.5977680206 -2.0671557681 H 1.0 -1.1085405155 1.2188907737 -0.8614599385 C 6.0 -0.7575939425 -1.0051260899 0.9795325580 H 1.0 -1.5577292561 -0.9861396993 0.2457917306 H 1.0 -0.9503838652 -1.5289152667 1.9099848971 INTERNUCLEAR DISTANCES (ANGS.) ------------------------------ 1 C 2 H 3 C 4 H 5 C 1 C 0.0000000 1.0891046 * 1.4643743 * 2.1754090 * 2.4850869 * 2 H 1.0891046 * 0.0000000 2.1735643 * 2.4756417 * 3.3584481 3 C 1.4643743 * 2.1735643 * 0.0000000 1.0893292 * 1.3331689 * 4 H 2.1754090 * 2.4756417 * 1.0893292 * 0.0000000 2.0874143 * 5 C 2.4850869 * 3.3584481 1.3331689 * 2.0874143 * 0.0000000 6 H 3.4673051 4.2480406 2.1106097 * 2.4189864 * 1.0848496 * 7 H 2.7609238 * 3.7321623 2.1153175 * 3.0683549 1.0863949 * 8 C 1.3330500 * 2.0882333 * 2.4855498 * 3.3617655 3.0711193 9 H 2.1138758 * 3.0677133 2.7603018 * 3.7335941 2.9096745 * 10 H 2.1111639 * 2.4213927 * 3.4680365 4.2525694 4.1299488 6 H 7 H 8 C 9 H 10 H 1 C 3.4673051 2.7609238 * 1.3330500 * 2.1138758 * 2.1111639 * 2 H 4.2480406 3.7321623 2.0882333 * 3.0677133 2.4213927 * 3 C 2.1106097 * 2.1153175 * 2.4855498 * 2.7603018 * 3.4680365 4 H 2.4189864 * 3.0683549 3.3617655 3.7335941 4.2525694 5 C 1.0848496 * 1.0863949 * 3.0711193 2.9096745 * 4.1299488 6 H 0.0000000 1.8529209 * 4.1310435 3.9091503 5.1986792 7 H 1.8529209 * 0.0000000 2.9083789 * 2.5079745 * 3.9059388 8 C 4.1310435 2.9083789 * 0.0000000 1.0857958 * 1.0850183 * 9 H 3.9091503 2.5079745 * 1.0857958 * 0.0000000 1.8528391 * 10 H 5.1986792 3.9059388 1.0850183 * 1.8528391 * 0.0000000 * ... LESS THAN 3.000 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 245.4 ( 4.1 MIN) TOTAL WALL CLOCK TIME= 247.6 SECONDS, CPU UTILIZATION IS 99.14% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 245.4 ( 4.1 MIN) TOTAL WALL CLOCK TIME= 247.6 SECONDS, CPU UTILIZATION IS 99.14% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8255968119 -155.8255968119 0.002093308 0.003757854 17703536 79795 2 1 0 -155.8257376179 -0.0001408060 0.000773829 0.000806117 16714522 122575 3 2 0 -155.8257411150 -0.0000034971 0.000497279 0.000351804 16082434 142277 4 3 0 -155.8257420875 -0.0000009725 0.000122966 0.000159539 15575950 156803 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 5 4 0 -155.8262222611 -0.0004801736 0.000890056 0.001467605 17703595 79798 6 5 0 -155.8262292185 -0.0000069574 0.000582024 0.000397254 16456973 129983 7 6 0 -155.8262295461 -0.0000003276 0.000300330 0.000285559 15753590 150629 8 7 0 -155.8262300186 -0.0000004726 0.000074003 0.000112903 15373409 163311 9 8 0 -155.8262300510 -0.0000000323 0.000021446 0.000028698 14624507 187298 10 9 0 -155.8262300543 -0.0000000034 0.000002060 0.000003099 13853466 206391 11 10 0 -155.8262300545 -0.0000000001 0.000001004 0.000002686 12809902 236423 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 9.2 SECONDS ( 0.8 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262300545 AFTER 11 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9909057818 TOTAL ELECTRON NUMBER = 30.0000053940 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 9.40 TOTAL CPU TIME= 254.8 ( 4.2 MIN) TOTAL WALL CLOCK TIME= 257.0 SECONDS, CPU UTILIZATION IS 99.14% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.02 TOTAL CPU TIME= 254.9 ( 4.2 MIN) TOTAL WALL CLOCK TIME= 257.1 SECONDS, CPU UTILIZATION IS 99.14% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700735 WORDS. CPU 0: STEP CPU TIME= 2.31 TOTAL CPU TIME= 257.2 ( 4.3 MIN) TOTAL WALL CLOCK TIME= 259.4 SECONDS, CPU UTILIZATION IS 99.15% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 257.5 ( 4.3 MIN) TOTAL WALL CLOCK TIME= 259.8 SECONDS, CPU UTILIZATION IS 99.15% NSERCH= 22 ENERGY= -155.8262301 ----------------------- GRADIENT (HARTREE/BOHR) ----------------------- ATOM ZNUC DE/DX DE/DY DE/DZ -------------------------------------------------------------- 1 C 6.0 0.0001649 -0.0002929 0.0000793 2 H 1.0 0.0001000 0.0000987 -0.0000303 3 C 6.0 0.0002519 -0.0001343 0.0000459 4 H 1.0 0.0001997 0.0000603 -0.0001108 5 C 6.0 -0.0002485 -0.0001441 0.0001498 6 H 1.0 0.0001348 0.0001638 -0.0000662 7 H 1.0 -0.0002682 0.0001111 -0.0000607 8 C 6.0 -0.0004461 0.0004493 -0.0003688 9 H 1.0 0.0001538 -0.0001723 0.0000803 10 H 1.0 -0.0000424 -0.0001396 0.0002817 MAXIMUM GRADIENT = 0.0004493 RMS GRADIENT = 0.0002016 NSERCH: 22 E= -155.8262300545 GRAD. MAX= 0.0004493 R.M.S.= 0.0002016 HESSIAN UPDATED USING THE BFGS FORMULA ACTUAL ENERGY CHANGE WAS -0.0000145110 PREDICTED ENERGY CHANGE WAS -0.0000231962 RATIO= 0.626 MIN SEARCH, CORRECT HESSIAN, TRYING PURE NR STEP NR STEP HAS LENGTH = 0.019056 RADIUS OF STEP TAKEN= 0.01906 CURRENT TRUST RADIUS= 0.06882 BEGINNING GEOMETRY SEARCH POINT NSERCH= 23 ... COORDINATES OF ALL ATOMS ARE (ANGS) ATOM CHARGE X Y Z ------------------------------------------------------------ C 6.0 0.4199428555 -0.4271745441 0.7413134467 H 1.0 1.2110504384 -0.5263889549 1.4831442709 C 6.0 0.7648229929 0.3223446227 -0.4683858803 H 1.0 1.8036674948 0.2580491097 -0.7885874537 C 6.0 -0.0759031982 1.0811832920 -1.1710475720 H 1.0 0.2461228394 1.5950735773 -2.0700295945 H 1.0 -1.1067830620 1.2222655699 -0.8596222736 C 6.0 -0.7562104293 -1.0071075179 0.9792468118 H 1.0 -1.5567627687 -0.9858852782 0.2457055228 H 1.0 -0.9489471629 -1.5323598765 1.9082627218 INTERNUCLEAR DISTANCES (ANGS.) ------------------------------ 1 C 2 H 3 C 4 H 5 C 1 C 0.0000000 1.0890398 * 1.4642724 * 2.1736656 * 2.4855847 * 2 H 1.0890398 * 0.0000000 2.1743821 * 2.4753390 * 3.3593560 3 C 1.4642724 * 2.1743821 * 0.0000000 1.0889724 * 1.3328129 * 4 H 2.1736656 * 2.4753390 * 1.0889724 * 0.0000000 2.0872498 * 5 C 2.4855847 * 3.3593560 1.3328129 * 2.0872498 * 0.0000000 6 H 3.4674703 4.2493215 2.1104861 * 2.4198499 * 1.0844135 * 7 H 2.7594456 * 3.7307774 2.1132517 * 3.0668358 1.0860954 * 8 C 1.3327682 * 2.0868920 * 2.4852819 * 3.3583976 3.0736855 9 H 2.1130902 * 3.0664607 2.7588317 * 3.7295611 2.9108258 * 10 H 2.1111762 * 2.4203910 * 3.4677652 4.2491708 4.1321865 6 H 7 H 8 C 9 H 10 H 1 C 3.4674703 2.7594456 * 1.3327682 * 2.1130902 * 2.1111762 * 2 H 4.2493215 3.7307774 2.0868920 * 3.0664607 2.4203910 * 3 C 2.1104861 * 2.1132517 * 2.4852819 * 2.7588317 * 3.4677652 4 H 2.4198499 * 3.0668358 3.3583976 3.7295611 4.2491708 5 C 1.0844135 * 1.0860954 * 3.0736855 2.9108258 * 4.1321865 6 H 0.0000000 1.8532205 * 4.1320824 3.9082444 5.1996002 7 H 1.8532205 * 0.0000000 2.9110900 * 2.5100122 * 3.9082043 8 C 4.1320824 2.9110900 * 0.0000000 1.0860098 * 1.0844852 * 9 H 3.9082444 2.5100122 * 1.0860098 * 0.0000000 1.8526119 * 10 H 5.1996002 3.9082043 1.0844852 * 1.8526119 * 0.0000000 * ... LESS THAN 3.000 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 257.5 ( 4.3 MIN) TOTAL WALL CLOCK TIME= 259.8 SECONDS, CPU UTILIZATION IS 99.15% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 257.5 ( 4.3 MIN) TOTAL WALL CLOCK TIME= 259.8 SECONDS, CPU UTILIZATION IS 99.15% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8257180395 -155.8257180395 0.000873933 0.001471325 17702288 79799 2 1 0 -155.8257384545 -0.0000204150 0.000468314 0.000286607 16528408 128014 3 2 0 -155.8257389205 -0.0000004660 0.000284374 0.000235261 15762388 150827 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 4 3 0 -155.8262257151 -0.0004867947 0.000913693 0.001449684 17702290 79801 5 4 0 -155.8262325227 -0.0000068076 0.000633801 0.000397658 16452611 130066 6 5 0 -155.8262328287 -0.0000003060 0.000342173 0.000292239 15742947 150899 7 6 0 -155.8262333312 -0.0000005025 0.000059249 0.000113205 15353811 163976 8 7 0 -155.8262333634 -0.0000000323 0.000015215 0.000028922 14646523 186074 9 8 0 -155.8262333668 -0.0000000034 0.000002279 0.000002444 13901212 204519 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 7.8 SECONDS ( 0.9 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262333668 AFTER 9 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9916412349 TOTAL ELECTRON NUMBER = 30.0000053417 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.02 TOTAL CPU TIME= 265.6 ( 4.4 MIN) TOTAL WALL CLOCK TIME= 267.8 SECONDS, CPU UTILIZATION IS 99.15% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 265.6 ( 4.4 MIN) TOTAL WALL CLOCK TIME= 267.9 SECONDS, CPU UTILIZATION IS 99.15% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700735 WORDS. CPU 0: STEP CPU TIME= 2.30 TOTAL CPU TIME= 267.9 ( 4.5 MIN) TOTAL WALL CLOCK TIME= 270.2 SECONDS, CPU UTILIZATION IS 99.15% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 268.2 ( 4.5 MIN) TOTAL WALL CLOCK TIME= 270.5 SECONDS, CPU UTILIZATION IS 99.14% NSERCH= 23 ENERGY= -155.8262334 ----------------------- GRADIENT (HARTREE/BOHR) ----------------------- ATOM ZNUC DE/DX DE/DY DE/DZ -------------------------------------------------------------- 1 C 6.0 -0.0000402 0.0000795 0.0000298 2 H 1.0 -0.0000511 -0.0000615 0.0000174 3 C 6.0 -0.0000609 0.0000452 -0.0001427 4 H 1.0 -0.0000677 -0.0000407 0.0000282 5 C 6.0 0.0000371 0.0001161 -0.0000788 6 H 1.0 0.0000449 -0.0000501 0.0000829 7 H 1.0 -0.0000183 -0.0000741 0.0000292 8 C 6.0 0.0001415 -0.0000734 0.0000330 9 H 1.0 0.0000590 0.0000271 0.0000331 10 H 1.0 -0.0000445 0.0000319 -0.0000322 MAXIMUM GRADIENT = 0.0001427 RMS GRADIENT = 0.0000642 NSERCH: 23 E= -155.8262333668 GRAD. MAX= 0.0001427 R.M.S.= 0.0000642 HESSIAN UPDATED USING THE BFGS FORMULA ACTUAL ENERGY CHANGE WAS -0.0000033124 PREDICTED ENERGY CHANGE WAS -0.0000041311 RATIO= 0.802 MIN SEARCH, CORRECT HESSIAN, TRYING PURE NR STEP NR STEP HAS LENGTH = 0.004319 RADIUS OF STEP TAKEN= 0.00432 CURRENT TRUST RADIUS= 0.05000 BEGINNING GEOMETRY SEARCH POINT NSERCH= 24 ... COORDINATES OF ALL ATOMS ARE (ANGS) ATOM CHARGE X Y Z ------------------------------------------------------------ C 6.0 0.4200194088 -0.4276169922 0.7413034253 H 1.0 1.2113012784 -0.5265833595 1.4830759649 C 6.0 0.7652668251 0.3223053249 -0.4679538891 H 1.0 1.8042851486 0.2589157792 -0.7881641994 C 6.0 -0.0757672963 1.0805591097 -1.1710012651 H 1.0 0.2451679604 1.5945401811 -2.0704554262 H 1.0 -1.1065311608 1.2226656345 -0.8596564384 C 6.0 -0.7566244757 -1.0068499929 0.9791064019 H 1.0 -1.5574247102 -0.9853139366 0.2457092604 H 1.0 -0.9486929782 -1.5326217482 1.9080361658 INTERNUCLEAR DISTANCES (ANGS.) ------------------------------ 1 C 2 H 3 C 4 H 5 C 1 C 0.0000000 1.0891041 * 1.4642003 * 2.1741182 * 2.4854192 * 2 H 1.0891041 * 0.0000000 2.1739541 * 2.4753122 * 3.3591038 3 C 1.4642003 * 2.1739541 * 0.0000000 1.0890877 * 1.3328776 * 4 H 2.1741182 * 2.4753122 * 1.0890877 * 0.0000000 2.0871653 * 5 C 2.4854192 * 3.3591038 1.3328776 * 2.0871653 * 0.0000000 6 H 3.4678063 4.2497252 2.1111834 * 2.4205391 * 1.0845247 * 7 H 2.7598663 * 3.7310340 2.1136952 * 3.0670469 1.0860958 * 8 C 1.3328736 * 2.0874322 * 2.4853150 * 3.3591169 3.0730776 9 H 2.1135100 * 3.0671410 2.7593621 * 3.7306963 2.9103623 * 10 H 2.1108468 * 2.4203883 * 3.4675267 4.2494696 4.1317291 6 H 7 H 8 C 9 H 10 H 1 C 3.4678063 2.7598663 * 1.3328736 * 2.1135100 * 2.1108468 * 2 H 4.2497252 3.7310340 2.0874322 * 3.0671410 2.4203883 * 3 C 2.1111834 * 2.1136952 * 2.4853150 * 2.7593621 * 3.4675267 4 H 2.4205391 * 3.0670469 3.3591169 3.7306963 4.2494696 5 C 1.0845247 * 1.0860958 * 3.0730776 2.9103623 * 4.1317291 6 H 0.0000000 1.8524080 * 4.1316639 3.9076344 5.1993116 7 H 1.8524080 * 0.0000000 2.9110519 * 2.5100423 * 3.9085347 8 C 4.1316639 2.9110519 * 0.0000000 1.0861014 * 1.0845445 * 9 H 3.9076344 2.5100423 * 1.0861014 * 0.0000000 1.8529519 * 10 H 5.1993116 3.9085347 1.0845445 * 1.8529519 * 0.0000000 * ... LESS THAN 3.000 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 268.2 ( 4.5 MIN) TOTAL WALL CLOCK TIME= 270.5 SECONDS, CPU UTILIZATION IS 99.15% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.02 TOTAL CPU TIME= 268.3 ( 4.5 MIN) TOTAL WALL CLOCK TIME= 270.6 SECONDS, CPU UTILIZATION IS 99.15% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8257336452 -155.8257336452 0.000858870 0.001459919 17702416 79803 2 1 0 -155.8257411087 -0.0000074635 0.000481304 0.000346205 16461742 129818 3 2 0 -155.8257414939 -0.0000003852 0.000240966 0.000230651 15714116 151565 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 4 3 0 -155.8262260582 -0.0004845642 0.000849533 0.001446284 17702461 79813 5 4 0 -155.8262328738 -0.0000068156 0.000554167 0.000361627 16452552 130126 6 5 0 -155.8262331945 -0.0000003207 0.000294711 0.000248478 15713695 151622 7 6 0 -155.8262336035 -0.0000004090 0.000051744 0.000084423 15282102 165014 8 7 0 -155.8262336296 -0.0000000261 0.000018066 0.000036342 14652199 186599 9 8 0 -155.8262336345 -0.0000000049 0.000003330 0.000002632 13971572 202122 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 7.8 SECONDS ( 0.9 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262336345 AFTER 9 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9914560066 TOTAL ELECTRON NUMBER = 30.0000053506 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.00 TOTAL CPU TIME= 276.3 ( 4.6 MIN) TOTAL WALL CLOCK TIME= 278.6 SECONDS, CPU UTILIZATION IS 99.15% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 276.3 ( 4.6 MIN) TOTAL WALL CLOCK TIME= 278.6 SECONDS, CPU UTILIZATION IS 99.15% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700735 WORDS. CPU 0: STEP CPU TIME= 2.31 TOTAL CPU TIME= 278.6 ( 4.6 MIN) TOTAL WALL CLOCK TIME= 281.0 SECONDS, CPU UTILIZATION IS 99.15% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 278.9 ( 4.6 MIN) TOTAL WALL CLOCK TIME= 281.3 SECONDS, CPU UTILIZATION IS 99.15% NSERCH= 24 ENERGY= -155.8262336 ----------------------- GRADIENT (HARTREE/BOHR) ----------------------- ATOM ZNUC DE/DX DE/DY DE/DZ -------------------------------------------------------------- 1 C 6.0 -0.0000301 -0.0000262 0.0000004 2 H 1.0 0.0000275 0.0000196 0.0000143 3 C 6.0 -0.0000015 -0.0000245 0.0000534 4 H 1.0 0.0000105 0.0000210 -0.0000153 5 C 6.0 0.0000685 -0.0000391 -0.0000120 6 H 1.0 -0.0000636 0.0000055 0.0000006 7 H 1.0 -0.0000022 0.0000468 -0.0000240 8 C 6.0 -0.0000171 -0.0000238 -0.0000088 9 H 1.0 -0.0000112 0.0000218 -0.0000135 10 H 1.0 0.0000192 -0.0000010 0.0000048 MAXIMUM GRADIENT = 0.0000685 RMS GRADIENT = 0.0000274 NSERCH: 24 E= -155.8262336345 GRAD. MAX= 0.0000685 R.M.S.= 0.0000274 HESSIAN UPDATED USING THE BFGS FORMULA ACTUAL ENERGY CHANGE WAS -0.0000002677 PREDICTED ENERGY CHANGE WAS -0.0000004460 RATIO= 0.600 MIN SEARCH, CORRECT HESSIAN, TRYING PURE NR STEP NR STEP HAS LENGTH = 0.002068 RADIUS OF STEP TAKEN= 0.00207 CURRENT TRUST RADIUS= 0.05000 BEGINNING GEOMETRY SEARCH POINT NSERCH= 25 ... COORDINATES OF ALL ATOMS ARE (ANGS) ATOM CHARGE X Y Z ------------------------------------------------------------ C 6.0 0.4200463635 -0.4276345498 0.7411524381 H 1.0 1.2113843747 -0.5268471315 1.4828072744 C 6.0 0.7652229409 0.3223958361 -0.4680855733 H 1.0 1.8042959077 0.2590401124 -0.7881163777 C 6.0 -0.0759104882 1.0806627223 -1.1710123718 H 1.0 0.2456660986 1.5947676667 -2.0702003098 H 1.0 -1.1067922771 1.2220953531 -0.8597837858 C 6.0 -0.7566413267 -1.0066695114 0.9791908996 H 1.0 -1.5575039947 -0.9854334879 0.2458939693 H 1.0 -0.9487675987 -1.5323770101 1.9081538369 INTERNUCLEAR DISTANCES (ANGS.) ------------------------------ 1 C 2 H 3 C 4 H 5 C 1 C 0.0000000 1.0890872 * 1.4642230 * 2.1740129 * 2.4854191 * 2 H 1.0890872 * 0.0000000 2.1739955 * 2.4751277 * 3.3591628 3 C 1.4642230 * 2.1739955 * 0.0000000 1.0890851 * 1.3328842 * 4 H 2.1740129 * 2.4751277 * 1.0890851 * 0.0000000 2.0873067 * 5 C 2.4854191 * 3.3591628 1.3328842 * 2.0873067 * 0.0000000 6 H 3.4675962 4.2494381 2.1108389 * 2.4201723 * 1.0845526 * 7 H 2.7596815 * 3.7310154 2.1136054 * 3.0670908 1.0860864 * 8 C 1.3328682 * 2.0873390 * 2.4853762 * 3.3591361 3.0730643 9 H 2.1135577 * 3.0670831 2.7595733 * 3.7308967 2.9105835 * 10 H 2.1109239 * 2.4203856 * 3.4676303 4.2495184 4.1317213 6 H 7 H 8 C 9 H 10 H 1 C 3.4675962 2.7596815 * 1.3328682 * 2.1135577 * 2.1109239 * 2 H 4.2494381 3.7310154 2.0873390 * 3.0670831 2.4203856 * 3 C 2.1108389 * 2.1136054 * 2.4853762 * 2.7595733 * 3.4676303 4 H 2.4201723 * 3.0670908 3.3591361 3.7308967 4.2495184 5 C 1.0845526 * 1.0860864 * 3.0730643 2.9105835 * 4.1317213 6 H 0.0000000 1.8528725 * 4.1316924 3.9080882 5.1993276 7 H 1.8528725 * 0.0000000 2.9106402 * 2.5097506 * 3.9081413 8 C 4.1316924 2.9106402 * 0.0000000 1.0860738 * 1.0845520 * 9 H 3.9080882 2.5097506 * 1.0860738 * 0.0000000 1.8527858 * 10 H 5.1993276 3.9081413 1.0845520 * 1.8527858 * 0.0000000 * ... LESS THAN 3.000 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 278.9 ( 4.6 MIN) TOTAL WALL CLOCK TIME= 281.3 SECONDS, CPU UTILIZATION IS 99.15% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.02 TOTAL CPU TIME= 279.0 ( 4.6 MIN) TOTAL WALL CLOCK TIME= 281.3 SECONDS, CPU UTILIZATION IS 99.15% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8257349059 -155.8257349059 0.000860572 0.001460620 17702433 79808 2 1 0 -155.8257419284 -0.0000070224 0.000455197 0.000335825 16454281 130000 3 2 0 -155.8257422758 -0.0000003474 0.000229674 0.000221983 15708079 151888 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 4 3 0 -155.8262261239 -0.0004838481 0.000846461 0.001449524 17702509 79812 5 4 0 -155.8262329563 -0.0000068323 0.000546000 0.000363380 16452381 130123 6 5 0 -155.8262332979 -0.0000003416 0.000290117 0.000250393 15714317 151537 7 6 0 -155.8262336879 -0.0000003900 0.000044631 0.000066991 15281139 165053 8 7 0 -155.8262337060 -0.0000000181 0.000018355 0.000034582 14587593 188590 9 8 0 -155.8262337109 -0.0000000049 0.000003458 0.000002425 13935223 203198 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 7.8 SECONDS ( 0.9 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262337109 AFTER 9 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9914592521 TOTAL ELECTRON NUMBER = 30.0000053525 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.02 TOTAL CPU TIME= 287.0 ( 4.8 MIN) TOTAL WALL CLOCK TIME= 289.4 SECONDS, CPU UTILIZATION IS 99.15% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 287.0 ( 4.8 MIN) TOTAL WALL CLOCK TIME= 289.4 SECONDS, CPU UTILIZATION IS 99.15% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700735 WORDS. CPU 0: STEP CPU TIME= 2.31 TOTAL CPU TIME= 289.3 ( 4.8 MIN) TOTAL WALL CLOCK TIME= 291.8 SECONDS, CPU UTILIZATION IS 99.16% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 289.7 ( 4.8 MIN) TOTAL WALL CLOCK TIME= 292.1 SECONDS, CPU UTILIZATION IS 99.15% NSERCH= 25 ENERGY= -155.8262337 ----------------------- GRADIENT (HARTREE/BOHR) ----------------------- ATOM ZNUC DE/DX DE/DY DE/DZ -------------------------------------------------------------- 1 C 6.0 -0.0000127 -0.0000195 0.0000070 2 H 1.0 0.0000163 0.0000032 0.0000068 3 C 6.0 0.0000075 0.0000113 -0.0000053 4 H 1.0 0.0000139 -0.0000037 -0.0000032 5 C 6.0 -0.0000273 0.0000061 0.0000035 6 H 1.0 0.0000153 -0.0000047 -0.0000044 7 H 1.0 -0.0000076 0.0000028 0.0000014 8 C 6.0 -0.0000069 0.0000130 -0.0000127 9 H 1.0 0.0000026 -0.0000052 0.0000038 10 H 1.0 -0.0000010 -0.0000033 0.0000032 MAXIMUM GRADIENT = 0.0000273 RMS GRADIENT = 0.0000099 NSERCH: 25 E= -155.8262337109 GRAD. MAX= 0.0000273 R.M.S.= 0.0000099 ***** EQUILIBRIUM GEOMETRY LOCATED ***** COORDINATES OF ALL ATOMS ARE (ANGS) ATOM CHARGE X Y Z ------------------------------------------------------------ C 6.0 0.4200463635 -0.4276345498 0.7411524381 H 1.0 1.2113843747 -0.5268471315 1.4828072744 C 6.0 0.7652229409 0.3223958361 -0.4680855733 H 1.0 1.8042959077 0.2590401124 -0.7881163777 C 6.0 -0.0759104882 1.0806627223 -1.1710123718 H 1.0 0.2456660986 1.5947676667 -2.0702003098 H 1.0 -1.1067922771 1.2220953531 -0.8597837858 C 6.0 -0.7566413267 -1.0066695114 0.9791908996 H 1.0 -1.5575039947 -0.9854334879 0.2458939693 H 1.0 -0.9487675987 -1.5323770101 1.9081538369 INTERNUCLEAR DISTANCES (ANGS.) ------------------------------ 1 C 2 H 3 C 4 H 5 C 1 C 0.0000000 1.0890872 * 1.4642230 * 2.1740129 * 2.4854191 * 2 H 1.0890872 * 0.0000000 2.1739955 * 2.4751277 * 3.3591628 3 C 1.4642230 * 2.1739955 * 0.0000000 1.0890851 * 1.3328842 * 4 H 2.1740129 * 2.4751277 * 1.0890851 * 0.0000000 2.0873067 * 5 C 2.4854191 * 3.3591628 1.3328842 * 2.0873067 * 0.0000000 6 H 3.4675962 4.2494381 2.1108389 * 2.4201723 * 1.0845526 * 7 H 2.7596815 * 3.7310154 2.1136054 * 3.0670908 1.0860864 * 8 C 1.3328682 * 2.0873390 * 2.4853762 * 3.3591361 3.0730643 9 H 2.1135577 * 3.0670831 2.7595733 * 3.7308967 2.9105835 * 10 H 2.1109239 * 2.4203856 * 3.4676303 4.2495184 4.1317213 6 H 7 H 8 C 9 H 10 H 1 C 3.4675962 2.7596815 * 1.3328682 * 2.1135577 * 2.1109239 * 2 H 4.2494381 3.7310154 2.0873390 * 3.0670831 2.4203856 * 3 C 2.1108389 * 2.1136054 * 2.4853762 * 2.7595733 * 3.4676303 4 H 2.4201723 * 3.0670908 3.3591361 3.7308967 4.2495184 5 C 1.0845526 * 1.0860864 * 3.0730643 2.9105835 * 4.1317213 6 H 0.0000000 1.8528725 * 4.1316924 3.9080882 5.1993276 7 H 1.8528725 * 0.0000000 2.9106402 * 2.5097506 * 3.9081413 8 C 4.1316924 2.9106402 * 0.0000000 1.0860738 * 1.0845520 * 9 H 3.9080882 2.5097506 * 1.0860738 * 0.0000000 1.8527858 * 10 H 5.1993276 3.9081413 1.0845520 * 1.8527858 * 0.0000000 * ... LESS THAN 3.000 NUCLEAR ENERGY = 105.0583326385 ELECTRONIC ENERGY = -260.8845663493 TOTAL ENERGY = -155.8262337109 ------------------ MOLECULAR ORBITALS ------------------ 1 2 3 4 5 -10.2319 -10.2316 -10.2205 -10.2205 -0.8323 A A A A A 1 C 1 S 0.398857 -0.397823 -0.023375 0.006590 -0.073722 2 C 1 S 0.325405 -0.324541 -0.019057 0.005383 -0.114091 3 C 1 X 0.000086 -0.000116 -0.000042 0.000019 -0.018538 4 C 1 Y 0.000052 -0.000100 -0.000029 -0.000010 0.002206 5 C 1 Z -0.000082 0.000151 0.000019 0.000014 -0.016908 6 C 1 S 0.014452 -0.013956 -0.000221 -0.000071 0.296845 7 C 1 X 0.000188 0.000218 -0.001077 0.000344 -0.024139 8 C 1 Y 0.000337 0.000465 -0.000531 0.000216 0.007509 9 C 1 Z -0.000479 -0.000770 0.000225 -0.000130 -0.029648 10 C 1 S 0.004124 -0.007834 -0.002286 0.000796 0.139641 11 C 1 X -0.000953 0.001405 0.000927 -0.000331 -0.008897 12 C 1 Y -0.000404 -0.000716 0.000535 -0.000101 0.000119 13 C 1 Z -0.000456 0.001868 -0.000268 -0.000083 -0.012902 14 C 1 XX -0.005327 0.005503 0.000989 -0.000284 0.005594 15 C 1 YY -0.005075 0.005382 0.000497 -0.000142 -0.001332 16 C 1 ZZ -0.005011 0.005910 0.000482 -0.000086 0.004719 17 C 1 XY -0.000064 0.000198 0.000326 -0.000137 0.006813 18 C 1 XZ -0.000182 -0.000125 -0.000083 0.000040 -0.002201 19 C 1 YZ -0.000091 -0.000509 -0.000154 -0.000053 -0.009116 20 H 2 S 0.000223 -0.000156 -0.000009 -0.000014 0.038119 21 H 2 S 0.000895 -0.001042 -0.000095 0.000093 0.049011 22 H 2 S -0.000622 0.000410 0.000019 0.000076 -0.001003 23 H 2 X -0.000332 0.000348 0.000128 -0.000036 -0.006628 24 H 2 Y 0.000042 -0.000040 0.000018 0.000003 0.001007 25 H 2 Z -0.000269 0.000359 0.000053 -0.000020 -0.006245 26 C 3 S 0.397801 0.398880 0.007544 0.023077 -0.073719 27 C 3 S 0.324543 0.325403 0.006141 0.018820 -0.114087 28 C 3 X 0.000032 0.000020 -0.000007 0.000034 -0.024116 29 C 3 Y -0.000062 -0.000112 -0.000025 -0.000025 0.001580 30 C 3 Z 0.000109 0.000182 0.000023 0.000027 0.007083 31 C 3 S 0.014414 0.013994 0.000182 0.000144 0.296818 32 C 3 X 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0.034315 0.045455 0.019376 -0.007720 89 C 8 Y -0.025601 -0.042980 0.024248 0.017140 0.047134 90 C 8 Z -0.032107 0.074089 0.098784 0.008946 0.006367 91 C 8 S 0.991778 0.396342 -0.529647 0.871299 -2.100704 92 C 8 X -0.133839 0.293167 0.381224 0.728441 -1.761630 93 C 8 Y -0.075020 -0.338741 -0.174395 0.718041 -0.979151 94 C 8 Z -0.062523 0.837074 0.715557 -0.795259 0.704698 95 C 8 XX -0.028969 -0.004835 0.017483 -0.006107 0.066251 96 C 8 YY -0.009981 -0.002111 -0.004473 -0.020794 0.038909 97 C 8 ZZ -0.020052 -0.008649 0.005948 -0.007284 0.030693 98 C 8 XY -0.004171 -0.002129 -0.002281 -0.008358 0.016211 99 C 8 XZ -0.014232 0.005258 0.021197 0.023417 -0.013833 100 C 8 YZ -0.003995 0.006093 0.011890 0.005615 0.005751 101 H 9 S -0.028793 -0.009001 0.028481 0.060219 -0.003504 102 H 9 S 0.041838 -0.007726 0.117940 0.462744 -0.174582 103 H 9 S -1.045345 0.906013 1.405097 -0.742519 -0.001637 104 H 9 X 0.021800 -0.010291 -0.014388 0.012713 -0.021027 105 H 9 Y 0.005512 0.000814 -0.003267 0.003528 -0.017381 106 H 9 Z 0.014198 -0.010952 -0.012470 0.005885 0.015991 107 H 10 S -0.003490 -0.000222 -0.022832 -0.023301 -0.033392 108 H 10 S 0.019252 -0.006676 -0.057824 0.123236 -0.482580 109 H 10 S -0.461220 -1.423717 -0.896348 0.673144 -0.290600 110 H 10 X 0.006214 0.006633 0.010779 0.026992 -0.017091 111 H 10 Y 0.002490 0.009130 0.013897 0.008931 -0.007635 112 H 10 Z -0.007601 -0.019729 -0.007740 0.002860 0.011899 --------------------------------------------------------------------- PROPERTIES FOR THE PBE0 DFT FUNCTIONAL (RHF TYPE) DENSITY MATRIX --------------------------------------------------------------------- ----------------- ENERGY COMPONENTS ----------------- WAVEFUNCTION NORMALIZATION = 1.0000000000 ONE ELECTRON ENERGY = -416.1276245687 TWO ELECTRON ENERGY = 155.2430582194 NUCLEAR REPULSION ENERGY = 105.0583326385 ------------------ TOTAL ENERGY = -155.8262337109 ELECTRON-ELECTRON POTENTIAL ENERGY = 155.2430582194 NUCLEUS-ELECTRON POTENTIAL ENERGY = -571.1296699052 NUCLEUS-NUCLEUS POTENTIAL ENERGY = 105.0583326385 ------------------ TOTAL POTENTIAL ENERGY = -310.8282790473 TOTAL KINETIC ENERGY = 155.0020453365 VIRIAL RATIO (V/T) = 2.0053172742 --------------------------------------- MULLIKEN AND LOWDIN POPULATION ANALYSES --------------------------------------- ATOMIC MULLIKEN POPULATION IN EACH MOLECULAR ORBITAL 1 2 3 4 5 2.000000 2.000000 2.000000 2.000000 2.000000 1 1.001144 0.995463 0.003224 0.000241 0.609482 2 0.000073 0.000160 0.000002 -0.000001 0.044599 3 0.995848 1.000761 0.000335 0.003128 0.609829 4 0.000072 0.000160 0.000001 -0.000000 0.044648 5 0.001437 0.001731 0.169094 1.827305 0.307248 6 -0.000017 -0.000004 0.000018 0.000062 0.014311 7 0.000007 0.000004 0.000012 0.000045 0.024020 8 0.001446 0.001724 1.827172 0.169224 0.307527 9 0.000007 0.000004 0.000057 -0.000001 0.024011 10 -0.000017 -0.000003 0.000085 -0.000005 0.014325 6 7 8 9 10 2.000000 2.000000 2.000000 2.000000 2.000000 1 0.355863 0.390154 0.287120 0.391710 0.366005 2 0.034216 0.065772 0.161867 0.137891 0.023140 3 0.355880 0.390184 0.287172 0.391738 0.365633 4 0.034223 0.065763 0.161903 0.137813 0.023051 5 0.504689 0.357469 0.349046 0.292922 0.420955 6 0.059711 0.095891 0.061961 0.126980 0.025481 7 0.045556 0.090669 0.139967 0.050515 0.164521 8 0.504603 0.357496 0.349040 0.292945 0.421209 9 0.045562 0.090700 0.139936 0.050521 0.164347 10 0.059696 0.095901 0.061988 0.126967 0.025658 11 12 13 14 15 2.000000 2.000000 2.000000 2.000000 2.000000 1 0.196206 0.258983 0.344361 0.599794 0.340901 2 0.050865 0.187180 0.140896 0.028408 0.008028 3 0.196537 0.259046 0.344334 0.599769 0.340976 4 0.050944 0.187275 0.140813 0.028423 0.008029 5 0.450113 0.311592 0.227137 0.360540 0.640078 6 0.266946 0.041597 0.171875 0.006500 0.005150 7 0.035827 0.200659 0.115703 0.004729 0.005834 8 0.449800 0.311534 0.227191 0.360606 0.640020 9 0.035998 0.200578 0.115795 0.004726 0.005835 10 0.266765 0.041555 0.171895 0.006505 0.005150 ----- POPULATIONS IN EACH AO ----- MULLIKEN LOWDIN 1 C 1 S 1.10491 1.04592 2 C 1 S 0.87923 0.90915 3 C 1 X 0.23317 0.22278 4 C 1 Y 0.18743 0.18362 5 C 1 Z 0.20807 0.20056 6 C 1 S 0.76423 0.40195 7 C 1 X 0.52538 0.49240 8 C 1 Y 0.45739 0.42987 9 C 1 Z 0.49996 0.46450 10 C 1 S 0.42532 0.23541 11 C 1 X 0.22717 0.29892 12 C 1 Y 0.32058 0.34720 13 C 1 Z 0.23842 0.30854 14 C 1 XX 0.01940 0.17036 15 C 1 YY 0.00015 0.13029 16 C 1 ZZ 0.01207 0.15429 17 C 1 XY 0.00905 0.01817 18 C 1 XZ 0.02088 0.04228 19 C 1 YZ 0.00784 0.01455 20 H 2 S 0.27038 0.26746 21 H 2 S 0.49172 0.42476 22 H 2 S 0.09602 0.17972 23 H 2 X 0.00990 0.02128 24 H 2 Y 0.00556 0.01491 25 H 2 Z 0.00953 0.02153 26 C 3 S 1.10491 1.04587 27 C 3 S 0.87923 0.90908 28 C 3 X 0.22772 0.21791 29 C 3 Y 0.19451 0.18941 30 C 3 Z 0.20644 0.19928 31 C 3 S 0.76421 0.40105 32 C 3 X 0.52514 0.48904 33 C 3 Y 0.46738 0.43887 34 C 3 Z 0.49022 0.45913 35 C 3 S 0.42569 0.23536 36 C 3 X 0.25550 0.31412 37 C 3 Y 0.30038 0.33856 38 C 3 Z 0.23049 0.30270 39 C 3 XX 0.01958 0.16974 40 C 3 YY 0.00422 0.13811 41 C 3 ZZ 0.01499 0.15794 42 C 3 XY 0.00718 0.01452 43 C 3 XZ 0.01283 0.02574 44 C 3 YZ 0.01057 0.01986 45 H 4 S 0.27038 0.26914 46 H 4 S 0.49172 0.42635 47 H 4 S 0.09604 0.17982 48 H 4 X 0.01401 0.02890 49 H 4 Y 0.00539 0.01452 50 H 4 Z 0.00559 0.01478 51 C 5 S 1.10488 1.04584 52 C 5 S 0.87930 0.90901 53 C 5 X 0.22432 0.21353 54 C 5 Y 0.19560 0.18974 55 C 5 Z 0.21131 0.20284 56 C 5 S 0.76120 0.40010 57 C 5 X 0.51375 0.48202 58 C 5 Y 0.45888 0.43783 59 C 5 Z 0.49083 0.46201 60 C 5 S 0.46219 0.25426 61 C 5 X 0.25358 0.32911 62 C 5 Y 0.33589 0.36463 63 C 5 Z 0.28324 0.34353 64 C 5 XX 0.01750 0.17012 65 C 5 YY -0.00084 0.13247 66 C 5 ZZ 0.00834 0.15210 67 C 5 XY 0.00592 0.01272 68 C 5 XZ 0.00826 0.01705 69 C 5 YZ 0.00720 0.01504 70 H 6 S 0.27002 0.26521 71 H 6 S 0.48577 0.42261 72 H 6 S 0.09498 0.18307 73 H 6 X 0.00574 0.01465 74 H 6 Y 0.00794 0.01846 75 H 6 Z 0.01202 0.02597 76 H 7 S 0.26938 0.26581 77 H 7 S 0.48251 0.42246 78 H 7 S 0.10049 0.18804 79 H 7 X 0.01393 0.02981 80 H 7 Y 0.00587 0.01504 81 H 7 Z 0.00588 0.01478 82 C 8 S 1.10488 1.04588 83 C 8 S 0.87930 0.90908 84 C 8 X 0.22888 0.21778 85 C 8 Y 0.18793 0.18343 86 C 8 Z 0.21443 0.20521 87 C 8 S 0.76121 0.40095 88 C 8 X 0.51437 0.48582 89 C 8 Y 0.44681 0.42741 90 C 8 Z 0.50230 0.46797 91 C 8 S 0.46228 0.25427 92 C 8 X 0.22038 0.30500 93 C 8 Y 0.35880 0.37791 94 C 8 Z 0.29360 0.35339 95 C 8 XX 0.01638 0.17078 96 C 8 YY -0.00452 0.12484 97 C 8 ZZ 0.00773 0.15108 98 C 8 XY 0.00665 0.01396 99 C 8 XZ 0.01476 0.03129 100 C 8 YZ 0.00540 0.01120 101 H 9 S 0.26938 0.26430 102 H 9 S 0.48250 0.42107 103 H 9 S 0.10050 0.18797 104 H 9 X 0.01022 0.02210 105 H 9 Y 0.00586 0.01537 106 H 9 Z 0.00961 0.02166 107 H 10 S 0.27002 0.26528 108 H 10 S 0.48576 0.42265 109 H 10 S 0.09498 0.18305 110 H 10 X 0.00522 0.01311 111 H 10 Y 0.00814 0.01913 112 H 10 Z 0.01233 0.02702 ----- MULLIKEN ATOMIC OVERLAP POPULATIONS ----- (OFF-DIAGONAL ELEMENTS NEED TO BE MULTIPLIED BY 2) 1 2 3 4 5 1 4.8992988 2 0.4130637 0.5536848 3 0.3855532 -0.0440729 4.8997019 4 -0.0440616 -0.0039119 0.4130862 0.5536732 5 -0.0740533 0.0055302 0.6384487 -0.0381632 4.8735184 6 0.0079660 -0.0003522 -0.0328684 -0.0106678 0.4065211 7 -0.0112158 0.0001760 -0.0415052 0.0078108 0.4129163 8 0.6384854 -0.0381668 -0.0739191 0.0055293 -0.0083340 9 -0.0415190 0.0078107 -0.0112201 0.0001764 0.0051245 10 -0.0328675 -0.0106643 0.0079666 -0.0003523 -0.0001529 6 7 8 9 10 6 0.5432426 7 -0.0370348 0.5403432 8 -0.0001542 0.0051285 4.8735076 9 -0.0002156 0.0016649 0.4129308 0.5403650 10 0.0000265 -0.0002156 0.4065300 -0.0370419 0.5432341 TOTAL MULLIKEN AND LOWDIN ATOMIC POPULATIONS ATOM MULL.POP. CHARGE LOW.POP. CHARGE 1 C 6.140650 -0.140650 6.070748 -0.070748 2 H 0.883097 0.116903 0.929661 0.070339 3 C 6.141171 -0.141171 6.066287 -0.066287 4 H 0.883119 0.116881 0.933501 0.066499 5 C 6.221356 -0.221356 6.133940 -0.133940 6 H 0.876463 0.123537 0.929972 0.070028 7 H 0.878068 0.121932 0.935930 0.064070 8 C 6.221537 -0.221537 6.137258 -0.137258 9 H 0.878076 0.121924 0.932458 0.067542 10 H 0.876463 0.123537 0.930245 0.069755 ------------------------------- BOND ORDER AND VALENCE ANALYSIS BOND ORDER THRESHOLD=0.050 ------------------------------- BOND BOND BOND ATOM PAIR DIST ORDER ATOM PAIR DIST ORDER ATOM PAIR DIST ORDER 1 2 1.089 0.960 1 3 1.464 1.068 1 8 1.333 1.893 3 4 1.089 0.960 3 5 1.333 1.893 5 6 1.085 0.963 5 7 1.086 0.964 5 8 3.073 0.081 8 9 1.086 0.965 8 10 1.085 0.963 TOTAL BONDED FREE ATOM VALENCE VALENCE VALENCE 1 C 3.900 3.900 -0.000 2 H 0.970 0.970 -0.000 3 C 3.900 3.900 -0.000 4 H 0.970 0.970 -0.000 5 C 3.894 3.894 -0.000 6 H 0.967 0.967 -0.000 7 H 0.976 0.976 0.000 8 C 3.894 3.894 -0.000 9 H 0.976 0.976 0.000 10 H 0.967 0.967 -0.000 --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.135597 -0.012009 0.031226 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.112318 -0.010077 0.025822 0.115688 ...... END OF PROPERTY EVALUATION ...... CPU 0: STEP CPU TIME= 0.03 TOTAL CPU TIME= 289.7 ( 4.8 MIN) TOTAL WALL CLOCK TIME= 292.2 SECONDS, CPU UTILIZATION IS 99.15% $VIB IVIB= 0 IATOM= 0 ICOORD= 0 E= -155.8262337109 -1.268644611E-05-1.945329594E-05 7.009556905E-06 1.627856288E-05 3.228542612E-06 6.822932706E-06 7.487790965E-06 1.133459019E-05-5.322160616E-06 1.393128853E-05 -3.733534462E-06-3.243382805E-06-2.728092791E-05 6.072177276E-06 3.467830449E-06 1.526126580E-05-4.712948821E-06-4.363538152E-06-7.619693440E-06 2.771479986E-06 1.357884086E-06-6.939368431E-06 1.296641915E-05-1.273884891E-05 2.555530385E-06 -5.221788857E-06 3.830953232E-06-9.880026747E-07-3.251641132E-06 3.178773103E-06 1.123178000E-01-1.007683032E-02 2.582203477E-02 ......END OF GEOMETRY SEARCH...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 289.7 ( 4.8 MIN) TOTAL WALL CLOCK TIME= 292.2 SECONDS, CPU UTILIZATION IS 99.15% ********************************************************* THE HESSIAN WILL NOW BE COMPUTED AT THE STATIONARY POINT. ********************************************************* --------------------------------- HESSIAN MATRIX CONTROL PARAMETERS --------------------------------- METHOD=SEMINUM NVIB = 2 VIBSIZ= 0.01000 RDHESS= F PURIFY= F PRTIFC= F VIBANL= F DECOMP= F PROJCT= F SCLFAC= 1.00000 PRTSCN= F NPRT = 0 PULCOR= F NPUN = 0 REDOVB= T THE VIB 0 GEOMETRY GRADIENT IS UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C -0.000012686 -0.000019453 0.000007010 2 H 0.000016279 0.000003229 0.000006823 3 C 0.000007488 0.000011335 -0.000005322 4 H 0.000013931 -0.000003734 -0.000003243 5 C -0.000027281 0.000006072 0.000003468 6 H 0.000015261 -0.000004713 -0.000004364 7 H -0.000007620 0.000002771 0.000001358 8 C -0.000006939 0.000012966 -0.000012739 9 H 0.000002556 -0.000005222 0.000003831 10 H -0.000000988 -0.000003252 0.000003179 $VIB IVIB= 0 IATOM= 0 ICOORD= 0 E= -155.8262337109 -1.268644611E-05-1.945329594E-05 7.009556905E-06 1.627856288E-05 3.228542612E-06 6.822932706E-06 7.487790965E-06 1.133459019E-05-5.322160616E-06 1.393128853E-05 -3.733534462E-06-3.243382805E-06-2.728092791E-05 6.072177276E-06 3.467830449E-06 1.526126580E-05-4.712948821E-06-4.363538152E-06-7.619693440E-06 2.771479986E-06 1.357884086E-06-6.939368431E-06 1.296641915E-05-1.273884891E-05 2.555530385E-06 -5.221788857E-06 3.830953232E-06-9.880026747E-07-3.251641132E-06 3.178773103E-06 1.123178000E-01-1.007683032E-02 2.582203477E-02 1 ATOM 1 ------------------- COORD 1 NUCLEAR COORDINATES ------------------- VIB 1 ATOM X Y Z 1 C 0.803773 -0.808112 1.400575 2 H 2.289185 -0.995597 2.802099 3 C 1.446062 0.609240 -0.884553 4 H 3.409625 0.489515 -1.489324 5 C -0.143450 2.042156 -2.212893 6 H 0.464242 3.013674 -3.912111 7 H -2.091534 2.309425 -1.624756 8 C -1.429845 -1.902330 1.850402 9 H -2.943256 -1.862199 0.464672 10 H -1.792911 -2.895773 3.605888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 289.7 ( 4.8 MIN) TOTAL WALL CLOCK TIME= 292.2 SECONDS, CPU UTILIZATION IS 99.15% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 289.7 ( 4.8 MIN) TOTAL WALL CLOCK TIME= 292.2 SECONDS, CPU UTILIZATION IS 99.15% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8257144423 -155.8257144423 0.001451968 0.001927627 17702118 79814 2 1 0 -155.8257336380 -0.0000191957 0.001372100 0.000510458 16527930 127500 3 2 0 -155.8257336968 -0.0000000588 0.000692371 0.000659731 15959111 145655 4 3 0 -155.8257362707 -0.0000025739 0.000148049 0.000195962 15663852 156487 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 5 4 0 -155.8261877126 -0.0004514420 0.000923564 0.001451023 17701900 79833 6 5 0 -155.8261947411 -0.0000070284 0.000455038 0.000344572 16455272 130010 7 6 0 -155.8261951141 -0.0000003731 0.000213385 0.000227335 15720121 151305 8 7 0 -155.8261954567 -0.0000003425 0.000025475 0.000031119 15290343 164343 9 8 0 -155.8261954627 -0.0000000060 0.000017748 0.000019817 14467940 191168 10 9 0 -155.8261954650 -0.0000000023 0.000002899 0.000005450 13510785 216930 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 7.9 SECONDS ( 0.8 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8261954650 AFTER 10 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9906137533 TOTAL ELECTRON NUMBER = 30.0000051886 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.20 TOTAL CPU TIME= 297.9 ( 5.0 MIN) TOTAL WALL CLOCK TIME= 300.4 SECONDS, CPU UTILIZATION IS 99.15% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 297.9 ( 5.0 MIN) TOTAL WALL CLOCK TIME= 300.5 SECONDS, CPU UTILIZATION IS 99.15% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.30 TOTAL CPU TIME= 300.2 ( 5.0 MIN) TOTAL WALL CLOCK TIME= 302.8 SECONDS, CPU UTILIZATION IS 99.16% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 300.6 ( 5.0 MIN) TOTAL WALL CLOCK TIME= 303.1 SECONDS, CPU UTILIZATION IS 99.16% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.137818 -0.012009 0.031226 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.112717 -0.009793 0.029708 0.116977 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C 0.007648950 0.001950657 0.000492773 2 H -0.001981447 0.000194935 -0.001375584 3 C -0.001107932 -0.000132353 0.000181673 4 H -0.000039809 -0.000180402 0.000244238 5 C 0.000136021 0.000078242 -0.000105297 6 H 0.000006155 0.000062430 -0.000002425 7 H -0.000012053 -0.000027983 -0.000025420 8 C -0.004456445 -0.001836959 0.000563407 9 H -0.000174520 -0.000102391 0.000049883 10 H -0.000018919 -0.000006177 -0.000023248 $VIB IVIB= 1 IATOM= 1 ICOORD= 1 E= -155.8261954650 7.648949650E-03 1.950657401E-03 4.927731790E-04-1.981446801E-03 1.949351903E-04 -1.375584273E-03-1.107932160E-03-1.323533080E-04 1.816725749E-04-3.980866266E-05 -1.804022646E-04 2.442379719E-04 1.360206219E-04 7.824234136E-05-1.052971524E-04 6.154995265E-06 6.243025020E-05-2.425338890E-06-1.205345845E-05-2.798281675E-05 -2.542006409E-05-4.456445317E-03-1.836958783E-03 5.634074106E-04-1.745195625E-04 -1.023906162E-04 4.988332807E-05-1.891930567E-05-6.177394352E-06-2.324763651E-05 1.127168763E-01-9.793145485E-03 2.970803142E-02 1 ATOM 1 ------------------- COORD 2 NUCLEAR COORDINATES ------------------- VIB 1 ATOM X Y Z 1 C 0.793773 -0.798112 1.400575 2 H 2.289185 -0.995597 2.802099 3 C 1.446062 0.609240 -0.884553 4 H 3.409625 0.489515 -1.489324 5 C -0.143450 2.042156 -2.212893 6 H 0.464242 3.013674 -3.912111 7 H -2.091534 2.309425 -1.624756 8 C -1.429845 -1.902330 1.850402 9 H -2.943256 -1.862199 0.464672 10 H -1.792911 -2.895773 3.605888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 300.6 ( 5.0 MIN) TOTAL WALL CLOCK TIME= 303.1 SECONDS, CPU UTILIZATION IS 99.16% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 300.6 ( 5.0 MIN) TOTAL WALL CLOCK TIME= 303.1 SECONDS, CPU UTILIZATION IS 99.16% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8257502652 -155.8257502652 0.001069074 0.001508229 17704104 79753 2 1 0 -155.8257679735 -0.0000177083 0.000947297 0.000420779 16529369 128262 3 2 0 -155.8257682719 -0.0000002984 0.000471078 0.000460569 15897863 147693 4 3 0 -155.8257696329 -0.0000013610 0.000114698 0.000203479 15589077 157926 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 5 4 0 -155.8262107665 -0.0004411336 0.000936132 0.001458362 17704044 79760 6 5 0 -155.8262177529 -0.0000069863 0.000441578 0.000336493 16458390 129982 7 6 0 -155.8262181242 -0.0000003713 0.000199426 0.000231240 15728213 151119 8 7 0 -155.8262184715 -0.0000003473 0.000026576 0.000038290 15302788 163985 9 8 0 -155.8262184780 -0.0000000066 0.000017202 0.000026882 14488840 190663 10 9 0 -155.8262184811 -0.0000000031 0.000002746 0.000005702 13649800 213245 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 8.0 SECONDS ( 0.8 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262184811 AFTER 10 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9911338533 TOTAL ELECTRON NUMBER = 30.0000051618 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.20 TOTAL CPU TIME= 308.8 ( 5.1 MIN) TOTAL WALL CLOCK TIME= 311.4 SECONDS, CPU UTILIZATION IS 99.16% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 308.8 ( 5.1 MIN) TOTAL WALL CLOCK TIME= 311.4 SECONDS, CPU UTILIZATION IS 99.16% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.30 TOTAL CPU TIME= 311.1 ( 5.2 MIN) TOTAL WALL CLOCK TIME= 313.7 SECONDS, CPU UTILIZATION IS 99.16% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.37 TOTAL CPU TIME= 311.5 ( 5.2 MIN) TOTAL WALL CLOCK TIME= 314.1 SECONDS, CPU UTILIZATION IS 99.16% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.135597 -0.009788 0.031226 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.115316 -0.011738 0.023322 0.118235 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C 0.001980556 0.003067668 -0.001822605 2 H 0.000166014 -0.000432117 0.000237854 3 C -0.000218384 -0.001103225 0.000769234 4 H 0.000020134 0.000011045 -0.000017034 5 C -0.000009795 -0.000101909 0.000268932 6 H 0.000055065 0.000069801 0.000055727 7 H -0.000044562 -0.000052962 -0.000046092 8 C -0.001803941 -0.001497011 0.000513953 9 H 0.000007183 0.000072970 0.000027721 10 H -0.000152271 -0.000034260 0.000012310 $VIB IVIB= 1 IATOM= 1 ICOORD= 2 E= -155.8262184811 1.980556313E-03 3.067668207E-03-1.822604521E-03 1.660144421E-04-4.321170417E-04 2.378537824E-04-2.183838538E-04-1.103225065E-03 7.692336499E-04 2.013402226E-05 1.104507123E-05-1.703395134E-05-9.795048865E-06-1.019088050E-04 2.689324111E-04 5.506495274E-05 6.980113655E-05 5.572674508E-05-4.456153478E-05-5.296240008E-05 -4.609227905E-05-1.803941100E-03-1.497011030E-03 5.139525033E-04 7.182526572E-06 7.297036222E-05 2.772148039E-05-1.522707190E-04-3.426043473E-05 1.231017894E-05 1.153162057E-01-1.173771238E-02 2.332235990E-02 1 ATOM 1 ------------------- COORD 3 NUCLEAR COORDINATES ------------------- VIB 1 ATOM X Y Z 1 C 0.793773 -0.808112 1.410575 2 H 2.289185 -0.995597 2.802099 3 C 1.446062 0.609240 -0.884553 4 H 3.409625 0.489515 -1.489324 5 C -0.143450 2.042156 -2.212893 6 H 0.464242 3.013674 -3.912111 7 H -2.091534 2.309425 -1.624756 8 C -1.429845 -1.902330 1.850402 9 H -2.943256 -1.862199 0.464672 10 H -1.792911 -2.895773 3.605888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 311.5 ( 5.2 MIN) TOTAL WALL CLOCK TIME= 314.1 SECONDS, CPU UTILIZATION IS 99.16% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 311.5 ( 5.2 MIN) TOTAL WALL CLOCK TIME= 314.1 SECONDS, CPU UTILIZATION IS 99.16% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8256456148 -155.8256456148 0.001149331 0.001910990 17700470 79845 2 1 0 -155.8256653129 -0.0000196982 0.000898529 0.000402598 16551909 126945 3 2 0 -155.8256652309 0.0000000820 0.000477105 0.000415125 15855593 148428 4 3 0 -155.8256664070 -0.0000011762 0.000114055 0.000176708 15537640 158833 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 5 4 0 -155.8262006734 -0.0005342663 0.000817049 0.001452497 17700244 79849 6 5 0 -155.8262075179 -0.0000068445 0.000501846 0.000353430 16450259 130146 7 6 0 -155.8262078649 -0.0000003470 0.000256705 0.000234964 15702964 151818 8 7 0 -155.8262082359 -0.0000003710 0.000044461 0.000077242 15250000 165389 9 8 0 -155.8262082548 -0.0000000189 0.000016876 0.000039222 14621869 188156 10 9 0 -155.8262082600 -0.0000000052 0.000001751 0.000002064 13962896 202431 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 8.0 SECONDS ( 0.8 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262082600 AFTER 10 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9914158974 TOTAL ELECTRON NUMBER = 30.0000055415 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.19 TOTAL CPU TIME= 319.7 ( 5.3 MIN) TOTAL WALL CLOCK TIME= 322.4 SECONDS, CPU UTILIZATION IS 99.16% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 319.7 ( 5.3 MIN) TOTAL WALL CLOCK TIME= 322.4 SECONDS, CPU UTILIZATION IS 99.16% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.30 TOTAL CPU TIME= 322.0 ( 5.4 MIN) TOTAL WALL CLOCK TIME= 324.7 SECONDS, CPU UTILIZATION IS 99.16% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.37 TOTAL CPU TIME= 322.3 ( 5.4 MIN) TOTAL WALL CLOCK TIME= 325.0 SECONDS, CPU UTILIZATION IS 99.17% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.135597 -0.012009 0.033446 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.114162 -0.014006 0.029302 0.118692 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C 0.000468084 -0.001820827 0.005077471 2 H -0.001347244 0.000229630 -0.001828643 3 C 0.000386169 0.000760653 -0.001975332 4 H 0.000019539 0.000067772 -0.000034771 5 C -0.000085082 0.000198696 -0.000215076 6 H 0.000020564 0.000048122 0.000030391 7 H 0.000000105 -0.000024131 -0.000006908 8 C 0.000493019 0.000523232 -0.001108004 9 H -0.000202671 -0.000123274 0.000061755 10 H 0.000247516 0.000140128 -0.000000883 $VIB IVIB= 1 IATOM= 1 ICOORD= 3 E= -155.8262082600 4.680838049E-04-1.820827317E-03 5.077471330E-03-1.347243893E-03 2.296299923E-04 -1.828643313E-03 3.861687159E-04 7.606527549E-04-1.975332104E-03 1.953893813E-05 6.777157206E-05-3.477129475E-05-8.508189882E-05 1.986958789E-04-2.150757041E-04 2.056429463E-05 4.812150738E-05 3.039070104E-05 1.052044028E-07-2.413100610E-05 -6.908046146E-06 4.930191838E-04 5.232318515E-04-1.108004148E-03-2.026707951E-04 -1.232737138E-04 6.175540340E-05 2.475164453E-04 1.401284797E-04-8.828237949E-07 1.141623127E-01-1.400643106E-02 2.930239043E-02 1 ATOM 2 ------------------- COORD 1 NUCLEAR COORDINATES ------------------- VIB 1 ATOM X Y Z 1 C 0.793773 -0.808112 1.400575 2 H 2.299185 -0.995597 2.802099 3 C 1.446062 0.609240 -0.884553 4 H 3.409625 0.489515 -1.489324 5 C -0.143450 2.042156 -2.212893 6 H 0.464242 3.013674 -3.912111 7 H -2.091534 2.309425 -1.624756 8 C -1.429845 -1.902330 1.850402 9 H -2.943256 -1.862199 0.464672 10 H -1.792911 -2.895773 3.605888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 322.3 ( 5.4 MIN) TOTAL WALL CLOCK TIME= 325.0 SECONDS, CPU UTILIZATION IS 99.17% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 322.4 ( 5.4 MIN) TOTAL WALL CLOCK TIME= 325.1 SECONDS, CPU UTILIZATION IS 99.16% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8257238611 -155.8257238611 0.001150260 0.001428954 17701488 79845 2 1 0 -155.8257339958 -0.0000101347 0.000803195 0.000383172 16479181 128989 3 2 0 -155.8257344219 -0.0000004261 0.000391706 0.000318669 15829991 148318 4 3 0 -155.8257351610 -0.0000007391 0.000094896 0.000147605 15501662 159594 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 5 4 0 -155.8262154558 -0.0004802948 0.000865996 0.001447502 17701496 79845 6 5 0 -155.8262223367 -0.0000068809 0.000523095 0.000352058 16452106 130170 7 6 0 -155.8262226818 -0.0000003451 0.000270945 0.000236721 15712029 151706 8 7 0 -155.8262230585 -0.0000003768 0.000041668 0.000075532 15264430 165329 9 8 0 -155.8262230771 -0.0000000186 0.000018237 0.000038910 14625009 188246 10 9 0 -155.8262230823 -0.0000000052 0.000002412 0.000002148 13960270 202541 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 8.0 SECONDS ( 0.8 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262230823 AFTER 10 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9903916740 TOTAL ELECTRON NUMBER = 30.0000053865 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.20 TOTAL CPU TIME= 330.6 ( 5.5 MIN) TOTAL WALL CLOCK TIME= 333.3 SECONDS, CPU UTILIZATION IS 99.17% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 330.6 ( 5.5 MIN) TOTAL WALL CLOCK TIME= 333.3 SECONDS, CPU UTILIZATION IS 99.17% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.30 TOTAL CPU TIME= 332.9 ( 5.5 MIN) TOTAL WALL CLOCK TIME= 335.6 SECONDS, CPU UTILIZATION IS 99.17% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 333.2 ( 5.6 MIN) TOTAL WALL CLOCK TIME= 336.0 SECONDS, CPU UTILIZATION IS 99.17% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.135784 -0.012009 0.031226 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.111517 -0.010516 0.023565 0.114464 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C -0.001981074 0.000123172 -0.001314343 2 H 0.002105112 -0.000105857 0.001472750 3 C 0.000076716 0.000000908 0.000051390 4 H 0.000020802 0.000002886 -0.000007884 5 C -0.000022997 -0.000010586 0.000013417 6 H 0.000016431 -0.000008951 -0.000004374 7 H -0.000006945 0.000000559 0.000001551 8 C -0.000189078 0.000035440 -0.000234738 9 H -0.000021310 -0.000054496 0.000006107 10 H 0.000002343 0.000016925 0.000016124 $VIB IVIB= 1 IATOM= 2 ICOORD= 1 E= -155.8262230823 -1.981073763E-03 1.231718831E-04-1.314342677E-03 2.105112192E-03-1.058568334E-04 1.472749919E-03 7.671580796E-05 9.075712775E-07 5.139034942E-05 2.080155982E-05 2.886236852E-06-7.884465708E-06-2.299717251E-05-1.058625704E-05 1.341734853E-05 1.643099948E-05-8.950703170E-06-4.374027529E-06-6.944835332E-06 5.587187247E-07 1.551438058E-06-1.890779725E-04 3.543961856E-05-2.347379290E-04-2.131006646E-05 -5.449563157E-05 6.106532909E-06 2.343250773E-06 1.692539673E-05 1.612351207E-05 1.115174882E-01-1.051647206E-02 2.356509877E-02 1 ATOM 2 ------------------- COORD 2 NUCLEAR COORDINATES ------------------- VIB 1 ATOM X Y Z 1 C 0.793773 -0.808112 1.400575 2 H 2.289185 -0.985597 2.802099 3 C 1.446062 0.609240 -0.884553 4 H 3.409625 0.489515 -1.489324 5 C -0.143450 2.042156 -2.212893 6 H 0.464242 3.013674 -3.912111 7 H -2.091534 2.309425 -1.624756 8 C -1.429845 -1.902330 1.850402 9 H -2.943256 -1.862199 0.464672 10 H -1.792911 -2.895773 3.605888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 333.2 ( 5.6 MIN) TOTAL WALL CLOCK TIME= 336.0 SECONDS, CPU UTILIZATION IS 99.17% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 333.2 ( 5.6 MIN) TOTAL WALL CLOCK TIME= 336.0 SECONDS, CPU UTILIZATION IS 99.17% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8257235665 -155.8257235665 0.000826467 0.001470344 17703174 79787 2 1 0 -155.8257321650 -0.0000085986 0.000450786 0.000318449 16471830 129462 3 2 0 -155.8257325022 -0.0000003372 0.000244833 0.000231134 15712990 151689 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 4 3 0 -155.8262242169 -0.0004917147 0.000864115 0.001445915 17703208 79792 5 4 0 -155.8262310254 -0.0000068085 0.000575679 0.000367822 16453170 130095 6 5 0 -155.8262313276 -0.0000003022 0.000309152 0.000256059 15716438 151607 7 6 0 -155.8262317616 -0.0000004340 0.000057851 0.000092261 15295131 164900 8 7 0 -155.8262317943 -0.0000000327 0.000017609 0.000034575 14683952 185307 9 8 0 -155.8262317989 -0.0000000047 0.000003848 0.000003321 13974191 201945 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 7.8 SECONDS ( 0.9 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262317989 AFTER 9 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9915885411 TOTAL ELECTRON NUMBER = 30.0000052940 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.01 TOTAL CPU TIME= 341.2 ( 5.7 MIN) TOTAL WALL CLOCK TIME= 344.1 SECONDS, CPU UTILIZATION IS 99.17% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 341.2 ( 5.7 MIN) TOTAL WALL CLOCK TIME= 344.1 SECONDS, CPU UTILIZATION IS 99.17% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.30 TOTAL CPU TIME= 343.5 ( 5.7 MIN) TOTAL WALL CLOCK TIME= 346.4 SECONDS, CPU UTILIZATION IS 99.17% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 343.9 ( 5.7 MIN) TOTAL WALL CLOCK TIME= 346.8 SECONDS, CPU UTILIZATION IS 99.17% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.135597 -0.011822 0.031226 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.112179 -0.007208 0.027056 0.115620 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C 0.000171868 -0.000452329 0.000225836 2 H -0.000090445 0.000379018 -0.000296767 3 C 0.000132724 0.000000195 0.000134301 4 H 0.000007116 -0.000004452 -0.000006771 5 C -0.000051126 0.000012518 0.000022436 6 H 0.000015270 -0.000017781 -0.000004851 7 H -0.000005972 0.000009139 0.000003152 8 C -0.000150239 0.000063152 -0.000096970 9 H -0.000053937 0.000068078 0.000046853 10 H 0.000024739 -0.000057537 -0.000027219 $VIB IVIB= 1 IATOM= 2 ICOORD= 2 E= -155.8262317989 1.718681397E-04-4.523285768E-04 2.258356721E-04-9.044477109E-05 3.790176379E-04 -2.967666839E-04 1.327244712E-04 1.948820423E-07 1.343010201E-04 7.116207954E-06 -4.451737589E-06-6.770812026E-06-5.112590795E-05 1.251765697E-05 2.243578915E-05 1.527028142E-05-1.778117725E-05-4.850814860E-06-5.971760059E-06 9.138627871E-06 3.151647572E-06-1.502385466E-04 6.315174048E-05-9.696968298E-05-5.393745744E-05 6.807780108E-05 4.685288872E-05 2.473934282E-05-5.753685460E-05-2.721902392E-05 1.121790151E-01-7.207902451E-03 2.705571267E-02 1 ATOM 2 ------------------- COORD 3 NUCLEAR COORDINATES ------------------- VIB 1 ATOM X Y Z 1 C 0.793773 -0.808112 1.400575 2 H 2.289185 -0.995597 2.812099 3 C 1.446062 0.609240 -0.884553 4 H 3.409625 0.489515 -1.489324 5 C -0.143450 2.042156 -2.212893 6 H 0.464242 3.013674 -3.912111 7 H -2.091534 2.309425 -1.624756 8 C -1.429845 -1.902330 1.850402 9 H -2.943256 -1.862199 0.464672 10 H -1.792911 -2.895773 3.605888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 343.9 ( 5.7 MIN) TOTAL WALL CLOCK TIME= 346.8 SECONDS, CPU UTILIZATION IS 99.17% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.02 TOTAL CPU TIME= 343.9 ( 5.7 MIN) TOTAL WALL CLOCK TIME= 346.8 SECONDS, CPU UTILIZATION IS 99.17% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8257340390 -155.8257340390 0.001164626 0.001418484 17701310 79857 2 1 0 -155.8257441898 -0.0000101507 0.000758313 0.000378862 16480455 128929 3 2 0 -155.8257446419 -0.0000004521 0.000376761 0.000286351 15824232 148508 4 3 0 -155.8257453033 -0.0000006614 0.000087630 0.000144581 15481393 160077 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 5 4 0 -155.8262166132 -0.0004713098 0.000863623 0.001446589 17701381 79856 6 5 0 -155.8262234976 -0.0000068844 0.000528617 0.000355350 16451824 130160 7 6 0 -155.8262238384 -0.0000003408 0.000275783 0.000238046 15711552 151721 8 7 0 -155.8262242216 -0.0000003832 0.000044357 0.000079042 15266224 165316 9 8 0 -155.8262242424 -0.0000000208 0.000018336 0.000038683 14635450 187793 10 9 0 -155.8262242476 -0.0000000052 0.000002524 0.000002146 13963784 202343 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 8.0 SECONDS ( 0.8 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262242476 AFTER 10 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9904540374 TOTAL ELECTRON NUMBER = 30.0000052600 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.19 TOTAL CPU TIME= 352.1 ( 5.9 MIN) TOTAL WALL CLOCK TIME= 355.0 SECONDS, CPU UTILIZATION IS 99.17% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 352.1 ( 5.9 MIN) TOTAL WALL CLOCK TIME= 355.0 SECONDS, CPU UTILIZATION IS 99.17% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.30 TOTAL CPU TIME= 354.4 ( 5.9 MIN) TOTAL WALL CLOCK TIME= 357.4 SECONDS, CPU UTILIZATION IS 99.17% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.37 TOTAL CPU TIME= 354.8 ( 5.9 MIN) TOTAL WALL CLOCK TIME= 357.7 SECONDS, CPU UTILIZATION IS 99.18% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.135597 -0.012009 0.031412 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.110191 -0.008363 0.025127 0.113328 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C -0.001352878 0.000204834 -0.001807717 2 H 0.001484288 -0.000301103 0.001881665 3 C -0.000193386 0.000035981 -0.000134455 4 H 0.000017919 -0.000004949 0.000004167 5 C -0.000001978 0.000024592 -0.000032781 6 H 0.000009782 0.000008563 -0.000003768 7 H -0.000009343 -0.000000431 0.000001247 8 C 0.000032426 0.000026746 0.000059888 9 H 0.000000380 0.000043752 0.000033901 10 H 0.000012791 -0.000037986 -0.000002147 $VIB IVIB= 1 IATOM= 2 ICOORD= 3 E= -155.8262242476 -1.352878486E-03 2.048337784E-04-1.807717498E-03 1.484287946E-03-3.011026616E-04 1.881664841E-03-1.933864694E-04 3.598072629E-05-1.344545881E-04 1.791874222E-05 -4.949010885E-06 4.166853996E-06-1.978092569E-06 2.459206490E-05-3.278110340E-05 9.781737113E-06 8.563446515E-06-3.767622977E-06-9.343329615E-06-4.305843569E-07 1.247045989E-06 3.242643302E-05 2.674617589E-05 5.988839669E-05 3.803741766E-07 4.375209446E-05 3.390085398E-05 1.279114534E-05-3.798602959E-05-2.147179809E-06 1.101907276E-01-8.363378233E-03 2.512747311E-02 1 ATOM 3 ------------------- COORD 1 NUCLEAR COORDINATES ------------------- VIB 1 ATOM X Y Z 1 C 0.793773 -0.808112 1.400575 2 H 2.289185 -0.995597 2.802099 3 C 1.456062 0.609240 -0.884553 4 H 3.409625 0.489515 -1.489324 5 C -0.143450 2.042156 -2.212893 6 H 0.464242 3.013674 -3.912111 7 H -2.091534 2.309425 -1.624756 8 C -1.429845 -1.902330 1.850402 9 H -2.943256 -1.862199 0.464672 10 H -1.792911 -2.895773 3.605888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 354.8 ( 5.9 MIN) TOTAL WALL CLOCK TIME= 357.7 SECONDS, CPU UTILIZATION IS 99.18% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 354.8 ( 5.9 MIN) TOTAL WALL CLOCK TIME= 357.8 SECONDS, CPU UTILIZATION IS 99.18% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8256923140 -155.8256923140 0.001074342 0.001504989 17700363 79857 2 1 0 -155.8257113192 -0.0000190053 0.001065346 0.000517893 16534061 127032 3 2 0 -155.8257114045 -0.0000000853 0.000573853 0.000564345 15907354 146412 4 3 0 -155.8257130178 -0.0000016132 0.000101433 0.000169368 15585825 158333 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 5 4 0 -155.8261903788 -0.0004773611 0.000890291 0.001471822 17700278 79864 6 5 0 -155.8261973267 -0.0000069479 0.000469256 0.000355708 16452665 130100 7 6 0 -155.8261977019 -0.0000003753 0.000226230 0.000235622 15717002 151371 8 7 0 -155.8261980474 -0.0000003455 0.000027889 0.000040433 15282998 164557 9 8 0 -155.8261980539 -0.0000000064 0.000018544 0.000026581 14476198 191272 10 9 0 -155.8261980562 -0.0000000023 0.000002575 0.000003949 13552758 215396 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 8.0 SECONDS ( 0.8 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8261980562 AFTER 10 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9907424843 TOTAL ELECTRON NUMBER = 30.0000055010 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.18 TOTAL CPU TIME= 363.0 ( 6.0 MIN) TOTAL WALL CLOCK TIME= 366.0 SECONDS, CPU UTILIZATION IS 99.17% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 363.0 ( 6.0 MIN) TOTAL WALL CLOCK TIME= 366.0 SECONDS, CPU UTILIZATION IS 99.18% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.30 TOTAL CPU TIME= 365.3 ( 6.1 MIN) TOTAL WALL CLOCK TIME= 368.3 SECONDS, CPU UTILIZATION IS 99.18% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 365.6 ( 6.1 MIN) TOTAL WALL CLOCK TIME= 368.7 SECONDS, CPU UTILIZATION IS 99.18% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.137818 -0.012009 0.031226 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.115395 -0.009294 0.021379 0.117726 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C -0.001131129 -0.000242064 0.000395697 2 H 0.000087077 0.000127948 -0.000194205 3 C 0.007137099 -0.001665705 0.000218841 4 H -0.003063574 0.000142487 0.000806749 5 C -0.002901524 0.001741816 -0.001397286 6 H 0.000096513 -0.000086610 0.000068680 7 H -0.000172993 0.000189328 -0.000155790 8 C -0.000034196 -0.000160642 0.000243434 9 H 0.000003740 0.000023886 0.000024221 10 H -0.000021014 -0.000070443 -0.000010341 $VIB IVIB= 1 IATOM= 3 ICOORD= 1 E= -155.8261980562 -1.131128563E-03-2.420639293E-04 3.956969097E-04 8.707689489E-05 1.279475730E-04 -1.942045726E-04 7.137098995E-03-1.665704724E-03 2.188412090E-04-3.063573900E-03 1.424870159E-04 8.067492042E-04-2.901523906E-03 1.741816106E-03-1.397285760E-03 9.651283148E-05-8.661045814E-05 6.867962113E-05-1.729926368E-04 1.893281087E-04 -1.557902096E-04-3.419555927E-05-1.606418876E-04 2.434336618E-04 3.739953167E-06 2.388555638E-05 2.422117629E-05-2.101411049E-05-7.044336088E-05-1.034123997E-05 1.153947916E-01-9.293873118E-03 2.137893490E-02 1 ATOM 3 ------------------- COORD 2 NUCLEAR COORDINATES ------------------- VIB 1 ATOM X Y Z 1 C 0.793773 -0.808112 1.400575 2 H 2.289185 -0.995597 2.802099 3 C 1.446062 0.619240 -0.884553 4 H 3.409625 0.489515 -1.489324 5 C -0.143450 2.042156 -2.212893 6 H 0.464242 3.013674 -3.912111 7 H -2.091534 2.309425 -1.624756 8 C -1.429845 -1.902330 1.850402 9 H -2.943256 -1.862199 0.464672 10 H -1.792911 -2.895773 3.605888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 365.7 ( 6.1 MIN) TOTAL WALL CLOCK TIME= 368.7 SECONDS, CPU UTILIZATION IS 99.18% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.02 TOTAL CPU TIME= 365.7 ( 6.1 MIN) TOTAL WALL CLOCK TIME= 368.7 SECONDS, CPU UTILIZATION IS 99.18% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8256668275 -155.8256668275 0.001151118 0.001520974 17701063 79827 2 1 0 -155.8256860294 -0.0000192019 0.000750506 0.000344820 16526371 127741 3 2 0 -155.8256858588 0.0000001707 0.000373323 0.000488428 15890434 148741 4 3 0 -155.8256871544 -0.0000012956 0.000093871 0.000184847 15609233 157147 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 5 4 0 -155.8262072239 -0.0005200696 0.000890128 0.001443259 17700964 79842 6 5 0 -155.8262140997 -0.0000068758 0.000528926 0.000348007 16453044 130028 7 6 0 -155.8262144500 -0.0000003503 0.000274226 0.000237195 15714495 151648 8 7 0 -155.8262148234 -0.0000003733 0.000038917 0.000069942 15260601 165315 9 8 0 -155.8262148396 -0.0000000162 0.000018674 0.000038308 14602052 188761 10 9 0 -155.8262148446 -0.0000000051 0.000002759 0.000002259 13940682 203073 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 8.0 SECONDS ( 0.8 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262148446 AFTER 10 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9919184825 TOTAL ELECTRON NUMBER = 30.0000055576 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.19 TOTAL CPU TIME= 373.9 ( 6.2 MIN) TOTAL WALL CLOCK TIME= 377.0 SECONDS, CPU UTILIZATION IS 99.18% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 373.9 ( 6.2 MIN) TOTAL WALL CLOCK TIME= 377.0 SECONDS, CPU UTILIZATION IS 99.18% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.30 TOTAL CPU TIME= 376.2 ( 6.3 MIN) TOTAL WALL CLOCK TIME= 379.3 SECONDS, CPU UTILIZATION IS 99.18% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 376.5 ( 6.3 MIN) TOTAL WALL CLOCK TIME= 379.6 SECONDS, CPU UTILIZATION IS 99.18% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.135597 -0.009788 0.031226 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.110036 -0.011271 0.022872 0.112952 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C -0.000155867 -0.001131753 0.000763293 2 H 0.000005575 -0.000008220 0.000031536 3 C -0.001714044 0.003762508 -0.002676035 4 H 0.000200287 -0.000430066 0.000016765 5 C 0.001667871 -0.002154804 0.001562353 6 H 0.000136229 -0.000052929 0.000062625 7 H 0.000017711 0.000053538 0.000048089 8 C -0.000159428 -0.000056212 0.000175465 9 H 0.000047882 -0.000073417 -0.000028468 10 H -0.000046217 0.000091357 0.000044377 $VIB IVIB= 1 IATOM= 3 ICOORD= 2 E= -155.8262148446 -1.558673233E-04-1.131753169E-03 7.632932742E-04 5.574854422E-06-8.219810481E-06 3.153585660E-05-1.714043696E-03 3.762507692E-03-2.676034674E-03 2.002874637E-04 -4.300662752E-04 1.676545733E-05 1.667871355E-03-2.154804499E-03 1.562352551E-03 1.362290478E-04-5.292865954E-05 6.262517384E-05 1.771142254E-05 5.353810837E-05 4.808861223E-05-1.594281208E-04-5.621244485E-05 1.754646414E-04 4.788206258E-05 -7.341748078E-05-2.846821001E-05-4.621706629E-05 9.135653898E-05 4.437731725E-05 1.100359080E-01-1.127094514E-02 2.287214476E-02 1 ATOM 3 ------------------- COORD 3 NUCLEAR COORDINATES ------------------- VIB 1 ATOM X Y Z 1 C 0.793773 -0.808112 1.400575 2 H 2.289185 -0.995597 2.802099 3 C 1.446062 0.609240 -0.874553 4 H 3.409625 0.489515 -1.489324 5 C -0.143450 2.042156 -2.212893 6 H 0.464242 3.013674 -3.912111 7 H -2.091534 2.309425 -1.624756 8 C -1.429845 -1.902330 1.850402 9 H -2.943256 -1.862199 0.464672 10 H -1.792911 -2.895773 3.605888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 376.5 ( 6.3 MIN) TOTAL WALL CLOCK TIME= 379.6 SECONDS, CPU UTILIZATION IS 99.18% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 376.6 ( 6.3 MIN) TOTAL WALL CLOCK TIME= 379.7 SECONDS, CPU UTILIZATION IS 99.18% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8257441171 -155.8257441171 0.001102425 0.001585668 17704088 79758 2 1 0 -155.8257627284 -0.0000186113 0.000983253 0.000409362 16536167 127449 3 2 0 -155.8257629577 -0.0000002293 0.000445093 0.000569980 15942575 146684 4 3 0 -155.8257647696 -0.0000018119 0.000131638 0.000247053 15639866 156239 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 5 4 0 -155.8262008145 -0.0004360449 0.000873731 0.001472807 17704024 79767 6 5 0 -155.8262078086 -0.0000069941 0.000429959 0.000354431 16457780 130005 7 6 0 -155.8262081801 -0.0000003715 0.000196154 0.000232070 15726933 151184 8 7 0 -155.8262085211 -0.0000003410 0.000028397 0.000033596 15293860 164165 9 8 0 -155.8262085272 -0.0000000061 0.000017232 0.000024152 14464558 191205 10 9 0 -155.8262085298 -0.0000000027 0.000002125 0.000005738 13590837 215134 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 7.9 SECONDS ( 0.8 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262085298 AFTER 10 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9911440786 TOTAL ELECTRON NUMBER = 30.0000052719 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.20 TOTAL CPU TIME= 384.8 ( 6.4 MIN) TOTAL WALL CLOCK TIME= 387.9 SECONDS, CPU UTILIZATION IS 99.19% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 384.8 ( 6.4 MIN) TOTAL WALL CLOCK TIME= 387.9 SECONDS, CPU UTILIZATION IS 99.19% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.30 TOTAL CPU TIME= 387.1 ( 6.5 MIN) TOTAL WALL CLOCK TIME= 390.2 SECONDS, CPU UTILIZATION IS 99.19% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 387.4 ( 6.5 MIN) TOTAL WALL CLOCK TIME= 390.6 SECONDS, CPU UTILIZATION IS 99.19% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.135597 -0.012009 0.033446 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.109704 -0.013424 0.026193 0.113584 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C 0.000183766 0.000763424 -0.002005612 2 H 0.000073835 0.000143294 -0.000123216 3 C 0.000247299 -0.002659497 0.005049701 4 H 0.000786575 -0.000001808 -0.000793165 5 C -0.001348130 0.001541439 -0.002064710 6 H -0.000166225 0.000158173 -0.000089105 7 H 0.000063288 -0.000073706 0.000075588 8 C 0.000186879 0.000124510 -0.000081046 9 H -0.000007025 -0.000016556 0.000002604 10 H -0.000020260 0.000020726 0.000028960 $VIB IVIB= 1 IATOM= 3 ICOORD= 3 E= -155.8262085298 1.837655255E-04 7.634235516E-04-2.005611855E-03 7.383474584E-05 1.432939033E-04 -1.232158621E-04 2.472993896E-04-2.659497016E-03 5.049700993E-03 7.865747715E-04 -1.807746453E-06-7.931646082E-04-1.348129986E-03 1.541439305E-03-2.064709649E-03 -1.662250144E-04 1.581732152E-04-8.910547619E-05 6.328762702E-05-7.370559294E-05 7.558812545E-05 1.868785163E-04 1.245096254E-04-8.104566461E-05-7.025298372E-06 -1.655568866E-05 2.603933592E-06-2.026027691E-05 2.072644399E-05 2.896006316E-05 1.097040489E-01-1.342400484E-02 2.619306882E-02 1 ATOM 4 ------------------- COORD 1 NUCLEAR COORDINATES ------------------- VIB 1 ATOM X Y Z 1 C 0.793773 -0.808112 1.400575 2 H 2.289185 -0.995597 2.802099 3 C 1.446062 0.609240 -0.884553 4 H 3.419625 0.489515 -1.489324 5 C -0.143450 2.042156 -2.212893 6 H 0.464242 3.013674 -3.912111 7 H -2.091534 2.309425 -1.624756 8 C -1.429845 -1.902330 1.850402 9 H -2.943256 -1.862199 0.464672 10 H -1.792911 -2.895773 3.605888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 387.4 ( 6.5 MIN) TOTAL WALL CLOCK TIME= 390.6 SECONDS, CPU UTILIZATION IS 99.19% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 387.4 ( 6.5 MIN) TOTAL WALL CLOCK TIME= 390.6 SECONDS, CPU UTILIZATION IS 99.19% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8257204301 -155.8257204301 0.001108500 0.001447567 17701200 79865 2 1 0 -155.8257315140 -0.0000110839 0.000918591 0.000485717 16478242 128892 3 2 0 -155.8257318682 -0.0000003543 0.000435370 0.000432985 15868647 147308 4 3 0 -155.8257329454 -0.0000010771 0.000122814 0.000159380 15548861 158262 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 5 4 0 -155.8262099143 -0.0004769689 0.000828557 0.001452548 17701172 79875 6 5 0 -155.8262167983 -0.0000068841 0.000503030 0.000354371 16450792 130174 7 6 0 -155.8262171503 -0.0000003520 0.000258106 0.000236279 15708158 151749 8 7 0 -155.8262175214 -0.0000003711 0.000042038 0.000073231 15254779 165321 9 8 0 -155.8262175380 -0.0000000166 0.000017182 0.000039309 14610744 188661 10 9 0 -155.8262175432 -0.0000000052 0.000001857 0.000002119 13955016 202730 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 7.9 SECONDS ( 0.8 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262175432 AFTER 10 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9900587683 TOTAL ELECTRON NUMBER = 30.0000053038 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.20 TOTAL CPU TIME= 395.6 ( 6.6 MIN) TOTAL WALL CLOCK TIME= 398.9 SECONDS, CPU UTILIZATION IS 99.19% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.02 TOTAL CPU TIME= 395.7 ( 6.6 MIN) TOTAL WALL CLOCK TIME= 398.9 SECONDS, CPU UTILIZATION IS 99.19% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.30 TOTAL CPU TIME= 398.0 ( 6.6 MIN) TOTAL WALL CLOCK TIME= 401.2 SECONDS, CPU UTILIZATION IS 99.19% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 398.3 ( 6.6 MIN) TOTAL WALL CLOCK TIME= 401.6 SECONDS, CPU UTILIZATION IS 99.19% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.135784 -0.012009 0.031226 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.109815 -0.009617 0.027405 0.113591 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C -0.000067301 -0.000013805 0.000012767 2 H 0.000023016 -0.000003646 0.000010748 3 C -0.002978249 0.000188503 0.000749830 4 H 0.003204595 -0.000216459 -0.000845522 5 C -0.000202489 0.000014988 0.000086387 6 H 0.000023429 -0.000017825 -0.000015234 7 H -0.000009344 0.000038577 -0.000009995 8 C 0.000006630 0.000017877 0.000004776 9 H 0.000002556 -0.000000826 0.000003741 10 H -0.000002843 -0.000007384 0.000002500 $VIB IVIB= 1 IATOM= 4 ICOORD= 1 E= -155.8262175432 -6.730138945E-05-1.380518043E-05 1.276699458E-05 2.301614862E-05-3.645661230E-06 1.074844445E-05-2.978248649E-03 1.885027860E-04 7.498304082E-04 3.204594951E-03 -2.164586136E-04-8.455216493E-04-2.024892237E-04 1.498757226E-05 8.638676094E-05 2.342881107E-05-1.782499439E-05-1.523359714E-05-9.344097682E-06 3.857705176E-05 -9.994816027E-06 6.630135613E-06 1.787679811E-05 4.776122249E-06 2.556149517E-06 -8.257193327E-07 3.741149889E-06-2.842836299E-06-7.384039178E-06 2.500182132E-06 1.098150254E-01-9.616597023E-03 2.740469905E-02 1 ATOM 4 ------------------- COORD 2 NUCLEAR COORDINATES ------------------- VIB 1 ATOM X Y Z 1 C 0.793773 -0.808112 1.400575 2 H 2.289185 -0.995597 2.802099 3 C 1.446062 0.609240 -0.884553 4 H 3.409625 0.499515 -1.489324 5 C -0.143450 2.042156 -2.212893 6 H 0.464242 3.013674 -3.912111 7 H -2.091534 2.309425 -1.624756 8 C -1.429845 -1.902330 1.850402 9 H -2.943256 -1.862199 0.464672 10 H -1.792911 -2.895773 3.605888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 398.3 ( 6.6 MIN) TOTAL WALL CLOCK TIME= 401.6 SECONDS, CPU UTILIZATION IS 99.19% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.02 TOTAL CPU TIME= 398.3 ( 6.6 MIN) TOTAL WALL CLOCK TIME= 401.6 SECONDS, CPU UTILIZATION IS 99.19% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8257329165 -155.8257329165 0.000838937 0.001460873 17702049 79818 2 1 0 -155.8257411505 -0.0000082340 0.000456649 0.000320659 16469183 129451 3 2 0 -155.8257414911 -0.0000003406 0.000235758 0.000223759 15709593 151802 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 4 3 0 -155.8262242360 -0.0004827449 0.000850215 0.001446650 17702072 79824 5 4 0 -155.8262310463 -0.0000068103 0.000555653 0.000359439 16452446 130109 6 5 0 -155.8262313417 -0.0000002954 0.000291246 0.000245053 15713546 151711 7 6 0 -155.8262317813 -0.0000004395 0.000057320 0.000105269 15298973 164717 8 7 0 -155.8262318174 -0.0000000361 0.000017268 0.000035784 14716388 184782 9 8 0 -155.8262318221 -0.0000000047 0.000002545 0.000002112 13979477 201709 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 7.8 SECONDS ( 0.9 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262318221 AFTER 9 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9915429048 TOTAL ELECTRON NUMBER = 30.0000053210 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 7.99 TOTAL CPU TIME= 406.3 ( 6.8 MIN) TOTAL WALL CLOCK TIME= 409.6 SECONDS, CPU UTILIZATION IS 99.19% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 406.3 ( 6.8 MIN) TOTAL WALL CLOCK TIME= 409.6 SECONDS, CPU UTILIZATION IS 99.19% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.30 TOTAL CPU TIME= 408.6 ( 6.8 MIN) TOTAL WALL CLOCK TIME= 412.0 SECONDS, CPU UTILIZATION IS 99.19% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 409.0 ( 6.8 MIN) TOTAL WALL CLOCK TIME= 412.3 SECONDS, CPU UTILIZATION IS 99.19% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.135597 -0.011822 0.031226 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.112739 -0.007333 0.026834 0.116120 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C -0.000189135 -0.000005071 0.000078626 2 H 0.000023114 0.000002468 0.000005723 3 C 0.000142544 -0.000411319 -0.000001347 4 H -0.000196512 0.000381914 -0.000105109 5 C 0.000183815 0.000026236 -0.000025707 6 H -0.000004639 -0.000052135 -0.000042738 7 H 0.000037663 0.000059080 0.000069210 8 C 0.000004699 0.000014178 0.000014069 9 H 0.000001388 0.000000751 0.000004967 10 H -0.000002936 -0.000016102 0.000002306 $VIB IVIB= 1 IATOM= 4 ICOORD= 2 E= -155.8262318221 -1.891350558E-04-5.070634283E-06 7.862555681E-05 2.311362052E-05 2.468064451E-06 5.722561568E-06 1.425440293E-04-4.113188433E-04-1.346597021E-06-1.965123111E-04 3.819136611E-04-1.051090790E-04 1.838146146E-04 2.623554933E-05-2.570697354E-05 -4.639401735E-06-5.213477813E-05-4.273812617E-05 3.766309279E-05 5.907977083E-05 6.921001981E-05 4.699329696E-06 1.417784509E-05 1.406903492E-05 1.387601105E-06 7.513311122E-07 4.967164855E-06-2.935519333E-06-1.610196614E-05 2.306437770E-06 1.127387360E-01-7.332844175E-03 2.683391157E-02 1 ATOM 4 ------------------- COORD 3 NUCLEAR COORDINATES ------------------- VIB 1 ATOM X Y Z 1 C 0.793773 -0.808112 1.400575 2 H 2.289185 -0.995597 2.802099 3 C 1.446062 0.609240 -0.884553 4 H 3.409625 0.489515 -1.479324 5 C -0.143450 2.042156 -2.212893 6 H 0.464242 3.013674 -3.912111 7 H -2.091534 2.309425 -1.624756 8 C -1.429845 -1.902330 1.850402 9 H -2.943256 -1.862199 0.464672 10 H -1.792911 -2.895773 3.605888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 409.0 ( 6.8 MIN) TOTAL WALL CLOCK TIME= 412.3 SECONDS, CPU UTILIZATION IS 99.19% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.02 TOTAL CPU TIME= 409.0 ( 6.8 MIN) TOTAL WALL CLOCK TIME= 412.3 SECONDS, CPU UTILIZATION IS 99.19% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8257332380 -155.8257332380 0.000916026 0.001465940 17703001 79783 2 1 0 -155.8257414848 -0.0000082468 0.000481318 0.000293935 16467004 129457 3 2 0 -155.8257417185 -0.0000002337 0.000242886 0.000233254 15713032 151839 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 4 3 0 -155.8262224899 -0.0004807714 0.000843387 0.001431291 17703195 79781 5 4 0 -155.8262292252 -0.0000067353 0.000563951 0.000337762 16454304 130088 6 5 0 -155.8262293715 -0.0000001462 0.000284918 0.000319914 15719916 151828 7 6 0 -155.8262299711 -0.0000005996 0.000071066 0.000135719 15377647 163371 8 7 0 -155.8262300313 -0.0000000602 0.000015571 0.000028328 14816000 181111 9 8 0 -155.8262300348 -0.0000000036 0.000001477 0.000001814 13970314 202001 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 7.8 SECONDS ( 0.9 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262300348 AFTER 9 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9918927323 TOTAL ELECTRON NUMBER = 30.0000053399 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.00 TOTAL CPU TIME= 417.0 ( 7.0 MIN) TOTAL WALL CLOCK TIME= 420.4 SECONDS, CPU UTILIZATION IS 99.20% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 417.0 ( 7.0 MIN) TOTAL WALL CLOCK TIME= 420.4 SECONDS, CPU UTILIZATION IS 99.20% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.30 TOTAL CPU TIME= 419.3 ( 7.0 MIN) TOTAL WALL CLOCK TIME= 422.7 SECONDS, CPU UTILIZATION IS 99.20% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 419.7 ( 7.0 MIN) TOTAL WALL CLOCK TIME= 423.1 SECONDS, CPU UTILIZATION IS 99.20% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.135597 -0.012009 0.031412 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.113846 -0.008532 0.026979 0.117309 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C 0.000235100 -0.000032828 -0.000025032 2 H 0.000011811 -0.000000408 0.000014531 3 C 0.000797227 0.000034115 -0.000788407 4 H -0.000845047 -0.000104096 0.000737046 5 C -0.000193591 0.000035219 0.000099370 6 H 0.000002890 -0.000045219 -0.000021336 7 H -0.000013044 0.000072422 0.000026102 8 C -0.000005058 0.000038941 -0.000053370 9 H 0.000003916 -0.000007127 0.000004441 10 H 0.000005795 0.000008982 0.000006655 $VIB IVIB= 1 IATOM= 4 ICOORD= 3 E= -155.8262300348 2.350996450E-04-3.282825093E-05-2.503191460E-05 1.181112803E-05-4.083922967E-07 1.453093296E-05 7.972273996E-04 3.411494051E-05-7.884072900E-04-8.450470304E-04 -1.040959070E-04 7.370461290E-04-1.935907919E-04 3.521883995E-05 9.937025048E-05 2.890396288E-06-4.521908792E-05-2.133575036E-05-1.304388549E-05 7.242160689E-05 2.610200219E-05-5.057904593E-06 3.894062734E-05-5.337045741E-05 3.916427003E-06 -7.126766171E-06 4.440880094E-06 5.794616496E-06 8.982389592E-06 6.655217586E-06 1.138456254E-01-8.532273767E-03 2.697918310E-02 1 ATOM 5 ------------------- COORD 1 NUCLEAR COORDINATES ------------------- VIB 1 ATOM X Y Z 1 C 0.793773 -0.808112 1.400575 2 H 2.289185 -0.995597 2.802099 3 C 1.446062 0.609240 -0.884553 4 H 3.409625 0.489515 -1.489324 5 C -0.133450 2.042156 -2.212893 6 H 0.464242 3.013674 -3.912111 7 H -2.091534 2.309425 -1.624756 8 C -1.429845 -1.902330 1.850402 9 H -2.943256 -1.862199 0.464672 10 H -1.792911 -2.895773 3.605888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 419.7 ( 7.0 MIN) TOTAL WALL CLOCK TIME= 423.1 SECONDS, CPU UTILIZATION IS 99.20% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 419.7 ( 7.0 MIN) TOTAL WALL CLOCK TIME= 423.1 SECONDS, CPU UTILIZATION IS 99.20% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8256616308 -155.8256616308 0.000995180 0.001523423 17702257 79815 2 1 0 -155.8256808253 -0.0000191945 0.000470629 0.000324423 16525815 127381 3 2 0 -155.8256809381 -0.0000001128 0.000304001 0.000388145 15824737 150149 4 3 0 -155.8256817956 -0.0000008575 0.000083863 0.000148468 15486420 161137 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 5 4 0 -155.8261924266 -0.0005106309 0.000946623 0.001462686 17702143 79825 6 5 0 -155.8261992309 -0.0000068044 0.000438937 0.000340644 16452727 130091 7 6 0 -155.8261995929 -0.0000003620 0.000192933 0.000230366 15732086 151017 8 7 0 -155.8261999494 -0.0000003564 0.000036908 0.000055729 15318759 163696 9 8 0 -155.8261999601 -0.0000000107 0.000018451 0.000031609 14530098 189292 10 9 0 -155.8261999642 -0.0000000041 0.000002395 0.000004880 13782542 209504 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 8.0 SECONDS ( 0.8 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8261999642 AFTER 10 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9921315299 TOTAL ELECTRON NUMBER = 30.0000052312 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.19 TOTAL CPU TIME= 427.9 ( 7.1 MIN) TOTAL WALL CLOCK TIME= 431.4 SECONDS, CPU UTILIZATION IS 99.20% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 427.9 ( 7.1 MIN) TOTAL WALL CLOCK TIME= 431.4 SECONDS, CPU UTILIZATION IS 99.20% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.30 TOTAL CPU TIME= 430.2 ( 7.2 MIN) TOTAL WALL CLOCK TIME= 433.7 SECONDS, CPU UTILIZATION IS 99.20% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.37 TOTAL CPU TIME= 430.6 ( 7.2 MIN) TOTAL WALL CLOCK TIME= 434.0 SECONDS, CPU UTILIZATION IS 99.20% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.137818 -0.012009 0.031226 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.112261 -0.011309 0.023081 0.115166 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C 0.000150364 -0.000002616 -0.000051065 2 H 0.000020862 -0.000020744 0.000032638 3 C -0.002886300 0.001709282 -0.001360322 4 H -0.000161852 0.000208133 -0.000169243 5 C 0.006761204 -0.001863065 -0.000075928 6 H -0.000805637 -0.000368205 0.000750656 7 H -0.003027333 0.000370434 0.000837973 8 C -0.000054466 -0.000018358 0.000029001 9 H 0.000011034 -0.000022947 -0.000003900 10 H -0.000007877 0.000008086 0.000010190 $VIB IVIB= 1 IATOM= 5 ICOORD= 1 E= -155.8261999642 1.503639995E-04-2.616021495E-06-5.106474126E-05 2.086152088E-05-2.074428627E-05 3.263829386E-05-2.886300308E-03 1.709282079E-03-1.360322272E-03-1.618516152E-04 2.081334029E-04-1.692428165E-04 6.761204311E-03-1.863065036E-03-7.592759310E-05 -8.056366326E-04-3.682049768E-04 7.506556121E-04-3.027333058E-03 3.704337170E-04 8.379733156E-04-5.446590682E-05-1.835801913E-05 2.900064248E-05 1.103430672E-05 -2.294696680E-05-3.900006005E-06-7.876617356E-06 8.086107543E-06 1.018956437E-05 1.122610146E-01-1.130850973E-02 2.308131667E-02 1 ATOM 5 ------------------- COORD 2 NUCLEAR COORDINATES ------------------- VIB 1 ATOM X Y Z 1 C 0.793773 -0.808112 1.400575 2 H 2.289185 -0.995597 2.802099 3 C 1.446062 0.609240 -0.884553 4 H 3.409625 0.489515 -1.489324 5 C -0.143450 2.052156 -2.212893 6 H 0.464242 3.013674 -3.912111 7 H -2.091534 2.309425 -1.624756 8 C -1.429845 -1.902330 1.850402 9 H -2.943256 -1.862199 0.464672 10 H -1.792911 -2.895773 3.605888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 430.6 ( 7.2 MIN) TOTAL WALL CLOCK TIME= 434.1 SECONDS, CPU UTILIZATION IS 99.20% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 430.6 ( 7.2 MIN) TOTAL WALL CLOCK TIME= 434.1 SECONDS, CPU UTILIZATION IS 99.20% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8257201958 -155.8257201958 0.001114305 0.001540767 17699059 79881 2 1 0 -155.8257354441 -0.0000152482 0.000870251 0.000408947 16519839 127963 3 2 0 -155.8257357816 -0.0000003375 0.000437566 0.000343422 15868741 147053 4 3 0 -155.8257367622 -0.0000009806 0.000102484 0.000143778 15530487 158413 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 5 4 0 -155.8262073053 -0.0004705432 0.000831334 0.001457269 17698967 79892 6 5 0 -155.8262141988 -0.0000068934 0.000493136 0.000352372 16447553 130204 7 6 0 -155.8262145397 -0.0000003409 0.000251445 0.000231597 15701956 151869 8 7 0 -155.8262149027 -0.0000003630 0.000041121 0.000077195 15243023 165562 9 8 0 -155.8262149210 -0.0000000184 0.000016973 0.000039857 14621937 188171 10 9 0 -155.8262149263 -0.0000000053 0.000001522 0.000002011 13960058 202453 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 8.0 SECONDS ( 0.8 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262149263 AFTER 10 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9908020467 TOTAL ELECTRON NUMBER = 30.0000052215 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.20 TOTAL CPU TIME= 438.8 ( 7.3 MIN) TOTAL WALL CLOCK TIME= 442.3 SECONDS, CPU UTILIZATION IS 99.20% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 438.8 ( 7.3 MIN) TOTAL WALL CLOCK TIME= 442.3 SECONDS, CPU UTILIZATION IS 99.20% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.31 TOTAL CPU TIME= 441.1 ( 7.4 MIN) TOTAL WALL CLOCK TIME= 444.6 SECONDS, CPU UTILIZATION IS 99.20% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 441.5 ( 7.4 MIN) TOTAL WALL CLOCK TIME= 445.0 SECONDS, CPU UTILIZATION IS 99.20% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.135597 -0.009788 0.031226 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.111216 -0.016798 0.024493 0.115113 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C 0.000058546 -0.000127673 0.000199779 2 H -0.000000406 0.000009764 0.000025466 3 C 0.001744290 -0.002135227 0.001527047 4 H 0.000022829 0.000015990 0.000025531 5 C -0.001858544 0.003747468 -0.002971176 6 H -0.000382766 -0.001045439 0.001229759 7 H 0.000377205 -0.000474886 -0.000027166 8 C 0.000037866 0.000017245 -0.000017354 9 H 0.000001172 -0.000009004 0.000004489 10 H -0.000000193 0.000001761 0.000003624 $VIB IVIB= 1 IATOM= 5 ICOORD= 2 E= -155.8262149263 5.854599156E-05-1.276725980E-04 1.997791342E-04-4.055337001E-07 9.764103803E-06 2.546607377E-05 1.744290252E-03-2.135226842E-03 1.527047195E-03 2.282928683E-05 1.599013690E-05 2.553116167E-05-1.858543839E-03 3.747467972E-03-2.971175516E-03 -3.827662041E-04-1.045439433E-03 1.229759005E-03 3.772054372E-04-4.748856666E-04 -2.716614059E-05 3.786574284E-05 1.724548266E-05-1.735370685E-05 1.171527138E-06 -9.004152283E-06 4.488888085E-06-1.926603125E-07 1.760996117E-06 3.623905943E-06 1.112156636E-01-1.679819674E-02 2.449281498E-02 1 ATOM 5 ------------------- COORD 3 NUCLEAR COORDINATES ------------------- VIB 1 ATOM X Y Z 1 C 0.793773 -0.808112 1.400575 2 H 2.289185 -0.995597 2.802099 3 C 1.446062 0.609240 -0.884553 4 H 3.409625 0.489515 -1.489324 5 C -0.143450 2.042156 -2.202893 6 H 0.464242 3.013674 -3.912111 7 H -2.091534 2.309425 -1.624756 8 C -1.429845 -1.902330 1.850402 9 H -2.943256 -1.862199 0.464672 10 H -1.792911 -2.895773 3.605888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 441.5 ( 7.4 MIN) TOTAL WALL CLOCK TIME= 445.0 SECONDS, CPU UTILIZATION IS 99.20% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 441.5 ( 7.4 MIN) TOTAL WALL CLOCK TIME= 445.0 SECONDS, CPU UTILIZATION IS 99.20% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8256928647 -155.8256928647 0.001049829 0.001553306 17706723 79733 2 1 0 -155.8257108763 -0.0000180115 0.000467419 0.000314747 16532957 127370 3 2 0 -155.8257111269 -0.0000002506 0.000273299 0.000312165 15819953 150582 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 4 3 0 -155.8261990127 -0.0004878858 0.000881710 0.001422657 17706736 79742 5 4 0 -155.8262055919 -0.0000065792 0.000650312 0.000320200 16457459 130017 6 5 0 -155.8262055047 0.0000000872 0.000319379 0.000475750 15771284 151072 7 6 0 -155.8262065069 -0.0000010022 0.000078022 0.000136035 15479483 161103 8 7 0 -155.8262065747 -0.0000000678 0.000015760 0.000022469 14846726 179287 9 8 0 -155.8262065776 -0.0000000028 0.000002953 0.000003668 13965178 202388 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 7.8 SECONDS ( 0.9 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262065776 AFTER 9 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9921082258 TOTAL ELECTRON NUMBER = 30.0000052296 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.00 TOTAL CPU TIME= 449.5 ( 7.5 MIN) TOTAL WALL CLOCK TIME= 453.1 SECONDS, CPU UTILIZATION IS 99.20% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 449.5 ( 7.5 MIN) TOTAL WALL CLOCK TIME= 453.1 SECONDS, CPU UTILIZATION IS 99.20% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.30 TOTAL CPU TIME= 451.8 ( 7.5 MIN) TOTAL WALL CLOCK TIME= 455.4 SECONDS, CPU UTILIZATION IS 99.20% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 452.1 ( 7.5 MIN) TOTAL WALL CLOCK TIME= 455.8 SECONDS, CPU UTILIZATION IS 99.20% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.135597 -0.012009 0.033446 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.110682 -0.011771 0.022918 0.113641 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C -0.000120245 0.000246949 -0.000212973 2 H 0.000026256 0.000022070 -0.000029320 3 C -0.001427357 0.001568619 -0.002080404 4 H 0.000097568 -0.000033415 0.000092553 5 C -0.000114868 -0.002962604 0.005413003 6 H 0.000798651 0.001175911 -0.002437219 7 H 0.000806725 -0.000001581 -0.000749281 8 C -0.000077554 0.000000830 -0.000004451 9 H 0.000006828 -0.000003281 0.000006656 10 H 0.000003997 -0.000013499 0.000001436 $VIB IVIB= 1 IATOM= 5 ICOORD= 3 E= -155.8262065776 -1.202448189E-04 2.469493749E-04-2.129734797E-04 2.625591061E-05 2.206968773E-05 -2.931983124E-05-1.427357029E-03 1.568618514E-03-2.080403914E-03 9.756750987E-05 -3.341457880E-05 9.255346085E-05-1.148679674E-04-2.962604139E-03 5.413002573E-03 7.986509378E-04 1.175911499E-03-2.437219444E-03 8.067252067E-04-1.580954849E-06 -7.492807242E-04-7.755442962E-05 8.299452870E-07-4.450910525E-06 6.828158774E-06 -3.280625569E-06 6.656342783E-06 3.996521042E-06-1.349872270E-05 1.435927210E-06 1.106823264E-01-1.177085079E-02 2.291763138E-02 1 ATOM 6 ------------------- COORD 1 NUCLEAR COORDINATES ------------------- VIB 1 ATOM X Y Z 1 C 0.793773 -0.808112 1.400575 2 H 2.289185 -0.995597 2.802099 3 C 1.446062 0.609240 -0.884553 4 H 3.409625 0.489515 -1.489324 5 C -0.143450 2.042156 -2.212893 6 H 0.474242 3.013674 -3.912111 7 H -2.091534 2.309425 -1.624756 8 C -1.429845 -1.902330 1.850402 9 H -2.943256 -1.862199 0.464672 10 H -1.792911 -2.895773 3.605888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 452.2 ( 7.5 MIN) TOTAL WALL CLOCK TIME= 455.8 SECONDS, CPU UTILIZATION IS 99.20% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 452.2 ( 7.5 MIN) TOTAL WALL CLOCK TIME= 455.8 SECONDS, CPU UTILIZATION IS 99.20% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8257339050 -155.8257339050 0.000894338 0.001472035 17702087 79810 2 1 0 -155.8257423189 -0.0000084139 0.000572423 0.000351572 16471783 129192 3 2 0 -155.8257427129 -0.0000003940 0.000297835 0.000234277 15738624 150993 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 4 3 0 -155.8262220667 -0.0004793538 0.000859408 0.001441443 17702290 79812 5 4 0 -155.8262288245 -0.0000067578 0.000585731 0.000325567 16452305 130120 6 5 0 -155.8262290223 -0.0000001978 0.000298309 0.000280996 15714432 151749 7 6 0 -155.8262295762 -0.0000005540 0.000070043 0.000129659 15346892 163800 8 7 0 -155.8262296316 -0.0000000554 0.000015427 0.000029830 14803493 181793 9 8 0 -155.8262296353 -0.0000000037 0.000002440 0.000002690 13974324 201906 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 7.8 SECONDS ( 0.9 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262296353 AFTER 9 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9910610471 TOTAL ELECTRON NUMBER = 30.0000052413 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 7.99 TOTAL CPU TIME= 460.2 ( 7.7 MIN) TOTAL WALL CLOCK TIME= 463.8 SECONDS, CPU UTILIZATION IS 99.20% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 460.2 ( 7.7 MIN) TOTAL WALL CLOCK TIME= 463.9 SECONDS, CPU UTILIZATION IS 99.20% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.31 TOTAL CPU TIME= 462.5 ( 7.7 MIN) TOTAL WALL CLOCK TIME= 466.2 SECONDS, CPU UTILIZATION IS 99.21% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 462.8 ( 7.7 MIN) TOTAL WALL CLOCK TIME= 466.5 SECONDS, CPU UTILIZATION IS 99.21% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.135784 -0.012009 0.031226 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.113865 -0.010318 0.027328 0.117553 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C -0.000020540 0.000020778 0.000012010 2 H 0.000017453 0.000003143 0.000001535 3 C 0.000087262 0.000132670 -0.000187564 4 H 0.000022493 -0.000023626 -0.000015739 5 C -0.000857309 -0.000388987 0.000801619 6 H 0.000800031 0.000371842 -0.000813791 7 H -0.000047060 -0.000122664 0.000213415 8 C -0.000009141 0.000013503 -0.000019602 9 H 0.000003882 -0.000000299 0.000004909 10 H 0.000002930 -0.000006361 0.000003207 $VIB IVIB= 1 IATOM= 6 ICOORD= 1 E= -155.8262296353 -2.054040271E-05 2.077842295E-05 1.200987558E-05 1.745314708E-05 3.143084277E-06 1.535471510E-06 8.726194336E-05 1.326699995E-04-1.875635412E-04 2.249254995E-05 -2.362560684E-05-1.573948811E-05-8.573091719E-04-3.889870206E-04 8.016190712E-04 8.000308171E-04 3.718424489E-04-8.137907898E-04-4.706038009E-05-1.226641361E-04 2.134150911E-04-9.140897704E-06 1.350305655E-05-1.960207725E-05 3.881994073E-06 -2.993098030E-07 4.909302460E-06 2.930400883E-06-6.360938863E-06 3.207084559E-06 1.138654477E-01-1.031843959E-02 2.732775318E-02 1 ATOM 6 ------------------- COORD 2 NUCLEAR COORDINATES ------------------- VIB 1 ATOM X Y Z 1 C 0.793773 -0.808112 1.400575 2 H 2.289185 -0.995597 2.802099 3 C 1.446062 0.609240 -0.884553 4 H 3.409625 0.489515 -1.489324 5 C -0.143450 2.042156 -2.212893 6 H 0.464242 3.023674 -3.912111 7 H -2.091534 2.309425 -1.624756 8 C -1.429845 -1.902330 1.850402 9 H -2.943256 -1.862199 0.464672 10 H -1.792911 -2.895773 3.605888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 462.8 ( 7.7 MIN) TOTAL WALL CLOCK TIME= 466.5 SECONDS, CPU UTILIZATION IS 99.20% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.02 TOTAL CPU TIME= 462.9 ( 7.7 MIN) TOTAL WALL CLOCK TIME= 466.6 SECONDS, CPU UTILIZATION IS 99.21% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8257225139 -155.8257225139 0.000946296 0.001447422 17700339 79847 2 1 0 -155.8257319254 -0.0000094115 0.000735767 0.000373114 16476986 129272 3 2 0 -155.8257323046 -0.0000003792 0.000382289 0.000272493 15772816 150293 4 3 0 -155.8257329324 -0.0000006279 0.000079603 0.000124255 15361410 163430 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 5 4 0 -155.8262209559 -0.0004880235 0.000895295 0.001464831 17700549 79844 6 5 0 -155.8262278618 -0.0000069059 0.000451988 0.000348668 16452867 130148 7 6 0 -155.8262282282 -0.0000003664 0.000211716 0.000231072 15720317 151311 8 7 0 -155.8262285729 -0.0000003447 0.000031926 0.000036815 15293916 164312 9 8 0 -155.8262285802 -0.0000000073 0.000019409 0.000022691 14490978 190721 10 9 0 -155.8262285832 -0.0000000030 0.000002411 0.000005076 13594613 214826 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 7.9 SECONDS ( 0.8 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262285832 AFTER 10 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9907520283 TOTAL ELECTRON NUMBER = 30.0000053957 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.18 TOTAL CPU TIME= 471.0 ( 7.9 MIN) TOTAL WALL CLOCK TIME= 474.8 SECONDS, CPU UTILIZATION IS 99.21% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 471.0 ( 7.9 MIN) TOTAL WALL CLOCK TIME= 474.8 SECONDS, CPU UTILIZATION IS 99.21% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.30 TOTAL CPU TIME= 473.4 ( 7.9 MIN) TOTAL WALL CLOCK TIME= 477.1 SECONDS, CPU UTILIZATION IS 99.21% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 473.7 ( 7.9 MIN) TOTAL WALL CLOCK TIME= 477.5 SECONDS, CPU UTILIZATION IS 99.21% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.135597 -0.011822 0.031226 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.112582 -0.007908 0.028040 0.116290 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C 0.000054444 0.000055038 0.000060067 2 H 0.000012492 -0.000009852 0.000020585 3 C -0.000074737 -0.000036527 0.000158080 4 H 0.000001490 -0.000051019 -0.000043385 5 C -0.000388275 -0.001039012 0.001200042 6 H 0.000389968 0.001031171 -0.001343125 7 H 0.000013057 0.000041520 -0.000031134 8 C -0.000011842 0.000019169 -0.000024989 9 H 0.000002133 -0.000002911 0.000002194 10 H 0.000001269 -0.000007577 0.000001663 $VIB IVIB= 1 IATOM= 6 ICOORD= 2 E= -155.8262285832 5.444401221E-05 5.503795960E-05 6.006666076E-05 1.249220501E-05-9.852473990E-06 2.058509473E-05-7.473693758E-05-3.652710069E-05 1.580800794E-04 1.489766656E-06 -5.101921527E-05-4.338457805E-05-3.882748958E-04-1.039012445E-03 1.200042355E-03 3.899684048E-04 1.031171370E-03-1.343124566E-03 1.305749027E-05 4.152044309E-05 -3.113360460E-05-1.184221583E-05 1.916921486E-05-2.498865866E-05 2.133018269E-06 -2.910999061E-06 2.194057315E-06 1.269152027E-06-7.576752815E-06 1.663160453E-06 1.125815314E-01-7.908218880E-03 2.803956244E-02 1 ATOM 6 ------------------- COORD 3 NUCLEAR COORDINATES ------------------- VIB 1 ATOM X Y Z 1 C 0.793773 -0.808112 1.400575 2 H 2.289185 -0.995597 2.802099 3 C 1.446062 0.609240 -0.884553 4 H 3.409625 0.489515 -1.489324 5 C -0.143450 2.042156 -2.212893 6 H 0.464242 3.013674 -3.902111 7 H -2.091534 2.309425 -1.624756 8 C -1.429845 -1.902330 1.850402 9 H -2.943256 -1.862199 0.464672 10 H -1.792911 -2.895773 3.605888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 473.7 ( 7.9 MIN) TOTAL WALL CLOCK TIME= 477.5 SECONDS, CPU UTILIZATION IS 99.21% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.02 TOTAL CPU TIME= 473.7 ( 7.9 MIN) TOTAL WALL CLOCK TIME= 477.5 SECONDS, CPU UTILIZATION IS 99.21% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8257156562 -155.8257156562 0.000876195 0.001471727 17704563 79732 2 1 0 -155.8257248535 -0.0000091973 0.000512451 0.000393166 16473946 129138 3 2 0 -155.8257244928 0.0000003607 0.000248914 0.000547359 15858488 148978 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 4 3 0 -155.8262134277 -0.0004889349 0.000845227 0.001447790 17704767 79729 5 4 0 -155.8262201749 -0.0000067472 0.000446799 0.000339112 16454086 129929 6 5 0 -155.8262203290 -0.0000001541 0.000222887 0.000248061 15734856 151347 7 6 0 -155.8262207868 -0.0000004578 0.000084077 0.000091284 15385971 162962 8 7 0 -155.8262208322 -0.0000000454 0.000016538 0.000022031 14577514 188622 9 8 0 -155.8262208348 -0.0000000026 0.000004272 0.000005531 13868293 205989 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 7.8 SECONDS ( 0.9 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262208348 AFTER 9 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9926888790 TOTAL ELECTRON NUMBER = 30.0000053203 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 7.99 TOTAL CPU TIME= 481.7 ( 8.0 MIN) TOTAL WALL CLOCK TIME= 485.6 SECONDS, CPU UTILIZATION IS 99.21% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 481.7 ( 8.0 MIN) TOTAL WALL CLOCK TIME= 485.6 SECONDS, CPU UTILIZATION IS 99.21% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.30 TOTAL CPU TIME= 484.0 ( 8.1 MIN) TOTAL WALL CLOCK TIME= 487.9 SECONDS, CPU UTILIZATION IS 99.21% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 484.4 ( 8.1 MIN) TOTAL WALL CLOCK TIME= 488.3 SECONDS, CPU UTILIZATION IS 99.21% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.135597 -0.012009 0.031412 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.113448 -0.007269 0.025227 0.116446 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C -0.000011453 0.000040030 0.000041803 2 H 0.000016663 0.000002749 0.000007670 3 C 0.000080252 0.000077826 -0.000091068 4 H 0.000003233 -0.000042548 -0.000020779 5 C 0.000740748 0.001251822 -0.002483649 6 H -0.000808946 -0.001374326 0.002587222 7 H -0.000011601 0.000040703 -0.000025754 8 C -0.000014402 0.000013866 -0.000021020 9 H 0.000003154 -0.000004131 0.000004435 10 H 0.000002353 -0.000005991 0.000001141 $VIB IVIB= 1 IATOM= 6 ICOORD= 3 E= -155.8262208348 -1.145348599E-05 4.003020572E-05 4.180298942E-05 1.666250257E-05 2.749213350E-06 7.669612849E-06 8.025158215E-05 7.782550523E-05-9.106814289E-05 3.233219989E-06 -4.254809061E-05-2.077949072E-05 7.407478560E-04 1.251821659E-03-2.483648682E-03 -8.089459699E-04-1.374325768E-03 2.587222435E-03-1.160086587E-05 4.070326204E-05 -2.575371167E-05-1.440169160E-05 1.386581218E-05-2.102034937E-05 3.153937818E-06 -4.130968108E-06 4.434588978E-06 2.352914874E-06-5.990831138E-06 1.140749870E-06 1.134477695E-01-7.269427779E-03 2.522746935E-02 1 ATOM 7 ------------------- COORD 1 NUCLEAR COORDINATES ------------------- VIB 1 ATOM X Y Z 1 C 0.793773 -0.808112 1.400575 2 H 2.289185 -0.995597 2.802099 3 C 1.446062 0.609240 -0.884553 4 H 3.409625 0.489515 -1.489324 5 C -0.143450 2.042156 -2.212893 6 H 0.464242 3.013674 -3.912111 7 H -2.081534 2.309425 -1.624756 8 C -1.429845 -1.902330 1.850402 9 H -2.943256 -1.862199 0.464672 10 H -1.792911 -2.895773 3.605888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 484.4 ( 8.1 MIN) TOTAL WALL CLOCK TIME= 488.3 SECONDS, CPU UTILIZATION IS 99.21% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 484.4 ( 8.1 MIN) TOTAL WALL CLOCK TIME= 488.3 SECONDS, CPU UTILIZATION IS 99.21% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8257156692 -155.8257156692 0.000909963 0.001467254 17703279 79765 2 1 0 -155.8257249291 -0.0000092599 0.000518941 0.000456354 16468497 129204 3 2 0 -155.8257244567 0.0000004724 0.000298495 0.000618178 15869810 148548 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 4 3 0 -155.8262098795 -0.0004854228 0.000840313 0.001446181 17703291 79769 5 4 0 -155.8262166271 -0.0000067476 0.000440848 0.000338943 16454328 129975 6 5 0 -155.8262167778 -0.0000001507 0.000223562 0.000248456 15732852 151390 7 6 0 -155.8262172365 -0.0000004586 0.000083294 0.000091869 15384382 162995 8 7 0 -155.8262172807 -0.0000000443 0.000016477 0.000022417 14576490 188682 9 8 0 -155.8262172834 -0.0000000027 0.000004223 0.000005356 13871355 205964 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 7.8 SECONDS ( 0.9 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262172834 AFTER 9 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9928584917 TOTAL ELECTRON NUMBER = 30.0000053744 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.00 TOTAL CPU TIME= 492.4 ( 8.2 MIN) TOTAL WALL CLOCK TIME= 496.3 SECONDS, CPU UTILIZATION IS 99.21% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 492.4 ( 8.2 MIN) TOTAL WALL CLOCK TIME= 496.3 SECONDS, CPU UTILIZATION IS 99.21% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.31 TOTAL CPU TIME= 494.7 ( 8.2 MIN) TOTAL WALL CLOCK TIME= 498.6 SECONDS, CPU UTILIZATION IS 99.21% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 495.1 ( 8.3 MIN) TOTAL WALL CLOCK TIME= 499.0 SECONDS, CPU UTILIZATION IS 99.21% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.135784 -0.012009 0.031226 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.110988 -0.008884 0.026825 0.114528 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C -0.000018131 -0.000057477 0.000014588 2 H 0.000017205 0.000004885 0.000005265 3 C -0.000159462 0.000036636 0.000064748 4 H 0.000012366 0.000041210 -0.000009238 5 C -0.003139725 0.000403906 0.000834457 6 H -0.000024937 0.000015290 -0.000008263 7 H 0.003306568 -0.000450533 -0.000896975 8 C 0.000000722 0.000011352 -0.000014210 9 H 0.000004559 -0.000003682 0.000006419 10 H 0.000000834 -0.000001586 0.000003209 $VIB IVIB= 1 IATOM= 7 ICOORD= 1 E= -155.8262172834 -1.813101785E-05-5.747732216E-05 1.458796696E-05 1.720524535E-05 4.885051657E-06 5.265005753E-06-1.594615347E-04 3.663556126E-05 6.474751320E-05 1.236586792E-05 4.121031280E-05-9.237807388E-06-3.139724846E-03 4.039059868E-04 8.344572575E-04 -2.493712863E-05 1.528987565E-05-8.263081338E-06 3.306567683E-03-4.505331818E-04 -8.969754078E-04 7.224356857E-07 1.135156139E-05-1.420970887E-05 4.559497106E-06 -3.682130091E-06 6.419421785E-06 8.337977009E-07-1.585715449E-06 3.208840263E-06 1.109875030E-01-8.884221195E-03 2.682484890E-02 1 ATOM 7 ------------------- COORD 2 NUCLEAR COORDINATES ------------------- VIB 1 ATOM X Y Z 1 C 0.793773 -0.808112 1.400575 2 H 2.289185 -0.995597 2.802099 3 C 1.446062 0.609240 -0.884553 4 H 3.409625 0.489515 -1.489324 5 C -0.143450 2.042156 -2.212893 6 H 0.464242 3.013674 -3.912111 7 H -2.091534 2.319425 -1.624756 8 C -1.429845 -1.902330 1.850402 9 H -2.943256 -1.862199 0.464672 10 H -1.792911 -2.895773 3.605888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 495.1 ( 8.3 MIN) TOTAL WALL CLOCK TIME= 499.0 SECONDS, CPU UTILIZATION IS 99.21% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 495.1 ( 8.3 MIN) TOTAL WALL CLOCK TIME= 499.0 SECONDS, CPU UTILIZATION IS 99.21% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8257249390 -155.8257249390 0.000852603 0.001454753 17701010 79851 2 1 0 -155.8257334204 -0.0000084813 0.000499077 0.000346463 16461719 129797 3 2 0 -155.8257337922 -0.0000003718 0.000235210 0.000233681 15713095 151458 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 4 3 0 -155.8262242120 -0.0004904198 0.000840305 0.001441539 17701002 79860 5 4 0 -155.8262309123 -0.0000067003 0.000549187 0.000350358 16448825 130247 6 5 0 -155.8262311602 -0.0000002478 0.000282018 0.000245571 15710090 151904 7 6 0 -155.8262316452 -0.0000004851 0.000062478 0.000121536 15324086 164329 8 7 0 -155.8262316922 -0.0000000470 0.000015956 0.000032798 14765002 183266 9 8 0 -155.8262316964 -0.0000000042 0.000001513 0.000001836 13977358 201845 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 7.9 SECONDS ( 0.9 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262316964 AFTER 9 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9912311997 TOTAL ELECTRON NUMBER = 30.0000053513 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.12 TOTAL CPU TIME= 503.2 ( 8.4 MIN) TOTAL WALL CLOCK TIME= 507.2 SECONDS, CPU UTILIZATION IS 99.21% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 503.2 ( 8.4 MIN) TOTAL WALL CLOCK TIME= 507.2 SECONDS, CPU UTILIZATION IS 99.21% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.31 TOTAL CPU TIME= 505.5 ( 8.4 MIN) TOTAL WALL CLOCK TIME= 509.5 SECONDS, CPU UTILIZATION IS 99.21% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 505.9 ( 8.4 MIN) TOTAL WALL CLOCK TIME= 509.9 SECONDS, CPU UTILIZATION IS 99.21% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.135597 -0.011822 0.031226 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.112649 -0.007120 0.026776 0.116006 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C -0.000043247 -0.000075019 -0.000019757 2 H 0.000014341 0.000009504 0.000003913 3 C 0.000194335 0.000062286 -0.000082208 4 H 0.000050162 0.000052642 0.000066322 5 C 0.000355131 -0.000477562 -0.000002244 6 H -0.000110241 0.000034319 0.000034232 7 H -0.000457278 0.000400507 -0.000006389 8 C 0.000005425 0.000006546 -0.000003411 9 H -0.000002873 -0.000012877 0.000007426 10 H -0.000005754 -0.000000347 0.000002115 $VIB IVIB= 1 IATOM= 7 ICOORD= 2 E= -155.8262316964 -4.324691818E-05-7.501883506E-05-1.975658478E-05 1.434131698E-05 9.504060934E-06 3.913172680E-06 1.943352742E-04 6.228551980E-05-8.220846781E-05 5.016171129E-05 5.264244594E-05 6.632248535E-05 3.551305875E-04-4.775617345E-04-2.243979080E-06 -1.102409288E-04 3.431927472E-05 3.423192092E-05-4.572782516E-04 4.005072373E-04 -6.388990105E-06 5.424516644E-06 6.546170721E-06-3.410655641E-06-2.873213306E-06 -1.287680297E-05 7.425982707E-06-5.754094791E-06-3.473369124E-07 2.115115754E-06 1.126485893E-01-7.119606419E-03 2.677634777E-02 1 ATOM 7 ------------------- COORD 3 NUCLEAR COORDINATES ------------------- VIB 1 ATOM X Y Z 1 C 0.793773 -0.808112 1.400575 2 H 2.289185 -0.995597 2.802099 3 C 1.446062 0.609240 -0.884553 4 H 3.409625 0.489515 -1.489324 5 C -0.143450 2.042156 -2.212893 6 H 0.464242 3.013674 -3.912111 7 H -2.091534 2.309425 -1.614756 8 C -1.429845 -1.902330 1.850402 9 H -2.943256 -1.862199 0.464672 10 H -1.792911 -2.895773 3.605888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 505.9 ( 8.4 MIN) TOTAL WALL CLOCK TIME= 509.9 SECONDS, CPU UTILIZATION IS 99.22% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 505.9 ( 8.4 MIN) TOTAL WALL CLOCK TIME= 509.9 SECONDS, CPU UTILIZATION IS 99.21% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8257304207 -155.8257304207 0.000883123 0.001461979 17703961 79752 2 1 0 -155.8257393131 -0.0000088924 0.000580111 0.000349687 16480715 128933 3 2 0 -155.8257396987 -0.0000003856 0.000303337 0.000234153 15738195 150830 4 3 0 -155.8257401183 -0.0000004196 0.000057555 0.000083273 15298757 164473 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 5 4 0 -155.8262225641 -0.0004824459 0.000895245 0.001463945 17703900 79762 6 5 0 -155.8262295493 -0.0000069852 0.000453941 0.000353694 16457324 129923 7 6 0 -155.8262299057 -0.0000003564 0.000212692 0.000235894 15729247 151108 8 7 0 -155.8262302542 -0.0000003485 0.000041689 0.000046078 15308462 164049 9 8 0 -155.8262302651 -0.0000000109 0.000021052 0.000026077 14524131 189649 10 9 0 -155.8262302689 -0.0000000038 0.000002163 0.000004832 13717821 211475 11 10 0 -155.8262302691 -0.0000000002 0.000001355 0.000001985 12854131 235358 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 9.1 SECONDS ( 0.8 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262302691 AFTER 11 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9910588599 TOTAL ELECTRON NUMBER = 30.0000055183 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 9.36 TOTAL CPU TIME= 515.3 ( 8.6 MIN) TOTAL WALL CLOCK TIME= 519.3 SECONDS, CPU UTILIZATION IS 99.21% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 515.3 ( 8.6 MIN) TOTAL WALL CLOCK TIME= 519.4 SECONDS, CPU UTILIZATION IS 99.21% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.30 TOTAL CPU TIME= 517.6 ( 8.6 MIN) TOTAL WALL CLOCK TIME= 521.7 SECONDS, CPU UTILIZATION IS 99.21% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 517.9 ( 8.6 MIN) TOTAL WALL CLOCK TIME= 522.0 SECONDS, CPU UTILIZATION IS 99.21% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.135597 -0.012009 0.031412 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.114394 -0.009390 0.027359 0.117995 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C -0.000039008 -0.000066543 -0.000001168 2 H 0.000016605 0.000004938 0.000006912 3 C -0.000150004 0.000058894 0.000068252 4 H 0.000002898 0.000064016 0.000021599 5 C 0.000828930 -0.000024680 -0.000755201 6 H 0.000227460 -0.000038010 -0.000031189 7 H -0.000888301 -0.000006522 0.000688717 8 C 0.000002751 0.000012068 -0.000006725 9 H 0.000000765 0.000000343 0.000005295 10 H -0.000002097 -0.000004504 0.000003509 $VIB IVIB= 1 IATOM= 7 ICOORD= 3 E= -155.8262302691 -3.900790577E-05-6.654261580E-05-1.168006681E-06 1.660509791E-05 4.937948344E-06 6.912462220E-06-1.500039986E-04 5.889357346E-05 6.825155232E-05 2.898235450E-06 6.401581665E-05 2.159917367E-05 8.289300005E-04-2.468002713E-05-7.552010408E-04 2.274600236E-04-3.800955594E-05-3.118932641E-05-8.883010837E-04-6.521805274E-06 6.887165101E-04 2.751402933E-06 1.206799790E-05-6.724567719E-06 7.650454404E-07 3.428364556E-07 5.294617484E-06-2.096817726E-06-4.504168658E-06 3.508625850E-06 1.143942872E-01-9.390024505E-03 2.735902121E-02 1 ATOM 8 ------------------- COORD 1 NUCLEAR COORDINATES ------------------- VIB 1 ATOM X Y Z 1 C 0.793773 -0.808112 1.400575 2 H 2.289185 -0.995597 2.802099 3 C 1.446062 0.609240 -0.884553 4 H 3.409625 0.489515 -1.489324 5 C -0.143450 2.042156 -2.212893 6 H 0.464242 3.013674 -3.912111 7 H -2.091534 2.309425 -1.624756 8 C -1.419845 -1.902330 1.850402 9 H -2.943256 -1.862199 0.464672 10 H -1.792911 -2.895773 3.605888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 518.0 ( 8.6 MIN) TOTAL WALL CLOCK TIME= 522.0 SECONDS, CPU UTILIZATION IS 99.21% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.02 TOTAL CPU TIME= 518.0 ( 8.6 MIN) TOTAL WALL CLOCK TIME= 522.1 SECONDS, CPU UTILIZATION IS 99.22% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8256596898 -155.8256596898 0.001023398 0.001634169 17704401 79764 2 1 0 -155.8256791670 -0.0000194772 0.000591275 0.000439103 16522402 127737 3 2 0 -155.8256789852 0.0000001818 0.000413244 0.000498585 15869697 150004 4 3 0 -155.8256804602 -0.0000014750 0.000092750 0.000146587 15538333 160351 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 5 4 0 -155.8261891657 -0.0005087055 0.000848610 0.001492504 17704534 79763 6 5 0 -155.8261960560 -0.0000068903 0.000408044 0.000344813 16459009 129975 7 6 0 -155.8261964145 -0.0000003585 0.000178059 0.000228007 15732711 151086 8 7 0 -155.8261967564 -0.0000003419 0.000036270 0.000052621 15309094 163877 9 8 0 -155.8261967660 -0.0000000096 0.000018438 0.000031214 14514723 189686 10 9 0 -155.8261967700 -0.0000000040 0.000002104 0.000004926 13763742 210000 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 8.0 SECONDS ( 0.8 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8261967700 AFTER 10 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9924490720 TOTAL ELECTRON NUMBER = 30.0000055622 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.19 TOTAL CPU TIME= 526.2 ( 8.8 MIN) TOTAL WALL CLOCK TIME= 530.3 SECONDS, CPU UTILIZATION IS 99.22% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 526.2 ( 8.8 MIN) TOTAL WALL CLOCK TIME= 530.3 SECONDS, CPU UTILIZATION IS 99.22% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.31 TOTAL CPU TIME= 528.5 ( 8.8 MIN) TOTAL WALL CLOCK TIME= 532.6 SECONDS, CPU UTILIZATION IS 99.22% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 528.8 ( 8.8 MIN) TOTAL WALL CLOCK TIME= 533.0 SECONDS, CPU UTILIZATION IS 99.22% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.137818 -0.012009 0.031226 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.110386 -0.009232 0.028776 0.114448 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C -0.004569850 -0.001862902 0.000528109 2 H -0.000167157 -0.000141162 0.000046849 3 C -0.000020451 -0.000141834 0.000187157 4 H 0.000028124 0.000008014 -0.000001331 5 C -0.000074633 0.000051200 -0.000067332 6 H 0.000013106 -0.000009349 -0.000010477 7 H 0.000001548 0.000015338 0.000010958 8 C 0.007408480 0.002401266 0.000338446 9 H -0.002008486 -0.000021420 -0.001431965 10 H -0.000610682 -0.000299150 0.000399587 $VIB IVIB= 1 IATOM= 8 ICOORD= 1 E= -155.8261967700 -4.569849647E-03-1.862902238E-03 5.281087161E-04-1.671571978E-04-1.411623148E-04 4.684930504E-05-2.045128188E-05-1.418340612E-04 1.871567089E-04 2.812416550E-05 8.014325216E-06-1.331312295E-06-7.463253200E-05 5.119968520E-05-6.733207786E-05 1.310557682E-05-9.348515700E-06-1.047679438E-05 1.548075582E-06 1.533776499E-05 1.095786966E-05 7.408480173E-03 2.401266320E-03 3.384458082E-04-2.008485688E-03 -2.142048012E-05-1.431964750E-03-6.106816439E-04-2.991504856E-04 3.995865270E-04 1.103858963E-01-9.231826411E-03 2.877644519E-02 1 ATOM 8 ------------------- COORD 2 NUCLEAR COORDINATES ------------------- VIB 1 ATOM X Y Z 1 C 0.793773 -0.808112 1.400575 2 H 2.289185 -0.995597 2.802099 3 C 1.446062 0.609240 -0.884553 4 H 3.409625 0.489515 -1.489324 5 C -0.143450 2.042156 -2.212893 6 H 0.464242 3.013674 -3.912111 7 H -2.091534 2.309425 -1.624756 8 C -1.429845 -1.892330 1.850402 9 H -2.943256 -1.862199 0.464672 10 H -1.792911 -2.895773 3.605888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 528.8 ( 8.8 MIN) TOTAL WALL CLOCK TIME= 533.0 SECONDS, CPU UTILIZATION IS 99.22% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 528.8 ( 8.8 MIN) TOTAL WALL CLOCK TIME= 533.0 SECONDS, CPU UTILIZATION IS 99.22% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8257001358 -155.8257001358 0.000858200 0.001508323 17706187 79731 2 1 0 -155.8257161932 -0.0000160574 0.000504453 0.000378191 16511720 128281 3 2 0 -155.8257163771 -0.0000001838 0.000313439 0.000289446 15780881 151600 4 3 0 -155.8257169964 -0.0000006193 0.000082138 0.000136753 15378967 163491 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 5 4 0 -155.8262109010 -0.0004939046 0.000881448 0.001479257 17706328 79728 6 5 0 -155.8262178402 -0.0000069392 0.000421337 0.000349323 16460404 129946 7 6 0 -155.8262182130 -0.0000003727 0.000186217 0.000231233 15732091 151064 8 7 0 -155.8262185541 -0.0000003411 0.000028637 0.000040710 15302817 163968 9 8 0 -155.8262185608 -0.0000000066 0.000016361 0.000028396 14486340 190596 10 9 0 -155.8262185639 -0.0000000031 0.000002022 0.000005723 13675113 212585 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 7.9 SECONDS ( 0.8 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262185639 AFTER 10 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9919595900 TOTAL ELECTRON NUMBER = 30.0000056358 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.19 TOTAL CPU TIME= 537.0 ( 9.0 MIN) TOTAL WALL CLOCK TIME= 541.3 SECONDS, CPU UTILIZATION IS 99.22% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 537.0 ( 9.0 MIN) TOTAL WALL CLOCK TIME= 541.3 SECONDS, CPU UTILIZATION IS 99.22% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.30 TOTAL CPU TIME= 539.3 ( 9.0 MIN) TOTAL WALL CLOCK TIME= 543.6 SECONDS, CPU UTILIZATION IS 99.22% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 539.7 ( 9.0 MIN) TOTAL WALL CLOCK TIME= 544.0 SECONDS, CPU UTILIZATION IS 99.22% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.135597 -0.009788 0.031226 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.113212 -0.016989 0.024265 0.117023 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C -0.001907924 -0.001527275 0.000522538 2 H 0.000038727 0.000053686 0.000021021 3 C -0.000168228 -0.000056760 0.000105727 4 H 0.000019341 -0.000002591 0.000022726 5 C -0.000058640 0.000010568 -0.000008835 6 H 0.000015696 0.000001372 -0.000002573 7 H -0.000008192 -0.000003807 0.000000337 8 C 0.002359543 0.003015628 -0.002043557 9 H -0.000019550 -0.000422954 0.000101761 10 H -0.000270773 -0.001067869 0.001280854 $VIB IVIB= 1 IATOM= 8 ICOORD= 2 E= -155.8262185639 -1.907923771E-03-1.527274551E-03 5.225380402E-04 3.872721503E-05 5.368646689E-05 2.102102106E-05-1.682282310E-04-5.675965917E-05 1.057270981E-04 1.934080410E-05 -2.590914675E-06 2.272584715E-05-5.863951467E-05 1.056838121E-05-8.835092642E-06 1.569555016E-05 1.372455380E-06-2.572836723E-06-8.191932173E-06-3.806822154E-06 3.368290235E-07 2.359542679E-03 3.015628369E-03-2.043556591E-03-1.954985190E-05 -4.229543995E-04 1.017613358E-04-2.707729467E-04-1.067869326E-03 1.280854349E-03 1.132122917E-01-1.698909670E-02 2.426526465E-02 1 ATOM 8 ------------------- COORD 3 NUCLEAR COORDINATES ------------------- VIB 1 ATOM X Y Z 1 C 0.793773 -0.808112 1.400575 2 H 2.289185 -0.995597 2.802099 3 C 1.446062 0.609240 -0.884553 4 H 3.409625 0.489515 -1.489324 5 C -0.143450 2.042156 -2.212893 6 H 0.464242 3.013674 -3.912111 7 H -2.091534 2.309425 -1.624756 8 C -1.429845 -1.902330 1.860402 9 H -2.943256 -1.862199 0.464672 10 H -1.792911 -2.895773 3.605888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 539.7 ( 9.0 MIN) TOTAL WALL CLOCK TIME= 544.0 SECONDS, CPU UTILIZATION IS 99.22% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.02 TOTAL CPU TIME= 539.7 ( 9.0 MIN) TOTAL WALL CLOCK TIME= 544.0 SECONDS, CPU UTILIZATION IS 99.22% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8256997118 -155.8256997118 0.000976391 0.001432436 17698843 79863 2 1 0 -155.8257176437 -0.0000179319 0.000523466 0.000310531 16500865 128234 3 2 0 -155.8257181045 -0.0000004607 0.000249775 0.000280082 15810346 149049 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 4 3 0 -155.8261979337 -0.0004798292 0.000954615 0.001462508 17698818 79866 5 4 0 -155.8262047681 -0.0000068344 0.000420263 0.000349074 16449848 130144 6 5 0 -155.8262051529 -0.0000003848 0.000190465 0.000243458 15727398 150922 7 6 0 -155.8262055247 -0.0000003718 0.000035389 0.000050176 15314008 163500 8 7 0 -155.8262055322 -0.0000000075 0.000014131 0.000032744 14484112 190442 9 8 0 -155.8262055362 -0.0000000040 0.000002683 0.000005282 13761465 209932 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 7.7 SECONDS ( 0.9 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262055362 AFTER 9 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9911902382 TOTAL ELECTRON NUMBER = 30.0000052692 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 7.99 TOTAL CPU TIME= 547.7 ( 9.1 MIN) TOTAL WALL CLOCK TIME= 552.0 SECONDS, CPU UTILIZATION IS 99.22% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 547.7 ( 9.1 MIN) TOTAL WALL CLOCK TIME= 552.0 SECONDS, CPU UTILIZATION IS 99.22% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.31 TOTAL CPU TIME= 550.0 ( 9.2 MIN) TOTAL WALL CLOCK TIME= 554.3 SECONDS, CPU UTILIZATION IS 99.22% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 550.4 ( 9.2 MIN) TOTAL WALL CLOCK TIME= 554.7 SECONDS, CPU UTILIZATION IS 99.22% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.135597 -0.012009 0.033446 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.114190 -0.011488 0.024944 0.117445 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C 0.000584341 0.000512559 -0.001095608 2 H -0.000206693 -0.000080517 0.000080598 3 C 0.000262749 0.000199800 -0.000073516 4 H 0.000031846 0.000023029 -0.000043772 5 C 0.000014099 0.000001563 0.000011830 6 H 0.000008396 -0.000017226 -0.000012471 7 H -0.000008827 0.000012088 0.000007175 8 C 0.000352872 -0.002057419 0.005656817 9 H -0.001392092 0.000118484 -0.001843894 10 H 0.000353310 0.001287640 -0.002687159 $VIB IVIB= 1 IATOM= 8 ICOORD= 3 E= -155.8262055362 5.843408492E-04 5.125585578E-04-1.095608381E-03-2.066925288E-04-8.051743681E-05 8.059781540E-05 2.627487395E-04 1.997995441E-04-7.351589518E-05 3.184593695E-05 2.302894117E-05-4.377236190E-05 1.409877906E-05 1.563237467E-06 1.182961886E-05 8.395594096E-06-1.722571663E-05-1.247059283E-05-8.827155839E-06 1.208849476E-05 7.175362435E-06 3.528716782E-04-2.057419364E-03 5.656817353E-03-1.392091734E-03 1.184836175E-04-1.843894127E-03 3.533098417E-04 1.287640125E-03-2.687158791E-03 1.141895898E-01-1.148773401E-02 2.494418208E-02 1 ATOM 9 ------------------- COORD 1 NUCLEAR COORDINATES ------------------- VIB 1 ATOM X Y Z 1 C 0.793773 -0.808112 1.400575 2 H 2.289185 -0.995597 2.802099 3 C 1.446062 0.609240 -0.884553 4 H 3.409625 0.489515 -1.489324 5 C -0.143450 2.042156 -2.212893 6 H 0.464242 3.013674 -3.912111 7 H -2.091534 2.309425 -1.624756 8 C -1.429845 -1.902330 1.850402 9 H -2.933256 -1.862199 0.464672 10 H -1.792911 -2.895773 3.605888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 550.4 ( 9.2 MIN) TOTAL WALL CLOCK TIME= 554.7 SECONDS, CPU UTILIZATION IS 99.22% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 550.4 ( 9.2 MIN) TOTAL WALL CLOCK TIME= 554.7 SECONDS, CPU UTILIZATION IS 99.22% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8257220951 -155.8257220951 0.000939128 0.001447986 17704113 79742 2 1 0 -155.8257307681 -0.0000086730 0.000456124 0.000287818 16477540 129054 3 2 0 -155.8257306699 0.0000000982 0.000261323 0.000397899 15791528 150561 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 4 3 0 -155.8262153899 -0.0004847200 0.000971015 0.001460629 17704258 79747 5 4 0 -155.8262221524 -0.0000067624 0.000499700 0.000317691 16456393 129976 6 5 0 -155.8262223013 -0.0000001489 0.000264775 0.000246381 15744705 150783 7 6 0 -155.8262227998 -0.0000004985 0.000082837 0.000110163 15406752 162085 8 7 0 -155.8262228526 -0.0000000528 0.000014866 0.000021832 14632075 187091 9 8 0 -155.8262228551 -0.0000000025 0.000004104 0.000005232 13896728 205297 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 7.8 SECONDS ( 0.9 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262228551 AFTER 9 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9925602433 TOTAL ELECTRON NUMBER = 30.0000053737 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.00 TOTAL CPU TIME= 558.4 ( 9.3 MIN) TOTAL WALL CLOCK TIME= 562.8 SECONDS, CPU UTILIZATION IS 99.22% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 558.4 ( 9.3 MIN) TOTAL WALL CLOCK TIME= 562.8 SECONDS, CPU UTILIZATION IS 99.22% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.30 TOTAL CPU TIME= 560.7 ( 9.3 MIN) TOTAL WALL CLOCK TIME= 565.1 SECONDS, CPU UTILIZATION IS 99.22% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 561.1 ( 9.4 MIN) TOTAL WALL CLOCK TIME= 565.5 SECONDS, CPU UTILIZATION IS 99.22% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.135784 -0.012009 0.031226 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.112450 -0.011020 0.024462 0.115607 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C -0.000190204 -0.000015186 -0.000199185 2 H -0.000007652 -0.000053611 0.000004745 3 C 0.000007345 0.000057951 -0.000016180 4 H 0.000014545 -0.000005181 -0.000001791 5 C -0.000019139 0.000005162 0.000007749 6 H 0.000016806 -0.000006017 -0.000002780 7 H -0.000004756 -0.000002868 -0.000000328 8 C -0.002050017 -0.000004735 -0.001450324 9 H 0.002174095 0.000037502 0.001600023 10 H 0.000058976 -0.000013017 0.000058070 $VIB IVIB= 1 IATOM= 9 ICOORD= 1 E= -155.8262228551 -1.902041704E-04-1.518570525E-05-1.991849102E-04-7.651928327E-06-5.361056145E-05 4.745253481E-06 7.345443478E-06 5.795087559E-05-1.617989713E-05 1.454499300E-05 -5.180932059E-06-1.791196755E-06-1.913884785E-05 5.161696096E-06 7.749051459E-06 1.680597656E-05-6.017406714E-06-2.779777846E-06-4.755868751E-06-2.867634049E-06 -3.280680165E-07-2.050016633E-03-4.734528545E-06-1.450323562E-03 2.174095363E-03 3.750153247E-05 1.600022614E-03 5.897567206E-05-1.301733608E-05 5.807049284E-05 1.124501689E-01-1.102005158E-02 2.446205640E-02 1 ATOM 9 ------------------- COORD 2 NUCLEAR COORDINATES ------------------- VIB 1 ATOM X Y Z 1 C 0.793773 -0.808112 1.400575 2 H 2.289185 -0.995597 2.802099 3 C 1.446062 0.609240 -0.884553 4 H 3.409625 0.489515 -1.489324 5 C -0.143450 2.042156 -2.212893 6 H 0.464242 3.013674 -3.912111 7 H -2.091534 2.309425 -1.624756 8 C -1.429845 -1.902330 1.850402 9 H -2.943256 -1.852199 0.464672 10 H -1.792911 -2.895773 3.605888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 561.1 ( 9.4 MIN) TOTAL WALL CLOCK TIME= 565.5 SECONDS, CPU UTILIZATION IS 99.22% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.02 TOTAL CPU TIME= 561.1 ( 9.4 MIN) TOTAL WALL CLOCK TIME= 565.5 SECONDS, CPU UTILIZATION IS 99.22% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8257394250 -155.8257394250 0.000888812 0.001468095 17703579 79764 2 1 0 -155.8257477849 -0.0000083598 0.000472122 0.000348519 16477656 129128 3 2 0 -155.8257481476 -0.0000003627 0.000249767 0.000231028 15727384 151389 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 4 3 0 -155.8262244905 -0.0004763429 0.000862838 0.001451978 17703747 79761 5 4 0 -155.8262314025 -0.0000069120 0.000573380 0.000371726 16455784 129978 6 5 0 -155.8262317408 -0.0000003383 0.000308922 0.000262879 15721549 151343 7 6 0 -155.8262321515 -0.0000004106 0.000049382 0.000072377 15296570 164793 8 7 0 -155.8262321721 -0.0000000206 0.000018237 0.000028108 14592395 187856 9 8 0 -155.8262321766 -0.0000000045 0.000003817 0.000002859 13929922 203483 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 7.8 SECONDS ( 0.9 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262321766 AFTER 9 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9914591131 TOTAL ELECTRON NUMBER = 30.0000051896 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 7.99 TOTAL CPU TIME= 569.1 ( 9.5 MIN) TOTAL WALL CLOCK TIME= 573.5 SECONDS, CPU UTILIZATION IS 99.22% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 569.1 ( 9.5 MIN) TOTAL WALL CLOCK TIME= 573.5 SECONDS, CPU UTILIZATION IS 99.22% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.30 TOTAL CPU TIME= 571.4 ( 9.5 MIN) TOTAL WALL CLOCK TIME= 575.9 SECONDS, CPU UTILIZATION IS 99.22% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.37 TOTAL CPU TIME= 571.8 ( 9.5 MIN) TOTAL WALL CLOCK TIME= 576.2 SECONDS, CPU UTILIZATION IS 99.22% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.135597 -0.011822 0.031226 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.112234 -0.006881 0.026913 0.115621 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C -0.000111059 0.000058991 -0.000110950 2 H -0.000033478 0.000076246 0.000055812 3 C 0.000036592 -0.000057132 -0.000016614 4 H 0.000018083 0.000002179 -0.000005143 5 C -0.000044784 0.000002260 0.000005495 6 H 0.000020306 -0.000002308 -0.000003314 7 H -0.000006179 -0.000004778 0.000007020 8 C -0.000017636 -0.000404344 0.000116554 9 H 0.000039791 0.000311701 -0.000138673 10 H 0.000098364 0.000017183 0.000089812 $VIB IVIB= 1 IATOM= 9 ICOORD= 2 E= -155.8262321766 -1.110590268E-04 5.899127166E-05-1.109502403E-04-3.347839841E-05 7.624604890E-05 5.581213603E-05 3.659203652E-05-5.713221402E-05-1.661353643E-05 1.808279986E-05 2.179139570E-06-5.143314644E-06-4.478422893E-05 2.260422641E-06 5.495214295E-06 2.030596080E-05-2.307710970E-06-3.313829769E-06-6.178702329E-06-4.777548222E-06 7.019765349E-06-1.763588311E-05-4.043436807E-04 1.165540194E-04 3.979107989E-05 3.117013283E-04-1.386726613E-04 9.836436256E-05 1.718294287E-05 8.981244733E-05 1.122340018E-01-6.880743098E-03 2.691288287E-02 1 ATOM 9 ------------------- COORD 3 NUCLEAR COORDINATES ------------------- VIB 1 ATOM X Y Z 1 C 0.793773 -0.808112 1.400575 2 H 2.289185 -0.995597 2.802099 3 C 1.446062 0.609240 -0.884553 4 H 3.409625 0.489515 -1.489324 5 C -0.143450 2.042156 -2.212893 6 H 0.464242 3.013674 -3.912111 7 H -2.091534 2.309425 -1.624756 8 C -1.429845 -1.902330 1.850402 9 H -2.943256 -1.862199 0.474672 10 H -1.792911 -2.895773 3.605888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 571.8 ( 9.5 MIN) TOTAL WALL CLOCK TIME= 576.2 SECONDS, CPU UTILIZATION IS 99.23% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 571.8 ( 9.5 MIN) TOTAL WALL CLOCK TIME= 576.2 SECONDS, CPU UTILIZATION IS 99.23% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8257150207 -155.8257150207 0.000877413 0.001442059 17701726 79831 2 1 0 -155.8257234546 -0.0000084339 0.000449666 0.000284047 16460670 129637 3 2 0 -155.8257234274 0.0000000272 0.000249277 0.000362646 15768995 151076 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 4 3 0 -155.8262168644 -0.0004934370 0.000969380 0.001466517 17701874 79837 5 4 0 -155.8262235806 -0.0000067162 0.000491768 0.000317311 16451511 130131 6 5 0 -155.8262237510 -0.0000001704 0.000258803 0.000236448 15735461 151037 7 6 0 -155.8262242246 -0.0000004736 0.000081816 0.000102602 15393582 162464 8 7 0 -155.8262242738 -0.0000000493 0.000015234 0.000022432 14601678 187814 9 8 0 -155.8262242764 -0.0000000026 0.000004186 0.000005499 13891898 205601 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 7.8 SECONDS ( 0.9 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262242764 AFTER 9 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9924325252 TOTAL ELECTRON NUMBER = 30.0000053146 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 7.98 TOTAL CPU TIME= 579.8 ( 9.7 MIN) TOTAL WALL CLOCK TIME= 584.3 SECONDS, CPU UTILIZATION IS 99.22% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.02 TOTAL CPU TIME= 579.8 ( 9.7 MIN) TOTAL WALL CLOCK TIME= 584.3 SECONDS, CPU UTILIZATION IS 99.23% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.30 TOTAL CPU TIME= 582.1 ( 9.7 MIN) TOTAL WALL CLOCK TIME= 586.6 SECONDS, CPU UTILIZATION IS 99.23% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.37 TOTAL CPU TIME= 582.4 ( 9.7 MIN) TOTAL WALL CLOCK TIME= 587.0 SECONDS, CPU UTILIZATION IS 99.23% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.135597 -0.012009 0.031412 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.109784 -0.009447 0.025697 0.113147 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C 0.000034852 0.000004447 0.000065835 2 H 0.000018716 0.000046281 0.000037099 3 C 0.000026706 -0.000019960 -0.000007992 4 H 0.000014488 -0.000002801 -0.000002595 5 C -0.000035560 0.000007261 0.000006227 6 H 0.000016413 -0.000007216 -0.000002693 7 H -0.000004082 0.000006175 0.000002890 8 C -0.001487834 0.000115741 -0.001878869 9 H 0.001596161 -0.000144066 0.001886697 10 H -0.000179860 -0.000005864 -0.000106599 $VIB IVIB= 1 IATOM= 9 ICOORD= 3 E= -155.8262242764 3.485177645E-05 4.447275268E-06 6.583530374E-05 1.871596636E-05 4.628099368E-05 3.709930371E-05 2.670624053E-05-1.996017198E-05-7.991565832E-06 1.448800693E-05 -2.801042551E-06-2.595338366E-06-3.555960268E-05 7.261498688E-06 6.227132618E-06 1.641315950E-05-7.215877563E-06-2.692818809E-06-4.082344421E-06 6.175425292E-06 2.889567043E-06-1.487834373E-03 1.157410981E-04-1.878869402E-03 1.596160877E-03 -1.440656854E-04 1.886697257E-03-1.798597061E-04-5.863513515E-06-1.065994390E-04 1.097840375E-01-9.447424256E-03 2.569749946E-02 1 ATOM 10 ------------------- COORD 1 NUCLEAR COORDINATES ------------------- VIB 1 ATOM X Y Z 1 C 0.793773 -0.808112 1.400575 2 H 2.289185 -0.995597 2.802099 3 C 1.446062 0.609240 -0.884553 4 H 3.409625 0.489515 -1.489324 5 C -0.143450 2.042156 -2.212893 6 H 0.464242 3.013674 -3.912111 7 H -2.091534 2.309425 -1.624756 8 C -1.429845 -1.902330 1.850402 9 H -2.943256 -1.862199 0.464672 10 H -1.782911 -2.895773 3.605888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 582.4 ( 9.7 MIN) TOTAL WALL CLOCK TIME= 587.0 SECONDS, CPU UTILIZATION IS 99.23% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 582.5 ( 9.7 MIN) TOTAL WALL CLOCK TIME= 587.0 SECONDS, CPU UTILIZATION IS 99.23% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8257343304 -155.8257343304 0.000918696 0.001471143 17703263 79773 2 1 0 -155.8257421687 -0.0000078383 0.000398151 0.000292771 16472415 129297 3 2 0 -155.8257424590 -0.0000002903 0.000185262 0.000214490 15702852 152007 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 4 3 0 -155.8262232146 -0.0004807555 0.000929533 0.001460014 17703355 79771 5 4 0 -155.8262300728 -0.0000068582 0.000429090 0.000341410 16455063 130017 6 5 0 -155.8262304415 -0.0000003687 0.000181905 0.000240000 15728982 151018 7 6 0 -155.8262307992 -0.0000003577 0.000036033 0.000043696 15308440 163776 8 7 0 -155.8262308069 -0.0000000076 0.000018093 0.000028392 14475116 190737 9 8 0 -155.8262308105 -0.0000000036 0.000002549 0.000005430 13724119 211448 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 7.7 SECONDS ( 0.9 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262308105 AFTER 9 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9917576460 TOTAL ELECTRON NUMBER = 30.0000053171 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 7.99 TOTAL CPU TIME= 590.5 ( 9.8 MIN) TOTAL WALL CLOCK TIME= 595.0 SECONDS, CPU UTILIZATION IS 99.23% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 590.5 ( 9.8 MIN) TOTAL WALL CLOCK TIME= 595.1 SECONDS, CPU UTILIZATION IS 99.23% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.30 TOTAL CPU TIME= 592.8 ( 9.9 MIN) TOTAL WALL CLOCK TIME= 597.4 SECONDS, CPU UTILIZATION IS 99.23% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.37 TOTAL CPU TIME= 593.1 ( 9.9 MIN) TOTAL WALL CLOCK TIME= 597.7 SECONDS, CPU UTILIZATION IS 99.23% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.135784 -0.012009 0.031226 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.114098 -0.011155 0.026046 0.117563 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C -0.000030945 -0.000172345 0.000255768 2 H 0.000019810 0.000028838 0.000020776 3 C -0.000013606 -0.000033192 -0.000025514 4 H 0.000012660 -0.000005772 0.000003508 5 C -0.000034473 0.000007200 0.000008504 6 H 0.000019150 -0.000002953 -0.000000511 7 H -0.000005090 -0.000002177 0.000000187 8 C -0.000610883 -0.000257134 0.000328263 9 H 0.000061855 0.000094413 -0.000174220 10 H 0.000581522 0.000343122 -0.000416761 $VIB IVIB= 1 IATOM= 10 ICOORD= 1 E= -155.8262308105 -3.094474186E-05-1.723446171E-04 2.557683738E-04 1.981040580E-05 2.883788681E-05 2.077578753E-05-1.360642892E-05-3.319224588E-05-2.551420742E-05 1.266038993E-05 -5.772247946E-06 3.508240825E-06-3.447325121E-05 7.199920016E-06 8.503527190E-06 1.914983141E-05-2.953091766E-06-5.108275825E-07-5.090250789E-06-2.177028433E-06 1.867413597E-07-6.108832661E-04-2.571339243E-04 3.282632323E-04 6.185516955E-05 9.441329901E-05-1.742197493E-04 5.815221422E-04 3.431220496E-04-4.167611188E-04 1.140977919E-01-1.115468884E-02 2.604566778E-02 1 ATOM 10 ------------------- COORD 2 NUCLEAR COORDINATES ------------------- VIB 1 ATOM X Y Z 1 C 0.793773 -0.808112 1.400575 2 H 2.289185 -0.995597 2.802099 3 C 1.446062 0.609240 -0.884553 4 H 3.409625 0.489515 -1.489324 5 C -0.143450 2.042156 -2.212893 6 H 0.464242 3.013674 -3.912111 7 H -2.091534 2.309425 -1.624756 8 C -1.429845 -1.902330 1.850402 9 H -2.943256 -1.862199 0.464672 10 H -1.792911 -2.885773 3.605888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 593.1 ( 9.9 MIN) TOTAL WALL CLOCK TIME= 597.8 SECONDS, CPU UTILIZATION IS 99.23% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 593.1 ( 9.9 MIN) TOTAL WALL CLOCK TIME= 597.8 SECONDS, CPU UTILIZATION IS 99.23% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8257301314 -155.8257301314 0.000909811 0.001452874 17704589 79735 2 1 0 -155.8257391913 -0.0000090600 0.000428465 0.000269262 16473615 129305 3 2 0 -155.8257393252 -0.0000001339 0.000228862 0.000242542 15744924 151132 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 4 3 0 -155.8262210321 -0.0004817068 0.000979140 0.001463245 17704546 79740 5 4 0 -155.8262277959 -0.0000067639 0.000499450 0.000333727 16456442 129993 6 5 0 -155.8262280014 -0.0000002055 0.000262208 0.000245426 15748530 150546 7 6 0 -155.8262284919 -0.0000004905 0.000081161 0.000107546 15406738 161948 8 7 0 -155.8262285428 -0.0000000510 0.000015133 0.000023035 14625085 187232 9 8 0 -155.8262285455 -0.0000000027 0.000004056 0.000005332 13907095 205266 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 7.8 SECONDS ( 0.9 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262285455 AFTER 9 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9921739165 TOTAL ELECTRON NUMBER = 30.0000053717 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.00 TOTAL CPU TIME= 601.1 ( 10.0 MIN) TOTAL WALL CLOCK TIME= 605.8 SECONDS, CPU UTILIZATION IS 99.23% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 601.2 ( 10.0 MIN) TOTAL WALL CLOCK TIME= 605.8 SECONDS, CPU UTILIZATION IS 99.23% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.30 TOTAL CPU TIME= 603.5 ( 10.1 MIN) TOTAL WALL CLOCK TIME= 608.1 SECONDS, CPU UTILIZATION IS 99.23% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 603.8 ( 10.1 MIN) TOTAL WALL CLOCK TIME= 608.5 SECONDS, CPU UTILIZATION IS 99.23% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.135597 -0.011822 0.031226 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.111245 -0.007742 0.027862 0.114942 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C -0.000015191 -0.000049643 0.000150095 2 H 0.000036815 -0.000051283 -0.000027884 3 C -0.000061135 0.000107325 0.000017522 4 H 0.000010516 -0.000016843 0.000009118 5 C -0.000016286 0.000011607 -0.000006935 6 H 0.000012230 -0.000009875 -0.000006144 7 H -0.000005120 0.000005532 0.000000059 8 C -0.000303741 -0.001047821 0.001261638 9 H -0.000007367 0.000015758 0.000000471 10 H 0.000349279 0.001035242 -0.001397941 $VIB IVIB= 1 IATOM= 10 ICOORD= 2 E= -155.8262285455 -1.519100497E-05-4.964314372E-05 1.500953038E-04 3.681526114E-05-5.128272255E-05 -2.788369279E-05-6.113458995E-05 1.073254917E-04 1.752215018E-05 1.051646201E-05 -1.684292075E-05 9.117586126E-06-1.628593327E-05 1.160665200E-05-6.934942827E-06 1.222956911E-05-9.874572293E-06-6.143723359E-06-5.120003148E-06 5.532371173E-06 5.916598674E-08-3.037411263E-04-1.047821365E-03 1.261638102E-03-7.367208673E-06 1.575824286E-05 4.712842771E-07 3.492785741E-04 1.035241966E-03-1.397941233E-03 1.112449579E-01-7.742202357E-03 2.786208547E-02 1 ATOM 10 ------------------- COORD 3 NUCLEAR COORDINATES ------------------- VIB 1 ATOM X Y Z 1 C 0.793773 -0.808112 1.400575 2 H 2.289185 -0.995597 2.802099 3 C 1.446062 0.609240 -0.884553 4 H 3.409625 0.489515 -1.489324 5 C -0.143450 2.042156 -2.212893 6 H 0.464242 3.013674 -3.912111 7 H -2.091534 2.309425 -1.624756 8 C -1.429845 -1.902330 1.850402 9 H -2.943256 -1.862199 0.464672 10 H -1.792911 -2.895773 3.615888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 603.8 ( 10.1 MIN) TOTAL WALL CLOCK TIME= 608.5 SECONDS, CPU UTILIZATION IS 99.23% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 603.8 ( 10.1 MIN) TOTAL WALL CLOCK TIME= 608.5 SECONDS, CPU UTILIZATION IS 99.23% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8257209553 -155.8257209553 0.001188504 0.001475218 17700104 79865 2 1 0 -155.8257314232 -0.0000104679 0.001019659 0.000560147 16472411 129277 3 2 0 -155.8257317273 -0.0000003041 0.000519391 0.000501503 15865521 148501 4 3 0 -155.8257330506 -0.0000013233 0.000107900 0.000125619 15477251 161662 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 5 4 0 -155.8262123664 -0.0004793158 0.000912325 0.001472953 17700007 79866 6 5 0 -155.8262192710 -0.0000069047 0.000437068 0.000340786 16452358 130143 7 6 0 -155.8262196479 -0.0000003769 0.000195578 0.000231909 15723142 151252 8 7 0 -155.8262199943 -0.0000003464 0.000021593 0.000032488 15293638 164137 9 8 0 -155.8262199998 -0.0000000055 0.000015237 0.000024499 14447443 191594 10 9 0 -155.8262200022 -0.0000000024 0.000002734 0.000006321 13579045 215126 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 7.9 SECONDS ( 0.8 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262200022 AFTER 10 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9902155626 TOTAL ELECTRON NUMBER = 30.0000053596 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.20 TOTAL CPU TIME= 612.0 ( 10.2 MIN) TOTAL WALL CLOCK TIME= 616.8 SECONDS, CPU UTILIZATION IS 99.23% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 612.0 ( 10.2 MIN) TOTAL WALL CLOCK TIME= 616.8 SECONDS, CPU UTILIZATION IS 99.23% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.30 TOTAL CPU TIME= 614.3 ( 10.2 MIN) TOTAL WALL CLOCK TIME= 619.1 SECONDS, CPU UTILIZATION IS 99.23% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 614.7 ( 10.2 MIN) TOTAL WALL CLOCK TIME= 619.5 SECONDS, CPU UTILIZATION IS 99.23% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.135597 -0.012009 0.031412 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.113032 -0.007436 0.024805 0.115960 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C -0.000039043 -0.000009537 0.000002344 2 H 0.000029468 -0.000026908 0.000001643 3 C -0.000006565 0.000052914 0.000019899 4 H 0.000013645 -0.000004671 -0.000000095 5 C -0.000020605 0.000006522 0.000000810 6 H 0.000014445 -0.000006540 -0.000005613 7 H -0.000006615 0.000001436 0.000001132 8 C 0.000376105 0.001278206 -0.002642814 9 H 0.000056259 0.000081348 -0.000105699 10 H -0.000417094 -0.001372770 0.002728393 $VIB IVIB= 1 IATOM= 10 ICOORD= 3 E= -155.8262200022 -3.904266114E-05-9.536938437E-06 2.343775455E-06 2.946798433E-05-2.690811174E-05 1.643199356E-06-6.565235948E-06 5.291392982E-05 1.989943493E-05 1.364511246E-05 -4.670748891E-06-9.539539888E-08-2.060536610E-05 6.521521431E-06 8.102228375E-07 1.444458176E-05-6.540066493E-06-5.612671051E-06-6.614500949E-06 1.435975554E-06 1.131593147E-06 3.761050767E-04 1.278205579E-03-2.642814093E-03 5.625940229E-05 8.134842026E-05-1.056993523E-04-4.170943934E-04-1.372769561E-03 2.728393286E-03 1.130316576E-01-7.435640795E-03 2.480545848E-02 1 ATOM 1 ------------------- COORD 1 NUCLEAR COORDINATES ------------------- VIB 2 ATOM X Y Z 1 C 0.783773 -0.808112 1.400575 2 H 2.289185 -0.995597 2.802099 3 C 1.446062 0.609240 -0.884553 4 H 3.409625 0.489515 -1.489324 5 C -0.143450 2.042156 -2.212893 6 H 0.464242 3.013674 -3.912111 7 H -2.091534 2.309425 -1.624756 8 C -1.429845 -1.902330 1.850402 9 H -2.943256 -1.862199 0.464672 10 H -1.792911 -2.895773 3.605888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 614.7 ( 10.2 MIN) TOTAL WALL CLOCK TIME= 619.5 SECONDS, CPU UTILIZATION IS 99.23% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 614.7 ( 10.2 MIN) TOTAL WALL CLOCK TIME= 619.5 SECONDS, CPU UTILIZATION IS 99.23% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8256482984 -155.8256482984 0.001029177 0.001721341 17703085 79773 2 1 0 -155.8256689335 -0.0000206351 0.000529866 0.000413828 16541291 127233 3 2 0 -155.8256684452 0.0000004883 0.000400537 0.000602186 15941827 147133 4 3 0 -155.8256702182 -0.0000017730 0.000099945 0.000156219 15669930 155717 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 5 4 0 -155.8261873924 -0.0005171742 0.000811195 0.001468987 17703449 79766 6 5 0 -155.8261942204 -0.0000068280 0.000481345 0.000343959 16454290 130039 7 6 0 -155.8261945691 -0.0000003487 0.000231143 0.000221687 15706585 151771 8 7 0 -155.8261949138 -0.0000003447 0.000034765 0.000067243 15235805 165632 9 8 0 -155.8261949268 -0.0000000130 0.000016147 0.000039568 14593304 189064 10 9 0 -155.8261949318 -0.0000000049 0.000001247 0.000002128 13933277 203284 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 7.9 SECONDS ( 0.8 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8261949318 AFTER 10 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9923200141 TOTAL ELECTRON NUMBER = 30.0000055020 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.20 TOTAL CPU TIME= 622.9 ( 10.4 MIN) TOTAL WALL CLOCK TIME= 627.7 SECONDS, CPU UTILIZATION IS 99.23% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 622.9 ( 10.4 MIN) TOTAL WALL CLOCK TIME= 627.7 SECONDS, CPU UTILIZATION IS 99.23% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.31 TOTAL CPU TIME= 625.2 ( 10.4 MIN) TOTAL WALL CLOCK TIME= 630.1 SECONDS, CPU UTILIZATION IS 99.23% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 625.6 ( 10.4 MIN) TOTAL WALL CLOCK TIME= 630.4 SECONDS, CPU UTILIZATION IS 99.23% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.133377 -0.012009 0.031226 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.111880 -0.010455 0.021966 0.114494 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C -0.007755819 -0.002064828 -0.000401935 2 H 0.001983604 -0.000184327 0.001343339 3 C 0.001123483 0.000157285 -0.000197118 4 H 0.000067879 0.000172292 -0.000249313 5 C -0.000191071 -0.000065918 0.000111955 6 H 0.000024188 -0.000072508 -0.000005161 7 H -0.000001753 0.000033145 0.000027915 8 C 0.004549804 0.001930487 -0.000618887 9 H 0.000181800 0.000093943 -0.000041127 10 H 0.000017884 0.000000428 0.000030331 $VIB IVIB= 2 IATOM= 1 ICOORD= 1 E= -155.8261949318 -7.755819002E-03-2.064827932E-03-4.019352560E-04 1.983604460E-03-1.843272812E-04 1.343339087E-03 1.123482827E-03 1.572848514E-04-1.971175061E-04 6.787851291E-05 1.722923874E-04-2.493133965E-04-1.910705431E-04-6.591811125E-05 1.119548082E-04 2.418798479E-05-7.250804385E-05-5.160668396E-06-1.752518770E-06 3.314512507E-05 2.791537120E-05 4.549804152E-03 1.930487270E-03-6.188866043E-04 1.817997755E-04 9.394337261E-05-4.112665013E-05 1.788435112E-05 4.283612336E-07 3.033081468E-05 1.118796013E-01-1.045450643E-02 2.196649563E-02 1 ATOM 1 ------------------- COORD 2 NUCLEAR COORDINATES ------------------- VIB 2 ATOM X Y Z 1 C 0.793773 -0.818112 1.400575 2 H 2.289185 -0.995597 2.802099 3 C 1.446062 0.609240 -0.884553 4 H 3.409625 0.489515 -1.489324 5 C -0.143450 2.042156 -2.212893 6 H 0.464242 3.013674 -3.912111 7 H -2.091534 2.309425 -1.624756 8 C -1.429845 -1.902330 1.850402 9 H -2.943256 -1.862199 0.464672 10 H -1.792911 -2.895773 3.605888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 625.6 ( 10.4 MIN) TOTAL WALL CLOCK TIME= 630.4 SECONDS, CPU UTILIZATION IS 99.23% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 625.6 ( 10.4 MIN) TOTAL WALL CLOCK TIME= 630.4 SECONDS, CPU UTILIZATION IS 99.23% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8256645515 -155.8256645515 0.000995154 0.001555679 17701277 79830 2 1 0 -155.8256830082 -0.0000184567 0.000730665 0.000321018 16524541 128125 3 2 0 -155.8256830020 0.0000000062 0.000385278 0.000431157 15838810 149709 4 3 0 -155.8256838783 -0.0000008763 0.000080449 0.000184968 15535326 159375 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 5 4 0 -155.8262105353 -0.0005266570 0.000812524 0.001461856 17701265 79838 6 5 0 -155.8262173836 -0.0000068482 0.000488604 0.000362350 16451131 130135 7 6 0 -155.8262177401 -0.0000003566 0.000248323 0.000239813 15705888 151755 8 7 0 -155.8262180976 -0.0000003575 0.000038799 0.000067106 15243126 165422 9 8 0 -155.8262181111 -0.0000000135 0.000016718 0.000039221 14582413 189418 10 9 0 -155.8262181161 -0.0000000050 0.000001771 0.000002225 13936132 203357 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 8.0 SECONDS ( 0.8 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262181161 AFTER 10 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9917759767 TOTAL ELECTRON NUMBER = 30.0000055057 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.19 TOTAL CPU TIME= 633.8 ( 10.6 MIN) TOTAL WALL CLOCK TIME= 638.7 SECONDS, CPU UTILIZATION IS 99.23% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.02 TOTAL CPU TIME= 633.8 ( 10.6 MIN) TOTAL WALL CLOCK TIME= 638.7 SECONDS, CPU UTILIZATION IS 99.23% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.30 TOTAL CPU TIME= 636.1 ( 10.6 MIN) TOTAL WALL CLOCK TIME= 641.0 SECONDS, CPU UTILIZATION IS 99.23% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 636.5 ( 10.6 MIN) TOTAL WALL CLOCK TIME= 641.4 SECONDS, CPU UTILIZATION IS 99.23% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.135597 -0.014229 0.031226 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.109311 -0.008505 0.028376 0.113253 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C -0.002034563 -0.003096941 0.001813890 2 H -0.000124671 0.000436311 -0.000216078 3 C 0.000226030 0.001123842 -0.000762005 4 H 0.000008438 -0.000018745 0.000010535 5 C -0.000044154 0.000113592 -0.000259786 6 H -0.000024567 -0.000079838 -0.000063657 7 H 0.000030323 0.000058231 0.000048605 8 C 0.001812888 0.001520519 -0.000544495 9 H -0.000001677 -0.000083478 -0.000019693 10 H 0.000151952 0.000026508 -0.000007317 $VIB IVIB= 2 IATOM= 1 ICOORD= 2 E= -155.8262181161 -2.034563115E-03-3.096940902E-03 1.813889621E-03-1.246710926E-04 4.363105881E-04 -2.160775628E-04 2.260299385E-04 1.123842320E-03-7.620050622E-04 8.438213552E-06 -1.874549366E-05 1.053476634E-05-4.415365853E-05 1.135921430E-04-2.597857127E-04 -2.456748830E-05-7.983765082E-05-6.365667836E-05 3.032348969E-05 5.823056793E-05 4.860510711E-05 1.812887975E-03 1.520519081E-03-5.444949131E-04-1.676710029E-06 -8.347833251E-05-1.969250992E-05 1.519524473E-04 2.650767880E-05-7.317055422E-06 1.093105567E-01-8.504914045E-03 2.837590990E-02 1 ATOM 1 ------------------- COORD 3 NUCLEAR COORDINATES ------------------- VIB 2 ATOM X Y Z 1 C 0.793773 -0.808112 1.390575 2 H 2.289185 -0.995597 2.802099 3 C 1.446062 0.609240 -0.884553 4 H 3.409625 0.489515 -1.489324 5 C -0.143450 2.042156 -2.212893 6 H 0.464242 3.013674 -3.912111 7 H -2.091534 2.309425 -1.624756 8 C -1.429845 -1.902330 1.850402 9 H -2.943256 -1.862199 0.464672 10 H -1.792911 -2.895773 3.605888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 636.5 ( 10.6 MIN) TOTAL WALL CLOCK TIME= 641.4 SECONDS, CPU UTILIZATION IS 99.23% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 636.5 ( 10.6 MIN) TOTAL WALL CLOCK TIME= 641.4 SECONDS, CPU UTILIZATION IS 99.23% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8257472459 -155.8257472459 0.001321544 0.001557782 17704693 79742 2 1 0 -155.8257669293 -0.0000196835 0.000706346 0.000395588 16529117 127570 3 2 0 -155.8257672127 -0.0000002833 0.000359030 0.000438281 15908255 147812 4 3 0 -155.8257685131 -0.0000013004 0.000101378 0.000217342 15574059 158030 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 5 4 0 -155.8262005844 -0.0004320713 0.000953487 0.001468748 17704782 79742 6 5 0 -155.8262075596 -0.0000069752 0.000441849 0.000347120 16459094 129948 7 6 0 -155.8262079299 -0.0000003703 0.000196204 0.000234207 15737635 150894 8 7 0 -155.8262082893 -0.0000003594 0.000034202 0.000050736 15322103 163622 9 8 0 -155.8262082985 -0.0000000092 0.000018428 0.000031085 14527725 189554 10 9 0 -155.8262083025 -0.0000000040 0.000002571 0.000005169 13762389 210066 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 8.0 SECONDS ( 0.8 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262083025 AFTER 10 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9915055787 TOTAL ELECTRON NUMBER = 30.0000050836 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.20 TOTAL CPU TIME= 644.7 ( 10.7 MIN) TOTAL WALL CLOCK TIME= 649.6 SECONDS, CPU UTILIZATION IS 99.23% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 644.7 ( 10.7 MIN) TOTAL WALL CLOCK TIME= 649.7 SECONDS, CPU UTILIZATION IS 99.23% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.31 TOTAL CPU TIME= 647.0 ( 10.8 MIN) TOTAL WALL CLOCK TIME= 652.0 SECONDS, CPU UTILIZATION IS 99.23% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.37 TOTAL CPU TIME= 647.3 ( 10.8 MIN) TOTAL WALL CLOCK TIME= 652.3 SECONDS, CPU UTILIZATION IS 99.23% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.135597 -0.012009 0.029005 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.110456 -0.006195 0.022355 0.112866 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C -0.000426635 0.001815970 -0.005094049 2 H 0.001338349 -0.000216559 0.001821305 3 C -0.000389069 -0.000770905 0.002006769 4 H 0.000008457 -0.000076091 0.000028749 5 C 0.000031269 -0.000188910 0.000224089 6 H 0.000009997 -0.000058169 -0.000038276 7 H -0.000014444 0.000029390 0.000009299 8 C -0.000518201 -0.000502766 0.001089082 9 H 0.000208769 0.000112720 -0.000054233 10 H -0.000248492 -0.000144680 0.000007266 $VIB IVIB= 2 IATOM= 1 ICOORD= 3 E= -155.8262083025 -4.266349969E-04 1.815970268E-03-5.094049420E-03 1.338348773E-03-2.165591305E-04 1.821305094E-03-3.890692584E-04-7.709050203E-04 2.006768588E-03 8.456775171E-06 -7.609112245E-05 2.874853029E-05 3.126945525E-05-1.889100516E-04 2.240887176E-04 9.997292635E-06-5.816894364E-05-3.827567118E-05-1.444391822E-05 2.939036669E-05 9.298660370E-06-5.182009347E-04-5.027661318E-04 1.089081881E-03 2.087688901E-04 1.127200482E-04-5.423287870E-05-2.484920783E-04-1.446802823E-04 7.266499177E-06 1.104561410E-01-6.195415937E-03 2.235508612E-02 1 ATOM 2 ------------------- COORD 1 NUCLEAR COORDINATES ------------------- VIB 2 ATOM X Y Z 1 C 0.793773 -0.808112 1.400575 2 H 2.279185 -0.995597 2.802099 3 C 1.446062 0.609240 -0.884553 4 H 3.409625 0.489515 -1.489324 5 C -0.143450 2.042156 -2.212893 6 H 0.464242 3.013674 -3.912111 7 H -2.091534 2.309425 -1.624756 8 C -1.429845 -1.902330 1.850402 9 H -2.943256 -1.862199 0.464672 10 H -1.792911 -2.895773 3.605888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 647.3 ( 10.8 MIN) TOTAL WALL CLOCK TIME= 652.3 SECONDS, CPU UTILIZATION IS 99.23% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 647.3 ( 10.8 MIN) TOTAL WALL CLOCK TIME= 652.4 SECONDS, CPU UTILIZATION IS 99.23% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8257210573 -155.8257210573 0.000865925 0.001492433 17703628 79762 2 1 0 -155.8257297240 -0.0000086667 0.000606275 0.000347759 16470086 129131 3 2 0 -155.8257295628 0.0000001612 0.000345858 0.000389630 15763601 151520 4 3 0 -155.8257305251 -0.0000009623 0.000071763 0.000116203 15439611 162429 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 5 4 0 -155.8262156685 -0.0004851434 0.000871470 0.001469116 17703644 79770 6 5 0 -155.8262226031 -0.0000069346 0.000438764 0.000345964 16456631 129959 7 6 0 -155.8262229697 -0.0000003666 0.000206103 0.000227831 15718470 151367 8 7 0 -155.8262232996 -0.0000003299 0.000021338 0.000028805 15278350 164512 9 8 0 -155.8262233050 -0.0000000054 0.000015958 0.000018666 14438309 192006 10 9 0 -155.8262233066 -0.0000000016 0.000002658 0.000005433 13424062 218756 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 7.9 SECONDS ( 0.8 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262233066 AFTER 10 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9925298227 TOTAL ELECTRON NUMBER = 30.0000053052 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.19 TOTAL CPU TIME= 655.5 ( 10.9 MIN) TOTAL WALL CLOCK TIME= 660.6 SECONDS, CPU UTILIZATION IS 99.23% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 655.5 ( 10.9 MIN) TOTAL WALL CLOCK TIME= 660.6 SECONDS, CPU UTILIZATION IS 99.23% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.30 TOTAL CPU TIME= 657.8 ( 11.0 MIN) TOTAL WALL CLOCK TIME= 662.9 SECONDS, CPU UTILIZATION IS 99.23% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 658.2 ( 11.0 MIN) TOTAL WALL CLOCK TIME= 663.3 SECONDS, CPU UTILIZATION IS 99.23% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.135411 -0.012009 0.031226 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.113137 -0.009668 0.028096 0.116974 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C 0.001984366 -0.000167394 0.001371050 2 H -0.002101116 0.000116463 -0.001501445 3 C -0.000064061 0.000022995 -0.000064139 4 H 0.000008013 -0.000010522 0.000001443 5 C -0.000031891 0.000023205 -0.000007006 6 H 0.000013928 -0.000000829 -0.000003660 7 H -0.000007368 0.000004735 0.000000957 8 C 0.000175718 -0.000009422 0.000210693 9 H 0.000026713 0.000044445 0.000001779 10 H -0.000004302 -0.000023677 -0.000009673 $VIB IVIB= 2 IATOM= 2 ICOORD= 1 E= -155.8262233066 1.984365791E-03-1.673937363E-04 1.371049933E-03-2.101115987E-03 1.164633812E-04 -1.501445225E-03-6.406140960E-05 2.299545882E-05-6.413864280E-05 8.012838475E-06 -1.052177502E-05 1.442874060E-06-3.189064009E-05 2.320484897E-05-7.005911363E-06 1.392778232E-05-8.292718337E-07-3.659873226E-06-7.367737850E-06 4.735039479E-06 9.574975291E-07 1.757182006E-04-9.421896417E-06 2.106933132E-04 2.671316378E-05 4.444490483E-05 1.779217875E-06-4.302002598E-06-2.367695376E-05-9.673182591E-06 1.131368333E-01-9.667971334E-03 2.809605815E-02 1 ATOM 2 ------------------- COORD 2 NUCLEAR COORDINATES ------------------- VIB 2 ATOM X Y Z 1 C 0.793773 -0.808112 1.400575 2 H 2.289185 -1.005597 2.802099 3 C 1.446062 0.609240 -0.884553 4 H 3.409625 0.489515 -1.489324 5 C -0.143450 2.042156 -2.212893 6 H 0.464242 3.013674 -3.912111 7 H -2.091534 2.309425 -1.624756 8 C -1.429845 -1.902330 1.850402 9 H -2.943256 -1.862199 0.464672 10 H -1.792911 -2.895773 3.605888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 658.2 ( 11.0 MIN) TOTAL WALL CLOCK TIME= 663.3 SECONDS, CPU UTILIZATION IS 99.23% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.02 TOTAL CPU TIME= 658.2 ( 11.0 MIN) TOTAL WALL CLOCK TIME= 663.3 SECONDS, CPU UTILIZATION IS 99.23% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8257396771 -155.8257396771 0.000912381 0.001449871 17701933 79823 2 1 0 -155.8257479660 -0.0000082890 0.000477615 0.000353334 16462454 129663 3 2 0 -155.8257483542 -0.0000003882 0.000230795 0.000223741 15724217 151347 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 4 3 0 -155.8262242433 -0.0004758890 0.000872702 0.001451615 17702138 79824 5 4 0 -155.8262310913 -0.0000068481 0.000530820 0.000362834 16452798 130127 6 5 0 -155.8262314548 -0.0000003635 0.000277474 0.000248813 15717380 151364 7 6 0 -155.8262318323 -0.0000003775 0.000044732 0.000053260 15279311 164822 8 7 0 -155.8262318428 -0.0000000105 0.000016745 0.000026844 14511484 190583 9 8 0 -155.8262318469 -0.0000000041 0.000002720 0.000002712 13840825 205752 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 7.8 SECONDS ( 0.9 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262318469 AFTER 9 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9913228889 TOTAL ELECTRON NUMBER = 30.0000053722 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 7.99 TOTAL CPU TIME= 666.2 ( 11.1 MIN) TOTAL WALL CLOCK TIME= 671.4 SECONDS, CPU UTILIZATION IS 99.23% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 666.2 ( 11.1 MIN) TOTAL WALL CLOCK TIME= 671.4 SECONDS, CPU UTILIZATION IS 99.23% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.30 TOTAL CPU TIME= 668.5 ( 11.1 MIN) TOTAL WALL CLOCK TIME= 673.7 SECONDS, CPU UTILIZATION IS 99.23% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 668.9 ( 11.1 MIN) TOTAL WALL CLOCK TIME= 674.0 SECONDS, CPU UTILIZATION IS 99.23% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.135597 -0.012195 0.031226 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.112423 -0.012951 0.024572 0.115803 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C -0.000206892 0.000416484 -0.000220544 2 H 0.000131755 -0.000376065 0.000318291 3 C -0.000117704 0.000023111 -0.000143832 4 H 0.000020714 -0.000002962 0.000000283 5 C -0.000003322 -0.000000480 -0.000015567 6 H 0.000015195 0.000008254 -0.000003918 7 H -0.000009237 -0.000003567 -0.000000408 8 C 0.000136987 -0.000037309 0.000071098 9 H 0.000059079 -0.000078375 -0.000039011 10 H -0.000026574 0.000050908 0.000033608 $VIB IVIB= 2 IATOM= 2 ICOORD= 2 E= -155.8262318469 -2.068924708E-04 4.164844562E-04-2.205440689E-04 1.317551511E-04-3.760648756E-04 3.182912567E-04-1.177042619E-04 2.311120875E-05-1.438322335E-04 2.071443606E-05 -2.961538178E-06 2.832650141E-07-3.322171057E-06-4.799263362E-07-1.556695121E-05 1.519499862E-05 8.253841077E-06-3.917588526E-06-9.237328051E-06-3.567384048E-06 -4.084992053E-07 1.369866789E-04-3.730885330E-05 7.109821053E-05 5.907853174E-05 -7.837497053E-05-3.901120847E-05-2.657356452E-05 5.090804187E-05 3.360781758E-05 1.124225308E-01-1.295123116E-02 2.457191644E-02 1 ATOM 2 ------------------- COORD 3 NUCLEAR COORDINATES ------------------- VIB 2 ATOM X Y Z 1 C 0.793773 -0.808112 1.400575 2 H 2.289185 -0.995597 2.792099 3 C 1.446062 0.609240 -0.884553 4 H 3.409625 0.489515 -1.489324 5 C -0.143450 2.042156 -2.212893 6 H 0.464242 3.013674 -3.912111 7 H -2.091534 2.309425 -1.624756 8 C -1.429845 -1.902330 1.850402 9 H -2.943256 -1.862199 0.464672 10 H -1.792911 -2.895773 3.605888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 668.9 ( 11.1 MIN) TOTAL WALL CLOCK TIME= 674.1 SECONDS, CPU UTILIZATION IS 99.23% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 668.9 ( 11.1 MIN) TOTAL WALL CLOCK TIME= 674.1 SECONDS, CPU UTILIZATION IS 99.23% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8257124759 -155.8257124759 0.000805170 0.001502576 17703938 79758 2 1 0 -155.8257210636 -0.0000085877 0.000568385 0.000339419 16470006 129204 3 2 0 -155.8257209568 0.0000001068 0.000335033 0.000356439 15759898 151543 4 3 0 -155.8257218179 -0.0000008611 0.000069191 0.000116193 15416513 162904 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 5 4 0 -155.8262166911 -0.0004948732 0.000873112 0.001470105 17704096 79764 6 5 0 -155.8262236220 -0.0000069309 0.000432681 0.000342148 16456876 129989 7 6 0 -155.8262239877 -0.0000003657 0.000199503 0.000224199 15719245 151357 8 7 0 -155.8262243159 -0.0000003282 0.000022443 0.000029485 15280545 164458 9 8 0 -155.8262243213 -0.0000000054 0.000015545 0.000018410 14436324 191881 10 9 0 -155.8262243230 -0.0000000017 0.000002655 0.000006112 13457844 218335 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 8.0 SECONDS ( 0.8 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262243230 AFTER 10 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9924665141 TOTAL ELECTRON NUMBER = 30.0000054137 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.18 TOTAL CPU TIME= 677.1 ( 11.3 MIN) TOTAL WALL CLOCK TIME= 682.3 SECONDS, CPU UTILIZATION IS 99.23% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 677.1 ( 11.3 MIN) TOTAL WALL CLOCK TIME= 682.3 SECONDS, CPU UTILIZATION IS 99.23% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.31 TOTAL CPU TIME= 679.4 ( 11.3 MIN) TOTAL WALL CLOCK TIME= 684.6 SECONDS, CPU UTILIZATION IS 99.23% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.37 TOTAL CPU TIME= 679.8 ( 11.3 MIN) TOTAL WALL CLOCK TIME= 685.0 SECONDS, CPU UTILIZATION IS 99.24% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.135597 -0.012009 0.031039 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.114466 -0.011829 0.026521 0.118092 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C 0.001365958 -0.000249262 0.001842322 2 H -0.001489912 0.000314021 -0.001888195 3 C 0.000208697 -0.000013303 0.000124140 4 H 0.000010756 -0.000002552 -0.000010820 5 C -0.000053079 -0.000012396 0.000039649 6 H 0.000020669 -0.000018427 -0.000004287 7 H -0.000005021 0.000005787 0.000001276 8 C -0.000048284 -0.000001006 -0.000086803 9 H 0.000004842 -0.000054586 -0.000026182 10 H -0.000014625 0.000031725 0.000008899 $VIB IVIB= 2 IATOM= 2 ICOORD= 3 E= -155.8262243230 1.365957829E-03-2.492623763E-04 1.842321981E-03-1.489912423E-03 3.140207725E-04 -1.888195369E-03 2.086973494E-04-1.330326281E-05 1.241400975E-04 1.075595728E-05 -2.551521245E-06-1.081972751E-05-5.307932657E-05-1.239648715E-05 3.964878360E-05 2.066851002E-05-1.842668143E-05-4.287428627E-06-5.021469475E-06 5.786741056E-06 1.276439095E-06-4.828362366E-05-1.005779933E-06-8.680255542E-05 4.842066593E-06 -5.458592018E-05-2.618171437E-05-1.462486965E-05 3.172451543E-05 8.899493967E-06 1.144661852E-01-1.182919365E-02 2.652140318E-02 1 ATOM 3 ------------------- COORD 1 NUCLEAR COORDINATES ------------------- VIB 2 ATOM X Y Z 1 C 0.793773 -0.808112 1.400575 2 H 2.289185 -0.995597 2.802099 3 C 1.436062 0.609240 -0.884553 4 H 3.409625 0.489515 -1.489324 5 C -0.143450 2.042156 -2.212893 6 H 0.464242 3.013674 -3.912111 7 H -2.091534 2.309425 -1.624756 8 C -1.429845 -1.902330 1.850402 9 H -2.943256 -1.862199 0.464672 10 H -1.792911 -2.895773 3.605888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 679.8 ( 11.3 MIN) TOTAL WALL CLOCK TIME= 685.0 SECONDS, CPU UTILIZATION IS 99.24% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 679.8 ( 11.3 MIN) TOTAL WALL CLOCK TIME= 685.0 SECONDS, CPU UTILIZATION IS 99.24% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8256805101 -155.8256805101 0.001090150 0.001551787 17704085 79747 2 1 0 -155.8257004821 -0.0000199721 0.000658475 0.000461801 16547483 126700 3 2 0 -155.8257002700 0.0000002121 0.000362946 0.000688395 15896081 148750 4 3 0 -155.8257015964 -0.0000013264 0.000115911 0.000163854 15600490 157859 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 5 4 0 -155.8261907989 -0.0004892025 0.000873220 0.001448146 17704208 79751 6 5 0 -155.8261977134 -0.0000069145 0.000494825 0.000348148 16455625 130008 7 6 0 -155.8261980820 -0.0000003686 0.000250502 0.000229108 15715913 151535 8 7 0 -155.8261984332 -0.0000003512 0.000035102 0.000057015 15252947 165263 9 8 0 -155.8261984429 -0.0000000097 0.000016683 0.000036661 14551898 190389 10 9 0 -155.8261984474 -0.0000000045 0.000001972 0.000002452 13884767 204774 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 7.9 SECONDS ( 0.8 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8261984474 AFTER 10 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9921833649 TOTAL ELECTRON NUMBER = 30.0000051849 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.19 TOTAL CPU TIME= 688.0 ( 11.5 MIN) TOTAL WALL CLOCK TIME= 693.3 SECONDS, CPU UTILIZATION IS 99.23% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 688.0 ( 11.5 MIN) TOTAL WALL CLOCK TIME= 693.3 SECONDS, CPU UTILIZATION IS 99.23% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.31 TOTAL CPU TIME= 690.3 ( 11.5 MIN) TOTAL WALL CLOCK TIME= 695.6 SECONDS, CPU UTILIZATION IS 99.24% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 690.7 ( 11.5 MIN) TOTAL WALL CLOCK TIME= 696.0 SECONDS, CPU UTILIZATION IS 99.24% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.133377 -0.012009 0.031226 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.109153 -0.010888 0.030348 0.113815 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C 0.001100504 0.000202327 -0.000379411 2 H -0.000053505 -0.000122195 0.000207998 3 C -0.007046405 0.001722115 -0.000306821 4 H 0.002996978 -0.000141171 -0.000775976 5 C 0.002865652 -0.001768839 0.001441933 6 H -0.000065332 0.000076745 -0.000076588 7 H 0.000161352 -0.000186453 0.000158290 8 C 0.000020061 0.000187594 -0.000269613 9 H 0.000001638 -0.000034219 -0.000016717 10 H 0.000019057 0.000064096 0.000016903 $VIB IVIB= 2 IATOM= 3 ICOORD= 1 E= -155.8261984474 1.100504476E-03 2.023265389E-04-3.794107104E-04-5.350524192E-05-1.221946663E-04 2.079983425E-04-7.046405218E-03 1.722114710E-03-3.068209611E-04 2.996977695E-03 -1.411706604E-04-7.759756517E-04 2.865652241E-03-1.768838913E-03 1.441933302E-03 -6.533204846E-05 7.674495560E-05-7.658791501E-05 1.613520997E-04-1.864531382E-04 1.582902725E-04 2.006087953E-05 1.875938699E-04-2.696126227E-04 1.637715796E-06 -3.421893655E-05-1.671706974E-05 1.905740224E-05 6.409624062E-05 1.690301388E-05 1.091528702E-01-1.088837036E-02 3.034817328E-02 1 ATOM 3 ------------------- COORD 2 NUCLEAR COORDINATES ------------------- VIB 2 ATOM X Y Z 1 C 0.793773 -0.808112 1.400575 2 H 2.289185 -0.995597 2.802099 3 C 1.446062 0.599240 -0.884553 4 H 3.409625 0.489515 -1.489324 5 C -0.143450 2.042156 -2.212893 6 H 0.464242 3.013674 -3.912111 7 H -2.091534 2.309425 -1.624756 8 C -1.429845 -1.902330 1.850402 9 H -2.943256 -1.862199 0.464672 10 H -1.792911 -2.895773 3.605888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 690.7 ( 11.5 MIN) TOTAL WALL CLOCK TIME= 696.0 SECONDS, CPU UTILIZATION IS 99.24% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 690.7 ( 11.5 MIN) TOTAL WALL CLOCK TIME= 696.0 SECONDS, CPU UTILIZATION IS 99.23% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8257394937 -155.8257394937 0.001090190 0.001607276 17703674 79765 2 1 0 -155.8257574035 -0.0000179097 0.001014848 0.000402472 16537060 127891 3 2 0 -155.8257576504 -0.0000002469 0.000487791 0.000513559 15908094 147137 4 3 0 -155.8257592108 -0.0000015604 0.000122427 0.000223864 15612136 157092 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 5 4 0 -155.8262074612 -0.0004482503 0.000876915 0.001473779 17703560 79771 6 5 0 -155.8262144144 -0.0000069532 0.000432849 0.000350271 16455757 130061 7 6 0 -155.8262147854 -0.0000003710 0.000198296 0.000229002 15724509 151265 8 7 0 -155.8262151240 -0.0000003386 0.000025659 0.000030256 15291937 164242 9 8 0 -155.8262151297 -0.0000000057 0.000016644 0.000022211 14454284 191429 10 9 0 -155.8262151320 -0.0000000024 0.000002368 0.000005821 13547107 216436 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 8.0 SECONDS ( 0.8 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262151320 AFTER 10 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9909962722 TOTAL ELECTRON NUMBER = 30.0000051267 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.20 TOTAL CPU TIME= 698.9 ( 11.6 MIN) TOTAL WALL CLOCK TIME= 704.2 SECONDS, CPU UTILIZATION IS 99.24% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 698.9 ( 11.6 MIN) TOTAL WALL CLOCK TIME= 704.3 SECONDS, CPU UTILIZATION IS 99.23% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.31 TOTAL CPU TIME= 701.2 ( 11.7 MIN) TOTAL WALL CLOCK TIME= 706.6 SECONDS, CPU UTILIZATION IS 99.24% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 701.5 ( 11.7 MIN) TOTAL WALL CLOCK TIME= 706.9 SECONDS, CPU UTILIZATION IS 99.24% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.135597 -0.014229 0.031226 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.114611 -0.008865 0.028780 0.118501 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C 0.000133766 0.001095379 -0.000768052 2 H 0.000027414 0.000014696 -0.000017906 3 C 0.001673543 -0.003725797 0.002657110 4 H -0.000160424 0.000418523 -0.000027624 5 C -0.001687167 0.002153389 -0.001525560 6 H -0.000104792 0.000043930 -0.000068585 7 H -0.000031411 -0.000047791 -0.000045381 8 C 0.000147236 0.000082344 -0.000202334 9 H -0.000042565 0.000063068 0.000036244 10 H 0.000044400 -0.000097743 -0.000037912 $VIB IVIB= 2 IATOM= 3 ICOORD= 2 E= -155.8262151320 1.337655347E-04 1.095379346E-03-7.680516011E-04 2.741381487E-05 1.469647856E-05 -1.790620227E-05 1.673543305E-03-3.725796589E-03 2.657109965E-03-1.604240832E-04 4.185230404E-04-2.762399728E-05-1.687166800E-03 2.153388819E-03-1.525560062E-03 -1.047920655E-04 4.393034803E-05-6.858543393E-05-3.141082782E-05-4.779066855E-05 -4.538145896E-05 1.472361259E-04 8.234392236E-05-2.023335354E-04-4.256451066E-05 6.306831998E-05 3.624432165E-05 4.439950606E-05-9.774301737E-05-3.791199575E-05 1.146109450E-01-8.864962059E-03 2.878048433E-02 1 ATOM 3 ------------------- COORD 3 NUCLEAR COORDINATES ------------------- VIB 2 ATOM X Y Z 1 C 0.793773 -0.808112 1.400575 2 H 2.289185 -0.995597 2.802099 3 C 1.446062 0.609240 -0.894553 4 H 3.409625 0.489515 -1.489324 5 C -0.143450 2.042156 -2.212893 6 H 0.464242 3.013674 -3.912111 7 H -2.091534 2.309425 -1.624756 8 C -1.429845 -1.902330 1.850402 9 H -2.943256 -1.862199 0.464672 10 H -1.792911 -2.895773 3.605888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 701.5 ( 11.7 MIN) TOTAL WALL CLOCK TIME= 706.9 SECONDS, CPU UTILIZATION IS 99.24% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 701.5 ( 11.7 MIN) TOTAL WALL CLOCK TIME= 706.9 SECONDS, CPU UTILIZATION IS 99.23% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8256462987 -155.8256462987 0.001288677 0.001953114 17700758 79829 2 1 0 -155.8256669476 -0.0000206489 0.000924175 0.000380696 16550524 127208 3 2 0 -155.8256666478 0.0000002998 0.000472354 0.000565574 15921595 147848 4 3 0 -155.8256682774 -0.0000016295 0.000089523 0.000206503 15642632 156509 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 5 4 0 -155.8262009965 -0.0005327191 0.000891947 0.001444073 17700740 79839 6 5 0 -155.8262078186 -0.0000068222 0.000527413 0.000342486 16451130 130084 7 6 0 -155.8262081668 -0.0000003481 0.000272093 0.000237476 15711047 151718 8 7 0 -155.8262085414 -0.0000003746 0.000037424 0.000070867 15262609 165300 9 8 0 -155.8262085577 -0.0000000163 0.000018651 0.000038551 14605006 188686 10 9 0 -155.8262085628 -0.0000000051 0.000002657 0.000002251 13942694 203047 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 8.0 SECONDS ( 0.8 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262085628 AFTER 10 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9917804644 TOTAL ELECTRON NUMBER = 30.0000054187 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.20 TOTAL CPU TIME= 709.7 ( 11.8 MIN) TOTAL WALL CLOCK TIME= 715.2 SECONDS, CPU UTILIZATION IS 99.24% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 709.8 ( 11.8 MIN) TOTAL WALL CLOCK TIME= 715.2 SECONDS, CPU UTILIZATION IS 99.24% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.31 TOTAL CPU TIME= 712.1 ( 11.9 MIN) TOTAL WALL CLOCK TIME= 717.5 SECONDS, CPU UTILIZATION IS 99.24% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 712.4 ( 11.9 MIN) TOTAL WALL CLOCK TIME= 717.9 SECONDS, CPU UTILIZATION IS 99.24% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.135597 -0.012009 0.029005 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.114953 -0.006730 0.025444 0.117928 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C -0.000195132 -0.000768156 0.001976606 2 H -0.000041460 -0.000134862 0.000135482 3 C -0.000278627 0.002673842 -0.005015457 4 H -0.000758486 -0.000006186 0.000779128 5 C 0.001322481 -0.001554030 0.002078636 6 H 0.000197100 -0.000171103 0.000081617 7 H -0.000077677 0.000078851 -0.000073011 8 C -0.000199033 -0.000097352 0.000054256 9 H 0.000012199 0.000006274 0.000005364 10 H 0.000018635 -0.000027278 -0.000022622 $VIB IVIB= 2 IATOM= 3 ICOORD= 3 E= -155.8262085628 -1.951315305E-04-7.681559191E-04 1.976605813E-03-4.146044825E-05-1.348624143E-04 1.354820648E-04-2.786271603E-04 2.673842317E-03-5.015456739E-03-7.584862080E-04 -6.186467749E-06 7.791275226E-04 1.322481430E-03-1.554030061E-03 2.078636364E-03 1.970998173E-04-1.711028067E-04 8.161730405E-05-7.767666557E-05 7.885116847E-05 -7.301068113E-05-1.990330382E-04-9.735244236E-05 5.425552530E-05 1.219898813E-05 6.274380724E-06 5.364498134E-06 1.863481528E-05-2.727775532E-05-2.262167166E-05 1.149532689E-01-6.730345944E-03 2.544428168E-02 1 ATOM 4 ------------------- COORD 1 NUCLEAR COORDINATES ------------------- VIB 2 ATOM X Y Z 1 C 0.793773 -0.808112 1.400575 2 H 2.289185 -0.995597 2.802099 3 C 1.446062 0.609240 -0.884553 4 H 3.399625 0.489515 -1.489324 5 C -0.143450 2.042156 -2.212893 6 H 0.464242 3.013674 -3.912111 7 H -2.091534 2.309425 -1.624756 8 C -1.429845 -1.902330 1.850402 9 H -2.943256 -1.862199 0.464672 10 H -1.792911 -2.895773 3.605888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 712.4 ( 11.9 MIN) TOTAL WALL CLOCK TIME= 717.9 SECONDS, CPU UTILIZATION IS 99.24% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 712.4 ( 11.9 MIN) TOTAL WALL CLOCK TIME= 717.9 SECONDS, CPU UTILIZATION IS 99.24% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8257114901 -155.8257114901 0.000928324 0.001473621 17703724 79746 2 1 0 -155.8257212429 -0.0000097528 0.000557528 0.000349124 16477612 129011 3 2 0 -155.8257209415 0.0000003014 0.000321303 0.000520675 15827635 149837 4 3 0 -155.8257222659 -0.0000013244 0.000092389 0.000128610 15528064 160042 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 5 4 0 -155.8262099039 -0.0004876380 0.000918161 0.001464782 17703857 79751 6 5 0 -155.8262168317 -0.0000069279 0.000444519 0.000338798 16456764 129939 7 6 0 -155.8262171953 -0.0000003636 0.000207221 0.000223459 15719113 151342 8 7 0 -155.8262175256 -0.0000003303 0.000019029 0.000030828 15280704 164480 9 8 0 -155.8262175309 -0.0000000053 0.000015289 0.000015941 14443890 191892 10 9 0 -155.8262175324 -0.0000000014 0.000003320 0.000006270 13426594 218851 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 8.0 SECONDS ( 0.8 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262175324 AFTER 10 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9928697280 TOTAL ELECTRON NUMBER = 30.0000053999 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.19 TOTAL CPU TIME= 720.6 ( 12.0 MIN) TOTAL WALL CLOCK TIME= 726.2 SECONDS, CPU UTILIZATION IS 99.24% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 720.6 ( 12.0 MIN) TOTAL WALL CLOCK TIME= 726.2 SECONDS, CPU UTILIZATION IS 99.24% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.31 TOTAL CPU TIME= 722.9 ( 12.0 MIN) TOTAL WALL CLOCK TIME= 728.5 SECONDS, CPU UTILIZATION IS 99.24% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 723.3 ( 12.1 MIN) TOTAL WALL CLOCK TIME= 728.8 SECONDS, CPU UTILIZATION IS 99.24% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.135411 -0.012009 0.031226 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.114818 -0.010588 0.024300 0.117838 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C 0.000040510 -0.000025478 0.000001723 2 H 0.000010103 0.000010035 0.000003343 3 C 0.003082438 -0.000172378 -0.000795712 4 H -0.003264591 0.000216714 0.000873356 5 C 0.000147161 -0.000002468 -0.000080296 6 H 0.000006946 0.000008127 0.000007355 7 H -0.000004904 -0.000033486 0.000012326 8 C -0.000021095 0.000007759 -0.000030127 9 H 0.000002612 -0.000009557 0.000003921 10 H 0.000000819 0.000000731 0.000004111 $VIB IVIB= 2 IATOM= 4 ICOORD= 1 E= -155.8262175324 4.050975806E-05-2.547800389E-05 1.722848130E-06 1.010250486E-05 1.003519788E-05 3.342650343E-06 3.082438339E-03-1.723783410E-04-7.957117873E-04-3.264590940E-03 2.167141660E-04 8.733557300E-04 1.471610549E-04-2.467965771E-06-8.029550031E-05 6.946382823E-06 8.127164647E-06 7.355129955E-06-4.903790661E-06-3.348554040E-05 1.232573000E-05-2.109460164E-05 7.758635823E-06-3.012671950E-05 2.612357904E-06 -9.556617335E-06 3.921269703E-06 8.189347507E-07 7.313040147E-07 4.110648999E-06 1.148176507E-01-1.058810189E-02 2.430009714E-02 1 ATOM 4 ------------------- COORD 2 NUCLEAR COORDINATES ------------------- VIB 2 ATOM X Y Z 1 C 0.793773 -0.808112 1.400575 2 H 2.289185 -0.995597 2.802099 3 C 1.446062 0.609240 -0.884553 4 H 3.409625 0.479515 -1.489324 5 C -0.143450 2.042156 -2.212893 6 H 0.464242 3.013674 -3.912111 7 H -2.091534 2.309425 -1.624756 8 C -1.429845 -1.902330 1.850402 9 H -2.943256 -1.862199 0.464672 10 H -1.792911 -2.895773 3.605888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 723.3 ( 12.1 MIN) TOTAL WALL CLOCK TIME= 728.8 SECONDS, CPU UTILIZATION IS 99.24% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 723.3 ( 12.1 MIN) TOTAL WALL CLOCK TIME= 728.9 SECONDS, CPU UTILIZATION IS 99.24% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8257303637 -155.8257303637 0.000897236 0.001459566 17702726 79791 2 1 0 -155.8257388757 -0.0000085120 0.000470544 0.000350733 16474253 129433 3 2 0 -155.8257392484 -0.0000003727 0.000237843 0.000234437 15727103 151275 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 4 3 0 -155.8262241354 -0.0004848870 0.000861557 0.001450837 17702934 79786 5 4 0 -155.8262309702 -0.0000068348 0.000547341 0.000370524 16453046 130109 6 5 0 -155.8262313202 -0.0000003500 0.000289261 0.000261377 15725542 151225 7 6 0 -155.8262317139 -0.0000003937 0.000045341 0.000077086 15304540 164578 8 7 0 -155.8262317284 -0.0000000146 0.000015052 0.000033938 14541319 189545 9 8 0 -155.8262317322 -0.0000000038 0.000001901 0.000002219 13840895 206050 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 7.8 SECONDS ( 0.9 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262317322 AFTER 9 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9913684518 TOTAL ELECTRON NUMBER = 30.0000053876 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.00 TOTAL CPU TIME= 731.3 ( 12.2 MIN) TOTAL WALL CLOCK TIME= 736.9 SECONDS, CPU UTILIZATION IS 99.24% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 731.3 ( 12.2 MIN) TOTAL WALL CLOCK TIME= 736.9 SECONDS, CPU UTILIZATION IS 99.24% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.30 TOTAL CPU TIME= 733.6 ( 12.2 MIN) TOTAL WALL CLOCK TIME= 739.2 SECONDS, CPU UTILIZATION IS 99.24% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 734.0 ( 12.2 MIN) TOTAL WALL CLOCK TIME= 739.6 SECONDS, CPU UTILIZATION IS 99.24% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.135597 -0.012195 0.031226 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.111870 -0.012845 0.024846 0.115314 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C 0.000164253 -0.000034438 -0.000065473 2 H 0.000009480 0.000003900 0.000008014 3 C -0.000141279 0.000437213 -0.000005778 4 H 0.000236275 -0.000391610 0.000094745 5 C -0.000237592 -0.000013937 0.000033299 6 H 0.000035178 0.000042453 0.000034435 7 H -0.000052158 -0.000053720 -0.000066687 8 C -0.000018502 0.000011874 -0.000039550 9 H 0.000003549 -0.000011220 0.000002518 10 H 0.000000797 0.000009484 0.000004478 $VIB IVIB= 2 IATOM= 4 ICOORD= 2 E= -155.8262317322 1.642529921E-04-3.443750693E-05-6.547334636E-05 9.479520812E-06 3.900382986E-06 8.013869415E-06-1.412790106E-04 4.372125405E-04-5.777807367E-06 2.362746357E-04 -3.916098705E-04 9.474530782E-05-2.375921537E-04-1.393690697E-05 3.329903392E-05 3.517827803E-05 4.245312850E-05 3.443452722E-05-5.215818173E-05-5.372008339E-05 -6.668730976E-05-1.850205724E-05 1.187400097E-05-3.954955194E-05 3.549408943E-06 -1.121985304E-05 2.517640907E-06 7.965676077E-07 9.484167838E-06 4.477636147E-06 1.118701648E-01-1.284549820E-02 2.484566643E-02 1 ATOM 4 ------------------- COORD 3 NUCLEAR COORDINATES ------------------- VIB 2 ATOM X Y Z 1 C 0.793773 -0.808112 1.400575 2 H 2.289185 -0.995597 2.802099 3 C 1.446062 0.609240 -0.884553 4 H 3.409625 0.489515 -1.499324 5 C -0.143450 2.042156 -2.212893 6 H 0.464242 3.013674 -3.912111 7 H -2.091534 2.309425 -1.624756 8 C -1.429845 -1.902330 1.850402 9 H -2.943256 -1.862199 0.464672 10 H -1.792911 -2.895773 3.605888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 734.0 ( 12.2 MIN) TOTAL WALL CLOCK TIME= 739.6 SECONDS, CPU UTILIZATION IS 99.24% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 734.0 ( 12.2 MIN) TOTAL WALL CLOCK TIME= 739.6 SECONDS, CPU UTILIZATION IS 99.24% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8257265551 -155.8257265551 0.000919845 0.001454700 17701714 79835 2 1 0 -155.8257351139 -0.0000085587 0.000473248 0.000388169 16484107 129102 3 2 0 -155.8257355231 -0.0000004093 0.000226396 0.000252992 15754808 150524 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 4 3 0 -155.8262223671 -0.0004868440 0.000884313 0.001463977 17701765 79843 5 4 0 -155.8262291640 -0.0000067969 0.000486651 0.000372538 16451574 130115 6 5 0 -155.8262294482 -0.0000002842 0.000223448 0.000262762 15750677 150626 7 6 0 -155.8262299100 -0.0000004618 0.000076533 0.000084385 15384572 162607 8 7 0 -155.8262299470 -0.0000000369 0.000019001 0.000024761 14569425 188580 9 8 0 -155.8262299503 -0.0000000034 0.000003728 0.000005043 13880609 206280 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 7.8 SECONDS ( 0.9 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262299503 AFTER 9 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9910215221 TOTAL ELECTRON NUMBER = 30.0000053564 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 7.99 TOTAL CPU TIME= 742.0 ( 12.4 MIN) TOTAL WALL CLOCK TIME= 747.7 SECONDS, CPU UTILIZATION IS 99.24% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 742.0 ( 12.4 MIN) TOTAL WALL CLOCK TIME= 747.7 SECONDS, CPU UTILIZATION IS 99.24% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.31 TOTAL CPU TIME= 744.3 ( 12.4 MIN) TOTAL WALL CLOCK TIME= 750.0 SECONDS, CPU UTILIZATION IS 99.24% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 744.7 ( 12.4 MIN) TOTAL WALL CLOCK TIME= 750.4 SECONDS, CPU UTILIZATION IS 99.24% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.135597 -0.012009 0.031039 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.110837 -0.011652 0.024716 0.114155 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C -0.000259152 -0.000005862 0.000039069 2 H 0.000021571 0.000006748 -0.000000307 3 C -0.000784369 -0.000010224 0.000783775 4 H 0.000873567 0.000095685 -0.000750220 5 C 0.000137759 -0.000022759 -0.000092880 6 H 0.000027745 0.000035107 0.000013241 7 H -0.000001223 -0.000066887 -0.000023534 8 C -0.000009796 -0.000013312 0.000027995 9 H 0.000001481 -0.000003245 0.000003387 10 H -0.000007582 -0.000015252 -0.000000526 $VIB IVIB= 2 IATOM= 4 ICOORD= 3 E= -155.8262299503 -2.591524908E-04-5.862485520E-06 3.906948665E-05 2.157139035E-05 6.748173952E-06 -3.074024259E-07-7.843688822E-04-1.022355586E-05 7.837745065E-04 8.735665915E-04 9.568540165E-05-7.502204820E-04 1.377590153E-04-2.275875952E-05-9.288035044E-05 2.774498540E-05 3.510707080E-05 1.324141927E-05-1.223433171E-06-6.688700112E-05 -2.353365937E-05-9.796145055E-06-1.331226338E-05 2.799523090E-05 1.481024956E-06 -3.244624324E-06 3.387436574E-06-7.582056358E-06-1.525195666E-05-5.261856956E-07 1.108365008E-01-1.165174215E-02 2.471639806E-02 1 ATOM 5 ------------------- COORD 1 NUCLEAR COORDINATES ------------------- VIB 2 ATOM X Y Z 1 C 0.793773 -0.808112 1.400575 2 H 2.289185 -0.995597 2.802099 3 C 1.446062 0.609240 -0.884553 4 H 3.409625 0.489515 -1.489324 5 C -0.153450 2.042156 -2.212893 6 H 0.464242 3.013674 -3.912111 7 H -2.091534 2.309425 -1.624756 8 C -1.429845 -1.902330 1.850402 9 H -2.943256 -1.862199 0.464672 10 H -1.792911 -2.895773 3.605888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 744.7 ( 12.4 MIN) TOTAL WALL CLOCK TIME= 750.4 SECONDS, CPU UTILIZATION IS 99.24% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.02 TOTAL CPU TIME= 744.7 ( 12.4 MIN) TOTAL WALL CLOCK TIME= 750.4 SECONDS, CPU UTILIZATION IS 99.24% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8257165524 -155.8257165524 0.001067661 0.001881314 17702641 79806 2 1 0 -155.8257342210 -0.0000176686 0.000894509 0.000468153 16528188 127453 3 2 0 -155.8257346325 -0.0000004115 0.000462010 0.000367249 15892831 146494 4 3 0 -155.8257356969 -0.0000010644 0.000114129 0.000139214 15561689 157546 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 5 4 0 -155.8261913979 -0.0004557010 0.000828738 0.001457906 17702492 79819 6 5 0 -155.8261984230 -0.0000070251 0.000494319 0.000351133 16456792 129980 7 6 0 -155.8261987656 -0.0000003426 0.000249619 0.000235120 15708920 151697 8 7 0 -155.8261991409 -0.0000003753 0.000042811 0.000084102 15254674 165327 9 8 0 -155.8261991623 -0.0000000214 0.000016800 0.000040238 14656311 187255 10 9 0 -155.8261991677 -0.0000000054 0.000001309 0.000001976 13981707 201919 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 8.0 SECONDS ( 0.8 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8261991677 AFTER 10 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9907937188 TOTAL ELECTRON NUMBER = 30.0000054337 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.18 TOTAL CPU TIME= 752.9 ( 12.5 MIN) TOTAL WALL CLOCK TIME= 758.6 SECONDS, CPU UTILIZATION IS 99.24% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.02 TOTAL CPU TIME= 752.9 ( 12.5 MIN) TOTAL WALL CLOCK TIME= 758.6 SECONDS, CPU UTILIZATION IS 99.24% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.31 TOTAL CPU TIME= 755.2 ( 12.6 MIN) TOTAL WALL CLOCK TIME= 761.0 SECONDS, CPU UTILIZATION IS 99.24% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.35 TOTAL CPU TIME= 755.5 ( 12.6 MIN) TOTAL WALL CLOCK TIME= 761.3 SECONDS, CPU UTILIZATION IS 99.24% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.133377 -0.012009 0.031226 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.112596 -0.008977 0.028647 0.116529 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C -0.000176717 -0.000037098 0.000065527 2 H 0.000012074 0.000027174 -0.000018439 3 C 0.002880473 -0.001645565 0.001310168 4 H 0.000187924 -0.000213508 0.000162370 5 C -0.006896799 0.001852271 0.000159167 6 H 0.000845794 0.000358292 -0.000759936 7 H 0.003107176 -0.000383321 -0.000872732 8 C 0.000040183 0.000044032 -0.000054242 9 H -0.000005903 0.000012432 0.000011720 10 H 0.000005795 -0.000014709 -0.000003601 $VIB IVIB= 2 IATOM= 5 ICOORD= 1 E= -155.8261991677 -1.767173002E-04-3.709820193E-05 6.552657060E-05 1.207417829E-05 2.717384664E-05 -1.843929730E-05 2.880472617E-03-1.645565303E-03 1.310167707E-03 1.879242371E-04 -2.135080229E-04 1.623696840E-04-6.896798756E-03 1.852271051E-03 1.591673436E-04 8.457939518E-04 3.582924992E-04-7.599362755E-04 3.107175879E-03-3.833206710E-04 -8.727322432E-04 4.018283108E-05 4.403225870E-05-5.424204955E-05-5.903016908E-06 1.243161007E-05 1.171979517E-05 5.795379210E-06-1.470906684E-05-3.601234785E-06 1.125956761E-01-8.976972567E-03 2.864679957E-02 1 ATOM 5 ------------------- COORD 2 NUCLEAR COORDINATES ------------------- VIB 2 ATOM X Y Z 1 C 0.793773 -0.808112 1.400575 2 H 2.289185 -0.995597 2.802099 3 C 1.446062 0.609240 -0.884553 4 H 3.409625 0.489515 -1.489324 5 C -0.143450 2.032156 -2.212893 6 H 0.464242 3.013674 -3.912111 7 H -2.091534 2.309425 -1.624756 8 C -1.429845 -1.902330 1.850402 9 H -2.943256 -1.862199 0.464672 10 H -1.792911 -2.895773 3.605888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 755.5 ( 12.6 MIN) TOTAL WALL CLOCK TIME= 761.3 SECONDS, CPU UTILIZATION IS 99.24% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 755.6 ( 12.6 MIN) TOTAL WALL CLOCK TIME= 761.3 SECONDS, CPU UTILIZATION IS 99.24% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8256928681 -155.8256928681 0.000944228 0.001540609 17706171 79738 2 1 0 -155.8257099560 -0.0000170879 0.000504846 0.000315275 16522283 127620 3 2 0 -155.8257100836 -0.0000001277 0.000286636 0.000368174 15819820 150769 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 4 3 0 -155.8262074138 -0.0004973302 0.000856354 0.001413730 17706018 79745 5 4 0 -155.8262139943 -0.0000065806 0.000624012 0.000314664 16457368 129973 6 5 0 -155.8262138776 0.0000001167 0.000302468 0.000485911 15766497 151227 7 6 0 -155.8262148846 -0.0000010070 0.000077948 0.000134523 15482529 161098 8 7 0 -155.8262149508 -0.0000000661 0.000014596 0.000021917 14844459 179331 9 8 0 -155.8262149536 -0.0000000028 0.000001814 0.000002370 13962796 202359 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 7.8 SECONDS ( 0.9 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262149536 AFTER 9 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9921083866 TOTAL ELECTRON NUMBER = 30.0000054560 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.00 TOTAL CPU TIME= 763.6 ( 12.7 MIN) TOTAL WALL CLOCK TIME= 769.4 SECONDS, CPU UTILIZATION IS 99.24% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 763.6 ( 12.7 MIN) TOTAL WALL CLOCK TIME= 769.4 SECONDS, CPU UTILIZATION IS 99.24% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.30 TOTAL CPU TIME= 765.9 ( 12.8 MIN) TOTAL WALL CLOCK TIME= 771.7 SECONDS, CPU UTILIZATION IS 99.24% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.37 TOTAL CPU TIME= 766.2 ( 12.8 MIN) TOTAL WALL CLOCK TIME= 772.1 SECONDS, CPU UTILIZATION IS 99.24% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.135597 -0.014229 0.031226 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.113474 -0.003597 0.027375 0.116785 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C -0.000084532 0.000088264 -0.000188050 2 H 0.000033170 -0.000003191 -0.000011712 3 C -0.001766637 0.002173309 -0.001568908 4 H 0.000005198 -0.000024011 -0.000032728 5 C 0.001856672 -0.003760583 0.002986346 6 H 0.000407010 0.001040714 -0.001216846 7 H -0.000400316 0.000487065 0.000033699 8 C -0.000051985 0.000008488 -0.000008165 9 H 0.000003511 -0.000001459 0.000002741 10 H -0.000002091 -0.000008596 0.000003621 $VIB IVIB= 2 IATOM= 5 ICOORD= 2 E= -155.8262149536 -8.453214103E-05 8.826444925E-05-1.880498341E-04 3.316998640E-05-3.191294696E-06 -1.171167758E-05-1.766636524E-03 2.173309316E-03-1.568907569E-03 5.197980700E-06 -2.401145394E-05-3.272794033E-05 1.856671984E-03-3.760583143E-03 2.986345694E-03 4.070100749E-04 1.040714288E-03-1.216845623E-03-4.003159176E-04 4.870653092E-04 3.369933745E-05-5.198525424E-05 8.487791219E-06-8.164577325E-06 3.511150502E-06 -1.459281431E-06 2.740928255E-06-2.091339427E-06-8.595979965E-06 3.621262383E-06 1.134742033E-01-3.597211079E-03 2.737468563E-02 1 ATOM 5 ------------------- COORD 3 NUCLEAR COORDINATES ------------------- VIB 2 ATOM X Y Z 1 C 0.793773 -0.808112 1.400575 2 H 2.289185 -0.995597 2.802099 3 C 1.446062 0.609240 -0.884553 4 H 3.409625 0.489515 -1.489324 5 C -0.143450 2.042156 -2.222893 6 H 0.464242 3.013674 -3.912111 7 H -2.091534 2.309425 -1.624756 8 C -1.429845 -1.902330 1.850402 9 H -2.943256 -1.862199 0.464672 10 H -1.792911 -2.895773 3.605888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 766.2 ( 12.8 MIN) TOTAL WALL CLOCK TIME= 772.1 SECONDS, CPU UTILIZATION IS 99.24% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 766.3 ( 12.8 MIN) TOTAL WALL CLOCK TIME= 772.1 SECONDS, CPU UTILIZATION IS 99.24% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8257018517 -155.8257018517 0.000989017 0.001358944 17698679 79881 2 1 0 -155.8257184248 -0.0000165731 0.000830751 0.000401245 16515006 127791 3 2 0 -155.8257187827 -0.0000003579 0.000415873 0.000355179 15865475 147275 4 3 0 -155.8257197125 -0.0000009297 0.000104280 0.000122506 15510476 158761 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 5 4 0 -155.8261988281 -0.0004791157 0.000835673 0.001452897 17698447 79895 6 5 0 -155.8262057300 -0.0000069019 0.000487095 0.000352691 16448199 130166 7 6 0 -155.8262060688 -0.0000003388 0.000244251 0.000231575 15699708 151892 8 7 0 -155.8262064392 -0.0000003704 0.000043258 0.000083810 15248347 165477 9 8 0 -155.8262064602 -0.0000000211 0.000016647 0.000040035 14643630 187435 10 9 0 -155.8262064655 -0.0000000053 0.000001302 0.000001935 13968266 202116 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 7.9 SECONDS ( 0.8 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262064655 AFTER 10 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9908099576 TOTAL ELECTRON NUMBER = 30.0000054199 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.19 TOTAL CPU TIME= 774.4 ( 12.9 MIN) TOTAL WALL CLOCK TIME= 780.4 SECONDS, CPU UTILIZATION IS 99.24% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 774.4 ( 12.9 MIN) TOTAL WALL CLOCK TIME= 780.4 SECONDS, CPU UTILIZATION IS 99.24% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.30 TOTAL CPU TIME= 776.8 ( 12.9 MIN) TOTAL WALL CLOCK TIME= 782.7 SECONDS, CPU UTILIZATION IS 99.24% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 777.1 ( 13.0 MIN) TOTAL WALL CLOCK TIME= 783.1 SECONDS, CPU UTILIZATION IS 99.24% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.135597 -0.012009 0.029005 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.113987 -0.008625 0.029003 0.117935 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C 0.000095730 -0.000282446 0.000226506 2 H 0.000006252 -0.000015911 0.000043226 3 C 0.001411885 -0.001519461 0.002063196 4 H -0.000068862 0.000025426 -0.000099438 5 C 0.000119838 0.002995332 -0.005462398 6 H -0.000797359 -0.001233584 0.002483623 7 H -0.000822383 0.000006138 0.000760234 8 C 0.000063576 0.000025235 -0.000021351 9 H -0.000002417 -0.000007145 0.000000377 10 H -0.000006260 0.000006415 0.000006025 $VIB IVIB= 2 IATOM= 5 ICOORD= 3 E= -155.8262064655 9.572972256E-05-2.824457575E-04 2.265058583E-04 6.251958706E-06-1.591124036E-05 4.322588961E-05 1.411884943E-03-1.519460569E-03 2.063195597E-03-6.886167462E-05 2.542625687E-05-9.943783889E-05 1.198381572E-04 2.995332430E-03-5.462397770E-03 -7.973594596E-04-1.233584135E-03 2.483622950E-03-8.223825310E-04 6.137613254E-06 7.602338435E-04 6.357576670E-05 2.523511139E-05-2.135051140E-05-2.416750181E-06 -7.144631431E-06 3.770461057E-07-6.260132573E-06 6.414922459E-06 6.024936567E-06 1.139873696E-01-8.624885645E-03 2.900347326E-02 1 ATOM 6 ------------------- COORD 1 NUCLEAR COORDINATES ------------------- VIB 2 ATOM X Y Z 1 C 0.793773 -0.808112 1.400575 2 H 2.289185 -0.995597 2.802099 3 C 1.446062 0.609240 -0.884553 4 H 3.409625 0.489515 -1.489324 5 C -0.143450 2.042156 -2.212893 6 H 0.454242 3.013674 -3.912111 7 H -2.091534 2.309425 -1.624756 8 C -1.429845 -1.902330 1.850402 9 H -2.943256 -1.862199 0.464672 10 H -1.792911 -2.895773 3.605888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 777.1 ( 13.0 MIN) TOTAL WALL CLOCK TIME= 783.1 SECONDS, CPU UTILIZATION IS 99.24% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.02 TOTAL CPU TIME= 777.1 ( 13.0 MIN) TOTAL WALL CLOCK TIME= 783.1 SECONDS, CPU UTILIZATION IS 99.24% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8257252439 -155.8257252439 0.000909436 0.001448405 17702876 79784 2 1 0 -155.8257334543 -0.0000082103 0.000493956 0.000319986 16467056 129381 3 2 0 -155.8257336756 -0.0000002214 0.000260857 0.000249012 15724646 151490 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 4 3 0 -155.8262224211 -0.0004887455 0.000856815 0.001451190 17703107 79783 5 4 0 -155.8262291976 -0.0000067765 0.000564098 0.000380360 16452555 130063 6 5 0 -155.8262294540 -0.0000002565 0.000290531 0.000280880 15747906 150938 7 6 0 -155.8262299356 -0.0000004815 0.000079011 0.000113399 15385344 163174 8 7 0 -155.8262299706 -0.0000000350 0.000020548 0.000023969 14595993 187862 9 8 0 -155.8262299736 -0.0000000030 0.000002591 0.000004066 13829090 206909 10 9 0 -155.8262299737 -0.0000000001 0.000001353 0.000003415 12867419 235010 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 9.0 SECONDS ( 0.9 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262299737 AFTER 10 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9918512802 TOTAL ELECTRON NUMBER = 30.0000054276 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 9.16 TOTAL CPU TIME= 786.3 ( 13.1 MIN) TOTAL WALL CLOCK TIME= 792.3 SECONDS, CPU UTILIZATION IS 99.24% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 786.3 ( 13.1 MIN) TOTAL WALL CLOCK TIME= 792.3 SECONDS, CPU UTILIZATION IS 99.24% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.31 TOTAL CPU TIME= 788.6 ( 13.1 MIN) TOTAL WALL CLOCK TIME= 794.6 SECONDS, CPU UTILIZATION IS 99.24% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 789.0 ( 13.1 MIN) TOTAL WALL CLOCK TIME= 795.0 SECONDS, CPU UTILIZATION IS 99.24% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.135411 -0.012009 0.031226 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.110760 -0.009965 0.024433 0.113860 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C -0.000003272 -0.000059326 0.000001717 2 H 0.000015134 0.000003203 0.000012391 3 C -0.000074199 -0.000108428 0.000175758 4 H 0.000005931 0.000016244 0.000009092 5 C 0.000794537 0.000400697 -0.000793857 6 H -0.000762280 -0.000382229 0.000807376 7 H 0.000033935 0.000128372 -0.000212880 8 C -0.000005009 0.000012315 -0.000005933 9 H 0.000000440 -0.000010159 0.000002056 10 H -0.000005217 -0.000000691 0.000004279 $VIB IVIB= 2 IATOM= 6 ICOORD= 1 E= -155.8262299737 -3.271967974E-06-5.932569683E-05 1.717395658E-06 1.513418432E-05 3.203387416E-06 1.239054630E-05-7.419853539E-05-1.084278982E-04 1.757582694E-04 5.930905916E-06 1.624445406E-05 9.092091281E-06 7.945372424E-04 4.006973830E-04-7.938568795E-04 -7.622804504E-04-3.822291334E-04 8.073755984E-04 3.393493129E-05 1.283723979E-04 -2.128796094E-04-5.009034813E-06 1.231535076E-05-5.933331610E-06 4.401910728E-07 -1.015936059E-05 2.056466627E-06-5.217466445E-06-6.908840248E-07 4.279452796E-06 1.107604399E-01-9.965033094E-03 2.443314069E-02 1 ATOM 6 ------------------- COORD 2 NUCLEAR COORDINATES ------------------- VIB 2 ATOM X Y Z 1 C 0.793773 -0.808112 1.400575 2 H 2.289185 -0.995597 2.802099 3 C 1.446062 0.609240 -0.884553 4 H 3.409625 0.489515 -1.489324 5 C -0.143450 2.042156 -2.212893 6 H 0.464242 3.003674 -3.912111 7 H -2.091534 2.309425 -1.624756 8 C -1.429845 -1.902330 1.850402 9 H -2.943256 -1.862199 0.464672 10 H -1.792911 -2.895773 3.605888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 789.0 ( 13.1 MIN) TOTAL WALL CLOCK TIME= 795.0 SECONDS, CPU UTILIZATION IS 99.24% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 789.0 ( 13.1 MIN) TOTAL WALL CLOCK TIME= 795.0 SECONDS, CPU UTILIZATION IS 99.24% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8257333964 -155.8257333964 0.000867429 0.001473252 17704208 79737 2 1 0 -155.8257418881 -0.0000084917 0.000494888 0.000314725 16466294 129447 3 2 0 -155.8257419482 -0.0000000601 0.000246076 0.000343403 15770950 150661 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 4 3 0 -155.8262209941 -0.0004790459 0.000861389 0.001454148 17704399 79739 5 4 0 -155.8262277306 -0.0000067365 0.000511985 0.000368083 16454738 129917 6 5 0 -155.8262278814 -0.0000001508 0.000240649 0.000306104 15759688 150639 7 6 0 -155.8262284468 -0.0000005653 0.000091813 0.000104414 15424707 162045 8 7 0 -155.8262284954 -0.0000000486 0.000016583 0.000021245 14564506 189061 9 8 0 -155.8262284980 -0.0000000026 0.000004358 0.000006289 13881462 205782 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 7.8 SECONDS ( 0.9 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262284980 AFTER 9 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9921654665 TOTAL ELECTRON NUMBER = 30.0000053030 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.00 TOTAL CPU TIME= 797.0 ( 13.3 MIN) TOTAL WALL CLOCK TIME= 803.1 SECONDS, CPU UTILIZATION IS 99.24% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 797.0 ( 13.3 MIN) TOTAL WALL CLOCK TIME= 803.1 SECONDS, CPU UTILIZATION IS 99.24% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.30 TOTAL CPU TIME= 799.3 ( 13.3 MIN) TOTAL WALL CLOCK TIME= 805.4 SECONDS, CPU UTILIZATION IS 99.24% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 799.7 ( 13.3 MIN) TOTAL WALL CLOCK TIME= 805.8 SECONDS, CPU UTILIZATION IS 99.24% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.135597 -0.012195 0.031226 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.112156 -0.012310 0.023681 0.115288 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C -0.000080529 -0.000095016 -0.000045745 2 H 0.000021050 0.000016323 -0.000006225 3 C 0.000089050 0.000060504 -0.000171468 4 H 0.000027610 0.000043616 0.000036967 5 C 0.000338176 0.001047793 -0.001209732 6 H -0.000364400 -0.001036830 0.001351936 7 H -0.000027706 -0.000036273 0.000034302 8 C -0.000003627 0.000005884 -0.000000029 9 H 0.000003398 -0.000007453 0.000005690 10 H -0.000003021 0.000001452 0.000004305 $VIB IVIB= 2 IATOM= 6 ICOORD= 2 E= -155.8262284980 -8.052897425E-05-9.501589309E-05-4.574512456E-05 2.105025118E-05 1.632316844E-05 -6.225204375E-06 8.904996526E-05 6.050431326E-05-1.714675748E-04 2.760953950E-05 4.361606842E-05 3.696684471E-05 3.381758262E-04 1.047793152E-03-1.209732379E-03 -3.644000506E-04-1.036830301E-03 1.351936079E-03-2.770569551E-05-3.627339473E-05 3.430201221E-05-3.627478489E-06 5.883771716E-06-2.886227024E-08 3.397774497E-06 -7.452546710E-06 5.689537308E-06-3.021157831E-06 1.451661793E-06 4.304672488E-06 1.121564505E-01-1.231015215E-02 2.368097868E-02 1 ATOM 6 ------------------- COORD 3 NUCLEAR COORDINATES ------------------- VIB 2 ATOM X Y Z 1 C 0.793773 -0.808112 1.400575 2 H 2.289185 -0.995597 2.802099 3 C 1.446062 0.609240 -0.884553 4 H 3.409625 0.489515 -1.489324 5 C -0.143450 2.042156 -2.212893 6 H 0.464242 3.013674 -3.922111 7 H -2.091534 2.309425 -1.624756 8 C -1.429845 -1.902330 1.850402 9 H -2.943256 -1.862199 0.464672 10 H -1.792911 -2.895773 3.605888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 799.7 ( 13.3 MIN) TOTAL WALL CLOCK TIME= 805.8 SECONDS, CPU UTILIZATION IS 99.24% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 799.7 ( 13.3 MIN) TOTAL WALL CLOCK TIME= 805.8 SECONDS, CPU UTILIZATION IS 99.24% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8257233455 -155.8257233455 0.001117324 0.001449355 17699889 79858 2 1 0 -155.8257339779 -0.0000106324 0.000956553 0.000432532 16477608 129034 3 2 0 -155.8257343256 -0.0000003477 0.000483144 0.000385728 15839480 148846 4 3 0 -155.8257354445 -0.0000011189 0.000102938 0.000146389 15459646 161891 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 5 4 0 -155.8262132806 -0.0004778361 0.000895699 0.001468106 17700099 79855 6 5 0 -155.8262201921 -0.0000069115 0.000446835 0.000351095 16453044 130145 7 6 0 -155.8262205686 -0.0000003765 0.000205995 0.000230601 15721381 151247 8 7 0 -155.8262209169 -0.0000003483 0.000025614 0.000031275 15293909 164207 9 8 0 -155.8262209229 -0.0000000060 0.000017635 0.000022416 14464414 191293 10 9 0 -155.8262209255 -0.0000000025 0.000002501 0.000005614 13559442 216027 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 8.0 SECONDS ( 0.8 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262209255 AFTER 10 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9902368044 TOTAL ELECTRON NUMBER = 30.0000053521 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.19 TOTAL CPU TIME= 807.9 ( 13.5 MIN) TOTAL WALL CLOCK TIME= 814.0 SECONDS, CPU UTILIZATION IS 99.24% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 807.9 ( 13.5 MIN) TOTAL WALL CLOCK TIME= 814.0 SECONDS, CPU UTILIZATION IS 99.24% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.30 TOTAL CPU TIME= 810.2 ( 13.5 MIN) TOTAL WALL CLOCK TIME= 816.3 SECONDS, CPU UTILIZATION IS 99.24% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.37 TOTAL CPU TIME= 810.5 ( 13.5 MIN) TOTAL WALL CLOCK TIME= 816.7 SECONDS, CPU UTILIZATION IS 99.24% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.135597 -0.012009 0.031039 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.111287 -0.012932 0.026509 0.115129 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C -0.000014161 -0.000079177 -0.000027066 2 H 0.000016822 0.000003582 0.000006741 3 C -0.000065487 -0.000053504 0.000079802 4 H 0.000025641 0.000034511 0.000013961 5 C -0.000770040 -0.001196088 0.002438282 6 H 0.000812977 0.001321177 -0.002544949 7 H -0.000003055 -0.000035400 0.000029088 8 C -0.000000953 0.000011329 -0.000004181 9 H 0.000002359 -0.000006220 0.000003438 10 H -0.000004104 -0.000000212 0.000004884 $VIB IVIB= 2 IATOM= 6 ICOORD= 3 E= -155.8262209255 -1.416081457E-05-7.917709581E-05-2.706633779E-05 1.682217052E-05 3.582446556E-06 6.741061535E-06-6.548694275E-05-5.350362126E-05 7.980205128E-05 2.564147028E-05 3.451074958E-05 1.396110535E-05-7.700403396E-04-1.196087732E-03 2.438282297E-03 8.129774526E-04 1.321177467E-03-2.544948647E-03-3.055295114E-06-3.540009441E-05 2.908829395E-05-9.531384934E-07 1.132942463E-05-4.181171806E-06 2.358939670E-06 -6.220022999E-06 3.437576034E-06-4.103502567E-06-2.115206408E-07 4.883770876E-06 1.112870327E-01-1.293173931E-02 2.650921629E-02 1 ATOM 7 ------------------- COORD 1 NUCLEAR COORDINATES ------------------- VIB 2 ATOM X Y Z 1 C 0.793773 -0.808112 1.400575 2 H 2.289185 -0.995597 2.802099 3 C 1.446062 0.609240 -0.884553 4 H 3.409625 0.489515 -1.489324 5 C -0.143450 2.042156 -2.212893 6 H 0.464242 3.013674 -3.912111 7 H -2.101534 2.309425 -1.624756 8 C -1.429845 -1.902330 1.850402 9 H -2.943256 -1.862199 0.464672 10 H -1.792911 -2.895773 3.605888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 810.5 ( 13.5 MIN) TOTAL WALL CLOCK TIME= 816.7 SECONDS, CPU UTILIZATION IS 99.24% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 810.6 ( 13.5 MIN) TOTAL WALL CLOCK TIME= 816.7 SECONDS, CPU UTILIZATION IS 99.24% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8257159416 -155.8257159416 0.001154664 0.001453519 17701699 79841 2 1 0 -155.8257272379 -0.0000112962 0.001039318 0.000462078 16477982 128944 3 2 0 -155.8257275479 -0.0000003100 0.000511546 0.000441871 15853608 148088 4 3 0 -155.8257289087 -0.0000013609 0.000107999 0.000138940 15495726 161013 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 5 4 0 -155.8262098090 -0.0004809002 0.000900368 0.001469013 17701711 79846 6 5 0 -155.8262167028 -0.0000068938 0.000446509 0.000350817 16452776 130137 7 6 0 -155.8262170802 -0.0000003774 0.000204431 0.000229986 15723322 151211 8 7 0 -155.8262174304 -0.0000003502 0.000026987 0.000034246 15296711 164133 9 8 0 -155.8262174367 -0.0000000063 0.000017904 0.000024245 14474892 191028 10 9 0 -155.8262174396 -0.0000000028 0.000002402 0.000005537 13598098 214916 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 8.0 SECONDS ( 0.8 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262174396 AFTER 10 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9900712272 TOTAL ELECTRON NUMBER = 30.0000053252 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.20 TOTAL CPU TIME= 818.8 ( 13.6 MIN) TOTAL WALL CLOCK TIME= 825.0 SECONDS, CPU UTILIZATION IS 99.24% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 818.8 ( 13.6 MIN) TOTAL WALL CLOCK TIME= 825.0 SECONDS, CPU UTILIZATION IS 99.24% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.30 TOTAL CPU TIME= 821.1 ( 13.7 MIN) TOTAL WALL CLOCK TIME= 827.3 SECONDS, CPU UTILIZATION IS 99.24% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 821.4 ( 13.7 MIN) TOTAL WALL CLOCK TIME= 827.7 SECONDS, CPU UTILIZATION IS 99.24% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.135411 -0.012009 0.031226 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.113792 -0.011305 0.024859 0.117023 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C -0.000007805 0.000017657 -0.000000217 2 H 0.000016272 0.000001526 0.000009090 3 C 0.000174502 -0.000012648 -0.000076040 4 H 0.000016538 -0.000048648 0.000002853 5 C 0.002994934 -0.000374659 -0.000794355 6 H 0.000056352 -0.000025143 -0.000000050 7 H -0.003233078 0.000439391 0.000865326 8 C -0.000016013 0.000013837 -0.000010852 9 H 0.000000925 -0.000006723 0.000001462 10 H -0.000002626 -0.000004590 0.000002783 $VIB IVIB= 2 IATOM= 7 ICOORD= 1 E= -155.8262174396 -7.805437568E-06 1.765678117E-05-2.171542418E-07 1.627155637E-05 1.525962030E-06 9.090437493E-06 1.745019594E-04-1.264775220E-05-7.603964235E-05 1.653838324E-05 -4.864771611E-05 2.852627085E-06 2.994934100E-03-3.746587562E-04-7.943546935E-04 5.635193998E-05-2.514327666E-05-5.035744848E-08-3.233078255E-03 4.393910540E-04 8.653256505E-04-1.601273059E-05 1.383712370E-05-1.085183765E-05 9.247879785E-07 -6.723446734E-06 1.462018866E-06-2.626303484E-06-4.589973001E-06 2.782951240E-06 1.137920925E-01-1.130514001E-02 2.485927954E-02 1 ATOM 7 ------------------- COORD 2 NUCLEAR COORDINATES ------------------- VIB 2 ATOM X Y Z 1 C 0.793773 -0.808112 1.400575 2 H 2.289185 -0.995597 2.802099 3 C 1.446062 0.609240 -0.884553 4 H 3.409625 0.489515 -1.489324 5 C -0.143450 2.042156 -2.212893 6 H 0.464242 3.013674 -3.912111 7 H -2.091534 2.299425 -1.624756 8 C -1.429845 -1.902330 1.850402 9 H -2.943256 -1.862199 0.464672 10 H -1.792911 -2.895773 3.605888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 821.4 ( 13.7 MIN) TOTAL WALL CLOCK TIME= 827.7 SECONDS, CPU UTILIZATION IS 99.25% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 821.4 ( 13.7 MIN) TOTAL WALL CLOCK TIME= 827.7 SECONDS, CPU UTILIZATION IS 99.24% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8257383894 -155.8257383894 0.000868188 0.001465819 17704243 79749 2 1 0 -155.8257468208 -0.0000084314 0.000449783 0.000325193 16474191 129120 3 2 0 -155.8257471523 -0.0000003315 0.000234017 0.000227610 15736031 151215 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 4 3 0 -155.8262240775 -0.0004769252 0.000875739 0.001455491 17704213 79757 5 4 0 -155.8262309942 -0.0000069168 0.000544037 0.000375415 16455681 129943 6 5 0 -155.8262313338 -0.0000003395 0.000280501 0.000266780 15740173 150850 7 6 0 -155.8262317487 -0.0000004149 0.000058566 0.000090058 15340337 163698 8 7 0 -155.8262317684 -0.0000000197 0.000021572 0.000032905 14568117 188577 9 8 0 -155.8262317720 -0.0000000036 0.000002019 0.000002383 13824205 207877 10 9 0 -155.8262317722 -0.0000000002 0.000000862 0.000001911 12723602 238701 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 8.9 SECONDS ( 0.9 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262317722 AFTER 10 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9916805577 TOTAL ELECTRON NUMBER = 30.0000053421 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 9.17 TOTAL CPU TIME= 830.6 ( 13.8 MIN) TOTAL WALL CLOCK TIME= 836.9 SECONDS, CPU UTILIZATION IS 99.25% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 830.6 ( 13.8 MIN) TOTAL WALL CLOCK TIME= 836.9 SECONDS, CPU UTILIZATION IS 99.25% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.31 TOTAL CPU TIME= 832.9 ( 13.9 MIN) TOTAL WALL CLOCK TIME= 839.2 SECONDS, CPU UTILIZATION IS 99.25% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.35 TOTAL CPU TIME= 833.3 ( 13.9 MIN) TOTAL WALL CLOCK TIME= 839.6 SECONDS, CPU UTILIZATION IS 99.25% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.135597 -0.012195 0.031226 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.112036 -0.013114 0.024928 0.115523 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C 0.000018322 0.000036254 0.000033807 2 H 0.000018413 -0.000003108 0.000010069 3 C -0.000181675 -0.000038705 0.000069899 4 H -0.000022060 -0.000060212 -0.000072898 5 C -0.000397850 0.000484202 0.000005530 6 H 0.000140610 -0.000043631 -0.000041677 7 H 0.000432446 -0.000390170 0.000012707 8 C -0.000019580 0.000019308 -0.000022148 9 H 0.000007719 0.000002483 -0.000000116 10 H 0.000003656 -0.000006421 0.000004826 $VIB IVIB= 2 IATOM= 7 ICOORD= 2 E= -155.8262317722 1.832186931E-05 3.625400192E-05 3.380669682E-05 1.841262086E-05-3.108351060E-06 1.006937690E-05-1.816754367E-04-3.870522473E-05 6.989908166E-05-2.205967068E-05 -6.021223596E-05-7.289780442E-05-3.978495964E-04 4.842015971E-04 5.530096095E-06 1.406097483E-04-4.363086490E-05-4.167663308E-05 4.324457949E-04-3.901695860E-04 1.270690392E-05-1.957989235E-05 1.930787513E-05-2.214795580E-05 7.718774703E-06 2.483315739E-06-1.157942259E-07 3.655788069E-06-6.420527321E-06 4.826032124E-06 1.120362066E-01-1.311438001E-02 2.492786595E-02 1 ATOM 7 ------------------- COORD 3 NUCLEAR COORDINATES ------------------- VIB 2 ATOM X Y Z 1 C 0.793773 -0.808112 1.400575 2 H 2.289185 -0.995597 2.802099 3 C 1.446062 0.609240 -0.884553 4 H 3.409625 0.489515 -1.489324 5 C -0.143450 2.042156 -2.212893 6 H 0.464242 3.013674 -3.912111 7 H -2.091534 2.309425 -1.634756 8 C -1.429845 -1.902330 1.850402 9 H -2.943256 -1.862199 0.464672 10 H -1.792911 -2.895773 3.605888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 833.3 ( 13.9 MIN) TOTAL WALL CLOCK TIME= 839.6 SECONDS, CPU UTILIZATION IS 99.25% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 833.3 ( 13.9 MIN) TOTAL WALL CLOCK TIME= 839.6 SECONDS, CPU UTILIZATION IS 99.25% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8257297576 -155.8257297576 0.000941028 0.001458514 17701235 79850 2 1 0 -155.8257377304 -0.0000079728 0.000497015 0.000323457 16457700 129840 3 2 0 -155.8257379633 -0.0000002328 0.000266118 0.000252271 15728760 151426 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 4 3 0 -155.8262228306 -0.0004848674 0.000854603 0.001454359 17701317 79852 5 4 0 -155.8262295427 -0.0000067120 0.000566964 0.000379324 16448942 130162 6 5 0 -155.8262297897 -0.0000002470 0.000292712 0.000286635 15745981 151023 7 6 0 -155.8262302786 -0.0000004889 0.000079723 0.000114624 15385765 163266 8 7 0 -155.8262303142 -0.0000000355 0.000020304 0.000023637 14592785 187905 9 8 0 -155.8262303171 -0.0000000029 0.000002537 0.000003967 13826834 206908 10 9 0 -155.8262303172 -0.0000000001 0.000001314 0.000003391 12856452 235359 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 9.0 SECONDS ( 0.9 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.0 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262303172 AFTER 10 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9918531892 TOTAL ELECTRON NUMBER = 30.0000051790 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 9.18 TOTAL CPU TIME= 842.5 ( 14.0 MIN) TOTAL WALL CLOCK TIME= 848.8 SECONDS, CPU UTILIZATION IS 99.25% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 842.5 ( 14.0 MIN) TOTAL WALL CLOCK TIME= 848.9 SECONDS, CPU UTILIZATION IS 99.25% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.31 TOTAL CPU TIME= 844.8 ( 14.1 MIN) TOTAL WALL CLOCK TIME= 851.2 SECONDS, CPU UTILIZATION IS 99.25% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 845.1 ( 14.1 MIN) TOTAL WALL CLOCK TIME= 851.5 SECONDS, CPU UTILIZATION IS 99.25% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.135597 -0.012009 0.031039 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.110266 -0.010866 0.024352 0.113445 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C 0.000014296 0.000028097 0.000015039 2 H 0.000016075 0.000001446 0.000007058 3 C 0.000164027 -0.000034483 -0.000080387 4 H 0.000025275 -0.000071824 -0.000028089 5 C -0.000881160 0.000036277 0.000754251 6 H -0.000198902 0.000027341 0.000023754 7 H 0.000873523 0.000012574 -0.000678383 8 C -0.000016766 0.000013766 -0.000018708 9 H 0.000003754 -0.000010808 0.000001798 10 H -0.000000123 -0.000002386 0.000003668 $VIB IVIB= 2 IATOM= 7 ICOORD= 3 E= -155.8262303172 1.429633358E-05 2.809678895E-05 1.503875465E-05 1.607549314E-05 1.445649522E-06 7.057748800E-06 1.640274847E-04-3.448293148E-05-8.038657338E-05 2.527542481E-05 -7.182386409E-05-2.808861059E-05-8.811600488E-04 3.627699439E-05 7.542512608E-04 -1.989021229E-04 2.734137447E-05 2.375355592E-05 8.735226935E-04 1.257422102E-05 -6.783833833E-04-1.676601082E-05 1.376553939E-05-1.870781219E-05 3.754000182E-06 -1.080813284E-05 1.797551942E-06-1.232473579E-07-2.385639335E-06 3.667507354E-06 1.102664330E-01-1.086588157E-02 2.435175340E-02 1 ATOM 8 ------------------- COORD 1 NUCLEAR COORDINATES ------------------- VIB 2 ATOM X Y Z 1 C 0.793773 -0.808112 1.400575 2 H 2.289185 -0.995597 2.802099 3 C 1.446062 0.609240 -0.884553 4 H 3.409625 0.489515 -1.489324 5 C -0.143450 2.042156 -2.212893 6 H 0.464242 3.013674 -3.912111 7 H -2.091534 2.309425 -1.624756 8 C -1.439845 -1.902330 1.850402 9 H -2.943256 -1.862199 0.464672 10 H -1.792911 -2.895773 3.605888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 845.1 ( 14.1 MIN) TOTAL WALL CLOCK TIME= 851.5 SECONDS, CPU UTILIZATION IS 99.25% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 845.2 ( 14.1 MIN) TOTAL WALL CLOCK TIME= 851.6 SECONDS, CPU UTILIZATION IS 99.25% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8257099693 -155.8257099693 0.001445765 0.002145738 17700676 79849 2 1 0 -155.8257275305 -0.0000175612 0.001148465 0.000529880 16516179 127911 3 2 0 -155.8257279943 -0.0000004638 0.000568272 0.000431248 15925244 145517 4 3 0 -155.8257295338 -0.0000015396 0.000125174 0.000167568 15621176 156239 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 5 4 0 -155.8261892422 -0.0004597084 0.000881697 0.001424409 17700465 79858 6 5 0 -155.8261961830 -0.0000069408 0.000523918 0.000352146 16451972 130096 7 6 0 -155.8261965206 -0.0000003376 0.000271864 0.000237656 15707767 151813 8 7 0 -155.8261968939 -0.0000003733 0.000042928 0.000077944 15260921 165410 9 8 0 -155.8261969141 -0.0000000202 0.000018596 0.000038949 14631098 187961 10 9 0 -155.8261969194 -0.0000000053 0.000002318 0.000002134 13963077 202372 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 8.1 SECONDS ( 0.8 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8261969194 AFTER 10 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9904831869 TOTAL ELECTRON NUMBER = 30.0000051628 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.33 TOTAL CPU TIME= 853.5 ( 14.2 MIN) TOTAL WALL CLOCK TIME= 859.9 SECONDS, CPU UTILIZATION IS 99.25% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 853.5 ( 14.2 MIN) TOTAL WALL CLOCK TIME= 859.9 SECONDS, CPU UTILIZATION IS 99.25% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.30 TOTAL CPU TIME= 855.8 ( 14.3 MIN) TOTAL WALL CLOCK TIME= 862.3 SECONDS, CPU UTILIZATION IS 99.25% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 856.1 ( 14.3 MIN) TOTAL WALL CLOCK TIME= 862.6 SECONDS, CPU UTILIZATION IS 99.25% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.133377 -0.012009 0.031226 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.114447 -0.010910 0.022920 0.117229 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C 0.004436345 0.001754638 -0.000483523 2 H 0.000197783 0.000145756 -0.000033693 3 C 0.000033639 0.000164817 -0.000198750 4 H 0.000000378 -0.000015528 -0.000005372 5 C 0.000019888 -0.000038633 0.000073796 6 H 0.000017247 -0.000000424 0.000002279 7 H -0.000015912 -0.000009792 -0.000008490 8 C -0.007337798 -0.002302160 -0.000451087 9 H 0.002045760 0.000011752 0.001488767 10 H 0.000602672 0.000289574 -0.000383926 $VIB IVIB= 2 IATOM= 8 ICOORD= 1 E= -155.8261969194 4.436345363E-03 1.754637929E-03-4.835225012E-04 1.977826756E-04 1.457557367E-04 -3.369253540E-05 3.363858032E-05 1.648167306E-04-1.987501757E-04 3.776174894E-07 -1.552849926E-05-5.372302394E-06 1.988773452E-05-3.863313855E-05 7.379595609E-05 1.724655772E-05-4.235383053E-07 2.278834911E-06-1.591193308E-05-9.792300838E-06 -8.490087715E-06-7.337798358E-03-2.302159661E-03-4.510874978E-04 2.045759714E-03 1.175232537E-05 1.488766572E-03 6.026720481E-04 2.895744163E-04-3.839262628E-04 1.144474445E-01-1.091048348E-02 2.291970563E-02 1 ATOM 8 ------------------- COORD 2 NUCLEAR COORDINATES ------------------- VIB 2 ATOM X Y Z 1 C 0.793773 -0.808112 1.400575 2 H 2.289185 -0.995597 2.802099 3 C 1.446062 0.609240 -0.884553 4 H 3.409625 0.489515 -1.489324 5 C -0.143450 2.042156 -2.212893 6 H 0.464242 3.013674 -3.912111 7 H -2.091534 2.309425 -1.624756 8 C -1.429845 -1.912330 1.850402 9 H -2.943256 -1.862199 0.464672 10 H -1.792911 -2.895773 3.605888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 856.1 ( 14.3 MIN) TOTAL WALL CLOCK TIME= 862.6 SECONDS, CPU UTILIZATION IS 99.25% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 856.2 ( 14.3 MIN) TOTAL WALL CLOCK TIME= 862.6 SECONDS, CPU UTILIZATION IS 99.25% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8257220578 -155.8257220578 0.001099537 0.001411380 17698878 79869 2 1 0 -155.8257375719 -0.0000155141 0.000767609 0.000377573 16510120 128512 3 2 0 -155.8257379785 -0.0000004066 0.000388054 0.000306022 15836444 147905 4 3 0 -155.8257387329 -0.0000007544 0.000067842 0.000120033 15483864 159537 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 5 4 0 -155.8262111997 -0.0004724668 0.000851140 0.001438925 17698885 79874 6 5 0 -155.8262180981 -0.0000068983 0.000533716 0.000349807 16450400 130120 7 6 0 -155.8262184215 -0.0000003235 0.000279673 0.000238176 15706861 151870 8 7 0 -155.8262188089 -0.0000003873 0.000049395 0.000088553 15263277 165428 9 8 0 -155.8262188350 -0.0000000261 0.000018158 0.000037819 14659570 186678 10 9 0 -155.8262188401 -0.0000000051 0.000002457 0.000002128 13969718 202028 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 8.0 SECONDS ( 0.8 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262188401 AFTER 10 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9909464802 TOTAL ELECTRON NUMBER = 30.0000051006 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.19 TOTAL CPU TIME= 864.4 ( 14.4 MIN) TOTAL WALL CLOCK TIME= 870.9 SECONDS, CPU UTILIZATION IS 99.25% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 864.4 ( 14.4 MIN) TOTAL WALL CLOCK TIME= 870.9 SECONDS, CPU UTILIZATION IS 99.25% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.31 TOTAL CPU TIME= 866.7 ( 14.4 MIN) TOTAL WALL CLOCK TIME= 873.2 SECONDS, CPU UTILIZATION IS 99.25% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 867.0 ( 14.5 MIN) TOTAL WALL CLOCK TIME= 873.6 SECONDS, CPU UTILIZATION IS 99.25% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.135597 -0.014229 0.031226 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.111593 -0.003057 0.027295 0.114923 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C 0.001858641 0.001490178 -0.000503544 2 H -0.000006138 -0.000047153 -0.000006816 3 C 0.000180224 0.000081546 -0.000115967 4 H 0.000009067 -0.000005192 -0.000029118 5 C 0.000003906 0.000001844 0.000015647 6 H 0.000014665 -0.000011206 -0.000005657 7 H -0.000006256 0.000009161 0.000002236 8 C -0.002343303 -0.002987653 0.002042860 9 H 0.000015488 0.000411812 -0.000103157 10 H 0.000273707 0.001056665 -0.001296483 $VIB IVIB= 2 IATOM= 8 ICOORD= 2 E= -155.8262188401 1.858640887E-03 1.490177776E-03-5.035437906E-04-6.137993274E-06-4.715344733E-05 -6.816286675E-06 1.802243354E-04 8.154607220E-05-1.159670668E-04 9.066951287E-06 -5.192134571E-06-2.911826093E-05 3.906029768E-06 1.843536019E-06 1.564703795E-05 1.466478853E-05-1.120633631E-05-5.657467931E-06-6.256190603E-06 9.160939897E-06 2.236223995E-06-2.343303449E-03-2.987652881E-03 2.042859508E-03 1.548763729E-05 4.118116213E-04-1.031571757E-04 2.737070034E-04 1.056664854E-03-1.296482721E-03 1.115931301E-01-3.056553634E-03 2.729472499E-02 1 ATOM 8 ------------------- COORD 3 NUCLEAR COORDINATES ------------------- VIB 2 ATOM X Y Z 1 C 0.793773 -0.808112 1.400575 2 H 2.289185 -0.995597 2.802099 3 C 1.446062 0.609240 -0.884553 4 H 3.409625 0.489515 -1.489324 5 C -0.143450 2.042156 -2.212893 6 H 0.464242 3.013674 -3.912111 7 H -2.091534 2.309425 -1.624756 8 C -1.429845 -1.902330 1.840402 9 H -2.943256 -1.862199 0.464672 10 H -1.792911 -2.895773 3.605888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 867.0 ( 14.5 MIN) TOTAL WALL CLOCK TIME= 873.6 SECONDS, CPU UTILIZATION IS 99.25% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.02 TOTAL CPU TIME= 867.1 ( 14.5 MIN) TOTAL WALL CLOCK TIME= 873.6 SECONDS, CPU UTILIZATION IS 99.25% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8256957493 -155.8256957493 0.000883364 0.001488292 17705898 79734 2 1 0 -155.8257130676 -0.0000173183 0.000492367 0.000359422 16516174 127528 3 2 0 -155.8257135133 -0.0000004456 0.000305177 0.000253913 15775906 150568 4 3 0 -155.8257138696 -0.0000003563 0.000069075 0.000091473 15292012 164557 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 5 4 0 -155.8261977657 -0.0004838962 0.000910996 0.001471458 17706252 79732 6 5 0 -155.8262047294 -0.0000069637 0.000398686 0.000333005 16459618 129960 7 6 0 -155.8262050980 -0.0000003686 0.000165426 0.000231352 15730084 151110 8 7 0 -155.8262054331 -0.0000003351 0.000031263 0.000043910 15299810 163981 9 8 0 -155.8262054400 -0.0000000069 0.000012856 0.000030240 14490660 190076 10 9 0 -155.8262054433 -0.0000000033 0.000002269 0.000005905 13717888 211308 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 7.9 SECONDS ( 0.8 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262054433 AFTER 10 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9917271618 TOTAL ELECTRON NUMBER = 30.0000054475 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.19 TOTAL CPU TIME= 875.2 ( 14.6 MIN) TOTAL WALL CLOCK TIME= 881.9 SECONDS, CPU UTILIZATION IS 99.25% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 875.3 ( 14.6 MIN) TOTAL WALL CLOCK TIME= 881.9 SECONDS, CPU UTILIZATION IS 99.25% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.30 TOTAL CPU TIME= 877.5 ( 14.6 MIN) TOTAL WALL CLOCK TIME= 884.2 SECONDS, CPU UTILIZATION IS 99.25% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 877.9 ( 14.6 MIN) TOTAL WALL CLOCK TIME= 884.5 SECONDS, CPU UTILIZATION IS 99.25% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.135597 -0.012009 0.029005 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.110629 -0.008632 0.026663 0.114123 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C -0.000597394 -0.000545640 0.001101250 2 H 0.000238781 0.000087644 -0.000065985 3 C -0.000250307 -0.000177903 0.000061698 4 H -0.000003125 -0.000030522 0.000037140 5 C -0.000069093 0.000010633 -0.000004953 6 H 0.000021904 0.000007211 0.000004796 7 H -0.000005084 -0.000006830 -0.000004775 8 C -0.000436693 0.002029479 -0.005631596 9 H 0.001438859 -0.000130177 0.001869996 10 H -0.000337847 -0.001243897 0.002632429 $VIB IVIB= 2 IATOM= 8 ICOORD= 3 E= -155.8262054433 -5.973940969E-04-5.456397200E-04 1.101249610E-03 2.387805221E-04 8.764429748E-05 -6.598510345E-05-2.503067145E-04-1.779028110E-04 6.169803301E-05-3.125035286E-06 -3.052211569E-05 3.713993982E-05-6.909317694E-05 1.063322530E-05-4.953061040E-06 2.190379492E-05 7.211225086E-06 4.796427441E-06-5.083682730E-06-6.829919654E-06 -4.774898511E-06-4.366930375E-04 2.029478884E-03-5.631596112E-03 1.438858891E-03 -1.301765190E-04 1.869995737E-03-3.378474638E-04-1.243896546E-03 2.632429427E-03 1.106289514E-01-8.631751226E-03 2.666252111E-02 1 ATOM 9 ------------------- COORD 1 NUCLEAR COORDINATES ------------------- VIB 2 ATOM X Y Z 1 C 0.793773 -0.808112 1.400575 2 H 2.289185 -0.995597 2.802099 3 C 1.446062 0.609240 -0.884553 4 H 3.409625 0.489515 -1.489324 5 C -0.143450 2.042156 -2.212893 6 H 0.464242 3.013674 -3.912111 7 H -2.091534 2.309425 -1.624756 8 C -1.429845 -1.902330 1.850402 9 H -2.953256 -1.862199 0.464672 10 H -1.792911 -2.895773 3.605888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 877.9 ( 14.6 MIN) TOTAL WALL CLOCK TIME= 884.6 SECONDS, CPU UTILIZATION IS 99.25% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 877.9 ( 14.6 MIN) TOTAL WALL CLOCK TIME= 884.6 SECONDS, CPU UTILIZATION IS 99.25% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8257219449 -155.8257219449 0.001100432 0.001471111 17700787 79878 2 1 0 -155.8257320490 -0.0000101041 0.000975714 0.000533898 16460475 129608 3 2 0 -155.8257323360 -0.0000002870 0.000494433 0.000449775 15836576 148930 4 3 0 -155.8257335073 -0.0000011713 0.000101745 0.000121611 15466171 161819 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 5 4 0 -155.8262153838 -0.0004818765 0.000912173 0.001471111 17700924 79878 6 5 0 -155.8262222725 -0.0000068886 0.000429496 0.000336823 16450907 130170 7 6 0 -155.8262226480 -0.0000003756 0.000191369 0.000231838 15719412 151322 8 7 0 -155.8262229904 -0.0000003424 0.000022546 0.000032475 15289473 164216 9 8 0 -155.8262229959 -0.0000000054 0.000014294 0.000024542 14440780 191679 10 9 0 -155.8262229981 -0.0000000023 0.000002730 0.000006505 13578231 215047 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 8.0 SECONDS ( 0.8 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262229981 AFTER 10 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9903633119 TOTAL ELECTRON NUMBER = 30.0000053431 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.19 TOTAL CPU TIME= 886.1 ( 14.8 MIN) TOTAL WALL CLOCK TIME= 892.8 SECONDS, CPU UTILIZATION IS 99.25% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 886.1 ( 14.8 MIN) TOTAL WALL CLOCK TIME= 892.8 SECONDS, CPU UTILIZATION IS 99.25% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.31 TOTAL CPU TIME= 888.4 ( 14.8 MIN) TOTAL WALL CLOCK TIME= 895.1 SECONDS, CPU UTILIZATION IS 99.25% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 888.8 ( 14.8 MIN) TOTAL WALL CLOCK TIME= 895.5 SECONDS, CPU UTILIZATION IS 99.25% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.135411 -0.012009 0.031226 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.112273 -0.009252 0.027306 0.115916 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C 0.000165066 -0.000024282 0.000212105 2 H 0.000040442 0.000059668 0.000009204 3 C 0.000005756 -0.000033237 0.000003898 4 H 0.000014447 -0.000002533 -0.000004735 5 C -0.000035995 0.000007675 -0.000001634 6 H 0.000013315 -0.000004440 -0.000004243 7 H -0.000008800 0.000008123 0.000002676 8 C 0.002004834 0.000030708 0.001380380 9 H -0.002138916 -0.000047697 -0.001548174 10 H -0.000060149 0.000006016 -0.000049479 $VIB IVIB= 2 IATOM= 9 ICOORD= 1 E= -155.8262229981 1.650663584E-04-2.428214561E-05 2.121052539E-04 4.044242654E-05 5.966751537E-05 9.203926586E-06 5.756088962E-06-3.323740547E-05 3.898425684E-06 1.444681394E-05 -2.533071605E-06-4.735312638E-06-3.599518574E-05 7.675335437E-06-1.633729002E-06 1.331548647E-05-4.439998493E-06-4.242594067E-06-8.800206649E-06 8.123148041E-06 2.676126776E-06 2.004833613E-03 3.070847167E-05 1.380380464E-03-2.138916125E-03 -4.769735924E-05-1.548173903E-03-6.014926971E-05 6.015509899E-06-4.947865789E-05 1.122728147E-01-9.251858675E-03 2.730637694E-02 1 ATOM 9 ------------------- COORD 2 NUCLEAR COORDINATES ------------------- VIB 2 ATOM X Y Z 1 C 0.793773 -0.808112 1.400575 2 H 2.289185 -0.995597 2.802099 3 C 1.446062 0.609240 -0.884553 4 H 3.409625 0.489515 -1.489324 5 C -0.143450 2.042156 -2.212893 6 H 0.464242 3.013674 -3.912111 7 H -2.091534 2.309425 -1.624756 8 C -1.429845 -1.902330 1.850402 9 H -2.943256 -1.872199 0.464672 10 H -1.792911 -2.895773 3.605888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 888.8 ( 14.8 MIN) TOTAL WALL CLOCK TIME= 895.5 SECONDS, CPU UTILIZATION IS 99.25% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 888.8 ( 14.8 MIN) TOTAL WALL CLOCK TIME= 895.5 SECONDS, CPU UTILIZATION IS 99.25% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8257247198 -155.8257247198 0.000832250 0.001452648 17701168 79853 2 1 0 -155.8257333342 -0.0000086144 0.000459333 0.000323351 16456253 130056 3 2 0 -155.8257336960 -0.0000003618 0.000229091 0.000225379 15716475 151621 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 4 3 0 -155.8262245741 -0.0004908780 0.000843939 0.001445487 17701347 79855 5 4 0 -155.8262313244 -0.0000067503 0.000538335 0.000360440 16449222 130256 6 5 0 -155.8262316554 -0.0000003310 0.000283066 0.000244102 15710656 151672 7 6 0 -155.8262320529 -0.0000003976 0.000047916 0.000081465 15277003 165114 8 7 0 -155.8262320757 -0.0000000228 0.000017981 0.000037569 14634455 187452 9 8 0 -155.8262320808 -0.0000000051 0.000002829 0.000002095 13965685 202328 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 7.8 SECONDS ( 0.9 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262320808 AFTER 9 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9914522472 TOTAL ELECTRON NUMBER = 30.0000055719 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.00 TOTAL CPU TIME= 896.8 ( 14.9 MIN) TOTAL WALL CLOCK TIME= 903.6 SECONDS, CPU UTILIZATION IS 99.25% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 896.8 ( 14.9 MIN) TOTAL WALL CLOCK TIME= 903.6 SECONDS, CPU UTILIZATION IS 99.25% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.30 TOTAL CPU TIME= 899.1 ( 15.0 MIN) TOTAL WALL CLOCK TIME= 905.9 SECONDS, CPU UTILIZATION IS 99.25% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.37 TOTAL CPU TIME= 899.5 ( 15.0 MIN) TOTAL WALL CLOCK TIME= 906.3 SECONDS, CPU UTILIZATION IS 99.25% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.135597 -0.012195 0.031226 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.112431 -0.013269 0.024741 0.115883 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C 0.000084887 -0.000097695 0.000125262 2 H 0.000065782 -0.000069872 -0.000042283 3 C -0.000021781 0.000079806 0.000005917 4 H 0.000009751 -0.000009666 -0.000001364 5 C -0.000009763 0.000009880 0.000001433 6 H 0.000010226 -0.000007127 -0.000005365 7 H -0.000009022 0.000010285 -0.000004281 8 C 0.000015351 0.000430152 -0.000132067 9 H -0.000045028 -0.000321390 0.000136827 10 H -0.000100403 -0.000024374 -0.000084079 $VIB IVIB= 2 IATOM= 9 ICOORD= 2 E= -155.8262320808 8.488730317E-05-9.769466360E-05 1.252624747E-04 6.578156587E-05-6.987177228E-05 -4.228285787E-05-2.178064916E-05 7.980634492E-05 5.916904113E-06 9.750752263E-06 -9.665735353E-06-1.364249599E-06-9.762790236E-06 9.880027095E-06 1.432697792E-06 1.022560145E-05-7.127083993E-06-5.365136348E-06-9.022434462E-06 1.028468538E-05 -4.281313732E-06 1.535102171E-05 4.301523396E-04-1.320666077E-04-4.502777487E-05 -3.213898939E-04 1.368272685E-04-1.004025957E-04-2.437424784E-05-8.407917978E-05 1.124305206E-01-1.326892640E-02 2.474084333E-02 1 ATOM 9 ------------------- COORD 3 NUCLEAR COORDINATES ------------------- VIB 2 ATOM X Y Z 1 C 0.793773 -0.808112 1.400575 2 H 2.289185 -0.995597 2.802099 3 C 1.446062 0.609240 -0.884553 4 H 3.409625 0.489515 -1.489324 5 C -0.143450 2.042156 -2.212893 6 H 0.464242 3.013674 -3.912111 7 H -2.091534 2.309425 -1.624756 8 C -1.429845 -1.902330 1.850402 9 H -2.943256 -1.862199 0.454672 10 H -1.792911 -2.895773 3.605888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 899.5 ( 15.0 MIN) TOTAL WALL CLOCK TIME= 906.3 SECONDS, CPU UTILIZATION IS 99.25% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 899.5 ( 15.0 MIN) TOTAL WALL CLOCK TIME= 906.3 SECONDS, CPU UTILIZATION IS 99.25% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8257321075 -155.8257321075 0.001103842 0.001478322 17703032 79782 2 1 0 -155.8257422809 -0.0000101734 0.000910640 0.000505959 16477606 129101 3 2 0 -155.8257425726 -0.0000002917 0.000475359 0.000426627 15824044 149077 4 3 0 -155.8257435986 -0.0000010260 0.000097025 0.000121602 15444570 162377 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 5 4 0 -155.8262167193 -0.0004731208 0.000913656 0.001466616 17703111 79781 6 5 0 -155.8262236752 -0.0000069558 0.000423003 0.000338003 16455513 130022 7 6 0 -155.8262240537 -0.0000003785 0.000183550 0.000233784 15725213 151130 8 7 0 -155.8262243983 -0.0000003447 0.000025638 0.000034424 15296688 164022 9 8 0 -155.8262244038 -0.0000000054 0.000012818 0.000026163 14448930 191276 10 9 0 -155.8262244062 -0.0000000024 0.000002633 0.000006592 13618368 213736 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 7.9 SECONDS ( 0.8 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262244062 AFTER 10 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9904892145 TOTAL ELECTRON NUMBER = 30.0000054064 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.19 TOTAL CPU TIME= 907.7 ( 15.1 MIN) TOTAL WALL CLOCK TIME= 914.5 SECONDS, CPU UTILIZATION IS 99.25% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 907.7 ( 15.1 MIN) TOTAL WALL CLOCK TIME= 914.5 SECONDS, CPU UTILIZATION IS 99.25% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.31 TOTAL CPU TIME= 910.0 ( 15.2 MIN) TOTAL WALL CLOCK TIME= 916.9 SECONDS, CPU UTILIZATION IS 99.25% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 910.4 ( 15.2 MIN) TOTAL WALL CLOCK TIME= 917.2 SECONDS, CPU UTILIZATION IS 99.25% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.135597 -0.012009 0.031039 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.114925 -0.010812 0.026068 0.118340 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C -0.000057148 -0.000043074 -0.000050501 2 H 0.000014316 -0.000039553 -0.000022892 3 C -0.000013749 0.000044072 -0.000004364 4 H 0.000014514 -0.000004931 -0.000003932 5 C -0.000019737 0.000005602 -0.000000104 6 H 0.000013712 -0.000003265 -0.000004299 7 H -0.000009420 -0.000000944 -0.000000530 8 C 0.001433225 -0.000088889 0.001834611 9 H -0.001551997 0.000131260 -0.001860592 10 H 0.000176285 -0.000000279 0.000112606 $VIB IVIB= 2 IATOM= 9 ICOORD= 3 E= -155.8262244062 -5.714824172E-05-4.307392238E-05-5.050111988E-05 1.431638760E-05-3.955307152E-05 -2.289245730E-05-1.374920679E-05 4.407218605E-05-4.364441338E-06 1.451353770E-05 -4.931034665E-06-3.932473234E-06-1.973656939E-05 5.602136831E-06-1.038533768E-07 1.371156887E-05-3.265392704E-06-4.299173426E-06-9.419756487E-06-9.436254996E-07 -5.301666596E-07 1.433224662E-03-8.888869956E-05 1.834610640E-03-1.551997202E-03 1.312603462E-04-1.860592470E-03 1.762848195E-04-2.789227917E-07 1.126055150E-04 1.149252112E-01-1.081182681E-02 2.606821891E-02 1 ATOM 10 ------------------- COORD 1 NUCLEAR COORDINATES ------------------- VIB 2 ATOM X Y Z 1 C 0.793773 -0.808112 1.400575 2 H 2.289185 -0.995597 2.802099 3 C 1.446062 0.609240 -0.884553 4 H 3.409625 0.489515 -1.489324 5 C -0.143450 2.042156 -2.212893 6 H 0.464242 3.013674 -3.912111 7 H -2.091534 2.309425 -1.624756 8 C -1.429845 -1.902330 1.850402 9 H -2.943256 -1.862199 0.464672 10 H -1.802911 -2.895773 3.605888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 910.4 ( 15.2 MIN) TOTAL WALL CLOCK TIME= 917.2 SECONDS, CPU UTILIZATION IS 99.25% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 910.4 ( 15.2 MIN) TOTAL WALL CLOCK TIME= 917.2 SECONDS, CPU UTILIZATION IS 99.25% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8257273664 -155.8257273664 0.000843698 0.001449319 17701358 79841 2 1 0 -155.8257357932 -0.0000084268 0.000622118 0.000392671 16460203 129778 3 2 0 -155.8257361549 -0.0000003617 0.000334122 0.000269610 15746260 150944 4 3 0 -155.8257366000 -0.0000004451 0.000054440 0.000080315 15301674 164712 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 5 4 0 -155.8262231364 -0.0004865364 0.000907887 0.001470019 17701308 79839 6 5 0 -155.8262300574 -0.0000069210 0.000403994 0.000331604 16453303 130089 7 6 0 -155.8262304230 -0.0000003656 0.000171852 0.000230311 15718218 151421 8 7 0 -155.8262307521 -0.0000003292 0.000027401 0.000034261 15278552 164388 9 8 0 -155.8262307575 -0.0000000053 0.000010988 0.000024437 14429406 191472 10 9 0 -155.8262307596 -0.0000000021 0.000002589 0.000006925 13582371 214635 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 8.0 SECONDS ( 0.8 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262307596 AFTER 10 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9911560358 TOTAL ELECTRON NUMBER = 30.0000053952 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.19 TOTAL CPU TIME= 918.6 ( 15.3 MIN) TOTAL WALL CLOCK TIME= 925.5 SECONDS, CPU UTILIZATION IS 99.25% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 918.6 ( 15.3 MIN) TOTAL WALL CLOCK TIME= 925.5 SECONDS, CPU UTILIZATION IS 99.25% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.30 TOTAL CPU TIME= 920.9 ( 15.3 MIN) TOTAL WALL CLOCK TIME= 927.8 SECONDS, CPU UTILIZATION IS 99.25% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 921.2 ( 15.4 MIN) TOTAL WALL CLOCK TIME= 928.2 SECONDS, CPU UTILIZATION IS 99.25% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.135411 -0.012009 0.031226 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.110591 -0.009084 0.025657 0.113891 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C 0.000005823 0.000132062 -0.000240526 2 H 0.000013049 -0.000022538 -0.000006511 3 C 0.000026664 0.000057171 0.000013694 4 H 0.000016234 -0.000001898 -0.000010050 5 C -0.000020749 0.000005415 -0.000001932 6 H 0.000011118 -0.000007277 -0.000006914 7 H -0.000008559 0.000007412 0.000002180 8 C 0.000602566 0.000287468 -0.000362790 9 H -0.000057372 -0.000104558 0.000181939 10 H -0.000588774 -0.000353256 0.000430910 $VIB IVIB= 2 IATOM= 10 ICOORD= 1 E= -155.8262307596 5.823364346E-06 1.320620652E-04-2.405255840E-04 1.304907509E-05-2.253813522E-05 -6.511145878E-06 2.666437040E-05 5.717093754E-05 1.369385258E-05 1.623355575E-05 -1.897826014E-06-1.005006382E-05-2.074912399E-05 5.415158667E-06-1.931615304E-06 1.111794909E-05-7.277301380E-06-6.913939007E-06-8.559139625E-06 7.411505745E-06 2.179651182E-06 6.025658662E-04 2.874679014E-04-3.627903629E-04-5.737234428E-05 -1.045580100E-04 1.819393507E-04-5.887735730E-04-3.532562959E-04 4.309098565E-04 1.105907672E-01-9.083606078E-03 2.565650595E-02 1 ATOM 10 ------------------- COORD 2 NUCLEAR COORDINATES ------------------- VIB 2 ATOM X Y Z 1 C 0.793773 -0.808112 1.400575 2 H 2.289185 -0.995597 2.802099 3 C 1.446062 0.609240 -0.884553 4 H 3.409625 0.489515 -1.489324 5 C -0.143450 2.042156 -2.212893 6 H 0.464242 3.013674 -3.912111 7 H -2.091534 2.309425 -1.624756 8 C -1.429845 -1.902330 1.850402 9 H -2.943256 -1.862199 0.464672 10 H -1.792911 -2.905773 3.605888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 921.2 ( 15.4 MIN) TOTAL WALL CLOCK TIME= 928.2 SECONDS, CPU UTILIZATION IS 99.25% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 921.2 ( 15.4 MIN) TOTAL WALL CLOCK TIME= 928.2 SECONDS, CPU UTILIZATION IS 99.25% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8257253973 -155.8257253973 0.001005697 0.001467290 17700409 79853 2 1 0 -155.8257344518 -0.0000090545 0.000800824 0.000455803 16467871 129556 3 2 0 -155.8257347873 -0.0000003356 0.000426436 0.000327375 15785435 150124 4 3 0 -155.8257355366 -0.0000007493 0.000084043 0.000111350 15386299 163469 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 5 4 0 -155.8262208308 -0.0004852941 0.000908734 0.001472906 17700379 79856 6 5 0 -155.8262277509 -0.0000069201 0.000423375 0.000338188 16452577 130120 7 6 0 -155.8262281232 -0.0000003723 0.000186825 0.000230736 15718663 151379 8 7 0 -155.8262284599 -0.0000003367 0.000022881 0.000032031 15283056 164334 9 8 0 -155.8262284650 -0.0000000051 0.000012245 0.000022598 14424729 191942 10 9 0 -155.8262284668 -0.0000000018 0.000002817 0.000007061 13541736 215908 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 7.9 SECONDS ( 0.8 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262284668 AFTER 10 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9907439541 TOTAL ELECTRON NUMBER = 30.0000053331 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.20 TOTAL CPU TIME= 929.4 ( 15.5 MIN) TOTAL WALL CLOCK TIME= 936.4 SECONDS, CPU UTILIZATION IS 99.25% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 929.5 ( 15.5 MIN) TOTAL WALL CLOCK TIME= 936.4 SECONDS, CPU UTILIZATION IS 99.25% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.30 TOTAL CPU TIME= 931.8 ( 15.5 MIN) TOTAL WALL CLOCK TIME= 938.8 SECONDS, CPU UTILIZATION IS 99.25% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 932.1 ( 15.5 MIN) TOTAL WALL CLOCK TIME= 939.1 SECONDS, CPU UTILIZATION IS 99.25% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.135597 -0.012195 0.031226 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.113461 -0.012493 0.023854 0.116612 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C -0.000009630 0.000010960 -0.000134956 2 H -0.000003739 0.000057322 0.000041846 3 C 0.000073979 -0.000082408 -0.000029711 4 H 0.000018436 0.000009054 -0.000015612 5 C -0.000038872 0.000001250 0.000013111 6 H 0.000017895 -0.000000626 -0.000000880 7 H -0.000008362 -0.000000323 0.000002289 8 C 0.000285450 0.001077015 -0.001269665 9 H 0.000011911 -0.000025935 0.000006334 10 H -0.000347068 -0.001046309 0.001387244 $VIB IVIB= 2 IATOM= 10 ICOORD= 2 E= -155.8262284668 -9.630276283E-06 1.096027329E-05-1.349560991E-04-3.739424578E-06 5.732207223E-05 4.184648524E-05 7.397879354E-05-8.240833627E-05-2.971118050E-05 1.843641390E-05 9.054248298E-06-1.561194178E-05-3.887162392E-05 1.249732446E-06 1.311141632E-05 1.789544274E-05-6.255360592E-07-8.796275891E-07-8.362018552E-06-3.233275565E-07 2.288813830E-06 2.854499197E-04 1.077015001E-03-1.269665410E-03 1.191092836E-05 -2.593508638E-05 6.333608438E-06-3.470681549E-04-1.046309041E-03 1.387243935E-03 1.134605590E-01-1.249340423E-02 2.385372036E-02 1 ATOM 10 ------------------- COORD 3 NUCLEAR COORDINATES ------------------- VIB 2 ATOM X Y Z 1 C 0.793773 -0.808112 1.400575 2 H 2.289185 -0.995597 2.802099 3 C 1.446062 0.609240 -0.884553 4 H 3.409625 0.489515 -1.489324 5 C -0.143450 2.042156 -2.212893 6 H 0.464242 3.013674 -3.912111 7 H -2.091534 2.309425 -1.624756 8 C -1.429845 -1.902330 1.850402 9 H -2.943256 -1.862199 0.464672 10 H -1.792911 -2.895773 3.595888 ...... END OF ONE-ELECTRON INTEGRALS ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 932.1 ( 15.5 MIN) TOTAL WALL CLOCK TIME= 939.1 SECONDS, CPU UTILIZATION IS 99.25% ...... END OF TWO-ELECTRON INTEGRALS ..... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 932.1 ( 15.5 MIN) TOTAL WALL CLOCK TIME= 939.1 SECONDS, CPU UTILIZATION IS 99.25% -------------------------- R-PBE0 SCF CALCULATION -------------------------- DENSITY MATRIX CONVERGENCE THRESHOLD= 2.00E-05 COARSE -> FINE DFT GRID SWITCH THRESHOLD= 3.00E-04 (SWITCH IN $DFT) HF -> DFT SWITCH THRESHOLD= 5.00E-03 (SWOFF IN $DFT) DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=T, DIRTHR= 0.00E+00 NITDIR=10 DFT CODE IS SWITCHING FROM THE FINE GRID NRAD= 96, NLEB= 590 TO THE COARSE GRID NRAD0= 24, NLEB0= 110 NONZERO BLOCKS ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED * * * INITIATING DIIS PROCEDURE * * * 1 0 0 -155.8257162397 -155.8257162397 0.000905899 0.001445340 17704887 79731 2 1 0 -155.8257257352 -0.0000094955 0.000459092 0.000318126 16468966 129400 3 2 0 -155.8257254549 0.0000002803 0.000269070 0.000463377 15814800 150055 DFT CODE IS SWITCHING BACK TO THE FINE GRID * * * INITIATING DIIS PROCEDURE * * * 4 3 0 -155.8262124523 -0.0004869974 0.000953232 0.001456398 17704593 79737 5 4 0 -155.8262192259 -0.0000067736 0.000473728 0.000307241 16455299 129964 6 5 0 -155.8262194022 -0.0000001763 0.000251600 0.000228254 15732014 151181 7 6 0 -155.8262198250 -0.0000004228 0.000075472 0.000108199 15380698 162718 8 7 0 -155.8262198732 -0.0000000481 0.000015273 0.000022590 14631233 187132 9 8 0 -155.8262198758 -0.0000000026 0.000003751 0.000004788 13881630 205623 ----------------- DENSITY CONVERGED ----------------- TIME TO FORM FOCK OPERATORS= 7.8 SECONDS ( 0.9 SEC/ITER) FOCK TIME ON FIRST ITERATION= 0.2, LAST ITERATION= 1.2 TIME TO SOLVE SCF EQUATIONS= 0.1 SECONDS ( 0.0 SEC/ITER) FINAL R-PBE0 ENERGY IS -155.8262198758 AFTER 9 ITERATIONS DFT EXCHANGE + CORRELATION ENERGY = -17.9927107837 TOTAL ELECTRON NUMBER = 30.0000053492 ...... END OF RHF CALCULATION ...... CPU 0: STEP CPU TIME= 8.00 TOTAL CPU TIME= 940.1 ( 15.7 MIN) TOTAL WALL CLOCK TIME= 947.2 SECONDS, CPU UTILIZATION IS 99.25% ..... END OF 1-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 940.1 ( 15.7 MIN) TOTAL WALL CLOCK TIME= 947.2 SECONDS, CPU UTILIZATION IS 99.25% MEMORY FOR GRID POINT CONTRIBUTIONS TO THE DFT GRADIENT= 700705 WORDS. CPU 0: STEP CPU TIME= 2.30 TOTAL CPU TIME= 942.4 ( 15.7 MIN) TOTAL WALL CLOCK TIME= 949.5 SECONDS, CPU UTILIZATION IS 99.25% ...... END OF 2-ELECTRON GRADIENT ...... CPU 0: STEP CPU TIME= 0.36 TOTAL CPU TIME= 942.8 ( 15.7 MIN) TOTAL WALL CLOCK TIME= 949.9 SECONDS, CPU UTILIZATION IS 99.25% --------------------- ELECTROSTATIC MOMENTS --------------------- POINT 1 X Y Z (BOHR) CHARGE 0.135597 -0.012009 0.031039 -0.00 (A.U.) DX DY DZ /D/ (DEBYE) 0.111683 -0.012811 0.026894 0.115587 UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C 0.000015540 -0.000028684 0.000010417 2 H 0.000003391 0.000033507 0.000012730 3 C 0.000020161 -0.000028863 -0.000032220 4 H 0.000015395 -0.000002969 -0.000006530 5 C -0.000034682 0.000006286 0.000005463 6 H 0.000015734 -0.000003866 -0.000001501 7 H -0.000006953 0.000003772 0.000001233 8 C -0.000407982 -0.001299667 0.002676872 9 H -0.000051378 -0.000092568 0.000113453 10 H 0.000430775 0.001413053 -0.002779920 $VIB IVIB= 2 IATOM= 10 ICOORD= 3 E= -155.8262198758 1.554027204E-05-2.868409232E-05 1.041708073E-05 3.391152860E-06 3.350664920E-05 1.273040203E-05 2.016076547E-05-2.886341487E-05-3.221957008E-05 1.539472265E-05 -2.968633918E-06-6.529507371E-06-3.468220642E-05 6.285920092E-06 5.463076305E-06 1.573404563E-05-3.866286739E-06-1.500569901E-06-6.953246371E-06 3.771653830E-06 1.233207302E-06-4.079820932E-04-1.299666539E-03 2.676872455E-03-5.137805666E-05 -9.256799159E-05 1.134532908E-04 4.307746440E-04 1.413052735E-03-2.779919865E-03 1.116826549E-01-1.281073026E-02 2.689439118E-02 ...... END OF NUMERICAL HESSIAN CALCULATION ...... CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 942.8 ( 15.7 MIN) TOTAL WALL CLOCK TIME= 949.9 SECONDS, CPU UTILIZATION IS 99.25% --------------- ENERGY GRADIENT --------------- UNITS ARE HARTREE/BOHR E'X E'Y E'Z 1 C -0.000012686 -0.000019453 0.000007010 2 H 0.000016279 0.000003229 0.000006823 3 C 0.000007488 0.000011335 -0.000005322 4 H 0.000013931 -0.000003734 -0.000003243 5 C -0.000027281 0.000006072 0.000003468 6 H 0.000015261 -0.000004713 -0.000004364 7 H -0.000007620 0.000002771 0.000001358 8 C -0.000006939 0.000012966 -0.000012739 9 H 0.000002556 -0.000005222 0.000003831 10 H -0.000000988 -0.000003252 0.000003179 ------------------------------- CARTESIAN FORCE CONSTANT MATRIX ------------------------------- 1 2 C H X Y Z X Y Z 1 C X 0.770238 0.200765 0.044736-0.198262 0.018951-0.135944 Y 0.200765 0.308230-0.181832 0.014531-0.043431 0.022701 Z 0.044736-0.181832 0.508576-0.134275 0.022314-0.182500 2 H X-0.198262 0.014531-0.134275 0.210311-0.011113 0.148710 Y 0.018951-0.043431 0.022314-0.011113 0.037754-0.030755 Z-0.135944 0.022701-0.182500 0.148710-0.030755 0.188493 3 C X-0.111576-0.022220 0.038759 0.007034 0.012514-0.020107 Y-0.014482-0.111355 0.076573-0.001098-0.001146 0.002468 Z 0.018942 0.076570-0.199108 0.005771 0.013907-0.012932 4 H X-0.005387 0.000584 0.000553 0.000643-0.000682 0.000364 Y-0.017652 0.001479 0.007199 0.000676-0.000073-0.000117 Z 0.024695-0.001363-0.003191-0.000477-0.000355 0.000746 5 C X 0.016354 0.001721-0.005824 0.000442-0.002393 0.002554 Y 0.007181-0.010786 0.019386-0.001684 0.000649 0.001854 Z-0.010831 0.026453-0.021966 0.001011 0.001900-0.003624 6 H X-0.000883 0.003993 0.000521 0.000121 0.000000-0.000544 Y 0.006748 0.007492 0.005303-0.000417-0.001305 0.001345 Z 0.000136 0.005965 0.003438-0.000022-0.000044 0.000036 7 H X-0.000516-0.003750 0.000734 0.000034 0.000166-0.000204 Y-0.003067-0.005562-0.002677-0.000206 0.000633-0.000309 Z-0.002666-0.004733-0.000810 0.000028 0.000176-0.000004 8 C X-0.450311-0.180859 0.050571-0.018243-0.014354 0.004031 Y-0.188350-0.150875 0.051302 0.002243 0.005033 0.001390 Z 0.059101 0.052916-0.109849-0.022273-0.008406 0.007332 9 H X-0.017790 0.000449-0.020568-0.002403-0.005657-0.000223 Y-0.009807 0.007828-0.011805-0.004955 0.007314 0.004911 Z 0.004575 0.002373 0.005808 0.000218 0.004292 0.003002 10 H X-0.001839-0.015216 0.024808 0.000335 0.002567 0.001368 Y-0.000304-0.003034 0.014247 0.002029-0.005426-0.003486 Z-0.002704 0.000969-0.000406 0.001297-0.003031-0.000553 3 4 C H X Y Z X Y Z 3 C X 0.709175-0.169385 0.026290-0.303031 0.014187 0.079108 Y-0.169385 0.374415-0.266662 0.018040-0.042428 0.002218 Z 0.026290-0.266662 0.503258 0.077265 0.000220-0.078612 4 H X-0.303031 0.018040 0.077265 0.323459-0.021649-0.085937 Y 0.014187-0.042428 0.000220-0.021649 0.038676-0.009991 Z 0.079108 0.002218-0.078612-0.085937-0.009991 0.074363 5 C X-0.288349 0.167747-0.133528-0.017486 0.021076-0.016574 Y 0.175540-0.215418 0.154786 0.000877 0.002004 0.002906 Z-0.141962 0.154400-0.207174 0.008328-0.002946 0.009606 6 H X 0.008083 0.012053-0.018166 0.000826-0.001992-0.001242 Y-0.008179-0.004847 0.016471-0.001302-0.004731-0.004017 Z 0.007275 0.006563-0.008540-0.001125-0.003856-0.001733 7 H X-0.016708 0.002460 0.007044-0.000215 0.004492-0.000598 Y 0.018795 0.005058-0.007617 0.003607 0.005641 0.006963 Z-0.015703 0.004671 0.007431-0.001117 0.006793 0.002483 8 C X-0.002709-0.015333 0.019295 0.001387 0.001169 0.000219 Y-0.017417-0.006922 0.011089 0.000510 0.000123 0.002602 Z 0.025653 0.018888-0.006763 0.001747 0.002679-0.004057 9 H X 0.000092 0.004541-0.000983 0.000001-0.000120 0.000134 Y 0.002912-0.006836-0.001134 0.000427 0.000595-0.000192 Z 0.002035-0.003219-0.000160-0.000005 0.000114 0.000060 10 H X-0.002009-0.004524-0.001953-0.000181-0.000190 0.000673 Y-0.006741 0.009471 0.002381-0.000401-0.001287 0.001224 Z-0.001349 0.004102 0.002593-0.000084-0.000097 0.000340 5 6 C H X Y Z X Y Z 5 C X 0.682900-0.185764-0.011745-0.082582-0.036324 0.075535 Y-0.185764 0.375403-0.297886-0.039487-0.104324 0.122363 Z-0.011745-0.297886 0.543770 0.079787 0.120482-0.246069 6 H X-0.082582-0.039487 0.079787 0.078116 0.037711-0.081077 Y-0.036324-0.104324 0.120482 0.037711 0.103400-0.134764 Z 0.075535 0.122363-0.246069-0.081077-0.134764 0.256609 7 H X-0.306729 0.038902 0.081448-0.004057 0.002030-0.000419 Y 0.037668-0.048093-0.000387-0.012547 0.003894 0.003800 Z 0.085520-0.003046-0.075474 0.021316-0.003270-0.002745 8 C X-0.004729 0.004492-0.007056-0.000207-0.000428-0.000655 Y-0.003123 0.000437-0.001222 0.000055 0.000647 0.000141 Z 0.004161-0.000456 0.000842-0.000679-0.001235-0.000853 9 H X 0.000845-0.000121 0.000466 0.000173-0.000071 0.000056 Y-0.001760-0.000379 0.000198 0.000499 0.000234 0.000104 Z-0.000786 0.000085 0.000315 0.000139-0.000186 0.000065 10 H X-0.000685 0.000092 0.000517 0.000404 0.000215 0.000321 Y 0.001135 0.000518-0.000999-0.000283-0.000457-0.000276 Z 0.000697 0.000006-0.000231-0.000059-0.000133-0.000196 7 8 H C X Y Z X Y Z 7 H X 0.326982-0.044491-0.088103 0.000855-0.000111-0.000178 Y-0.044491 0.039534-0.000955 0.001253-0.000643 0.000941 Z-0.088103-0.000955 0.068355 0.000974-0.000090 0.000598 8 C X 0.000855 0.001253 0.000974 0.737314 0.235157 0.039477 Y-0.000111-0.000643-0.000090 0.235157 0.300164-0.204333 Z-0.000178 0.000941 0.000598 0.039477-0.204333 0.564421 9 H X 0.000192-0.000540-0.000150-0.202727-0.001762-0.141541 Y 0.000147-0.000761 0.000561-0.001654-0.041732 0.012432 Z 0.000257 0.000367 0.000173-0.146045 0.010239-0.185684 10 H X 0.000173-0.000475-0.000099-0.060670-0.027227 0.034555 Y 0.000156 0.000298-0.000109-0.029448-0.106234 0.126571 Z 0.000019-0.000126-0.000007 0.039190 0.128880-0.265982 9 10 H H X Y Z X Y Z 9 H X 0.215651 0.004250 0.157409 0.005959-0.000958 0.005380 Y 0.004250 0.031655-0.013771 0.009943 0.002081 0.008695 Z 0.157409-0.013771 0.187364-0.017808-0.000286-0.010959 10 H X 0.005959 0.009943-0.017808 0.058515 0.034818-0.042389 Y-0.000958 0.002081-0.000286 0.034818 0.104078-0.139275 Z 0.005380 0.008695-0.010959-0.042389-0.139275 0.275416 ------------------------ ---------------- DIPOLE DERIVATIVE TENSOR (DEBYE/ANGSTROM) ------------------------ ---------------- ATOM MU-X MU-Y MU-Z C D/DX 0.174495595 0.049597807 0.816257508 D/DY 0.506082459 -0.163643433 -0.471613485 D/DZ 0.403817316 -0.764784320 0.729851616 H D/DX -0.150908747 -0.081322282 -0.429921530 D/DY -0.020281325 0.538481904 0.236596967 D/DZ -0.324350725 0.433563362 -0.104211073 C D/DX 0.581390081 0.149684521 -0.853497033 D/DY -0.429938415 -0.223609042 -0.457852477 D/DZ -0.470636116 -0.691075272 0.057837964 H D/DX -0.325791202 0.132587526 0.204907265 D/DY 0.087797260 0.604832007 0.202346883 D/DZ 0.242623475 0.292292870 0.213600644 C D/DX -0.029819999 -0.223501206 -0.521616732 D/DY -0.213709290 -1.167702196 -0.166247573 D/DZ -0.284819530 -0.307123853 -0.572432159 H D/DX 0.295197281 -0.039275813 0.264204005 D/DY 0.099290067 0.453661798 0.338642872 D/DZ 0.228646159 0.619279710 -0.066092571 H D/DX -0.369998513 0.263140190 0.233558344 D/DY 0.085486612 0.514916902 0.178961205 D/DZ 0.386889080 0.137966046 0.284673453 C D/DX -0.385473404 0.161718775 0.629337222 D/DY 0.257210941 -1.288473377 -0.287565214 D/DZ 0.330975120 -0.260759581 -0.209526761 H D/DX -0.048481860 -0.184570635 -0.275401158 D/DY -0.014361781 0.602349382 0.199344558 D/DZ -0.495067034 0.143144989 -0.079285394 H D/DX 0.421450377 -0.171199880 0.056539512 D/DY -0.273603028 0.577898419 0.412968724 D/DZ 0.142744154 0.474589945 -0.131291473 -------------------------------------------------------- NORMAL COORDINATE ANALYSIS IN THE HARMONIC APPROXIMATION -------------------------------------------------------- ATOMIC WEIGHTS (AMU) 1 C 12.00000 2 H 1.00782 3 C 12.00000 4 H 1.00782 5 C 12.00000 6 H 1.00782 7 H 1.00782 8 C 12.00000 9 H 1.00782 10 H 1.00782 MODES 1 TO 6 ARE TAKEN AS ROTATIONS AND TRANSLATIONS. ANALYZING SYMMETRY OF NORMAL MODES... FREQUENCIES IN CM**-1, IR INTENSITIES IN DEBYE**2/AMU-ANGSTROM**2, REDUCED MASSES IN AMU. 1 2 3 4 5 FREQUENCY: 2.69 2.14 0.10 0.07 0.02 SYMMETRY: A A A A A REDUCED MASS: 3.37004 2.93978 5.40506 5.41135 5.41378 IR INTENSITY: 0.00084 0.00053 0.00131 0.00152 0.00341 1 C X 0.00862488 -0.08368133 0.13477565 0.00270027 -0.02166176 Y -0.08612203 -0.00006232 0.01264063 0.09959612 0.09310250 Z -0.05341980 0.03882638 0.01612636 -0.09321179 0.09874070 2 H X 0.02330737 -0.16835577 0.13509775 0.00283937 -0.02288762 Y -0.18189147 -0.00214732 0.01262601 0.10089804 0.09409489 Z -0.08190266 0.12889135 0.01577560 -0.09319316 0.10018566 3 C X -0.00543615 0.05759048 0.13420233 0.00136665 -0.01988059 Y 0.04280516 -0.00534009 0.01273286 0.10045443 0.09211703 Z 0.02250440 0.07583674 0.01603798 -0.09305293 0.09863382 4 H X -0.01343432 0.09352064 0.13403219 0.00148293 -0.01931101 Y 0.06135105 -0.01195582 0.01274268 0.10239800 0.09220836 Z -0.00714005 0.19379467 0.01550067 -0.09303764 0.10046057 5 C X -0.00826590 0.14142815 0.13387478 0.00000970 -0.01896937 Y 0.13483810 -0.00268411 0.01282767 0.09906934 0.09114885 Z 0.12517764 -0.02161771 0.01653985 -0.09291283 0.09650067 6 H X -0.01937245 0.24607320 0.13343340 -0.00090763 -0.01763586 Y 0.22959343 -0.00700078 0.01291760 0.09983560 0.09042988 Z 0.17539493 0.01333274 0.01641869 -0.09279683 0.09656574 7 H X 0.00082533 0.10693464 0.13402937 -0.00025112 -0.01955230 Y 0.11716628 0.00381775 0.01282974 0.09714165 0.09104761 Z 0.16330972 -0.13882950 0.01706657 -0.09290047 0.09461530 8 C X 0.00416934 -0.11387930 0.13491811 0.00374823 -0.02184527 Y -0.09296878 0.00703634 0.01257093 0.09738908 0.09286890 Z -0.09205826 -0.09319342 0.01659684 -0.09336738 0.09726030 9 H X -0.01158560 -0.03034753 0.13459782 0.00372867 -0.02059052 Y 0.00226601 0.00943112 0.01257619 0.09605154 0.09188048 Z -0.07210539 -0.18435458 0.01695408 -0.09340038 0.09586501 10 H X 0.01574614 -0.22238414 0.13534343 0.00466976 -0.02323297 Y -0.19327538 0.01068572 0.01249726 0.09685611 0.09365062 Z -0.14642650 -0.11358236 0.01664489 -0.09346889 0.09741323 TRANS. SAYVETZ X -0.01544270 0.04313615 7.26609545 0.10555053 -1.11245828 Y 0.01811498 -0.00974940 0.68605077 5.35593010 4.98848879 Z 0.05782137 -0.10331222 0.88274249 -5.03370910 5.28330988 TOTAL 0.06252951 0.11237968 7.35160140 7.35087447 7.35091471 ROT. SAYVETZ X 17.35795021 1.77551906 0.00866366 0.06760495 -0.10803319 Y -0.51266853-16.23713879 0.06428483 0.13349229 -0.19030643 Z 1.80964685 -9.52849512 0.04014901 0.21704293 -0.10490228 TOTAL 17.45955573 18.91003341 0.07628592 0.26362522 0.24267715 6 7 8 9 10 FREQUENCY: 3.33 170.40 271.93 469.52 621.14 SYMMETRY: A A A A A REDUCED MASS: 2.31101 1.56673 2.41788 1.35538 1.70435 IR INTENSITY: 0.00240 0.00507 0.00061 0.48591 0.24652 1 C X 0.00229405 -0.03531441 -0.05627737 -0.03869976 -0.08715160 Y -0.07054763 0.08655214 -0.01699540 -0.01923206 0.07764331 Z -0.04367113 0.04367479 -0.02330843 -0.08573138 -0.04981142 2 H X 0.05919331 -0.10524559 0.01405106 -0.13114539 -0.08171465 Y -0.21560434 0.34072448 -0.02720694 0.24625609 -0.13801602 Z -0.12378757 0.15445678 -0.09714715 0.05189475 -0.08198433 3 C X 0.00625964 -0.02666907 -0.05672111 0.06839316 0.11184372 Y -0.10274157 -0.08136471 0.02708885 -0.02859769 0.05981732 Z -0.06252151 -0.05828906 -0.00284009 -0.06083582 -0.00386470 4 H X -0.03557367 -0.08312874 -0.02474942 0.13486498 0.08489139 Y -0.26649345 -0.32499281 0.02798714 0.22347381 -0.15299590 Z -0.16593706 -0.19837559 0.09490490 0.11322192 -0.04338514 5 C X 0.06136933 0.02928998 0.07442028 0.00792240 0.02032972 Y 0.04920066 0.06093863 0.08694914 0.00067686 -0.03947671 Z 0.03544902 0.03161480 -0.09726837 0.04901738 0.02307427 6 H X 0.05713554 -0.00673204 0.25727678 -0.03974030 -0.27659499 Y 0.01467260 -0.06153365 0.09969111 0.34305189 -0.16779375 Z 0.01419137 -0.05203882 -0.02539480 0.22821862 -0.15378240 7 H X 0.11512611 0.11422596 0.02650915 -0.04332144 0.10563809 Y 0.21174572 0.30061016 0.12953768 -0.31995611 -0.05693665 Z 0.13965156 0.20405774 -0.27433984 0.02366411 0.31499563 8 C X -0.06941999 0.02922555 0.00875521 -0.02825614 -0.03464100 Y 0.11812714 -0.06584177 -0.09431756 0.00420148 -0.03417749 Z 0.06074848 -0.01783622 0.11646186 0.04039907 0.00996529 9 H X -0.13833698 0.13877559 -0.11808147 -0.02586904 -0.24016428 Y 0.26488863 -0.32308266 -0.12205555 -0.32205955 -0.02623398 Z 0.14027891 -0.14495137 0.25376981 0.02777842 0.23527754 10 H X -0.06419796 -0.01816090 0.20049017 -0.00634343 0.28436809 Y 0.13089583 0.06436953 -0.14020124 0.34061641 -0.21782309 Z 0.06905309 0.04681401 0.13092631 0.23582237 -0.02540350 TRANS. SAYVETZ X -0.00066940 -0.00157018 0.00040217 -0.00011161 0.00002683 Y 0.06966461 -0.00052398 0.00020029 -0.00003289 -0.00006767 Z -0.04591672 0.00001233 -0.00009379 0.00011686 0.00000185 TOTAL 0.08343830 0.00165535 0.00045897 0.00016490 0.00007282 ROT. SAYVETZ X -1.81198916 0.01054801 0.00038088 0.00322964 0.00206649 Y 0.59215627 0.00510145 -0.01017730 -0.00184200 -0.00225599 Z-11.37438441 -0.01430296 -0.00906434 0.00003154 -0.00155647 TOTAL 11.53302105 0.01848945 0.01363396 0.00371814 0.00343256 11 12 13 14 15 FREQUENCY: 761.75 894.04 946.61 947.84 1019.87 SYMMETRY: A A A A A REDUCED MASS: 1.63208 1.95200 1.37405 1.34932 1.12649 IR INTENSITY: 0.12263 0.03108 0.24423 2.03708 0.02102 1 C X -0.03066889 -0.00890132 -0.01543352 -0.00863605 -0.02422425 Y 0.11351973 0.05234660 0.04008472 0.02137508 0.06012210 Z 0.05379327 -0.09678418 0.00995409 0.01222915 0.00119579 2 H X 0.07879844 -0.02137340 -0.00864092 -0.00448916 0.22693779 Y -0.04033907 -0.00981069 0.02687757 -0.00732769 -0.37644754 Z -0.08717178 -0.09903016 -0.00040190 0.00399918 -0.32647548 3 C X -0.02280358 -0.05928547 -0.01377064 0.00947969 -0.03079648 Y -0.10889608 -0.04663390 -0.03067010 0.02900998 -0.05495873 Z -0.06620617 0.08140687 -0.01249549 0.02014788 -0.01381851 4 H X 0.03884208 -0.06104424 -0.01125126 0.00376273 0.12167493 Y 0.03077864 0.01655592 -0.02504644 -0.00119578 0.34366421 Z 0.11465371 0.07989113 -0.00240648 0.00690061 0.40537041 5 C X 0.01253857 -0.00900197 0.02364527 -0.02883601 0.01833424 Y -0.01249934 -0.06167670 0.06038291 -0.08997101 0.01566468 Z 0.01855504 0.07629132 0.05945935 -0.06594361 -0.00518187 6 H X 0.06631935 0.34078396 -0.05050154 0.10054951 -0.14146433 Y 0.37302786 -0.17492379 -0.26957598 0.37046600 -0.14641287 Z 0.26082132 0.13887716 -0.15543574 0.24407374 -0.15309482 7 H X -0.04045004 -0.03239155 -0.11422101 0.14153284 0.10046749 Y -0.24007699 0.19376163 -0.30195431 0.38493699 0.13237075 Z -0.05362696 -0.13737801 -0.23082529 0.27948519 0.21808835 8 C X 0.02125285 0.03533602 0.04572551 0.02822764 0.01134050 Y 0.00949896 0.06003385 -0.08894777 -0.07474553 -0.01836397 Z -0.01069318 -0.07030193 -0.05721612 -0.03670238 0.01210202 9 H X -0.01854594 -0.11991128 -0.19394773 -0.13589077 0.16194862 Y 0.24538581 -0.18258219 0.42424383 0.31111318 -0.15669026 Z 0.03964084 0.10085414 0.21837623 0.15271015 -0.15817733 10 H X 0.10929128 0.39190794 -0.09976132 -0.10825031 -0.16774366 Y -0.38813082 0.10847784 0.37348223 0.30335776 0.17416921 Z -0.22008356 0.02861538 0.17423322 0.14956665 0.08219154 TRANS. SAYVETZ X -0.00008437 -0.00036480 -0.00006725 0.00001631 0.00003065 Y -0.00002673 -0.00006266 0.00000839 0.00002530 -0.00000721 Z 0.00004548 0.00004968 -0.00001024 0.00005551 0.00000312 TOTAL 0.00009950 0.00037346 0.00006854 0.00006315 0.00003164 ROT. SAYVETZ X -0.00088032 0.00199356 -0.00059095 -0.00037595 0.00005496 Y -0.00006173 -0.00325223 0.00008459 -0.00092591 0.00045978 Z 0.00090076 -0.00284987 0.00121371 0.00013010 -0.00017815 TOTAL 0.00126101 0.00476163 0.00135258 0.00100775 0.00049614 16 17 18 19 20 FREQUENCY: 1036.18 1069.18 1101.40 1307.37 1339.56 SYMMETRY: A A A A A REDUCED MASS: 1.09179 1.50814 1.60028 1.25244 1.29835 IR INTENSITY: 0.75023 0.01056 0.14013 0.00627 0.00467 1 C X 0.01293282 0.02447101 0.04508727 -0.03798550 0.05130182 Y -0.04709070 0.00990934 -0.04639870 -0.00431545 -0.00945373 Z -0.03056115 0.10902679 0.06084165 -0.04059886 0.05001500 2 H X -0.14089565 -0.13177297 -0.10712571 -0.37762298 0.37431061 Y 0.47432677 -0.37273109 -0.07636231 -0.27190666 0.26934698 Z 0.20218072 0.22715834 0.21429386 0.28366004 -0.24423707 3 C X -0.00625903 0.06659995 -0.07440927 0.05126677 0.06805253 Y -0.04559305 -0.01828384 -0.03566401 -0.01207426 -0.00097674 Z -0.03484503 -0.08745804 0.03378922 -0.02070416 -0.02243237 4 H X 0.11647890 0.04384210 -0.01069776 0.16752267 0.17856585 Y 0.45342406 0.37979586 -0.08801744 -0.32280827 -0.31498837 Z 0.26222856 -0.24637641 0.23953048 0.41261862 0.36856000 5 C X 0.00029853 -0.04728893 0.03378799 -0.07223606 -0.06794530 Y 0.00279813 0.01429257 0.04637756 0.02397005 0.01729050 Z 0.01276534 0.01121639 -0.07520060 -0.00126091 0.00638300 6 H X -0.03579739 0.14091189 -0.32499623 -0.04648113 -0.04356221 Y -0.22126323 -0.07428506 0.19234525 0.02031465 0.01172775 Z -0.12922578 0.01937218 -0.11828003 -0.00394723 0.00021494 7 H X 0.07939874 -0.07423947 0.08011701 -0.11569097 -0.11720942 Y 0.26909756 0.21477220 -0.16716499 0.18341728 0.19575887 Z 0.15146333 -0.17465182 0.20518393 -0.20441912 -0.22342052 8 C X -0.00532937 -0.03934334 0.01069975 0.06776020 -0.06085143 Y 0.00342023 -0.00627449 0.04828514 0.01145840 -0.00607821 Z 0.01159515 -0.03199377 -0.08030580 0.03063937 -0.03608825 9 H X -0.08979859 -0.17956081 -0.18657664 0.21965194 -0.23625958 Y 0.28231548 -0.19339691 -0.14118021 0.15163158 -0.16602180 Z 0.11096724 0.11810851 0.14230238 -0.12552653 0.14456616 10 H X 0.05106220 0.14807367 0.36869001 0.04775927 -0.04325112 Y -0.22836735 0.05010886 0.13037692 0.01267210 -0.00509881 Z -0.10889334 0.04696321 0.04180982 0.01772455 -0.02041312 TRANS. SAYVETZ X 0.00001062 0.00010586 -0.00001355 -0.00001686 0.00016659 Y 0.00000463 0.00002017 0.00002325 0.00001176 0.00003385 Z -0.00000336 -0.00000339 0.00000599 -0.00001004 -0.00000326 TOTAL 0.00001206 0.00010782 0.00002756 0.00002288 0.00017002 ROT. SAYVETZ X -0.00129270 0.00086425 0.00089211 0.00019551 -0.00071520 Y 0.00071018 -0.00142701 -0.00105144 -0.00067231 0.00035847 Z 0.00144350 -0.00177934 -0.00049871 -0.00049328 -0.00005542 TOTAL 0.00206376 0.00243913 0.00146632 0.00085647 0.00080193 21 22 23 24 25 FREQUENCY: 1427.82 1459.08 1700.30 1710.79 3144.92 SYMMETRY: A A A A A REDUCED MASS: 1.14924 1.24664 5.67473 4.11433 1.07857 IR INTENSITY: 0.07238 0.30255 0.06290 0.09429 0.14262 1 C X -0.06007249 -0.03467890 0.10805160 0.12239034 0.03877205 Y -0.02630738 -0.04590897 0.07984784 0.05390239 -0.00442776 Z 0.02386257 0.06038779 -0.06921614 -0.03079551 0.03561925 2 H X 0.13511419 0.11880353 -0.02878867 -0.05185161 -0.46093003 Y 0.12365921 0.06917330 -0.02380918 -0.08920737 0.05739865 Z -0.16725689 -0.08254672 0.08068833 0.15817050 -0.43123373 3 C X 0.03875402 0.00243825 0.05216924 -0.08595269 -0.05021468 Y -0.03443788 0.04933487 -0.09402024 0.07235541 0.00353402 Z 0.04558419 -0.06836851 0.10607716 -0.07872072 0.01488552 4 H X -0.02477669 0.05754433 0.01361889 -0.03775472 0.60067553 Y 0.13567533 -0.08600241 0.02472981 -0.09016447 -0.03706660 Z -0.20143773 0.12510339 -0.08388387 0.16122456 -0.18432968 5 C X 0.02319202 -0.03685113 -0.06962524 0.07751013 -0.00530455 Y -0.01245845 0.01609167 0.07158561 -0.07074145 0.00876406 Z 0.00769796 -0.00801604 -0.06789804 0.06721918 -0.00974092 6 H X -0.41420665 0.43915799 0.11592844 -0.14437006 -0.06234623 Y 0.16715250 -0.18945579 0.01596667 0.02044603 -0.09345615 Z -0.06000811 0.05450225 -0.04905426 0.06096121 0.16662487 7 H X -0.05358127 0.03515651 -0.05229154 0.05252446 0.12823105 Y 0.23612161 -0.21568408 -0.09881597 0.07056696 -0.01639837 Z -0.31981654 0.30401079 0.11965874 -0.13781554 -0.04230054 8 C X -0.02686829 -0.03872801 -0.10308048 -0.10955167 0.01108234 Y -0.00830808 -0.00935854 -0.05624215 -0.05407089 0.00769732 Z -0.00386673 -0.00938562 0.02811391 0.02408623 -0.00619687 9 H X 0.22798095 0.19553619 0.02203560 0.02495584 -0.10414029 Y 0.21329953 0.19122854 0.10122945 0.07270668 0.00390634 Z -0.25867142 -0.24612961 -0.12640656 -0.14382164 -0.10029516 10 H X 0.42702117 0.43775779 0.07823435 0.10424723 -0.03401019 Y 0.09469445 0.10982801 -0.03323460 -0.00165379 -0.09974990 Z 0.13459287 0.14722605 0.09385321 0.11823008 0.17998077 TRANS. SAYVETZ X -0.00005675 0.00016578 0.00008239 0.00009571 0.00002982 Y 0.00005608 0.00004980 0.00000986 -0.00009593 -0.00000491 Z -0.00009003 -0.00005784 0.00005098 0.00011706 0.00002986 TOTAL 0.00012030 0.00018251 0.00009739 0.00017907 0.00004249 ROT. SAYVETZ X -0.00041150 -0.00058249 0.00021712 -0.00043712 -0.00012417 Y 0.00125340 0.00054108 -0.00032653 -0.00008313 0.00000282 Z 0.00109912 0.00059974 -0.00036659 -0.00009506 -0.00001379 TOTAL 0.00171709 0.00099587 0.00053680 0.00045499 0.00012496 26 27 28 29 30 FREQUENCY: 3151.73 3155.11 3164.11 3245.34 3246.72 SYMMETRY: A A A A A REDUCED MASS: 1.06191 1.06951 1.08888 1.11602 1.11640 IR INTENSITY: 0.53596 0.12612 0.04283 0.33141 0.14905 1 C X -0.01961876 -0.02071335 -0.03823533 -0.00590148 0.00546028 Y 0.00460347 -0.00139717 0.00277297 0.00026888 -0.00068153 Z -0.02198870 -0.01200960 -0.03164598 -0.00474049 0.00509453 2 H X 0.26321093 0.17825887 0.40118587 0.05512800 -0.05348898 Y -0.03479225 -0.02007542 -0.05396025 -0.00593939 0.00695975 Z 0.24969392 0.16270239 0.37847030 0.05092364 -0.04956359 3 C X -0.02924506 0.02111976 -0.04844468 0.00669937 0.00773965 Y -0.00017503 -0.00518060 0.00501343 -0.00086884 -0.00051092 Z 0.01139661 -0.00120240 0.01176223 -0.00150099 -0.00232326 4 H X 0.36449260 -0.20643427 0.53213706 -0.06575862 -0.07576622 Y -0.02054246 0.01494391 -0.02890158 0.00498941 0.00444880 Z -0.11431753 0.06036647 -0.16536440 0.01980829 0.02281423 5 C X -0.02330672 -0.03409829 0.02509329 0.04304048 0.04687337 Y 0.02117329 0.02470920 -0.01508776 0.01536616 0.01669515 Z -0.01858469 -0.01841392 0.00873071 -0.04363691 -0.04745418 6 H X -0.12392861 -0.12458530 0.06201112 -0.14245841 -0.15481675 Y -0.18444248 -0.18416059 0.09342861 -0.23337884 -0.25276422 Z 0.32625121 0.32436863 -0.16344719 0.40700700 0.44017498 7 H X 0.38360619 0.48513246 -0.32052151 -0.38195175 -0.41716619 Y -0.05028978 -0.06364246 0.04212734 0.05528898 0.06168637 Z -0.12119734 -0.15087779 0.09896210 0.11149685 0.12163721 8 C X -0.03334518 0.04209808 0.02733943 -0.01802073 0.01658966 Y -0.01665556 0.01768679 0.00981414 0.02246925 -0.02067903 Z 0.00569869 -0.00048113 0.00366613 -0.06238647 0.05740669 9 H X 0.30488388 -0.37218743 -0.23710580 0.32515357 -0.30023281 Y -0.01037128 0.01265778 0.00798717 -0.00548696 0.00390819 Z 0.28657813 -0.34673988 -0.22001145 0.29193629 -0.26924293 10 H X 0.06415923 -0.06021912 -0.02992003 -0.09751147 0.08870538 Y 0.19396080 -0.18624132 -0.09059321 -0.25883890 0.23738271 Z -0.34751733 0.33253685 0.16051866 0.45555850 -0.41729131 TRANS. SAYVETZ X 0.00006713 0.00005676 0.00001018 0.00000756 0.00004765 Y 0.00004344 -0.00003696 0.00000743 -0.00000968 -0.00001222 Z -0.00005894 0.00006401 -0.00001746 0.00001210 0.00002867 TOTAL 0.00009934 0.00009319 0.00002154 0.00001724 0.00005694 ROT. SAYVETZ X -0.00001638 -0.00016451 0.00002792 -0.00001244 -0.00011756 Y 0.00004520 -0.00006819 -0.00001809 -0.00014614 0.00003372 Z 0.00006584 -0.00014794 0.00003521 -0.00004662 -0.00006375 TOTAL 0.00008152 0.00023152 0.00004844 0.00015390 0.00013792 REFERENCE ON SAYVETZ CONDITIONS - A. SAYVETZ, J.CHEM.PHYS., 7, 383-389(1939). NOTE - THE MODES J,K ARE ORTHONORMALIZED ACCORDING TO SUM ON I M(I) * (X(I,J)*X(I,K) + Y(I,J)*Y(I,K) + Z(I,J)*Z(I,K)) = DELTA(J,K) ------------------------------- THERMOCHEMISTRY AT T= 298.15 K ------------------------------- USING IDEAL GAS, RIGID ROTOR, HARMONIC NORMAL MODE APPROXIMATIONS. P= 1.01325E+05 PASCAL. ALL FREQUENCIES ARE SCALED BY 1.00000 THE MOMENTS OF INERTIA ARE (IN AMU*BOHR**2) 83.36144 319.28699 392.92240 THE ROTATIONAL SYMMETRY NUMBER IS 1.0 THE ROTATIONAL CONSTANTS ARE (IN GHZ) 21.62976 5.64723 4.58892 THE HARMONIC ZERO POINT ENERGY IS (SCALED BY 1.000) 0.085119 HARTREE/MOLECULE 18681.354213 CM**-1/MOLECULE 53.412726 KCAL/MOL 223.478844 KJ/MOL Q LN Q ELEC. 1.00000E+00 0.000000 TRANS. 1.56175E+07 16.563900 ROT. 3.66073E+04 10.508004 VIB. 3.13824E+00 1.143663 TOT. 1.79418E+12 28.215567 E H G CV CP S KJ/MOL KJ/MOL KJ/MOL J/MOL-K J/MOL-K J/MOL-K ELEC. 0.000 0.000 0.000 0.000 0.000 0.000 TRANS. 3.718 6.197 -41.061 12.472 20.786 158.505 ROT. 3.718 3.718 -26.049 12.472 12.472 99.839 VIB. 228.344 228.344 220.644 41.090 41.090 25.827 TOTAL 235.781 238.260 153.534 66.033 74.348 284.172 VIB. THERMAL CORRECTION E(T)-E(0) = H(T)-H(0) = 4865.266 J/MOL E H G CV CP S KCAL/MOL KCAL/MOL KCAL/MOL CAL/MOL-K CAL/MOL-K CAL/MOL-K ELEC. 0.000 0.000 0.000 0.000 0.000 0.000 TRANS. 0.889 1.481 -9.814 2.981 4.968 37.884 ROT. 0.889 0.889 -6.226 2.981 2.981 23.862 VIB. 54.576 54.576 52.735 9.821 9.821 6.173 TOTAL 56.353 56.945 36.696 15.782 17.770 67.919 VIB. THERMAL CORRECTION E(T)-E(0) = H(T)-H(0) = 1162.826 CAL/MOL ......END OF NORMAL COORDINATE ANALYSIS...... CPU 0: STEP CPU TIME= 0.01 TOTAL CPU TIME= 942.8 ( 15.7 MIN) TOTAL WALL CLOCK TIME= 949.9 SECONDS, CPU UTILIZATION IS 99.25% 1121202 WORDS OF DYNAMIC MEMORY USED EXECUTION OF GAMESS TERMINATED NORMALLY Wed Jan 23 21:20:06 2013 DDI: 263624 bytes (0.3 MB / 0 MWords) used by master data server. ---------------------------------------- CPU timing information for all processes ======================================== 0: 938.894 + 3.912 = 942.806 1: 937.542 + 5.268 = 942.810 2: 936.810 + 3.964 = 940.774 3: 936.782 + 4.544 = 941.326 4: 936.574 + 4.88 = 940.662 5: 936.534 + 3.20 = 939.554 ---------------------------------------- ddikick.x: exited gracefully. ----- accounting info ----- Dictionary file copied to NFS disk total 884 -rw-r--r-- 1 www-data www-data 970 Jan 23 21:04 butadieneDFT.inp -rw------- 1 www-data www-data 895801 Jan 23 21:20 butadieneDFT.out -rw-r--r-- 1 www-data www-data 1510 Jan 23 21:04 butadieneDFT.sub Files used on the master node thebrain were: -rw------- 1 www-data www-data 970 Jan 23 21:04 /home/www-data/scr/butadieneDFT.F05 -rw------- 1 www-data www-data 2584880 Jan 23 21:20 /home/www-data/scr/butadieneDFT.F10 -rw------- 1 www-data www-data 5094256 Jan 23 21:19 /home/www-data/scr/butadieneDFT.F22 -rw------- 1 www-data www-data 5094256 Jan 23 21:19 /home/www-data/scr/butadieneDFT.F22.001 -rw------- 1 www-data www-data 5094256 Jan 23 21:19 /home/www-data/scr/butadieneDFT.F22.002 -rw------- 1 www-data www-data 5094256 Jan 23 21:19 /home/www-data/scr/butadieneDFT.F22.003 -rw------- 1 www-data www-data 5094256 Jan 23 21:19 /home/www-data/scr/butadieneDFT.F22.004 -rw------- 1 www-data www-data 5094256 Jan 23 21:19 /home/www-data/scr/butadieneDFT.F22.005 --- Cleaning up scratch directories on 1 remote nodes. --- Wed Jan 23 21:20:09 EST 2013 0.0u 0.0s 15:52.96 0.0% 0+0k 0+5080io 0pf+0w ch5m3d-1.2.5+dfsg/qchem/data/admin/butadiene/butadiene.inp0000755000175000017500000000171212230555426023435 0ustar georgeskgeorgesk! ! GAMESS Calculation input file ! 1,3-butadiene in s-cis conformation with DFT Functional ! $CONTRL SCFTYP=RHF MAXIT=50 RUNTYP=OPTIMIZE COORD=UNIQUE MULT=1 DFTTYP=PBE0 ICHARG=0 MOLPLT=.FALSE. PLTORB=.FALSE. $END $SYSTEM TIMLIM=480 MWORDS=6 $END $STATPT OPTTOL=0.00005 NSTEP=30 HSSEND=.TRUE. $END $DFT METHOD=GRID NLEB=590 $END $BASIS GBASIS=N311 NGAUSS=6 NDFUNC=1 NPFUNC=1 $END $SCF DIRSCF=.T. $END $GUESS GUESS=HUCKEL $END $DATA 1,3-butadiene in s-cis conformation with DFT Functional C1 C 6 0.406 -0.421 0.749 H 1 1.178 -0.471 1.500 C 6 0.755 0.318 -0.482 H 1 1.773 0.209 -0.820 C 6 -0.066 1.097 -1.164 H 1 0.252 1.595 -2.062 H 1 -1.077 1.275 -0.843 C 6 -0.747 -1.025 0.976 H 1 -1.533 -1.043 0.242 H 1 -0.940 -1.534 1.904 $END ch5m3d-1.2.5+dfsg/qchem/password.php0000644000175000017500000001066312230555424017377 0ustar georgeskgeorgesk CH5M3D

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color: black; } #Toolbar li.UserName { font-family: Times-Roman,Bookman,serif; font-weight: bold; font-style: italic; text-align: right; } ch5m3d-1.2.5+dfsg/qchem/icon_textfile.png0000755000175000017500000000051412230555426020365 0ustar georgeskgeorgeskPNG  IHDRbgAMA asRGB cHRMz&u0`:pQ< PLTE tRNS@fbKGD L pHYsHHFk>!IDATc` ``[jXcM©D'(I%tEXtdate:create2013-03-08T13:03:25-05:00,'%tEXtdate:modify2013-03-08T09:48:50-05:00owIENDB`ch5m3d-1.2.5+dfsg/qchem/icon_folder.png0000755000175000017500000000053512230555426020017 0ustar georgeskgeorgeskPNG  IHDRRgAMA asRGB cHRMz&u0`:pQ<PLTE-0ktRNS@fbKGDo pHYsHHFk>,IDATc`LJJ` `  &.`` c8Sʀl j "%tEXtdate:create2013-03-08T09:39:39-05:00U%tEXtdate:modify2013-03-08T09:39:26-05:00 5IENDB`ch5m3d-1.2.5+dfsg/qchem/newpass.php0000755000175000017500000000272712230555424017222 0ustar georgeskgeorgesk ch5m3d-1.2.5+dfsg/qchem/ch5m3dq.full.js0000644000175000017500000055661312230555426017603 0ustar georgeskgeorgesk// // -------------------- periodic.js -------------------- // //# function element(Z,param) //# //# Define public routine to store and return elemental information //# //# Parameters: //# Z = Atomic number of element //# param: //# symbol - Elemental symbol //# block - "s", "p", "d", or "f" block //# valence - # of valence electrons //# mass - Atomic mass //# radius - Covalent radius of atom //# EN - Electronegativity of atom //# color - color of atom (based on JMol) //# gradient - gradient color for atom //# label - color for label //# //# Return value: //# Variable containing requested information //# function element(Z,param) { if ( typeof element.elem == 'undefined' ) { element.elem = []; // // Load parameters for all elements // // Parameters: // Atomic number // Element symbol // Block (s, p, d, or f) // Number of valence electrons // Atomic mass // Covalent radii (in pm). From www.webelements.com // Jmol CPK colors (rgb). From jmol.sourceforge.net/jscolors/ // Electronegativities from Wikipedia, citing WebElements as their source // element.elem[0] = addElement(0, 'X', 's', 0, 0, 0, 0, 0, 0, 0); element.elem[1] = addElement(1, 'H', 's', 1, 1.0079, 31, 255, 255, 255, 2.2); element.elem[2] = addElement(2, 'He', 's', 2, 4.0026, 28, 217, 255, 255, 0); element.elem[3] = addElement(3, 'Li', 's', 1, 6.941, 128, 204, 128, 255, 0.98); element.elem[4] = addElement(4, 'Be', 's', 2, 9.0122, 96, 194, 255, 0, 1.57); element.elem[5] = addElement(5, 'B', 'p', 3, 10.811, 84, 255, 181, 181, 2.04); element.elem[6] = addElement(6, 'C', 'p', 4, 12.0107, 76, 144, 144, 144, 2.55); element.elem[7] = addElement(7, 'N', 'p', 5, 14.0067, 71, 48, 80, 248, 3.04); element.elem[8] = addElement(8, 'O', 'p', 6, 15.9994, 66, 255, 13, 13, 3.44); element.elem[9] = addElement(9, 'F', 'p', 7, 18.9984, 57, 144, 224, 80, 3.98); element.elem[10] = addElement(10, 'Ne', 'p', 8, 20.1797, 58, 179, 227, 245, 0); element.elem[11] = addElement(11, 'Na', 's', 1, 22.9897, 166, 171, 92, 242, 0.93); element.elem[12] = addElement(12, 'Mg', 's', 2, 24.305, 141, 138, 255, 0, 1.31); element.elem[13] = addElement(13, 'Al', 'p', 3, 26.9815, 121, 191, 166, 166, 1.61); element.elem[14] = addElement(14, 'Si', 'p', 4, 28.0855, 111, 240, 200, 160, 1.9); element.elem[15] = addElement(15, 'P', 'p', 5, 30.9738, 107, 255, 128, 0, 2.19); element.elem[16] = addElement(16, 'S', 'p', 6, 32.065, 105, 255, 255, 48, 2.58); element.elem[17] = addElement(17, 'Cl', 'p', 7, 35.453, 102, 31, 240, 31, 3.16); element.elem[18] = addElement(18, 'Ar', 'p', 8, 39.948, 106, 128, 209, 227, 0); element.elem[19] = addElement(19, 'K', 's', 1, 39.0983, 203, 143, 64, 212, 0.82); element.elem[20] = addElement(20, 'Ca', 's', 2, 40.078, 176, 61, 255, 0, 1); element.elem[21] = addElement(21, 'Sc', 'd', 3, 44.9559, 170, 230, 230, 230, 1.36); element.elem[22] = addElement(22, 'Ti', 'd', 4, 47.867, 160, 191, 194, 199, 1.54); element.elem[23] = addElement(23, 'V', 'd', 5, 50.9415, 153, 166, 166, 171, 1.63); element.elem[24] = addElement(24, 'Cr', 'd', 6, 51.9961, 139, 138, 153, 199, 1.66); element.elem[25] = addElement(25, 'Mn', 'd', 7, 54.938, 139, 156, 122, 199, 1.55); element.elem[26] = addElement(26, 'Fe', 'd', 8, 55.845, 132, 224, 102, 51, 1.83); element.elem[27] = addElement(27, 'Co', 'd', 9, 58.9332, 126, 240, 144, 160, 1.88); element.elem[28] = addElement(28, 'Ni', 'd', 10, 58.6934, 124, 80, 208, 80, 1.91); element.elem[29] = addElement(29, 'Cu', 'd', 11, 63.546, 132, 200, 128, 51, 1.9); element.elem[30] = addElement(30, 'Zn', 'd', 2, 65.39, 122, 125, 128, 176, 1.65); element.elem[31] = addElement(31, 'Ga', 'p', 3, 69.723, 122, 194, 143, 143, 1.81); element.elem[32] = addElement(32, 'Ge', 'p', 4, 72.64, 120, 102, 143, 143, 2.01); element.elem[33] = addElement(33, 'As', 'p', 5, 74.9216, 119, 189, 128, 227, 2.18); element.elem[34] = addElement(34, 'Se', 'p', 6, 78.96, 120, 255, 161, 0, 2.55); element.elem[35] = addElement(35, 'Br', 'p', 7, 79.904, 120, 166, 41, 41, 2.96); element.elem[36] = addElement(36, 'Kr', 'p', 8, 83.8, 116, 92, 184, 209, 3); element.elem[37] = addElement(37, 'Rb', 's', 1, 85.4678, 220, 112, 46, 176, 0.82); element.elem[38] = addElement(38, 'Sr', 's', 2, 87.62, 195, 0, 255, 0, 0.95); element.elem[39] = addElement(39, 'Y', 'd', 3, 88.9059, 190, 148, 255, 255, 1.22); element.elem[40] = addElement(40, 'Zr', 'd', 4, 91.224, 175, 148, 224, 224, 1.33); element.elem[41] = addElement(41, 'Nb', 'd', 5, 92.9064, 164, 115, 194, 201, 1.6); element.elem[42] = addElement(42, 'Mo', 'd', 6, 95.94, 154, 84, 181, 181, 2.16); element.elem[43] = addElement(43, 'Tc', 'd', 7, 98, 147, 59, 158, 158, 1.9); element.elem[44] = addElement(44, 'Ru', 'd', 8, 101.07, 146, 36, 143, 143, 2.2); element.elem[45] = addElement(45, 'Rh', 'd', 9, 102.9055, 142, 10, 125, 140, 2.28); element.elem[46] = addElement(46, 'Pd', 'd', 10, 106.42, 139, 0, 105, 133, 2.2); element.elem[47] = addElement(47, 'Ag', 'd', 11, 107.8682, 145, 192, 192, 192, 1.93); element.elem[48] = addElement(48, 'Cd', 'd', 2, 112.411, 144, 255, 217, 143, 1.69); element.elem[49] = addElement(49, 'In', 'p', 3, 114.818, 142, 166, 117, 115, 1.78); element.elem[50] = addElement(50, 'Sn', 'p', 4, 118.71, 139, 102, 128, 128, 1.96); element.elem[51] = addElement(51, 'Sb', 'p', 5, 121.76, 139, 158, 99, 181, 2.05); element.elem[52] = addElement(52, 'Te', 'p', 6, 127.6, 138, 212, 122, 0, 2.1); element.elem[53] = addElement(53, 'I', 'p', 7, 126.9045, 139, 148, 0, 148, 2.66); element.elem[54] = addElement(54, 'Xe', 'p', 8, 131.293, 140, 66, 158, 176, 2.6); element.elem[55] = addElement(55, 'Cs', 's', 1, 132.9055, 244, 87, 23, 143, 0.79); element.elem[56] = addElement(56, 'Ba', 's', 2, 137.327, 215, 0, 201, 0, 0.89); element.elem[57] = addElement(57, 'La', 'd', 3, 138.9055, 207, 112, 212, 255, 1.1); element.elem[58] = addElement(58, 'Ce', 'f', 4, 140.116, 204, 255, 255, 199, 1.12); element.elem[59] = addElement(59, 'Pr', 'f', 5, 140.9077, 203, 217, 255, 199, 1.13); element.elem[60] = addElement(60, 'Nd', 'f', 6, 144.24, 201, 199, 255, 199, 1.14); element.elem[61] = addElement(61, 'Pm', 'f', 7, 145, 199, 163, 255, 199, 0); element.elem[62] = addElement(62, 'Sm', 'f', 8, 150.36, 198, 143, 255, 199, 1.17); element.elem[63] = addElement(63, 'Eu', 'f', 9, 151.964, 198, 97, 255, 199, 0); element.elem[64] = addElement(64, 'Gd', 'f', 10, 157.25, 196, 69, 255, 199, 1.2); element.elem[65] = addElement(65, 'Tb', 'f', 11, 158.9253, 194, 48, 255, 199, 0); element.elem[66] = addElement(66, 'Dy', 'f', 12, 162.5, 192, 31, 255, 199, 1.22); element.elem[67] = addElement(67, 'Ho', 'f', 13, 164.9303, 192, 0, 255, 156, 1.23); element.elem[68] = addElement(68, 'Er', 'f', 14, 167.259, 189, 0, 230, 117, 1.24); element.elem[69] = addElement(69, 'Tm', 'f', 15, 168.9342, 190, 0, 212, 82, 1.25); element.elem[70] = addElement(70, 'Yb', 'f', 16, 173.04, 187, 0, 191, 56, 0); element.elem[71] = addElement(71, 'Lu', 'f', 17, 174.967, 187, 0, 171, 36, 1.27); element.elem[72] = addElement(72, 'Hf', 'd', 4, 178.49, 175, 77, 194, 255, 1.3); element.elem[73] = addElement(73, 'Ta', 'd', 5, 180.9479, 170, 77, 166, 255, 1.5); element.elem[74] = addElement(74, 'W', 'd', 6, 183.84, 162, 33, 148, 214, 2.36); element.elem[75] = addElement(75, 'Re', 'd', 7, 186.207, 151, 38, 125, 171, 1.9); element.elem[76] = addElement(76, 'Os', 'd', 8, 190.23, 144, 38, 102, 150, 2.2); element.elem[77] = addElement(77, 'Ir', 'd', 9, 192.217, 141, 23, 84, 135, 2.2); element.elem[78] = addElement(78, 'Pt', 'd', 10, 195.078, 136, 208, 208, 224, 2.28); element.elem[79] = addElement(79, 'Au', 'd', 11, 196.9665, 136, 255, 209, 35, 2.54); element.elem[80] = addElement(80, 'Hg', 'd', 2, 200.59, 132, 184, 184, 208, 2); element.elem[81] = addElement(81, 'Tl', 'p', 3, 204.3833, 145, 166, 84, 77, 1.62); element.elem[82] = addElement(82, 'Pb', 'p', 4, 207.2, 146, 87, 89, 97, 2.33); element.elem[83] = addElement(83, 'Bi', 'p', 5, 208.9804, 148, 158, 79, 181, 2.02); element.elem[84] = addElement(84, 'Po', 'p', 6, 209, 140, 171, 92, 0, 2); element.elem[85] = addElement(85, 'At', 'p', 7, 210, 150, 117, 79, 69, 2.2); element.elem[86] = addElement(86, 'Rn', 'p', 8, 222, 150, 66, 130, 150, 0); element.elem[87] = addElement(87, 'Fr', 's', 1, 223, 260, 66, 0, 102, 0.7); element.elem[88] = addElement(88, 'Ra', 's', 2, 226, 221, 0, 125, 0, 0.9); element.elem[89] = addElement(89, 'Ac', 'd', 3, 227, 215, 112, 171, 250, 1.1); element.elem[90] = addElement(90, 'Th', 'f', 4, 232.0381, 206, 0, 186, 255, 1.3); element.elem[91] = addElement(91, 'Pa', 'f', 5, 231.0359, 200, 0, 161, 255, 1.5); element.elem[92] = addElement(92, 'U', 'f', 6, 238.0289, 196, 0, 143, 255, 1.38); element.elem[93] = addElement(93, 'Np', 'f', 7, 237, 190, 0, 128, 255, 1.36); element.elem[94] = addElement(94, 'Pu', 'f', 8, 244, 187, 0, 107, 255, 1.28); element.elem[95] = addElement(95, 'Am', 'f', 9, 243, 180, 84, 92, 242, 1.3); element.elem[96] = addElement(96, 'Cm', 'f', 10, 247, 169, 120, 92, 227, 1.3); element.elem[97] = addElement(97, 'Bk', 'f', 11, 247, 168, 138, 79, 227, 1.3); element.elem[98] = addElement(98, 'Cf', 'f', 12, 251, 168, 161, 54, 212, 1.3); element.elem[99] = addElement(99, 'Es', 'f', 13, 252, 165, 179, 31, 212, 1.3); element.elem[100] = addElement(100, 'Fm', 'f', 14, 257, 167, 179, 31, 186, 1.3); element.elem[101] = addElement(101, 'Md', 'f', 15, 258, 173, 179, 13, 166, 1.3); element.elem[102] = addElement(102, 'No', 'f', 16, 259, 176, 189, 13, 135, 1.3); element.elem[103] = addElement(103, 'Lr', 'f', 17, 262, 161, 199, 0, 102, 0); element.elem[104] = addElement(104, 'Rf', 'd', 4, 267, 157, 204, 0, 89, 0); element.elem[105] = addElement(105, 'Db', 'd', 5, 268, 149, 209, 0, 79, 0); element.elem[106] = addElement(106, 'Sg', 'd', 6, 269, 143, 217, 0, 69, 0); element.elem[107] = addElement(107, 'Bh', 'd', 7, 270, 141, 224, 0, 56, 0); element.elem[108] = addElement(108, 'Hs', 'd', 8, 269, 134, 230, 0, 46, 0); element.elem[109] = addElement(109, 'Mt', 'd', 9, 278, 129, 235, 0, 38, 0); element.elem[110] = addElement(110, 'Ds', 'd', 10, 281, 0, 0, 0, 28, 0); element.elem[111] = addElement(111, 'Rg', 'd', 11, 281, 0, 0, 0, 28, 0); element.elem[112] = addElement(112, 'Cn', 'd', 12, 285, 0, 0, 0, 28, 0); element.elem[113] = addElement(113, 'Uut', 'p', 3, 286, 0, 0, 0, 28, 0); element.elem[114] = addElement(114, 'Fl', 'p', 4, 289, 0, 0, 0, 28, 0); element.elem[115] = addElement(115, 'Uup', 'p', 5, 288, 0, 0, 0, 28, 0); element.elem[116] = addElement(116, 'Lv', 'p', 6, 293, 0, 0, 0, 28, 0); element.elem[117] = addElement(117, 'Uus', 'p', 7, 294, 0, 0, 0, 28, 0); element.elem[118] = addElement(118, 'Uuo', 'p', 8, 294, 0, 0, 0, 28, 0); } // Make sure element requested is defined. if ( (Z < 0) || (Z > element.elem.length) ) { alert("Element "+Z+" is not defined."); return 0; } // Determine what information is requested and return value switch (param) { case "symbol": return element.elem[Z].symbol; break; case "block": return element.elem[Z].block; break; case "valence": return element.elem[Z].valence; break; case "mass": return element.elem[Z].mass; break; case "radius": return element.elem[Z].radius; break; case "EN": return element.elem[Z].EN; break; case "color": return element.elem[Z].color; break; case "gradient": return element.elem[Z].gradient; break; case "label": return element.elem[Z].label; break; case "max": return element.elem.length; break; default: alert("Param "+param+" is not defined."); return 0; break; } // End of element routine } /// /// Define internal structure for elemental information /// function elementObject() { this.symbol = "?"; this.block = "?"; this.valence = 0; this.mass = 0.0; this.radius = 0.0; this.EN = 0.0; this.color = "rgb(88,88,88)"; this.gradient = "rgb(88,88,88)"; this.label = "rgb(255,255,255)"; } /// /// Internal routine to add information for elements /// function addElement(Z, Symbol, block, valence, mass, radius, red, green, blue, EN) { // Declare local variables var atomR, sum; var element = new elementObject(); // Add elemental information element.symbol = Symbol; element.block = block; element.valence = valence; element.mass = mass; (radius <= 0) ? atomR = 0.1 : atomR = radius / 100.0; element.radius = atomR; element.color = "rgb("+red+","+green+","+blue+")"; element.gradient = "rgb("+Math.floor(red/2)+","+Math.floor(green/2)+","+Math.floor(blue/2)+")"; sum = red + green + blue; element.label = (sum > 384) ? "rgb(0,0,0)" : "rgb(255,255,255)"; element.EN = EN; // End of addElement routine return element; } //# function drawPeriodic() //# //# Writes html code to a division named "ptable". The periodic table is written as a table, and each element //# is linked to to the pickElem() routine. //# function drawPeriodic() { // Declare local variables var html; var PerDivision = "ptable"; html = ""; html += ""; html += ""; // html += ""; // html += ""; html += ""; html += ""; html += "\n"; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += "\n"; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += "\n"; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += "\n"; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += "\n"; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += "\n"; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += "\n"; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += "\n"; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += "
H MainMetals"; html += "
Metals
He
LiBe BCNOFNe
NaMg AlSiPSClAr
KCaScTiVCrMnFeCoNiCuZnGaGeAsSeBrKr
RbSrYZrNbMoTcRuRhPdAgCdInSnSbTeIXe
CsBaLaHfTaWReOsIrPtAuHgTlPbBiPoAtRn
FrRaAcRfDbSgBhHsMtDsRgCnUutFlUupLvUusUuo
 CePrNdPmSmEuGdTbDyHoErTmYbLu 
 ThPaUNpPuAmCmBkCfEsFmMdNoLr 
\n"; // Write html code to division var divID = document.getElementById(PerDivision); if ( divID ) { divID.innerHTML = html; } // End of drawPeriodic routine } // // -------------------- molecule.js -------------------- // //# function Mol(value) //# //# Define public routine to store and return molecule arrays //# //# Parameter: //# value = If value given, then set as active molecule //# //# Return value: //# Pointer to current array for molecular coordinates, ex. //# var molecule = Mol(); //# //# Molecular values stored in 'zeroth' element of array //# molecule[0].molIndex - ID number for this molecule //# molecule[0].numatoms - # of atoms in this molecule //# molecule[0].AtomScale - Scale factor to control size of molecule displayed //# molecule[0].showlabels - 0=don't show elemental symbols, 1=show symbols //# molecule[0].showcharges - 0=don't show charges, 1=show charges //# molecule[0].gradients - 0=don't shade atoms, 1=use shading //# molecule[0].formula - Simple text string containing molecular formula //# molecule[0].weight - Molecular weight //# molecule[0].charge - Charge of molecule //# //# Atomic values in remaining elements of array //# molecule[i].atomicnumber - Atomic number (Z) for atom //# molecule[i].x - x coordinate of atom //# molecule[i].y - y coordinate of atom //# molecule[i].z - z coordinate of atom //# molecule[i].charge - Estimate of atomic charge //# molecule[i].highlite - 0=don't highlight atom, 1=highlight atom //# molecule[i].hide - 0=display atom, 1=do not display atom //# function Mol(value) { // Declare local variables var id; var param = value || 0; // Determine which molecule to use if(typeof Mol.molecule === "undefined") Mol.molecule = 1; if ( param > 0 ) { Mol.molecule = param; BondMatrix(param); } id = Mol.molecule; // Initialize molecular array if necessary if ( typeof Mol.moly === "undefined" ) Mol.moly = []; if ( typeof Mol.moly[id] === "undefined" ) { Mol.moly[id] = []; Mol.moly[id][0] = new molObject(); Mol.moly[id][0].molIndex = id; Mol.moly[id][0].numatoms = 0; Mol.moly[id][0].AtomScale = 1.0; Mol.moly[id][0].showlabels = 0; Mol.moly[id][0].showcharges = 0; Mol.moly[id][0].gradients = 1; Mol.moly[id][0].highlite = 0; Mol.moly[id][0].formula = ""; Mol.moly[id][0].weight = 0.0; Mol.moly[id][0].charge = 999; } // End of Mol routine return Mol.moly[id]; } //# function BondMatrix(value) //# //# Define public routine to store and return Bond Matrix //# //# Parameter: //# value = If value given, then set as active matrix //# //# Return value: //# Pointer to current bond matrix, ex. //# var bonds = BondMatrix(); //# bonds[i][j] then gives indication of bond between atoms "i" and "j" //# function BondMatrix(value) { // Declare local variables var id; var param = value || 0; // Determine which bond matrix to use if(typeof BondMatrix.id === "undefined") BondMatrix.id = 1; if ( param > 0 ) BondMatrix.id = param; id = BondMatrix.id; // Initialize molecular array if necessary if ( typeof BondMatrix.bonds === "undefined" ) BondMatrix.bonds = []; if ( typeof BondMatrix.bonds[id] === "undefined" ) { BondMatrix.bonds[id] = []; } // End of BondMatrix routine return BondMatrix.bonds[id]; } /// /// Private routine to store name for active window. /// /// Parameter: /// mywin = If name of window exists, then set as active window/molecule. /// Otherwise, create new window with this name. /// /// Return value: /// Name of active Canvas/window /// function activeWin(mywin) { // Declare local variables var i, active; var param = mywin || " "; // Initialize links if (typeof activeWin.mol === "undefined") { activeWin.mol = []; activeWin.mol[0] = "Dummy"; } // Define defaults for active window and molecule if (typeof activeWin.win === "undefined") { var tag = document.getElementsByTagName("canvas"); if ( tag[0] ) { activeWin.win = tag[0].id; activeWin.mol[1] = activeWin.win; } else { // alert("No canvas element found."); return; } } // User requested to set/view Window information if ( param.length > 1 ) activeWin.win = param; // Find active molecule active=-1; for (i=0; i118) ) { InfoWin("*** ERROR Reading XYZ file. ***\n"); return; } x = parseFloat(current[1]); y = parseFloat(current[2]); z = parseFloat(current[3]); addAtom(A, x, y, z); InfoWin(" "+current[0]+"("+A+") "+x+", "+y+", "+z+"\n"); } // Create bonds for (i=1; i < numatoms; i++) { for (j=i+1; j <= numatoms; j++) { bond = 1.2 * (element(molecule[i].atomicnumber,"radius") + element(molecule[j].atomicnumber,"radius")); dx = molecule[i].x - molecule[j].x; dy = molecule[i].y - molecule[j].y; dz = molecule[i].z - molecule[j].z; r = Math.sqrt(dx*dx+dy*dy+dz*dz); if (r <= bond) addBond(i,j); } } // Finished with readXYZfile routine formula(); InfoWin("Finished reading XYZ input file.\n"); } /// function readMOLfile(molfile,lines) /// /// Read MDL .mol file (V2000 format) /// /// molfile: name of .mol file /// lines: Array holding content of .mol file /// /// Data stored in molecule array and bond matrix /// function readMOLfile(molfile,lines) { // Declare local variables var i, j; var x, y, z; var bond1, bond2; var A, symbol; var Qtitle = new Array(); var molecule = Mol(); // Write file information to information window var molname = escape(molfile.name); InfoWin("File Name = "+molname,1); InfoWin("\nFile Type = "+molfile.type); InfoWin("\nFile Size = "+molfile.size); // Reset molecule object and contents delMolecule(); // Read data Qtitle = lines[0]; Qtitle = Qtitle.replace(/\s+$/,""); var molAtoms = parseFloat(lines[3].substr(0,3)); var molBonds = parseFloat(lines[3].substr(3,3)); InfoWin("\n\n"+Qtitle); InfoWin("\n"+molAtoms+" atoms and "+molBonds+" bonds."); // Read coordinates j = molAtoms+4; for (i=4; i < j; i++) { x = parseFloat(lines[i].substr(0,10)); y = parseFloat(lines[i].substr(10,10)); z = parseFloat(lines[i].substr(20,10)); symbol = lines[i].substr(31,3); symbol = symbol.replace(/\s+/,""); A = lookupSymbol(symbol); InfoWin("\n "+symbol+"("+A+") "+x+", "+y+", "+z); addAtom(A, x, y, z); } j = 4 + molAtoms + molBonds; for (i = 4+molAtoms; i < j; i++) { bond1 = parseFloat(lines[i].substr(0,3)); bond2 = parseFloat(lines[i].substr(3,3)); InfoWin("\n Bond from "+bond1+" to "+bond2); addBond(bond1,bond2); } // Finished formula(); } /// /// Read GAMESS input file contain full set of x,y,z coordinates /// /// lines: Array holding content of .inp file /// function readINPfile(lines) { // Declare local variables var i, j; var x, y, z; var bond1, bond2; var A, symbol; var numatoms; var Qtitle = new Array(); var molecule = Mol(); // Inform user that file being read InfoWin("--- Reading Gamess input file ---\n",1); // Reset molecule object and contents delMolecule(); // Read title from file i = 0; lines[i].toLowerCase(); while ( lines[i].toLowerCase().indexOf('$data') < 0 ) { i++; } i++; Qtitle = lines[i]; Qtitle = Qtitle.replace(/\s+$/,""); InfoWin("\n\nTitle: [" + Qtitle + "]\n"); // Advance to start of coordinates i++; if ( lines[i].toLowerCase().indexOf('c1') < 0 ) i++; // Read coordinates i++; while ( lines[i].toLowerCase().indexOf('$end') < 0 ) { InfoWin(" Line = [" + lines[i] + "]\n"); current = lines[i].replace(/\s+/g," ").replace(/^\s+/,"").split(' '); A = parseInt(current[1]); x = parseFloat(current[2]); y = parseFloat(current[3]); z = parseFloat(current[4]); addAtom(A, x, y, z); i++; } // Calculate bonds for (i=1; i < molecule[0].numatoms; i++) { ra = element(molecule[i].atomicnumber,"radius"); for (j=i+1; j <= molecule[0].numatoms; j++) { rb = element(molecule[i].atomicnumber,"radius"); r = 0.9*distance(molecule, i, j); if ( r <= (ra+rb) ) addBond(i, j); } } // Finished with readINPfile routine InfoWin("Finished reading input file.\n"); formula(); return; } //# function lookupSymbol(symbol) //# //# Given elemental symbol, lookup and return atomic number (Z) //# function lookupSymbol(symbol) { var i; for (i = 1; i < element(1,"max"); i++) { if ( element(i,"symbol") == symbol ) return i; } return 0; } /// /// Routine to remove and initialize molecule object /// function delMolecule() { var molecule = Mol(); molecule[0] = new molObject(); molecule[0].molIndex = 1; molecule[0].numatoms = 0; molecule[0].AtomScale = 1.0; molecule[0].showlabels = 0; molecule[0].showcharges = 0; buttonColor("ChargeButton",0); } /// /// Routine to save/restore molecular coordinates, bonds, ... /// /// Parameter: mode /// pop - restore last saved set of coordinates /// save - store current information /// redo - 'Undo' last pop /// function Undo(mode) { // Declare local variables var i, pos; var maxBonds; var MAXSAVE=10; var molecule = Mol(); var bonds = BondMatrix(); // Initialization of variables if ( typeof Undo.num == 'undefined' ) { Undo.num = 0; Undo.mol = []; Undo.bonds = []; for (i=0; i < MAXSAVE; i++) { Undo.mol[i] = []; Undo.mol[i][0] = 0; Undo.bonds[i] = []; } } // Save current geometry information if ( mode == "save") { pos = Undo.num; // InfoWin(" --- Saving geometry in slot " + pos + " ---\n"); Undo.mol[pos] = null; Undo.mol[pos] = []; Undo.mol[pos][0] = molecule[0].numatoms; for (i=1; i <= molecule[0].numatoms; i++) { Undo.mol[pos][i] = new atomObject(); Undo.mol[pos][i].atomicnumber = molecule[i].atomicnumber; Undo.mol[pos][i].x = molecule[i].x; Undo.mol[pos][i].y = molecule[i].y; Undo.mol[pos][i].z = molecule[i].z; Undo.mol[pos][i].bonds = []; Undo.mol[pos][i].charge = molecule[i].charge; Undo.mol[pos][i].highlite = molecule[i].highlite; } Undo.bonds[pos] = null; Undo.bonds[pos] = []; for (i=1; i <= molecule[0].numatoms; i++) { Undo.bonds[pos][i] = []; for (j=0; j <= molecule[0].numatoms; j++) { Undo.bonds[pos][i][j] = bonds[i][j]; } } // alert("Coordinate set "+Undo.num+" contains "+Undo.mol[pos][0]+" atoms."); Undo.num = ( (Undo.num+1) % MAXSAVE ); return; } // Set position of 'last saved' geometry information if ( mode == "pop") { Undo('save'); pos = ( (Undo.num+MAXSAVE-2) % MAXSAVE ); Undo.num = pos; // InfoWin(" --- Attempting to restore from slot " + pos + " ---\n"); if ( Undo.mol[pos][0] < 1 ) { alert("ERROR: No saved coordinates to restore."); return; } } // Attempt to reverse last 'undo' (pop) if ( mode == "redo") { pos = ( (Undo.num+1) % MAXSAVE ); Undo.num = pos; // InfoWin(" --- Attempting to go back to slot " + pos + " ---\n"); if ( Undo.mol[pos][0] < 1 ) { alert("ERROR: No saved coordinates to restore."); return; } } if ( (mode == "redo") || (mode == "pop") ) { molecule[0].numatoms = Undo.mol[pos][0]; for (i=1; i <= Undo.mol[pos][0]; i++) { molecule[i].atomicnumber = Undo.mol[pos][i].atomicnumber; molecule[i].x = Undo.mol[pos][i].x; molecule[i].y = Undo.mol[pos][i].y; molecule[i].z = Undo.mol[pos][i].z; molecule[i].charge = Undo.mol[pos][i].charge; molecule[i].highlite = Undo.mol[pos][i].highlite; } for (i=1; i <= molecule[0].numatoms; i++) { for (j=0; j <= molecule[0].numatoms; j++) { bonds[i][j] = Undo.bonds[pos][i][j]; } } centerMolecule(); drawMolecule(); return; } // End of Undo routine } //# function addAtom(AtomicNum, x, y, z) //# //# Routine to add atomic information to molecule array. //# //# Parameters are the atomic # and (x,y,z) coordinates of the atom. //# function addAtom(AtomicNum, x, y, z) { // Declare local variables var i; var numatoms; var molecule = Mol(); var bonds = BondMatrix(); // Create/fill molecular array molecule[0].numatoms++; numatoms = molecule[0].numatoms; molecule[0].showcharges = 0; buttonColor("ChargeButton",0); molecule[numatoms] = new atomObject(); molecule[numatoms].atomicnumber = AtomicNum; molecule[numatoms].x = x; molecule[numatoms].y = y; molecule[numatoms].z = z; molecule[numatoms].charge = 0.0; molecule[numatoms].highlite = 0; // Initialize bond matrix if (typeof bonds[numatoms] === "undefined") { bonds[numatoms] = []; } bonds[numatoms][0] = 0; for (i=1; i <= numatoms; i++) { bonds[i][numatoms] = 0; bonds[numatoms][i] = 0; } // End of addAtom routine } //# function addBond(atom1, atom2) //# //# Routine to add bonding information to bonds array //# (Note that atom numbers start at 1) //# function addBond(atom1, atom2) { // Define local variables var i, j; var newbond; var molecule = Mol(); var numatoms = molecule[0].numatoms; var bonds = BondMatrix(); // Add bonds to matrix bonds[atom1][0]++; bonds[atom1][atom2] = 1; bonds[atom2][0]++; bonds[atom2][atom1] = 1; // End of addBond routine } //# function delAtom(atomNum) //# //# Routine to remove selected atom, directly-bonded Hydrogens, and //# cleanup molecule object (remove blank slots) and update bond arrays. //# //# atomNum is the position of the atom to delete in the molecule array //# function delAtom(atomNum) { // Declare local variables var i, j, k, Hi=0; var bondedAtom, bi; var numatoms; var newNum, maxBonds, maxBondsB, maxBondsI, maxBondsJ; var HList = new Array(); var molecule = Mol(); var bonds = BondMatrix(); // See if there are any attached hydrogen atoms molecule[0].showcharges = 0; buttonColor("ChargeButton",0); newNum = atomNum; for (i=1; i < atomNum; i++) { if ( (bonds[atomNum][i] > 0) && (molecule[i].atomicnumber == 1) ) { HList[Hi++] = i; newNum--; } } for (i=atomNum+1; i <= molecule[0].numatoms; i++) { if ( (bonds[atomNum][i] > 0) && (molecule[i].atomicnumber == 1) ) { HList[Hi++] = i; } } // Remove attached hydrogen atoms HList.sort(function(a,b){ return(b-a); }); for (i=0; i < Hi; i++) { delAtom(HList[i]); } atomNum = newNum; // Remove atom and shift 'higher' atoms in molecule object to fill gaps for (i=atomNum; i < molecule[0].numatoms; i++) { j=i+1; molecule[i].atomicnumber = molecule[j].atomicnumber; molecule[i].x = molecule[j].x; molecule[i].y = molecule[j].y; molecule[i].z = molecule[j].z; molecule[i].charge = molecule[j].charge; molecule[i].highlite = molecule[j].highlite; } molecule[0].numatoms--; // Remove bonds to atom being deleted numatoms = molecule[0].numatoms; for (i=1; i < atomNum; i++) { if ( bonds[i][atomNum] > 0 ) bonds[i][0]--; for (j=atomNum; j <= numatoms; j++) bonds[i][j] = bonds[i][j+1]; bonds[i][numatoms+1] = 0; } for (i=atomNum; i <= numatoms; i++) { if ( bonds[i+1][atomNum] > 0 ) bonds[i+1][0]--; for (j=0; j < atomNum ; j++) bonds[i][j] = bonds[i+1][j]; for (j=atomNum; j <= numatoms; j++) bonds[i][j] = bonds[i+1][j+1]; bonds[i][numatoms+1] = 0; } for (i=0; i<=numatoms+1; i++) bonds[numatoms+1][i] = 0; // Finished with delAtom routine drawMolecule(); } //# function delBond(atom1, atom2) //# //# Routine to remove bond from bonds array. //# function delBond(atom1, atom2) { var i, maxBonds; var bonds = BondMatrix(); // Remove bond on atom1 if ( bonds[atom1][atom2] > 0 ) { bonds[atom1][atom2] = 0; bonds[atom1][0]--; } // Remove bond on atom2 if ( bonds[atom2][atom1] > 0 ) { bonds[atom2][atom1] = 0; bonds[atom2][0]--; } // Finished with delBond routine } //# function hideH() //# //# Do not display any hydrogen atoms in molecule //# function hideH() { var i; var molecule = Mol(); // Loop over all atoms, setting hide flag to 0 for all atoms for (i=1; i <= molecule[0].numatoms; i++) { if ( molecule[i].atomicnumber == 1 ) { molecule[i].hide = 1; } } // Finished with hideH routine drawMolecule(); } //# function showAll() //# //# Show all atoms in molecule //# function showAll() { var i; var molecule = Mol(); // Loop over all atoms, setting hide flag to 0 for all atoms for (i=1; i < molecule[0].numatoms; i++) { molecule[i].hide = 0; } // Finished with showAll routine } //# function centerMolecule() //# //# Find center of molecule and move coordinates to center. //# function centerMolecule() { // Define local variables var i, A, numatoms; var molSize = 0.0; var xc, yc, zc; var xyz; var activeCanvas = activeWin(""); var molecule = Mol(); // Get height of Canvas var canvas = document.getElementById(activeCanvas); var height = canvas.height; // Find center of molecule xc = 0.0; yc = 0.0; zc = 0.0; numatoms = molecule[0].numatoms; for (i=1; i <= numatoms; i++) { xc += molecule[i].x; yc += molecule[i].y; zc += molecule[i].z; } xc /= numatoms; yc /= numatoms; zc /= numatoms; // Translate coordinates to center molSize = 0.0; for (i=1; i <= numatoms; i++) { A = molecule[i].atomicnumber; molecule[i].x -= xc; molecule[i].y -= yc; molecule[i].z -= zc; xyz = Math.abs(molecule[i].x); xyz = Math.max(xyz,Math.abs(molecule[i].y)); xyz = Math.max(xyz,Math.abs(molecule[i].z)); xyz += element(A,"radius"); molSize = Math.max(molSize,xyz); } molecule[0].AtomScale = 0.5*height/molSize; // Finished with centerMolecule routine } /// /// Display parameters (mainly for debugging) /// function showGlobal() { // Declare local variables var i; var molecule = Mol(); InfoWin("numatoms = " + molecule[0].numatoms,1); InfoWin("\nAtomScale = " + molecule[0].AtomScale.toFixed(6)); InfoWin("\n"); for (i=1; i<=molecule[0].numatoms; i++) { A = molecule[i].atomicnumber; InfoWin(i + " " + element(A,"symbol")); InfoWin(" (" + molecule[i].x.toFixed(4)); InfoWin(", " + molecule[i].y.toFixed(4)); InfoWin(", " + molecule[i].z.toFixed(4)); InfoWin(")\n"); } } //# function showCoord(mode) //# //# Display molecular coordinates and bonds in information window. //# //# Parameter: //# mode=0: Write .xyz formatted file //# mode>0: Write coordinates and bond information //# function showCoord(mode) { // Declare local variables var i; var space; var molecule = Mol(); var bonds = BondMatrix(); // If no coordinates available, return if ( molecule[0].weight <= 0.0 ) return; // Loop over all atoms and bonds if ( mode ) { InfoWin("Molecular Coordinates and Bond Information\n",1); InfoWin(" "+molecule[0].formula+" ("+molecule[0].weight.toFixed(2)+" g/mol)"); if ( (molecule[0].charge != 999) && (molecule[0].charge != 0) ) InfoWin(" Charge = "+molecule[0].charge); InfoWin("\n"); } else { InfoWin("Molecular Coordinates in .xyz format\n",1); InfoWin("--------------------\n"); InfoWin(molecule[0].numatoms + "\n"); InfoWin(molecule[0].formula+" ("+molecule[0].weight.toFixed(2)+" g/mol) in xyz format: From CH5M3D\n"); } for (i=1; i<=molecule[0].numatoms; i++) { space = ""; if (i < 100) space = " "; if (i < 10) space = " "; if ( mode ) { InfoWin(space+i+": "); } InfoWin(element(molecule[i].atomicnumber,"symbol") + " "); if ( element(molecule[i].atomicnumber,"symbol").length < 2 ) InfoWin(" "); InfoWin(XYZpretty(molecule[i].x)); InfoWin(XYZpretty(molecule[i].y)); InfoWin(XYZpretty(molecule[i].z)); if ( mode ) { InfoWin(" "); for (j=1; j <=molecule[0].numatoms; j++) { if ( bonds[i][j] > 0 ) InfoWin(" "+j+","); } } InfoWin("\n"); } // End of showCoord routine } /// /// Helper routine to make coordinates line up in columns /// function XYZpretty(coord) { // Declare local variables var space = " "; var mystr = new Array(); if ( coord >= 100.0) { mystr = space + " " + coord.toFixed(4); return mystr; } if ( coord >= 10.0) { mystr = space + " " + coord.toFixed(4); return mystr; } if ( coord >= 0.0) { mystr = space + " " + coord.toFixed(4); return mystr; } if ( coord >= -10.0) { mystr = space + " " + coord.toFixed(4); return mystr; } if ( coord >= -100.0) { mystr = space + " " + coord.toFixed(4); return mystr; } mystr = space + coord.toFixed(4); return mystr; // Finished with XYZpretty } //# function formula() //# //# Display molecular formula to division with an id = "formula". //# Note that the contents of this division will be overwritten. //# function formula() { var i, j, A; var found, num; var molweight; var molformula = new Array(); var formulaStr="

Formula = "; var molecule = Mol(); // If no molecule loaded, return if (molecule[0].numatoms < 1) return; // Look for carbon and place in first slot num = 0; for (i=1; i<=molecule[0].numatoms; i++) if ( molecule[i].atomicnumber == 6 ) { molformula[num] = []; molformula[num][0] = 6; molformula[num][1] = 0; num++; i = molecule[0].numatoms+1; } // Look for hydrogen in next slot for (i=1; i<=molecule[0].numatoms; i++) if ( molecule[i].atomicnumber == 1 ) { molformula[num] = []; molformula[num][0] = 1; molformula[num][1] = 0; num++; i = molecule[0].numatoms+1; } // Loop over all atoms in molecule for (i=1; i<=molecule[0].numatoms; i++) { A = molecule[i].atomicnumber; found = 0; for (j=0; j < num; j++) { if (molformula[j][0] == A) { molformula[j][1]++; found = 1; j = num; } } if (found == 0) { molformula[num] = new Array(2); molformula[num][0] = molecule[i].atomicnumber; molformula[num][1] = 1; num++; } } // Calculate molecular weight and output formula molweight = 0.0; molecule[0].formula = ""; for (i=0; i 1) { formulaStr += ""+molformula[i][1]+""; molecule[0].formula += molformula[i][1] + " "; } } formulaStr += "

"; molecule[0].weight = molweight; // Write formula to screen if ( document.getElementById("formula") ) document.getElementById("formula").innerHTML = formulaStr; if ( molweight > 0.0 ) InfoWin(molecule[0].formula+" has a molecular weight of "+molweight.toFixed(2)+"\n"); // End formula routine } //# function RotateMolecule(axis) //# //# Routine to start/stop rotation of molecule. //# //# Parameter: //# axis = rotation axis. Allowed values are "x", "y", or "z" //# ("s" can be used to stop all rotations) //# //# Buttons must be created in html with: //# id="rotateX" (or rotateY or rotateZ) //# function RotateMolecule(axis) { // Declare local variables var delay = 20; // Delay between redrawing screen, in ms // Parameter validation axis = axis[0].toLowerCase(); if ( (axis != "x") && (axis != "y") && (axis != "z") && (axis != "s") ) { return; } // If first call, initialize "active" variable if(typeof RotateMolecule.RX === "undefined") { RotateMolecule.RX = 0; RotateMolecule.RY = 0; RotateMolecule.RZ = 0; } // Start/Stop rotation switch (axis) { case 'x': if ( RotateMolecule.RX == 0 ) { // Start rotation RotateMolecule.RX = 1; RotateX_ID = setInterval( "rotateX()", delay ); buttonColor("rotateX",1); } else { // Stop rotation RotateMolecule.RX = 0; clearInterval( RotateX_ID ); buttonColor("rotateX",0); } break; case 'y': if ( RotateMolecule.RY == 0 ) { // Start rotation RotateMolecule.RY = 1; RotateY_ID = setInterval( "rotateY()", delay ); buttonColor("rotateY",1); } else { // Stop rotation RotateMolecule.RY = 0; clearInterval( RotateY_ID ); buttonColor("rotateY",0); } break; case 'z': if ( RotateMolecule.RZ == 0 ) { // Start rotation RotateMolecule.RZ = 1; RotateZ_ID = setInterval( "rotateZ()", delay ); buttonColor("rotateZ",1); } else { // Stop rotation RotateMolecule.RZ = 0; clearInterval( RotateZ_ID ); buttonColor("rotateZ",0); } break; case 's': if ( RotateMolecule.RX != 0 ) { RotateMolecule.RX = 0; clearInterval( RotateX_ID); } if ( RotateMolecule.RY != 0 ) { RotateMolecule.RY = 0; clearInterval( RotateY_ID); } if ( RotateMolecule.RZ != 0 ) { RotateMolecule.RZ = 0; clearInterval( RotateZ_ID); } buttonColor("rotateX",0); buttonColor("rotateY",0); buttonColor("rotateZ",0); break; } // End of RotateMolecule function } // // Private function to perform rotation of molecule about x-axis // function rotateX() { // Declare local variables var i, x, y, z; var angle = 1.0; var cosA = Math.cos(-angle*Math.PI/180); var sinA = Math.sin(-angle*Math.PI/180); var molecule = Mol(); // Draw molecule and display on canvas for (i=1; i <= molecule[0].numatoms; i++) { y = molecule[i].y; z = molecule[i].z; molecule[i].y = cosA*y + sinA*z; molecule[i].z = -sinA*y + cosA*z; } drawMolecule(); // End of rotateX function } // // Private function to perform rotation of molecule about y-axis // function rotateY() { // Declare local variables var i, x, y, z; var angle = 1.0; var cosA = Math.cos(-angle*Math.PI/180); var sinA = Math.sin(-angle*Math.PI/180); var molecule = Mol(); // Draw molecule and display on canvas for (i=1; i <= molecule[0].numatoms; i++) { x = molecule[i].x; z = molecule[i].z; molecule[i].x = cosA*x + sinA*z; molecule[i].z = -sinA*x + cosA*z; } drawMolecule(); // End of rotateY function } // // Private function to perform rotation of molecule about z-axis // function rotateZ() { // Declare local variables var i, x, y, z; var angle = 1.0; var cosA = Math.cos(-angle*Math.PI/180); var sinA = Math.sin(-angle*Math.PI/180); var molecule = Mol(); // Draw molecule and display on canvas for (i=1; i <= molecule[0].numatoms; i++) { x = molecule[i].x; y = molecule[i].y; molecule[i].x = cosA*x + sinA*y; molecule[i].y = -sinA*x + cosA*y; } drawMolecule(); // End of rotateZ function } // // -------------------- drawmolecule.js -------------------- // //# function drawMolecule() //# //# Draw atoms and bonds. //# function drawMolecule() { // Define local variables var i, j, k; var x, y, r; var bonds = BondMatrix(); var molecule = Mol(); var A, numatoms=molecule[0].numatoms; var bondto, maxBonds; var x1, y1, x2, y2; var AtomSize = 0.50; var SimpleSwitch = 250; // Create connection to active Canvas var mycanvas = activeWin(""); var canvas = document.getElementById(mycanvas); if ( ! canvas ) return; var ctx = canvas.getContext('2d'); var width = canvas.width; var height = canvas.height; var centerx = canvas.width/2; var centery = canvas.height/2; // Clear screen before drawing molecule clear(ctx, width, height); // Define properties of lines ctx.strokeStyle = "rgb(0, 0, 255)"; ctx.lineWidth = 3.0; // Depth sort: Draw from back to front if ( typeof drawMolecule.deep == 'undefined' ) { drawMolecule.deep = []; } if ( drawMolecule.deep.length != numatoms ) { j=0; drawMolecule.deep = []; for (i=drawMolecule.deep.length; i SimpleSwitch ) molecule[0].gradients = 0; // Loop over all atoms in molecule for (i = 0; i < numatoms; i++) { atom = drawMolecule.deep[i].id; if ( ! molecule[atom].hide ) { if ( molecule[0].gradients ) { drawAtom(ctx, atom, AtomSize, centerx, centery); } else { drawAtomPlain(ctx, atom, AtomSize, centerx, centery); } if ( molecule[0].showcharges != 0 ) DrawChargeCloud(ctx, atom, AtomSize*1.5, centerx, centery); if ( molecule[atom].highlite != 0 ) DrawAtomHilite(ctx, atom, AtomSize*1.5, centerx, centery); // Loop over all bonds on current atom for (j = 1; j <= numatoms; j++) { if ( (bonds[atom][j] > 0) && (j != atom) && !molecule[j].hide ) { for (k=i+1; k < numatoms; k++) { if (drawMolecule.deep[k].id == j) { drawBond(ctx, atom, j, AtomSize, centerx, centery, molecule[0].gradients); } } } } } } // Finished with drawMolecule routine } //# function showLabels() //# //# Routine to toggle display of atomic labels. //# function showLabels() { // Local variables var molecule = Mol(); if ( molecule[0].showlabels == 0 ) { buttonColor("LabelButton",1); molecule[0].showlabels = 1; drawMolecule(); return; } buttonColor("LabelButton",0); molecule[0].showlabels = 0; drawMolecule(); return; } /// /// Routine to draw a single atom /// function drawAtom(ctx, atomNum, AtomSize, centerx, centery) { // Define local variables var A; var x, y, r; var xoff, yoff, roff; var molecule = Mol(); var activeCanvas = activeWin(""); // Get parameters for atom A = molecule[atomNum].atomicnumber; x = molecule[0].AtomScale*molecule[atomNum].x + centerx; y = molecule[0].AtomScale*molecule[atomNum].y + centery; r = molecule[0].AtomScale*AtomSize*element(A,"radius"); xoff = x-(0.20*r); yoff = y-(0.20*r); roff = 0.30*r; x = Math.floor(x+0.5); y = Math.floor(y+0.5); r = Math.floor(r+0.5); xoff = Math.floor(xoff+0.5); yoff = Math.floor(yoff+0.5); AtomColor = ctx.createRadialGradient(xoff, yoff, roff, x, y, r); AtomColor.addColorStop(0, element(A,"color")); AtomColor.addColorStop(1, element(A,"gradient")); // Plot atom as a gradient shaded circle ctx.beginPath(); ctx.arc(x, y, r, 0, 2*Math.PI, false); ctx.fillStyle = AtomColor; ctx.fill(); ctx.lineWidth = 0.01; ctx.strokeStyle = "black"; ctx.stroke(); ctx.closePath(); // Draw label for atom if ( molecule[0].showlabels != 0 ) atomLabel(ctx,A,atomNum,x,y); // End of drawAtom routine } /// /// Routine to draw a single atom without gradient /// function drawAtomPlain(ctx, atomNum, AtomSize, centerx, centery) { // Define local variables var A; var x, y, r; var xoff, yoff, roff; var molecule = Mol(); var activeCanvas = activeWin(""); // Get parameters for atom A = molecule[atomNum].atomicnumber; x = molecule[0].AtomScale*molecule[atomNum].x + centerx; y = molecule[0].AtomScale*molecule[atomNum].y + centery; r = molecule[0].AtomScale*AtomSize*element(A,"radius"); xoff = x-(0.20*r); yoff = y-(0.20*r); roff = 0.30*r; x = Math.floor(x+0.5); y = Math.floor(y+0.5); r = Math.floor(r+0.5); xoff = Math.floor(xoff+0.5); yoff = Math.floor(yoff+0.5); // Plot atom as a solid shaded circle ctx.beginPath(); ctx.arc(x, y, r, 0, 2*Math.PI, false); ctx.fillStyle = element(A,"color"); ctx.fill(); ctx.lineWidth = 1; ctx.strokeStyle = "black"; ctx.stroke(); ctx.closePath(); // Draw label for atom if ( molecule[0].showlabels != 0 ) atomLabel(ctx,A,atomNum,x,y); // End of drawAtomPlain routine } /// /// Routine to draw charge cloud around a single atom /// function DrawChargeCloud(ctx, atomNum, AtomSize, centerx, centery) { // Define local variables var A; var x, y, r; var colR, colB, colG, deltaRGB; var molecule = Mol(); var activeCanvas = activeWin(""); // Get parameters for atom A = molecule[atomNum].atomicnumber; x = molecule[0].AtomScale*molecule[atomNum].x + centerx; y = molecule[0].AtomScale*molecule[atomNum].y + centery; r = molecule[0].AtomScale*AtomSize*element(A,"radius"); // Set colors based on charge var q = molecule[atomNum].charge; // Positive charges shown in blue if (q >= 0) { (q > 1.0) ? deltaRGB = 1.0 : deltaRGB = q; colR = 0; colG = 0; colB = 255; } // Positive charges shown in red if (q < 0) { (q < -1.0) ? deltaRGB = 1.0 : deltaRGB = -q; colR = 255; colG = 0; colB = 0; } AtomColor = "rgba("+colR+","+colG+","+colB+","+deltaRGB+")"; // AtomColor = "rgba("+colR+","+colG+","+colB+",0.75)"; // Plot charge cloud as a semi-transparent circle ctx.beginPath(); ctx.arc(x, y, r, 0, 2*Math.PI, false); ctx.fillStyle = AtomColor; ctx.fill(); ctx.lineWidth = 0.01; ctx.strokeStyle = "black"; ctx.stroke(); ctx.closePath(); // End DrawChargeCloud routine } /// /// Routine to draw a single atom with a highlight /// function DrawAtomHilite(ctx, atomNum, AtomSize, centerx, centery) { // Define local variables var A; var x, y, r; var colR, colB, colG, deltaRGB; var molecule = Mol(); var activeCanvas = activeWin(""); // Get parameters for atom A = molecule[atomNum].atomicnumber; x = molecule[0].AtomScale*molecule[atomNum].x + centerx; y = molecule[0].AtomScale*molecule[atomNum].y + centery; r = molecule[0].AtomScale*AtomSize*element(A,"radius"); // Set highlight color to yellow AtomColor = "rgba(255,255,0,0.5)"; // Plot charge cloud as a semi-transparent circle ctx.beginPath(); ctx.arc(x, y, r, 0, 2*Math.PI, false); ctx.fillStyle = AtomColor; ctx.fill(); ctx.lineWidth = 0.01; ctx.strokeStyle = "black"; ctx.stroke(); ctx.closePath(); // End DrawAtomHilite routine } /// /// Helper routine to draw label for atom /// Parameters: /// Atomic number, atom #, (x,y) coordinates /// function atomLabel(ctx,A,i,ax,ay) { var label = element(A,"symbol"); var fontsize = 14; var x = parseFloat(ax); var y = parseFloat(ay) + fontsize/2; var molecule = Mol(); ctx.lineWidth = 1.0; ctx.textAlign = "center"; ctx.font = "normal " + fontsize + "px sans-serif"; ctx.fillStyle = element(A,"label"); ctx.beginPath(); ctx.fillText(label,x,y); var w = 10.0 / molecule[0].AtomScale; ctx.fillRect(x,y,w*1.5,w); ctx.closePath(); } /// /// Routine to draw a single bond /// function drawBond(ctx, atom1, atom2, AtomSize, centerx, centery, smallMolecule) { // Define local variables var i, j, k; var x1, y1, z1, x2, y2, z2; var dx, dy, dz; var xoff, yoff; var dist, r; var molecule = Mol(); var activeCanvas = activeWin(""); var AtomScale = molecule[0].AtomScale; var BondWidth = Math.floor(0.10*AtomScale + 0.5); var BondColor = "rgb(200,128,51)"; // Get parameters for atoms r = AtomScale * AtomSize * element(molecule[atom1].atomicnumber,"radius") - 2; x1 = AtomScale*molecule[atom1].x + centerx; y1 = AtomScale*molecule[atom1].y + centery; z1 = AtomScale*molecule[atom1].z; x2 = AtomScale*molecule[atom2].x + centerx; y2 = AtomScale*molecule[atom2].y + centery; z2 = AtomScale*molecule[atom2].z; // For large molecules, use simpler plot if ( ! smallMolecule ) { ctx.beginPath(); ctx.moveTo(xoff, yoff); ctx.lineTo(x2, y2); ctx.lineWidth = BondWidth; ctx.strokeStyle = BondColor; ctx.stroke(); ctx.closePath(); } // Calculate intersection of bond with sphere dx = x2 - x1; dy = y2 - y1; dz = z2 - z1; dist = Math.sqrt(dx*dx + dy*dy + dz*dz); xoff = x1 + r*dx/dist; yoff = y1 + r*dy/dist; // Draw bond ctx.beginPath(); ctx.moveTo(xoff, yoff); ctx.lineTo(x2, y2); ctx.lineWidth = BondWidth + 2; ctx.strokeStyle = "rgb(0,0,0)"; ctx.stroke(); ctx.moveTo(xoff, yoff); ctx.lineTo(x2, y2); ctx.lineWidth = BondWidth; ctx.strokeStyle = BondColor; ctx.stroke(); ctx.closePath(); } /// /// Clear drawing window (canvas) /// function clear(ctx, width, height) { // Clear plot area ctx.fillStyle = "rgb(255,255,255)"; ctx.fillRect(0, 0, width, height); // ctx.clearRect(0, 0, width, height); // Show border around plot area ctx.beginPath(); ctx.rect(1,1,width-1,height-1); ctx.lineWidth = 2; ctx.strokeStyle = "rgb(95,95,127)"; ctx.stroke(); ctx.closePath(); } /// /// Draw atoms and bonds with highlighting /// function drawHighlight(mycanvas, sequence, AtomSize, centerx, centery) { // Define local variables var i, j, k; var x, y, r; var A; var maxBonds, bondto; var x1, y1, x2, y2; var molecule = Mol(); var bonds = BondMatrix(); // Create connection to Canvas var canvas = document.getElementById(mycanvas); var ctx = canvas.getContext('2d'); var width = canvas.width; var height = canvas.height; // Clear screen before drawing molecule clear(ctx, width, height); // Define properties of lines ctx.strokeStyle = "rgb(0, 0, 255)"; ctx.lineWidth = 3.0; // Depth sort: Draw from back to front if ( typeof drawHighlight.deep == 'undefined' ) { drawHighlight.deep = []; } if ( drawHighlight.deep.length != molecule[0].numatoms ) { j=0; drawHighlight.deep = []; for (i=drawHighlight.deep.length; i 0) { highbond = 0; if (hilite > 0) { for (ih=1; ih < sequence[0]*3; ih++) { if (bondto == sequence[ih]) highbond = 1; } } for (k=i+1; k < molecule[0].numatoms; k++) { if (drawHighlight.deep[k].id == bondto) { HighlightBond(ctx,atom,bondto,highbond, AtomSize, centerx, centery); } } } } } // Finished with drawHighlight routine } /// /// Routine to draw a single highlighted atom /// function HighlightAtom(ctx, atomNum, hilite, AtomSize, centerx, centery) { // Define local variables var A; var x, y, r; var xoff, yoff, roff; var istart, ilength, colorstr; var myrgb = new Array(); var bcolor = "rgb(191,191,191)"; var hcolor = "rgb(255, 0, 0)"; var gcolor = "rgb(127, 0, 0)"; var molecule = Mol(); var activeCanvas = activeWin(""); // Get parameters for atom A = molecule[atomNum].atomicnumber; x = molecule[0].AtomScale*molecule[atomNum].x + centerx; y = molecule[0].AtomScale*molecule[atomNum].y + centery; r = molecule[0].AtomScale*AtomSize*element(A,"radius"); xoff = x-(0.20*r); yoff = y-(0.20*r); roff = 0.30*r; x = Math.floor(x+0.5); y = Math.floor(y+0.5); r = Math.floor(r+0.5); xoff = Math.floor(xoff+0.5); yoff = Math.floor(yoff+0.5); AtomColor = ctx.createRadialGradient(xoff, yoff, roff, x, y, r); alpha = 0.33; if (hilite > 0) alpha = 1.0; istart = element(A,"color").indexOf("(") + 1; ilength = element(A,"color").indexOf(")") - istart; colorstr = element(A,"color").substr(istart,ilength); myrgb = colorstr.replace(/,/g," ").split(' '); hcolor = "rgba("+myrgb[0]+","+myrgb[1]+","+myrgb[2]+","+alpha+")"; istart = element(A,"gradient").indexOf("(") + 1; ilength = element(A,"gradient").indexOf(")") - istart; colorstr = element(A,"gradient").substr(istart,ilength); myrgb = colorstr.replace(/,/g," ").split(' '); gcolor = "rgba("+myrgb[0]+","+myrgb[1]+","+myrgb[2]+","+alpha+")"; AtomColor.addColorStop(0, hcolor); AtomColor.addColorStop(1, gcolor); // Plot atom as a gradient shaded circle ctx.beginPath(); ctx.arc(x, y, r, 0, 2*Math.PI, false); ctx.fillStyle = AtomColor; ctx.fill(); ctx.lineWidth = 0.01; ctx.strokeStyle = "black"; ctx.stroke(); ctx.closePath(); // Draw label if highlighted atom if (hilite > 0) atomLabel(ctx,A,atomNum,x,y); } /// /// Routine to draw a single highlighted bond /// function HighlightBond(ctx, atom1, atom2, highlite, AtomSize, centerx, centery) { // Define local variables var i, j, k; var x1, y1, z1, x2, y2, z2; var dx, dy, dz; var xoff, yoff; var dist, r; var AtomScale = molecule[0].AtomScale; var BondWidth = Math.floor(0.10*AtomScale + 0.5); var BondColor = "rgba(200,128,51,1.0)"; var bcolor = "rgba(191,191,191,0.33)"; var molecule = Mol(); var activeCanvas = activeWin(""); // Get parameters for atoms r = AtomScale * AtomSize * element(molecule[atom1].atomicnumber,"radius"); x1 = AtomScale*molecule[atom1].x + centerx; y1 = AtomScale*molecule[atom1].y + centery; z1 = AtomScale*molecule[atom1].z; x2 = AtomScale*molecule[atom2].x + centerx; y2 = AtomScale*molecule[atom2].y + centery; z2 = AtomScale*molecule[atom2].z; // Calculate intersection of bond with sphere dx = x2 - x1; dy = y2 - y1; dz = z2 - z1; dist = Math.sqrt(dx*dx + dy*dy + dz*dz); xoff = x1 + r*dx/dist; yoff = y1 + r*dy/dist; // Draw bond ctx.beginPath(); ctx.moveTo(xoff, yoff); ctx.lineTo(x2, y2); ctx.lineWidth = BondWidth + 2; ctx.strokeStyle = "rgba(0,0,0,0.33)"; if ( highlite > 0 ) ctx.strokeStyle = "rgba(0,0,0,1.0)"; ctx.stroke(); ctx.moveTo(xoff, yoff); ctx.lineTo(x2, y2); ctx.lineWidth = BondWidth; if ( highlite > 0 ) { ctx.strokeStyle = BondColor; } else { ctx.strokeStyle = bcolor; } ctx.stroke(); ctx.closePath(); } // -------------------- mouse.js file -------------------- /// /// Routine to save number of atom selected with mouseDown event /// option = "Set" or "Show" /// value = Number of selected atom /// 0 = MouseDown, but not on atom /// -1 = Mouse not down /// function mouseState(option, value) { // Initialize parameters as necessary if ( typeof mouseState.DownAtom == 'undefined' ) mouseState.DownAtom = -1; // Show number of atom selected by mouseDown if ( option == "Show" ) return mouseState.DownAtom; if ( option == "Set" ) mouseState.DownAtom = value; // End of mouseState routine } //# function parameters() //# //# Define constants used to control drawing. //# Get/set values using: //# var param = parameters(); //# //# param.mode = Interface mode. Set to "Draw" or "View" //# param.element = Type of element to add next. Default = "C" //# param.clouds = # of hybrid orbitals. Default = 4 //# param.bondmode = Bond mode. Set to "Add", "Delete", or "Rotate" //# param.atommode = Add atom mode. Set to "Add" or "Delete" //# function parameters() { // Initialize parameter array if necessary if ( typeof parameters.values === "undefined" ) parameters.values = new paramObject(); // Define default values for parameters if ( typeof parameters.values.mode == 'undefined' ) parameters.values.mode = "View"; if ( typeof parameters.values.elem == 'undefined' ) parameters.values.elem = "C"; if ( typeof parameters.values.clouds == 'undefined' ) parameters.values.clouds = 4; if ( typeof parameters.values.add == 'undefined' ) parameters.values.add = "Add"; if ( typeof parameters.values.bond == 'undefined' ) parameters.values.bond = "Add"; // End of parameters routine return parameters.values; } /// /// Define structure for drawing parameters /// function paramObject() { this.mode = "View"; this.element = "C"; this.clouds = 4; this.bondmode = "Add"; this.atommode = "Add"; } /// /// Routine to handle mouse press /// function MouseDown(evt) { // Declare local variables var cx, cy; var windowName = evt.target.id; var activecanvas = activeWin(windowName); var canvas = document.getElementById(activecanvas); var width = canvas.width; var height = canvas.height; // Map touch screen and mouse buttons cx = evt.pageX; cy = evt.pageY; // If touch screen if (evt.targetTouches) { if (evt.targetTouches.length == 1) { cx = evt.targetTouches[0].pageX; cy = evt.targetTouches[0].pageY; } } // Save selected atom mouseState( "Set", onAtom(cx, cy, canvas, width, height) ); } /// /// Routine to handle mouse up /// function MouseUp(evt) { // Declare local variables var cx, cy; var mouseOnAtom, UpAtom; var activecanvas = activeWin(""); var molecule = Mol(); var canvas = document.getElementById(activecanvas); var width = canvas.width; var height = canvas.height; var param = parameters(); // Map touch screen and mouse buttons cx = evt.pageX; cy = evt.pageY; // If touch screen if (evt.targetTouches) { cx = evt.targetTouches[0].pageX; cy = evt.targetTouches[0].pageY; } // See which atom (if any) mouse is currently on mouseOnAtom = mouseState("Show"); mouseState("Set", -1); Upatom = onAtom(cx, cy, canvas, width, height); // If 'click' moves to blank space, exit if ( Upatom == 0 ) { viewGeom(0); return; } // If 'click' stays on a same atom, proceed if ( Upatom == mouseOnAtom ) { // Show geometry information if (param.mode == "View") { if ( evt.shiftKey > 0) { molecule[Upatom].highlite = ( (molecule[Upatom].highlite+1) % 2); drawMolecule(); } else { viewGeom(mouseOnAtom); } } // Add or Remove atom(s) if (param.mode == "Draw") { // Save Molecular information Undo("save"); molecule[0].charge = 999; if (param.atommode == "Delete") { delAtom(Upatom); } else { newAtom(Upatom); } } } // If 'click' moves to a different atom, draw or remove bond if ( (Upatom != mouseOnAtom) && (param.mode == "Draw") ) { // Save Molecular information Undo("save"); if (param.bondmode == "Add") { molecule[0].charge = 999; addBond(mouseOnAtom,Upatom); } if (param.bondmode == "Delete") { molecule[0].charge = 999; delBond(mouseOnAtom,Upatom); } if (param.bondmode == "Rotate") { BondRotation("Set",mouseOnAtom,Upatom); } drawMolecule(); } // Finished with MouseUp routine } /// /// Is mouse within radius of atom? /// Parameters - mouse coordinates /// Return - number of atom or zero if none /// function onAtom(mx, my, canvas, width, height) { // Declare local variables var i, A, dx, dy; var radius, delta; var AtomSize = 0.50; var molecule = Mol(); // Convert mouse position to atomic coordinate system mx = (mx - canvas.offsetLeft - width/2); my = (my - canvas.offsetTop - height/2); // Loop over all atoms, looking for first match for (i=1; i <= molecule[0].numatoms; i++) { A = molecule[i].atomicnumber; radius = molecule[0].AtomScale*AtomSize*element(A,"radius"); radius = radius*radius; dx = molecule[0].AtomScale*molecule[i].x - mx; dy = molecule[0].AtomScale*molecule[i].y - my; delta = dx*dx + dy*dy; if (delta <= radius) { return i; } } return 0; } /// /// Routine to deal with scroll wheel /// function MouseWheel(evt) { // Local variable var molecule = Mol(); // Stop window scrolling if (evt.preventDefault) evt.preventDefault(); // Firefox and Opera use detail, Chrome uses wheelDelta(?) var delta = evt.detail ? evt.detail*(-1) : evt.wheelDelta; var newScale = (delta > 0) ? 1.1 : 0.9; molecule[0].AtomScale = molecule[0].AtomScale*newScale; drawMolecule(); return false; } /// /// Alter molecule IFF mouse is pressed /// function MouseMove(evt) { var newx, newy; var dx, dy, tx, ty, da; var x, y, z; var xc, yc; var cosx, cosy, cosz, sinx, siny, sinz; var cosA, sinA; var step=2; // Smaller values make less sensitive var molecule = Mol(); var param = parameters(); // Save old (x,y) coordinates if ( typeof MouseMove.cx == 'undefined' ) MouseMove.cx = 250; if ( typeof MouseMove.cy == 'undefined' ) MouseMove.cy = 250; // Only rotate if mouse pressed, but not on an atom if ( mouseState("Show") == 0 ) { // Map touch screen and mouse buttons newx = evt.pageX; newy = evt.pageY; // If touch screen if (evt.targetTouches) { if (evt.targetTouches.length == 1) { newx = evt.targetTouches[0].pageX; newy = evt.targetTouches[0].pageY; } } // Record movement dx = (MouseMove.cx - newx); dy = (MouseMove.cy - newy); MouseMove.cx = newx; MouseMove.cy = newy; if ( Math.abs(dx)+Math.abs(dy) > 10) return; // Handle special case of rotation about a bond if ( param.bondmode == "Rotate" ) { da = dx + dy; BondRotation("Rotate",da); drawMolecule(); return; } // If key pressed, rotate around z-axis if ( evt.shiftKey > 0) { cosz = Math.cos(dx*step*Math.PI/180); sinz = Math.sin(dx*step*Math.PI/180); for (i=1; i <= molecule[0].numatoms; i++) { x = molecule[i].x; y = molecule[i].y; molecule[i].x = cosz*x + sinz*y; molecule[i].y = -sinz*x + cosz*y; } drawMolecule(); return; } // If key pressed, translate along x- or y-axis if ( evt.ctrlKey > 0) { tx = dx*0.01; ty = dy*0.01; for (i=1; i <= molecule[0].numatoms; i++) { x = molecule[i].x; y = molecule[i].y; molecule[i].x = x - tx; molecule[i].y = y - ty; } drawMolecule(); return; } // Rotate entire molecule cosx = Math.cos(dy*step*Math.PI/180); sinx = Math.sin(dy*step*Math.PI/180); cosy = Math.cos(dx*step*Math.PI/180); siny = Math.sin(dx*step*Math.PI/180); for (i=1; i <= molecule[0].numatoms; i++) { x = molecule[i].x; y = molecule[i].y; z = molecule[i].z; molecule[i].x = cosy*x + siny*z; molecule[i].y = -sinx*siny*x + cosx*y + sinx*cosy*z; molecule[i].z = -cosx*siny*x - sinx*y + cosx*cosy*z; } drawMolecule(); } } /// /// VIEW MODE: Routine to display geometry information to user /// function viewGeom(OnAtom) { // Declare local variables var i, A1, A2, A3, A4; var dx, dy, dz, d; var dux, duy, duz, dvx, dvy, dvz, du, dv; var label; var activecanvas = activeWin(""); var canvas = document.getElementById(activecanvas); var ctx = canvas.getContext('2d'); var width = canvas.width; var height = canvas.height; var molecule = Mol(); // Initialize geom array if necessary if ( typeof viewGeom.geom == 'undefined' ) { viewGeom.geom = [0,0,0,0,0]; } // If valid atom not sent, zero array if (OnAtom == 0) { for (i=0; i < 5; i++) viewGeom.geom[i] = 0; drawMolecule(); return; } // If duplicate atom sent, zero array and return if (OnAtom) { for (i=1; i < 5; i++) { if (viewGeom.geom[i] == OnAtom) viewGeom(0); } } // Display appropriate information to user viewGeom.geom[0] = viewGeom.geom[0] + 1; sw = viewGeom.geom[0]; viewGeom.geom[sw] = OnAtom; //InfoWin("\nMouse on atom #"+OnAtom+" Switch = "+sw); switch (sw) { case 1: A1 = molecule[viewGeom.geom[1]].atomicnumber; label = element(A1,"symbol") + viewGeom.geom[1].toString(); if ( molecule[0].showcharges != 0 ) { label += ": Charge = "; if ( molecule[viewGeom.geom[1]].charge > 0 ) label += "+"; label += molecule[viewGeom.geom[1]].charge.toFixed(2); } drawMolecule(); geomLabel(ctx,label,width); break; case 2: // Bond distance dx = molecule[viewGeom.geom[1]].x - molecule[viewGeom.geom[2]].x; dy = molecule[viewGeom.geom[1]].y - molecule[viewGeom.geom[2]].y; dz = molecule[viewGeom.geom[1]].z - molecule[viewGeom.geom[2]].z; d = Math.sqrt(dx*dx+dy*dy+dz*dz); d = d.toFixed(3); d = d.toString(); A1 = molecule[viewGeom.geom[1]].atomicnumber; A2 = molecule[viewGeom.geom[2]].atomicnumber; label = element(A1,"symbol") + viewGeom.geom[1].toString() + "--"; label += element(A2,"symbol") + viewGeom.geom[2].toString(); label += " = " + d; drawMolecule(); geomLabel(ctx,label,width); break; case 3: // Bond angle A1 = molecule[viewGeom.geom[1]].atomicnumber; A2 = molecule[viewGeom.geom[2]].atomicnumber; A3 = molecule[viewGeom.geom[3]].atomicnumber; label = element(A1,"symbol") + viewGeom.geom[1].toString() + "--"; label += element(A2,"symbol") + viewGeom.geom[2].toString() + "--"; label += element(A3,"symbol") + viewGeom.geom[3].toString(); ang = angle(molecule,viewGeom.geom[1],viewGeom.geom[2],viewGeom.geom[3]); ang = ang.toFixed(1); ang = ang.toString(); label += " = " + ang + "ᵒ"; drawMolecule(); geomLabel(ctx,label,width); break; case 4: // Dihedral angle A1 = molecule[viewGeom.geom[1]].atomicnumber; A2 = molecule[viewGeom.geom[2]].atomicnumber; A3 = molecule[viewGeom.geom[3]].atomicnumber; A4 = molecule[viewGeom.geom[4]].atomicnumber; label = element(A1,"symbol") + viewGeom.geom[1].toString() + "--"; label += element(A2,"symbol") + viewGeom.geom[2].toString() + "--"; label += element(A3,"symbol") + viewGeom.geom[3].toString() + "--"; label += element(A4,"symbol") + viewGeom.geom[4].toString(); ang = dihedral(molecule,viewGeom.geom[1],viewGeom.geom[2],viewGeom.geom[3],viewGeom.geom[4]); ang = ang.toFixed(1); ang = ang.toString(); label += " = " + ang; drawMolecule(); geomLabel(ctx,label,width); for (i=0; i < 5; i++) viewGeom.geom[i] = 0; break; } } /// /// VIEW MODE: /// Helper routine to show geometry information /// Parameters - mouse coordinates /// function geomLabel(ctx,label,width) { ctx.lineWidth = 1.0; ctx.textAlign = "right"; ctx.textBaseline = "top"; ctx.font = "normal 18px sans-serif"; ctx.fillStyle = "#000000"; ctx.beginPath(); ctx.fillText(label,width-5,5); ctx.closePath(); } /// /// Routine to select current element for drawing /// function pickElem(elem) { var tablesize = element(1,"max"); var i, str, mystyle; var mode; var param = parameters(); var backcolor = "silver"; var active = "lightskyblue"; // If first time routine called, set defaults if ( typeof pickElem.metals == 'undefined' ) { pickElem.metals = "none"; pickElem.myfont = "14px"; if (document.getElementById('pchooser') ) document.getElementById('pchooser').innerHTML = "Metals"; } // Change display of periodic table if (elem == "PView") { if (document.getElementById('pchooser') ) { if ( document.getElementById('pchooser').innerHTML == "Metals" ) { pickElem.metals = "table-cell"; pickElem.myfont = "10px"; document.getElementById('pchooser').innerHTML = "Organic"; } else { pickElem.metals = "none"; pickElem.myfont = "14px"; document.getElementById('pchooser').innerHTML = "Metals"; } } } // Turn off display for metals // if (elem == "MOff") { // pickElem.metals = "none"; // pickElem.myfont = "14px"; // if (document.getElementById('MOn') ) // document.getElementById('MOn').style.color = "navy"; // if (document.getElementById('MOff') ) // document.getElementById('MOff').style.color = "antiquewhite"; // if (document.getElementById('pchooser') ) // document.getElementById('pchooser').innerHTML = "Metals"; // } // Turn on display for metals // if (elem == "MOn") { // pickElem.metals = "table-cell"; // pickElem.myfont = "10px"; // if (document.getElementById('pchooser') ) // document.getElementById('pchooser').innerHTML = "Organic"; // } // Set display options depending on selected view if (document.getElementById('Row1') ) document.getElementById('Row1').style.display = pickElem.metals; if (document.getElementById('Row2') ) document.getElementById('Row2').style.display = pickElem.metals; if (document.getElementById('Row3') ) document.getElementById('Row3').style.display = pickElem.metals; if (document.getElementById('RowLa') ) document.getElementById('RowLa').style.display = pickElem.metals; if (document.getElementById('RowAc') ) document.getElementById('RowAc').style.display = pickElem.metals; if (document.getElementById('RowLa2') ) document.getElementById('RowLa2').style.display = pickElem.metals; if (document.getElementById('RowAc2') ) document.getElementById('RowAc2').style.display = pickElem.metals; // if (document.getElementById('Mon') ) // document.getElementById('MOn').style.fontSize = pickElem.myfont; // if (document.getElementById('Moff') ) // document.getElementById('MOff').style.fontSize = pickElem.myfont; // Loop over all elements in table for (i=1; i 0) { found = 0; if ( atm == atom1 ) found = 1; for (j=1; j <= RList[0]; j++) { if ( atm == RList[j] ) { found = 1; j = RList[0] + 1; } } if (found == 0) { RList[0]++; RList[RList[0]] = atm; rotlist(RList, atom2, atm); } } } // End of rotlist routine return RList; } // -------------------- End of mouse.js file -------------------- // // -------------------- charges.js -------------------- // //# function setCharge() //# //# Routine to set the molecular charge using value of select form with id="SelectCharge". //# function setCharge() { var molecule = Mol(); var ChargeForm = document.getElementById("SelectCharge"); if ( ChargeForm ) { molecule[0].charge = ChargeForm.value * 1; } // End of setCharge routine } //# function simpleQ() //# //# Public routine to (somewhat arbitrarily) assign electron configuration, //# including bond orders, and calculate the charges on each atom. //# function simpleQ() { // Define local variables var i, j; var BondMtx = []; var BondWin = document.getElementById("bondMatrix"); var molecule = Mol(); var numatoms=molecule[0].numatoms; // If no atoms defined, exit if ( numatoms < 1 ) { InfoWin("Cannot set charges. No atoms found.\n",1); return; } // Toggle charge button if ( molecule[0].showcharges != 0 ) { buttonColor("ChargeButton",0); molecule[0].showcharges = 0; if ( document.getElementById("SelectCharge") ) { document.getElementById("SelectCharge").value = 0; } drawMolecule(); return; } // Change color of charge button buttonColor("ChargeButton",1); molecule[0].showcharges = 1; // Clear information and bond windows InfoWin("",1); if ( BondWin ) BondWin.innerHTML = ""; // Initialize Bond Matrix for (i = 0; i <= numatoms; i++) { BondMtx[i] = []; for (j = 0; j <= numatoms; j++) BondMtx[i][j] = 0.0; } // Initialize calculated atomic charges for (i=1; i <= numatoms; i++) molecule[i].charge = 0.0; // Place electrons for single bonds in BondMtx. sigmaBonds(BondMtx); // If no charge explicitly set, try to calculate "best" charge if ( molecule[0].charge == 999 ) formalcharge(); // Adjust electrons is necessary to match charge checkcharge(BondMtx); // Create list of atoms with less than octet of electrons checkOctet(BondMtx); // Then, loop over all atoms and share electrons to form pi bonds limitShare(BondMtx); formPi(BondMtx); // Look for atoms that still have less than full octet // If violations of octet rule found, try to form 'dative' bonds checkOctet(BondMtx); formDative(BondMtx); // Calculate charges atomicCharge(BondMtx); // Write bond matrix to output window if ( BondWin ) showBondMatrix(BondMtx, BondWin); // Draw molecule, showing charges drawMolecule(); // Finished with simpleQ routine return; } /// /// Calculate formal charges based on "ideal" number of bonds /// (for main group elements only). Since multiple bonds may /// not yet be known, negative formal charges limited to -1. /// function formalcharge() { // Declare local variables var i, num; var octet, qbonds; var formalpos, formalneg; var molecule = Mol(); var numatoms = molecule[0].numatoms; var bonds = BondMatrix(); // Calculate formal charges based on number of bonds formalpos = 0.0; formalneg = 0.0; for (i=1; i <= numatoms; i++) { octet = 0; if (element(molecule[i].atomicnumber,"block") == "s") octet = 2; if (element(molecule[i].atomicnumber,"block") == "p") octet = 8; if ( octet > 0 ) { qbonds = bonds[i][0] + element(molecule[i].atomicnumber,"valence") - octet; if ( qbonds < 0 ) formalneg += qbonds; if ( qbonds > 0 ) formalpos += qbonds; } } // Since multiple bonds not yet known, "scale down" negative charges while ( formalneg <= -2 ) formalneg += 2; // Store formal charge prediction of molecular charge molecule[0].charge = formalpos + formalneg; // End formalcharge routine return; } /// /// Look for mismatch between molecular charge and the calculated charge /// based on the electron assignment. If difference found, try to /// add/remove appropriate number of electrons to fix. /// function checkcharge(BondMtx) { // Declare local variables var i, j, num; var totalq; var deltaq, electrons; var molecule = Mol(); var numatoms = molecule[0].numatoms; var block, numetals; var eerror; var bonds = BondMatrix(); var AlmostZero = 0.00001; // Count electrons to determine current charge totalq = 0; for (i=1; i <= numatoms; i++) { totalq += element(molecule[i].atomicnumber,"valence"); for (j=i; j <= numatoms; j++) { totalq -= BondMtx[i][j]; } } // If values don't match, try to add/remove electrons. deltaq = totalq - molecule[0].charge; if ( Math.abs(deltaq) < AlmostZero ) { return; } // If too many electrons present, remove from lone pairs if ( deltaq < -AlmostZero ) { // Remove electrons from metals first numetals = 0; for (i=1; i <= molecule[0].numatoms; i++) { block = element(molecule[i].atomicnumber,"block"); if ( (block == "d") || (block == "f") ) { numetals++; } } if ( numetals > 0 ) { electrons = -deltaq / numetals; for (i=1; i <= molecule[0].numatoms; i++) { block = element(molecule[i].atomicnumber,"block"); if ( (block == "d") || (block == "f") ) { BondMtx[i][i] -= electrons; } } } else { // No metals present, so remove from lone pairs num = 0; for (i=1; i <= molecule[0].numatoms; i++) { if ( BondMtx[i][i] > 0 ) num++; } eerror = -deltaq; if ( num > 0 ) { eerror = 0; electrons = -deltaq / num; for (i=1; i <= molecule[0].numatoms; i++) { if ( BondMtx[i][i] > 0 ) { BondMtx[i][i] -= electrons; if ( BondMtx[i][i] < 0 ) { eerror -= BondMtx[i][i]; BondMtx[i][i] = 0.0; } } } } // Solve (rare) case where couldn't remove enough e- from one or more atoms if ( eerror > 0 ) { num = 0; for (i=1; i <= molecule[0].numatoms; i++) { if ( BondMtx[i][i] > 0 ) num++; } if ( num > 0 ) { electrons = eerror / num; for (i=1; i <= molecule[0].numatoms; i++) { if ( BondMtx[i][i] > 0 ) { BondMtx[i][i] -= electrons; } } } } } } // If not enough electrons present, add to atoms short of full octet if ( deltaq > AlmostZero ) { // Create list of atoms that with less than octet of electrons checkOctet(BondMtx); // Count number of atoms short of full octet num = 0; for (i=1; i <= molecule[0].numatoms; i++) { if ( BondMtx[i][0] > 0.0 ) num++; } // If atoms found that need electrons, add them eerror = deltaq; if ( num > 0 ) { eerror = 0; electrons = deltaq/num; for ( i=1; i <= molecule[0].numatoms; i++ ) { if ( BondMtx[i][0] > 0.0 ) { if ( electrons <= BondMtx[i][0]) { BondMtx[i][i] += electrons; } else { BondMtx[i][i] += BondMtx[i][0]; eerror += electrons - BondMtx[i][0]; BondMtx[i][0] = 0; } } } // Try again if one or more atoms couldn't accept enough e- if ( eerror > 0 ) { num = 0; for (i=1; i <= molecule[0].numatoms; i++) { if ( BondMtx[i][0] > 0.0 ) num++; } if ( num > 0 ) { electrons = eerror/num; eerror = 0; for ( i=1; i <= molecule[0].numatoms; i++ ) { if ( BondMtx[i][0] > 0.0 ) { if ( electrons <= BondMtx[i][0]) { BondMtx[i][i] += electrons; } else { BondMtx[i][i] += BondMtx[i][0]; eerror += electrons - BondMtx[i][0]; BondMtx[i][0] = 0; } } } } } } // If all else fails, add electrons to atoms that can violate octet rule if ( eerror > 0 ) { num = 0; for (i=1; i <= molecule[0].numatoms; i++) { if ( molecule[i].atomicnumber > 12 ) num++; } if ( num > 0 ) { electrons = eerror/num; for (i=1; i <= molecule[0].numatoms; i++) { if ( molecule[i].atomicnumber > 12 ) BondMtx[i][i] += electrons; } } } } // Electron adjustment complete. Check to see if charges match now. // Count electrons to determine current charge totalq = 0; for (i=1; i <= numatoms; i++) { totalq += element(molecule[i].atomicnumber,"valence"); for (j=i; j <= numatoms; j++) { totalq -= BondMtx[i][j]; } } deltaq = totalq - molecule[0].charge; if ( Math.abs(deltaq) > AlmostZero ) { InfoWin("ERROR: Unable to assign electrons to balance charge.\n",1); InfoWin(" Assigned charge = "+molecule[0].charge+"\n"); InfoWin("Charge based on e- = "+totalq+"\n\n"); } // End checkcharge routine return; } /// /// Place valence electrons for single bonds in BondMtx. /// Remaining electrons initially assumed to be lone pairs. /// function sigmaBonds(BondMtx) { // Declare local variables var i, j; var lone; var molecule = Mol(); var numatoms=molecule[0].numatoms; var bonds = BondMatrix(); // Place electrons in bonds for (i=1; i < numatoms; i++) { // Bonds assumed to be single bonds for (j=i+1; j <= numatoms; j++) { if (bonds[i][j] > 0) { BondMtx[i][j] = 2.0; BondMtx[j][i] = 2.0; } } } // Place remaining electrons in lone pairs for (i=1; i <= numatoms; i++) { lone = element(molecule[i].atomicnumber,"valence") - bonds[i][0]; // First-row main-group elements cannot have more than 8 electrons if ( (molecule[i].atomicnumber<11) && (bonds[i][0] > 3) ) lone = 0; if (lone > 0) BondMtx[i][i] = lone; } // Finished with sigmaBonds routine return BondMtx; } /// /// Check if all main group atoms obey octet rule or not. /// # of missing electrons stored in BondMtx[i][0] /// function checkOctet(BondMtx) { // Declare local variables var i, j, octet; var molecule = Mol(); var numatoms=molecule[0].numatoms; // Find/store # of missing electrons for ( i=1; i <= numatoms; i++ ) { octet = 0; BondMtx[i][0] = 0.0; if (element(molecule[i].atomicnumber,"block") == "p") { octet = 8; for ( j=1; j <= numatoms; j++) { octet -= BondMtx[i][j]; } } if ( octet > 0 ) BondMtx[i][0] = octet; } // Finished with checkOctet routine return BondMtx; } /// /// Limit number of electrons any one atom can share /// to form pi bonds. /// function limitShare(BondMtx) { // Declare local variables var i, j, nb; var molecule = Mol(); var numatoms=molecule[0].numatoms; var bonds = BondMatrix(); for ( i=1; i <= numatoms; i++ ) { if ( BondMtx[i][0] > 0 ) { nb = 0; for ( j=1; j <= numatoms; j++ ) { if ( (bonds[i][j] > 0) && (BondMtx[j][0] > 0) ) { nb++; } } (nb > 0) ? BondMtx[i][0] = BondMtx[i][0]/nb : BondMtx[i][0] = 0; } } // Finished with limitShare routine return BondMtx; } /// /// Loop over all atoms and share electrons to form pi bonds /// function formPi(BondMtx) { // Declare local variables var i, j, nb; var electrons; var molecule = Mol(); var numatoms=molecule[0].numatoms; var bonds = BondMatrix(); for ( i=1; i < numatoms; i++ ) { if ( BondMtx[i][0] > 0.0 ) { for (j=i+1; j <= numatoms; j++) { if (bonds[i][j] > 0) { electrons = Math.min(BondMtx[i][0],BondMtx[j][0]); if ( electrons > 0.0 ) { BondMtx[i][j] += 2.0*electrons; BondMtx[j][i] += 2.0*electrons; BondMtx[i][i] -= electrons; BondMtx[j][j] -= electrons; } } } } } // Simple error checking for (i=1; i <= numatoms; i++) { if ( BondMtx[i][i] < 0.0 ) { InfoWin("ERROR in formPi: Atom "+i+" has "+BondMtx[i][i].toFixed(3)+" lone pairs.\n"); BondMtx[i][i] = 0.0; } } // Finished with formPi routine return BondMtx; } /// /// Use lone pairs on one atom to form 'dative' bonds with neighbor(s) /// function formDative(BondMtx) { // Define local variables var i, j, k, nb; var dative; var easy; var donor = new Array(); var molecule = Mol(); var numatoms = molecule[0].numatoms; var bonds = BondMatrix(); // See if dative bonds necessary dative = 0; for ( i=1; i <= numatoms; i++ ) { if ( BondMtx[i][0] > 0.0 ) { dative = 1; } } if ( dative == 0 ) { return; } // Initialize donor array for ( i=1; i <= numatoms; i++ ) { donor[i] = 0.0; } // Loop over all atoms for ( i=1; i <= numatoms; i++ ) { // If atom has less than octet of electrons, look for donors if ( BondMtx[i][0] > 0.0 ) { // Count potential donors (atoms with lone pairs) nb = 0; for (j = 1; j <= numatoms; j++) { if ( bonds[i][j] > 0 ) if ( BondMtx[j][j] > 0 ) nb++; } // Request equal number of electrons from all neighbors if ( nb > 0 ) { BondMtx[i][0] = BondMtx[i][0]/nb; for (j = 1; j <= numatoms; j++) { if ( bonds[i][j] > 0 ) { if ( BondMtx[j][j] > 0 ) donor[j] += BondMtx[i][0]; } } } } } // Verify enough electrons available to form all requested dative bonds easy = 1; for ( i=1; i <= numatoms; i++ ) { if ( donor[i] > BondMtx[i][i] ) easy = 0; } // If 'easy' solution exists, use it if ( easy > 0 ) { for ( i=1; i <= numatoms; i++ ) { if ( BondMtx[i][0] > 0.0 ) { for ( j = 1; j <= numatoms; j++) { if ( bonds[i][j] > 0 ) { if ( donor[j] > 0 ) { BondMtx[i][j] += BondMtx[i][0]; BondMtx[j][i] += BondMtx[i][0]; BondMtx[j][j] -= BondMtx[i][0]; } } } } } } // Finished with formDative routine return BondMtx; } /// /// Calculate charges on all atoms /// function atomicCharge(BondMtx) { // Declare parameters var ALPHA = 0.5; // Fraction of charge to mix with EN var MIX = 0.5; // Reduce effects of formal charges (1=no reduction) var MAXSTEP = 15; var CONVERGED = 0.001; // Declare local variables var i, j, loop; var Z, mixfactor; var q, delta, dmax; var molcharge = 0.0; var atomEN = new Array(); var molecule = Mol(); var numatoms=molecule[0].numatoms; var bonds = BondMatrix(); // Calculate charge on molecule for (i=1; i <= numatoms; i++) { molcharge += element(molecule[i].atomicnumber,"valence"); for (j=1; j <= numatoms; j++) { if ( i == j ) { molcharge -= BondMtx[i][i]; } else { molcharge -= 0.5*BondMtx[i][j]; } } } delta = Math.abs(molcharge - molecule[0].charge); if ( delta > 0.001 ) alert("Error: Electron assignment does NOT match molecular charge."); // InfoWin("Molecular charge = "+molcharge.toFixed(2)+"\n"); // Initialize electronegativity array and set mixing factor mixfactor = MIX; // If molecule has a charge, use 100% formal charge method if ( Math.abs(molcharge) > 0.001 ) mixfactor = 1.0; for ( i=1; i <= numatoms; i++ ) { Z = molecule[i].atomicnumber; if ( (element(Z,"block")=="d") || (element(Z,"block")=="f") ) mixfactor = 0.0; q = element(Z,"EN") || 0; if ( q == 0 ) { q = 1.0; InfoWin("WARNING: No electronegativity defined for "); InfoWin(element(molecule[i].atomicnumber,"symbol")+"\n"); } atomEN[i] = q; } // Inform user of method used to calculate charges if (mixfactor==1.0) InfoWin("Using 100% formal charge method to calculate charges.\n"); if (mixfactor==0.0) InfoWin("Using 100% bond polarity method to calculate charges.\n"); if (mixfactor==MIX) InfoWin("Using mixture of formal charge and bond polarity method to calculate charges.\n"); // Perform iterations until charges remain constant loop = 0; dmax = 100.0; while ( (loopCONVERGED) ) { loop++; // Calculate charges for each atom for ( i=1; i <= numatoms; i++ ) { Z = molecule[i].atomicnumber; q = mixfactor * (element(Z,"valence") - BondMtx[i][i]); for ( j = 1; j <= numatoms; j++) { if ( bonds[i][j] > 0 ) { q += (1.0-mixfactor) * 0.5 * BondMtx[i][j]; q -= BondMtx[i][j]*atomEN[i]/(atomEN[i]+atomEN[j]); } } molecule[i].charge = q; } // Calculate new electronegativity values for each atom dmax = 0.0; for ( i=1; i <= numatoms; i++ ) { q = atomEN[i]; atomEN[i] = element(molecule[i].atomicnumber,"EN") || 1.0; atomEN[i] += ALPHA*molecule[i].charge; delta = Math.abs(q - atomEN[i]); if ( delta > dmax ) dmax = delta; } } // Finished with atomicCharge routine return BondMtx; } /// /// Calculate molecular dipole /// Assumes point charges on nuclear centers, with charge /// vector originating from origin. /// function dipoleMoment() { // Declare local variables var i; var dx, dy, dz, dipole; var DEBYE = 4.8032; var molecule = Mol(); var numatoms=molecule[0].numatoms; // Calculate x,y,z components of dipole vector dx = 0.0; dy = 0.0; dz = 0.0; for ( i=1; i <= numatoms; i++ ) { dx += molecule[i].x * molecule[i].charge; dy += molecule[i].y * molecule[i].charge; dz += molecule[i].z * molecule[i].charge; } // Calculate length of dipole vector and scale to Debye units dipole = DEBYE * Math.sqrt(dx*dx+dy*dy+dz*dz); // Finished with dipoleMoment routine return dipole; } //# function showBondMatrix(BondMtx,BondWin) //# //# Write Bond information to output window. //# function showBondMatrix(BondMtx,BondWin) { // Define local variables var i, j; var numstr, plus; var dq, dipole; var qsign = ""; var symbol; var molcharge; var bondtable = new Array(); var entry = new Array(); var molecule = Mol(); var numatoms=molecule[0].numatoms; // Calculate molecular charge molcharge = 0; for (i=1; i <= numatoms; i++) molcharge += molecule[i].charge; // Show Charge and Dipole moment dipole = dipoleMoment(); BondWin.innerHTML = "

Molecular charge = "+molcharge.toFixed(1)+ ", Dipole ≈ "+dipole.toFixed(1)+" D"; // Write Bond matrix to Information Window //--- Header --- InfoWin("Bond Matrix: Off-diagonal = e- in bonds, diagonal = unshared e-\n"); InfoWin(" "); for (i=1; i <= numatoms; i++) { symbol = element(molecule[i].atomicnumber,"symbol"); if (symbol.length < 2) symbol += " "; InfoWin(" "+symbol+" "); if ( (i%5) == 0 ) InfoWin(" "); } InfoWin("\n"); //--- One row for each atom --- for (i=1; i <= numatoms; i++) { symbol = element(molecule[i].atomicnumber,"symbol"); if (symbol.length < 2) symbol += " "; if ( i < 10 ) InfoWin(" "); InfoWin(i+" "+symbol+" "); for (j=1; j <= numatoms; j++) { InfoWin(BondMtx[i][j].toFixed(1)+" "); if ( (j%5) == 0 ) InfoWin(" "); } InfoWin(" q = "); if ( molecule[i].charge > 0 ) InfoWin("+"); InfoWin(molecule[i].charge.toFixed(2)+"\n"); if ( (i%5) == 0 ) InfoWin("\n"); } // End of showBondMatrix routine return; } // -------------------- Section to handle Reading Files -------------------- /// /// Routine to get filename of local input file from user /// function MyFileReader(evt) { var validExtension; var localfile = evt.target.files[0]; // Call routine to read and process data if (localfile) { var fr = new FileReader(); fr.onload = function(fh) { validExtension = 0; var ext = extension(localfile.name); // Read contents and split data into lines var contents = fh.target.result; var lines = contents.split("\n"); if ( ext == "xyz" ) { validExtension = 1; readXYZfile(lines); } if ( ext == "mol" ) { validExtension = 1; readMOLfile(localfile,lines); } if ( ext == "inp" ) { validExtension = 1; readINPfile(localfile,lines); } if ( validExtension == 0 ) { InfoWin("*** ERROR: Invalid file type for "+localfile.name+". ***",1); return; } centerMolecule(); drawMolecule(); } fr.readAsText(localfile); } else { alert("Failed to load file"); } } /// /// Routine to determine extension for filename /// function extension(myfilename) { var extension = myfilename.substring(myfilename.lastIndexOf('.')+1); return extension.toLowerCase(); } //# //# function showgallery(title,base,List,Desc,size) //# //# Routine to display multiple files stored on the web server. //# //# Parameters: //# title: Title to display before gallery //# (If title = "delete", clear gallery) //# base: Path to directory (relative to web root) containing images //# List: Array containing a list of filenames (including extensions) //# Desc: Array containing descriptions for each file //# size: integer width (in px) for each frame //# function showgallery(title,base,List,Desc,size) { // Declare local variables var i, start, pos; var html; var frame, canvas; var framestr, canvasstr; var csize; // If title = "delete", clear gallery if ( title == "delete" ) { if ( typeof showgallery.num != "undefined" ) { showgallery.num = 0; delete showgallery.list; } return; } // If no gallery division present, exit if ( ! document.getElementById("gallery") ) { alert("Warning: showgallery called, but no

exists on html page."); return; } // Set up storage to keep track of all files to load in all galleries if ( typeof showgallery.list === "undefined" ) { showgallery.num = 0; showgallery.list = []; } start = showgallery.num; // Define base names to use for each frame and canvas canvas = "gallerycanvas"; frame = "galleryframe"; // Add files to list for display in all galleries pos = start; for (i=0; i < List.length; i++) { showgallery.list[pos] = base + List[i]; showgallery.num++; pos++; } // Set dimension for canvas csize = "width=\"" + size + "\" height=\"" + size + "\">"; // Create content and add to web page html = ""; if ( title ) { html = "

" + title + "

\n"; } pos = start; for (i=0; i < List.length; i++) { canvasstr = canvas + pos; framestr = frame + pos; html += "
"; html += ""; html += Desc[i]; html += "

\n"; pos++; } html += "

 

\n\n"; document.getElementById("gallery").innerHTML += html; // If debug window exists, write output to this window if ( document.getElementById("debug") ) { document.getElementById("debug").innerHTML += html; } // Set correct size for each box px = size + "px"; pos = start; for (i=0; i < List.length; i++) { framestr = frame + pos; if ( document.getElementById(framestr) ) document.getElementById(framestr).style.width = px; pos++; } // Updating HTML appears to erase old molecules, so load all molecules in list for (i=0; i < showgallery.num; i++) { canvasstr = canvas + i; activeWin(canvasstr); delMolecule(); readServerFile(showgallery.list[i]); if ( document.getElementById("debug") ) { html = "\n\nProcessed molecule "+i; html += " named "+showgallery.list[i]; document.getElementById("debug").innerHTML += html; } } } //# //# function galleryUniform() //# //# Routine to force all molecules that are part of a "gallery" to be displayed with the same size scale. //# function galleryUniform() { // Declare local variables var i, num, scale; var framestr; var frame = "gallerycanvas"; var molecule = []; // Find number of gallery images on page num = 0; framestr = frame + num; while ( document.getElementById(framestr) ) { num++; framestr = frame + num; } // Find scale factor for largest molecule scale = 1000; for (i=0; i < num; i++) { framestr = frame + i; activeWin(framestr); molecule = Mol(); if ( molecule[0].AtomScale < scale ) { scale = molecule[0].AtomScale; } } // Scale molecules if ( scale < 1000.0 ) { for (i=0; i < num; i++) { framestr = frame + i; activeWin(framestr); molecule = Mol(); molecule[0].AtomScale = scale; drawMolecule(); } } } //# //# function galleryReset() //# //# For molecules that are part of a "gallery", this routine optimizes the size of each molecule individually. //# function galleryReset() { // Declare local variables var i, num; var framestr; var frame = "gallerycanvas"; // Find number of gallery images on page num = 0; framestr = frame + num; while ( document.getElementById(framestr) ) { num++; framestr = frame + num; } // Reset view for each molecule for (i=0; i < num; i++) { framestr = frame + i; activeWin(framestr); centerMolecule(); drawMolecule(); } } //# //# function readServerFile(filename) //# //# Routine to read contents of file stored on the web server. //# //# Parameter: //# filename: Name (URL) of file (including path) //# function readServerFile(filename) { // Define local variables var lines; var validExtension; var fileinfo = new Array(); var ext = extension(filename); var xmlhttp; // Use XML to get contents of file from "server" xmlhttp=new XMLHttpRequest(); xmlhttp.open('GET', filename, false); xmlhttp.send(); lines = xmlhttp.responseText.split('\n'); // Call routine to read and process data validExtension = 0; if ( ext == "xyz" ) { validExtension = 1; readXYZfile(lines); } if ( ext == "mol" ) { validExtension = 1; readMOLfile(localfile,lines); } if ( ext == "inp" ) { validExtension = 1; readINPfile(localfile,lines); } if ( validExtension == 0 ) { InfoWin("*** ERROR: Invalid file type. ***",1); return; } // Update display centerMolecule(); drawMolecule(); } //# //# function InfoWin(mytext,mode) //# //# Routine to write text to information window (textarea with an id of "information"). //# //# Parameters: //# mytext: String to write to output window //# mode: If >0, then clear text window //# function InfoWin(mytext,mode) { var outstring = mytext || ""; var clearwin = mode || 0; if ( ! document.getElementById("information") ) return; if ( clearwin > 0 ) document.getElementById("information").value = outstring; else document.getElementById("information").value += outstring; } //# function loadMolecule() //# //# Routine to load molecular information for methane molecule. //# function loadMolecule() { // Add atomic coordinates to molecule array addAtom(6, 0.000, 0.000, 0.000); addAtom(1, 0.874, 0.618, 0.000); addAtom(1, -0.874, 0.618, 0.000); addAtom(1, 0.000, -0.618, 0.874); addAtom(1, 0.000, -0.618, -0.874); // Add bonds to bond array addBond(1, 2); addBond(1, 3); addBond(1, 4); addBond(1, 5); } //# function resetView() //# //# Routine to reset view. Center, rescale, and remove highlights. //# function resetView() { // Define local variables var i; var molecule = Mol(); // Remove highlights and show all atoms for ( i=1; i <= molecule[0].numatoms; i++ ) { molecule[i].highlite = 0; molecule[i].hide = 0; } // Clear Information Window InfoWin("",1); // Formula, center, scale, and draw formula(); centerMolecule(); drawMolecule(); } //# function buttonColor(button, mode) //# //# Set color of buttons //# //# Parameters //# button - string containing ID name for button //# mode - 0=inactive, 1=active //# function buttonColor(button, mode) { mode = mode || 0; var buttoncolor = "silver"; if ( mode ) buttoncolor = "lightskyblue"; if ( document.getElementById(button) ) document.getElementById(button).style.backgroundColor = buttoncolor; } //# function initialize() //# //# Initialization Routines //# - Load properties of elements //# - Define Handlers for mouse events //# - Draw molecule //# function initialize() { // Define handler for drawing area (canvas) // activeWin defines routines to handle mouse events var activeCanvas = activeWin(); var molfile = document.getElementById('molfile'); // If no canvas element found, see if userDefined() creates one. if ( ! activeCanvas ) { userDefined(); activeCanvas = activeWin(""); if ( ! activeCanvas ) { alert("No canvas present. Either create a canvas or remove onLoad=initialize() statement from ."); } return; } // Handler for loading files. After file selected, calls "MyFileReader" if ( molfile ) { // Verify browser supports HTML5 FileReader if (window.File && window.FileReader && window.FileList && window.Blob) { molfile.addEventListener('change', MyFileReader, false); } else { alert('The File APIs are not fully supported by your browser.'); } } // Create periodic table drawPeriodic(); // Initialize molecular geometry var molecule = Mol(); // Set display mode to View viewmode(); // Draw molecule if ( typeof molecule == 'undefined' ) delMolecule(); if (molecule[0].numatoms < 1) { delMolecule(); loadMolecule(); formula(); // Display molecular formula centerMolecule(); // Center molecule } drawMolecule(); // Set default drawing atom pickClouds(4); pickElem("C"); // Execute user-defined routine userDefined(); } // -------------------- build.js file -------------------- /// /// Routine to add/change atoms and add H /// function newAtom(OnAtom) { // Declare local variables var i, j, k, numbonds; var vx, vy, vz, vd; var Rij, Rnew; var elem, pos; var errorH; var bondlist = []; var param = parameters(); var molecule = Mol(); var bonds = BondMatrix(); var activeCanvas = activeWin(""); // Lookup information for current element atomicNumber = lookupSymbol(param.element); // Set number of bonds on selected atom numbonds = bonds[OnAtom][0]; // // If number of bonds == 0, arbitrarily add new atom along // x axis and attach the appropriate number of hydrogen atoms. // if (numbonds == 0) { Rnew = element(atomicNumber,"radius") + element(molecule[OnAtom].atomicnumber,"radius"); dx = molecule[OnAtom].x + Rnew; dy = molecule[OnAtom].y; dz = molecule[OnAtom].z; addAtom(atomicNumber, dx, dy, dz); addBond(OnAtom,molecule[0].numatoms); addH(molecule[0].numatoms); centerMolecule(); drawMolecule(activeCanvas); return; } // Create list of atoms bonded to current atom pos = 0; for (i=1; i <= molecule[0].numatoms; i++) { if ( (bonds[OnAtom][i] > 0) && (i != OnAtom)) bondlist[++pos] = i; } bondlist[0] = pos; if ( bondlist[0] != bonds[OnAtom][0]) alert("ERROR: Supposed to be "+numbonds+" bonds on atom "+OnAtom+", but "+pos+" bonds found."); // If atom to add is H, add one H if (atomicNumber == 1) { vx = 0.0; vy = 0.0; vz = 0.0; for (i=1; i <= numbonds; i++) { j = bondlist[i]; dx = molecule[j].x - molecule[OnAtom].x; dy = molecule[j].y - molecule[OnAtom].y; dz = molecule[j].z - molecule[OnAtom].z; dd = Math.sqrt(dx*dx+dy*dy+dz*dz); vx += dx/dd; vy += dy/dd; vz += dz/dd; } vd = Math.sqrt(vx*vx+vy*vy+vz*vz); Rnew = element(1,"radius") + element(molecule[OnAtom].atomicnumber,"radius"); vx = molecule[OnAtom].x - vx*Rnew/vd; vy = molecule[OnAtom].y - vy*Rnew/vd; vz = molecule[OnAtom].z - vz*Rnew/vd; addAtom(1, vx, vy, vz); // Check to be sure new H atom not too close to other bonded atoms for (pos=1; pos <= numbonds; pos++) { errorH = 0; Rij = distance(molecule,bondlist[pos],molecule[0].numatoms); if ( Rij < 0.2 ) errorH = 1; } if ( (errorH) && (numbonds>1) ) { // If bonded atoms all close to a plane, place H above/below plane i = bondlist[1]; j = bondlist[2]; vx = (molecule[i].y-molecule[OnAtom].y) * (molecule[j].z-molecule[OnAtom].z); vx -= (molecule[i].z-molecule[OnAtom].z) * (molecule[j].y-molecule[OnAtom].y); vy = (molecule[i].z-molecule[OnAtom].z) * (molecule[j].x-molecule[OnAtom].x); vy -= (molecule[i].x-molecule[OnAtom].x) * (molecule[j].z-molecule[OnAtom].z); vz = (molecule[i].x-molecule[OnAtom].x) * (molecule[j].y-molecule[OnAtom].y); vz -= (molecule[i].y-molecule[OnAtom].y) * (molecule[j].x-molecule[OnAtom].x); vd = Math.sqrt(vx*vx+vy*vy+vz*vz); molecule[molecule[0].numatoms].x = molecule[OnAtom].x - vx*Rnew/vd; molecule[molecule[0].numatoms].y = molecule[OnAtom].y - vy*Rnew/vd; molecule[molecule[0].numatoms].z = molecule[OnAtom].z - vz*Rnew/vd; errorH = 0; for (pos=1; pos <= numbonds; pos++) { Rij = distance(molecule,bondlist[pos],molecule[0].numatoms); if ( Rij < 0.2 ) errorH = 1; } } if ( errorH ) { alert("Error adding H atom"); delAtom(molecule[0].numatoms); return; } // If no errors, continue addBond(OnAtom,molecule[0].numatoms); centerMolecule(); drawMolecule(activeCanvas); numbonds = 0; return; } // // If number of bonds == 1, change to new atom type, // change bond length, and add appropriate # of H. // if (numbonds == 1) { i = OnAtom; j =bondlist[1]; dx = molecule[i].x - molecule[j].x; dy = molecule[i].y - molecule[j].y; dz = molecule[i].z - molecule[j].z; Rij = Math.sqrt(dx*dx+dy*dy+dz*dz); Rnew = element(atomicNumber,"radius") + element(molecule[j].atomicnumber,"radius"); dx *= Rnew/Rij; dy *= Rnew/Rij; dz *= Rnew/Rij; molecule[i].atomicnumber = atomicNumber; molecule[i].x = dx + molecule[j].x; molecule[i].y = dy + molecule[j].y; molecule[i].z = dz + molecule[j].z; addH(OnAtom); centerMolecule(); drawMolecule(activeCanvas); } // If number of bonds > 1, then simply change atom type if (numbonds > 1) { molecule[OnAtom].atomicnumber = atomicNumber; drawMolecule(activeCanvas); } // Finished with newAtom routine } /// /// Routine to add H atoms to 'atom' /// function addH(atom) { var i, j, clouds, Z, numH; var atom1, atom2; var errmsg; var param = parameters(); var molecule = Mol(); var bonds = BondMatrix(); var activeCanvas = activeWin(""); // Only automatically add H atoms to p-block elements if ( element(molecule[atom].atomicnumber,"block") != "p" ) return; // Determine how many H atoms to add clouds = param.clouds; Z = molecule[atom].atomicnumber; valence = element(Z,"valence"); numH = 3 + clouds - valence; if (numH < 1) clouds = 1; if ( clouds <= 1 ) return; // Find first atom bonded to current atom atom1 = 0; i = 0; while ( (atom1==0) && (i < molecule[0].numatoms) ) { i++; if ( (bonds[atom][i]>0) && (i != atom) ) atom1 = i; } // Find first atom bonded to atom1 atom2 = 0; if ( atom1 ) { i = 0; while ( (atom2==0) && (i < molecule[0].numatoms) ) { i++; if ( bonds[atom1][i]>0 ) if ( (i != atom) && (i != atom1) ) atom2 = i; } } // Call appropriate routines to add hydrogen atom(s) switch (clouds) { case 2: add1H(atom,atom1); break; case 3: add2H(atom,atom1,atom2,numH); break; case 4: add3H(atom,atom1,atom2,numH); break; default: break; } // Draw molecule centerMolecule(); drawMolecule(activeCanvas); // Finished } /// /// Routine to add one H atom to sp hybridized atom /// function add1H(atom,i) { // Declare local variables var j, dx, dy, dz; var Za, Rai, RH; var Hx, Hy, Hz; var molecule = Mol(); // Calculate H--atom bond length Za = molecule[atom].atomicnumber; RH = element(Za,"radius") + element(1,"radius"); // If atom has zero bonds, add H along x-axis if (i == 0) { dx = molecule[atom].x + RH; dy = molecule[atom].y; dz = molecule[atom].z; addAtom(1, Hx, Hy, Hz); addBond(atom,molecule[0].numatoms); return; } // Calculate vector atom->i dx = molecule[i].x - molecule[atom].x; dy = molecule[i].y - molecule[atom].y; dz = molecule[i].z - molecule[atom].z; Rai = Math.sqrt(dx*dx+dy*dy+dz*dz); // Calculate position of new H Hx = molecule[atom].x - dx*RH/Rai; Hy = molecule[atom].y - dy*RH/Rai; Hz = molecule[atom].z - dz*RH/Rai; addAtom(1, Hx, Hy, Hz); addBond(atom,molecule[0].numatoms); // End add1H routine } /// /// Routine to add up to 2 H atoms to sp2 hybridized atom /// function add2H(atom,i,j,numH) { // Declare local variables var Za, Zi, Zj, RaH; var daiX, daiY, daiZ, Rai; var dijX, dijY, dijZ, Rij, ang; var dpX, dpY, dpZ, dpd; var Hx, Hy, Hz, dHx, dHy, dHz; var LX, LY, LZ, Lscale; var base; var aug = new Array(); var molecule = Mol(); // Lookup atomic numbers and calculate X-H Bond length Za = molecule[atom].atomicnumber; RaH = element(Za,"radius") + element(1,"radius"); // If atom contains zero bonds, add 2H in xy plane if (i == 0) { Hx = molecule[atom].x + 0.5*RaH; Hy = molecule[atom].y + RaH*Math.sqrt(3)/2; Hz = molecule[atom].z; addAtom(1, Hx, Hy, Hz); addBond(atom,molecule[0].numatoms); if (numH > 1) { Hy = molecule[atom].y - RaH*Math.sqrt(3)/2; addAtom(1, Hx, Hy, Hz); addBond(atom,molecule[0].numatoms); } return; } // Lookup atomic numbers for first bonded atom Zi = molecule[i].atomicnumber; daiX = molecule[i].x - molecule[atom].x; daiY = molecule[i].y - molecule[atom].y; daiZ = molecule[i].z - molecule[atom].z; Rai = Math.sqrt(daiX*daiX + daiY*daiY + daiZ*daiZ); // If atom contains only one bond, pick arbitrary atom for second point if (j == 0) { for (var ii=1; ii 1) { Hy = molecule[atom].y - RaH*Math.sqrt(3)/2; addAtom(1, Hx, Hy, Hz); addBond(atom,molecule[0].numatoms); } return; } // Lookup atomic numbers for second bonded atom Zj = molecule[j].atomicnumber; dijX = molecule[j].x - molecule[i].x; dijY = molecule[j].y - molecule[i].y; dijZ = molecule[j].z - molecule[i].z; Rij = Math.sqrt(dijX*dijX + dijY*dijY + dijZ*dijZ); // ----- Add first H ----- // Dot-product of HA*Ai aug[0] = daiX; aug[1] = daiY; aug[2] = daiZ; aug[3] = -RaH*Rai/2; // Dot-product of HA*ij ang = (-daiX*dijX-daiY*dijY-daiZ*dijZ)/(Rai*Rij); ang = Math.acos(-1/2) + Math.PI - Math.acos(ang); aug[4] = dijX; aug[5] = dijY; aug[6] = dijZ; aug[7] = RaH*Rij*Math.cos(ang); // Calculate cross product (ji x ai) dpX = dijZ*daiY - dijY*daiZ; dpY = dijX*daiZ - dijZ*daiX; dpZ = dijY*daiX - dijX*daiY; dpd = Math.sqrt(dpX*dpX+dpY*dpY+dpZ*dpZ); // Dot-product of HA * ( ji X ai ) aug[8] = dpX; aug[9] = dpY; aug[10] = dpZ; aug[11] = 0.0; // Calculate coordinates of H1 var coord = gaussElim(aug); Hx = molecule[atom].x + coord[0]; Hy = molecule[atom].y + coord[1]; Hz = molecule[atom].z + coord[2]; addAtom(1, Hx, Hy, Hz); addBond(atom,molecule[0].numatoms); // ----- Add second H ----- if (numH == 1) { return; } // Dot-product of HA*Ai aug[0] = daiX; aug[1] = daiY; aug[2] = daiZ; aug[3] = -RaH*Rai/2; // Dot-product of HA*ij ang = (-daiX*dijX-daiY*dijY-daiZ*dijZ)/(Rai*Rij); ang = Math.acos(ang) - Math.acos(0.5); aug[4] = dijX; aug[5] = dijY; aug[6] = dijZ; aug[7] = RaH*Rij*Math.cos(ang); // Dot-product of LH2* (iA x ij) aug[8] = dpX; aug[9] = dpY; aug[10] = dpZ; aug[11] = 0.0; // Calculate coordinates for H2 debug = "\nRow 1: "+aug[0].toFixed(4)+" "+aug[1].toFixed(4); debug += " "+aug[2].toFixed(4)+" "+aug[3].toFixed(4); debug += "\nRow 2: "+aug[4].toFixed(4)+" "+aug[5].toFixed(4); debug += " "+aug[6].toFixed(4)+" "+aug[7].toFixed(4); debug += "\nRow 3: "+aug[8].toFixed(4)+" "+aug[9].toFixed(4); debug += " "+aug[10].toFixed(4)+" "+aug[11].toFixed(4); coord = gaussElim(aug); Hx = molecule[atom].x + coord[0]; Hy = molecule[atom].y + coord[1]; Hz = molecule[atom].z + coord[2]; debug = "H2 at: ("+Hx.toFixed(4)+", "+Hy.toFixed(4)+", "+Hz.toFixed(4)+")"; addAtom(1, Hx, Hy, Hz); addBond(atom,molecule[0].numatoms); debug = "atom = "+atom+" i = "+i+" numatoms = "+molecule[0].numatoms; debug += "\n"+element(molecule[molecule[0].numatoms].atomicnumber,"symbol"); debug += "\nRow 1: "+aug[0].toFixed(4)+" "+aug[1].toFixed(4); debug += " "+aug[2].toFixed(4)+" "+aug[3].toFixed(4); debug += "\nRow 2: "+aug[4].toFixed(4)+" "+aug[5].toFixed(4); debug += " "+aug[6].toFixed(4)+" "+aug[7].toFixed(4); debug += "\nRow 3: "+aug[8].toFixed(4)+" "+aug[9].toFixed(4); debug += " "+aug[10].toFixed(4)+" "+aug[11].toFixed(4); debug += "\nCross: "+dpX.toFixed(4)+" "+dpY.toFixed(4)+" "+dpZ.toFixed(4); //alert(debug); // End of add2H routine } /// /// Routine to add H atoms to sp3 hybridized atom /// function add3H(atom,i,j,numH) { // Declare local variables var Za, Zi, Zj, RaH; var daiX, daiY, daiZ, Rai; var dijX, dijY, dijZ, Rij, ang; var dpX, dpY, dpZ, dpd; var Hx, Hy, Hz, dHx, dHy, dHz; var LX, LY, LZ, Lscale; var base; var aug = new Array(); var molecule = Mol(); // Lookup atomic numbers and calculate X-H Bond length Za = molecule[atom].atomicnumber; Zi = molecule[i].atomicnumber; Zj = molecule[j].atomicnumber; RaH = element(Za,"radius") + element(1,"radius"); // ----- Add first H ----- // Dot-product of HA*Ai daiX = molecule[i].x - molecule[atom].x; daiY = molecule[i].y - molecule[atom].y; daiZ = molecule[i].z - molecule[atom].z; Rai = Math.sqrt(daiX*daiX + daiY*daiY + daiZ*daiZ); aug[0] = daiX; aug[1] = daiY; aug[2] = daiZ; aug[3] = -RaH*Rai/3; // Dot-product of HA*ij dijX = molecule[j].x - molecule[i].x; dijY = molecule[j].y - molecule[i].y; dijZ = molecule[j].z - molecule[i].z; Rij = Math.sqrt(dijX*dijX + dijY*dijY + dijZ*dijZ); ang = (-daiX*dijX-daiY*dijY-daiZ*dijZ)/(Rai*Rij); ang = Math.acos(-1/3) + Math.PI - Math.acos(ang); aug[4] = dijX; aug[5] = dijY; aug[6] = dijZ; aug[7] = RaH*Rij*Math.cos(ang); // Cross-product ji X ai dpX = dijZ*daiY - dijY*daiZ; dpY = dijX*daiZ - dijZ*daiX; dpZ = dijY*daiX - dijX*daiY; dpd = Math.sqrt(dpX*dpX+dpY*dpY+dpZ*dpZ); // Handle special case where j=0 and i located at (0,0,0) if (dpd == 0) { dpX = molecule[atom].y; dpY = -molecule[atom].x; dpZ = molecule[atom].z; dpd = Math.sqrt(dpX*dpX+dpY*dpY+dpZ*dpZ); } // Dot-product of HA * ( ji X ai ) aug[8] = dpX; aug[9] = dpY; aug[10] = dpZ; aug[11] = 0.0; var coord = gaussElim(aug); Hx = molecule[atom].x + coord[0]; Hy = molecule[atom].y + coord[1]; Hz = molecule[atom].z + coord[2]; addAtom(1, Hx, Hy, Hz); addBond(atom,molecule[0].numatoms); // ----- Add second H ----- if (numH == 1) { return; } // Create point L base = molecule[0].numatoms; Lscale = RaH/(Rai*3); LX = molecule[atom].x - daiX*Lscale; LY = molecule[atom].y - daiY*Lscale; LZ = molecule[atom].z - daiZ*Lscale; // Dot-product of LH2*LH aug[0] = molecule[base].x - LX; aug[1] = molecule[base].y - LY; aug[2] = molecule[base].z - LZ; aug[3] = -RaH*RaH*4/9; // Dot-product of LH2*LA dHx = coord[0]; dHy = coord[1]; dHz = coord[2]; aug[4] = molecule[atom].x - LX; aug[5] = molecule[atom].y - LY; aug[6] = molecule[atom].z - LZ; aug[7] = 0.0; // Dot-product of LH2* (iA x ij) aug[8] = dpX; aug[9] = dpY; aug[10] = dpZ; aug[11] = RaH*dpd*Math.sqrt(2/3); // Calculate coordinates for H2 coord = gaussElim(aug); Hx = LX + coord[0]; Hy = LY + coord[1]; Hz = LZ + coord[2]; addAtom(1, Hx, Hy, Hz); addBond(atom,molecule[0].numatoms); // ----- Add third H ----- if (numH == 2) { return; } // Dot-product of LH2*LH aug[0] = molecule[base].x - LX; aug[1] = molecule[base].y - LY; aug[2] = molecule[base].z - LZ; aug[3] = -RaH*RaH*4/9; // Dot-product of LH2*LA dHx = coord[0]; dHy = coord[1]; dHz = coord[2]; aug[4] = molecule[atom].x - LX; aug[5] = molecule[atom].y - LY; aug[6] = molecule[atom].z - LZ; aug[7] = 0.0; // Dot-product of LH2* (iA x ij) dpd = Math.sqrt(dpX*dpX+dpY*dpY+dpZ*dpZ); aug[8] = dpX; aug[9] = dpY; aug[10] = dpZ; aug[11] = -RaH*dpd*Math.sqrt(2/3); debug = "atom = "+atom+" i = "+i+" numatoms = "+molecule[0].numatoms; debug += "\n"+element(molecule[molecule[0].numatoms].atomicnumber,"symbol"); debug += "\nRow 1: "+aug[0].toFixed(4)+" "+aug[1].toFixed(4); debug += " "+aug[2].toFixed(4)+" "+aug[3].toFixed(4); debug += "\nRow 2: "+aug[4].toFixed(4)+" "+aug[5].toFixed(4); debug += " "+aug[6].toFixed(4)+" "+aug[7].toFixed(4); debug += "\nRow 3: "+aug[8].toFixed(4)+" "+aug[9].toFixed(4); debug += " "+aug[10].toFixed(4)+" "+aug[11].toFixed(4); debug += "\nCross: "+dpX.toFixed(4)+" "+dpY.toFixed(4)+" "+dpZ.toFixed(4); //alert(debug); // Calculate coordinates for H3 coord = gaussElim(aug); // Hx = molecule[atom].x + coord[0]; // Hy = molecule[atom].y + coord[1]; // Hz = molecule[atom].z + coord[2]; Hx = LX + coord[0]; Hy = LY + coord[1]; Hz = LZ + coord[2]; addAtom(1, Hx, Hy, Hz); addBond(atom,molecule[0].numatoms); // End of add3H routine } /// /// Use gaussian elimination to solve for new coordinates. /// Argument is augmented matrix of the form: /// | ax ay az = ac | /// | bx by bz = bc | /// | cx cy cz = cc | /// /// Returns a matrix containing the solution (x,y,z) /// function gaussElim(aug) { // var aug = [2, -2, 0, -6, 1, -1, 1, 1, 0, 3, -2, -5]; // var aug = [1, -2, 1, 0, 2, 1, -3, 5, 4, -7, 1, -1]; var x, y, z, c; var coord = new Array(); var ax = parseFloat(aug[0]); var ay = parseFloat(aug[1]); var az = parseFloat(aug[2]); var ac = parseFloat(aug[3]); var bx = parseFloat(aug[4]); var by = parseFloat(aug[5]); var bz = parseFloat(aug[6]); var bc = parseFloat(aug[7]); var cx = parseFloat(aug[8]); var cy = parseFloat(aug[9]); var cz = parseFloat(aug[10]); var cc = parseFloat(aug[11]); //alert("| "+ax.toFixed(4)+" "+ay.toFixed(4)+" "+az.toFixed(4)+" = "+ac.toFixed(4)+" |\n"+ // "| "+bx.toFixed(4)+" "+by.toFixed(4)+" "+bz.toFixed(4)+" = "+bc.toFixed(4)+" |\n"+ // "| "+cx.toFixed(4)+" "+cy.toFixed(4)+" "+cz.toFixed(4)+" = "+cc.toFixed(4)+" |\n"); // Swap rows to place largest X variable in first row if ( (Math.abs(bx) > Math.abs(ax)) && (Math.abs(bx) > Math.abs(cx)) ) { x=ax; y=ay; z=az; c=ac; ax=bx; ay=by; az=bz; ac=bc; bx=x; by=y; bz=z; bc=c; } if ( (Math.abs(cx) > Math.abs(ax)) && (Math.abs(cx) > Math.abs(bx)) ) { x=ax; y=ay; z=az; c=ac; ax=cx; ay=cy; az=cz; ac=cc; cx=x; cy=y; cz=z; cc=c; } if ( Math.abs(cx) > Math.abs(bx) ) { x=bx; y=by; z=bz; c=bc; bx=cx; by=cy; bz=cz; bc=cc; cx=x; cy=y; cz=z; cc=c; } // Add rows to "zero-out" first column if ( (ax != 0) && (bx != 0 ) ) { factor = -ax/bx; bx = 0.0; by = by*factor + ay; bz = bz*factor + az; bc = bc*factor + ac; } if ( (ax != 0) && (cx != 0 ) ) { factor = -ax/cx; cx = 0.0; cy = cy*factor + ay; cz = cz*factor + az; cc = cc*factor + ac; } // Swap rows to place largest Y variable in second row if (Math.abs(cy) > Math.abs(by)) { y=by; z=bz; c=bc; by=cy; bz=cz; bc=cc; cy=y; cz=z; cc=c; } // Add rows to "zero-out" second column if ( (by != 0) && (cy != 0 ) ) { factor = -by/cy; cy = 0.0; cz = cz*factor + bz; cc = cc*factor + bc; } //alert("| "+ax.toFixed(4)+" "+ay.toFixed(4)+" "+az.toFixed(4)+" = "+ac.toFixed(4)+" |\n"+ // "| "+bx.toFixed(4)+" "+by.toFixed(4)+" "+bz.toFixed(4)+" = "+bc.toFixed(4)+" |\n"+ // "| "+cx.toFixed(4)+" "+cy.toFixed(4)+" "+cz.toFixed(4)+" = "+cc.toFixed(4)+" |\n"); // Solve coord[2] = 0.0; if (cz != 0) { coord[2] = cc/cz; } coord[1] = 0.0; if (by != 0) { coord[1] = (bc-(bz*coord[2]))/by; } coord[0] = 0.0; if (ax != 0) { coord[0] = (ac - (az*coord[2]) - (ay*coord[1]))/ax; } //alert("dx = "+coord[0].toFixed(4)+", dy = "+coord[1].toFixed(4)+", dz = "+coord[2].toFixed(4)); // Return answer return coord; } // // -------------------- mechanics.js -------------------- // //# function mechanics() //# //# Simple routine to perform crude optimization of structure. //# function mechanics() { // Define local variables var i, j, k; var Z; var loop; var erg, deltaE; var molOLD = new Array(); var molNEW = new Array(); var molecule = Mol(); // Drawing Canvas info var activecanvas = activeWin(""); var canvas = document.getElementById(activecanvas); var ctx = canvas.getContext('2d'); var width = canvas.width; // Parameters var MAXSTEP=0.2; var MAXLOOP=500; var ETHRESH = 0.0000002; // Save Molecular information Undo("save"); // Clear information window InfoWin("Simple Geometry Optimization starting\n",1); geomLabel(ctx,"Simple Geometry Optimization started",width); // Determine hybridization of all atoms in molecule molOLD = hybridization(); var DEBUG=0; // Debug hybridization routine if (DEBUG > 0) { InfoWin("Hybridization\n"); for (i=1; i <= molecule[0].numatoms; i++) { Z = molecule[i].atomicnumber; InfoWin(element(Z,"symbol")+" has "+molOLD[i].hybrid+" hybrid orbitals\n"); } } // Calculate energy of initial geometry erg = mechEnergy(molOLD); molOLD[0].energy = erg; molOLD[0].step = MAXSTEP; // Populate molNEW array molNEW[0] = new energyObject(); molNEW[0].energy = molOLD[0].energy; molNEW[0].step = molOLD[0].step; for (i=1; i <= molecule[0].numatoms; i++) { molNEW[i] = new mechanicsObject(); molNEW[i].hybrid = molOLD[i].hybrid; molNEW[i].x = molOLD[i].x; molNEW[i].y = molOLD[i].y; molNEW[i].z = molOLD[i].z; } // Call routine to calculate new geometry loop = 0; deltaE = ETHRESH*2.0; InfoWin(0+": Energy = "+erg.toFixed(8)+"\n"); while ( (loopETHRESH) ) { molNEW = optimize(molOLD); deltaE = Math.abs( molOLD[0].energy - molNEW[0].energy ); // Don't allow step size to increase too much if ( molNEW[0].step > MAXSTEP ) molNEW[0].step = MAXSTEP; // Copy values from molNEW array into molOLD molOLD[0].energy = molNEW[0].energy; molOLD[0].step = molNEW[0].step; for (i=1; i <= molecule[0].numatoms; i++) { molOLD[i].hybrid = molNEW[i].hybrid; molOLD[i].x = molNEW[i].x; molOLD[i].y = molNEW[i].y; molOLD[i].z = molNEW[i].z; } // Force at least 3 iterations loop++; if (loop < 3) if ( deltaE < ETHRESH ) deltaE = ETHRESH*2.0; // If structure approaching convergence, increase step size if ( deltaE < ETHRESH ) { if ( molNEW[0].step < MAXSTEP ) { molOLD[0].step *= 1.5; molNEW = optimize(molOLD); deltaE = Math.abs( molOLD[0].energy - molNEW[0].energy ); if ( deltaE > ETHRESH ) { molOLD[0].energy = molNEW[0].energy; molOLD[0].step = molNEW[0].step; for (i=1; i <= molecule[0].numatoms; i++) { molOLD[i].hybrid = molNEW[i].hybrid; molOLD[i].x = molNEW[i].x; molOLD[i].y = molNEW[i].y; molOLD[i].z = molNEW[i].z; } } } } // Save current structure and display geometry every 5 steps InfoWin(loop+": Energy = "+molNEW[0].energy.toFixed(8)+"\n"); //InfoWin(" Step = "+molNEW[0].step.toFixed(5)+"\n"); DEBUG=1; if ( (DEBUG>0) && (loop%5 == 0) ) { for (i=1; i <= molecule[0].numatoms; i++) { molecule[i].x = molNEW[i].x; molecule[i].y = molNEW[i].y; molecule[i].z = molNEW[i].z; } centerMolecule(); drawMolecule(); geomLabel(ctx,"Simple Geometry Optimization in progress.",width); } } // Save optimized coordinates and display structure InfoWin("Final Energy at loop "+loop+" = "+molNEW[0].energy.toFixed(8)+"\n"); InfoWin("Geometry Optimization complete.\n"); if ( loop >= MAXLOOP ) InfoWin("Too many steps. Optimization may not be complete.\n"); for (i=1; i <= molecule[0].numatoms; i++) { molecule[i].x = molNEW[i].x; molecule[i].y = molNEW[i].y; molecule[i].z = molNEW[i].z; } centerMolecule(); drawMolecule(); // Finished with mechanics routine } /// /// Define object to hold temporary molecular information /// function mechanicsObject() { this.hybrid = 0; this.x = 0.0; this.y = 0.0; this.z = 0.0; } /// /// Define object to hold temporary energy/optimization information /// function energyObject() { this.energy = 0.0; this.rstep = 0; this.astep = 0; } //# function distance(mol, atomA, atomB) //# //# Calculate the distance between two atoms in mol array. //# function distance(mol, atomA, atomB) { // Calculate distance between atoms var dx = mol[atomA].x - mol[atomB].x; var dy = mol[atomA].y - mol[atomB].y; var dz = mol[atomA].z - mol[atomB].z; var r = Math.sqrt(dx*dx+dy*dy+dz*dz); // Exit distance routine return r; } //# function angle(mol, atomA, atomB, atomC) //# //# Calculate the angle between A--B--C in mol array //# function angle(mol, atomA, atomB, atomC) { // Calculate vector BA var dax = mol[atomA].x - mol[atomB].x; var day = mol[atomA].y - mol[atomB].y; var daz = mol[atomA].z - mol[atomB].z; var ra = Math.sqrt(dax*dax+day*day+daz*daz); // Calculate vector BC var dbx = mol[atomC].x - mol[atomB].x; var dby = mol[atomC].y - mol[atomB].y; var dbz = mol[atomC].z - mol[atomB].z; var rb = Math.sqrt(dbx*dbx+dby*dby+dbz*dbz); // Calculate bond angle var ang = (dax*dbx + day*dby + daz*dbz) / (ra*rb); if (ang > 1.0) ang = 1.0; if (ang < -1.0) ang = -1.0; ang = Math.acos(ang) * 180.0 / Math.PI; // Exit distance routine return ang; } //# function dihedral(mol, atomA, atomB, atomC, atomD) //# //# Routine to calculate the dihedral angle for A--B--C--D //# function dihedral(mol, atomA, atomB, atomC, atomD) { // Define local variables var i, j, k; var dux, duy, duz; var dvx, dvy, dvz; var crossA, crossAx, crossAy, crossAz; var crossB, crossBx, crossBy, crossBz; // Calculate cross product of BA x BC dux = mol[atomA].x - mol[atomB].x; duy = mol[atomA].y - mol[atomB].y; duz = mol[atomA].z - mol[atomB].z; dvx = mol[atomC].x - mol[atomB].x; dvy = mol[atomC].y - mol[atomB].y; dvz = mol[atomC].z - mol[atomB].z; crossAx = duy*dvz - duz*dvy; crossAy = duz*dvx - dux*dvz; crossAz = dux*dvy - duy*dvx; crossA = Math.sqrt(crossAx*crossAx + crossAy*crossAy + crossAz*crossAz); // Calculate cross product of CD x CB dux = mol[atomD].x - mol[atomC].x; duy = mol[atomD].y - mol[atomC].y; duz = mol[atomD].z - mol[atomC].z; crossBx = duz*dvy - duy*dvz; crossBy = dux*dvz - duz*dvx; crossBz = duy*dvx - dux*dvy; crossB = Math.sqrt(crossBx*crossBx + crossBy*crossBy + crossBz*crossBz); // Use dot product to calculate dihedral angle ang = (-crossAx*crossBx-crossAy*crossBy-crossAz*crossBz)/(crossA*crossB); if (ang > 1.0) ang = 1.0; if (ang < -1.0) ang = -1.0; ang = Math.acos(ang) * 180.0 / Math.PI; // Finished with dihedral routine return ang; } /// /// Determine number of hybrid orbitals on all atoms /// function hybridization() { // Define local variables var i, j, k; var valence; var optmol = new Array(); var molecule = Mol(); var bonds = BondMatrix(); // Copy molecule data into local array optmol[0] = new energyObject(); optmol[0].energy = 0.0; optmol[0].step = 0.0; for (i=1; i <= molecule[0].numatoms; i++) { optmol[i] = new mechanicsObject(); optmol[i].hybrid = 0; optmol[i].x = molecule[i].x; optmol[i].y = molecule[i].y; optmol[i].z = molecule[i].z; } // Loop over all atoms in molecule for (i=1; i <= molecule[0].numatoms; i++) { valence = element(molecule[i].atomicnumber,"valence"); switch (valence) { case 1: case 2: case 3: optmol[i].hybrid = bonds[i][0]; break; default: optmol[i].hybrid = valence + bonds[i][0] - 4; break; } while ( (optmol[i].hybrid>bonds[i][0]) && (optmol[i].hybrid>=5) ) { optmol[i].hybrid = optmol[i].hybrid-1; } } // Look for delocalized lone pairs for (i=1; i <= molecule[0].numatoms; i++) { if ( (optmol[i].hybrid == 4) && (bonds[i][0]<4) ) { for (j=1; j <= molecule[0].numatoms; j++) { k = bonds[i][j]; if (k > 0) { if ( optmol[k].hybrid == 3 ) { optmol[i].hybrid = 3; // InfoWin("Delocalized lone pair found on atom "+i+" bonded to "+bonds[i][j]+"\n"); } } } } } // End hybridization routine return optmol; } /// /// Calculate the mechanics energy of the current geometry /// function mechEnergy(current) { // Define local variables var i, j, k; var ii, bi, bj, ia, ja; var r0, r1, r2; var dx, dy, dz, r, dr; var atomA, atomB, maxBonds; var da, dax, day, daz; var db, dbx, dby, dbz; var ang; var tetra = Math.acos(-1/3.0) * 180.0 / Math.PI; var energy = 0.0; var molecule = Mol(); var bonds = BondMatrix(); // Parameters var penaltyR = 20000.0; var penaltyA = 10.0; var penaltyD = 5.0; var penaltyVDW = 500.0; // Look for hybridization error DEBUG=1; if ( DEBUG > 0 ) { var hytotal = 0; for (i=1; i <= molecule[0].numatoms; i++) { hytotal += current[i].hybrid; } if (hytotal < molecule[0].numatoms) InfoWin("*** Too few hybrid orbitals ("+hytotal+") returned at end of optimize\n"); } // Calculate energy penalty for bond lengths for (i=1; i <= molecule[0].numatoms; i++) { r1 = element(molecule[i].atomicnumber,"radius"); if ( current[i].hybrid == 3 ) r1 -= 0.05; if ( current[i].hybrid == 2 ) r1 -= 0.10; for (j=1; j <= molecule[0].numatoms; j++) { if ( bonds[i][j] > 0) { k = j; r2 = element(molecule[k].atomicnumber,"radius"); if ( current[k].hybrid == 3 ) r2 -= 0.05; if ( current[k].hybrid == 2 ) r2 -= 0.10; r0 = r1 + r2; // Ideal bond length dx = current[i].x - current[k].x; dy = current[i].y - current[k].y; dz = current[i].z - current[k].z; r = Math.sqrt(dx*dx+dy*dy+dz*dz); energy += penaltyR*(r-r0)*(r-r0); } } } // Calculate energy penalty for bond angles for (i=1; i <= molecule[0].numatoms; i++) { if (current[i].hybrid > 1) { for (j=1; j < molecule[0].numatoms; j++) { if (bonds[i][j] > 0) { atomA = j; dax = current[atomA].x - current[i].x; day = current[atomA].y - current[i].y; daz = current[atomA].z - current[i].z; da = Math.sqrt(dax*dax + day*day + daz*daz); for (k=j+1; k <= molecule[0].numatoms; k++) { if (bonds[i][k] > 0) { atomB = k; dbx = current[atomB].x - current[i].x; dby = current[atomB].y - current[i].y; dbz = current[atomB].z - current[i].z; db = Math.sqrt(dbx*dbx + dby*dby + dbz*dbz); ang = (dax*dbx+day*dby+daz*dbz)/(da*db); if (ang > 1.0) ang = 1.0; if (ang < -1.0) ang = -1.0; ang = Math.acos(ang) * 180.0 / Math.PI; switch (current[i].hybrid) { case 2: energy += penaltyA*(ang-180.0)*(ang-180.0); break; case 3: energy += penaltyA*(ang-120.0)*(ang-120.0); break; case 4: energy += penaltyA*(ang-tetra)*(ang-tetra); break; case 5: case 6: if (ang < 100.0) energy += penaltyA*(ang-90.0)*(ang-90.0); break; } } } } } } } // Calculate energy penalty for sp3-sp3 dihedral angles for (i=1; i < molecule[0].numatoms; i++) { if (current[i].hybrid == 4) { for (ii=i+1; ii<=molecule[0].numatoms; ii++) { if ( (bonds[i][ii] > 0) && (current[ii].hybrid == 4) ) { j = ii; for (bi=1; bi<=molecule[0].numatoms; bi++) { if ( (bonds[i][bi]>0) && (bi!=j) && (bi!=i) ) { ia = bi; for (bj=1; bj<=molecule[j].numatoms; bj++) { if ( (bonds[j][bj]>0) && (bj!=j) && (bj!=i) && (bj!=ia) ) { ja = molecule[j].bonds[bj]; ang = Math.abs(dihedral(current, ia, i, j, ja)); while (ang > 120.0) ang -= 120.0; energy += penaltyD*(ang-60.0)*(ang-60.0); // InfoWin("Dihedral: "+ia+"-"+i+"-"+j+"-"+ja); // InfoWin(" = "+ang+"\n"); } } } } } } } } // Calculate energy penalty for sp2-sp2 dihedral angles (pi bonds) for (i=1; i < molecule[0].numatoms; i++) { if (current[i].hybrid == 3) { for (ii=i+1; ii<=molecule[i].numatoms; ii++) { if ( (bonds[i][ii]>0) && (current[j].hybrid == 3) ) { j = ii; for (bi=1; bi<=molecule[i].numatoms; bi++) { if ( (bonds[i][bi]>0) && (bi!=j) && (bi!=i) ) { ia = bi; for (bj=1; bj<=molecule[j].numatoms; bj++) { if ( (bonds[j][bj]>0) && (bj!=i) && (bj!=j) && (bj!=ia) ) { ja = bj; ang = Math.abs(dihedral(current, ia, i, j, ja)); if (ang > 180.0) ang -= 180.0; if (ang > 135.0) ang = 180.0 - ang; energy += penaltyD*ang*ang; // InfoWin("Dihedral: "+ia+"-"+i+"-"+j+"-"+ja); // InfoWin(" = "+ang+"\n"); } } } } } } } } // Calculate energy penalty for van der Waal's repulsion for (i=1; i < molecule[0].numatoms; i++) { r1 = element(molecule[i].atomicnumber,"radius"); for (j=i+1; j <= molecule[0].numatoms; j++) { r2 = element(molecule[j].atomicnumber,"radius"); r = distance(current, i, j); if ( r < 0.1 ) r = 0.1; r = r/(r1+r2); energy += penaltyVDW / (r*r*r*r*r*r); } } // End of mechEnergy routine return energy; } /// /// Calculate 'optimal' change in all coordinates /// function changexyz(current) { // Define local variables var molecule = Mol(); var i, j, k; var ixyz; var delta = []; var EZero, energyX, energyY, energyZ; var stepx, stepy, stepz; var stepfactor; var oldx, oldy, oldz; var randomnumber; // Parameters var stepsize = current[0].step; // Debug hybridization routine var DEBUG=0; if (DEBUG > 0) { InfoWin("Hybridization\n"); for (i=1; i <= molecule[0].numatoms; i++) { Z = molecule[i].atomicnumber; InfoWin(element(Z,"symbol")+" has "+current[i].hybrid+" hybrid orbitals\n"); } } // Initialize delta array for (i=0; i <= molecule[0].numatoms; i++) { delta[i] = [0.0, 0.0, 0.0]; } // Populate trial array var trial = new Array(); trial[0] = new energyObject(); trial[0].energy = current[0].energy; trial[0].step = current[0].step; for (i=1; i <= molecule[0].numatoms; i++) { trial[i] = new mechanicsObject(); trial[i].hybrid = current[i].hybrid; trial[i].x = current[i].x; trial[i].y = current[i].y; trial[i].z = current[i].z; } // Loop over all coordinates, looking for 'best' changes EZero = mechEnergy(trial); for (i=1; i <= molecule[0].numatoms; i++) { // Save current coordinates oldx = trial[i].x; oldy = trial[i].y; oldz = trial[i].z; // Loop over changes in all coordinates for (ixyz=0; ixyz<6; ixyz++) { stepx = 0.0; stepy = 0.0; stepz = 0.0; energyX = EZero; energyY = EZero; energyZ = EZero; (ixyz%2) ? stepfactor=1.0 : stepfactor=-1.0; switch (ixyz) { case 0: case 1: trial[i].x = oldx + stepfactor*stepsize; Energy = mechEnergy(trial); while ( (Energy>EZero) && (stepfactor>0.1) ) { stepfactor *= 0.75; trial[i].x = oldx + stepfactor*stepsize; Energy = mechEnergy(trial); } if ( Energy < energyX ) stepx = stepfactor; trial[i].x = oldx; delta[i][0] = stepx*stepsize; break; case 2: case 3: trial[i].y = oldy + stepfactor*stepsize; Energy = mechEnergy(trial); while ( (Energy>EZero) && (stepfactor>0.1) ) { stepfactor *= 0.75; trial[i].y = oldy + stepfactor*stepsize; Energy = mechEnergy(trial); } if ( Energy < energyY ) stepy = stepfactor; trial[i].y = oldy; delta[i][1] = stepy*stepsize; break; case 4: case 5: trial[i].z = oldz + stepfactor*stepsize; Energy = mechEnergy(trial); while ( (Energy>EZero) && (stepfactor>0.1) ) { stepfactor *= 0.75; trial[i].z = oldz + stepfactor*stepsize; Energy = mechEnergy(trial); } if ( Energy < energyZ ) stepz = stepfactor; trial[i].z = oldz; delta[i][2] = stepz*stepsize; break; } } // Finished loop for atom 'i' } // End of changexyz routine return delta; } /// /// Simple molecular mechanics (kind of) geometry optimization /// function optimize(current) { // Define local variables var i, j, k; var ib; var newstep; var EFit; var EMin; var beststep, trial; var maxstep; var delta = new Array(); var molNEW = new Array(); var molecule = Mol(); // Parameters var MINSTEP=0.001; var step = current[0].step; var eINITIAL = current[0].energy; // Look for a few obvious errors DEBUG=1; if ( DEBUG > 0 ) { var erg = mechEnergy(current); if (erg != eINITIAL) InfoWin("*** Call to mechEnergy changed energy from "+eINITIAL+" to "+erg+"\n"); var hytotal = 0; for (i=1; i <= molecule[0].numatoms; i++) { hytotal += current[i].hybrid; } if (hytotal < molecule[0].numatoms) InfoWin("*** Too few hybrid orbitals ("+hytotal+")\n"); } // Initialize delta array for (i=0; i <= molecule[0].numatoms; i++) { delta[i] = [0.0, 0.0, 0.0]; } // Call routine to calculate changes in coordinates // and find maximum change. delta = changexyz(current); maxstep = 0.0; for (i=0; i <= molecule[0].numatoms; i++) { for (j=0; j < 3; j++) { if ( Math.abs(delta[i][j]) > maxstep ) maxstep = Math.abs(delta[i][j]); } } // Simple line search to find best change in coordinates EMin = current[0].energy; beststep = 0.0; trial = 1.0; EFit = trialEnergy(current,delta,trial); while ( (EFit > EMin) && (trial > 0.002) ) { trial *= 0.75; EFit = trialEnergy(current,delta,trial); } if (EFit < EMin) { beststep = trial; EMin = EFit; } // Determine new step sizes for next iteration newstep = (beststep+0.5) * (current[0].step + maxstep); if (newstep < MINSTEP) newstep = MINSTEP; // Populate molNEW object with new geometry molNEW[0] = new energyObject(); molNEW[0].energy = EMin; molNEW[0].step = newstep; for (i=1; i <= molecule[0].numatoms; i++) { molNEW[i] = new mechanicsObject(); molNEW[i].hybrid = current[i].hybrid; molNEW[i].x = current[i].x + beststep*delta[i][0]; molNEW[i].y = current[i].y + beststep*delta[i][1]; molNEW[i].z = current[i].z + beststep*delta[i][2]; } // DEBUG: Show changes in coordinates from optimization DEBUG = 0; if (DEBUG > 0) { for (i=0; i <= molecule[0].numatoms; i++) { InfoWin("Change in coordinates = ("); for (j=0; j < 3; j++) { InfoWin(delta[i][j].toFixed(5)); if (j<2) InfoWin(", "); } InfoWin(")\n"); } InfoWin("--- Max change = "+maxstep.toFixed(5)+"\n"); } // Finished with optimize routine return (molNEW); } /// /// Calculate the mechanics energy of the current geometry /// function trialEnergy(current,delta,step) { // Define local variables var i; var trial = new Array(); var molecule = Mol(); // Populate array trial[0] = new energyObject(); trial[0].energy = current[0].energy; trial[0].step = current[0].step; for (i=1; i <= molecule[0].numatoms; i++) { trial[i] = new mechanicsObject(); trial[i].hybrid = current[i].hybrid; trial[i].x = current[i].x + step*delta[i][0]; trial[i].y = current[i].y + step*delta[i][1]; trial[i].z = current[i].z + step*delta[i][2]; } // End of trialEnergy routine return mechEnergy(trial); } /// /// Routine to process data collected from user /// and create GAMESS input file. /// function createQC() { // Declare local variables var i; var contents = ""; var xyzstring = Array(); var molecule = Mol(); // Name for input file var NameForm = document.getElementById("Name"); var filename = NameForm.value; // Verify input filename entered if ( filename.length < 1 ) { alert("Filename must be given."); return; } // Close parameter input box and open submit job box hideQCEdit(); showQCSubmit(); // Name for input file filename = filename.replace(/^\s+/,""); filename = filename.replace(/\s+$/,""); i = filename.indexOf(" "); while (i > 0) { filename = filename.replace(/\s+/,"_"); i = filename.indexOf(" "); } i = filename.search(/\W/); while (i > 0) { filename = filename.replace(/\W/,""); i = filename.search(/\W/); } // Comment to include in input file var CommentForm = document.getElementById("Comment"); var comment = CommentForm.value; comment = comment.replace(/^\s+/,""); comment = comment.replace(/\s+$/,""); // Molecular charge var chargeForm = document.getElementById("Charge"); var charge = chargeForm.value; // Type of calculation var TypeForm = document.SelectType; for (i=0; i < TypeForm.Type.length; i++) if (TypeForm.Type[i].checked) { calcType = TypeForm.Type[i].value; } // Basis set to use var BasisForm = document.SelectBasis; for (i=0; i < BasisForm.Basis.length; i++) if (BasisForm.Basis[i].checked) { basisSet = BasisForm.Basis[i].value; } // RHF or DFT? for (i=0; i < document.SelectDFT.DFT.length; i++) if (document.SelectDFT.DFT[i].checked) { DFT = document.SelectDFT.DFT[i].value; } // Use PCM solvent model? for (i=0; i < document.SelectPCM.PCM.length; i++) if (document.SelectPCM.PCM[i].checked) { PCM = document.SelectPCM.PCM[i].value; } // // Populating contents for input file // // Store filename InfoWin("!! filename=" + filename + "\n",1); // Comments InfoWin("!\n! GAMESS Calculation input file\n"); InfoWin("! " + comment + "\n!\n"); // Control and System options var HSSEND = ""; if (calcType == "FULL") { calcType = "OPTIMIZE"; HSSEND="HSSEND=.TRUE. "; } InfoWin(" $CONTRL SCFTYP=RHF MAXIT=50 RUNTYP=" + calcType + "\n"); InfoWin(" COORD=UNIQUE MULT=1\n"); InfoWin(" ICHARG=" + charge + "\n"); if ( DFT != "NONE" ) { InfoWin(" DFTTYP=" + DFT + "\n"); } InfoWin(" MOLPLT=.FALSE. PLTORB=.FALSE. $END\n"); InfoWin(" $SYSTEM TIMLIM=480 MWORDS=6 $END\n\n"); // Stationary point options InfoWin(" $STATPT OPTTOL=0.00005 NSTEP=60 " + HSSEND + "$END\n\n"); // DFT Options if ( DFT != "NONE") { InfoWin(" $DFT METHOD=GRID NLEB=590 $END\n\n"); } // Basis set Options switch (basisSet) { case "STO-3G": InfoWin(" $BASIS GBASIS=STO NGAUSS=3 $END\n\n"); break; case "3-21G": InfoWin(" $BASIS GBASIS=N21 NGAUSS=3 $END\n\n"); break; case "6-31G*": InfoWin(" $BASIS GBASIS=N31 NGAUSS=6\n"); InfoWin(" NDFUNC=1 NPFUNC=0 $END\n\n"); break; case "6-311G**": InfoWin(" $BASIS GBASIS=N311 NGAUSS=6\n"); InfoWin(" NDFUNC=1 NPFUNC=1 $END\n\n"); break; } // PCM Options if ( PCM != "None") { InfoWin(" $PCM SOLVNT=" + PCM + " $END\n\n"); } // Miscellaneous options InfoWin(" $SCF DIRSCF=.T. $END\n"); InfoWin(" $GUESS GUESS=HUCKEL $END\n\n"); // Add coordinates InfoWin(" $DATA\n"); InfoWin(" " + comment + "\n"); InfoWin(" C1\n"); for (i=1; i <= molecule[0].numatoms; i++) { A = molecule[i].atomicnumber; x = molecule[i].x; y = molecule[i].y; z = molecule[i].z; xyzstring = showxyz(x,y,z); symbol = element(A,"symbol"); space = " "; if (symbol.length == 1) space = " "; if (A < 10) space += " "; InfoWin(" " + symbol + space + A + " " + xyzstring + "\n"); } InfoWin(" $END\n"); } /// /// Format x,y,z coordinates /// function showxyz(x, y, z) { var string = Array(); var space = Array(); space = ""; if (x > 10) space = " "; if ( (x >= 0) && (x < 10) ) space = " "; if ( (x < 0) && (x > -10) ) space = " "; string = space + x.toFixed(3); space = ""; if (y > 10) space = " "; if ( (y >= 0) && (y < 10) ) space = " "; if ( (y < 0) && (y > -10) ) space = " "; string += " " + space + y.toFixed(3); space = ""; if (z > 10) space = " "; if ( (z >= 0) && (z < 10) ) space = " "; if ( (z < 0) && (z > -10) ) space = " "; string += " " + space + z.toFixed(3); return string; } /// /// Routine to open PHP file to create GAMESS input file /// function writeQC() { // Declare local variables var i; var url = "write.php"; var contents = ""; var lines = Array(); var filename = Array(); // Close job submission box hideQCSubmit(); // Create XML object // Should(?) work for IE7+, Firefox, Chrome, Opera, Safari try { var xmlhttp = new XMLHttpRequest(); } catch(e) { InfoWin("\nUnable to write data."); return; } // Respond to php output xmlhttp.onreadystatechange = function() { if(xmlhttp.readyState == 4 && xmlhttp.status==200) { InfoWin("\n"+xmlhttp.responseText,1); } } // Read information from textbox var InfoBox = document.getElementById("information"); lines = InfoBox.value; // Name of input file var pos = lines.indexOf("\n"); filename = lines.substr(12,pos-12); lines = lines.substr(pos+1); // Get directory path var path = ""; // Combine information to send to PHP file contents = "path=" + path; contents += "&filename=" + filename; contents += "&contents=" + lines; // "Post" data to php routine xmlhttp.open("POST",url,true); xmlhttp.setRequestHeader("Content-type","application/x-www-form-urlencoded"); xmlhttp.send(contents); } /// /// Routine to show jobs running on batch queue /// function showQueue() { // Create XML object // Should(?) work for IE7+, Firefox, Chrome, Opera, Safari try { var xmlhttp = new XMLHttpRequest(); } catch(e) { InfoWin("\nUnable to write data."); return; } // Respond to php output xmlhttp.onreadystatechange = function() { if(xmlhttp.readyState == 4 && xmlhttp.status==200) { InfoWin(xmlhttp.responseText,1); } } // "Post" data to php routine xmlhttp.open("POST","showqueue.php",true); xmlhttp.setRequestHeader("Content-type","application/x-www-form-urlencoded"); xmlhttp.send(); } /// /// Routine to enable display of Quantum Chemistry input form /// function showQCEdit() { document.getElementById("paramDiv").style.display = "inline"; } /// /// Routine to hide display of Quantum Chemistry input form /// function hideQCEdit() { document.getElementById("paramDiv").style.display = "none"; } /// /// Routine to enable display of job submission form /// function showQCSubmit() { document.getElementById("submitDiv").style.display = "inline"; } /// /// Routine to hide display of job submission form /// function hideQCSubmit() { document.getElementById("submitDiv").style.display = "none"; } /// /// Routine to hide or display window containing /// list of files in user's directory. /// function toggleDirWin() { // Initialize parameter as necessary if ( typeof toggleDirWin.state == 'undefined' ) { toggleDirWin.state = "1"; } // Toggle state of window showing directory listing if (toggleDirWin.state == "0") { // If state=0, hide window document.getElementById("dirDiv").style.display = "none"; document.getElementById("ServerBtn").value = "Show Server files"; toggleDirWin.state = "1"; } else { // If state=1, show window document.getElementById("dirDiv").style.display = "inline"; document.getElementById("ServerBtn").value = "Hide Server files"; toggleDirWin.state = "0"; dirList(""); } // End of toggleDirWin routine } /// /// Routine to show contents of file /// or delete file/directory. /// /// Parameters: /// myfile = filename or directory /// function showname(myfile) { // Declare local variables var mode="show"; var url = "read.php"; // Initialize parameters as necessary if ( typeof showname.mode == 'undefined' ) showname.mode = "show"; // If filename/directory not given, exit if ( typeof myfile == 'undefined' ) return; // Trim leading slashes from filename while ( myfile[0] == "/") { alert ("Leading // found in "+myfile[0]); myfile = myfile.substring(1); } // Close Server Directory Window toggleDirWin(); // Create XML object // Should(?) work for IE7+, Firefox, Chrome, Opera, Safari try { var xmlhttp = new XMLHttpRequest(); } catch(e) { InfoWin("\nUnable to read data."); return; } // Respond to php output xmlhttp.onreadystatechange = function() { if(xmlhttp.readyState == 4 && xmlhttp.status==200) { lines = xmlhttp.responseText; InfoWin(lines,1); if ( myfile.indexOf('.mol') > 1) { // Save Molecular information Undo("save"); var fileinfo = new Array(); fileinfo.name = myfile; fileinfo.type = "mol file"; fileinfo.size = "Not known"; var pos = lines.indexOf("\n"); lines = lines.substr(pos+1); lines = lines.split("\n"); readMOLfile(fileinfo,lines); centerMolecule(); drawMolecule(); formula(); } if ( myfile.indexOf('.inp') > 1) { // Save Molecular information Undo("save"); lines = lines.split("\n"); readINPfile(lines); centerMolecule(); drawMolecule(); formula(); } } } // "Post" data to php routine contents = "filename=" + myfile; xmlhttp.open("POST",url,true); xmlhttp.setRequestHeader("Content-type","application/x-www-form-urlencoded"); xmlhttp.send(contents); // End of showname routine } /// /// Routine to fill or clear delete window. /// If 'filename' empty, then clear window. Otherwise, add new entry. /// function fillDelWin(filename) { // Declare local variables var i, j, pos; var contents; var delbox = document.getElementById('delDiv'); // Define mode: 0=empty, 1=not empty if ( typeof fillDelWin.num == 'undefined' ) { fillDelWin.num = 0; fillDelWin.sname = new Array(); fillDelWin.full = new Array(); } // Define filename as empty string if necessary if ( typeof filename == 'undefined' ) filename = ""; // If empty string passed, clear window and turn off display if ( filename.length < 1 ) { delbox.innerHTML = ""; delbox.style.display = "none"; fillDelWin.num = 0; return; } // If filename begins with "-", search for and remove from array if ( filename.substring(0,1) == "-" ) { for (i=0; i < fillDelWin.num; i++) { if ( filename.substring(1) == fillDelWin.full[i] ) { for (j=i; j < fillDelWin.num-1; j++) { fillDelWin.full[j] = fillDelWin.full[j+1]; fillDelWin.sname[j] = fillDelWin.sname[j+1]; } i=fillDelWin.num; fillDelWin.num--; } } if ( fillDelWin.num <= 0 ) { delbox.innerHTML = ""; delbox.style.display = "none"; return; } } // Store filename and filename with full path if ( filename.substring(0,1) != "-" ) { pos = filename.lastIndexOf('/') + 1; fillDelWin.full[fillDelWin.num] = filename; fillDelWin.sname[fillDelWin.num] = filename.substring(pos); fillDelWin.num++; } // Make delete window visible delbox.style.display = "inline"; // Create contents of window contents = "
"; for (i=0; i < fillDelWin.num; i++) { contents += " "; } delbox.innerHTML = contents; // End of fillDelWin routine } /// /// Routine to delete file on server /// function deleteFile(filename) { // Declare local variables var url = "delete.php"; // Update delete window fillDelWin("-"+filename); // Create XML object // Should(?) work for IE7+, Firefox, Chrome, Opera, Safari try { var xmlhttp = new XMLHttpRequest(); } catch(e) { InfoWin("\nUnable to write data."); return; } // Respond to php output xmlhttp.onreadystatechange = function() { if(xmlhttp.readyState == 4 && xmlhttp.status==200) { InfoWin(xmlhttp.responseText,1); dirList("."); // Update server window } } // "Post" data to php routine contents = "filename=" + filename; xmlhttp.open("POST",url,true); xmlhttp.setRequestHeader("Content-type","application/x-www-form-urlencoded"); xmlhttp.send(contents); // End deleteFile routine } /// /// Routine to update list of available files on server /// function dirList(subdir) { // Declare local variables var url = "dirlist.php"; // Get current path subdir = subdir || ""; path = filepath(subdir); InfoWin("Full directory path = "+path+"\n"); // Create XML object // Should(?) work for IE7+, Firefox, Chrome, Opera, Safari try { var xmlhttp = new XMLHttpRequest(); } catch(e) { InfoWin("\nUnable to write data."); return; } // Respond to php output xmlhttp.onreadystatechange = function() { if(xmlhttp.readyState == 4 && xmlhttp.status==200) { var rvalue = xmlhttp.responseText; document.getElementById('dirWindow').innerHTML = rvalue; } } // "Post" data to php routine contents = "path=" + path; xmlhttp.open("POST",url,true); xmlhttp.setRequestHeader("Content-type","application/x-www-form-urlencoded"); xmlhttp.send(contents); } /// /// Routine to save (and return) current subdirectory path for files /// function filepath(subdir) { // Initialize parameter if necessary if ( typeof filepath.current == 'undefined' ) { filepath.current = ""; } // If no subdirectory string passed, set to empty string subdir = subdir || ""; if ( subdir == "." ) subdir = ""; if ( subdir == ".." ) subdir = ""; // If subdirectory passed as parameter, add to string. Otherwise, reset to base. if ( subdir.length <= 0 ) { filepath.current = ""; } else { filepath.current += "/"+subdir; } // End filepath routine return filepath.current; } // // -------------------- peptide.js -------------------- // /// /// Routine to determine information about peptide structures /// function peptideInfo() { // Define local variables var i, chainlength; var AtomSize = 0.50; var sequence = new Array(); var activecanvas = activeWin(""); var canvas = document.getElementById(activecanvas); var centerx = canvas.width/2; var centery = canvas.height/2; // Clear information window InfoWin("Information about Amino Acid/Peptide Structure\n",1); // Look for peptide backbone sequence = backbone(); chainlength = sequence[0]*3; // If not an amino acid/peptide, exit. if (chainlength < 1) { InfoWin("\nThis compound does not appear to an amino acid/peptide.\n"); return; } InfoWin("\nFinal Ordered sequence contains "+sequence[0]+" amino acids.\n"); for (i=1; i<=chainlength; i++) { InfoWin(sequence[i]); if (i < chainlength) InfoWin(" - "); } InfoWin("\n"); // If amino acid or peptide, show information if (chainlength > 1) { // Determine whether amino acid(s) is(are) D or L DorL(sequence); // Calculate dihedral angles along backbone backangles(sequence); // Draw molecule with backbone highlighted drawHighlight(activecanvas, sequence, AtomSize, centerx, centery); } // Finished with peptideInfo routine } /// /// Routine to determine information about peptide structures /// function backbone() { // Define local variables var i, j, k; var bi, bii, kO, bkO; var maxBonds, maxBondsK, maxBondsKO; var numbonds, numamino, attach; var chain = new Array(); var bbone = new Array(); var sequence = new Array(); var molecule = Mol(); // Flag to determine if backbone found numamino = 0; // Loop over all molecules for (i=1; i <= molecule[0].numatoms; i++) { attach = -1; // Look for alpha-Carbon (CA) if ( molecule[i].atomicnumber == 6 ) { maxBonds = molecule[i].bonds[0]; for (bi=1; bi <= maxBonds; bi++) { j = molecule[i].bonds[bi]; // Look for Nitrogen bonded to CA if ( molecule[j].atomicnumber == 7 ) { for (bii=1; bii <= maxBonds; bii++) { k = molecule[i].bonds[bii]; // Looking for Carbonyl carbon if ( molecule[k].atomicnumber == 6 ) { // Look for Nitrogen on next amino acid maxBondsK = molecule[k].bonds[0]; for ( bk=1; bk <= maxBondsK; bk++) { kN = molecule[k].bonds[bk]; if ( molecule[kN].atomicnumber == 7 ) attach = kN; } // Look for Oxygen in carbonyl for ( bk=1; bk <= maxBondsK; bk++) { kO = molecule[k].bonds[bk]; if ( molecule[kO].atomicnumber == 8 ) { numbonds = molecule[k].bonds[0]; if ( numbonds == 1) { unique = 1; for (na=0; na < numamino; na++) { if ( chain[na][0] == j ) unique = 0; } if (unique > 0) { chain[numamino] = new Array(); chain[numamino][0] = j; chain[numamino][1] = i; chain[numamino][2] = k; chain[numamino][3] = attach; numamino++; // InfoWin("--- Amino acid "+numamino+" = "+j+"-"+i+"-"+k+" attached to "+attach+"\n"); } } } } } } } } } } // If no amino acids found, return empty array. sequence[0] = 0; if ( numamino == 0 ) return sequence; // Determine proper sequence of amino acids lookfor = -1; pos = numamino; found = 1; while ( found > 0 ) { found = 0; for (i=0; i < numamino; i++) { if (chain[i][3] == lookfor) { found = 1; pos--; bbone[pos] = i; lookfor = chain[i][0]; i = numamino; } } } // Store sequence of individual atoms pos=1; sequence[0] = numamino; for (i=0; i < numamino; i++) { j = bbone[i]; sequence[pos++] = chain[j][0]; sequence[pos++] = chain[j][1]; sequence[pos++] = chain[j][2]; } // Finished with backbone routine return sequence; } /// /// Routine to whether amino acid(s) is(are) "D" or "L" /// function DorL(sequence) { // Define local variables var i, j, k; var iH, iR, iN, iCA, iCO; var midX, midY, midZ; var vmNx, vmNy, vmNz; var vmCx, vmCy, vmCz; var vCH, vCHx, vCHy, vCHz; var cross, crossX, crossY, crossZ; var maxBonds, ang; var numamino; var molecule = Mol(); // Calculate the number of amino acids present numamino = sequence[0]; if ( numamino < 1) return; // Send header to information window InfoWin("\nDetermining the configuration of "+numamino+" amino acid(s).\n"); // Loop over all amino acids for (i=0; i < numamino; i++) { iH = 0; iR = 0; iN = sequence[i*3+1]; iCA = sequence[i*3+2]; iCO = sequence[i*3+3]; maxBonds = molecule[iCA].bonds[0]; for (j=1; j <= maxBonds; j++) { k = molecule[iCA].bonds[j]; // Look for H attached to alpha-carbon if (molecule[k].atomicnumber == 1) iH = k; // Look for first carbon on side chain (R group) if ( (k != iCO) && (molecule[k].atomicnumber == 6) ) iR = k; } if ( (iH > 0) && (iR > 0) ) { midX = (molecule[iCO].x + molecule[iN].x + molecule[iR].x)/3.0; midY = (molecule[iCO].y + molecule[iN].y + molecule[iR].y)/3.0; midZ = (molecule[iCO].z + molecule[iN].z + molecule[iR].z)/3.0; // InfoWin("Carbon"+iCA+" connected to N"+iN+", C(O)"+iCO+", H"+iH+", and R"+iR+"\n"); vmNx = molecule[iN].x - midX; vmNy = molecule[iN].y - midY; vmNz = molecule[iN].z - midZ; vmCx = molecule[iCO].x - midX; vmCy = molecule[iCO].y - midY; vmCz = molecule[iCO].z - midZ; crossX = vmNy*vmCz - vmNz*vmCy; crossY = vmNz*vmCx - vmNx*vmCz; crossZ = vmNx*vmCy - vmNy*vmCx; cross = Math.sqrt(crossX*crossX + crossY*crossY + crossZ*crossZ); vCHx = molecule[iH].x - molecule[iCA].x; vCHy = molecule[iH].y - molecule[iCA].y; vCHz = molecule[iH].z - molecule[iCA].z; vCH = Math.sqrt(vCHx*vCHx + vCHy*vCHy + vCHz*vCHz); ang = (crossX*vCHx+crossY*vCHy+crossZ*vCHz)/(cross*vCH); if (ang < -0.5) InfoWin(" - Amino acid "+(i+1)+" is L.\n"); if (ang > 0.5) InfoWin(" - Amino acid "+(i+1)+" is D.\n"); if (Math.abs(ang) < 0.5) InfoWin(" - Cannot determine whether amino acid "+(i+1)+" is D or L.\n"); } } // Finished with DorL routine return; } /// /// Calculate appropriate dihedral angles along backbone /// function backangles(seq) { // Define local variables var i, chainlength; var aNames = ['psi', 'omega', 'phi']; var describe = ["N-CA-C-N", "CA-C-N-CA", "C-N-CA-C"]; var molecule = Mol(); // Only show dihedrals for dipeptides or larger if (seq[0] < 2) return; // Header for information window InfoWin("\nShowing dihedral angles along backbone. (Omega should be ~180)\n"); // Calculate starting points for dihedrals pos = 0; iA = 1; iB = 2; iC = 3; iD = 4; // Walk down chain, showing dihedral angles chainlength = seq[0]*3; while ( iD <= chainlength ) { ang = dihedral(molecule, seq[iA], seq[iB], seq[iC], seq[iD]); InfoWin(" Angle "+aNames[pos%3]+" ("+describe[pos%3]+") = "+ang.toFixed(3)+" degrees.\n"); pos++; iA++; iB++; iC++; iD++; } } ch5m3d-1.2.5+dfsg/qchem/delete.php0000755000175000017500000000174412230555424017002 0ustar georgeskgeorgesk ch5m3d-1.2.5+dfsg/qchem/dirlist.php0000755000175000017500000000522412230555424017207 0ustar georgeskgeorgesk 2) $mypath = "$mypath/$subdir"; // // Set allowed extensions to show user // $molext = array (".xyz", ".mol"); $txtext = array (".inp", ".out", ".sum"); // // Read sorted list of files and directories into array // $filelist = scandir($mypath); // // Set values for icon images // $iconFolder = ""; $iconMol = ""; $iconText = ""; $iconDelete = ""; // // Output list of all directories // if (strlen($subdir) > 2) { echo "
 
"; echo "
"; echo "$iconFolder Home Directory
"; } for ($i=0; $i < count($filelist); $i++) { if (strlen($filelist[$i]) > 2) { if ( strpos($filelist[$i], ".") === false ) { echo "
 
"; echo "
"; echo "$iconFolder $filelist[$i]
"; } } } // // Output list of all files // for ($i=0; $i < count($filelist); $i++) { if (strlen($filelist[$i]) > 2) { // If file is of 'molecule' type, show file for ($j=0; $j < count($molext); $j++) { if (strpos($filelist[$i],$molext[$j]) > 0) { echo "
"; echo "$iconDelete
"; echo "
"; echo "$iconMol $filelist[$i]
"; } } // If file is of allowed 'text' type, show file for ($j=0; $j < count($txtext); $j++) { if (strpos($filelist[$i],$txtext[$j]) > 0) { echo "
"; echo "$iconDelete
"; echo "
"; echo "$iconText $filelist[$i]
"; } } } } // Finished return; ?> ch5m3d-1.2.5+dfsg/qchem/write.php0000755000175000017500000000232112230555424016662 0ustar georgeskgeorgesk 2) $path = "$path/$subdir"; // // File written to new subdirectory based on filename // Build new path and full filename // $path = "$path/$filename"; $suffix = ".inp"; $fullname = "$path/$filename$suffix"; echo "File = [$filename] (Full name = $fullname)\n"; // // Create new subdirectory // mkdir($path, 0755); // // Open file handle for new file and write contents to disk // $fh = fopen($fullname,'w') or die("Unable to open file $fullname"); fwrite($fh, $contents); fclose($fh); // Start batch job system("cd $path; /usr/local/bin/subgms $filename batch 4"); echo "Calculation should be submitted to batch queue.\n"; //echo "$filename$suffix file created, but calculation NOT actually submitted. See write.php.\n"; ?> ch5m3d-1.2.5+dfsg/qchem/qchem.php0000644000175000017500000004037112230555424016631 0ustar georgeskgeorgesk CH5M3D

CH5M3D

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Formula =

Current Element:

H   Organic Metals He
Li Be   B C N O F Ne
Na Mg   Al Si P S Cl Ar
K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr
Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe
Cs Ba La Hf Ta W Re Os Ir Pt Au Hg Tl Pb Bi Po At Rn
Fr Ra Ac Rf Db Sg Bh Hs Mt Ds Rg Cn Uut Fl Uup Lv Uus Uuo
  Ce Pr Nd Pm Sm Eu Gd Tb Dy Ho Er Tm Yb Lu  
  Th Pa U Np Pu Am Cm Bk Cf Es Fm Md No Lr  

Hybridization:

   

 

Parameters for quantum mechanical calculation




Single-Point Energy       Geometry Optimization       Optimization and Frequency
STO-3G       3-21G       6-31G*       6-311G**

None       B3LYP       B97-D       PBE0       M11       wB97X-D      

None       Water       Methanol       Ethanol       Acetone       THF      

You may edit the data in the Information box below. When finished, submit the job by pressing the [Start Calculation] button.

Information

ch5m3d-1.2.5+dfsg/qchem/read.php0000755000175000017500000000073412230555424016451 0ustar georgeskgeorgesk ch5m3d-1.2.5+dfsg/qchem/showqueue.php0000755000175000017500000000020612230555424017555 0ustar georgeskgeorgesk ch5m3d-1.2.5+dfsg/qchem/account0000755000175000017500000000006012230555426016376 0ustar georgeskgeorgeskadmin, 5baa61e4c9b93f3f0682250b6cf8331b7ee68fd8 ch5m3d-1.2.5+dfsg/ch5m3d.full.js0000644000175000017500000050235712230555424016317 0ustar georgeskgeorgesk// // -------------------- periodic.js -------------------- // //# function element(Z,param) //# //# Define public routine to store and return elemental information //# //# Parameters: //# Z = Atomic number of element //# param: //# symbol - Elemental symbol //# block - "s", "p", "d", or "f" block //# valence - # of valence electrons //# mass - Atomic mass //# radius - Covalent radius of atom //# EN - Electronegativity of atom //# color - color of atom (based on JMol) //# gradient - gradient color for atom //# label - color for label //# //# Return value: //# Variable containing requested information //# function element(Z,param) { if ( typeof element.elem == 'undefined' ) { element.elem = []; // // Load parameters for all elements // // Parameters: // Atomic number // Element symbol // Block (s, p, d, or f) // Number of valence electrons // Atomic mass // Covalent radii (in pm). From www.webelements.com // Jmol CPK colors (rgb). From jmol.sourceforge.net/jscolors/ // Electronegativities from Wikipedia, citing WebElements as their source // element.elem[0] = addElement(0, 'X', 's', 0, 0, 0, 0, 0, 0, 0); element.elem[1] = addElement(1, 'H', 's', 1, 1.0079, 31, 255, 255, 255, 2.2); element.elem[2] = addElement(2, 'He', 's', 2, 4.0026, 28, 217, 255, 255, 0); element.elem[3] = addElement(3, 'Li', 's', 1, 6.941, 128, 204, 128, 255, 0.98); element.elem[4] = addElement(4, 'Be', 's', 2, 9.0122, 96, 194, 255, 0, 1.57); element.elem[5] = addElement(5, 'B', 'p', 3, 10.811, 84, 255, 181, 181, 2.04); element.elem[6] = addElement(6, 'C', 'p', 4, 12.0107, 76, 144, 144, 144, 2.55); element.elem[7] = addElement(7, 'N', 'p', 5, 14.0067, 71, 48, 80, 248, 3.04); element.elem[8] = addElement(8, 'O', 'p', 6, 15.9994, 66, 255, 13, 13, 3.44); element.elem[9] = addElement(9, 'F', 'p', 7, 18.9984, 57, 144, 224, 80, 3.98); element.elem[10] = addElement(10, 'Ne', 'p', 8, 20.1797, 58, 179, 227, 245, 0); element.elem[11] = addElement(11, 'Na', 's', 1, 22.9897, 166, 171, 92, 242, 0.93); element.elem[12] = addElement(12, 'Mg', 's', 2, 24.305, 141, 138, 255, 0, 1.31); element.elem[13] = addElement(13, 'Al', 'p', 3, 26.9815, 121, 191, 166, 166, 1.61); element.elem[14] = addElement(14, 'Si', 'p', 4, 28.0855, 111, 240, 200, 160, 1.9); element.elem[15] = addElement(15, 'P', 'p', 5, 30.9738, 107, 255, 128, 0, 2.19); element.elem[16] = addElement(16, 'S', 'p', 6, 32.065, 105, 255, 255, 48, 2.58); element.elem[17] = addElement(17, 'Cl', 'p', 7, 35.453, 102, 31, 240, 31, 3.16); element.elem[18] = addElement(18, 'Ar', 'p', 8, 39.948, 106, 128, 209, 227, 0); element.elem[19] = addElement(19, 'K', 's', 1, 39.0983, 203, 143, 64, 212, 0.82); element.elem[20] = addElement(20, 'Ca', 's', 2, 40.078, 176, 61, 255, 0, 1); element.elem[21] = addElement(21, 'Sc', 'd', 3, 44.9559, 170, 230, 230, 230, 1.36); element.elem[22] = addElement(22, 'Ti', 'd', 4, 47.867, 160, 191, 194, 199, 1.54); element.elem[23] = addElement(23, 'V', 'd', 5, 50.9415, 153, 166, 166, 171, 1.63); element.elem[24] = addElement(24, 'Cr', 'd', 6, 51.9961, 139, 138, 153, 199, 1.66); element.elem[25] = addElement(25, 'Mn', 'd', 7, 54.938, 139, 156, 122, 199, 1.55); element.elem[26] = addElement(26, 'Fe', 'd', 8, 55.845, 132, 224, 102, 51, 1.83); element.elem[27] = addElement(27, 'Co', 'd', 9, 58.9332, 126, 240, 144, 160, 1.88); element.elem[28] = addElement(28, 'Ni', 'd', 10, 58.6934, 124, 80, 208, 80, 1.91); element.elem[29] = addElement(29, 'Cu', 'd', 11, 63.546, 132, 200, 128, 51, 1.9); element.elem[30] = addElement(30, 'Zn', 'd', 2, 65.39, 122, 125, 128, 176, 1.65); element.elem[31] = addElement(31, 'Ga', 'p', 3, 69.723, 122, 194, 143, 143, 1.81); element.elem[32] = addElement(32, 'Ge', 'p', 4, 72.64, 120, 102, 143, 143, 2.01); element.elem[33] = addElement(33, 'As', 'p', 5, 74.9216, 119, 189, 128, 227, 2.18); element.elem[34] = addElement(34, 'Se', 'p', 6, 78.96, 120, 255, 161, 0, 2.55); element.elem[35] = addElement(35, 'Br', 'p', 7, 79.904, 120, 166, 41, 41, 2.96); element.elem[36] = addElement(36, 'Kr', 'p', 8, 83.8, 116, 92, 184, 209, 3); element.elem[37] = addElement(37, 'Rb', 's', 1, 85.4678, 220, 112, 46, 176, 0.82); element.elem[38] = addElement(38, 'Sr', 's', 2, 87.62, 195, 0, 255, 0, 0.95); element.elem[39] = addElement(39, 'Y', 'd', 3, 88.9059, 190, 148, 255, 255, 1.22); element.elem[40] = addElement(40, 'Zr', 'd', 4, 91.224, 175, 148, 224, 224, 1.33); element.elem[41] = addElement(41, 'Nb', 'd', 5, 92.9064, 164, 115, 194, 201, 1.6); element.elem[42] = addElement(42, 'Mo', 'd', 6, 95.94, 154, 84, 181, 181, 2.16); element.elem[43] = addElement(43, 'Tc', 'd', 7, 98, 147, 59, 158, 158, 1.9); element.elem[44] = addElement(44, 'Ru', 'd', 8, 101.07, 146, 36, 143, 143, 2.2); element.elem[45] = addElement(45, 'Rh', 'd', 9, 102.9055, 142, 10, 125, 140, 2.28); element.elem[46] = addElement(46, 'Pd', 'd', 10, 106.42, 139, 0, 105, 133, 2.2); element.elem[47] = addElement(47, 'Ag', 'd', 11, 107.8682, 145, 192, 192, 192, 1.93); element.elem[48] = addElement(48, 'Cd', 'd', 2, 112.411, 144, 255, 217, 143, 1.69); element.elem[49] = addElement(49, 'In', 'p', 3, 114.818, 142, 166, 117, 115, 1.78); element.elem[50] = addElement(50, 'Sn', 'p', 4, 118.71, 139, 102, 128, 128, 1.96); element.elem[51] = addElement(51, 'Sb', 'p', 5, 121.76, 139, 158, 99, 181, 2.05); element.elem[52] = addElement(52, 'Te', 'p', 6, 127.6, 138, 212, 122, 0, 2.1); element.elem[53] = addElement(53, 'I', 'p', 7, 126.9045, 139, 148, 0, 148, 2.66); element.elem[54] = addElement(54, 'Xe', 'p', 8, 131.293, 140, 66, 158, 176, 2.6); element.elem[55] = addElement(55, 'Cs', 's', 1, 132.9055, 244, 87, 23, 143, 0.79); element.elem[56] = addElement(56, 'Ba', 's', 2, 137.327, 215, 0, 201, 0, 0.89); element.elem[57] = addElement(57, 'La', 'd', 3, 138.9055, 207, 112, 212, 255, 1.1); element.elem[58] = addElement(58, 'Ce', 'f', 4, 140.116, 204, 255, 255, 199, 1.12); element.elem[59] = addElement(59, 'Pr', 'f', 5, 140.9077, 203, 217, 255, 199, 1.13); element.elem[60] = addElement(60, 'Nd', 'f', 6, 144.24, 201, 199, 255, 199, 1.14); element.elem[61] = addElement(61, 'Pm', 'f', 7, 145, 199, 163, 255, 199, 0); element.elem[62] = addElement(62, 'Sm', 'f', 8, 150.36, 198, 143, 255, 199, 1.17); element.elem[63] = addElement(63, 'Eu', 'f', 9, 151.964, 198, 97, 255, 199, 0); element.elem[64] = addElement(64, 'Gd', 'f', 10, 157.25, 196, 69, 255, 199, 1.2); element.elem[65] = addElement(65, 'Tb', 'f', 11, 158.9253, 194, 48, 255, 199, 0); element.elem[66] = addElement(66, 'Dy', 'f', 12, 162.5, 192, 31, 255, 199, 1.22); element.elem[67] = addElement(67, 'Ho', 'f', 13, 164.9303, 192, 0, 255, 156, 1.23); element.elem[68] = addElement(68, 'Er', 'f', 14, 167.259, 189, 0, 230, 117, 1.24); element.elem[69] = addElement(69, 'Tm', 'f', 15, 168.9342, 190, 0, 212, 82, 1.25); element.elem[70] = addElement(70, 'Yb', 'f', 16, 173.04, 187, 0, 191, 56, 0); element.elem[71] = addElement(71, 'Lu', 'f', 17, 174.967, 187, 0, 171, 36, 1.27); element.elem[72] = addElement(72, 'Hf', 'd', 4, 178.49, 175, 77, 194, 255, 1.3); element.elem[73] = addElement(73, 'Ta', 'd', 5, 180.9479, 170, 77, 166, 255, 1.5); element.elem[74] = addElement(74, 'W', 'd', 6, 183.84, 162, 33, 148, 214, 2.36); element.elem[75] = addElement(75, 'Re', 'd', 7, 186.207, 151, 38, 125, 171, 1.9); element.elem[76] = addElement(76, 'Os', 'd', 8, 190.23, 144, 38, 102, 150, 2.2); element.elem[77] = addElement(77, 'Ir', 'd', 9, 192.217, 141, 23, 84, 135, 2.2); element.elem[78] = addElement(78, 'Pt', 'd', 10, 195.078, 136, 208, 208, 224, 2.28); element.elem[79] = addElement(79, 'Au', 'd', 11, 196.9665, 136, 255, 209, 35, 2.54); element.elem[80] = addElement(80, 'Hg', 'd', 2, 200.59, 132, 184, 184, 208, 2); element.elem[81] = addElement(81, 'Tl', 'p', 3, 204.3833, 145, 166, 84, 77, 1.62); element.elem[82] = addElement(82, 'Pb', 'p', 4, 207.2, 146, 87, 89, 97, 2.33); element.elem[83] = addElement(83, 'Bi', 'p', 5, 208.9804, 148, 158, 79, 181, 2.02); element.elem[84] = addElement(84, 'Po', 'p', 6, 209, 140, 171, 92, 0, 2); element.elem[85] = addElement(85, 'At', 'p', 7, 210, 150, 117, 79, 69, 2.2); element.elem[86] = addElement(86, 'Rn', 'p', 8, 222, 150, 66, 130, 150, 0); element.elem[87] = addElement(87, 'Fr', 's', 1, 223, 260, 66, 0, 102, 0.7); element.elem[88] = addElement(88, 'Ra', 's', 2, 226, 221, 0, 125, 0, 0.9); element.elem[89] = addElement(89, 'Ac', 'd', 3, 227, 215, 112, 171, 250, 1.1); element.elem[90] = addElement(90, 'Th', 'f', 4, 232.0381, 206, 0, 186, 255, 1.3); element.elem[91] = addElement(91, 'Pa', 'f', 5, 231.0359, 200, 0, 161, 255, 1.5); element.elem[92] = addElement(92, 'U', 'f', 6, 238.0289, 196, 0, 143, 255, 1.38); element.elem[93] = addElement(93, 'Np', 'f', 7, 237, 190, 0, 128, 255, 1.36); element.elem[94] = addElement(94, 'Pu', 'f', 8, 244, 187, 0, 107, 255, 1.28); element.elem[95] = addElement(95, 'Am', 'f', 9, 243, 180, 84, 92, 242, 1.3); element.elem[96] = addElement(96, 'Cm', 'f', 10, 247, 169, 120, 92, 227, 1.3); element.elem[97] = addElement(97, 'Bk', 'f', 11, 247, 168, 138, 79, 227, 1.3); element.elem[98] = addElement(98, 'Cf', 'f', 12, 251, 168, 161, 54, 212, 1.3); element.elem[99] = addElement(99, 'Es', 'f', 13, 252, 165, 179, 31, 212, 1.3); element.elem[100] = addElement(100, 'Fm', 'f', 14, 257, 167, 179, 31, 186, 1.3); element.elem[101] = addElement(101, 'Md', 'f', 15, 258, 173, 179, 13, 166, 1.3); element.elem[102] = addElement(102, 'No', 'f', 16, 259, 176, 189, 13, 135, 1.3); element.elem[103] = addElement(103, 'Lr', 'f', 17, 262, 161, 199, 0, 102, 0); element.elem[104] = addElement(104, 'Rf', 'd', 4, 267, 157, 204, 0, 89, 0); element.elem[105] = addElement(105, 'Db', 'd', 5, 268, 149, 209, 0, 79, 0); element.elem[106] = addElement(106, 'Sg', 'd', 6, 269, 143, 217, 0, 69, 0); element.elem[107] = addElement(107, 'Bh', 'd', 7, 270, 141, 224, 0, 56, 0); element.elem[108] = addElement(108, 'Hs', 'd', 8, 269, 134, 230, 0, 46, 0); element.elem[109] = addElement(109, 'Mt', 'd', 9, 278, 129, 235, 0, 38, 0); element.elem[110] = addElement(110, 'Ds', 'd', 10, 281, 0, 0, 0, 28, 0); element.elem[111] = addElement(111, 'Rg', 'd', 11, 281, 0, 0, 0, 28, 0); element.elem[112] = addElement(112, 'Cn', 'd', 12, 285, 0, 0, 0, 28, 0); element.elem[113] = addElement(113, 'Uut', 'p', 3, 286, 0, 0, 0, 28, 0); element.elem[114] = addElement(114, 'Fl', 'p', 4, 289, 0, 0, 0, 28, 0); element.elem[115] = addElement(115, 'Uup', 'p', 5, 288, 0, 0, 0, 28, 0); element.elem[116] = addElement(116, 'Lv', 'p', 6, 293, 0, 0, 0, 28, 0); element.elem[117] = addElement(117, 'Uus', 'p', 7, 294, 0, 0, 0, 28, 0); element.elem[118] = addElement(118, 'Uuo', 'p', 8, 294, 0, 0, 0, 28, 0); } // Make sure element requested is defined. if ( (Z < 0) || (Z > element.elem.length) ) { alert("Element "+Z+" is not defined."); return 0; } // Determine what information is requested and return value switch (param) { case "symbol": return element.elem[Z].symbol; break; case "block": return element.elem[Z].block; break; case "valence": return element.elem[Z].valence; break; case "mass": return element.elem[Z].mass; break; case "radius": return element.elem[Z].radius; break; case "EN": return element.elem[Z].EN; break; case "color": return element.elem[Z].color; break; case "gradient": return element.elem[Z].gradient; break; case "label": return element.elem[Z].label; break; case "max": return element.elem.length; break; default: alert("Param "+param+" is not defined."); return 0; break; } // End of element routine } /// /// Define internal structure for elemental information /// function elementObject() { this.symbol = "?"; this.block = "?"; this.valence = 0; this.mass = 0.0; this.radius = 0.0; this.EN = 0.0; this.color = "rgb(88,88,88)"; this.gradient = "rgb(88,88,88)"; this.label = "rgb(255,255,255)"; } /// /// Internal routine to add information for elements /// function addElement(Z, Symbol, block, valence, mass, radius, red, green, blue, EN) { // Declare local variables var atomR, sum; var element = new elementObject(); // Add elemental information element.symbol = Symbol; element.block = block; element.valence = valence; element.mass = mass; (radius <= 0) ? atomR = 0.1 : atomR = radius / 100.0; element.radius = atomR; element.color = "rgb("+red+","+green+","+blue+")"; element.gradient = "rgb("+Math.floor(red/2)+","+Math.floor(green/2)+","+Math.floor(blue/2)+")"; sum = red + green + blue; element.label = (sum > 384) ? "rgb(0,0,0)" : "rgb(255,255,255)"; element.EN = EN; // End of addElement routine return element; } //# function drawPeriodic() //# //# Writes html code to a division named "ptable". The periodic table is written as a table, and each element //# is linked to to the pickElem() routine. //# function drawPeriodic() { // Declare local variables var html; var PerDivision = "ptable"; html = ""; html += ""; html += ""; // html += ""; // html += ""; html += ""; html += ""; html += "\n"; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += "\n"; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += "\n"; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += "\n"; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += "\n"; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += "\n"; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += "\n"; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += "\n"; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += ""; html += "
H MainMetals"; html += "
Metals
He
LiBe BCNOFNe
NaMg AlSiPSClAr
KCaScTiVCrMnFeCoNiCuZnGaGeAsSeBrKr
RbSrYZrNbMoTcRuRhPdAgCdInSnSbTeIXe
CsBaLaHfTaWReOsIrPtAuHgTlPbBiPoAtRn
FrRaAcRfDbSgBhHsMtDsRgCnUutFlUupLvUusUuo
 CePrNdPmSmEuGdTbDyHoErTmYbLu 
 ThPaUNpPuAmCmBkCfEsFmMdNoLr 
\n"; // Write html code to division var divID = document.getElementById(PerDivision); if ( divID ) { divID.innerHTML = html; } // End of drawPeriodic routine } // // -------------------- molecule.js -------------------- // //# function Mol(value) //# //# Define public routine to store and return molecule arrays //# //# Parameter: //# value = If value given, then set as active molecule //# //# Return value: //# Pointer to current array for molecular coordinates, ex. //# var molecule = Mol(); //# //# Molecular values stored in 'zeroth' element of array //# molecule[0].molIndex - ID number for this molecule //# molecule[0].numatoms - # of atoms in this molecule //# molecule[0].AtomScale - Scale factor to control size of molecule displayed //# molecule[0].showlabels - 0=don't show elemental symbols, 1=show symbols //# molecule[0].showcharges - 0=don't show charges, 1=show charges //# molecule[0].gradients - 0=don't shade atoms, 1=use shading //# molecule[0].formula - Simple text string containing molecular formula //# molecule[0].weight - Molecular weight //# molecule[0].charge - Charge of molecule //# //# Atomic values in remaining elements of array //# molecule[i].atomicnumber - Atomic number (Z) for atom //# molecule[i].x - x coordinate of atom //# molecule[i].y - y coordinate of atom //# molecule[i].z - z coordinate of atom //# molecule[i].charge - Estimate of atomic charge //# molecule[i].highlite - 0=don't highlight atom, 1=highlight atom //# molecule[i].hide - 0=display atom, 1=do not display atom //# function Mol(value) { // Declare local variables var id; var param = value || 0; // Determine which molecule to use if(typeof Mol.molecule === "undefined") Mol.molecule = 1; if ( param > 0 ) { Mol.molecule = param; BondMatrix(param); } id = Mol.molecule; // Initialize molecular array if necessary if ( typeof Mol.moly === "undefined" ) Mol.moly = []; if ( typeof Mol.moly[id] === "undefined" ) { Mol.moly[id] = []; Mol.moly[id][0] = new molObject(); Mol.moly[id][0].molIndex = id; Mol.moly[id][0].numatoms = 0; Mol.moly[id][0].AtomScale = 1.0; Mol.moly[id][0].showlabels = 0; Mol.moly[id][0].showcharges = 0; Mol.moly[id][0].gradients = 1; Mol.moly[id][0].highlite = 0; Mol.moly[id][0].formula = ""; Mol.moly[id][0].weight = 0.0; Mol.moly[id][0].charge = 999; } // End of Mol routine return Mol.moly[id]; } //# function BondMatrix(value) //# //# Define public routine to store and return Bond Matrix //# //# Parameter: //# value = If value given, then set as active matrix //# //# Return value: //# Pointer to current bond matrix, ex. //# var bonds = BondMatrix(); //# bonds[i][j] then gives indication of bond between atoms "i" and "j" //# function BondMatrix(value) { // Declare local variables var id; var param = value || 0; // Determine which bond matrix to use if(typeof BondMatrix.id === "undefined") BondMatrix.id = 1; if ( param > 0 ) BondMatrix.id = param; id = BondMatrix.id; // Initialize molecular array if necessary if ( typeof BondMatrix.bonds === "undefined" ) BondMatrix.bonds = []; if ( typeof BondMatrix.bonds[id] === "undefined" ) { BondMatrix.bonds[id] = []; } // End of BondMatrix routine return BondMatrix.bonds[id]; } /// /// Private routine to store name for active window. /// /// Parameter: /// mywin = If name of window exists, then set as active window/molecule. /// Otherwise, create new window with this name. /// /// Return value: /// Name of active Canvas/window /// function activeWin(mywin) { // Declare local variables var i, active; var param = mywin || " "; // Initialize links if (typeof activeWin.mol === "undefined") { activeWin.mol = []; activeWin.mol[0] = "Dummy"; } // Define defaults for active window and molecule if (typeof activeWin.win === "undefined") { var tag = document.getElementsByTagName("canvas"); if ( tag[0] ) { activeWin.win = tag[0].id; activeWin.mol[1] = activeWin.win; } else { // alert("No canvas element found."); return; } } // User requested to set/view Window information if ( param.length > 1 ) activeWin.win = param; // Find active molecule active=-1; for (i=0; i118) ) { InfoWin("*** ERROR Reading XYZ file. ***\n"); return; } x = parseFloat(current[1]); y = parseFloat(current[2]); z = parseFloat(current[3]); addAtom(A, x, y, z); InfoWin(" "+current[0]+"("+A+") "+x+", "+y+", "+z+"\n"); } // Create bonds for (i=1; i < numatoms; i++) { for (j=i+1; j <= numatoms; j++) { bond = 1.2 * (element(molecule[i].atomicnumber,"radius") + element(molecule[j].atomicnumber,"radius")); dx = molecule[i].x - molecule[j].x; dy = molecule[i].y - molecule[j].y; dz = molecule[i].z - molecule[j].z; r = Math.sqrt(dx*dx+dy*dy+dz*dz); if (r <= bond) addBond(i,j); } } // Finished with readXYZfile routine formula(); InfoWin("Finished reading XYZ input file.\n"); } /// function readMOLfile(molfile,lines) /// /// Read MDL .mol file (V2000 format) /// /// molfile: name of .mol file /// lines: Array holding content of .mol file /// /// Data stored in molecule array and bond matrix /// function readMOLfile(molfile,lines) { // Declare local variables var i, j; var x, y, z; var bond1, bond2; var A, symbol; var Qtitle = new Array(); var molecule = Mol(); // Write file information to information window var molname = escape(molfile.name); InfoWin("File Name = "+molname,1); InfoWin("\nFile Type = "+molfile.type); InfoWin("\nFile Size = "+molfile.size); // Reset molecule object and contents delMolecule(); // Read data Qtitle = lines[0]; Qtitle = Qtitle.replace(/\s+$/,""); var molAtoms = parseFloat(lines[3].substr(0,3)); var molBonds = parseFloat(lines[3].substr(3,3)); InfoWin("\n\n"+Qtitle); InfoWin("\n"+molAtoms+" atoms and "+molBonds+" bonds."); // Read coordinates j = molAtoms+4; for (i=4; i < j; i++) { x = parseFloat(lines[i].substr(0,10)); y = parseFloat(lines[i].substr(10,10)); z = parseFloat(lines[i].substr(20,10)); symbol = lines[i].substr(31,3); symbol = symbol.replace(/\s+/,""); A = lookupSymbol(symbol); InfoWin("\n "+symbol+"("+A+") "+x+", "+y+", "+z); addAtom(A, x, y, z); } j = 4 + molAtoms + molBonds; for (i = 4+molAtoms; i < j; i++) { bond1 = parseFloat(lines[i].substr(0,3)); bond2 = parseFloat(lines[i].substr(3,3)); InfoWin("\n Bond from "+bond1+" to "+bond2); addBond(bond1,bond2); } // Finished formula(); } /// /// Read GAMESS input file contain full set of x,y,z coordinates /// /// lines: Array holding content of .inp file /// function readINPfile(lines) { // Declare local variables var i, j; var x, y, z; var bond1, bond2; var A, symbol; var numatoms; var Qtitle = new Array(); var molecule = Mol(); // Inform user that file being read InfoWin("--- Reading Gamess input file ---\n",1); // Reset molecule object and contents delMolecule(); // Read title from file i = 0; lines[i].toLowerCase(); while ( lines[i].toLowerCase().indexOf('$data') < 0 ) { i++; } i++; Qtitle = lines[i]; Qtitle = Qtitle.replace(/\s+$/,""); InfoWin("\n\nTitle: [" + Qtitle + "]\n"); // Advance to start of coordinates i++; if ( lines[i].toLowerCase().indexOf('c1') < 0 ) i++; // Read coordinates i++; while ( lines[i].toLowerCase().indexOf('$end') < 0 ) { InfoWin(" Line = [" + lines[i] + "]\n"); current = lines[i].replace(/\s+/g," ").replace(/^\s+/,"").split(' '); A = parseInt(current[1]); x = parseFloat(current[2]); y = parseFloat(current[3]); z = parseFloat(current[4]); addAtom(A, x, y, z); i++; } // Calculate bonds for (i=1; i < molecule[0].numatoms; i++) { ra = element(molecule[i].atomicnumber,"radius"); for (j=i+1; j <= molecule[0].numatoms; j++) { rb = element(molecule[i].atomicnumber,"radius"); r = 0.9*distance(molecule, i, j); if ( r <= (ra+rb) ) addBond(i, j); } } // Finished with readINPfile routine InfoWin("Finished reading input file.\n"); formula(); return; } //# function lookupSymbol(symbol) //# //# Given elemental symbol, lookup and return atomic number (Z) //# function lookupSymbol(symbol) { var i; for (i = 1; i < element(1,"max"); i++) { if ( element(i,"symbol") == symbol ) return i; } return 0; } /// /// Routine to remove and initialize molecule object /// function delMolecule() { var molecule = Mol(); molecule[0] = new molObject(); molecule[0].molIndex = 1; molecule[0].numatoms = 0; molecule[0].AtomScale = 1.0; molecule[0].showlabels = 0; molecule[0].showcharges = 0; buttonColor("ChargeButton",0); } /// /// Routine to save/restore molecular coordinates, bonds, ... /// /// Parameter: mode /// pop - restore last saved set of coordinates /// save - store current information /// redo - 'Undo' last pop /// function Undo(mode) { // Declare local variables var i, pos; var maxBonds; var MAXSAVE=10; var molecule = Mol(); var bonds = BondMatrix(); // Initialization of variables if ( typeof Undo.num == 'undefined' ) { Undo.num = 0; Undo.mol = []; Undo.bonds = []; for (i=0; i < MAXSAVE; i++) { Undo.mol[i] = []; Undo.mol[i][0] = 0; Undo.bonds[i] = []; } } // Save current geometry information if ( mode == "save") { pos = Undo.num; // InfoWin(" --- Saving geometry in slot " + pos + " ---\n"); Undo.mol[pos] = null; Undo.mol[pos] = []; Undo.mol[pos][0] = molecule[0].numatoms; for (i=1; i <= molecule[0].numatoms; i++) { Undo.mol[pos][i] = new atomObject(); Undo.mol[pos][i].atomicnumber = molecule[i].atomicnumber; Undo.mol[pos][i].x = molecule[i].x; Undo.mol[pos][i].y = molecule[i].y; Undo.mol[pos][i].z = molecule[i].z; Undo.mol[pos][i].bonds = []; Undo.mol[pos][i].charge = molecule[i].charge; Undo.mol[pos][i].highlite = molecule[i].highlite; } Undo.bonds[pos] = null; Undo.bonds[pos] = []; for (i=1; i <= molecule[0].numatoms; i++) { Undo.bonds[pos][i] = []; for (j=0; j <= molecule[0].numatoms; j++) { Undo.bonds[pos][i][j] = bonds[i][j]; } } // alert("Coordinate set "+Undo.num+" contains "+Undo.mol[pos][0]+" atoms."); Undo.num = ( (Undo.num+1) % MAXSAVE ); return; } // Set position of 'last saved' geometry information if ( mode == "pop") { Undo('save'); pos = ( (Undo.num+MAXSAVE-2) % MAXSAVE ); Undo.num = pos; // InfoWin(" --- Attempting to restore from slot " + pos + " ---\n"); if ( Undo.mol[pos][0] < 1 ) { alert("ERROR: No saved coordinates to restore."); return; } } // Attempt to reverse last 'undo' (pop) if ( mode == "redo") { pos = ( (Undo.num+1) % MAXSAVE ); Undo.num = pos; // InfoWin(" --- Attempting to go back to slot " + pos + " ---\n"); if ( Undo.mol[pos][0] < 1 ) { alert("ERROR: No saved coordinates to restore."); return; } } if ( (mode == "redo") || (mode == "pop") ) { molecule[0].numatoms = Undo.mol[pos][0]; for (i=1; i <= Undo.mol[pos][0]; i++) { molecule[i].atomicnumber = Undo.mol[pos][i].atomicnumber; molecule[i].x = Undo.mol[pos][i].x; molecule[i].y = Undo.mol[pos][i].y; molecule[i].z = Undo.mol[pos][i].z; molecule[i].charge = Undo.mol[pos][i].charge; molecule[i].highlite = Undo.mol[pos][i].highlite; } for (i=1; i <= molecule[0].numatoms; i++) { for (j=0; j <= molecule[0].numatoms; j++) { bonds[i][j] = Undo.bonds[pos][i][j]; } } centerMolecule(); drawMolecule(); return; } // End of Undo routine } //# function addAtom(AtomicNum, x, y, z) //# //# Routine to add atomic information to molecule array. //# //# Parameters are the atomic # and (x,y,z) coordinates of the atom. //# function addAtom(AtomicNum, x, y, z) { // Declare local variables var i; var numatoms; var molecule = Mol(); var bonds = BondMatrix(); // Create/fill molecular array molecule[0].numatoms++; numatoms = molecule[0].numatoms; molecule[0].showcharges = 0; buttonColor("ChargeButton",0); molecule[numatoms] = new atomObject(); molecule[numatoms].atomicnumber = AtomicNum; molecule[numatoms].x = x; molecule[numatoms].y = y; molecule[numatoms].z = z; molecule[numatoms].charge = 0.0; molecule[numatoms].highlite = 0; // Initialize bond matrix if (typeof bonds[numatoms] === "undefined") { bonds[numatoms] = []; } bonds[numatoms][0] = 0; for (i=1; i <= numatoms; i++) { bonds[i][numatoms] = 0; bonds[numatoms][i] = 0; } // End of addAtom routine } //# function addBond(atom1, atom2) //# //# Routine to add bonding information to bonds array //# (Note that atom numbers start at 1) //# function addBond(atom1, atom2) { // Define local variables var i, j; var newbond; var molecule = Mol(); var numatoms = molecule[0].numatoms; var bonds = BondMatrix(); // Add bonds to matrix bonds[atom1][0]++; bonds[atom1][atom2] = 1; bonds[atom2][0]++; bonds[atom2][atom1] = 1; // End of addBond routine } //# function delAtom(atomNum) //# //# Routine to remove selected atom, directly-bonded Hydrogens, and //# cleanup molecule object (remove blank slots) and update bond arrays. //# //# atomNum is the position of the atom to delete in the molecule array //# function delAtom(atomNum) { // Declare local variables var i, j, k, Hi=0; var bondedAtom, bi; var numatoms; var newNum, maxBonds, maxBondsB, maxBondsI, maxBondsJ; var HList = new Array(); var molecule = Mol(); var bonds = BondMatrix(); // See if there are any attached hydrogen atoms molecule[0].showcharges = 0; buttonColor("ChargeButton",0); newNum = atomNum; for (i=1; i < atomNum; i++) { if ( (bonds[atomNum][i] > 0) && (molecule[i].atomicnumber == 1) ) { HList[Hi++] = i; newNum--; } } for (i=atomNum+1; i <= molecule[0].numatoms; i++) { if ( (bonds[atomNum][i] > 0) && (molecule[i].atomicnumber == 1) ) { HList[Hi++] = i; } } // Remove attached hydrogen atoms HList.sort(function(a,b){ return(b-a); }); for (i=0; i < Hi; i++) { delAtom(HList[i]); } atomNum = newNum; // Remove atom and shift 'higher' atoms in molecule object to fill gaps for (i=atomNum; i < molecule[0].numatoms; i++) { j=i+1; molecule[i].atomicnumber = molecule[j].atomicnumber; molecule[i].x = molecule[j].x; molecule[i].y = molecule[j].y; molecule[i].z = molecule[j].z; molecule[i].charge = molecule[j].charge; molecule[i].highlite = molecule[j].highlite; } molecule[0].numatoms--; // Remove bonds to atom being deleted numatoms = molecule[0].numatoms; for (i=1; i < atomNum; i++) { if ( bonds[i][atomNum] > 0 ) bonds[i][0]--; for (j=atomNum; j <= numatoms; j++) bonds[i][j] = bonds[i][j+1]; bonds[i][numatoms+1] = 0; } for (i=atomNum; i <= numatoms; i++) { if ( bonds[i+1][atomNum] > 0 ) bonds[i+1][0]--; for (j=0; j < atomNum ; j++) bonds[i][j] = bonds[i+1][j]; for (j=atomNum; j <= numatoms; j++) bonds[i][j] = bonds[i+1][j+1]; bonds[i][numatoms+1] = 0; } for (i=0; i<=numatoms+1; i++) bonds[numatoms+1][i] = 0; // Finished with delAtom routine drawMolecule(); } //# function delBond(atom1, atom2) //# //# Routine to remove bond from bonds array. //# function delBond(atom1, atom2) { var i, maxBonds; var bonds = BondMatrix(); // Remove bond on atom1 if ( bonds[atom1][atom2] > 0 ) { bonds[atom1][atom2] = 0; bonds[atom1][0]--; } // Remove bond on atom2 if ( bonds[atom2][atom1] > 0 ) { bonds[atom2][atom1] = 0; bonds[atom2][0]--; } // Finished with delBond routine } //# function hideH() //# //# Do not display any hydrogen atoms in molecule //# function hideH() { var i; var molecule = Mol(); // Loop over all atoms, setting hide flag to 0 for all atoms for (i=1; i <= molecule[0].numatoms; i++) { if ( molecule[i].atomicnumber == 1 ) { molecule[i].hide = 1; } } // Finished with hideH routine drawMolecule(); } //# function showAll() //# //# Show all atoms in molecule //# function showAll() { var i; var molecule = Mol(); // Loop over all atoms, setting hide flag to 0 for all atoms for (i=1; i < molecule[0].numatoms; i++) { molecule[i].hide = 0; } // Finished with showAll routine } //# function centerMolecule() //# //# Find center of molecule and move coordinates to center. //# function centerMolecule() { // Define local variables var i, A, numatoms; var molSize = 0.0; var xc, yc, zc; var xyz; var activeCanvas = activeWin(""); var molecule = Mol(); // Get height of Canvas var canvas = document.getElementById(activeCanvas); var height = canvas.height; // Find center of molecule xc = 0.0; yc = 0.0; zc = 0.0; numatoms = molecule[0].numatoms; for (i=1; i <= numatoms; i++) { xc += molecule[i].x; yc += molecule[i].y; zc += molecule[i].z; } xc /= numatoms; yc /= numatoms; zc /= numatoms; // Translate coordinates to center molSize = 0.0; for (i=1; i <= numatoms; i++) { A = molecule[i].atomicnumber; molecule[i].x -= xc; molecule[i].y -= yc; molecule[i].z -= zc; xyz = Math.abs(molecule[i].x); xyz = Math.max(xyz,Math.abs(molecule[i].y)); xyz = Math.max(xyz,Math.abs(molecule[i].z)); xyz += element(A,"radius"); molSize = Math.max(molSize,xyz); } molecule[0].AtomScale = 0.5*height/molSize; // Finished with centerMolecule routine } /// /// Display parameters (mainly for debugging) /// function showGlobal() { // Declare local variables var i; var molecule = Mol(); InfoWin("numatoms = " + molecule[0].numatoms,1); InfoWin("\nAtomScale = " + molecule[0].AtomScale.toFixed(6)); InfoWin("\n"); for (i=1; i<=molecule[0].numatoms; i++) { A = molecule[i].atomicnumber; InfoWin(i + " " + element(A,"symbol")); InfoWin(" (" + molecule[i].x.toFixed(4)); InfoWin(", " + molecule[i].y.toFixed(4)); InfoWin(", " + molecule[i].z.toFixed(4)); InfoWin(")\n"); } } //# function showCoord(mode) //# //# Display molecular coordinates and bonds in information window. //# //# Parameter: //# mode=0: Write .xyz formatted file //# mode>0: Write coordinates and bond information //# function showCoord(mode) { // Declare local variables var i; var space; var molecule = Mol(); var bonds = BondMatrix(); // If no coordinates available, return if ( molecule[0].weight <= 0.0 ) return; // Loop over all atoms and bonds if ( mode ) { InfoWin("Molecular Coordinates and Bond Information\n",1); InfoWin(" "+molecule[0].formula+" ("+molecule[0].weight.toFixed(2)+" g/mol)"); if ( (molecule[0].charge != 999) && (molecule[0].charge != 0) ) InfoWin(" Charge = "+molecule[0].charge); InfoWin("\n"); } else { InfoWin("Molecular Coordinates in .xyz format\n",1); InfoWin("--------------------\n"); InfoWin(molecule[0].numatoms + "\n"); InfoWin(molecule[0].formula+" ("+molecule[0].weight.toFixed(2)+" g/mol) in xyz format: From CH5M3D\n"); } for (i=1; i<=molecule[0].numatoms; i++) { space = ""; if (i < 100) space = " "; if (i < 10) space = " "; if ( mode ) { InfoWin(space+i+": "); } InfoWin(element(molecule[i].atomicnumber,"symbol") + " "); if ( element(molecule[i].atomicnumber,"symbol").length < 2 ) InfoWin(" "); InfoWin(XYZpretty(molecule[i].x)); InfoWin(XYZpretty(molecule[i].y)); InfoWin(XYZpretty(molecule[i].z)); if ( mode ) { InfoWin(" "); for (j=1; j <=molecule[0].numatoms; j++) { if ( bonds[i][j] > 0 ) InfoWin(" "+j+","); } } InfoWin("\n"); } // End of showCoord routine } /// /// Helper routine to make coordinates line up in columns /// function XYZpretty(coord) { // Declare local variables var space = " "; var mystr = new Array(); if ( coord >= 100.0) { mystr = space + " " + coord.toFixed(4); return mystr; } if ( coord >= 10.0) { mystr = space + " " + coord.toFixed(4); return mystr; } if ( coord >= 0.0) { mystr = space + " " + coord.toFixed(4); return mystr; } if ( coord >= -10.0) { mystr = space + " " + coord.toFixed(4); return mystr; } if ( coord >= -100.0) { mystr = space + " " + coord.toFixed(4); return mystr; } mystr = space + coord.toFixed(4); return mystr; // Finished with XYZpretty } //# function formula() //# //# Display molecular formula to division with an id = "formula". //# Note that the contents of this division will be overwritten. //# function formula() { var i, j, A; var found, num; var molweight; var molformula = new Array(); var formulaStr="

Formula = "; var molecule = Mol(); // If no molecule loaded, return if (molecule[0].numatoms < 1) return; // Look for carbon and place in first slot num = 0; for (i=1; i<=molecule[0].numatoms; i++) if ( molecule[i].atomicnumber == 6 ) { molformula[num] = []; molformula[num][0] = 6; molformula[num][1] = 0; num++; i = molecule[0].numatoms+1; } // Look for hydrogen in next slot for (i=1; i<=molecule[0].numatoms; i++) if ( molecule[i].atomicnumber == 1 ) { molformula[num] = []; molformula[num][0] = 1; molformula[num][1] = 0; num++; i = molecule[0].numatoms+1; } // Loop over all atoms in molecule for (i=1; i<=molecule[0].numatoms; i++) { A = molecule[i].atomicnumber; found = 0; for (j=0; j < num; j++) { if (molformula[j][0] == A) { molformula[j][1]++; found = 1; j = num; } } if (found == 0) { molformula[num] = new Array(2); molformula[num][0] = molecule[i].atomicnumber; molformula[num][1] = 1; num++; } } // Calculate molecular weight and output formula molweight = 0.0; molecule[0].formula = ""; for (i=0; i 1) { formulaStr += ""+molformula[i][1]+""; molecule[0].formula += molformula[i][1] + " "; } } formulaStr += "

"; molecule[0].weight = molweight; // Write formula to screen if ( document.getElementById("formula") ) document.getElementById("formula").innerHTML = formulaStr; if ( molweight > 0.0 ) InfoWin(molecule[0].formula+" has a molecular weight of "+molweight.toFixed(2)+"\n"); // End formula routine } //# function RotateMolecule(axis) //# //# Routine to start/stop rotation of molecule. //# //# Parameter: //# axis = rotation axis. Allowed values are "x", "y", or "z" //# ("s" can be used to stop all rotations) //# //# Buttons must be created in html with: //# id="rotateX" (or rotateY or rotateZ) //# function RotateMolecule(axis) { // Declare local variables var delay = 20; // Delay between redrawing screen, in ms // Parameter validation axis = axis[0].toLowerCase(); if ( (axis != "x") && (axis != "y") && (axis != "z") && (axis != "s") ) { return; } // If first call, initialize "active" variable if(typeof RotateMolecule.RX === "undefined") { RotateMolecule.RX = 0; RotateMolecule.RY = 0; RotateMolecule.RZ = 0; } // Start/Stop rotation switch (axis) { case 'x': if ( RotateMolecule.RX == 0 ) { // Start rotation RotateMolecule.RX = 1; RotateX_ID = setInterval( "rotateX()", delay ); buttonColor("rotateX",1); } else { // Stop rotation RotateMolecule.RX = 0; clearInterval( RotateX_ID ); buttonColor("rotateX",0); } break; case 'y': if ( RotateMolecule.RY == 0 ) { // Start rotation RotateMolecule.RY = 1; RotateY_ID = setInterval( "rotateY()", delay ); buttonColor("rotateY",1); } else { // Stop rotation RotateMolecule.RY = 0; clearInterval( RotateY_ID ); buttonColor("rotateY",0); } break; case 'z': if ( RotateMolecule.RZ == 0 ) { // Start rotation RotateMolecule.RZ = 1; RotateZ_ID = setInterval( "rotateZ()", delay ); buttonColor("rotateZ",1); } else { // Stop rotation RotateMolecule.RZ = 0; clearInterval( RotateZ_ID ); buttonColor("rotateZ",0); } break; case 's': if ( RotateMolecule.RX != 0 ) { RotateMolecule.RX = 0; clearInterval( RotateX_ID); } if ( RotateMolecule.RY != 0 ) { RotateMolecule.RY = 0; clearInterval( RotateY_ID); } if ( RotateMolecule.RZ != 0 ) { RotateMolecule.RZ = 0; clearInterval( RotateZ_ID); } buttonColor("rotateX",0); buttonColor("rotateY",0); buttonColor("rotateZ",0); break; } // End of RotateMolecule function } // // Private function to perform rotation of molecule about x-axis // function rotateX() { // Declare local variables var i, x, y, z; var angle = 1.0; var cosA = Math.cos(-angle*Math.PI/180); var sinA = Math.sin(-angle*Math.PI/180); var molecule = Mol(); // Draw molecule and display on canvas for (i=1; i <= molecule[0].numatoms; i++) { y = molecule[i].y; z = molecule[i].z; molecule[i].y = cosA*y + sinA*z; molecule[i].z = -sinA*y + cosA*z; } drawMolecule(); // End of rotateX function } // // Private function to perform rotation of molecule about y-axis // function rotateY() { // Declare local variables var i, x, y, z; var angle = 1.0; var cosA = Math.cos(-angle*Math.PI/180); var sinA = Math.sin(-angle*Math.PI/180); var molecule = Mol(); // Draw molecule and display on canvas for (i=1; i <= molecule[0].numatoms; i++) { x = molecule[i].x; z = molecule[i].z; molecule[i].x = cosA*x + sinA*z; molecule[i].z = -sinA*x + cosA*z; } drawMolecule(); // End of rotateY function } // // Private function to perform rotation of molecule about z-axis // function rotateZ() { // Declare local variables var i, x, y, z; var angle = 1.0; var cosA = Math.cos(-angle*Math.PI/180); var sinA = Math.sin(-angle*Math.PI/180); var molecule = Mol(); // Draw molecule and display on canvas for (i=1; i <= molecule[0].numatoms; i++) { x = molecule[i].x; y = molecule[i].y; molecule[i].x = cosA*x + sinA*y; molecule[i].y = -sinA*x + cosA*y; } drawMolecule(); // End of rotateZ function } // // -------------------- drawmolecule.js -------------------- // //# function drawMolecule() //# //# Draw atoms and bonds. //# function drawMolecule() { // Define local variables var i, j, k; var x, y, r; var bonds = BondMatrix(); var molecule = Mol(); var A, numatoms=molecule[0].numatoms; var bondto, maxBonds; var x1, y1, x2, y2; var AtomSize = 0.50; var SimpleSwitch = 250; // Create connection to active Canvas var mycanvas = activeWin(""); var canvas = document.getElementById(mycanvas); if ( ! canvas ) return; var ctx = canvas.getContext('2d'); var width = canvas.width; var height = canvas.height; var centerx = canvas.width/2; var centery = canvas.height/2; // Clear screen before drawing molecule clear(ctx, width, height); // Define properties of lines ctx.strokeStyle = "rgb(0, 0, 255)"; ctx.lineWidth = 3.0; // Depth sort: Draw from back to front if ( typeof drawMolecule.deep == 'undefined' ) { drawMolecule.deep = []; } if ( drawMolecule.deep.length != numatoms ) { j=0; drawMolecule.deep = []; for (i=drawMolecule.deep.length; i SimpleSwitch ) molecule[0].gradients = 0; // Loop over all atoms in molecule for (i = 0; i < numatoms; i++) { atom = drawMolecule.deep[i].id; if ( ! molecule[atom].hide ) { if ( molecule[0].gradients ) { drawAtom(ctx, atom, AtomSize, centerx, centery); } else { drawAtomPlain(ctx, atom, AtomSize, centerx, centery); } if ( molecule[0].showcharges != 0 ) DrawChargeCloud(ctx, atom, AtomSize*1.5, centerx, centery); if ( molecule[atom].highlite != 0 ) DrawAtomHilite(ctx, atom, AtomSize*1.5, centerx, centery); // Loop over all bonds on current atom for (j = 1; j <= numatoms; j++) { if ( (bonds[atom][j] > 0) && (j != atom) && !molecule[j].hide ) { for (k=i+1; k < numatoms; k++) { if (drawMolecule.deep[k].id == j) { drawBond(ctx, atom, j, AtomSize, centerx, centery, molecule[0].gradients); } } } } } } // Finished with drawMolecule routine } //# function showLabels() //# //# Routine to toggle display of atomic labels. //# function showLabels() { // Local variables var molecule = Mol(); if ( molecule[0].showlabels == 0 ) { buttonColor("LabelButton",1); molecule[0].showlabels = 1; drawMolecule(); return; } buttonColor("LabelButton",0); molecule[0].showlabels = 0; drawMolecule(); return; } /// /// Routine to draw a single atom /// function drawAtom(ctx, atomNum, AtomSize, centerx, centery) { // Define local variables var A; var x, y, r; var xoff, yoff, roff; var molecule = Mol(); var activeCanvas = activeWin(""); // Get parameters for atom A = molecule[atomNum].atomicnumber; x = molecule[0].AtomScale*molecule[atomNum].x + centerx; y = molecule[0].AtomScale*molecule[atomNum].y + centery; r = molecule[0].AtomScale*AtomSize*element(A,"radius"); xoff = x-(0.20*r); yoff = y-(0.20*r); roff = 0.30*r; x = Math.floor(x+0.5); y = Math.floor(y+0.5); r = Math.floor(r+0.5); xoff = Math.floor(xoff+0.5); yoff = Math.floor(yoff+0.5); AtomColor = ctx.createRadialGradient(xoff, yoff, roff, x, y, r); AtomColor.addColorStop(0, element(A,"color")); AtomColor.addColorStop(1, element(A,"gradient")); // Plot atom as a gradient shaded circle ctx.beginPath(); ctx.arc(x, y, r, 0, 2*Math.PI, false); ctx.fillStyle = AtomColor; ctx.fill(); ctx.lineWidth = 0.01; ctx.strokeStyle = "black"; ctx.stroke(); ctx.closePath(); // Draw label for atom if ( molecule[0].showlabels != 0 ) atomLabel(ctx,A,atomNum,x,y); // End of drawAtom routine } /// /// Routine to draw a single atom without gradient /// function drawAtomPlain(ctx, atomNum, AtomSize, centerx, centery) { // Define local variables var A; var x, y, r; var xoff, yoff, roff; var molecule = Mol(); var activeCanvas = activeWin(""); // Get parameters for atom A = molecule[atomNum].atomicnumber; x = molecule[0].AtomScale*molecule[atomNum].x + centerx; y = molecule[0].AtomScale*molecule[atomNum].y + centery; r = molecule[0].AtomScale*AtomSize*element(A,"radius"); xoff = x-(0.20*r); yoff = y-(0.20*r); roff = 0.30*r; x = Math.floor(x+0.5); y = Math.floor(y+0.5); r = Math.floor(r+0.5); xoff = Math.floor(xoff+0.5); yoff = Math.floor(yoff+0.5); // Plot atom as a solid shaded circle ctx.beginPath(); ctx.arc(x, y, r, 0, 2*Math.PI, false); ctx.fillStyle = element(A,"color"); ctx.fill(); ctx.lineWidth = 1; ctx.strokeStyle = "black"; ctx.stroke(); ctx.closePath(); // Draw label for atom if ( molecule[0].showlabels != 0 ) atomLabel(ctx,A,atomNum,x,y); // End of drawAtomPlain routine } /// /// Routine to draw charge cloud around a single atom /// function DrawChargeCloud(ctx, atomNum, AtomSize, centerx, centery) { // Define local variables var A; var x, y, r; var colR, colB, colG, deltaRGB; var molecule = Mol(); var activeCanvas = activeWin(""); // Get parameters for atom A = molecule[atomNum].atomicnumber; x = molecule[0].AtomScale*molecule[atomNum].x + centerx; y = molecule[0].AtomScale*molecule[atomNum].y + centery; r = molecule[0].AtomScale*AtomSize*element(A,"radius"); // Set colors based on charge var q = molecule[atomNum].charge; // Positive charges shown in blue if (q >= 0) { (q > 1.0) ? deltaRGB = 1.0 : deltaRGB = q; colR = 0; colG = 0; colB = 255; } // Positive charges shown in red if (q < 0) { (q < -1.0) ? deltaRGB = 1.0 : deltaRGB = -q; colR = 255; colG = 0; colB = 0; } AtomColor = "rgba("+colR+","+colG+","+colB+","+deltaRGB+")"; // AtomColor = "rgba("+colR+","+colG+","+colB+",0.75)"; // Plot charge cloud as a semi-transparent circle ctx.beginPath(); ctx.arc(x, y, r, 0, 2*Math.PI, false); ctx.fillStyle = AtomColor; ctx.fill(); ctx.lineWidth = 0.01; ctx.strokeStyle = "black"; ctx.stroke(); ctx.closePath(); // End DrawChargeCloud routine } /// /// Routine to draw a single atom with a highlight /// function DrawAtomHilite(ctx, atomNum, AtomSize, centerx, centery) { // Define local variables var A; var x, y, r; var colR, colB, colG, deltaRGB; var molecule = Mol(); var activeCanvas = activeWin(""); // Get parameters for atom A = molecule[atomNum].atomicnumber; x = molecule[0].AtomScale*molecule[atomNum].x + centerx; y = molecule[0].AtomScale*molecule[atomNum].y + centery; r = molecule[0].AtomScale*AtomSize*element(A,"radius"); // Set highlight color to yellow AtomColor = "rgba(255,255,0,0.5)"; // Plot charge cloud as a semi-transparent circle ctx.beginPath(); ctx.arc(x, y, r, 0, 2*Math.PI, false); ctx.fillStyle = AtomColor; ctx.fill(); ctx.lineWidth = 0.01; ctx.strokeStyle = "black"; ctx.stroke(); ctx.closePath(); // End DrawAtomHilite routine } /// /// Helper routine to draw label for atom /// Parameters: /// Atomic number, atom #, (x,y) coordinates /// function atomLabel(ctx,A,i,ax,ay) { var label = element(A,"symbol"); var fontsize = 14; var x = parseFloat(ax); var y = parseFloat(ay) + fontsize/2; var molecule = Mol(); ctx.lineWidth = 1.0; ctx.textAlign = "center"; ctx.font = "normal " + fontsize + "px sans-serif"; ctx.fillStyle = element(A,"label"); ctx.beginPath(); ctx.fillText(label,x,y); var w = 10.0 / molecule[0].AtomScale; ctx.fillRect(x,y,w*1.5,w); ctx.closePath(); } /// /// Routine to draw a single bond /// function drawBond(ctx, atom1, atom2, AtomSize, centerx, centery, smallMolecule) { // Define local variables var i, j, k; var x1, y1, z1, x2, y2, z2; var dx, dy, dz; var xoff, yoff; var dist, r; var molecule = Mol(); var activeCanvas = activeWin(""); var AtomScale = molecule[0].AtomScale; var BondWidth = Math.floor(0.10*AtomScale + 0.5); var BondColor = "rgb(200,128,51)"; // Get parameters for atoms r = AtomScale * AtomSize * element(molecule[atom1].atomicnumber,"radius") - 2; x1 = AtomScale*molecule[atom1].x + centerx; y1 = AtomScale*molecule[atom1].y + centery; z1 = AtomScale*molecule[atom1].z; x2 = AtomScale*molecule[atom2].x + centerx; y2 = AtomScale*molecule[atom2].y + centery; z2 = AtomScale*molecule[atom2].z; // For large molecules, use simpler plot if ( ! smallMolecule ) { ctx.beginPath(); ctx.moveTo(xoff, yoff); ctx.lineTo(x2, y2); ctx.lineWidth = BondWidth; ctx.strokeStyle = BondColor; ctx.stroke(); ctx.closePath(); } // Calculate intersection of bond with sphere dx = x2 - x1; dy = y2 - y1; dz = z2 - z1; dist = Math.sqrt(dx*dx + dy*dy + dz*dz); xoff = x1 + r*dx/dist; yoff = y1 + r*dy/dist; // Draw bond ctx.beginPath(); ctx.moveTo(xoff, yoff); ctx.lineTo(x2, y2); ctx.lineWidth = BondWidth + 2; ctx.strokeStyle = "rgb(0,0,0)"; ctx.stroke(); ctx.moveTo(xoff, yoff); ctx.lineTo(x2, y2); ctx.lineWidth = BondWidth; ctx.strokeStyle = BondColor; ctx.stroke(); ctx.closePath(); } /// /// Clear drawing window (canvas) /// function clear(ctx, width, height) { // Clear plot area ctx.fillStyle = "rgb(255,255,255)"; ctx.fillRect(0, 0, width, height); // ctx.clearRect(0, 0, width, height); // Show border around plot area ctx.beginPath(); ctx.rect(1,1,width-1,height-1); ctx.lineWidth = 2; ctx.strokeStyle = "rgb(95,95,127)"; ctx.stroke(); ctx.closePath(); } /// /// Draw atoms and bonds with highlighting /// function drawHighlight(mycanvas, sequence, AtomSize, centerx, centery) { // Define local variables var i, j, k; var x, y, r; var A; var maxBonds, bondto; var x1, y1, x2, y2; var molecule = Mol(); var bonds = BondMatrix(); // Create connection to Canvas var canvas = document.getElementById(mycanvas); var ctx = canvas.getContext('2d'); var width = canvas.width; var height = canvas.height; // Clear screen before drawing molecule clear(ctx, width, height); // Define properties of lines ctx.strokeStyle = "rgb(0, 0, 255)"; ctx.lineWidth = 3.0; // Depth sort: Draw from back to front if ( typeof drawHighlight.deep == 'undefined' ) { drawHighlight.deep = []; } if ( drawHighlight.deep.length != molecule[0].numatoms ) { j=0; drawHighlight.deep = []; for (i=drawHighlight.deep.length; i 0) { highbond = 0; if (hilite > 0) { for (ih=1; ih < sequence[0]*3; ih++) { if (bondto == sequence[ih]) highbond = 1; } } for (k=i+1; k < molecule[0].numatoms; k++) { if (drawHighlight.deep[k].id == bondto) { HighlightBond(ctx,atom,bondto,highbond, AtomSize, centerx, centery); } } } } } // Finished with drawHighlight routine } /// /// Routine to draw a single highlighted atom /// function HighlightAtom(ctx, atomNum, hilite, AtomSize, centerx, centery) { // Define local variables var A; var x, y, r; var xoff, yoff, roff; var istart, ilength, colorstr; var myrgb = new Array(); var bcolor = "rgb(191,191,191)"; var hcolor = "rgb(255, 0, 0)"; var gcolor = "rgb(127, 0, 0)"; var molecule = Mol(); var activeCanvas = activeWin(""); // Get parameters for atom A = molecule[atomNum].atomicnumber; x = molecule[0].AtomScale*molecule[atomNum].x + centerx; y = molecule[0].AtomScale*molecule[atomNum].y + centery; r = molecule[0].AtomScale*AtomSize*element(A,"radius"); xoff = x-(0.20*r); yoff = y-(0.20*r); roff = 0.30*r; x = Math.floor(x+0.5); y = Math.floor(y+0.5); r = Math.floor(r+0.5); xoff = Math.floor(xoff+0.5); yoff = Math.floor(yoff+0.5); AtomColor = ctx.createRadialGradient(xoff, yoff, roff, x, y, r); alpha = 0.33; if (hilite > 0) alpha = 1.0; istart = element(A,"color").indexOf("(") + 1; ilength = element(A,"color").indexOf(")") - istart; colorstr = element(A,"color").substr(istart,ilength); myrgb = colorstr.replace(/,/g," ").split(' '); hcolor = "rgba("+myrgb[0]+","+myrgb[1]+","+myrgb[2]+","+alpha+")"; istart = element(A,"gradient").indexOf("(") + 1; ilength = element(A,"gradient").indexOf(")") - istart; colorstr = element(A,"gradient").substr(istart,ilength); myrgb = colorstr.replace(/,/g," ").split(' '); gcolor = "rgba("+myrgb[0]+","+myrgb[1]+","+myrgb[2]+","+alpha+")"; AtomColor.addColorStop(0, hcolor); AtomColor.addColorStop(1, gcolor); // Plot atom as a gradient shaded circle ctx.beginPath(); ctx.arc(x, y, r, 0, 2*Math.PI, false); ctx.fillStyle = AtomColor; ctx.fill(); ctx.lineWidth = 0.01; ctx.strokeStyle = "black"; ctx.stroke(); ctx.closePath(); // Draw label if highlighted atom if (hilite > 0) atomLabel(ctx,A,atomNum,x,y); } /// /// Routine to draw a single highlighted bond /// function HighlightBond(ctx, atom1, atom2, highlite, AtomSize, centerx, centery) { // Define local variables var i, j, k; var x1, y1, z1, x2, y2, z2; var dx, dy, dz; var xoff, yoff; var dist, r; var AtomScale = molecule[0].AtomScale; var BondWidth = Math.floor(0.10*AtomScale + 0.5); var BondColor = "rgba(200,128,51,1.0)"; var bcolor = "rgba(191,191,191,0.33)"; var molecule = Mol(); var activeCanvas = activeWin(""); // Get parameters for atoms r = AtomScale * AtomSize * element(molecule[atom1].atomicnumber,"radius"); x1 = AtomScale*molecule[atom1].x + centerx; y1 = AtomScale*molecule[atom1].y + centery; z1 = AtomScale*molecule[atom1].z; x2 = AtomScale*molecule[atom2].x + centerx; y2 = AtomScale*molecule[atom2].y + centery; z2 = AtomScale*molecule[atom2].z; // Calculate intersection of bond with sphere dx = x2 - x1; dy = y2 - y1; dz = z2 - z1; dist = Math.sqrt(dx*dx + dy*dy + dz*dz); xoff = x1 + r*dx/dist; yoff = y1 + r*dy/dist; // Draw bond ctx.beginPath(); ctx.moveTo(xoff, yoff); ctx.lineTo(x2, y2); ctx.lineWidth = BondWidth + 2; ctx.strokeStyle = "rgba(0,0,0,0.33)"; if ( highlite > 0 ) ctx.strokeStyle = "rgba(0,0,0,1.0)"; ctx.stroke(); ctx.moveTo(xoff, yoff); ctx.lineTo(x2, y2); ctx.lineWidth = BondWidth; if ( highlite > 0 ) { ctx.strokeStyle = BondColor; } else { ctx.strokeStyle = bcolor; } ctx.stroke(); ctx.closePath(); } // -------------------- mouse.js file -------------------- /// /// Routine to save number of atom selected with mouseDown event /// option = "Set" or "Show" /// value = Number of selected atom /// 0 = MouseDown, but not on atom /// -1 = Mouse not down /// function mouseState(option, value) { // Initialize parameters as necessary if ( typeof mouseState.DownAtom == 'undefined' ) mouseState.DownAtom = -1; // Show number of atom selected by mouseDown if ( option == "Show" ) return mouseState.DownAtom; if ( option == "Set" ) mouseState.DownAtom = value; // End of mouseState routine } //# function parameters() //# //# Define constants used to control drawing. //# Get/set values using: //# var param = parameters(); //# //# param.mode = Interface mode. Set to "Draw" or "View" //# param.element = Type of element to add next. Default = "C" //# param.clouds = # of hybrid orbitals. Default = 4 //# param.bondmode = Bond mode. Set to "Add", "Delete", or "Rotate" //# param.atommode = Add atom mode. Set to "Add" or "Delete" //# function parameters() { // Initialize parameter array if necessary if ( typeof parameters.values === "undefined" ) parameters.values = new paramObject(); // Define default values for parameters if ( typeof parameters.values.mode == 'undefined' ) parameters.values.mode = "View"; if ( typeof parameters.values.elem == 'undefined' ) parameters.values.elem = "C"; if ( typeof parameters.values.clouds == 'undefined' ) parameters.values.clouds = 4; if ( typeof parameters.values.add == 'undefined' ) parameters.values.add = "Add"; if ( typeof parameters.values.bond == 'undefined' ) parameters.values.bond = "Add"; // End of parameters routine return parameters.values; } /// /// Define structure for drawing parameters /// function paramObject() { this.mode = "View"; this.element = "C"; this.clouds = 4; this.bondmode = "Add"; this.atommode = "Add"; } /// /// Routine to handle mouse press /// function MouseDown(evt) { // Declare local variables var cx, cy; var windowName = evt.target.id; var activecanvas = activeWin(windowName); var canvas = document.getElementById(activecanvas); var width = canvas.width; var height = canvas.height; // Map touch screen and mouse buttons cx = evt.pageX; cy = evt.pageY; // If touch screen if (evt.targetTouches) { if (evt.targetTouches.length == 1) { cx = evt.targetTouches[0].pageX; cy = evt.targetTouches[0].pageY; } } // Save selected atom mouseState( "Set", onAtom(cx, cy, canvas, width, height) ); } /// /// Routine to handle mouse up /// function MouseUp(evt) { // Declare local variables var cx, cy; var mouseOnAtom, UpAtom; var activecanvas = activeWin(""); var molecule = Mol(); var canvas = document.getElementById(activecanvas); var width = canvas.width; var height = canvas.height; var param = parameters(); // Map touch screen and mouse buttons cx = evt.pageX; cy = evt.pageY; // If touch screen if (evt.targetTouches) { cx = evt.targetTouches[0].pageX; cy = evt.targetTouches[0].pageY; } // See which atom (if any) mouse is currently on mouseOnAtom = mouseState("Show"); mouseState("Set", -1); Upatom = onAtom(cx, cy, canvas, width, height); // If 'click' moves to blank space, exit if ( Upatom == 0 ) { viewGeom(0); return; } // If 'click' stays on a same atom, proceed if ( Upatom == mouseOnAtom ) { // Show geometry information if (param.mode == "View") { if ( evt.shiftKey > 0) { molecule[Upatom].highlite = ( (molecule[Upatom].highlite+1) % 2); drawMolecule(); } else { viewGeom(mouseOnAtom); } } // Add or Remove atom(s) if (param.mode == "Draw") { // Save Molecular information Undo("save"); molecule[0].charge = 999; if (param.atommode == "Delete") { delAtom(Upatom); } else { newAtom(Upatom); } } } // If 'click' moves to a different atom, draw or remove bond if ( (Upatom != mouseOnAtom) && (param.mode == "Draw") ) { // Save Molecular information Undo("save"); if (param.bondmode == "Add") { molecule[0].charge = 999; addBond(mouseOnAtom,Upatom); } if (param.bondmode == "Delete") { molecule[0].charge = 999; delBond(mouseOnAtom,Upatom); } if (param.bondmode == "Rotate") { BondRotation("Set",mouseOnAtom,Upatom); } drawMolecule(); } // Finished with MouseUp routine } /// /// Is mouse within radius of atom? /// Parameters - mouse coordinates /// Return - number of atom or zero if none /// function onAtom(mx, my, canvas, width, height) { // Declare local variables var i, A, dx, dy; var radius, delta; var AtomSize = 0.50; var molecule = Mol(); // Convert mouse position to atomic coordinate system mx = (mx - canvas.offsetLeft - width/2); my = (my - canvas.offsetTop - height/2); // Loop over all atoms, looking for first match for (i=1; i <= molecule[0].numatoms; i++) { A = molecule[i].atomicnumber; radius = molecule[0].AtomScale*AtomSize*element(A,"radius"); radius = radius*radius; dx = molecule[0].AtomScale*molecule[i].x - mx; dy = molecule[0].AtomScale*molecule[i].y - my; delta = dx*dx + dy*dy; if (delta <= radius) { return i; } } return 0; } /// /// Routine to deal with scroll wheel /// function MouseWheel(evt) { // Local variable var molecule = Mol(); // Stop window scrolling if (evt.preventDefault) evt.preventDefault(); // Firefox and Opera use detail, Chrome uses wheelDelta(?) var delta = evt.detail ? evt.detail*(-1) : evt.wheelDelta; var newScale = (delta > 0) ? 1.1 : 0.9; molecule[0].AtomScale = molecule[0].AtomScale*newScale; drawMolecule(); return false; } /// /// Alter molecule IFF mouse is pressed /// function MouseMove(evt) { var newx, newy; var dx, dy, tx, ty, da; var x, y, z; var xc, yc; var cosx, cosy, cosz, sinx, siny, sinz; var cosA, sinA; var step=2; // Smaller values make less sensitive var molecule = Mol(); var param = parameters(); // Save old (x,y) coordinates if ( typeof MouseMove.cx == 'undefined' ) MouseMove.cx = 250; if ( typeof MouseMove.cy == 'undefined' ) MouseMove.cy = 250; // Only rotate if mouse pressed, but not on an atom if ( mouseState("Show") == 0 ) { // Map touch screen and mouse buttons newx = evt.pageX; newy = evt.pageY; // If touch screen if (evt.targetTouches) { if (evt.targetTouches.length == 1) { newx = evt.targetTouches[0].pageX; newy = evt.targetTouches[0].pageY; } } // Record movement dx = (MouseMove.cx - newx); dy = (MouseMove.cy - newy); MouseMove.cx = newx; MouseMove.cy = newy; if ( Math.abs(dx)+Math.abs(dy) > 10) return; // Handle special case of rotation about a bond if ( param.bondmode == "Rotate" ) { da = dx + dy; BondRotation("Rotate",da); drawMolecule(); return; } // If key pressed, rotate around z-axis if ( evt.shiftKey > 0) { cosz = Math.cos(dx*step*Math.PI/180); sinz = Math.sin(dx*step*Math.PI/180); for (i=1; i <= molecule[0].numatoms; i++) { x = molecule[i].x; y = molecule[i].y; molecule[i].x = cosz*x + sinz*y; molecule[i].y = -sinz*x + cosz*y; } drawMolecule(); return; } // If key pressed, translate along x- or y-axis if ( evt.ctrlKey > 0) { tx = dx*0.01; ty = dy*0.01; for (i=1; i <= molecule[0].numatoms; i++) { x = molecule[i].x; y = molecule[i].y; molecule[i].x = x - tx; molecule[i].y = y - ty; } drawMolecule(); return; } // Rotate entire molecule cosx = Math.cos(dy*step*Math.PI/180); sinx = Math.sin(dy*step*Math.PI/180); cosy = Math.cos(dx*step*Math.PI/180); siny = Math.sin(dx*step*Math.PI/180); for (i=1; i <= molecule[0].numatoms; i++) { x = molecule[i].x; y = molecule[i].y; z = molecule[i].z; molecule[i].x = cosy*x + siny*z; molecule[i].y = -sinx*siny*x + cosx*y + sinx*cosy*z; molecule[i].z = -cosx*siny*x - sinx*y + cosx*cosy*z; } drawMolecule(); } } /// /// VIEW MODE: Routine to display geometry information to user /// function viewGeom(OnAtom) { // Declare local variables var i, A1, A2, A3, A4; var dx, dy, dz, d; var dux, duy, duz, dvx, dvy, dvz, du, dv; var label; var activecanvas = activeWin(""); var canvas = document.getElementById(activecanvas); var ctx = canvas.getContext('2d'); var width = canvas.width; var height = canvas.height; var molecule = Mol(); // Initialize geom array if necessary if ( typeof viewGeom.geom == 'undefined' ) { viewGeom.geom = [0,0,0,0,0]; } // If valid atom not sent, zero array if (OnAtom == 0) { for (i=0; i < 5; i++) viewGeom.geom[i] = 0; drawMolecule(); return; } // If duplicate atom sent, zero array and return if (OnAtom) { for (i=1; i < 5; i++) { if (viewGeom.geom[i] == OnAtom) viewGeom(0); } } // Display appropriate information to user viewGeom.geom[0] = viewGeom.geom[0] + 1; sw = viewGeom.geom[0]; viewGeom.geom[sw] = OnAtom; //InfoWin("\nMouse on atom #"+OnAtom+" Switch = "+sw); switch (sw) { case 1: A1 = molecule[viewGeom.geom[1]].atomicnumber; label = element(A1,"symbol") + viewGeom.geom[1].toString(); if ( molecule[0].showcharges != 0 ) { label += ": Charge = "; if ( molecule[viewGeom.geom[1]].charge > 0 ) label += "+"; label += molecule[viewGeom.geom[1]].charge.toFixed(2); } drawMolecule(); geomLabel(ctx,label,width); break; case 2: // Bond distance dx = molecule[viewGeom.geom[1]].x - molecule[viewGeom.geom[2]].x; dy = molecule[viewGeom.geom[1]].y - molecule[viewGeom.geom[2]].y; dz = molecule[viewGeom.geom[1]].z - molecule[viewGeom.geom[2]].z; d = Math.sqrt(dx*dx+dy*dy+dz*dz); d = d.toFixed(3); d = d.toString(); A1 = molecule[viewGeom.geom[1]].atomicnumber; A2 = molecule[viewGeom.geom[2]].atomicnumber; label = element(A1,"symbol") + viewGeom.geom[1].toString() + "--"; label += element(A2,"symbol") + viewGeom.geom[2].toString(); label += " = " + d; drawMolecule(); geomLabel(ctx,label,width); break; case 3: // Bond angle A1 = molecule[viewGeom.geom[1]].atomicnumber; A2 = molecule[viewGeom.geom[2]].atomicnumber; A3 = molecule[viewGeom.geom[3]].atomicnumber; label = element(A1,"symbol") + viewGeom.geom[1].toString() + "--"; label += element(A2,"symbol") + viewGeom.geom[2].toString() + "--"; label += element(A3,"symbol") + viewGeom.geom[3].toString(); ang = angle(molecule,viewGeom.geom[1],viewGeom.geom[2],viewGeom.geom[3]); ang = ang.toFixed(1); ang = ang.toString(); label += " = " + ang + "ᵒ"; drawMolecule(); geomLabel(ctx,label,width); break; case 4: // Dihedral angle A1 = molecule[viewGeom.geom[1]].atomicnumber; A2 = molecule[viewGeom.geom[2]].atomicnumber; A3 = molecule[viewGeom.geom[3]].atomicnumber; A4 = molecule[viewGeom.geom[4]].atomicnumber; label = element(A1,"symbol") + viewGeom.geom[1].toString() + "--"; label += element(A2,"symbol") + viewGeom.geom[2].toString() + "--"; label += element(A3,"symbol") + viewGeom.geom[3].toString() + "--"; label += element(A4,"symbol") + viewGeom.geom[4].toString(); ang = dihedral(molecule,viewGeom.geom[1],viewGeom.geom[2],viewGeom.geom[3],viewGeom.geom[4]); ang = ang.toFixed(1); ang = ang.toString(); label += " = " + ang; drawMolecule(); geomLabel(ctx,label,width); for (i=0; i < 5; i++) viewGeom.geom[i] = 0; break; } } /// /// VIEW MODE: /// Helper routine to show geometry information /// Parameters - mouse coordinates /// function geomLabel(ctx,label,width) { ctx.lineWidth = 1.0; ctx.textAlign = "right"; ctx.textBaseline = "top"; ctx.font = "normal 18px sans-serif"; ctx.fillStyle = "#000000"; ctx.beginPath(); ctx.fillText(label,width-5,5); ctx.closePath(); } /// /// Routine to select current element for drawing /// function pickElem(elem) { var tablesize = element(1,"max"); var i, str, mystyle; var mode; var param = parameters(); var backcolor = "silver"; var active = "lightskyblue"; // If first time routine called, set defaults if ( typeof pickElem.metals == 'undefined' ) { pickElem.metals = "none"; pickElem.myfont = "14px"; if (document.getElementById('pchooser') ) document.getElementById('pchooser').innerHTML = "Metals"; } // Change display of periodic table if (elem == "PView") { if (document.getElementById('pchooser') ) { if ( document.getElementById('pchooser').innerHTML == "Metals" ) { pickElem.metals = "table-cell"; pickElem.myfont = "10px"; document.getElementById('pchooser').innerHTML = "Organic"; } else { pickElem.metals = "none"; pickElem.myfont = "14px"; document.getElementById('pchooser').innerHTML = "Metals"; } } } // Turn off display for metals // if (elem == "MOff") { // pickElem.metals = "none"; // pickElem.myfont = "14px"; // if (document.getElementById('MOn') ) // document.getElementById('MOn').style.color = "navy"; // if (document.getElementById('MOff') ) // document.getElementById('MOff').style.color = "antiquewhite"; // if (document.getElementById('pchooser') ) // document.getElementById('pchooser').innerHTML = "Metals"; // } // Turn on display for metals // if (elem == "MOn") { // pickElem.metals = "table-cell"; // pickElem.myfont = "10px"; // if (document.getElementById('pchooser') ) // document.getElementById('pchooser').innerHTML = "Organic"; // } // Set display options depending on selected view if (document.getElementById('Row1') ) document.getElementById('Row1').style.display = pickElem.metals; if (document.getElementById('Row2') ) document.getElementById('Row2').style.display = pickElem.metals; if (document.getElementById('Row3') ) document.getElementById('Row3').style.display = pickElem.metals; if (document.getElementById('RowLa') ) document.getElementById('RowLa').style.display = pickElem.metals; if (document.getElementById('RowAc') ) document.getElementById('RowAc').style.display = pickElem.metals; if (document.getElementById('RowLa2') ) document.getElementById('RowLa2').style.display = pickElem.metals; if (document.getElementById('RowAc2') ) document.getElementById('RowAc2').style.display = pickElem.metals; // if (document.getElementById('Mon') ) // document.getElementById('MOn').style.fontSize = pickElem.myfont; // if (document.getElementById('Moff') ) // document.getElementById('MOff').style.fontSize = pickElem.myfont; // Loop over all elements in table for (i=1; i 0) { found = 0; if ( atm == atom1 ) found = 1; for (j=1; j <= RList[0]; j++) { if ( atm == RList[j] ) { found = 1; j = RList[0] + 1; } } if (found == 0) { RList[0]++; RList[RList[0]] = atm; rotlist(RList, atom2, atm); } } } // End of rotlist routine return RList; } // -------------------- End of mouse.js file -------------------- // // -------------------- charges.js -------------------- // //# function setCharge() //# //# Routine to set the molecular charge using value of select form with id="SelectCharge". //# function setCharge() { var molecule = Mol(); var ChargeForm = document.getElementById("SelectCharge"); if ( ChargeForm ) { molecule[0].charge = ChargeForm.value * 1; } // End of setCharge routine } //# function simpleQ() //# //# Public routine to (somewhat arbitrarily) assign electron configuration, //# including bond orders, and calculate the charges on each atom. //# function simpleQ() { // Define local variables var i, j; var BondMtx = []; var BondWin = document.getElementById("bondMatrix"); var molecule = Mol(); var numatoms=molecule[0].numatoms; // If no atoms defined, exit if ( numatoms < 1 ) { InfoWin("Cannot set charges. No atoms found.\n",1); return; } // Toggle charge button if ( molecule[0].showcharges != 0 ) { buttonColor("ChargeButton",0); molecule[0].showcharges = 0; if ( document.getElementById("SelectCharge") ) { document.getElementById("SelectCharge").value = 0; } drawMolecule(); return; } // Change color of charge button buttonColor("ChargeButton",1); molecule[0].showcharges = 1; // Clear information and bond windows InfoWin("",1); if ( BondWin ) BondWin.innerHTML = ""; // Initialize Bond Matrix for (i = 0; i <= numatoms; i++) { BondMtx[i] = []; for (j = 0; j <= numatoms; j++) BondMtx[i][j] = 0.0; } // Initialize calculated atomic charges for (i=1; i <= numatoms; i++) molecule[i].charge = 0.0; // Place electrons for single bonds in BondMtx. sigmaBonds(BondMtx); // If no charge explicitly set, try to calculate "best" charge if ( molecule[0].charge == 999 ) formalcharge(); // Adjust electrons is necessary to match charge checkcharge(BondMtx); // Create list of atoms with less than octet of electrons checkOctet(BondMtx); // Then, loop over all atoms and share electrons to form pi bonds limitShare(BondMtx); formPi(BondMtx); // Look for atoms that still have less than full octet // If violations of octet rule found, try to form 'dative' bonds checkOctet(BondMtx); formDative(BondMtx); // Calculate charges atomicCharge(BondMtx); // Write bond matrix to output window if ( BondWin ) showBondMatrix(BondMtx, BondWin); // Draw molecule, showing charges drawMolecule(); // Finished with simpleQ routine return; } /// /// Calculate formal charges based on "ideal" number of bonds /// (for main group elements only). Since multiple bonds may /// not yet be known, negative formal charges limited to -1. /// function formalcharge() { // Declare local variables var i, num; var octet, qbonds; var formalpos, formalneg; var molecule = Mol(); var numatoms = molecule[0].numatoms; var bonds = BondMatrix(); // Calculate formal charges based on number of bonds formalpos = 0.0; formalneg = 0.0; for (i=1; i <= numatoms; i++) { octet = 0; if (element(molecule[i].atomicnumber,"block") == "s") octet = 2; if (element(molecule[i].atomicnumber,"block") == "p") octet = 8; if ( octet > 0 ) { qbonds = bonds[i][0] + element(molecule[i].atomicnumber,"valence") - octet; if ( qbonds < 0 ) formalneg += qbonds; if ( qbonds > 0 ) formalpos += qbonds; } } // Since multiple bonds not yet known, "scale down" negative charges while ( formalneg <= -2 ) formalneg += 2; // Store formal charge prediction of molecular charge molecule[0].charge = formalpos + formalneg; // End formalcharge routine return; } /// /// Look for mismatch between molecular charge and the calculated charge /// based on the electron assignment. If difference found, try to /// add/remove appropriate number of electrons to fix. /// function checkcharge(BondMtx) { // Declare local variables var i, j, num; var totalq; var deltaq, electrons; var molecule = Mol(); var numatoms = molecule[0].numatoms; var block, numetals; var eerror; var bonds = BondMatrix(); var AlmostZero = 0.00001; // Count electrons to determine current charge totalq = 0; for (i=1; i <= numatoms; i++) { totalq += element(molecule[i].atomicnumber,"valence"); for (j=i; j <= numatoms; j++) { totalq -= BondMtx[i][j]; } } // If values don't match, try to add/remove electrons. deltaq = totalq - molecule[0].charge; if ( Math.abs(deltaq) < AlmostZero ) { return; } // If too many electrons present, remove from lone pairs if ( deltaq < -AlmostZero ) { // Remove electrons from metals first numetals = 0; for (i=1; i <= molecule[0].numatoms; i++) { block = element(molecule[i].atomicnumber,"block"); if ( (block == "d") || (block == "f") ) { numetals++; } } if ( numetals > 0 ) { electrons = -deltaq / numetals; for (i=1; i <= molecule[0].numatoms; i++) { block = element(molecule[i].atomicnumber,"block"); if ( (block == "d") || (block == "f") ) { BondMtx[i][i] -= electrons; } } } else { // No metals present, so remove from lone pairs num = 0; for (i=1; i <= molecule[0].numatoms; i++) { if ( BondMtx[i][i] > 0 ) num++; } eerror = -deltaq; if ( num > 0 ) { eerror = 0; electrons = -deltaq / num; for (i=1; i <= molecule[0].numatoms; i++) { if ( BondMtx[i][i] > 0 ) { BondMtx[i][i] -= electrons; if ( BondMtx[i][i] < 0 ) { eerror -= BondMtx[i][i]; BondMtx[i][i] = 0.0; } } } } // Solve (rare) case where couldn't remove enough e- from one or more atoms if ( eerror > 0 ) { num = 0; for (i=1; i <= molecule[0].numatoms; i++) { if ( BondMtx[i][i] > 0 ) num++; } if ( num > 0 ) { electrons = eerror / num; for (i=1; i <= molecule[0].numatoms; i++) { if ( BondMtx[i][i] > 0 ) { BondMtx[i][i] -= electrons; } } } } } } // If not enough electrons present, add to atoms short of full octet if ( deltaq > AlmostZero ) { // Create list of atoms that with less than octet of electrons checkOctet(BondMtx); // Count number of atoms short of full octet num = 0; for (i=1; i <= molecule[0].numatoms; i++) { if ( BondMtx[i][0] > 0.0 ) num++; } // If atoms found that need electrons, add them eerror = deltaq; if ( num > 0 ) { eerror = 0; electrons = deltaq/num; for ( i=1; i <= molecule[0].numatoms; i++ ) { if ( BondMtx[i][0] > 0.0 ) { if ( electrons <= BondMtx[i][0]) { BondMtx[i][i] += electrons; } else { BondMtx[i][i] += BondMtx[i][0]; eerror += electrons - BondMtx[i][0]; BondMtx[i][0] = 0; } } } // Try again if one or more atoms couldn't accept enough e- if ( eerror > 0 ) { num = 0; for (i=1; i <= molecule[0].numatoms; i++) { if ( BondMtx[i][0] > 0.0 ) num++; } if ( num > 0 ) { electrons = eerror/num; eerror = 0; for ( i=1; i <= molecule[0].numatoms; i++ ) { if ( BondMtx[i][0] > 0.0 ) { if ( electrons <= BondMtx[i][0]) { BondMtx[i][i] += electrons; } else { BondMtx[i][i] += BondMtx[i][0]; eerror += electrons - BondMtx[i][0]; BondMtx[i][0] = 0; } } } } } } // If all else fails, add electrons to atoms that can violate octet rule if ( eerror > 0 ) { num = 0; for (i=1; i <= molecule[0].numatoms; i++) { if ( molecule[i].atomicnumber > 12 ) num++; } if ( num > 0 ) { electrons = eerror/num; for (i=1; i <= molecule[0].numatoms; i++) { if ( molecule[i].atomicnumber > 12 ) BondMtx[i][i] += electrons; } } } } // Electron adjustment complete. Check to see if charges match now. // Count electrons to determine current charge totalq = 0; for (i=1; i <= numatoms; i++) { totalq += element(molecule[i].atomicnumber,"valence"); for (j=i; j <= numatoms; j++) { totalq -= BondMtx[i][j]; } } deltaq = totalq - molecule[0].charge; if ( Math.abs(deltaq) > AlmostZero ) { InfoWin("ERROR: Unable to assign electrons to balance charge.\n",1); InfoWin(" Assigned charge = "+molecule[0].charge+"\n"); InfoWin("Charge based on e- = "+totalq+"\n\n"); } // End checkcharge routine return; } /// /// Place valence electrons for single bonds in BondMtx. /// Remaining electrons initially assumed to be lone pairs. /// function sigmaBonds(BondMtx) { // Declare local variables var i, j; var lone; var molecule = Mol(); var numatoms=molecule[0].numatoms; var bonds = BondMatrix(); // Place electrons in bonds for (i=1; i < numatoms; i++) { // Bonds assumed to be single bonds for (j=i+1; j <= numatoms; j++) { if (bonds[i][j] > 0) { BondMtx[i][j] = 2.0; BondMtx[j][i] = 2.0; } } } // Place remaining electrons in lone pairs for (i=1; i <= numatoms; i++) { lone = element(molecule[i].atomicnumber,"valence") - bonds[i][0]; // First-row main-group elements cannot have more than 8 electrons if ( (molecule[i].atomicnumber<11) && (bonds[i][0] > 3) ) lone = 0; if (lone > 0) BondMtx[i][i] = lone; } // Finished with sigmaBonds routine return BondMtx; } /// /// Check if all main group atoms obey octet rule or not. /// # of missing electrons stored in BondMtx[i][0] /// function checkOctet(BondMtx) { // Declare local variables var i, j, octet; var molecule = Mol(); var numatoms=molecule[0].numatoms; // Find/store # of missing electrons for ( i=1; i <= numatoms; i++ ) { octet = 0; BondMtx[i][0] = 0.0; if (element(molecule[i].atomicnumber,"block") == "p") { octet = 8; for ( j=1; j <= numatoms; j++) { octet -= BondMtx[i][j]; } } if ( octet > 0 ) BondMtx[i][0] = octet; } // Finished with checkOctet routine return BondMtx; } /// /// Limit number of electrons any one atom can share /// to form pi bonds. /// function limitShare(BondMtx) { // Declare local variables var i, j, nb; var molecule = Mol(); var numatoms=molecule[0].numatoms; var bonds = BondMatrix(); for ( i=1; i <= numatoms; i++ ) { if ( BondMtx[i][0] > 0 ) { nb = 0; for ( j=1; j <= numatoms; j++ ) { if ( (bonds[i][j] > 0) && (BondMtx[j][0] > 0) ) { nb++; } } (nb > 0) ? BondMtx[i][0] = BondMtx[i][0]/nb : BondMtx[i][0] = 0; } } // Finished with limitShare routine return BondMtx; } /// /// Loop over all atoms and share electrons to form pi bonds /// function formPi(BondMtx) { // Declare local variables var i, j, nb; var electrons; var molecule = Mol(); var numatoms=molecule[0].numatoms; var bonds = BondMatrix(); for ( i=1; i < numatoms; i++ ) { if ( BondMtx[i][0] > 0.0 ) { for (j=i+1; j <= numatoms; j++) { if (bonds[i][j] > 0) { electrons = Math.min(BondMtx[i][0],BondMtx[j][0]); if ( electrons > 0.0 ) { BondMtx[i][j] += 2.0*electrons; BondMtx[j][i] += 2.0*electrons; BondMtx[i][i] -= electrons; BondMtx[j][j] -= electrons; } } } } } // Simple error checking for (i=1; i <= numatoms; i++) { if ( BondMtx[i][i] < 0.0 ) { InfoWin("ERROR in formPi: Atom "+i+" has "+BondMtx[i][i].toFixed(3)+" lone pairs.\n"); BondMtx[i][i] = 0.0; } } // Finished with formPi routine return BondMtx; } /// /// Use lone pairs on one atom to form 'dative' bonds with neighbor(s) /// function formDative(BondMtx) { // Define local variables var i, j, k, nb; var dative; var easy; var donor = new Array(); var molecule = Mol(); var numatoms = molecule[0].numatoms; var bonds = BondMatrix(); // See if dative bonds necessary dative = 0; for ( i=1; i <= numatoms; i++ ) { if ( BondMtx[i][0] > 0.0 ) { dative = 1; } } if ( dative == 0 ) { return; } // Initialize donor array for ( i=1; i <= numatoms; i++ ) { donor[i] = 0.0; } // Loop over all atoms for ( i=1; i <= numatoms; i++ ) { // If atom has less than octet of electrons, look for donors if ( BondMtx[i][0] > 0.0 ) { // Count potential donors (atoms with lone pairs) nb = 0; for (j = 1; j <= numatoms; j++) { if ( bonds[i][j] > 0 ) if ( BondMtx[j][j] > 0 ) nb++; } // Request equal number of electrons from all neighbors if ( nb > 0 ) { BondMtx[i][0] = BondMtx[i][0]/nb; for (j = 1; j <= numatoms; j++) { if ( bonds[i][j] > 0 ) { if ( BondMtx[j][j] > 0 ) donor[j] += BondMtx[i][0]; } } } } } // Verify enough electrons available to form all requested dative bonds easy = 1; for ( i=1; i <= numatoms; i++ ) { if ( donor[i] > BondMtx[i][i] ) easy = 0; } // If 'easy' solution exists, use it if ( easy > 0 ) { for ( i=1; i <= numatoms; i++ ) { if ( BondMtx[i][0] > 0.0 ) { for ( j = 1; j <= numatoms; j++) { if ( bonds[i][j] > 0 ) { if ( donor[j] > 0 ) { BondMtx[i][j] += BondMtx[i][0]; BondMtx[j][i] += BondMtx[i][0]; BondMtx[j][j] -= BondMtx[i][0]; } } } } } } // Finished with formDative routine return BondMtx; } /// /// Calculate charges on all atoms /// function atomicCharge(BondMtx) { // Declare parameters var ALPHA = 0.5; // Fraction of charge to mix with EN var MIX = 0.5; // Reduce effects of formal charges (1=no reduction) var MAXSTEP = 15; var CONVERGED = 0.001; // Declare local variables var i, j, loop; var Z, mixfactor; var q, delta, dmax; var molcharge = 0.0; var atomEN = new Array(); var molecule = Mol(); var numatoms=molecule[0].numatoms; var bonds = BondMatrix(); // Calculate charge on molecule for (i=1; i <= numatoms; i++) { molcharge += element(molecule[i].atomicnumber,"valence"); for (j=1; j <= numatoms; j++) { if ( i == j ) { molcharge -= BondMtx[i][i]; } else { molcharge -= 0.5*BondMtx[i][j]; } } } delta = Math.abs(molcharge - molecule[0].charge); if ( delta > 0.001 ) alert("Error: Electron assignment does NOT match molecular charge."); // InfoWin("Molecular charge = "+molcharge.toFixed(2)+"\n"); // Initialize electronegativity array and set mixing factor mixfactor = MIX; // If molecule has a charge, use 100% formal charge method if ( Math.abs(molcharge) > 0.001 ) mixfactor = 1.0; for ( i=1; i <= numatoms; i++ ) { Z = molecule[i].atomicnumber; if ( (element(Z,"block")=="d") || (element(Z,"block")=="f") ) mixfactor = 0.0; q = element(Z,"EN") || 0; if ( q == 0 ) { q = 1.0; InfoWin("WARNING: No electronegativity defined for "); InfoWin(element(molecule[i].atomicnumber,"symbol")+"\n"); } atomEN[i] = q; } // Inform user of method used to calculate charges if (mixfactor==1.0) InfoWin("Using 100% formal charge method to calculate charges.\n"); if (mixfactor==0.0) InfoWin("Using 100% bond polarity method to calculate charges.\n"); if (mixfactor==MIX) InfoWin("Using mixture of formal charge and bond polarity method to calculate charges.\n"); // Perform iterations until charges remain constant loop = 0; dmax = 100.0; while ( (loopCONVERGED) ) { loop++; // Calculate charges for each atom for ( i=1; i <= numatoms; i++ ) { Z = molecule[i].atomicnumber; q = mixfactor * (element(Z,"valence") - BondMtx[i][i]); for ( j = 1; j <= numatoms; j++) { if ( bonds[i][j] > 0 ) { q += (1.0-mixfactor) * 0.5 * BondMtx[i][j]; q -= BondMtx[i][j]*atomEN[i]/(atomEN[i]+atomEN[j]); } } molecule[i].charge = q; } // Calculate new electronegativity values for each atom dmax = 0.0; for ( i=1; i <= numatoms; i++ ) { q = atomEN[i]; atomEN[i] = element(molecule[i].atomicnumber,"EN") || 1.0; atomEN[i] += ALPHA*molecule[i].charge; delta = Math.abs(q - atomEN[i]); if ( delta > dmax ) dmax = delta; } } // Finished with atomicCharge routine return BondMtx; } /// /// Calculate molecular dipole /// Assumes point charges on nuclear centers, with charge /// vector originating from origin. /// function dipoleMoment() { // Declare local variables var i; var dx, dy, dz, dipole; var DEBYE = 4.8032; var molecule = Mol(); var numatoms=molecule[0].numatoms; // Calculate x,y,z components of dipole vector dx = 0.0; dy = 0.0; dz = 0.0; for ( i=1; i <= numatoms; i++ ) { dx += molecule[i].x * molecule[i].charge; dy += molecule[i].y * molecule[i].charge; dz += molecule[i].z * molecule[i].charge; } // Calculate length of dipole vector and scale to Debye units dipole = DEBYE * Math.sqrt(dx*dx+dy*dy+dz*dz); // Finished with dipoleMoment routine return dipole; } //# function showBondMatrix(BondMtx,BondWin) //# //# Write Bond information to output window. //# function showBondMatrix(BondMtx,BondWin) { // Define local variables var i, j; var numstr, plus; var dq, dipole; var qsign = ""; var symbol; var molcharge; var bondtable = new Array(); var entry = new Array(); var molecule = Mol(); var numatoms=molecule[0].numatoms; // Calculate molecular charge molcharge = 0; for (i=1; i <= numatoms; i++) molcharge += molecule[i].charge; // Show Charge and Dipole moment dipole = dipoleMoment(); BondWin.innerHTML = "

Molecular charge = "+molcharge.toFixed(1)+ ", Dipole ≈ "+dipole.toFixed(1)+" D"; // Write Bond matrix to Information Window //--- Header --- InfoWin("Bond Matrix: Off-diagonal = e- in bonds, diagonal = unshared e-\n"); InfoWin(" "); for (i=1; i <= numatoms; i++) { symbol = element(molecule[i].atomicnumber,"symbol"); if (symbol.length < 2) symbol += " "; InfoWin(" "+symbol+" "); if ( (i%5) == 0 ) InfoWin(" "); } InfoWin("\n"); //--- One row for each atom --- for (i=1; i <= numatoms; i++) { symbol = element(molecule[i].atomicnumber,"symbol"); if (symbol.length < 2) symbol += " "; if ( i < 10 ) InfoWin(" "); InfoWin(i+" "+symbol+" "); for (j=1; j <= numatoms; j++) { InfoWin(BondMtx[i][j].toFixed(1)+" "); if ( (j%5) == 0 ) InfoWin(" "); } InfoWin(" q = "); if ( molecule[i].charge > 0 ) InfoWin("+"); InfoWin(molecule[i].charge.toFixed(2)+"\n"); if ( (i%5) == 0 ) InfoWin("\n"); } // End of showBondMatrix routine return; } // -------------------- Section to handle Reading Files -------------------- /// /// Routine to get filename of local input file from user /// function MyFileReader(evt) { var validExtension; var localfile = evt.target.files[0]; // Call routine to read and process data if (localfile) { var fr = new FileReader(); fr.onload = function(fh) { validExtension = 0; var ext = extension(localfile.name); // Read contents and split data into lines var contents = fh.target.result; var lines = contents.split("\n"); if ( ext == "xyz" ) { validExtension = 1; readXYZfile(lines); } if ( ext == "mol" ) { validExtension = 1; readMOLfile(localfile,lines); } if ( ext == "inp" ) { validExtension = 1; readINPfile(localfile,lines); } if ( validExtension == 0 ) { InfoWin("*** ERROR: Invalid file type for "+localfile.name+". ***",1); return; } centerMolecule(); drawMolecule(); } fr.readAsText(localfile); } else { alert("Failed to load file"); } } /// /// Routine to determine extension for filename /// function extension(myfilename) { var extension = myfilename.substring(myfilename.lastIndexOf('.')+1); return extension.toLowerCase(); } //# //# function showgallery(title,base,List,Desc,size) //# //# Routine to display multiple files stored on the web server. //# //# Parameters: //# title: Title to display before gallery //# (If title = "delete", clear gallery) //# base: Path to directory (relative to web root) containing images //# List: Array containing a list of filenames (including extensions) //# Desc: Array containing descriptions for each file //# size: integer width (in px) for each frame //# function showgallery(title,base,List,Desc,size) { // Declare local variables var i, start, pos; var html; var frame, canvas; var framestr, canvasstr; var csize; // If title = "delete", clear gallery if ( title == "delete" ) { if ( typeof showgallery.num != "undefined" ) { showgallery.num = 0; delete showgallery.list; } return; } // If no gallery division present, exit if ( ! document.getElementById("gallery") ) { alert("Warning: showgallery called, but no

exists on html page."); return; } // Set up storage to keep track of all files to load in all galleries if ( typeof showgallery.list === "undefined" ) { showgallery.num = 0; showgallery.list = []; } start = showgallery.num; // Define base names to use for each frame and canvas canvas = "gallerycanvas"; frame = "galleryframe"; // Add files to list for display in all galleries pos = start; for (i=0; i < List.length; i++) { showgallery.list[pos] = base + List[i]; showgallery.num++; pos++; } // Set dimension for canvas csize = "width=\"" + size + "\" height=\"" + size + "\">"; // Create content and add to web page html = ""; if ( title ) { html = "

" + title + "

\n"; } pos = start; for (i=0; i < List.length; i++) { canvasstr = canvas + pos; framestr = frame + pos; html += "
"; html += ""; html += Desc[i]; html += "

\n"; pos++; } html += "

 

\n\n"; document.getElementById("gallery").innerHTML += html; // If debug window exists, write output to this window if ( document.getElementById("debug") ) { document.getElementById("debug").innerHTML += html; } // Set correct size for each box px = size + "px"; pos = start; for (i=0; i < List.length; i++) { framestr = frame + pos; if ( document.getElementById(framestr) ) document.getElementById(framestr).style.width = px; pos++; } // Updating HTML appears to erase old molecules, so load all molecules in list for (i=0; i < showgallery.num; i++) { canvasstr = canvas + i; activeWin(canvasstr); delMolecule(); readServerFile(showgallery.list[i]); if ( document.getElementById("debug") ) { html = "\n\nProcessed molecule "+i; html += " named "+showgallery.list[i]; document.getElementById("debug").innerHTML += html; } } } //# //# function galleryUniform() //# //# Routine to force all molecules that are part of a "gallery" to be displayed with the same size scale. //# function galleryUniform() { // Declare local variables var i, num, scale; var framestr; var frame = "gallerycanvas"; var molecule = []; // Find number of gallery images on page num = 0; framestr = frame + num; while ( document.getElementById(framestr) ) { num++; framestr = frame + num; } // Find scale factor for largest molecule scale = 1000; for (i=0; i < num; i++) { framestr = frame + i; activeWin(framestr); molecule = Mol(); if ( molecule[0].AtomScale < scale ) { scale = molecule[0].AtomScale; } } // Scale molecules if ( scale < 1000.0 ) { for (i=0; i < num; i++) { framestr = frame + i; activeWin(framestr); molecule = Mol(); molecule[0].AtomScale = scale; drawMolecule(); } } } //# //# function galleryReset() //# //# For molecules that are part of a "gallery", this routine optimizes the size of each molecule individually. //# function galleryReset() { // Declare local variables var i, num; var framestr; var frame = "gallerycanvas"; // Find number of gallery images on page num = 0; framestr = frame + num; while ( document.getElementById(framestr) ) { num++; framestr = frame + num; } // Reset view for each molecule for (i=0; i < num; i++) { framestr = frame + i; activeWin(framestr); centerMolecule(); drawMolecule(); } } //# //# function readServerFile(filename) //# //# Routine to read contents of file stored on the web server. //# //# Parameter: //# filename: Name (URL) of file (including path) //# function readServerFile(filename) { // Define local variables var lines; var validExtension; var fileinfo = new Array(); var ext = extension(filename); var xmlhttp; // Use XML to get contents of file from "server" xmlhttp=new XMLHttpRequest(); xmlhttp.open('GET', filename, false); xmlhttp.send(); lines = xmlhttp.responseText.split('\n'); // Call routine to read and process data validExtension = 0; if ( ext == "xyz" ) { validExtension = 1; readXYZfile(lines); } if ( ext == "mol" ) { validExtension = 1; readMOLfile(localfile,lines); } if ( ext == "inp" ) { validExtension = 1; readINPfile(localfile,lines); } if ( validExtension == 0 ) { InfoWin("*** ERROR: Invalid file type. ***",1); return; } // Update display centerMolecule(); drawMolecule(); } //# //# function InfoWin(mytext,mode) //# //# Routine to write text to information window (textarea with an id of "information"). //# //# Parameters: //# mytext: String to write to output window //# mode: If >0, then clear text window //# function InfoWin(mytext,mode) { var outstring = mytext || ""; var clearwin = mode || 0; if ( ! document.getElementById("information") ) return; if ( clearwin > 0 ) document.getElementById("information").value = outstring; else document.getElementById("information").value += outstring; } //# function loadMolecule() //# //# Routine to load molecular information for methane molecule. //# function loadMolecule() { // Add atomic coordinates to molecule array addAtom(6, 0.000, 0.000, 0.000); addAtom(1, 0.874, 0.618, 0.000); addAtom(1, -0.874, 0.618, 0.000); addAtom(1, 0.000, -0.618, 0.874); addAtom(1, 0.000, -0.618, -0.874); // Add bonds to bond array addBond(1, 2); addBond(1, 3); addBond(1, 4); addBond(1, 5); } //# function resetView() //# //# Routine to reset view. Center, rescale, and remove highlights. //# function resetView() { // Define local variables var i; var molecule = Mol(); // Remove highlights and show all atoms for ( i=1; i <= molecule[0].numatoms; i++ ) { molecule[i].highlite = 0; molecule[i].hide = 0; } // Clear Information Window InfoWin("",1); // Formula, center, scale, and draw formula(); centerMolecule(); drawMolecule(); } //# function buttonColor(button, mode) //# //# Set color of buttons //# //# Parameters //# button - string containing ID name for button //# mode - 0=inactive, 1=active //# function buttonColor(button, mode) { mode = mode || 0; var buttoncolor = "silver"; if ( mode ) buttoncolor = "lightskyblue"; if ( document.getElementById(button) ) document.getElementById(button).style.backgroundColor = buttoncolor; } //# function initialize() //# //# Initialization Routines //# - Load properties of elements //# - Define Handlers for mouse events //# - Draw molecule //# function initialize() { // Define handler for drawing area (canvas) // activeWin defines routines to handle mouse events var activeCanvas = activeWin(); var molfile = document.getElementById('molfile'); // If no canvas element found, see if userDefined() creates one. if ( ! activeCanvas ) { userDefined(); activeCanvas = activeWin(""); if ( ! activeCanvas ) { alert("No canvas present. Either create a canvas or remove onLoad=initialize() statement from ."); } return; } // Handler for loading files. After file selected, calls "MyFileReader" if ( molfile ) { // Verify browser supports HTML5 FileReader if (window.File && window.FileReader && window.FileList && window.Blob) { molfile.addEventListener('change', MyFileReader, false); } else { alert('The File APIs are not fully supported by your browser.'); } } // Create periodic table drawPeriodic(); // Initialize molecular geometry var molecule = Mol(); // Set display mode to View viewmode(); // Draw molecule if ( typeof molecule == 'undefined' ) delMolecule(); if (molecule[0].numatoms < 1) { delMolecule(); loadMolecule(); formula(); // Display molecular formula centerMolecule(); // Center molecule } drawMolecule(); // Set default drawing atom pickClouds(4); pickElem("C"); // Execute user-defined routine userDefined(); } // -------------------- build.js file -------------------- /// /// Routine to add/change atoms and add H /// function newAtom(OnAtom) { // Declare local variables var i, j, k, numbonds; var vx, vy, vz, vd; var Rij, Rnew; var elem, pos; var errorH; var bondlist = []; var param = parameters(); var molecule = Mol(); var bonds = BondMatrix(); var activeCanvas = activeWin(""); // Lookup information for current element atomicNumber = lookupSymbol(param.element); // Set number of bonds on selected atom numbonds = bonds[OnAtom][0]; // // If number of bonds == 0, arbitrarily add new atom along // x axis and attach the appropriate number of hydrogen atoms. // if (numbonds == 0) { Rnew = element(atomicNumber,"radius") + element(molecule[OnAtom].atomicnumber,"radius"); dx = molecule[OnAtom].x + Rnew; dy = molecule[OnAtom].y; dz = molecule[OnAtom].z; addAtom(atomicNumber, dx, dy, dz); addBond(OnAtom,molecule[0].numatoms); addH(molecule[0].numatoms); centerMolecule(); drawMolecule(activeCanvas); return; } // Create list of atoms bonded to current atom pos = 0; for (i=1; i <= molecule[0].numatoms; i++) { if ( (bonds[OnAtom][i] > 0) && (i != OnAtom)) bondlist[++pos] = i; } bondlist[0] = pos; if ( bondlist[0] != bonds[OnAtom][0]) alert("ERROR: Supposed to be "+numbonds+" bonds on atom "+OnAtom+", but "+pos+" bonds found."); // If atom to add is H, add one H if (atomicNumber == 1) { vx = 0.0; vy = 0.0; vz = 0.0; for (i=1; i <= numbonds; i++) { j = bondlist[i]; dx = molecule[j].x - molecule[OnAtom].x; dy = molecule[j].y - molecule[OnAtom].y; dz = molecule[j].z - molecule[OnAtom].z; dd = Math.sqrt(dx*dx+dy*dy+dz*dz); vx += dx/dd; vy += dy/dd; vz += dz/dd; } vd = Math.sqrt(vx*vx+vy*vy+vz*vz); Rnew = element(1,"radius") + element(molecule[OnAtom].atomicnumber,"radius"); vx = molecule[OnAtom].x - vx*Rnew/vd; vy = molecule[OnAtom].y - vy*Rnew/vd; vz = molecule[OnAtom].z - vz*Rnew/vd; addAtom(1, vx, vy, vz); // Check to be sure new H atom not too close to other bonded atoms for (pos=1; pos <= numbonds; pos++) { errorH = 0; Rij = distance(molecule,bondlist[pos],molecule[0].numatoms); if ( Rij < 0.2 ) errorH = 1; } if ( (errorH) && (numbonds>1) ) { // If bonded atoms all close to a plane, place H above/below plane i = bondlist[1]; j = bondlist[2]; vx = (molecule[i].y-molecule[OnAtom].y) * (molecule[j].z-molecule[OnAtom].z); vx -= (molecule[i].z-molecule[OnAtom].z) * (molecule[j].y-molecule[OnAtom].y); vy = (molecule[i].z-molecule[OnAtom].z) * (molecule[j].x-molecule[OnAtom].x); vy -= (molecule[i].x-molecule[OnAtom].x) * (molecule[j].z-molecule[OnAtom].z); vz = (molecule[i].x-molecule[OnAtom].x) * (molecule[j].y-molecule[OnAtom].y); vz -= (molecule[i].y-molecule[OnAtom].y) * (molecule[j].x-molecule[OnAtom].x); vd = Math.sqrt(vx*vx+vy*vy+vz*vz); molecule[molecule[0].numatoms].x = molecule[OnAtom].x - vx*Rnew/vd; molecule[molecule[0].numatoms].y = molecule[OnAtom].y - vy*Rnew/vd; molecule[molecule[0].numatoms].z = molecule[OnAtom].z - vz*Rnew/vd; errorH = 0; for (pos=1; pos <= numbonds; pos++) { Rij = distance(molecule,bondlist[pos],molecule[0].numatoms); if ( Rij < 0.2 ) errorH = 1; } } if ( errorH ) { alert("Error adding H atom"); delAtom(molecule[0].numatoms); return; } // If no errors, continue addBond(OnAtom,molecule[0].numatoms); centerMolecule(); drawMolecule(activeCanvas); numbonds = 0; return; } // // If number of bonds == 1, change to new atom type, // change bond length, and add appropriate # of H. // if (numbonds == 1) { i = OnAtom; j =bondlist[1]; dx = molecule[i].x - molecule[j].x; dy = molecule[i].y - molecule[j].y; dz = molecule[i].z - molecule[j].z; Rij = Math.sqrt(dx*dx+dy*dy+dz*dz); Rnew = element(atomicNumber,"radius") + element(molecule[j].atomicnumber,"radius"); dx *= Rnew/Rij; dy *= Rnew/Rij; dz *= Rnew/Rij; molecule[i].atomicnumber = atomicNumber; molecule[i].x = dx + molecule[j].x; molecule[i].y = dy + molecule[j].y; molecule[i].z = dz + molecule[j].z; addH(OnAtom); centerMolecule(); drawMolecule(activeCanvas); } // If number of bonds > 1, then simply change atom type if (numbonds > 1) { molecule[OnAtom].atomicnumber = atomicNumber; drawMolecule(activeCanvas); } // Finished with newAtom routine } /// /// Routine to add H atoms to 'atom' /// function addH(atom) { var i, j, clouds, Z, numH; var atom1, atom2; var errmsg; var param = parameters(); var molecule = Mol(); var bonds = BondMatrix(); var activeCanvas = activeWin(""); // Only automatically add H atoms to p-block elements if ( element(molecule[atom].atomicnumber,"block") != "p" ) return; // Determine how many H atoms to add clouds = param.clouds; Z = molecule[atom].atomicnumber; valence = element(Z,"valence"); numH = 3 + clouds - valence; if (numH < 1) clouds = 1; if ( clouds <= 1 ) return; // Find first atom bonded to current atom atom1 = 0; i = 0; while ( (atom1==0) && (i < molecule[0].numatoms) ) { i++; if ( (bonds[atom][i]>0) && (i != atom) ) atom1 = i; } // Find first atom bonded to atom1 atom2 = 0; if ( atom1 ) { i = 0; while ( (atom2==0) && (i < molecule[0].numatoms) ) { i++; if ( bonds[atom1][i]>0 ) if ( (i != atom) && (i != atom1) ) atom2 = i; } } // Call appropriate routines to add hydrogen atom(s) switch (clouds) { case 2: add1H(atom,atom1); break; case 3: add2H(atom,atom1,atom2,numH); break; case 4: add3H(atom,atom1,atom2,numH); break; default: break; } // Draw molecule centerMolecule(); drawMolecule(activeCanvas); // Finished } /// /// Routine to add one H atom to sp hybridized atom /// function add1H(atom,i) { // Declare local variables var j, dx, dy, dz; var Za, Rai, RH; var Hx, Hy, Hz; var molecule = Mol(); // Calculate H--atom bond length Za = molecule[atom].atomicnumber; RH = element(Za,"radius") + element(1,"radius"); // If atom has zero bonds, add H along x-axis if (i == 0) { dx = molecule[atom].x + RH; dy = molecule[atom].y; dz = molecule[atom].z; addAtom(1, Hx, Hy, Hz); addBond(atom,molecule[0].numatoms); return; } // Calculate vector atom->i dx = molecule[i].x - molecule[atom].x; dy = molecule[i].y - molecule[atom].y; dz = molecule[i].z - molecule[atom].z; Rai = Math.sqrt(dx*dx+dy*dy+dz*dz); // Calculate position of new H Hx = molecule[atom].x - dx*RH/Rai; Hy = molecule[atom].y - dy*RH/Rai; Hz = molecule[atom].z - dz*RH/Rai; addAtom(1, Hx, Hy, Hz); addBond(atom,molecule[0].numatoms); // End add1H routine } /// /// Routine to add up to 2 H atoms to sp2 hybridized atom /// function add2H(atom,i,j,numH) { // Declare local variables var Za, Zi, Zj, RaH; var daiX, daiY, daiZ, Rai; var dijX, dijY, dijZ, Rij, ang; var dpX, dpY, dpZ, dpd; var Hx, Hy, Hz, dHx, dHy, dHz; var LX, LY, LZ, Lscale; var base; var aug = new Array(); var molecule = Mol(); // Lookup atomic numbers and calculate X-H Bond length Za = molecule[atom].atomicnumber; RaH = element(Za,"radius") + element(1,"radius"); // If atom contains zero bonds, add 2H in xy plane if (i == 0) { Hx = molecule[atom].x + 0.5*RaH; Hy = molecule[atom].y + RaH*Math.sqrt(3)/2; Hz = molecule[atom].z; addAtom(1, Hx, Hy, Hz); addBond(atom,molecule[0].numatoms); if (numH > 1) { Hy = molecule[atom].y - RaH*Math.sqrt(3)/2; addAtom(1, Hx, Hy, Hz); addBond(atom,molecule[0].numatoms); } return; } // Lookup atomic numbers for first bonded atom Zi = molecule[i].atomicnumber; daiX = molecule[i].x - molecule[atom].x; daiY = molecule[i].y - molecule[atom].y; daiZ = molecule[i].z - molecule[atom].z; Rai = Math.sqrt(daiX*daiX + daiY*daiY + daiZ*daiZ); // If atom contains only one bond, pick arbitrary atom for second point if (j == 0) { for (var ii=1; ii 1) { Hy = molecule[atom].y - RaH*Math.sqrt(3)/2; addAtom(1, Hx, Hy, Hz); addBond(atom,molecule[0].numatoms); } return; } // Lookup atomic numbers for second bonded atom Zj = molecule[j].atomicnumber; dijX = molecule[j].x - molecule[i].x; dijY = molecule[j].y - molecule[i].y; dijZ = molecule[j].z - molecule[i].z; Rij = Math.sqrt(dijX*dijX + dijY*dijY + dijZ*dijZ); // ----- Add first H ----- // Dot-product of HA*Ai aug[0] = daiX; aug[1] = daiY; aug[2] = daiZ; aug[3] = -RaH*Rai/2; // Dot-product of HA*ij ang = (-daiX*dijX-daiY*dijY-daiZ*dijZ)/(Rai*Rij); ang = Math.acos(-1/2) + Math.PI - Math.acos(ang); aug[4] = dijX; aug[5] = dijY; aug[6] = dijZ; aug[7] = RaH*Rij*Math.cos(ang); // Calculate cross product (ji x ai) dpX = dijZ*daiY - dijY*daiZ; dpY = dijX*daiZ - dijZ*daiX; dpZ = dijY*daiX - dijX*daiY; dpd = Math.sqrt(dpX*dpX+dpY*dpY+dpZ*dpZ); // Dot-product of HA * ( ji X ai ) aug[8] = dpX; aug[9] = dpY; aug[10] = dpZ; aug[11] = 0.0; // Calculate coordinates of H1 var coord = gaussElim(aug); Hx = molecule[atom].x + coord[0]; Hy = molecule[atom].y + coord[1]; Hz = molecule[atom].z + coord[2]; addAtom(1, Hx, Hy, Hz); addBond(atom,molecule[0].numatoms); // ----- Add second H ----- if (numH == 1) { return; } // Dot-product of HA*Ai aug[0] = daiX; aug[1] = daiY; aug[2] = daiZ; aug[3] = -RaH*Rai/2; // Dot-product of HA*ij ang = (-daiX*dijX-daiY*dijY-daiZ*dijZ)/(Rai*Rij); ang = Math.acos(ang) - Math.acos(0.5); aug[4] = dijX; aug[5] = dijY; aug[6] = dijZ; aug[7] = RaH*Rij*Math.cos(ang); // Dot-product of LH2* (iA x ij) aug[8] = dpX; aug[9] = dpY; aug[10] = dpZ; aug[11] = 0.0; // Calculate coordinates for H2 debug = "\nRow 1: "+aug[0].toFixed(4)+" "+aug[1].toFixed(4); debug += " "+aug[2].toFixed(4)+" "+aug[3].toFixed(4); debug += "\nRow 2: "+aug[4].toFixed(4)+" "+aug[5].toFixed(4); debug += " "+aug[6].toFixed(4)+" "+aug[7].toFixed(4); debug += "\nRow 3: "+aug[8].toFixed(4)+" "+aug[9].toFixed(4); debug += " "+aug[10].toFixed(4)+" "+aug[11].toFixed(4); coord = gaussElim(aug); Hx = molecule[atom].x + coord[0]; Hy = molecule[atom].y + coord[1]; Hz = molecule[atom].z + coord[2]; debug = "H2 at: ("+Hx.toFixed(4)+", "+Hy.toFixed(4)+", "+Hz.toFixed(4)+")"; addAtom(1, Hx, Hy, Hz); addBond(atom,molecule[0].numatoms); debug = "atom = "+atom+" i = "+i+" numatoms = "+molecule[0].numatoms; debug += "\n"+element(molecule[molecule[0].numatoms].atomicnumber,"symbol"); debug += "\nRow 1: "+aug[0].toFixed(4)+" "+aug[1].toFixed(4); debug += " "+aug[2].toFixed(4)+" "+aug[3].toFixed(4); debug += "\nRow 2: "+aug[4].toFixed(4)+" "+aug[5].toFixed(4); debug += " "+aug[6].toFixed(4)+" "+aug[7].toFixed(4); debug += "\nRow 3: "+aug[8].toFixed(4)+" "+aug[9].toFixed(4); debug += " "+aug[10].toFixed(4)+" "+aug[11].toFixed(4); debug += "\nCross: "+dpX.toFixed(4)+" "+dpY.toFixed(4)+" "+dpZ.toFixed(4); //alert(debug); // End of add2H routine } /// /// Routine to add H atoms to sp3 hybridized atom /// function add3H(atom,i,j,numH) { // Declare local variables var Za, Zi, Zj, RaH; var daiX, daiY, daiZ, Rai; var dijX, dijY, dijZ, Rij, ang; var dpX, dpY, dpZ, dpd; var Hx, Hy, Hz, dHx, dHy, dHz; var LX, LY, LZ, Lscale; var base; var aug = new Array(); var molecule = Mol(); // Lookup atomic numbers and calculate X-H Bond length Za = molecule[atom].atomicnumber; Zi = molecule[i].atomicnumber; Zj = molecule[j].atomicnumber; RaH = element(Za,"radius") + element(1,"radius"); // ----- Add first H ----- // Dot-product of HA*Ai daiX = molecule[i].x - molecule[atom].x; daiY = molecule[i].y - molecule[atom].y; daiZ = molecule[i].z - molecule[atom].z; Rai = Math.sqrt(daiX*daiX + daiY*daiY + daiZ*daiZ); aug[0] = daiX; aug[1] = daiY; aug[2] = daiZ; aug[3] = -RaH*Rai/3; // Dot-product of HA*ij dijX = molecule[j].x - molecule[i].x; dijY = molecule[j].y - molecule[i].y; dijZ = molecule[j].z - molecule[i].z; Rij = Math.sqrt(dijX*dijX + dijY*dijY + dijZ*dijZ); ang = (-daiX*dijX-daiY*dijY-daiZ*dijZ)/(Rai*Rij); ang = Math.acos(-1/3) + Math.PI - Math.acos(ang); aug[4] = dijX; aug[5] = dijY; aug[6] = dijZ; aug[7] = RaH*Rij*Math.cos(ang); // Cross-product ji X ai dpX = dijZ*daiY - dijY*daiZ; dpY = dijX*daiZ - dijZ*daiX; dpZ = dijY*daiX - dijX*daiY; dpd = Math.sqrt(dpX*dpX+dpY*dpY+dpZ*dpZ); // Handle special case where j=0 and i located at (0,0,0) if (dpd == 0) { dpX = molecule[atom].y; dpY = -molecule[atom].x; dpZ = molecule[atom].z; dpd = Math.sqrt(dpX*dpX+dpY*dpY+dpZ*dpZ); } // Dot-product of HA * ( ji X ai ) aug[8] = dpX; aug[9] = dpY; aug[10] = dpZ; aug[11] = 0.0; var coord = gaussElim(aug); Hx = molecule[atom].x + coord[0]; Hy = molecule[atom].y + coord[1]; Hz = molecule[atom].z + coord[2]; addAtom(1, Hx, Hy, Hz); addBond(atom,molecule[0].numatoms); // ----- Add second H ----- if (numH == 1) { return; } // Create point L base = molecule[0].numatoms; Lscale = RaH/(Rai*3); LX = molecule[atom].x - daiX*Lscale; LY = molecule[atom].y - daiY*Lscale; LZ = molecule[atom].z - daiZ*Lscale; // Dot-product of LH2*LH aug[0] = molecule[base].x - LX; aug[1] = molecule[base].y - LY; aug[2] = molecule[base].z - LZ; aug[3] = -RaH*RaH*4/9; // Dot-product of LH2*LA dHx = coord[0]; dHy = coord[1]; dHz = coord[2]; aug[4] = molecule[atom].x - LX; aug[5] = molecule[atom].y - LY; aug[6] = molecule[atom].z - LZ; aug[7] = 0.0; // Dot-product of LH2* (iA x ij) aug[8] = dpX; aug[9] = dpY; aug[10] = dpZ; aug[11] = RaH*dpd*Math.sqrt(2/3); // Calculate coordinates for H2 coord = gaussElim(aug); Hx = LX + coord[0]; Hy = LY + coord[1]; Hz = LZ + coord[2]; addAtom(1, Hx, Hy, Hz); addBond(atom,molecule[0].numatoms); // ----- Add third H ----- if (numH == 2) { return; } // Dot-product of LH2*LH aug[0] = molecule[base].x - LX; aug[1] = molecule[base].y - LY; aug[2] = molecule[base].z - LZ; aug[3] = -RaH*RaH*4/9; // Dot-product of LH2*LA dHx = coord[0]; dHy = coord[1]; dHz = coord[2]; aug[4] = molecule[atom].x - LX; aug[5] = molecule[atom].y - LY; aug[6] = molecule[atom].z - LZ; aug[7] = 0.0; // Dot-product of LH2* (iA x ij) dpd = Math.sqrt(dpX*dpX+dpY*dpY+dpZ*dpZ); aug[8] = dpX; aug[9] = dpY; aug[10] = dpZ; aug[11] = -RaH*dpd*Math.sqrt(2/3); debug = "atom = "+atom+" i = "+i+" numatoms = "+molecule[0].numatoms; debug += "\n"+element(molecule[molecule[0].numatoms].atomicnumber,"symbol"); debug += "\nRow 1: "+aug[0].toFixed(4)+" "+aug[1].toFixed(4); debug += " "+aug[2].toFixed(4)+" "+aug[3].toFixed(4); debug += "\nRow 2: "+aug[4].toFixed(4)+" "+aug[5].toFixed(4); debug += " "+aug[6].toFixed(4)+" "+aug[7].toFixed(4); debug += "\nRow 3: "+aug[8].toFixed(4)+" "+aug[9].toFixed(4); debug += " "+aug[10].toFixed(4)+" "+aug[11].toFixed(4); debug += "\nCross: "+dpX.toFixed(4)+" "+dpY.toFixed(4)+" "+dpZ.toFixed(4); //alert(debug); // Calculate coordinates for H3 coord = gaussElim(aug); // Hx = molecule[atom].x + coord[0]; // Hy = molecule[atom].y + coord[1]; // Hz = molecule[atom].z + coord[2]; Hx = LX + coord[0]; Hy = LY + coord[1]; Hz = LZ + coord[2]; addAtom(1, Hx, Hy, Hz); addBond(atom,molecule[0].numatoms); // End of add3H routine } /// /// Use gaussian elimination to solve for new coordinates. /// Argument is augmented matrix of the form: /// | ax ay az = ac | /// | bx by bz = bc | /// | cx cy cz = cc | /// /// Returns a matrix containing the solution (x,y,z) /// function gaussElim(aug) { // var aug = [2, -2, 0, -6, 1, -1, 1, 1, 0, 3, -2, -5]; // var aug = [1, -2, 1, 0, 2, 1, -3, 5, 4, -7, 1, -1]; var x, y, z, c; var coord = new Array(); var ax = parseFloat(aug[0]); var ay = parseFloat(aug[1]); var az = parseFloat(aug[2]); var ac = parseFloat(aug[3]); var bx = parseFloat(aug[4]); var by = parseFloat(aug[5]); var bz = parseFloat(aug[6]); var bc = parseFloat(aug[7]); var cx = parseFloat(aug[8]); var cy = parseFloat(aug[9]); var cz = parseFloat(aug[10]); var cc = parseFloat(aug[11]); //alert("| "+ax.toFixed(4)+" "+ay.toFixed(4)+" "+az.toFixed(4)+" = "+ac.toFixed(4)+" |\n"+ // "| "+bx.toFixed(4)+" "+by.toFixed(4)+" "+bz.toFixed(4)+" = "+bc.toFixed(4)+" |\n"+ // "| "+cx.toFixed(4)+" "+cy.toFixed(4)+" "+cz.toFixed(4)+" = "+cc.toFixed(4)+" |\n"); // Swap rows to place largest X variable in first row if ( (Math.abs(bx) > Math.abs(ax)) && (Math.abs(bx) > Math.abs(cx)) ) { x=ax; y=ay; z=az; c=ac; ax=bx; ay=by; az=bz; ac=bc; bx=x; by=y; bz=z; bc=c; } if ( (Math.abs(cx) > Math.abs(ax)) && (Math.abs(cx) > Math.abs(bx)) ) { x=ax; y=ay; z=az; c=ac; ax=cx; ay=cy; az=cz; ac=cc; cx=x; cy=y; cz=z; cc=c; } if ( Math.abs(cx) > Math.abs(bx) ) { x=bx; y=by; z=bz; c=bc; bx=cx; by=cy; bz=cz; bc=cc; cx=x; cy=y; cz=z; cc=c; } // Add rows to "zero-out" first column if ( (ax != 0) && (bx != 0 ) ) { factor = -ax/bx; bx = 0.0; by = by*factor + ay; bz = bz*factor + az; bc = bc*factor + ac; } if ( (ax != 0) && (cx != 0 ) ) { factor = -ax/cx; cx = 0.0; cy = cy*factor + ay; cz = cz*factor + az; cc = cc*factor + ac; } // Swap rows to place largest Y variable in second row if (Math.abs(cy) > Math.abs(by)) { y=by; z=bz; c=bc; by=cy; bz=cz; bc=cc; cy=y; cz=z; cc=c; } // Add rows to "zero-out" second column if ( (by != 0) && (cy != 0 ) ) { factor = -by/cy; cy = 0.0; cz = cz*factor + bz; cc = cc*factor + bc; } //alert("| "+ax.toFixed(4)+" "+ay.toFixed(4)+" "+az.toFixed(4)+" = "+ac.toFixed(4)+" |\n"+ // "| "+bx.toFixed(4)+" "+by.toFixed(4)+" "+bz.toFixed(4)+" = "+bc.toFixed(4)+" |\n"+ // "| "+cx.toFixed(4)+" "+cy.toFixed(4)+" "+cz.toFixed(4)+" = "+cc.toFixed(4)+" |\n"); // Solve coord[2] = 0.0; if (cz != 0) { coord[2] = cc/cz; } coord[1] = 0.0; if (by != 0) { coord[1] = (bc-(bz*coord[2]))/by; } coord[0] = 0.0; if (ax != 0) { coord[0] = (ac - (az*coord[2]) - (ay*coord[1]))/ax; } //alert("dx = "+coord[0].toFixed(4)+", dy = "+coord[1].toFixed(4)+", dz = "+coord[2].toFixed(4)); // Return answer return coord; } // // -------------------- mechanics.js -------------------- // //# function mechanics() //# //# Simple routine to perform crude optimization of structure. //# function mechanics() { // Define local variables var i, j, k; var Z; var loop; var erg, deltaE; var molOLD = new Array(); var molNEW = new Array(); var molecule = Mol(); // Drawing Canvas info var activecanvas = activeWin(""); var canvas = document.getElementById(activecanvas); var ctx = canvas.getContext('2d'); var width = canvas.width; // Parameters var MAXSTEP=0.2; var MAXLOOP=500; var ETHRESH = 0.0000002; // Save Molecular information Undo("save"); // Clear information window InfoWin("Simple Geometry Optimization starting\n",1); geomLabel(ctx,"Simple Geometry Optimization started",width); // Determine hybridization of all atoms in molecule molOLD = hybridization(); var DEBUG=0; // Debug hybridization routine if (DEBUG > 0) { InfoWin("Hybridization\n"); for (i=1; i <= molecule[0].numatoms; i++) { Z = molecule[i].atomicnumber; InfoWin(element(Z,"symbol")+" has "+molOLD[i].hybrid+" hybrid orbitals\n"); } } // Calculate energy of initial geometry erg = mechEnergy(molOLD); molOLD[0].energy = erg; molOLD[0].step = MAXSTEP; // Populate molNEW array molNEW[0] = new energyObject(); molNEW[0].energy = molOLD[0].energy; molNEW[0].step = molOLD[0].step; for (i=1; i <= molecule[0].numatoms; i++) { molNEW[i] = new mechanicsObject(); molNEW[i].hybrid = molOLD[i].hybrid; molNEW[i].x = molOLD[i].x; molNEW[i].y = molOLD[i].y; molNEW[i].z = molOLD[i].z; } // Call routine to calculate new geometry loop = 0; deltaE = ETHRESH*2.0; InfoWin(0+": Energy = "+erg.toFixed(8)+"\n"); while ( (loopETHRESH) ) { molNEW = optimize(molOLD); deltaE = Math.abs( molOLD[0].energy - molNEW[0].energy ); // Don't allow step size to increase too much if ( molNEW[0].step > MAXSTEP ) molNEW[0].step = MAXSTEP; // Copy values from molNEW array into molOLD molOLD[0].energy = molNEW[0].energy; molOLD[0].step = molNEW[0].step; for (i=1; i <= molecule[0].numatoms; i++) { molOLD[i].hybrid = molNEW[i].hybrid; molOLD[i].x = molNEW[i].x; molOLD[i].y = molNEW[i].y; molOLD[i].z = molNEW[i].z; } // Force at least 3 iterations loop++; if (loop < 3) if ( deltaE < ETHRESH ) deltaE = ETHRESH*2.0; // If structure approaching convergence, increase step size if ( deltaE < ETHRESH ) { if ( molNEW[0].step < MAXSTEP ) { molOLD[0].step *= 1.5; molNEW = optimize(molOLD); deltaE = Math.abs( molOLD[0].energy - molNEW[0].energy ); if ( deltaE > ETHRESH ) { molOLD[0].energy = molNEW[0].energy; molOLD[0].step = molNEW[0].step; for (i=1; i <= molecule[0].numatoms; i++) { molOLD[i].hybrid = molNEW[i].hybrid; molOLD[i].x = molNEW[i].x; molOLD[i].y = molNEW[i].y; molOLD[i].z = molNEW[i].z; } } } } // Save current structure and display geometry every 5 steps InfoWin(loop+": Energy = "+molNEW[0].energy.toFixed(8)+"\n"); //InfoWin(" Step = "+molNEW[0].step.toFixed(5)+"\n"); DEBUG=1; if ( (DEBUG>0) && (loop%5 == 0) ) { for (i=1; i <= molecule[0].numatoms; i++) { molecule[i].x = molNEW[i].x; molecule[i].y = molNEW[i].y; molecule[i].z = molNEW[i].z; } centerMolecule(); drawMolecule(); geomLabel(ctx,"Simple Geometry Optimization in progress.",width); } } // Save optimized coordinates and display structure InfoWin("Final Energy at loop "+loop+" = "+molNEW[0].energy.toFixed(8)+"\n"); InfoWin("Geometry Optimization complete.\n"); if ( loop >= MAXLOOP ) InfoWin("Too many steps. Optimization may not be complete.\n"); for (i=1; i <= molecule[0].numatoms; i++) { molecule[i].x = molNEW[i].x; molecule[i].y = molNEW[i].y; molecule[i].z = molNEW[i].z; } centerMolecule(); drawMolecule(); // Finished with mechanics routine } /// /// Define object to hold temporary molecular information /// function mechanicsObject() { this.hybrid = 0; this.x = 0.0; this.y = 0.0; this.z = 0.0; } /// /// Define object to hold temporary energy/optimization information /// function energyObject() { this.energy = 0.0; this.rstep = 0; this.astep = 0; } //# function distance(mol, atomA, atomB) //# //# Calculate the distance between two atoms in mol array. //# function distance(mol, atomA, atomB) { // Calculate distance between atoms var dx = mol[atomA].x - mol[atomB].x; var dy = mol[atomA].y - mol[atomB].y; var dz = mol[atomA].z - mol[atomB].z; var r = Math.sqrt(dx*dx+dy*dy+dz*dz); // Exit distance routine return r; } //# function angle(mol, atomA, atomB, atomC) //# //# Calculate the angle between A--B--C in mol array //# function angle(mol, atomA, atomB, atomC) { // Calculate vector BA var dax = mol[atomA].x - mol[atomB].x; var day = mol[atomA].y - mol[atomB].y; var daz = mol[atomA].z - mol[atomB].z; var ra = Math.sqrt(dax*dax+day*day+daz*daz); // Calculate vector BC var dbx = mol[atomC].x - mol[atomB].x; var dby = mol[atomC].y - mol[atomB].y; var dbz = mol[atomC].z - mol[atomB].z; var rb = Math.sqrt(dbx*dbx+dby*dby+dbz*dbz); // Calculate bond angle var ang = (dax*dbx + day*dby + daz*dbz) / (ra*rb); if (ang > 1.0) ang = 1.0; if (ang < -1.0) ang = -1.0; ang = Math.acos(ang) * 180.0 / Math.PI; // Exit distance routine return ang; } //# function dihedral(mol, atomA, atomB, atomC, atomD) //# //# Routine to calculate the dihedral angle for A--B--C--D //# function dihedral(mol, atomA, atomB, atomC, atomD) { // Define local variables var i, j, k; var dux, duy, duz; var dvx, dvy, dvz; var crossA, crossAx, crossAy, crossAz; var crossB, crossBx, crossBy, crossBz; // Calculate cross product of BA x BC dux = mol[atomA].x - mol[atomB].x; duy = mol[atomA].y - mol[atomB].y; duz = mol[atomA].z - mol[atomB].z; dvx = mol[atomC].x - mol[atomB].x; dvy = mol[atomC].y - mol[atomB].y; dvz = mol[atomC].z - mol[atomB].z; crossAx = duy*dvz - duz*dvy; crossAy = duz*dvx - dux*dvz; crossAz = dux*dvy - duy*dvx; crossA = Math.sqrt(crossAx*crossAx + crossAy*crossAy + crossAz*crossAz); // Calculate cross product of CD x CB dux = mol[atomD].x - mol[atomC].x; duy = mol[atomD].y - mol[atomC].y; duz = mol[atomD].z - mol[atomC].z; crossBx = duz*dvy - duy*dvz; crossBy = dux*dvz - duz*dvx; crossBz = duy*dvx - dux*dvy; crossB = Math.sqrt(crossBx*crossBx + crossBy*crossBy + crossBz*crossBz); // Use dot product to calculate dihedral angle ang = (-crossAx*crossBx-crossAy*crossBy-crossAz*crossBz)/(crossA*crossB); if (ang > 1.0) ang = 1.0; if (ang < -1.0) ang = -1.0; ang = Math.acos(ang) * 180.0 / Math.PI; // Finished with dihedral routine return ang; } /// /// Determine number of hybrid orbitals on all atoms /// function hybridization() { // Define local variables var i, j, k; var valence; var optmol = new Array(); var molecule = Mol(); var bonds = BondMatrix(); // Copy molecule data into local array optmol[0] = new energyObject(); optmol[0].energy = 0.0; optmol[0].step = 0.0; for (i=1; i <= molecule[0].numatoms; i++) { optmol[i] = new mechanicsObject(); optmol[i].hybrid = 0; optmol[i].x = molecule[i].x; optmol[i].y = molecule[i].y; optmol[i].z = molecule[i].z; } // Loop over all atoms in molecule for (i=1; i <= molecule[0].numatoms; i++) { valence = element(molecule[i].atomicnumber,"valence"); switch (valence) { case 1: case 2: case 3: optmol[i].hybrid = bonds[i][0]; break; default: optmol[i].hybrid = valence + bonds[i][0] - 4; break; } while ( (optmol[i].hybrid>bonds[i][0]) && (optmol[i].hybrid>=5) ) { optmol[i].hybrid = optmol[i].hybrid-1; } } // Look for delocalized lone pairs for (i=1; i <= molecule[0].numatoms; i++) { if ( (optmol[i].hybrid == 4) && (bonds[i][0]<4) ) { for (j=1; j <= molecule[0].numatoms; j++) { k = bonds[i][j]; if (k > 0) { if ( optmol[k].hybrid == 3 ) { optmol[i].hybrid = 3; // InfoWin("Delocalized lone pair found on atom "+i+" bonded to "+bonds[i][j]+"\n"); } } } } } // End hybridization routine return optmol; } /// /// Calculate the mechanics energy of the current geometry /// function mechEnergy(current) { // Define local variables var i, j, k; var ii, bi, bj, ia, ja; var r0, r1, r2; var dx, dy, dz, r, dr; var atomA, atomB, maxBonds; var da, dax, day, daz; var db, dbx, dby, dbz; var ang; var tetra = Math.acos(-1/3.0) * 180.0 / Math.PI; var energy = 0.0; var molecule = Mol(); var bonds = BondMatrix(); // Parameters var penaltyR = 20000.0; var penaltyA = 10.0; var penaltyD = 5.0; var penaltyVDW = 500.0; // Look for hybridization error DEBUG=1; if ( DEBUG > 0 ) { var hytotal = 0; for (i=1; i <= molecule[0].numatoms; i++) { hytotal += current[i].hybrid; } if (hytotal < molecule[0].numatoms) InfoWin("*** Too few hybrid orbitals ("+hytotal+") returned at end of optimize\n"); } // Calculate energy penalty for bond lengths for (i=1; i <= molecule[0].numatoms; i++) { r1 = element(molecule[i].atomicnumber,"radius"); if ( current[i].hybrid == 3 ) r1 -= 0.05; if ( current[i].hybrid == 2 ) r1 -= 0.10; for (j=1; j <= molecule[0].numatoms; j++) { if ( bonds[i][j] > 0) { k = j; r2 = element(molecule[k].atomicnumber,"radius"); if ( current[k].hybrid == 3 ) r2 -= 0.05; if ( current[k].hybrid == 2 ) r2 -= 0.10; r0 = r1 + r2; // Ideal bond length dx = current[i].x - current[k].x; dy = current[i].y - current[k].y; dz = current[i].z - current[k].z; r = Math.sqrt(dx*dx+dy*dy+dz*dz); energy += penaltyR*(r-r0)*(r-r0); } } } // Calculate energy penalty for bond angles for (i=1; i <= molecule[0].numatoms; i++) { if (current[i].hybrid > 1) { for (j=1; j < molecule[0].numatoms; j++) { if (bonds[i][j] > 0) { atomA = j; dax = current[atomA].x - current[i].x; day = current[atomA].y - current[i].y; daz = current[atomA].z - current[i].z; da = Math.sqrt(dax*dax + day*day + daz*daz); for (k=j+1; k <= molecule[0].numatoms; k++) { if (bonds[i][k] > 0) { atomB = k; dbx = current[atomB].x - current[i].x; dby = current[atomB].y - current[i].y; dbz = current[atomB].z - current[i].z; db = Math.sqrt(dbx*dbx + dby*dby + dbz*dbz); ang = (dax*dbx+day*dby+daz*dbz)/(da*db); if (ang > 1.0) ang = 1.0; if (ang < -1.0) ang = -1.0; ang = Math.acos(ang) * 180.0 / Math.PI; switch (current[i].hybrid) { case 2: energy += penaltyA*(ang-180.0)*(ang-180.0); break; case 3: energy += penaltyA*(ang-120.0)*(ang-120.0); break; case 4: energy += penaltyA*(ang-tetra)*(ang-tetra); break; case 5: case 6: if (ang < 100.0) energy += penaltyA*(ang-90.0)*(ang-90.0); break; } } } } } } } // Calculate energy penalty for sp3-sp3 dihedral angles for (i=1; i < molecule[0].numatoms; i++) { if (current[i].hybrid == 4) { for (ii=i+1; ii<=molecule[0].numatoms; ii++) { if ( (bonds[i][ii] > 0) && (current[ii].hybrid == 4) ) { j = ii; for (bi=1; bi<=molecule[0].numatoms; bi++) { if ( (bonds[i][bi]>0) && (bi!=j) && (bi!=i) ) { ia = bi; for (bj=1; bj<=molecule[j].numatoms; bj++) { if ( (bonds[j][bj]>0) && (bj!=j) && (bj!=i) && (bj!=ia) ) { ja = molecule[j].bonds[bj]; ang = Math.abs(dihedral(current, ia, i, j, ja)); while (ang > 120.0) ang -= 120.0; energy += penaltyD*(ang-60.0)*(ang-60.0); // InfoWin("Dihedral: "+ia+"-"+i+"-"+j+"-"+ja); // InfoWin(" = "+ang+"\n"); } } } } } } } } // Calculate energy penalty for sp2-sp2 dihedral angles (pi bonds) for (i=1; i < molecule[0].numatoms; i++) { if (current[i].hybrid == 3) { for (ii=i+1; ii<=molecule[i].numatoms; ii++) { if ( (bonds[i][ii]>0) && (current[j].hybrid == 3) ) { j = ii; for (bi=1; bi<=molecule[i].numatoms; bi++) { if ( (bonds[i][bi]>0) && (bi!=j) && (bi!=i) ) { ia = bi; for (bj=1; bj<=molecule[j].numatoms; bj++) { if ( (bonds[j][bj]>0) && (bj!=i) && (bj!=j) && (bj!=ia) ) { ja = bj; ang = Math.abs(dihedral(current, ia, i, j, ja)); if (ang > 180.0) ang -= 180.0; if (ang > 135.0) ang = 180.0 - ang; energy += penaltyD*ang*ang; // InfoWin("Dihedral: "+ia+"-"+i+"-"+j+"-"+ja); // InfoWin(" = "+ang+"\n"); } } } } } } } } // Calculate energy penalty for van der Waal's repulsion for (i=1; i < molecule[0].numatoms; i++) { r1 = element(molecule[i].atomicnumber,"radius"); for (j=i+1; j <= molecule[0].numatoms; j++) { r2 = element(molecule[j].atomicnumber,"radius"); r = distance(current, i, j); if ( r < 0.1 ) r = 0.1; r = r/(r1+r2); energy += penaltyVDW / (r*r*r*r*r*r); } } // End of mechEnergy routine return energy; } /// /// Calculate 'optimal' change in all coordinates /// function changexyz(current) { // Define local variables var molecule = Mol(); var i, j, k; var ixyz; var delta = []; var EZero, energyX, energyY, energyZ; var stepx, stepy, stepz; var stepfactor; var oldx, oldy, oldz; var randomnumber; // Parameters var stepsize = current[0].step; // Debug hybridization routine var DEBUG=0; if (DEBUG > 0) { InfoWin("Hybridization\n"); for (i=1; i <= molecule[0].numatoms; i++) { Z = molecule[i].atomicnumber; InfoWin(element(Z,"symbol")+" has "+current[i].hybrid+" hybrid orbitals\n"); } } // Initialize delta array for (i=0; i <= molecule[0].numatoms; i++) { delta[i] = [0.0, 0.0, 0.0]; } // Populate trial array var trial = new Array(); trial[0] = new energyObject(); trial[0].energy = current[0].energy; trial[0].step = current[0].step; for (i=1; i <= molecule[0].numatoms; i++) { trial[i] = new mechanicsObject(); trial[i].hybrid = current[i].hybrid; trial[i].x = current[i].x; trial[i].y = current[i].y; trial[i].z = current[i].z; } // Loop over all coordinates, looking for 'best' changes EZero = mechEnergy(trial); for (i=1; i <= molecule[0].numatoms; i++) { // Save current coordinates oldx = trial[i].x; oldy = trial[i].y; oldz = trial[i].z; // Loop over changes in all coordinates for (ixyz=0; ixyz<6; ixyz++) { stepx = 0.0; stepy = 0.0; stepz = 0.0; energyX = EZero; energyY = EZero; energyZ = EZero; (ixyz%2) ? stepfactor=1.0 : stepfactor=-1.0; switch (ixyz) { case 0: case 1: trial[i].x = oldx + stepfactor*stepsize; Energy = mechEnergy(trial); while ( (Energy>EZero) && (stepfactor>0.1) ) { stepfactor *= 0.75; trial[i].x = oldx + stepfactor*stepsize; Energy = mechEnergy(trial); } if ( Energy < energyX ) stepx = stepfactor; trial[i].x = oldx; delta[i][0] = stepx*stepsize; break; case 2: case 3: trial[i].y = oldy + stepfactor*stepsize; Energy = mechEnergy(trial); while ( (Energy>EZero) && (stepfactor>0.1) ) { stepfactor *= 0.75; trial[i].y = oldy + stepfactor*stepsize; Energy = mechEnergy(trial); } if ( Energy < energyY ) stepy = stepfactor; trial[i].y = oldy; delta[i][1] = stepy*stepsize; break; case 4: case 5: trial[i].z = oldz + stepfactor*stepsize; Energy = mechEnergy(trial); while ( (Energy>EZero) && (stepfactor>0.1) ) { stepfactor *= 0.75; trial[i].z = oldz + stepfactor*stepsize; Energy = mechEnergy(trial); } if ( Energy < energyZ ) stepz = stepfactor; trial[i].z = oldz; delta[i][2] = stepz*stepsize; break; } } // Finished loop for atom 'i' } // End of changexyz routine return delta; } /// /// Simple molecular mechanics (kind of) geometry optimization /// function optimize(current) { // Define local variables var i, j, k; var ib; var newstep; var EFit; var EMin; var beststep, trial; var maxstep; var delta = new Array(); var molNEW = new Array(); var molecule = Mol(); // Parameters var MINSTEP=0.001; var step = current[0].step; var eINITIAL = current[0].energy; // Look for a few obvious errors DEBUG=1; if ( DEBUG > 0 ) { var erg = mechEnergy(current); if (erg != eINITIAL) InfoWin("*** Call to mechEnergy changed energy from "+eINITIAL+" to "+erg+"\n"); var hytotal = 0; for (i=1; i <= molecule[0].numatoms; i++) { hytotal += current[i].hybrid; } if (hytotal < molecule[0].numatoms) InfoWin("*** Too few hybrid orbitals ("+hytotal+")\n"); } // Initialize delta array for (i=0; i <= molecule[0].numatoms; i++) { delta[i] = [0.0, 0.0, 0.0]; } // Call routine to calculate changes in coordinates // and find maximum change. delta = changexyz(current); maxstep = 0.0; for (i=0; i <= molecule[0].numatoms; i++) { for (j=0; j < 3; j++) { if ( Math.abs(delta[i][j]) > maxstep ) maxstep = Math.abs(delta[i][j]); } } // Simple line search to find best change in coordinates EMin = current[0].energy; beststep = 0.0; trial = 1.0; EFit = trialEnergy(current,delta,trial); while ( (EFit > EMin) && (trial > 0.002) ) { trial *= 0.75; EFit = trialEnergy(current,delta,trial); } if (EFit < EMin) { beststep = trial; EMin = EFit; } // Determine new step sizes for next iteration newstep = (beststep+0.5) * (current[0].step + maxstep); if (newstep < MINSTEP) newstep = MINSTEP; // Populate molNEW object with new geometry molNEW[0] = new energyObject(); molNEW[0].energy = EMin; molNEW[0].step = newstep; for (i=1; i <= molecule[0].numatoms; i++) { molNEW[i] = new mechanicsObject(); molNEW[i].hybrid = current[i].hybrid; molNEW[i].x = current[i].x + beststep*delta[i][0]; molNEW[i].y = current[i].y + beststep*delta[i][1]; molNEW[i].z = current[i].z + beststep*delta[i][2]; } // DEBUG: Show changes in coordinates from optimization DEBUG = 0; if (DEBUG > 0) { for (i=0; i <= molecule[0].numatoms; i++) { InfoWin("Change in coordinates = ("); for (j=0; j < 3; j++) { InfoWin(delta[i][j].toFixed(5)); if (j<2) InfoWin(", "); } InfoWin(")\n"); } InfoWin("--- Max change = "+maxstep.toFixed(5)+"\n"); } // Finished with optimize routine return (molNEW); 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K^XXkk" Ǝx!Xx]1&꺦Sd2 F￿bpuBk=H{}>ȑ#^($1@amks3gPeIhάI[;[;ѨqƀL2Gm4i͏.soGqv4heʹ`Mm dQd 9WUs~/>O>ypw6Cr::9[6._ֳQ\R>\Q1y5;x`_4*|l椀V3̛4WD`9eB2NRv}ǎpĩ28cD,m 29훶y<2dnǺN\K-b:~?vqn鯪:G߽ )`]>!UT}/ERRjP& hjaT*uIۗ_rt~r9%W^iyٳ $MQ(e(Ґ{5Wld~McW֭~M#7me R)0TU|Gs[dr>ϳ۽^Tǽ-q07iRޓO~i[S 9277;hY;{zr *EƓ' 3CYp9"D״ƍ)L!$P*C;mKC3)΁sf|@B d:4_d +uoDcc98rsXH:L߾_xtjaO%>[f!VޤI~_ZJ8؜h4:w;LvF1Im'zhuFcEl#a^MscΆaqvc9|I\0o,6֧n6rf~NMFBx;C==Snz&IaAQ~L\xQH/nZINu3v8Kٱgt_G^xΧvL3t]MH"+Eu ӫ*</v.;+/E?'6L0j``G]rMցYu(8e& u[~8 dL,΁1 )E E@ͭa2}^EH^ֲw*"_uGXb1%_{@֮/i[u9 A 0 y%tEXtdate:create2013-03-11T17:21:52-04:00p"%tEXtdate:modify2013-03-11T13:44:52-04:00wtEXtSoftwareShutterc IENDB`ch5m3d-1.2.5+dfsg/doc/drawing.html0000644000175000017500000001556112230555426017021 0ustar georgeskgeorgesk CH5M3D

CH5M3D

Drawing Molecules

In Draw Mode, you have the option of adding or deleting atoms and/or bonds to any structure shown in the display window. The image below shows the buttons initially displayed when first entering Draw Mode.

Draw Mode Buttons

Rotating the Entire Molecule

In draw mode, you can rotate the molecule in the same manner as performed in View mode by selecting a blank portion of the screen and "dragging" the pointer.

Adding Atoms

Initially, a subset of the periodic table is shown, with Carbon highlighted. To add a methyl group to the methane molecule shown, click on any of the hydrogen atoms. By default, the atom added is assumed to be sp3 hybridized. To add a CH2 group, select before clicking on an H.

In general, clicking on any atom will convert the atom into the selected element type shown on the periodic table. If the selected atom has only one bond, the new atom is added with a reasonable value for the bond length and the appropriate number of hydrogen atoms added. If the selected atom has two or more bonds, it is replaced with the new atom type, but bond distances are not changed and additional hydrogen atoms are not added.

Hydrogen is an exception to this pattern. If H is selected on the periodic table, clicking on any atom will add a single H atom (it will not replace the atom with H).

Adding Metals

Initially, only a subset of the periodic table is shown, with main group elements (excluding the noble gases) displayed. To add any of the remaining elements, select the Metals link above Oxygen/Fluorine. To revert back to showing only main group elements, select the Organic link.

Deleting Atoms

To delete an atom, select the button, then click on the atom to be removed. This atom and any hydrogen atoms attached to this atom should be removed.

Adding Bonds

To add a bond, place the pointer on the first atom and press down (but do not release). Drag the pointer to the second atom, then release the mouse. A bond should be shown connecting these atoms. Note that when adding bonds, the number of bonded atoms increases, so it may be necessary to delete one or more atoms.

Removing Bonds

Deleting bonds is done in a similar manner. Select , then place the pointer on the first atom and press down (but do not release). Drag the pointer to the second atom, then release the mouse. The bond connecting these atoms should be removed.

Rotating Around a Bond

It is also possible to rotate around bonds. To do this, first press the button. Then move the mouse pointer over the first atom, press and hold the mouse button, "drag" to the second bonded atom and release the mouse button. (Note that if the atoms are not bonded, rotation will not behave as expected). A new view of the molecule will be displayed with the molecule oriented so that you are looking "down" the selected bond. The second atom selected will be in front, eclipsing the first atom selected.

To rotate around this bond, use the mouse pointer to select a blank portion of the drawing window and "drag" the pointer while holding the mouse button down. To get out of bond rotation mode, press the , which should change color to indicate that it is no longer active.

Undo

When significant changes are made to the molecule (atoms added, atoms deleted, rotation about bonds, etc.), the molecular coordinates are saved. Currently, ten sets of saved coordinates are saved. Pressing the button restores the most recent set of coordinates. This may be repeated up to the the limit of saved sets of coordinates. There is also a button, that reverses the effects of the Undo.

Structure Optimization

At the bottom of the Draw mode window is an button. This button will cause a crude geometry optimization to be performed. It is not necessary to use this, but it can be useful when significant changes have occurred. This is most common when H atoms have been added or when bonds have been added or removed. At this point, the optimization routine is very crude, and it may be necessary to optimize a structure multiple times before a reasonable structure is obtained.

ch5m3d-1.2.5+dfsg/doc/introduction.html0000644000175000017500000001053612230555426020104 0ustar georgeskgeorgesk CH5M3D

CH5M3D

CH5M3D Overview

This web interface has been developed to allow users to create and visualize 3-dimensional drawings of simple molecules without requiring the download of any additional software. In addition to creating structures, users can also load existing XYZ formatted files (such as those generated by Open Babel) containing 3-dimensional coordinates. A small selection of .xyz formatted files is available from the project home page.

Once molecules are created or read from a file, users can examine geometry information (bond lengths, angles, and dihedral angles) and modify these structures. Routines to perform a crude geometry optimization and a simple calculation of atomic charges are also available.

This web interface relies on HTML5 (in particular, the HTML5 Canvas), and as such requires a modern web browser to run. The advantage of this approach is the no additional plugins or Java is required to use this program. Support for mobile devices is currently only partially implemented, but is planned to be included in future versions.

Screenshots

Initial View of Interface
Initial view of CH5M3D Interface
Image with labels added
Image with labels added
Image with highlighting
Image with highlighting
Draw Mode interface
Draw Mode interface
Example of charge calculation
Example of charge calculation

 

ch5m3d-1.2.5+dfsg/doc/apidoc.html0000644000175000017500000002407312230555430016616 0ustar georgeskgeorgesk CH5M3D

CH5M3D

 

function element(Z,param)

Define public routine to store and return elemental information

Parameters:

Z = Atomic number of element

param:

  symbol - Elemental symbol

  block - "s", "p", "d", or "f" block

  valence - # of valence electrons

  mass - Atomic mass

  radius - Covalent radius of atom

  EN   - Electronegativity of atom

  color - color of atom (based on JMol)

  gradient - gradient color for atom

  label - color for label

Return value:

Variable containing requested information

 

function drawPeriodic()

Writes html code to a division named "ptable". The periodic table is written as a table, and each element

is linked to to the pickElem() routine.

 

function Mol(value)

Define public routine to store and return molecule arrays

Parameter:

value = If value given, then set as active molecule

Return value:

Pointer to current array for molecular coordinates, ex.

var molecule = Mol();

Molecular values stored in 'zeroth' element of array

molecule[0].molIndex - ID number for this molecule

molecule[0].numatoms - # of atoms in this molecule

molecule[0].AtomScale - Scale factor to control size of molecule displayed

molecule[0].showlabels - 0=don't show elemental symbols, 1=show symbols

molecule[0].showcharges - 0=don't show charges, 1=show charges

molecule[0].gradients - 0=don't shade atoms, 1=use shading

molecule[0].formula - Simple text string containing molecular formula

molecule[0].weight   - Molecular weight

molecule[0].charge   - Charge of molecule

Atomic values in remaining elements of array

molecule[i].atomicnumber - Atomic number (Z) for atom

molecule[i].x     - x coordinate of atom

molecule[i].y     - y coordinate of atom

molecule[i].z     - z coordinate of atom

molecule[i].charge   - Estimate of atomic charge

molecule[i].highlite - 0=don't highlight atom, 1=highlight atom

molecule[i].hide   - 0=display atom, 1=do not display atom

 

function BondMatrix(value)

Define public routine to store and return Bond Matrix

Parameter:

value = If value given, then set as active matrix

Return value:

Pointer to current bond matrix, ex.

var bonds = BondMatrix();

bonds[i][j] then gives indication of bond between atoms "i" and "j"

 

function lookupSymbol(symbol)

Given elemental symbol, lookup and return atomic number (Z)

 

function addAtom(AtomicNum, x, y, z)

Routine to add atomic information to molecule array.

Parameters are the atomic # and (x,y,z) coordinates of the atom.

 

function addBond(atom1, atom2)

Routine to add bonding information to bonds array

(Note that atom numbers start at 1)

 

function delAtom(atomNum)

Routine to remove selected atom, directly-bonded Hydrogens, and

cleanup molecule object (remove blank slots) and update bond arrays.

atomNum is the position of the atom to delete in the molecule array

 

function delBond(atom1, atom2)

Routine to remove bond from bonds array.

 

function hideH()

Do not display any hydrogen atoms in molecule

 

function showAll()

Show all atoms in molecule

 

function centerMolecule()

Find center of molecule and move coordinates to center.

 

function showCoord(mode)

Display molecular coordinates and bonds in information window.

Parameter:

mode=0: Write .xyz formatted file

mode>0: Write coordinates and bond information

 

function formula()

Display molecular formula to division with an id = "formula".

Note that the contents of this division will be overwritten.

 

function RotateMolecule(axis)

Routine to start/stop rotation of molecule.

Parameter:

axis = rotation axis. Allowed values are "x", "y", or "z"

  ("s" can be used to stop all rotations)

Buttons must be created in html with:

id="rotateX" (or rotateY or rotateZ)

 

function drawMolecule()

Draw atoms and bonds.

 

function showLabels()

Routine to toggle display of atomic labels.

 

function parameters()

Define constants used to control drawing.

Get/set values using:

var param = parameters();

param.mode = Interface mode. Set to "Draw" or "View"

param.element = Type of element to add next. Default = "C"

param.clouds = # of hybrid orbitals. Default = 4

param.bondmode = Bond mode. Set to "Add", "Delete", or "Rotate"

param.atommode = Add atom mode. Set to "Add" or "Delete"

 

function drawmode()

Routine to enable display of "draw mode" interface.

 

function viewmode()

Routine to enable display of "view mode" interface.

 

function setCharge()

Routine to set the molecular charge using value of select form with id="SelectCharge".

 

function simpleQ()

Public routine to (somewhat arbitrarily) assign electron configuration,

including bond orders, and calculate the charges on each atom.

 

function showBondMatrix(BondMtx,BondWin)

Write Bond information to output window.

 

function showgallery(title,base,List,Desc,size)

Routine to display multiple files stored on the web server.

Parameters:

title: Title to display before gallery

  (If title = "delete", clear gallery)

base: Path to directory (relative to web root) containing images

List: Array containing a list of filenames (including extensions)

Desc: Array containing descriptions for each file

size: integer width (in px) for each frame

 

function galleryUniform()

Routine to force all molecules that are part of a "gallery" to be displayed with the same size scale.

 

function galleryReset()

For molecules that are part of a "gallery", this routine optimizes the size of each molecule individually.

 

function readServerFile(filename)

Routine to read contents of file stored on the web server.

Parameter:

filename: Name (URL) of file (including path)

 

function InfoWin(mytext,mode)

Routine to write text to information window (textarea with an id of "information").

Parameters:

mytext: String to write to output window

mode: If >0, then clear text window

 

function loadMolecule()

Routine to load molecular information for methane molecule.

 

function resetView()

Routine to reset view. Center, rescale, and remove highlights.

 

function buttonColor(button, mode)

Set color of buttons

Parameters

button - string containing ID name for button

mode - 0=inactive, 1=active

 

function initialize()

Initialization Routines

- Load properties of elements

- Define Handlers for mouse events

- Draw molecule

 

function mechanics()

Simple routine to perform crude optimization of structure.

 

function distance(mol, atomA, atomB)

Calculate the distance between two atoms in mol array.

 

function angle(mol, atomA, atomB, atomC)

Calculate the angle between A--B--C in mol array

 

function dihedral(mol, atomA, atomB, atomC, atomD)

Routine to calculate the dihedral angle for A--B--C--D

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About CH5M3D

 

CH5M3D Version 1.2.5

Project Homepage

Description

This program uses a combination of HTML5 and javascript to interactively draw 3-dimensional structures of small molecules.

License

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

To view a copy of the GNU General Public License, see http://www.gnu.org/licenses/gpl.html.

Author

Dr. Clarke Earley
Associate Professor of Chemistry
Kent State University at Stark
cearley@kent.edu

Acknowledgements

The support of Kent State University at Stark is gratefully acknowledged.

 

CH5M3D Overview

This web interface has been developed to allow users to create and visualize 3-dimensional drawings of simple molecules without requiring the download of any additional software. In addition to creating structures, users can also load existing XYZ formatted files (such as those generated by Open Babel) containing 3-dimensional coordinates. A small selection of .xyz formatted files is available from the project home page.

Once molecules are created or read from a file, users can examine geometry information (bond lengths, angles, and dihedral angles) and modify these structures. Routines to perform a crude geometry optimization and a simple calculation of atomic charges are also available.

This web interface relies on HTML5 (in particular, the HTML5 Canvas), and as such requires a modern web browser to run. The advantage of this approach is the no additional plugins or Java is required to use this program. Support for mobile devices is currently only partially implemented, but is planned to be included in future versions.

Screenshots

Initial View of Interface
Initial view of CH5M3D Interface
Image with labels added
Image with labels added
Image with highlighting
Image with highlighting
Draw Mode interface
Draw Mode interface
Example of charge calculation
Example of charge calculation

 

Installation

This "program" can be downloaded as a single zip file containing the following files.

  • index.html - The main HTML file loaded by a web browser.
  • ch5m3d.js - The javascript code required to generate the web interface.
  • ch5m3d.css - CSS code controlling the appearance of the web pages.
  • documentation.pdf - A PDF version of the documentation.
  • doc/ - A directory containing html documentation files and the GNU license.
  • molecules/ - A directory containing a small number of .xyz formatted files of molecular coordinates.
  • variations/ - A directory containing a few html files that illustrate different ways that web pages can use the javascript code to provide different views.
  • qchem/ - A directory containing a php files and support files that provide a simple front-end interface to the quantum mechanical program GAMESS. (Note that it is very unlikely that this will work without modification).

Testing

A live version of this program is available at the Project Web page on SourceForge. Note that a suitable web browser that supports HTML5 is required to run this program.

Installation on a Web Server

No special steps are required to install this program on a web server other than placing the "unzipped" directory tree in a location where it can be accessed by the web server. All file locations are coded as "relative" directories, so the actual path/directory location for these files does not matter.

If it is desired to change the relative location of any of these files, note that index.html assumes that ch5m3d.js and ch5m3d.css are both located in the same directory as index.html. All of the documentation files assume that ch5m3d.css is located "up" one directory (../ch5m3d.css).

Supported Web Browsers

The interactive drawing window used on this website requires HTML5, which is NOT supported by version 8 or lower of Microsoft Internet Explorer. To use this site, you will need to use a browser that supports the Canvas element and a few other features of HTML5. Listed below are several freely available web browsers that should work with this interface.

  • Mozilla Firefox - Available for Microsoft Windows, Apple, Linux, and Android.
  • Google Chrome - Available for Microsoft Windows, Apple, Linux, Android, and iOS.
  • Opera - While not as popular, is available for Microsoft Windows, Apple, Linux, Android, and iOS.
  • Apple Safari - Should already be installed on current Mac computers.

Currently, touch screen devices are NOT fully supported by this interface. While the web page will load, several important tasks do not function properly on tablets or other touch screen devices.

User Interface: View Mode

The image below shows the initial view that should be presented when this page is first loaded. The most important sections are labeled in red. Upon initially loading this page, you should be in View Mode, indicated by both the highlighted [View Mode] tab and the text "View Mode" displayed below this button. You can switch between View Mode and Draw Mode at any time by selecting the appropriate tab.

View Mode Interface with sections labeled

Initially, the methane molecule (CH4) should be displayed in the Drawing Window. While in View mode, you can use your mouse/pointer to perform the following tasks.

  • Rotate Molecule - Move the pointer to any blank portion of the Drawing Window and hold the mouse button down. Dragging the pointer should cause the molecule to rotate. To stop rotation, simply release the mouse button. Simultaneously pressing <Shift> while dragging the mouse pointer will cause the molecule to rotate around the z-axis. It is also possible to 'translate' a molecule by pressing the <Ctrl> key while dragging the mouse.
  • Zoom - If a mouse scroll wheel is available, this can be used to either zoom-in or zoom-out the current view.
  • Identify Atom - Move the pointer over any atom in a molecule and click on this atom to select. The Elemental symbol followed by a number should be displayed. The number is the position of the atom in the set of coordinates for this molecule, starting at 1. If the [Charges] button is active, then the calculated charge on this atom will also be displayed.
  • Highlight Atom - Move the pointer over any atom in a molecule, hold down the <Shift> key and click on this atom. A semitransparent yellow circle should appear over this atom. <Shift>-click on this atom a second time to turn off the highlight. Any number of atoms may be highlighted. The [Reset View] button may also be used to remove all highlights.
  • Measure Bond Lengths - Move the pointer to the first atom of the bond and select. The label for this atom should appear in the upper-right corner of the display window. Then, move the pointer to the second atom and select this atom. The bond length (in Angstroms) will be shown at the top right of the drawing window.
  • Measure Bond Angles - By selecting three atoms, the bond angle (in degrees) around the central atom (the second atom selected) will be shown.
  • Measure Dihedral Angles - By selecting four atoms, the dihedral angle (in degrees) will be shown. For example, if all four atoms lie in a plane, the dihedral angle will be either 0° or 180°.

For all of the operations, clicking on a blank portion of the screen will clear the list of selected atoms and allow you to start measuring a different set of lengths/angles. Clicking on the same atom twice will cause the atom list to be reset and this selected atom will be placed as the first atom on the list.

To the right of the Drawing Window are several buttons. These provide the following options:

  • [Show coordinates] This button will print the coordinates in .xyz format in the Information Window. For security reasons, it is not possible for javascript to write files to a user's computer. To save the coordinates of molecules created using this program, it is required that users open a text editor, copy the coordinates from the Information Window into their editor and save this as an .xyz file. When saving this file, but sure that it is saved as an unformatted text file.
  • [Labels] This button toggles the display of labels (elemental symbols) for each atom.
  • [Charges] Selecting this button causes a crude computation of atomic charge to be performed. Charges are shown as semi-transparent spheres around each atom. Negative charges are shown in red, and positive charges are shown as blue spheres. The intensity of these colors is used to indicate the magnitude of the charges. This charge calculation is based on a combination of formal charges and electronegativity differences. In addition, the dipole moment of the molecule based on these approximate point charges is displayed in the Information window near the bottom of the screen. Note that these calculated charges should not be considered to be accurate values but instead treated as a crude, first approximation.
  • [Reset View] This button centers and rescales the molecule to fit the display, and removes all highlights.
  • [Browse...] By selecting this button, users can load .xyz formatted files. Files of this format can be generated using the Open Babel program. A few sample .xyz files are available in the molecules folder on the CH5M3D Web site.

To save an image of a molecule, first rotate the molecule to get it into the desired orientation. Then, perform a right-click using the mouse pointer and select "Save Image As...".

User Interface: Keyboard and Mouse

While most common operations can be performed using only a mouse, a few operations require a combination of both keyboard and mouse. Note that these operations only work in View Mode. Note that in these descriptions, the screen is assumed to show the X-axis (horizontal) and the Y-axid (vertical), with the Z-axis coming "out" of this plane. The possible combinations and their results are outlined below.

  • Selecting a blank portion of the screen:
    • Mouse only - Dragging the mouse results in rotating the molecule around the X- and Y-axes.
    • <Shift> + Mouse - Rotation will occur around the Z-axis.
    • <Ctrl> + Mouse - The molecule will be translated along the X- and Y-axes.
  • Selecting a single atom:
    • Mouse only - The label for this atom is shown. (If the charges button is pressed, the calculated charge on this atom is also shown).
    • <Shift> + Mouse - The selected atom is highlighted. If this atom is already highlighted, this operation will cause the highlight to be removed.

A [Reset View] button is provided that will allow automatic re-scaling and re-centering of the molecule. This button will also remove all highlights from the displayed structure.

Drawing Molecules

In Draw Mode, you have the option of adding or deleting atoms and/or bonds to any structure shown in the display window. The image below shows the buttons initially displayed when first entering Draw Mode.

Draw Mode Buttons

Rotating the Entire Molecule

In draw mode, you can rotate the molecule in the same manner as performed in View mode by selecting a blank portion of the screen and "dragging" the pointer.

Adding Atoms

Initially, a subset of the periodic table is shown, with Carbon highlighted. To add a methyl group to the methane molecule shown, click on any of the hydrogen atoms. By default, the atom added is assumed to be sp3 hybridized. To add a CH2 group, select [sp2] before clicking on an H.

In general, clicking on any atom will convert the atom into the selected element type shown on the periodic table. If the selected atom has only one bond, the new atom is added with a reasonable value for the bond length and the appropriate number of hydrogen atoms added. If the selected atom has two or more bonds, it is replaced with the new atom type, but bond distances are not changed and additional hydrogen atoms are not added.

Hydrogen is an exception to this pattern. If H is selected on the periodic table, clicking on any atom will add a single H atom (it will not replace the atom with H).

Adding Metals

Initially, only a subset of the periodic table is shown, with main group elements (excluding the noble gases) displayed. To add any of the remaining elements, select the Metals link above Oxygen/Fluorine. To revert back to showing only main group elements, select the Organic link.

Deleting Atoms

To delete an atom, select the [Delete Atom] button, then click on the atom to be removed. This atom and any hydrogen atoms attached to this atom should be removed.

Adding Bonds

To add a bond, place the pointer on the first atom and press down (but do not release). Drag the pointer to the second atom, then release the mouse. A bond should be shown connecting these atoms. Note that when adding bonds, the number of bonded atoms increases, so it may be necessary to delete one or more atoms.

Removing Bonds

Deleting bonds is done in a similar manner. Select [Delete Bond], then place the pointer on the first atom and press down (but do not release). Drag the pointer to the second atom, then release the mouse. The bond connecting these atoms should be removed.

Rotating Around a Bond

It is also possible to rotate around bonds. To do this, first press the [Rotate Bond] button. Then move the mouse pointer over the first atom, press and hold the mouse button, "drag" to the second bonded atom and release the mouse button. (Note that if the atoms are not bonded, rotation will not behave as expected). A new view of the molecule will be displayed with the molecule oriented so that you are looking "down" the selected bond. The second atom selected will be in front, eclipsing the first atom selected.

To rotate around this bond, use the mouse pointer to select a blank portion of the drawing window and "drag" the pointer while holding the mouse button down. To get out of bond rotation mode, press the [Rotate Bond], which should change color to indicate that it is no longer active.

Undo

When significant changes are made to the molecule (atoms added, atoms deleted, rotation about bonds, etc.), the molecular coordinates are saved. Currently, ten sets of saved coordinates are saved. Pressing the [Undo] button restores the most recent set of coordinates. This may be repeated up to the the limit of saved sets of coordinates. There is also a [Redo] button, that reverses the effects of the Undo.

Structure Optimization

At the bottom of the Draw mode window is an [Optimize Structure] button. This button will cause a crude geometry optimization to be performed. It is not necessary to use this, but it can be useful when significant changes have occurred. This is most common when H atoms have been added or when bonds have been added or removed. At this point, the optimization routine is very crude, and it may be necessary to optimize a structure multiple times before a reasonable structure is obtained.

File Format for Molecules

Currently, the only format supported by this program for reading molecular coordinates is the .xyz format. These files can be created using the Open Babel program. Sample files in this format are available in the molecules directory.

Example

On the default page is a [Show coordinates] button that displays coordinates for the current molecule in the information box at the bottom of the screen. An example of the output produced for the methane molecule is:


5
CH4   (16.04 g/mol) in xyz format: From CH5M3D
C         0.0000       0.0000       0.0000
H         0.8740       0.6180       0.0000
H        -0.8740       0.6180       0.0000
H         0.0000      -0.6180       0.8740
H         0.0000      -0.6180      -0.8740

The first line contains the number of atoms in the molecule.

The second line is a comment. This line must be present, but can be blank or contain any text.

The remaining lines contain the elemental symbol (1-3 characters) and x, y, z cartesian coordinates. All of these values are separated by one or more spaces.

This program attempts to be flexible in reading these files, and does not require data to be present in specific columns. The one restriction that is enforced is that files must be named with the extension ".xyz".

Description of Variations

The following files are provided with this distribution to illustrate different ways that this interface can be used.

Pre-load

This simple page loads and displays the structure of a molecule from a file stored on the server. The name of this file is part of the web page html and cannot be changed by the user. While the molecule can be rotated and information displayed, the user cannot change this structure.

Chooser

This page allows the user to select the file to be viewed from a list of files stored on the server using either buttons or from a drop-down select list. While the molecule can be rotated and information displayed, the user cannot alter any of these structures.

Gallery

This page loads a list of files from the server and displays each of these in a separate division along with a description. Each of the molecules can be rotated independently and information displayed. However, the user cannot change any of these structures.

Viewer (only)

This page allows loading and viewing of molecules from files stored on the user's computer, but does not allow for any editting of these structures.

View 2 Windows

This page illustrates that more than one molecule can be loaded on a page. This page also does not allow for any editting of either structure. To switch between active windows, use the mouse to click on any portion of a drawing canvas.

Two Windows

This page illustrates that more than one molecule can be loaded on a page, and that these windows do not have to be the same size. In this view, both View Mode and Draw Mode are enabled, so either (or both) of the structures being displayed can be altered.

Javascript

This page illustrates how a user might create a simple function that interacts with functions contained within the CH5M3D library to gather information about the active molecule and interact with (alter) this structure. In this example, mirror images of a chiral molecule are generated with the user chosing the mirror plane to use.

Quantum Chemistry Interface

This page illustrates a simple interface that has been used to create input files for the quantum mechanical program GAMESS. This page makes calls to several PHP files, and uses a very simple authorization scheme. To view this page, use the username "admin" and the password "password".

Because this interface makes calls to the underlying operating system, it is unlikely that this interface will work without modification. All of the files used to create this page are located in the qchem subdirectory.

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CH5M3D

Description of Variations

The following files are provided with this distribution to illustrate different ways that this interface can be used.

Pre-load

This simple page loads and displays the structure of a molecule from a file stored on the server. The name of this file is part of the web page html and cannot be changed by the user. While the molecule can be rotated and information displayed, the user cannot change this structure.

Chooser

This page allows the user to select the file to be viewed from a list of files stored on the server using either buttons or from a drop-down select list. While the molecule can be rotated and information displayed, the user cannot alter any of these structures.

Gallery

This page loads a list of files from the server and displays each of these in a separate division along with a description. Each of the molecules can be rotated independently and information displayed. However, the user cannot change any of these structures.

Viewer (only)

This page allows loading and viewing of molecules from files stored on the user's computer, but does not allow for any editting of these structures.

View 2 Windows

This page illustrates that more than one molecule can be loaded on a page. This page also does not allow for any editting of either structure. To switch between active windows, use the mouse to click on any portion of a drawing canvas.

Two Windows

This page illustrates that more than one molecule can be loaded on a page, and that these windows do not have to be the same size. In this view, both View Mode and Draw Mode are enabled, so either (or both) of the structures being displayed can be altered.

Javascript

This page illustrates how a user might create a simple function that interacts with functions contained within the CH5M3D library to gather information about the active molecule and interact with (alter) this structure. In this example, mirror images of a chiral molecule are generated with the user chosing the mirror plane to use.

Quantum Chemistry Interface

This page illustrates a simple interface that has been used to create input files for the quantum mechanical program GAMESS. This page makes calls to several PHP files, and uses a very simple authorization scheme. To view this page, use the username "admin" and the password "password".

Because this interface makes calls to the underlying operating system, it is unlikely that this interface will work without modification. All of the files used to create this page are located in the qchem subdirectory.

ch5m3d-1.2.5+dfsg/doc/about.html0000644000175000017500000000675512230555426016505 0ustar georgeskgeorgesk CH5M3D

CH5M3D

 

CH5M3D Version 1.2.5

Project Homepage

Description

This program uses a combination of HTML5 and javascript to interactively draw 3-dimensional structures of small molecules.

License

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

To view a copy of the GNU General Public License, see http://www.gnu.org/licenses/gpl.html.

Author

Dr. Clarke Earley
Associate Professor of Chemistry
Kent State University at Stark
cearley@kent.edu

Acknowledgements

The support of Kent State University at Stark is gratefully acknowledged.

 

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CH5M3D

File Format for Molecules

Currently, the only format supported by this program for reading molecular coordinates is the .xyz format. These files can be created using the Open Babel program. Sample files in this format are available in the molecules directory.

Example

On the default page is a button that displays coordinates for the current molecule in the information box at the bottom of the screen. An example of the output produced for the methane molecule is:


5
CH4   (16.04 g/mol) in xyz format: From CH5M3D
C         0.0000       0.0000       0.0000
H         0.8740       0.6180       0.0000
H        -0.8740       0.6180       0.0000
H         0.0000      -0.6180       0.8740
H         0.0000      -0.6180      -0.8740

The first line contains the number of atoms in the molecule.

The second line is a comment. This line must be present, but can be blank or contain any text.

The remaining lines contain the elemental symbol (1-3 characters) and x, y, z cartesian coordinates. All of these values are separated by one or more spaces.

This program attempts to be flexible in reading these files, and does not require data to be present in specific columns. The one restriction that is enforced is that files must be named with the extension ".xyz".

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CH5M3D

User Interface: Keyboard and Mouse

While most common operations can be performed using only a mouse, a few operations require a combination of both keyboard and mouse. Note that these operations only work in View Mode. Note that in these descriptions, the screen is assumed to show the X-axis (horizontal) and the Y-axid (vertical), with the Z-axis coming "out" of this plane. The possible combinations and their results are outlined below.

  • Selecting a blank portion of the screen:
    • Mouse only - Dragging the mouse results in rotating the molecule around the X- and Y-axes.
    • <Shift> + Mouse - Rotation will occur around the Z-axis.
    • <Ctrl> + Mouse - The molecule will be translated along the X- and Y-axes.
  • Selecting a single atom:
    • Mouse only - The label for this atom is shown. (If the charges button is pressed, the calculated charge on this atom is also shown).
    • <Shift> + Mouse - The selected atom is highlighted. If this atom is already highlighted, this operation will cause the highlight to be removed.

A button is provided that will allow automatic re-scaling and re-centering of the molecule. This button will also remove all highlights from the displayed structure.

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CH5M3D

Installation

This "program" can be downloaded as a single zip file containing the following files.

  • index.html - The main HTML file loaded by a web browser.
  • ch5m3d.js - The javascript code required to generate the web interface.
  • ch5m3d.css - CSS code controlling the appearance of the web pages.
  • documentation.pdf - A PDF version of the documentation.
  • doc/ - A directory containing html documentation files and the GNU license.
  • molecules/ - A directory containing a small number of .xyz formatted files of molecular coordinates.
  • variations/ - A directory containing a few html files that illustrate different ways that web pages can use the javascript code to provide different views.
  • qchem/ - A directory containing a php files and support files that provide a simple front-end interface to the quantum mechanical program GAMESS. (Note that it is very unlikely that this will work without modification).

Testing

A live version of this program is available at the Project Web page on SourceForge. Note that a suitable web browser that supports HTML5 is required to run this program.

Installation on a Web Server

No special steps are required to install this program on a web server other than placing the "unzipped" directory tree in a location where it can be accessed by the web server. All file locations are coded as "relative" directories, so the actual path/directory location for these files does not matter.

If it is desired to change the relative location of any of these files, note that index.html assumes that ch5m3d.js and ch5m3d.css are both located in the same directory as index.html. All of the documentation files assume that ch5m3d.css is located "up" one directory (../ch5m3d.css).

ch5m3d-1.2.5+dfsg/doc/view.html0000644000175000017500000001757412230555426016346 0ustar georgeskgeorgesk CH5M3D

CH5M3D

User Interface: View Mode

The image below shows the initial view that should be presented when this page is first loaded. The most important sections are labeled in red. Upon initially loading this page, you should be in View Mode, indicated by both the highlighted tab and the text "View Mode" displayed below this button. You can switch between View Mode and Draw Mode at any time by selecting the appropriate tab.

View Mode Interface with sections labeled

Initially, the methane molecule (CH4) should be displayed in the Drawing Window. While in View mode, you can use your mouse/pointer to perform the following tasks.

  • Rotate Molecule - Move the pointer to any blank portion of the Drawing Window and hold the mouse button down. Dragging the pointer should cause the molecule to rotate. To stop rotation, simply release the mouse button. Simultaneously pressing <Shift> while dragging the mouse pointer will cause the molecule to rotate around the z-axis. It is also possible to 'translate' a molecule by pressing the <Ctrl> key while dragging the mouse.
  • Zoom - If a mouse scroll wheel is available, this can be used to either zoom-in or zoom-out the current view.
  • Identify Atom - Move the pointer over any atom in a molecule and click on this atom to select. The Elemental symbol followed by a number should be displayed. The number is the position of the atom in the set of coordinates for this molecule, starting at 1. If the button is active, then the calculated charge on this atom will also be displayed.
  • Highlight Atom - Move the pointer over any atom in a molecule, hold down the <Shift> key and click on this atom. A semitransparent yellow circle should appear over this atom. <Shift>-click on this atom a second time to turn off the highlight. Any number of atoms may be highlighted. The button may also be used to remove all highlights.
  • Measure Bond Lengths - Move the pointer to the first atom of the bond and select. The label for this atom should appear in the upper-right corner of the display window. Then, move the pointer to the second atom and select this atom. The bond length (in Angstroms) will be shown at the top right of the drawing window.
  • Measure Bond Angles - By selecting three atoms, the bond angle (in degrees) around the central atom (the second atom selected) will be shown.
  • Measure Dihedral Angles - By selecting four atoms, the dihedral angle (in degrees) will be shown. For example, if all four atoms lie in a plane, the dihedral angle will be either 0° or 180°.

For all of the operations, clicking on a blank portion of the screen will clear the list of selected atoms and allow you to start measuring a different set of lengths/angles. Clicking on the same atom twice will cause the atom list to be reset and this selected atom will be placed as the first atom on the list.

To the right of the Drawing Window are several buttons. These provide the following options:

  • This button will print the coordinates in .xyz format in the Information Window. For security reasons, it is not possible for javascript to write files to a user's computer. To save the coordinates of molecules created using this program, it is required that users open a text editor, copy the coordinates from the Information Window into their editor and save this as an .xyz file. When saving this file, but sure that it is saved as an unformatted text file.
  • This button toggles the display of labels (elemental symbols) for each atom.
  • Selecting this button causes a crude computation of atomic charge to be performed. Charges are shown as semi-transparent spheres around each atom. Negative charges are shown in red, and positive charges are shown as blue spheres. The intensity of these colors is used to indicate the magnitude of the charges. This charge calculation is based on a combination of formal charges and electronegativity differences. In addition, the dipole moment of the molecule based on these approximate point charges is displayed in the Information window near the bottom of the screen. Note that these calculated charges should not be considered to be accurate values but instead treated as a crude, first approximation.
  • This button centers and rescales the molecule to fit the display, and removes all highlights.
  • By selecting this button, users can load .xyz formatted files. Files of this format can be generated using the Open Babel program. A few sample .xyz files are available in the molecules folder on the CH5M3D Web site.

To save an image of a molecule, first rotate the molecule to get it into the desired orientation. Then, perform a right-click using the mouse pointer and select "Save Image As...".

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CH5M3D

 

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H   Organic Metals He
Li Be   B C N O F Ne
Na Mg   Al Si P S Cl Ar
K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr
Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe
Cs Ba La Hf Ta W Re Os Ir Pt Au Hg Tl Pb Bi Po At Rn
Fr Ra Ac Rf Db Sg Bh Hs Mt Ds Rg Cn Uut Fl Uup Lv Uus Uuo
  Ce Pr Nd Pm Sm Eu Gd Tb Dy Ho Er Tm Yb Lu  
  Th Pa U Np Pu Am Cm Bk Cf Es Fm Md No Lr  

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ch5m3d-1.2.5+dfsg/variations/serverView.html0000644000175000017500000000524012230555424021130 0ustar georgeskgeorgesk CH5M3D

CH5M3D

 

 

ch5m3d-1.2.5+dfsg/variations/gallery.html0000644000175000017500000000611712230555422020430 0ustar georgeskgeorgesk CH5M3D

CH5M3D

ch5m3d-1.2.5+dfsg/variations/chooser.html0000644000175000017500000000555312230555424020440 0ustar georgeskgeorgesk CH5M3D

CH5M3D

 

 

ch5m3d-1.2.5+dfsg/variations/viewer2x.html0000644000175000017500000000612312230555424020543 0ustar georgeskgeorgesk CH5M3D

CH5M3D

 

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CH5M3D

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ch5m3d-1.2.5+dfsg/variations/viewer300.html0000644000175000017500000000527012230555424020516 0ustar georgeskgeorgesk CH5M3D

CH5M3D

 

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CH5M3D

 

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%%EOF ch5m3d-1.2.5+dfsg/COPYING.txt0000755000175000017500000010451312230555426015603 0ustar georgeskgeorgesk GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007 Copyright (C) 2007 Free Software Foundation, Inc. Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. Preamble The GNU General Public License is a free, copyleft license for software and other kinds of works. The licenses for most software and other practical works are designed to take away your freedom to share and change the works. By contrast, the GNU General Public License is intended to guarantee your freedom to share and change all versions of a program--to make sure it remains free software for all its users. We, the Free Software Foundation, use the GNU General Public License for most of our software; it applies also to any other work released this way by its authors. You can apply it to your programs, too. When we speak of free software, we are referring to freedom, not price. Our General Public Licenses are designed to make sure that you have the freedom to distribute copies of free software (and charge for them if you wish), that you receive source code or can get it if you want it, that you can change the software or use pieces of it in new free programs, and that you know you can do these things. To protect your rights, we need to prevent others from denying you these rights or asking you to surrender the rights. Therefore, you have certain responsibilities if you distribute copies of the software, or if you modify it: responsibilities to respect the freedom of others. For example, if you distribute copies of such a program, whether gratis or for a fee, you must pass on to the recipients the same freedoms that you received. You must make sure that they, too, receive or can get the source code. And you must show them these terms so they know their rights. 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Regardless of what server hosts the Corresponding Source, you remain obligated to ensure that it is available for as long as needed to satisfy these requirements. e) Convey the object code using peer-to-peer transmission, provided you inform other peers where the object code and Corresponding Source of the work are being offered to the general public at no charge under subsection 6d. A separable portion of the object code, whose source code is excluded from the Corresponding Source as a System Library, need not be included in conveying the object code work. A "User Product" is either (1) a "consumer product", which means any tangible personal property which is normally used for personal, family, or household purposes, or (2) anything designed or sold for incorporation into a dwelling. In determining whether a product is a consumer product, doubtful cases shall be resolved in favor of coverage. For a particular product received by a particular user, "normally used" refers to a typical or common use of that class of product, regardless of the status of the particular user or of the way in which the particular user actually uses, or expects or is expected to use, the product. A product is a consumer product regardless of whether the product has substantial commercial, industrial or non-consumer uses, unless such uses represent the only significant mode of use of the product. "Installation Information" for a User Product means any methods, procedures, authorization keys, or other information required to install and execute modified versions of a covered work in that User Product from a modified version of its Corresponding Source. The information must suffice to ensure that the continued functioning of the modified object code is in no case prevented or interfered with solely because modification has been made. If you convey an object code work under this section in, or with, or specifically for use in, a User Product, and the conveying occurs as part of a transaction in which the right of possession and use of the User Product is transferred to the recipient in perpetuity or for a fixed term (regardless of how the transaction is characterized), the Corresponding Source conveyed under this section must be accompanied by the Installation Information. But this requirement does not apply if neither you nor any third party retains the ability to install modified object code on the User Product (for example, the work has been installed in ROM). The requirement to provide Installation Information does not include a requirement to continue to provide support service, warranty, or updates for a work that has been modified or installed by the recipient, or for the User Product in which it has been modified or installed. Access to a network may be denied when the modification itself materially and adversely affects the operation of the network or violates the rules and protocols for communication across the network. Corresponding Source conveyed, and Installation Information provided, in accord with this section must be in a format that is publicly documented (and with an implementation available to the public in source code form), and must require no special password or key for unpacking, reading or copying. 7. Additional Terms. "Additional permissions" are terms that supplement the terms of this License by making exceptions from one or more of its conditions. Additional permissions that are applicable to the entire Program shall be treated as though they were included in this License, to the extent that they are valid under applicable law. If additional permissions apply only to part of the Program, that part may be used separately under those permissions, but the entire Program remains governed by this License without regard to the additional permissions. When you convey a copy of a covered work, you may at your option remove any additional permissions from that copy, or from any part of it. (Additional permissions may be written to require their own removal in certain cases when you modify the work.) You may place additional permissions on material, added by you to a covered work, for which you have or can give appropriate copyright permission. Notwithstanding any other provision of this License, for material you add to a covered work, you may (if authorized by the copyright holders of that material) supplement the terms of this License with terms: a) Disclaiming warranty or limiting liability differently from the terms of sections 15 and 16 of this License; or b) Requiring preservation of specified reasonable legal notices or author attributions in that material or in the Appropriate Legal Notices displayed by works containing it; or c) Prohibiting misrepresentation of the origin of that material, or requiring that modified versions of such material be marked in reasonable ways as different from the original version; or d) Limiting the use for publicity purposes of names of licensors or authors of the material; or e) Declining to grant rights under trademark law for use of some trade names, trademarks, or service marks; or f) Requiring indemnification of licensors and authors of that material by anyone who conveys the material (or modified versions of it) with contractual assumptions of liability to the recipient, for any liability that these contractual assumptions directly impose on those licensors and authors. All other non-permissive additional terms are considered "further restrictions" within the meaning of section 10. If the Program as you received it, or any part of it, contains a notice stating that it is governed by this License along with a term that is a further restriction, you may remove that term. If a license document contains a further restriction but permits relicensing or conveying under this License, you may add to a covered work material governed by the terms of that license document, provided that the further restriction does not survive such relicensing or conveying. If you add terms to a covered work in accord with this section, you must place, in the relevant source files, a statement of the additional terms that apply to those files, or a notice indicating where to find the applicable terms. Additional terms, permissive or non-permissive, may be stated in the form of a separately written license, or stated as exceptions; the above requirements apply either way. 8. Termination. You may not propagate or modify a covered work except as expressly provided under this License. Any attempt otherwise to propagate or modify it is void, and will automatically terminate your rights under this License (including any patent licenses granted under the third paragraph of section 11). However, if you cease all violation of this License, then your license from a particular copyright holder is reinstated (a) provisionally, unless and until the copyright holder explicitly and finally terminates your license, and (b) permanently, if the copyright holder fails to notify you of the violation by some reasonable means prior to 60 days after the cessation. Moreover, your license from a particular copyright holder is reinstated permanently if the copyright holder notifies you of the violation by some reasonable means, this is the first time you have received notice of violation of this License (for any work) from that copyright holder, and you cure the violation prior to 30 days after your receipt of the notice. Termination of your rights under this section does not terminate the licenses of parties who have received copies or rights from you under this License. If your rights have been terminated and not permanently reinstated, you do not qualify to receive new licenses for the same material under section 10. 9. Acceptance Not Required for Having Copies. You are not required to accept this License in order to receive or run a copy of the Program. Ancillary propagation of a covered work occurring solely as a consequence of using peer-to-peer transmission to receive a copy likewise does not require acceptance. However, nothing other than this License grants you permission to propagate or modify any covered work. These actions infringe copyright if you do not accept this License. Therefore, by modifying or propagating a covered work, you indicate your acceptance of this License to do so. 10. Automatic Licensing of Downstream Recipients. Each time you convey a covered work, the recipient automatically receives a license from the original licensors, to run, modify and propagate that work, subject to this License. You are not responsible for enforcing compliance by third parties with this License. An "entity transaction" is a transaction transferring control of an organization, or substantially all assets of one, or subdividing an organization, or merging organizations. If propagation of a covered work results from an entity transaction, each party to that transaction who receives a copy of the work also receives whatever licenses to the work the party's predecessor in interest had or could give under the previous paragraph, plus a right to possession of the Corresponding Source of the work from the predecessor in interest, if the predecessor has it or can get it with reasonable efforts. You may not impose any further restrictions on the exercise of the rights granted or affirmed under this License. For example, you may not impose a license fee, royalty, or other charge for exercise of rights granted under this License, and you may not initiate litigation (including a cross-claim or counterclaim in a lawsuit) alleging that any patent claim is infringed by making, using, selling, offering for sale, or importing the Program or any portion of it. 11. Patents. A "contributor" is a copyright holder who authorizes use under this License of the Program or a work on which the Program is based. The work thus licensed is called the contributor's "contributor version". A contributor's "essential patent claims" are all patent claims owned or controlled by the contributor, whether already acquired or hereafter acquired, that would be infringed by some manner, permitted by this License, of making, using, or selling its contributor version, but do not include claims that would be infringed only as a consequence of further modification of the contributor version. For purposes of this definition, "control" includes the right to grant patent sublicenses in a manner consistent with the requirements of this License. Each contributor grants you a non-exclusive, worldwide, royalty-free patent license under the contributor's essential patent claims, to make, use, sell, offer for sale, import and otherwise run, modify and propagate the contents of its contributor version. In the following three paragraphs, a "patent license" is any express agreement or commitment, however denominated, not to enforce a patent (such as an express permission to practice a patent or covenant not to sue for patent infringement). To "grant" such a patent license to a party means to make such an agreement or commitment not to enforce a patent against the party. If you convey a covered work, knowingly relying on a patent license, and the Corresponding Source of the work is not available for anyone to copy, free of charge and under the terms of this License, through a publicly available network server or other readily accessible means, then you must either (1) cause the Corresponding Source to be so available, or (2) arrange to deprive yourself of the benefit of the patent license for this particular work, or (3) arrange, in a manner consistent with the requirements of this License, to extend the patent license to downstream recipients. "Knowingly relying" means you have actual knowledge that, but for the patent license, your conveying the covered work in a country, or your recipient's use of the covered work in a country, would infringe one or more identifiable patents in that country that you have reason to believe are valid. If, pursuant to or in connection with a single transaction or arrangement, you convey, or propagate by procuring conveyance of, a covered work, and grant a patent license to some of the parties receiving the covered work authorizing them to use, propagate, modify or convey a specific copy of the covered work, then the patent license you grant is automatically extended to all recipients of the covered work and works based on it. A patent license is "discriminatory" if it does not include within the scope of its coverage, prohibits the exercise of, or is conditioned on the non-exercise of one or more of the rights that are specifically granted under this License. You may not convey a covered work if you are a party to an arrangement with a third party that is in the business of distributing software, under which you make payment to the third party based on the extent of your activity of conveying the work, and under which the third party grants, to any of the parties who would receive the covered work from you, a discriminatory patent license (a) in connection with copies of the covered work conveyed by you (or copies made from those copies), or (b) primarily for and in connection with specific products or compilations that contain the covered work, unless you entered into that arrangement, or that patent license was granted, prior to 28 March 2007. Nothing in this License shall be construed as excluding or limiting any implied license or other defenses to infringement that may otherwise be available to you under applicable patent law. 12. No Surrender of Others' Freedom. If conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the conditions of this License, they do not excuse you from the conditions of this License. If you cannot convey a covered work so as to satisfy simultaneously your obligations under this License and any other pertinent obligations, then as a consequence you may not convey it at all. For example, if you agree to terms that obligate you to collect a royalty for further conveying from those to whom you convey the Program, the only way you could satisfy both those terms and this License would be to refrain entirely from conveying the Program. 13. Use with the GNU Affero General Public License. Notwithstanding any other provision of this License, you have permission to link or combine any covered work with a work licensed under version 3 of the GNU Affero General Public License into a single combined work, and to convey the resulting work. The terms of this License will continue to apply to the part which is the covered work, but the special requirements of the GNU Affero General Public License, section 13, concerning interaction through a network will apply to the combination as such. 14. Revised Versions of this License. The Free Software Foundation may publish revised and/or new versions of the GNU General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns. Each version is given a distinguishing version number. If the Program specifies that a certain numbered version of the GNU General Public License "or any later version" applies to it, you have the option of following the terms and conditions either of that numbered version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of the GNU General Public License, you may choose any version ever published by the Free Software Foundation. If the Program specifies that a proxy can decide which future versions of the GNU General Public License can be used, that proxy's public statement of acceptance of a version permanently authorizes you to choose that version for the Program. Later license versions may give you additional or different permissions. However, no additional obligations are imposed on any author or copyright holder as a result of your choosing to follow a later version. 15. Disclaimer of Warranty. THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION. 16. Limitation of Liability. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. 17. Interpretation of Sections 15 and 16. If the disclaimer of warranty and limitation of liability provided above cannot be given local legal effect according to their terms, reviewing courts shall apply local law that most closely approximates an absolute waiver of all civil liability in connection with the Program, unless a warranty or assumption of liability accompanies a copy of the Program in return for a fee. END OF TERMS AND CONDITIONS How to Apply These Terms to Your New Programs If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms. To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively state the exclusion of warranty; and each file should have at least the "copyright" line and a pointer to where the full notice is found. Copyright (C) This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see . Also add information on how to contact you by electronic and paper mail. If the program does terminal interaction, make it output a short notice like this when it starts in an interactive mode: Copyright (C) This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. This is free software, and you are welcome to redistribute it under certain conditions; type `show c' for details. The hypothetical commands `show w' and `show c' should show the appropriate parts of the General Public License. Of course, your program's commands might be different; for a GUI interface, you would use an "about box". You should also get your employer (if you work as a programmer) or school, if any, to sign a "copyright disclaimer" for the program, if necessary. For more information on this, and how to apply and follow the GNU GPL, see . The GNU General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Lesser General Public License instead of this License. But first, please read .