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Today is 28Apr2008 at 16: 2:51 For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or PAW Current dimensions of program pwscf are: Max number of different atomic species (ntypx) = 10 Max number of k-points (npk) = 40000 Max angular momentum in pseudopotentials (lmaxx) = 3 gamma-point specific algorithms are used initial path length = 4.2553 bohr initial inter-image distance = 0.7092 bohr calculation = neb restart_mode = from_scratch opt_scheme = broyden num_of_images = 7 nstep = 50 CI_scheme = auto first_last_opt = F coarse-grained phase-space = F use_freezing = F ds = 2.0000 a.u. k_max = 0.3000 a.u. k_min = 0.2000 a.u. suggested k_max = 0.1542 a.u. suggested k_min = 0.1028 a.u. path_thr = 0.1000 eV / A ------------------------------ iteration 1 ------------------------------ tcpu = 0.0 self-consistency for image 1 tcpu = 0.4 self-consistency for image 2 tcpu = 0.9 self-consistency for image 3 tcpu = 1.4 self-consistency for image 4 tcpu = 1.9 self-consistency for image 5 tcpu = 2.4 self-consistency for image 6 tcpu = 2.8 self-consistency for image 7 activation energy (->) = 1.705764 eV activation energy (<-) = 1.705764 eV image energy (eV) error (eV/A) frozen 1 -49.5015717 0.010088 T 2 -49.0010335 2.084250 F 3 -48.1936447 2.303345 F 4 -47.7958079 1.708818 F 5 -48.1936447 2.303352 F 6 -49.0010335 2.084248 F 7 -49.5015717 0.010106 T climbing image = 4 path length = 4.255 bohr inter-image distance = 0.709 bohr ------------------------------ iteration 2 ------------------------------ tcpu = 3.2 self-consistency for image 2 tcpu = 3.7 self-consistency for image 3 tcpu = 4.1 self-consistency for image 4 tcpu = 4.7 self-consistency for image 5 tcpu = 5.2 self-consistency for image 6 activation energy (->) = 1.463729 eV activation energy (<-) = 1.463729 eV image energy (eV) error (eV/A) frozen 1 -49.5015717 0.010088 T 2 -49.1182224 1.626556 F 3 -48.3973162 2.006061 F 4 -48.0378432 1.727851 F 5 -48.3973172 2.006061 F 6 -49.1182222 1.626556 F 7 -49.5015717 0.010106 T climbing image = 4 path length = 4.293 bohr inter-image distance = 0.715 bohr ------------------------------ iteration 3 ------------------------------ tcpu = 5.7 self-consistency for image 2 tcpu = 6.1 self-consistency for image 3 tcpu = 6.6 self-consistency for image 4 tcpu = 7.0 self-consistency for image 5 tcpu = 7.5 self-consistency for image 6 activation energy (->) = 1.098989 eV activation energy (<-) = 1.098989 eV image energy (eV) error (eV/A) frozen 1 -49.5015717 0.010088 T 2 -49.3117485 1.332428 F 3 -48.7120300 1.599538 F 4 -48.4025832 1.696518 F 5 -48.7120303 1.599537 F 6 -49.3117490 1.332424 F 7 -49.5015717 0.010106 T climbing image = 4 path length = 4.457 bohr inter-image distance = 0.743 bohr ------------------------------ iteration 4 ------------------------------ tcpu = 7.9 self-consistency for image 2 tcpu = 8.3 self-consistency for image 3 tcpu = 8.8 self-consistency for image 4 tcpu = 9.3 self-consistency for image 5 tcpu = 9.9 self-consistency for image 6 activation energy (->) = 0.736032 eV activation energy (<-) = 0.736032 eV image energy (eV) error (eV/A) frozen 1 -49.5015717 0.010088 T 2 -49.4419538 0.967940 F 3 -49.0138211 1.611376 F 4 -48.7655401 1.535157 F 5 -49.0138209 1.611375 F 6 -49.4419540 0.967935 F 7 -49.5015717 0.010106 T climbing image = 4 path length = 4.720 bohr inter-image distance = 0.787 bohr ------------------------------ iteration 5 ------------------------------ tcpu = 10.4 self-consistency for image 2 tcpu = 10.8 self-consistency for image 3 tcpu = 11.3 self-consistency for image 4 tcpu = 11.7 self-consistency for image 5 tcpu = 12.2 self-consistency for image 6 activation energy (->) = 0.416523 eV activation energy (<-) = 0.416523 eV image energy (eV) error (eV/A) frozen 1 -49.5015717 0.010088 T 2 -49.4475593 1.270664 F 3 -49.2552417 1.404518 F 4 -49.0850482 1.145325 F 5 -49.2552413 1.404517 F 6 -49.4475591 1.270664 F 7 -49.5015717 0.010106 T climbing image = 4 path length = 5.051 bohr inter-image distance = 0.842 bohr ------------------------------ iteration 6 ------------------------------ tcpu = 12.7 self-consistency for image 2 tcpu = 13.0 self-consistency for image 3 tcpu = 13.6 self-consistency for image 4 tcpu = 14.0 self-consistency for image 5 tcpu = 14.6 self-consistency for image 6 activation energy (->) = 0.212480 eV activation energy (<-) = 0.212480 eV image energy (eV) error (eV/A) frozen 1 -49.5015717 0.010088 T 2 -49.3551546 2.335058 F 3 -49.3494621 1.813497 F 4 -49.2890913 0.273185 F 5 -49.3494621 1.813491 F 6 -49.3551544 2.335058 F 7 -49.5015717 0.010106 T climbing image = 4 path length = 5.415 bohr inter-image distance = 0.903 bohr ------------------------------ iteration 7 ------------------------------ tcpu = 14.9 self-consistency for image 2 tcpu = 15.3 self-consistency for image 3 tcpu = 15.8 self-consistency for image 4 tcpu = 16.3 self-consistency for image 5 tcpu = 16.7 self-consistency for image 6 activation energy (->) = 0.309394 eV activation energy (<-) = 0.309394 eV image energy (eV) error (eV/A) frozen 1 -49.5015717 0.010088 T 2 -49.4633298 0.843368 F 3 -49.3387899 0.644622 F 4 -49.1921777 0.868610 F 5 -49.3387896 0.644623 F 6 -49.4633298 0.843365 F 7 -49.5015717 0.010106 T climbing image = 4 path length = 5.104 bohr inter-image distance = 0.851 bohr ------------------------------ iteration 8 ------------------------------ tcpu = 17.1 self-consistency for image 2 tcpu = 17.5 self-consistency for image 3 tcpu = 17.9 self-consistency for image 4 tcpu = 18.3 self-consistency for image 5 tcpu = 18.7 self-consistency for image 6 activation energy (->) = 0.258082 eV activation energy (<-) = 0.258082 eV image energy (eV) error (eV/A) frozen 1 -49.5015717 0.010088 T 2 -49.4700498 0.152243 F 3 -49.3626600 0.444364 F 4 -49.2434895 0.651593 F 5 -49.3626597 0.444365 F 6 -49.4700498 0.152243 F 7 -49.5015717 0.010106 T climbing image = 4 path length = 5.153 bohr inter-image distance = 0.859 bohr ------------------------------ iteration 9 ------------------------------ tcpu = 19.1 self-consistency for image 2 tcpu = 19.4 self-consistency for image 3 tcpu = 19.8 self-consistency for image 4 tcpu = 20.2 self-consistency for image 5 tcpu = 20.6 self-consistency for image 6 activation energy (->) = 0.223970 eV activation energy (<-) = 0.223970 eV image energy (eV) error (eV/A) frozen 1 -49.5015717 0.010088 T 2 -49.4688392 0.343489 F 3 -49.3763949 0.367419 F 4 -49.2776018 0.412481 F 5 -49.3763947 0.367419 F 6 -49.4688391 0.343489 F 7 -49.5015717 0.010106 T climbing image = 4 path length = 5.215 bohr inter-image distance = 0.869 bohr ------------------------------ iteration 10 ------------------------------ tcpu = 20.9 self-consistency for image 2 tcpu = 21.3 self-consistency for image 3 tcpu = 21.7 self-consistency for image 4 tcpu = 22.0 self-consistency for image 5 tcpu = 22.4 self-consistency for image 6 activation energy (->) = 0.219823 eV activation energy (<-) = 0.219823 eV image energy (eV) error (eV/A) frozen 1 -49.5015717 0.010088 T 2 -49.4707563 0.170855 F 3 -49.3718313 0.271386 F 4 -49.2817489 0.369262 F 5 -49.3718311 0.271386 F 6 -49.4707563 0.170856 F 7 -49.5015717 0.010106 T climbing image = 4 path length = 5.215 bohr inter-image distance = 0.869 bohr ------------------------------ iteration 11 ------------------------------ tcpu = 22.8 self-consistency for image 2 tcpu = 23.2 self-consistency for image 3 tcpu = 23.6 self-consistency for image 4 tcpu = 24.0 self-consistency for image 5 tcpu = 24.4 self-consistency for image 6 activation energy (->) = 0.213924 eV activation energy (<-) = 0.213924 eV image energy (eV) error (eV/A) frozen 1 -49.5015717 0.010088 T 2 -49.4700770 0.049788 F 3 -49.3706616 0.177726 F 4 -49.2876475 0.295103 F 5 -49.3706614 0.177726 F 6 -49.4700770 0.049788 F 7 -49.5015717 0.010106 T climbing image = 4 path length = 5.240 bohr inter-image distance = 0.873 bohr ------------------------------ iteration 12 ------------------------------ tcpu = 24.8 self-consistency for image 2 tcpu = 25.2 self-consistency for image 3 tcpu = 25.6 self-consistency for image 4 tcpu = 26.0 self-consistency for image 5 tcpu = 26.4 self-consistency for image 6 activation energy (->) = 0.205188 eV activation energy (<-) = 0.205188 eV image energy (eV) error (eV/A) frozen 1 -49.5015717 0.010088 T 2 -49.4688491 0.140232 F 3 -49.3705456 0.080977 F 4 -49.2963836 0.094863 F 5 -49.3705455 0.080977 F 6 -49.4688490 0.140232 F 7 -49.5015717 0.010106 T climbing image = 4 path length = 5.294 bohr inter-image distance = 0.882 bohr ------------------------------ iteration 13 ------------------------------ tcpu = 26.8 self-consistency for image 2 tcpu = 27.2 self-consistency for image 3 tcpu = 27.5 self-consistency for image 4 tcpu = 27.9 self-consistency for image 5 tcpu = 28.3 self-consistency for image 6 activation energy (->) = 0.204271 eV activation energy (<-) = 0.204271 eV image energy (eV) error (eV/A) frozen 1 -49.5015717 0.010088 T 2 -49.4686052 0.045064 F 3 -49.3702112 0.042258 F 4 -49.2973011 0.015888 F 5 -49.3702110 0.042258 F 6 -49.4686052 0.045064 F 7 -49.5015717 0.010106 T climbing image = 4 path length = 5.312 bohr inter-image distance = 0.885 bohr --------------------------------------------------------------------------- neb: convergence achieved in 13 iterations PWSCF : 28.62s CPU time, 33.03s wall time init_run : 4.20s CPU ( 67 calls, 0.063 s avg) electrons : 19.76s CPU ( 67 calls, 0.295 s avg) update_pot : 2.13s CPU ( 60 calls, 0.036 s avg) forces : 0.54s CPU ( 67 calls, 0.008 s avg) Called by init_run: wfcinit : 0.01s CPU ( 67 calls, 0.000 s avg) potinit : 1.58s CPU ( 67 calls, 0.024 s avg) Called by electrons: c_bands : 2.66s CPU ( 565 calls, 0.005 s avg) sum_band : 2.80s CPU ( 565 calls, 0.005 s avg) v_of_rho : 13.19s CPU ( 692 calls, 0.019 s avg) newd : 0.55s CPU ( 632 calls, 0.001 s avg) mix_rho : 0.94s CPU ( 565 calls, 0.002 s avg) Called by c_bands: init_us_2 : 0.09s CPU ( 2518 calls, 0.000 s avg) regterg : 2.55s CPU ( 1130 calls, 0.002 s avg) Called by *egterg: h_psi : 1.87s CPU ( 2956 calls, 0.001 s avg) s_psi : 0.04s CPU ( 3066 calls, 0.000 s avg) g_psi : 0.07s CPU ( 1812 calls, 0.000 s avg) rdiaghg : 0.30s CPU ( 2822 calls, 0.000 s avg) Called by h_psi: add_vuspsi : 0.05s CPU ( 2956 calls, 0.000 s avg) General routines calbec : 0.10s CPU ( 4842 calls, 0.000 s avg) cft3 : 3.72s CPU ( 19013 calls, 0.000 s avg) cft3s : 2.08s CPU ( 21918 calls, 0.000 s avg) interpolate : 1.09s CPU ( 2394 calls, 0.000 s avg) davcio : 0.03s CPU ( 4208 calls, 0.000 s avg) NEB/examples/example01/reference/asymmetric_H2+H.path0000644000700200004540000000634212053145633021607 0ustar marsamoscmRESTART INFORMATION 13 50 0 NUMBER OF IMAGES 8 ENERGIES, POSITIONS AND GRADIENTS Image: 1 -1.8191493670 -4.566700090000 0.000000000000 0.000000000000 0.000196343081 0.000000000000 0.000000000000 1 0 0 0.000000000000 0.000000000000 0.000000000000 0.000000000000 0.000000000000 0.000000000000 0 0 0 1.557766760000 0.000000000000 0.000000000000 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0.0000000000 0.0000000000 3 H -1.8714286233 0.0000000000 0.0000000000 H 0.0000000000 0.0000000000 0.0000000000 H 0.8349215369 0.0000000000 0.0000000000 3 H -1.4065859742 0.0000000000 0.0000000000 H 0.0000000000 0.0000000000 0.0000000000 H 0.8818384013 0.0000000000 0.0000000000 3 H -1.0524649767 0.0000000000 0.0000000000 H 0.0000000000 0.0000000000 0.0000000000 H 1.0524643124 0.0000000000 0.0000000000 3 H -0.8818385490 0.0000000000 0.0000000000 H 0.0000000000 0.0000000000 0.0000000000 H 1.4065853106 0.0000000000 0.0000000000 3 H -0.8349215547 0.0000000000 0.0000000000 H 0.0000000000 0.0000000000 0.0000000000 H 1.8714281947 0.0000000000 0.0000000000 3 H -0.8243346657 0.0000000000 0.0000000000 H 0.0000000000 0.0000000000 0.0000000000 H 2.4165936061 0.0000000000 0.0000000000 NEB/examples/example01/reference/H2+H-cp.out0000644000700200004540000005602312053145633017626 0ustar marsamoscm=------------------------------------------------------------------------------= CP: variable-cell Car-Parrinello molecular dynamics using norm-conserving and ultrasoft Vanderbilt pseudopotentials Version: 4.0 - Mon Apr 28 15:32:33 CEST 2008 Authors: Alfredo Pasquarello, Kari Laasonen, Andrea Trave, Roberto Car, Paolo Giannozzi, Nicola Marzari, Carlo Cavazzoni, Guido Chiarotti, Sandro Scandolo, Paolo Focher, Gerardo Ballabio, and others =------------------------------------------------------------------------------= This run was started on: 16: 4:37 28Apr2008 Serial Build Warning: card K_POINTS { GAMMA } ignored Job Title: MD Simulation Atomic Pseudopotentials Parameters ---------------------------------- Reading pseudopotential for specie # 1 from file : /home/giannozz/espresso/pseudo/HUSPBE.RRKJ3 file type is 2: RRKJ3 Main Simulation Parameters (from input) --------------------------------------- Restart Mode = -1 from_scratch Number of MD Steps = 50 Print out every 50 MD Steps Reads from unit = 50 Writes to unit = 50 MD Simulation time step = 10.00 Electronic fictitious mass (emass) = 250.00 emass cut-off = 2.50 Simulation Cell Parameters (from input) external pressure = 0.00 [GPa] wmass (calculated) = 418.87 [AU] initial cell from CELL_PARAMETERS card 12.00000000 0.00000000 0.00000000 0.00000000 5.00000000 0.00000000 0.00000000 0.00000000 5.00000000 ibrav = 0 alat = 1.00000000 a1 = 12.00000000 0.00000000 0.00000000 a2 = 0.00000000 5.00000000 0.00000000 a3 = 0.00000000 0.00000000 5.00000000 b1 = 0.08333333 0.00000000 0.00000000 b2 = 0.00000000 0.20000000 0.00000000 b3 = 0.00000000 0.00000000 0.20000000 omega = 300.00000000 Energy Cut-offs --------------- Ecutwfc = 20.0 Ry, Ecutrho = 100.0 Ry, Ecuts = 80.0 Ry Gcutwfc = 0.7 , Gcutrho = 1.6 Gcuts = 1.4 NOTA BENE: refg, mmx = 0.050000 2400 Eigenvalues calculated without the kinetic term contribution Orthog. with lagrange multipliers : eps = 0.10E-07, max = 250 verlet algorithm for electron dynamics with friction frice = 0.2000 , grease = 1.0000 Electron dynamics : the temperature is not controlled initial random displacement of el. coordinates with amplitude= 0.020000 Electronic states ----------------- Local Spin Density calculation Number of Electron = 3 Spins up = 2, occupations: 1.00 1.00 Spins down = 1, occupations: 1.00 Exchange and correlations functionals ------------------------------------- Using Local Density Approximation with Exchange functional: SLATER Correlation functional: PERDEW AND WANG Using Generalized Gradient Corrections with Exchange functional: PERDEW BURKE ERNZERHOF Correlation functional: PERDEW BURKE ERNZERHOF Exchange-correlation = SLA -PW -PBX -PBC (1434) Ions Simulation Parameters -------------------------- Ions are not allowed to move Ionic position (from input) sorted by specie, and converted to real a.u. coordinates Species 1 atoms = 3 mass = 1837.36 (a.u.), 1.01 (amu) rcmax = 0.50 (a.u.) 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 Ionic position read from input file Cell Dynamics Parameters (from STDIN) ------------------------------------- Starting cell generated from CELLDM Constant VOLUME Molecular dynamics cell parameters are not allowed to move Verbosity: iprsta = 1 initial path length = 4.2553 bohr initial inter-image distance = 0.7092 bohr calculation = neb restart_mode = from_scratch opt_scheme = broyden num_of_images = 7 nstep = 50 CI_scheme = auto first_last_opt = F coarse-grained phase-space = F use_freezing = F ds = 2.0000 a.u. k_max = 0.3000 a.u. k_min = 0.2000 a.u. suggested k_max = 0.1542 a.u. suggested k_min = 0.1028 a.u. path_thr = 0.1000 eV / A ------------------------------ iteration 1 ------------------------------ tcpu = 0.0 self-consistency for image 1 Delta V(G=0): 0.007854Ry, 0.213707eV tcpu = 1.0 self-consistency for image 2 Delta V(G=0): 0.007854Ry, 0.213707eV tcpu = 2.0 self-consistency for image 3 Delta V(G=0): 0.007854Ry, 0.213707eV tcpu = 3.4 self-consistency for image 4 Delta V(G=0): 0.007854Ry, 0.213707eV tcpu = 4.4 self-consistency for image 5 Delta V(G=0): 0.007854Ry, 0.213707eV tcpu = 6.0 self-consistency for image 6 Delta V(G=0): 0.007854Ry, 0.213707eV tcpu = 7.1 self-consistency for image 7 Delta V(G=0): 0.007854Ry, 0.213707eV activation energy (->) = 1.706820 eV activation energy (<-) = 1.707019 eV image energy (eV) error (eV/A) frozen 1 -49.5053029 0.013776 T 2 -49.0039505 2.083667 F 3 -48.1964753 2.304139 F 4 -47.7984832 1.716077 F 5 -48.1965105 2.304518 F 6 -49.0040482 2.086521 F 7 -49.5055023 0.018591 T climbing image = 4 path length = 4.255 bohr inter-image distance = 0.709 bohr ------------------------------ iteration 2 ------------------------------ tcpu = 8.0 self-consistency for image 2 Delta V(G=0): 0.007854Ry, 0.213707eV tcpu = 8.6 self-consistency for image 3 Delta V(G=0): 0.007854Ry, 0.213707eV tcpu = 9.3 self-consistency for image 4 Delta V(G=0): 0.007854Ry, 0.213707eV tcpu = 10.0 self-consistency for image 5 Delta V(G=0): 0.007854Ry, 0.213707eV tcpu = 10.7 self-consistency for image 6 Delta V(G=0): 0.007854Ry, 0.213707eV activation energy (->) = 1.464164 eV activation energy (<-) = 1.464364 eV image energy (eV) error (eV/A) frozen 1 -49.5053029 0.013776 T 2 -49.1210138 1.603467 F 3 -48.4003663 2.013713 F 4 -48.0411387 1.704188 F 5 -48.4004563 2.010021 F 6 -49.1214711 1.602840 F 7 -49.5055023 0.018591 T climbing image = 4 path length = 4.293 bohr inter-image distance = 0.715 bohr ------------------------------ iteration 3 ------------------------------ tcpu = 11.3 self-consistency for image 2 Delta V(G=0): 0.007854Ry, 0.213707eV tcpu = 12.0 self-consistency for image 3 Delta V(G=0): 0.007854Ry, 0.213707eV tcpu = 12.7 self-consistency for image 4 Delta V(G=0): 0.007854Ry, 0.213707eV tcpu = 13.4 self-consistency for image 5 Delta V(G=0): 0.007854Ry, 0.213707eV tcpu = 14.1 self-consistency for image 6 Delta V(G=0): 0.007854Ry, 0.213707eV activation energy (->) = 1.101964 eV activation energy (<-) = 1.102163 eV image energy (eV) error (eV/A) frozen 1 -49.5053029 0.013776 T 2 -49.3125870 1.362486 F 3 -48.7179788 1.613610 F 4 -48.4033392 1.707762 F 5 -48.7186163 1.615709 F 6 -49.3128139 1.365536 F 7 -49.5055023 0.018591 T climbing image = 4 path length = 4.456 bohr inter-image distance = 0.743 bohr ------------------------------ iteration 4 ------------------------------ tcpu = 14.8 self-consistency for image 2 Delta V(G=0): 0.007854Ry, 0.213707eV tcpu = 15.5 self-consistency for image 3 Delta V(G=0): 0.007854Ry, 0.213707eV tcpu = 16.2 self-consistency for image 4 Delta V(G=0): 0.007854Ry, 0.213707eV tcpu = 16.9 self-consistency for image 5 Delta V(G=0): 0.007854Ry, 0.213707eV tcpu = 17.6 self-consistency for image 6 Delta V(G=0): 0.007854Ry, 0.213707eV activation energy (->) = 0.740525 eV activation energy (<-) = 0.740725 eV image energy (eV) error (eV/A) frozen 1 -49.5053029 0.013776 T 2 -49.4442681 0.994205 F 3 -49.0198636 1.615521 F 4 -48.7647775 1.556996 F 5 -49.0205216 1.611525 F 6 -49.4445084 0.995376 F 7 -49.5055023 0.018591 T climbing image = 4 path length = 4.719 bohr inter-image distance = 0.787 bohr ------------------------------ iteration 5 ------------------------------ tcpu = 18.3 self-consistency for image 2 Delta V(G=0): 0.007854Ry, 0.213707eV tcpu = 19.0 self-consistency for image 3 Delta V(G=0): 0.007854Ry, 0.213707eV tcpu = 19.7 self-consistency for image 4 Delta V(G=0): 0.007854Ry, 0.213707eV tcpu = 20.4 self-consistency for image 5 Delta V(G=0): 0.007854Ry, 0.213707eV tcpu = 21.1 self-consistency for image 6 Delta V(G=0): 0.007854Ry, 0.213707eV activation energy (->) = 0.421357 eV activation energy (<-) = 0.421557 eV image energy (eV) error (eV/A) frozen 1 -49.5053029 0.013776 T 2 -49.4523419 1.233088 F 3 -49.2598346 1.426914 F 4 -49.0839456 1.175916 F 5 -49.2603274 1.422410 F 6 -49.4524385 1.235352 F 7 -49.5055023 0.018591 T climbing image = 4 path length = 5.051 bohr inter-image distance = 0.842 bohr ------------------------------ iteration 6 ------------------------------ tcpu = 21.8 self-consistency for image 2 Delta V(G=0): 0.007854Ry, 0.213707eV tcpu = 22.5 self-consistency for image 3 Delta V(G=0): 0.007854Ry, 0.213707eV tcpu = 23.2 self-consistency for image 4 Delta V(G=0): 0.007854Ry, 0.213707eV tcpu = 23.9 self-consistency for image 5 Delta V(G=0): 0.007854Ry, 0.213707eV tcpu = 24.6 self-consistency for image 6 Delta V(G=0): 0.007854Ry, 0.213707eV activation energy (->) = 0.214883 eV activation energy (<-) = 0.215083 eV image energy (eV) error (eV/A) frozen 1 -49.5053029 0.013776 T 2 -49.3533841 2.402947 F 3 -49.3517161 1.826382 F 4 -49.2904198 0.322579 F 5 -49.3518471 1.826289 F 6 -49.3534898 2.406525 F 7 -49.5055023 0.018591 T climbing image = 4 path length = 5.419 bohr inter-image distance = 0.903 bohr ------------------------------ iteration 7 ------------------------------ tcpu = 25.2 self-consistency for image 2 Delta V(G=0): 0.007854Ry, 0.213707eV tcpu = 25.8 self-consistency for image 3 Delta V(G=0): 0.007854Ry, 0.213707eV tcpu = 26.5 self-consistency for image 4 Delta V(G=0): 0.007854Ry, 0.213707eV tcpu = 27.2 self-consistency for image 5 Delta V(G=0): 0.007854Ry, 0.213707eV tcpu = 27.9 self-consistency for image 6 Delta V(G=0): 0.007854Ry, 0.213707eV activation energy (->) = 0.312407 eV activation energy (<-) = 0.312607 eV image energy (eV) error (eV/A) frozen 1 -49.5053029 0.013776 T 2 -49.4667503 0.841746 F 3 -49.3427158 0.634265 F 4 -49.1928956 0.868299 F 5 -49.3429931 0.631461 F 6 -49.4669234 0.841671 F 7 -49.5055023 0.018591 T climbing image = 4 path length = 5.108 bohr inter-image distance = 0.851 bohr ------------------------------ iteration 8 ------------------------------ tcpu = 28.5 self-consistency for image 2 Delta V(G=0): 0.007854Ry, 0.213707eV tcpu = 29.1 self-consistency for image 3 Delta V(G=0): 0.007854Ry, 0.213707eV tcpu = 29.6 self-consistency for image 4 Delta V(G=0): 0.007854Ry, 0.213707eV tcpu = 30.3 self-consistency for image 5 Delta V(G=0): 0.007854Ry, 0.213707eV tcpu = 30.8 self-consistency for image 6 Delta V(G=0): 0.007854Ry, 0.213707eV activation energy (->) = 0.259295 eV activation energy (<-) = 0.259495 eV image energy (eV) error (eV/A) frozen 1 -49.5053029 0.013776 T 2 -49.4738151 0.126010 F 3 -49.3664683 0.476758 F 4 -49.2460077 0.640546 F 5 -49.3666244 0.475901 F 6 -49.4739795 0.126609 F 7 -49.5055023 0.018591 T climbing image = 4 path length = 5.158 bohr inter-image distance = 0.860 bohr ------------------------------ iteration 9 ------------------------------ tcpu = 31.4 self-consistency for image 2 Delta V(G=0): 0.007854Ry, 0.213707eV tcpu = 31.9 self-consistency for image 3 Delta V(G=0): 0.007854Ry, 0.213707eV tcpu = 32.4 self-consistency for image 4 Delta V(G=0): 0.007854Ry, 0.213707eV tcpu = 33.0 self-consistency for image 5 Delta V(G=0): 0.007854Ry, 0.213707eV tcpu = 33.6 self-consistency for image 6 Delta V(G=0): 0.007854Ry, 0.213707eV activation energy (->) = 0.224273 eV activation energy (<-) = 0.224473 eV image energy (eV) error (eV/A) frozen 1 -49.5053029 0.013776 T 2 -49.4722725 0.335928 F 3 -49.3809791 0.341345 F 4 -49.2810295 0.391091 F 5 -49.3811032 0.342656 F 6 -49.4724243 0.336179 F 7 -49.5055023 0.018591 T climbing image = 4 path length = 5.227 bohr inter-image distance = 0.871 bohr ------------------------------ iteration 10 ------------------------------ tcpu = 34.1 self-consistency for image 2 Delta V(G=0): 0.007854Ry, 0.213707eV tcpu = 34.5 self-consistency for image 3 Delta V(G=0): 0.007854Ry, 0.213707eV tcpu = 34.9 self-consistency for image 4 Delta V(G=0): 0.007854Ry, 0.213707eV tcpu = 35.3 self-consistency for image 5 Delta V(G=0): 0.007854Ry, 0.213707eV tcpu = 35.7 self-consistency for image 6 Delta V(G=0): 0.007854Ry, 0.213707eV activation energy (->) = 0.220754 eV activation energy (<-) = 0.220954 eV image energy (eV) error (eV/A) frozen 1 -49.5053029 0.013776 T 2 -49.4742267 0.162027 F 3 -49.3767259 0.259062 F 4 -49.2845486 0.468793 F 5 -49.3768406 0.259544 F 6 -49.4743823 0.162278 F 7 -49.5055023 0.018591 T climbing image = 4 path length = 5.222 bohr inter-image distance = 0.870 bohr ------------------------------ iteration 11 ------------------------------ tcpu = 36.1 self-consistency for image 2 Delta V(G=0): 0.007854Ry, 0.213707eV tcpu = 36.7 self-consistency for image 3 Delta V(G=0): 0.007854Ry, 0.213707eV tcpu = 37.1 self-consistency for image 4 Delta V(G=0): 0.007854Ry, 0.213707eV tcpu = 37.6 self-consistency for image 5 Delta V(G=0): 0.007854Ry, 0.213707eV tcpu = 38.1 self-consistency for image 6 Delta V(G=0): 0.007854Ry, 0.213707eV activation energy (->) = 0.211773 eV activation energy (<-) = 0.211972 eV image energy (eV) error (eV/A) frozen 1 -49.5053029 0.013776 T 2 -49.4737553 0.080149 F 3 -49.3748274 0.151361 F 4 -49.2935300 0.266174 F 5 -49.3749462 0.151961 F 6 -49.4739116 0.080431 F 7 -49.5055023 0.018591 T climbing image = 4 path length = 5.253 bohr inter-image distance = 0.875 bohr ------------------------------ iteration 12 ------------------------------ tcpu = 38.6 self-consistency for image 2 Delta V(G=0): 0.007854Ry, 0.213707eV tcpu = 39.0 self-consistency for image 3 Delta V(G=0): 0.007854Ry, 0.213707eV tcpu = 39.5 self-consistency for image 4 Delta V(G=0): 0.007854Ry, 0.213707eV tcpu = 40.0 self-consistency for image 5 Delta V(G=0): 0.007854Ry, 0.213707eV tcpu = 40.4 self-consistency for image 6 Delta V(G=0): 0.007854Ry, 0.213707eV activation energy (->) = 0.205463 eV activation energy (<-) = 0.205663 eV image energy (eV) error (eV/A) frozen 1 -49.5053029 0.013776 T 2 -49.4725003 0.159280 F 3 -49.3737690 0.064155 F 4 -49.2998396 0.093780 F 5 -49.3738751 0.064558 F 6 -49.4726533 0.159521 F 7 -49.5055023 0.018591 T climbing image = 4 path length = 5.301 bohr inter-image distance = 0.883 bohr ------------------------------ iteration 13 ------------------------------ tcpu = 40.9 self-consistency for image 2 Delta V(G=0): 0.007854Ry, 0.213707eV tcpu = 41.3 self-consistency for image 3 Delta V(G=0): 0.007854Ry, 0.213707eV tcpu = 41.6 self-consistency for image 4 Delta V(G=0): 0.007854Ry, 0.213707eV tcpu = 42.1 self-consistency for image 5 Delta V(G=0): 0.007854Ry, 0.213707eV tcpu = 42.4 self-consistency for image 6 Delta V(G=0): 0.007854Ry, 0.213707eV activation energy (->) = 0.205203 eV activation energy (<-) = 0.205403 eV image energy (eV) error (eV/A) frozen 1 -49.5053029 0.013776 T 2 -49.4720920 0.089708 F 3 -49.3727786 0.129620 F 4 -49.3000997 0.069168 F 5 -49.3728742 0.129744 F 6 -49.4722415 0.089827 F 7 -49.5055023 0.018591 T climbing image = 4 path length = 5.316 bohr inter-image distance = 0.886 bohr ------------------------------ iteration 14 ------------------------------ tcpu = 42.8 self-consistency for image 2 Delta V(G=0): 0.007854Ry, 0.213707eV tcpu = 43.2 self-consistency for image 3 Delta V(G=0): 0.007854Ry, 0.213707eV tcpu = 43.6 self-consistency for image 4 Delta V(G=0): 0.007854Ry, 0.213707eV tcpu = 43.8 self-consistency for image 5 Delta V(G=0): 0.007854Ry, 0.213707eV tcpu = 44.2 self-consistency for image 6 Delta V(G=0): 0.007854Ry, 0.213707eV activation energy (->) = 0.205154 eV activation energy (<-) = 0.205354 eV image energy (eV) error (eV/A) frozen 1 -49.5053029 0.013776 T 2 -49.4716578 0.050724 F 3 -49.3723127 0.073745 F 4 -49.3001487 0.033927 F 5 -49.3724038 0.073851 F 6 -49.4718036 0.050893 F 7 -49.5055023 0.018591 T climbing image = 4 path length = 5.327 bohr inter-image distance = 0.888 bohr --------------------------------------------------------------------------- neb: convergence achieved in 14 iterations CP : 44.55s CPU time, 47.82s wall time This run was terminated on: 16: 5:25 28Apr2008 =------------------------------------------------------------------------------= JOB DONE. =------------------------------------------------------------------------------= NEB/examples/example01/reference/asymmetric_H2+H.dat0000644000700200004540000000067012053145633021421 0ustar marsamoscm 0.0000000000 0.0000000000 0.0100963663 0.1433063024 0.0179993198 0.0009983401 0.2769409464 0.0739866830 0.0332125059 0.3898177167 0.1530895575 0.0263775812 0.4896495899 0.2035773796 0.0415057207 0.6303004094 0.1406655125 0.0356538303 0.7988159856 0.0358412408 0.0089619046 1.0000000000 0.0000000000 0.0100962236 NEB/examples/example01/reference/asymmetric_H2+H.out0000644000700200004540000004332712053145633021466 0ustar marsamoscm Program PWSCF v.4.0 starts ... Today is 28Apr2008 at 16: 4: 4 For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or PAW Current dimensions of program pwscf are: Max number of different atomic species (ntypx) = 10 Max number of k-points (npk) = 40000 Max angular momentum in pseudopotentials (lmaxx) = 3 gamma-point specific algorithms are used reading file 'asymmetric_H2+H.path' calculation = neb restart_mode = restart opt_scheme = broyden num_of_images = 8 nstep = 50 CI_scheme = manual first_last_opt = F coarse-grained phase-space = F use_freezing = F ds = 2.0000 a.u. k_max = 0.3000 a.u. k_min = 0.2000 a.u. suggested k_max = 0.1542 a.u. suggested k_min = 0.1028 a.u. path_thr = 0.0500 eV / A list of climbing images : 5, ------------------------------ iteration 1 ------------------------------ tcpu = 0.0 self-consistency for image 1 tcpu = 0.4 self-consistency for image 2 tcpu = 0.9 self-consistency for image 3 tcpu = 1.3 self-consistency for image 4 tcpu = 1.8 self-consistency for image 5 tcpu = 2.3 self-consistency for image 6 tcpu = 2.8 self-consistency for image 7 tcpu = 3.2 self-consistency for image 8 activation energy (->) = 0.187378 eV activation energy (<-) = 0.187378 eV image energy (eV) error (eV/A) frozen 1 -49.5015717 0.010096 T 2 -49.4774302 0.113478 F 3 -49.4008026 0.049398 F 4 -49.3141933 0.067750 F 5 -49.3141932 0.192473 F 6 -49.4008026 0.049396 F 7 -49.4774302 0.113478 F 8 -49.5015717 0.010096 T path length = 5.308 bohr inter-image distance = 0.758 bohr ------------------------------ iteration 2 ------------------------------ tcpu = 3.7 self-consistency for image 2 tcpu = 3.9 self-consistency for image 3 tcpu = 4.2 self-consistency for image 4 tcpu = 4.4 self-consistency for image 5 tcpu = 4.7 self-consistency for image 6 tcpu = 5.0 self-consistency for image 7 activation energy (->) = 0.189149 eV activation energy (<-) = 0.189149 eV image energy (eV) error (eV/A) frozen 1 -49.5015717 0.010096 T 2 -49.4769474 0.003956 F 3 -49.4010805 0.082582 F 4 -49.3139435 0.134011 F 5 -49.3124224 0.194121 F 6 -49.4010805 0.164267 F 7 -49.4769474 0.003956 F 8 -49.5015717 0.010096 T path length = 5.311 bohr inter-image distance = 0.759 bohr ------------------------------ iteration 3 ------------------------------ tcpu = 5.3 self-consistency for image 2 tcpu = 5.6 self-consistency for image 3 tcpu = 5.8 self-consistency for image 4 tcpu = 6.1 self-consistency for image 5 tcpu = 6.5 self-consistency for image 6 tcpu = 6.8 self-consistency for image 7 activation energy (->) = 0.192038 eV activation energy (<-) = 0.192038 eV image energy (eV) error (eV/A) frozen 1 -49.5015717 0.010096 T 2 -49.4769470 0.071773 F 3 -49.3994647 0.181555 F 4 -49.3163218 0.029046 F 5 -49.3095334 0.183653 F 6 -49.3977523 0.079662 F 7 -49.4769470 0.157609 F 8 -49.5015717 0.010096 T path length = 5.317 bohr inter-image distance = 0.760 bohr ------------------------------ iteration 4 ------------------------------ tcpu = 7.1 self-consistency for image 2 tcpu = 7.3 self-consistency for image 3 tcpu = 7.6 self-consistency for image 4 tcpu = 8.0 self-consistency for image 5 tcpu = 8.3 self-consistency for image 6 tcpu = 8.7 self-consistency for image 7 activation energy (->) = 0.195400 eV activation energy (<-) = 0.195400 eV image energy (eV) error (eV/A) frozen 1 -49.5015717 0.010096 T 2 -49.4766365 0.034165 F 3 -49.4000984 0.211539 F 4 -49.3182326 0.107686 F 5 -49.3061720 0.152027 F 6 -49.3941356 0.102662 F 7 -49.4762623 0.195274 F 8 -49.5015717 0.010096 T path length = 5.324 bohr inter-image distance = 0.761 bohr ------------------------------ iteration 5 ------------------------------ tcpu = 9.0 self-consistency for image 2 tcpu = 9.2 self-consistency for image 3 tcpu = 9.6 self-consistency for image 4 tcpu = 9.9 self-consistency for image 5 tcpu = 10.4 self-consistency for image 6 tcpu = 10.7 self-consistency for image 7 activation energy (->) = 0.199625 eV activation energy (<-) = 0.199625 eV image energy (eV) error (eV/A) frozen 1 -49.5015717 0.010096 T 2 -49.4765285 0.160271 F 3 -49.4018047 0.257557 F 4 -49.3215498 0.198449 F 5 -49.3019466 0.086410 F 6 -49.3881423 0.140185 F 7 -49.4748028 0.209403 F 8 -49.5015717 0.010096 T path length = 5.334 bohr inter-image distance = 0.762 bohr ------------------------------ iteration 6 ------------------------------ tcpu = 11.0 self-consistency for image 2 tcpu = 11.3 self-consistency for image 3 tcpu = 11.6 self-consistency for image 4 tcpu = 12.0 self-consistency for image 5 tcpu = 12.5 self-consistency for image 6 tcpu = 12.9 self-consistency for image 7 activation energy (->) = 0.203647 eV activation energy (<-) = 0.203647 eV image energy (eV) error (eV/A) frozen 1 -49.5015717 0.010096 T 2 -49.4769983 0.287124 F 3 -49.4057130 0.281846 F 4 -49.3270607 0.272051 F 5 -49.2979247 0.091678 F 6 -49.3792132 0.168367 F 7 -49.4721138 0.172866 F 8 -49.5015717 0.010096 T path length = 5.347 bohr inter-image distance = 0.764 bohr ------------------------------ iteration 7 ------------------------------ tcpu = 13.2 self-consistency for image 2 tcpu = 13.5 self-consistency for image 3 tcpu = 14.0 self-consistency for image 4 tcpu = 14.4 self-consistency for image 5 tcpu = 14.8 self-consistency for image 6 tcpu = 15.3 self-consistency for image 7 activation energy (->) = 0.205849 eV activation energy (<-) = 0.205849 eV image energy (eV) error (eV/A) frozen 1 -49.5015717 0.010096 T 2 -49.4784065 0.314140 F 3 -49.4115903 0.304261 F 4 -49.3348670 0.237444 F 5 -49.2957224 0.131525 F 6 -49.3689823 0.113501 F 7 -49.4686221 0.113339 F 8 -49.5015717 0.010096 T path length = 5.357 bohr inter-image distance = 0.765 bohr ------------------------------ iteration 8 ------------------------------ tcpu = 15.6 self-consistency for image 2 tcpu = 16.0 self-consistency for image 3 tcpu = 16.4 self-consistency for image 4 tcpu = 16.8 self-consistency for image 5 tcpu = 17.3 self-consistency for image 6 tcpu = 17.7 self-consistency for image 7 activation energy (->) = 0.202920 eV activation energy (<-) = 0.202920 eV image energy (eV) error (eV/A) frozen 1 -49.5015717 0.010096 T 2 -49.4827947 0.077763 F 3 -49.4256962 0.230817 F 4 -49.3517716 0.028452 F 5 -49.2986522 0.193375 F 6 -49.3524389 0.181586 F 7 -49.4619944 0.015421 F 8 -49.5015717 0.010096 T path length = 5.349 bohr inter-image distance = 0.764 bohr ------------------------------ iteration 9 ------------------------------ tcpu = 18.1 self-consistency for image 2 tcpu = 18.4 self-consistency for image 3 tcpu = 18.7 self-consistency for image 4 tcpu = 19.2 self-consistency for image 5 tcpu = 19.6 self-consistency for image 6 tcpu = 20.0 self-consistency for image 7 activation energy (->) = 0.203288 eV activation energy (<-) = 0.203288 eV image energy (eV) error (eV/A) frozen 1 -49.5015717 0.010096 T 2 -49.4817891 0.156545 F 3 -49.4228309 0.118817 F 4 -49.3461761 0.139930 F 5 -49.2982840 0.102704 F 6 -49.3598131 0.039646 F 7 -49.4645375 0.031809 F 8 -49.5015717 0.010096 T path length = 5.337 bohr inter-image distance = 0.762 bohr ------------------------------ iteration 10 ------------------------------ tcpu = 20.3 self-consistency for image 2 tcpu = 20.7 self-consistency for image 3 tcpu = 21.0 self-consistency for image 4 tcpu = 21.3 self-consistency for image 5 tcpu = 21.6 self-consistency for image 6 tcpu = 22.0 self-consistency for image 7 activation energy (->) = 0.203076 eV activation energy (<-) = 0.203076 eV image energy (eV) error (eV/A) frozen 1 -49.5015717 0.010096 T 2 -49.4823791 0.085936 F 3 -49.4240539 0.138135 F 4 -49.3476273 0.047371 F 5 -49.2984959 0.073186 F 6 -49.3601684 0.052550 F 7 -49.4646856 0.029408 F 8 -49.5015717 0.010096 T path length = 5.331 bohr inter-image distance = 0.762 bohr ------------------------------ iteration 11 ------------------------------ tcpu = 22.2 self-consistency for image 2 tcpu = 22.5 self-consistency for image 3 tcpu = 22.9 self-consistency for image 4 tcpu = 23.2 self-consistency for image 5 tcpu = 23.6 self-consistency for image 6 tcpu = 24.0 self-consistency for image 7 activation energy (->) = 0.203338 eV activation energy (<-) = 0.203338 eV image energy (eV) error (eV/A) frozen 1 -49.5015717 0.010096 T 2 -49.4831711 0.076684 F 3 -49.4272905 0.050912 F 4 -49.3484726 0.030972 F 5 -49.2982338 0.046480 F 6 -49.3619657 0.035207 F 7 -49.4652501 0.040443 F 8 -49.5015717 0.010096 T path length = 5.321 bohr inter-image distance = 0.760 bohr ------------------------------ iteration 12 ------------------------------ tcpu = 24.3 self-consistency for image 2 tcpu = 24.5 self-consistency for image 3 tcpu = 24.8 self-consistency for image 4 tcpu = 25.2 self-consistency for image 5 tcpu = 25.5 self-consistency for image 6 tcpu = 25.8 self-consistency for image 7 activation energy (->) = 0.203567 eV activation energy (<-) = 0.203567 eV image energy (eV) error (eV/A) frozen 1 -49.5015717 0.010096 T 2 -49.4837747 0.049946 F 3 -49.4275612 0.034964 F 4 -49.3493257 0.088492 F 5 -49.2980046 0.050744 F 6 -49.3628491 0.039936 F 7 -49.4656940 0.021716 F 8 -49.5015717 0.010096 T path length = 5.319 bohr inter-image distance = 0.760 bohr ------------------------------ iteration 13 ------------------------------ tcpu = 26.1 self-consistency for image 2 tcpu = 26.4 self-consistency for image 3 tcpu = 26.6 self-consistency for image 4 tcpu = 26.9 self-consistency for image 5 tcpu = 27.2 self-consistency for image 6 tcpu = 27.4 self-consistency for image 7 activation energy (->) = 0.203577 eV activation energy (<-) = 0.203577 eV image energy (eV) error (eV/A) frozen 1 -49.5015717 0.010096 T 2 -49.4835724 0.000998 F 3 -49.4275850 0.033213 F 4 -49.3484822 0.026378 F 5 -49.2979943 0.041506 F 6 -49.3609062 0.035654 F 7 -49.4657305 0.008962 F 8 -49.5015717 0.010096 T path length = 5.321 bohr inter-image distance = 0.760 bohr --------------------------------------------------------------------------- neb: convergence achieved in 13 iterations PWSCF : 27.57s CPU time, 33.32s wall time init_run : 4.93s CPU ( 80 calls, 0.062 s avg) electrons : 17.19s CPU ( 80 calls, 0.215 s avg) update_pot : 2.53s CPU ( 72 calls, 0.035 s avg) forces : 0.64s CPU ( 80 calls, 0.008 s avg) Called by init_run: wfcinit : 0.01s CPU ( 80 calls, 0.000 s avg) potinit : 1.86s CPU ( 80 calls, 0.023 s avg) Called by electrons: c_bands : 2.41s CPU ( 518 calls, 0.005 s avg) sum_band : 2.58s CPU ( 518 calls, 0.005 s avg) v_of_rho : 12.17s CPU ( 647 calls, 0.019 s avg) newd : 0.48s CPU ( 575 calls, 0.001 s avg) mix_rho : 0.72s CPU ( 518 calls, 0.001 s avg) Called by c_bands: init_us_2 : 0.07s CPU ( 2380 calls, 0.000 s avg) regterg : 2.33s CPU ( 1036 calls, 0.002 s avg) Called by *egterg: h_psi : 1.71s CPU ( 2751 calls, 0.001 s avg) s_psi : 0.04s CPU ( 2883 calls, 0.000 s avg) g_psi : 0.07s CPU ( 1699 calls, 0.000 s avg) rdiaghg : 0.25s CPU ( 2545 calls, 0.000 s avg) Called by h_psi: add_vuspsi : 0.04s CPU ( 2751 calls, 0.000 s avg) General routines calbec : 0.08s CPU ( 4691 calls, 0.000 s avg) cft3 : 3.41s CPU ( 17637 calls, 0.000 s avg) cft3s : 1.99s CPU ( 20182 calls, 0.000 s avg) interpolate : 0.99s CPU ( 2186 calls, 0.000 s avg) davcio : 0.02s CPU ( 4088 calls, 0.000 s avg) NEB/examples/example01/reference/asymmetric_H2+H.axsf0000644000700200004540000000525412053145633021615 0ustar marsamoscm ANIMSTEPS 8 CRYSTAL PRIMVEC 6.3501265031 0.0000000000 0.0000000000 0.0000000000 2.6458860429 0.0000000000 0.0000000000 0.0000000000 2.6458860429 PRIMCOORD 1 3 1 H -2.4165936061 0.0000000000 0.0000000000 -0.0003710347 0.0000000000 0.0000000000 H 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 H 0.8243346657 0.0000000000 0.0000000000 0.0001122209 0.0000000000 0.0000000000 PRIMCOORD 2 3 1 H -2.0131348464 0.0000000000 0.0000000000 -0.0031551452 0.0000000000 0.0000000000 H 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 H 0.8297340455 0.0000000000 0.0000000000 -0.0001286373 0.0000000000 0.0000000000 PRIMCOORD 3 3 1 H -1.6372800206 0.0000000000 0.0000000000 -0.0079100579 0.0000000000 0.0000000000 H 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Today is 28Apr2008 at 16: 3:24 For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or PAW Current dimensions of program pwscf are: Max number of different atomic species (ntypx) = 10 Max number of k-points (npk) = 40000 Max angular momentum in pseudopotentials (lmaxx) = 3 gamma-point specific algorithms are used initial path length = 4.2553 bohr initial inter-image distance = 0.6079 bohr calculation = neb restart_mode = from_scratch opt_scheme = broyden num_of_images = 8 nstep = 50 CI_scheme = no-CI first_last_opt = F coarse-grained phase-space = F use_freezing = F ds = 2.0000 a.u. k_max = 0.3000 a.u. k_min = 0.2000 a.u. suggested k_max = 0.1542 a.u. suggested k_min = 0.1028 a.u. path_thr = 0.2000 eV / A ------------------------------ iteration 1 ------------------------------ tcpu = 0.0 self-consistency for image 1 tcpu = 0.4 self-consistency for image 2 tcpu = 0.9 self-consistency for image 3 tcpu = 1.4 self-consistency for image 4 tcpu = 1.9 self-consistency for image 5 tcpu = 2.4 self-consistency for image 6 tcpu = 2.9 self-consistency for image 7 tcpu = 3.4 self-consistency for image 8 activation energy (->) = 1.627022 eV activation energy (<-) = 1.627022 eV image energy (eV) error (eV/A) frozen 1 -49.5015717 0.010088 T 2 -49.1100937 1.835344 F 3 -48.4128430 2.249257 F 4 -47.8745493 1.873407 F 5 -47.8745493 1.873413 F 6 -48.4128430 2.249255 F 7 -49.1100937 1.835338 F 8 -49.5015717 0.010093 T path length = 4.255 bohr inter-image distance = 0.608 bohr ------------------------------ iteration 2 ------------------------------ tcpu = 3.8 self-consistency for image 2 tcpu = 4.2 self-consistency for image 3 tcpu = 4.7 self-consistency for image 4 tcpu = 5.3 self-consistency for image 5 tcpu = 5.8 self-consistency for image 6 tcpu = 6.3 self-consistency for image 7 activation energy (->) = 1.385583 eV activation energy (<-) = 1.385583 eV image energy (eV) error (eV/A) frozen 1 -49.5015717 0.010088 T 2 -49.2214735 1.451931 F 3 -48.6082420 1.970743 F 4 -48.1159885 1.928491 F 5 -48.1159893 1.928493 F 6 -48.6082417 1.970743 F 7 -49.2214729 1.451933 F 8 -49.5015717 0.010093 T path length = 4.295 bohr inter-image distance = 0.614 bohr ------------------------------ iteration 3 ------------------------------ tcpu = 6.7 self-consistency for image 2 tcpu = 7.1 self-consistency for image 3 tcpu = 7.6 self-consistency for image 4 tcpu = 8.0 self-consistency for image 5 tcpu = 8.5 self-consistency for image 6 tcpu = 9.0 self-consistency for image 7 activation energy (->) = 1.058298 eV activation energy (<-) = 1.058298 eV image energy (eV) error (eV/A) frozen 1 -49.5015717 0.010088 T 2 -49.3736163 1.177830 F 3 -48.8763153 1.635196 F 4 -48.4432734 1.701393 F 5 -48.4432736 1.701394 F 6 -48.8763160 1.635202 F 7 -49.3736161 1.177833 F 8 -49.5015717 0.010093 T path length = 4.449 bohr inter-image distance = 0.636 bohr ------------------------------ iteration 4 ------------------------------ tcpu = 9.4 self-consistency for image 2 tcpu = 9.8 self-consistency for image 3 tcpu = 10.3 self-consistency for image 4 tcpu = 10.7 self-consistency for image 5 tcpu = 11.1 self-consistency for image 6 tcpu = 11.5 self-consistency for image 7 activation energy (->) = 0.729986 eV activation energy (<-) = 0.729986 eV image energy (eV) error (eV/A) frozen 1 -49.5015717 0.010088 T 2 -49.4648004 0.703411 F 3 -49.1209357 1.468089 F 4 -48.7715863 1.582543 F 5 -48.7715862 1.582546 F 6 -49.1209363 1.468082 F 7 -49.4648004 0.703410 F 8 -49.5015717 0.010093 T path length = 4.688 bohr inter-image distance = 0.670 bohr ------------------------------ iteration 5 ------------------------------ tcpu = 12.0 self-consistency for image 2 tcpu = 12.4 self-consistency for image 3 tcpu = 12.9 self-consistency for image 4 tcpu = 13.3 self-consistency for image 5 tcpu = 13.8 self-consistency for image 6 tcpu = 14.2 self-consistency for image 7 activation energy (->) = 0.437319 eV activation energy (<-) = 0.437319 eV image energy (eV) error (eV/A) frozen 1 -49.5015717 0.010088 T 2 -49.4604312 0.963408 F 3 -49.3093591 1.228156 F 4 -49.0642529 1.312634 F 5 -49.0642525 1.312638 F 6 -49.3093594 1.228151 F 7 -49.4604311 0.963407 F 8 -49.5015717 0.010093 T path length = 4.984 bohr inter-image distance = 0.712 bohr ------------------------------ iteration 6 ------------------------------ tcpu = 14.7 self-consistency for image 2 tcpu = 15.1 self-consistency for image 3 tcpu = 15.6 self-consistency for image 4 tcpu = 16.0 self-consistency for image 5 tcpu = 16.5 self-consistency for image 6 tcpu = 17.0 self-consistency for image 7 activation energy (->) = 0.230914 eV activation energy (<-) = 0.230914 eV image energy (eV) error (eV/A) frozen 1 -49.5015717 0.010088 T 2 -49.3750319 2.172361 F 3 -49.3809319 1.351127 F 4 -49.2706578 0.882927 F 5 -49.2706575 0.882931 F 6 -49.3809318 1.351133 F 7 -49.3750315 2.172370 F 8 -49.5015717 0.010093 T path length = 5.311 bohr inter-image distance = 0.759 bohr ------------------------------ iteration 7 ------------------------------ tcpu = 17.4 self-consistency for image 2 tcpu = 17.9 self-consistency for image 3 tcpu = 18.3 self-consistency for image 4 tcpu = 18.7 self-consistency for image 5 tcpu = 19.1 self-consistency for image 6 tcpu = 19.5 self-consistency for image 7 activation energy (->) = 0.298844 eV activation energy (<-) = 0.298844 eV image energy (eV) error (eV/A) frozen 1 -49.5015717 0.010088 T 2 -49.4725159 0.651347 F 3 -49.3807825 0.581731 F 4 -49.2027284 1.052881 F 5 -49.2027282 1.052885 F 6 -49.3807826 0.581727 F 7 -49.4725159 0.651347 F 8 -49.5015717 0.010093 T path length = 5.080 bohr inter-image distance = 0.726 bohr ------------------------------ iteration 8 ------------------------------ tcpu = 20.0 self-consistency for image 2 tcpu = 20.3 self-consistency for image 3 tcpu = 20.8 self-consistency for image 4 tcpu = 21.2 self-consistency for image 5 tcpu = 21.7 self-consistency for image 6 tcpu = 22.1 self-consistency for image 7 activation energy (->) = 0.225903 eV activation energy (<-) = 0.225903 eV image energy (eV) error (eV/A) frozen 1 -49.5015717 0.010088 T 2 -49.4763129 0.242904 F 3 -49.3998549 0.170294 F 4 -49.2756691 0.682831 F 5 -49.2756691 0.682831 F 6 -49.3998549 0.170293 F 7 -49.4763129 0.242907 F 8 -49.5015717 0.010093 T path length = 5.183 bohr inter-image distance = 0.740 bohr ------------------------------ iteration 9 ------------------------------ tcpu = 22.5 self-consistency for image 2 tcpu = 22.8 self-consistency for image 3 tcpu = 23.1 self-consistency for image 4 tcpu = 23.5 self-consistency for image 5 tcpu = 24.0 self-consistency for image 6 tcpu = 24.3 self-consistency for image 7 activation energy (->) = 0.196775 eV activation energy (<-) = 0.196775 eV image energy (eV) error (eV/A) frozen 1 -49.5015717 0.010088 T 2 -49.4770211 0.212660 F 3 -49.4056477 0.225879 F 4 -49.3047968 0.386084 F 5 -49.3047967 0.386085 F 6 -49.4056476 0.225880 F 7 -49.4770211 0.212661 F 8 -49.5015717 0.010093 T path length = 5.247 bohr inter-image distance = 0.750 bohr ------------------------------ iteration 10 ------------------------------ tcpu = 24.6 self-consistency for image 2 tcpu = 24.9 self-consistency for image 3 tcpu = 25.3 self-consistency for image 4 tcpu = 25.7 self-consistency for image 5 tcpu = 26.1 self-consistency for image 6 tcpu = 26.5 self-consistency for image 7 activation energy (->) = 0.189973 eV activation energy (<-) = 0.189973 eV image energy (eV) error (eV/A) frozen 1 -49.5015717 0.010088 T 2 -49.4783379 0.149293 F 3 -49.4032631 0.149214 F 4 -49.3115985 0.306126 F 5 -49.3115985 0.306126 F 6 -49.4032631 0.149214 F 7 -49.4783379 0.149293 F 8 -49.5015717 0.010093 T path length = 5.262 bohr inter-image distance = 0.752 bohr ------------------------------ iteration 11 ------------------------------ tcpu = 26.8 self-consistency for image 2 tcpu = 27.1 self-consistency for image 3 tcpu = 27.4 self-consistency for image 4 tcpu = 27.8 self-consistency for image 5 tcpu = 28.1 self-consistency for image 6 tcpu = 28.4 self-consistency for image 7 activation energy (->) = 0.191342 eV activation energy (<-) = 0.191342 eV image energy (eV) error (eV/A) frozen 1 -49.5015717 0.010088 T 2 -49.4777188 0.019079 F 3 -49.4031214 0.193809 F 4 -49.3102299 0.269075 F 5 -49.3102299 0.269075 F 6 -49.4031214 0.193809 F 7 -49.4777188 0.019080 F 8 -49.5015717 0.010093 T path length = 5.268 bohr inter-image distance = 0.753 bohr ------------------------------ iteration 12 ------------------------------ tcpu = 28.7 self-consistency for image 2 tcpu = 29.2 self-consistency for image 3 tcpu = 29.6 self-consistency for image 4 tcpu = 30.1 self-consistency for image 5 tcpu = 30.6 self-consistency for image 6 tcpu = 31.0 self-consistency for image 7 activation energy (->) = 0.347502 eV activation energy (<-) = 0.347502 eV image energy (eV) error (eV/A) frozen 1 -49.5015717 0.010088 T 2 -49.4498141 1.050581 F 3 -49.3787783 0.436889 F 4 -49.1540696 1.942535 F 5 -49.1540695 1.942536 F 6 -49.3787783 0.436887 F 7 -49.4498145 1.050573 F 8 -49.5015717 0.010093 T path length = 5.722 bohr inter-image distance = 0.817 bohr ------------------------------ iteration 13 ------------------------------ tcpu = 31.5 self-consistency for image 2 tcpu = 32.0 self-consistency for image 3 tcpu = 32.4 self-consistency for image 4 tcpu = 32.9 self-consistency for image 5 tcpu = 33.3 self-consistency for image 6 tcpu = 33.8 self-consistency for image 7 activation energy (->) = 0.187378 eV activation energy (<-) = 0.187378 eV image energy (eV) error (eV/A) frozen 1 -49.5015717 0.010088 T 2 -49.4774302 0.113427 F 3 -49.4008026 0.049248 F 4 -49.3141932 0.067385 F 5 -49.3141932 0.067385 F 6 -49.4008026 0.049248 F 7 -49.4774302 0.113427 F 8 -49.5015717 0.010093 T path length = 5.308 bohr inter-image distance = 0.758 bohr --------------------------------------------------------------------------- neb: convergence achieved in 13 iterations PWSCF : 34.19s CPU time, 39.52s wall time init_run : 5.01s CPU ( 80 calls, 0.063 s avg) electrons : 23.71s CPU ( 80 calls, 0.296 s avg) update_pot : 2.54s CPU ( 72 calls, 0.035 s avg) forces : 0.64s CPU ( 80 calls, 0.008 s avg) Called by init_run: wfcinit : 0.01s CPU ( 80 calls, 0.000 s avg) potinit : 1.89s CPU ( 80 calls, 0.024 s avg) Called by electrons: c_bands : 3.25s CPU ( 678 calls, 0.005 s avg) sum_band : 3.38s CPU ( 678 calls, 0.005 s avg) v_of_rho : 15.74s CPU ( 828 calls, 0.019 s avg) newd : 0.65s CPU ( 756 calls, 0.001 s avg) mix_rho : 1.12s CPU ( 678 calls, 0.002 s avg) Called by c_bands: init_us_2 : 0.10s CPU ( 3020 calls, 0.000 s avg) regterg : 3.12s CPU ( 1356 calls, 0.002 s avg) Called by *egterg: h_psi : 2.34s CPU ( 3587 calls, 0.001 s avg) s_psi : 0.05s CPU ( 3719 calls, 0.000 s avg) g_psi : 0.09s CPU ( 2215 calls, 0.000 s avg) rdiaghg : 0.33s CPU ( 3423 calls, 0.000 s avg) Called by h_psi: add_vuspsi : 0.06s CPU ( 3587 calls, 0.000 s avg) General routines calbec : 0.12s CPU ( 5847 calls, 0.000 s avg) cft3 : 4.39s CPU ( 22760 calls, 0.000 s avg) cft3s : 2.61s CPU ( 26484 calls, 0.000 s avg) interpolate : 1.29s CPU ( 2868 calls, 0.000 s avg) davcio : 0.03s CPU ( 5048 calls, 0.000 s avg) NEB/examples/example01/reference/symmetric_H2+H.int0000644000700200004540000002210712053145633021301 0ustar marsamoscm 0.0000000000 0.0000000000 0.0040000000 0.0000134361 0.0080000000 0.0000537795 0.0120000000 0.0001210828 0.0160000000 0.0002153986 0.0200000000 0.0003367795 0.0240000000 0.0004852780 0.0280000000 0.0006609467 0.0320000000 0.0008638383 0.0360000000 0.0010940052 0.0400000000 0.0013515002 0.0440000000 0.0016363758 0.0480000000 0.0019486845 0.0520000000 0.0022884790 0.0560000000 0.0026558118 0.0600000000 0.0030507356 0.0640000000 0.0034733029 0.0680000000 0.0039235663 0.0720000000 0.0044015784 0.0760000000 0.0049073918 0.0800000000 0.0054410591 0.0840000000 0.0060026329 0.0880000000 0.0065921656 0.0920000000 0.0072097101 0.0960000000 0.0078553187 0.1000000000 0.0085290442 0.1040000000 0.0092309390 0.1080000000 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0.8800000000 0.0123212614 0.8840000000 0.0115061630 0.8880000000 0.0107194444 0.8920000000 0.0099610530 0.8960000000 0.0092309362 0.9000000000 0.0085290414 0.9040000000 0.0078553160 0.9080000000 0.0072097074 0.9120000000 0.0065921631 0.9160000000 0.0060026304 0.9200000000 0.0054410568 0.9240000000 0.0049073896 0.9280000000 0.0044015764 0.9320000000 0.0039235644 0.9360000000 0.0034733011 0.9400000000 0.0030507340 0.9440000000 0.0026558104 0.9480000000 0.0022884777 0.9520000000 0.0019486833 0.9560000000 0.0016363747 0.9600000000 0.0013514993 0.9640000000 0.0010940045 0.9680000000 0.0008638377 0.9720000000 0.0006609462 0.9760000000 0.0004852776 0.9800000000 0.0003367792 0.9840000000 0.0002153984 0.9880000000 0.0001210827 0.9920000000 0.0000537795 0.9960000000 0.0000134361 1.0000000000 0.0000000000 NEB/examples/example01/reference/H2+H.dat0000644000700200004540000000060112053145633017156 0ustar marsamoscm 0.0000000000 0.0000000000 0.0100883972 0.1939686614 0.0329664722 0.0450635505 0.3601677336 0.1313605248 0.0422584381 0.4999998398 0.2042705973 0.0158879326 0.6398320260 0.1313607025 0.0422582542 0.8060311860 0.0329665290 0.0450635459 1.0000000000 0.0000000000 0.0101062036 NEB/examples/example01/reference/asymmetric_H2+H.xyz0000644000700200004540000000240012053145633021474 0ustar marsamoscm 3 H -2.4165936061 0.0000000000 0.0000000000 H 0.0000000000 0.0000000000 0.0000000000 H 0.8243346657 0.0000000000 0.0000000000 3 H -2.0131348464 0.0000000000 0.0000000000 H 0.0000000000 0.0000000000 0.0000000000 H 0.8297340455 0.0000000000 0.0000000000 3 H -1.6372800206 0.0000000000 0.0000000000 H 0.0000000000 0.0000000000 0.0000000000 H 0.8472607656 0.0000000000 0.0000000000 3 H -1.3238851688 0.0000000000 0.0000000000 H 0.0000000000 0.0000000000 0.0000000000 H 0.9000945015 0.0000000000 0.0000000000 3 H -1.0748823172 0.0000000000 0.0000000000 H 0.0000000000 0.0000000000 0.0000000000 H 1.0305089178 0.0000000000 0.0000000000 3 H -0.8858875397 0.0000000000 0.0000000000 H 0.0000000000 0.0000000000 0.0000000000 H 1.3785193956 0.0000000000 0.0000000000 3 H -0.8347866509 0.0000000000 0.0000000000 H 0.0000000000 0.0000000000 0.0000000000 H 1.8502339974 0.0000000000 0.0000000000 3 H -0.8243346657 0.0000000000 0.0000000000 H 0.0000000000 0.0000000000 0.0000000000 H 2.4165936061 0.0000000000 0.0000000000 NEB/examples/example01/check-neb.x.j0000755000700200004540000001175112053145633016345 0ustar marsamoscm#!/bin/sh # Automated checks for neb.x - PG 2011 # Same logic of "check-pw.x.j" # You shouldn't need to modify anything below this line. # taken from examples - not sure it is really needed if test "`echo -e`" = "-e" ; then ECHO=echo ; else ECHO="echo -e" ; fi ESPRESSO_ROOT=`cd ../.. ; pwd` . $ESPRESSO_ROOT/examples/environment_variables ESPRESSO_TMPDIR=$ESPRESSO_ROOT/tmp/ ESPRESSO_PSEUDO=$ESPRESSO_ROOT/pseudo/ # no need to specify outdir and pseudo_dir in all *.in files export ESPRESSO_TMPDIR ESPRESSO_PSEUDO if test ! -d $ESPRESSO_TMPDIR then mkdir $ESPRESSO_TMPDIR fi # this is the current directory, where the test is executed TESTDIR=`pwd` # With no arguments, checks all *.in files # With an argument, checks files (ending with .in) matching the argument if test $# = 0 then files=`/bin/ls *.in` else files=`/bin/ls $*| grep "\.in$"` fi ######################################################################## # function to get pseudopotentials from the web if missing ######################################################################## get_pp () { ppfiles=`grep UPF $1.in | awk '{print $3}'` for ppfile in $ppfiles do if ! test -f $ESPRESSO_PSEUDO/$ppfile ; then $ECHO "Downloading $ppfile to $ESPRESSO_PSEUDO...\c" $WGET $ESPRESSO_PSEUDO/$ppfile \ http://www.quantum-espresso.org/pseudo/1.3/UPF/$ppfile \ 2> /dev/null if test $? != 0; then $ECHO "failed!" $ECHO "test $1 will not be executed" # status=1 else $ECHO "success" # status=0 fi fi done } ######################################################################## # function to test NEB calculations - usage: check_neb "file prefix" ######################################################################## check_neb () { # get reference number of neb iterations n0=`grep 'neb: convergence' $1.ref | awk '{print $1}'` # get reference activation energy (truncated to 4 significant digits) e0=`grep 'activation energy' $1.ref | tail -1 | awk '{printf "%8.4f\n", $5}'` # n1=`grep 'neb: convergence' $1.out | awk '{print $1}'` e1=`grep 'activation energy' $1.out | tail -1 | awk '{printf "%8.4f\n", $5}'` if test "$e1" = "$e0" then if test "$n1" = "$n0" then $ECHO "passed" fi fi if test "$e1" != "$e0" then $ECHO "discrepancy in activation energy detected" $ECHO "Reference: $e0, You got: $e1" fi if test "$n1" != "$n0" then $ECHO "discrepancy in number of neb iterations detected" $ECHO "Reference: $n0, You got: $n1" fi } ######################################################################## # function to get wall times - usage: get_times "file prefix" ######################################################################## get_times () { # convert from "1h23m45.6s" to seconds # the following line prevents cases such as "2m 7.5s" grep 'WALL$' $1.ref | sed 's/m /m0/' > $1.tmp # in order to get cpu instead of wall time, replace $3 to $5 tref=`awk '{ str = $5; h = m = s = 0; if (split(str, x, "h") == 2) { h = x[1]; str = x[2]; } if (split(str, x, "m") == 2) { m = x[1]; str = x[2]; } if (split(str, x, "s") == 2) { s = x[1]; str = x[2]; } t += h * 3600 + m * 60 + s; } END { printf("%.2f\n", t); }' \ $1.tmp` # as above for file *.out grep 'WALL$' $1.out | sed 's/m /m0/' > $1.tmp tout=`awk '{ str = $5; h = m = s = 0; if (split(str, x, "h") == 2) { h = x[1]; str = x[2]; } if (split(str, x, "m") == 2) { m = x[1]; str = x[2]; } if (split(str, x, "s") == 2) { s = x[1]; str = x[2]; } t += h * 3600 + m * 60 + s; } END { printf("%.2f\n", t); }' \ $1.tmp` /bin/rm $1.tmp # accumulate data totref=`echo $totref $tref | awk '{print $1+$2}'` totout=`echo $totout $tout | awk '{print $1+$2}'` } ######################################################################## # Perform here required checks ######################################################################## for file in $files do name=`basename $file .in` get_pp $name $ECHO "Checking $name...\c" ### # run the code in the scratch directory # cd $ESPRESSO_TMPDIR $PARA_PREFIX $ESPRESSO_ROOT/bin/neb.x $PARA_POSTFIX \ -inp $TESTDIR/$name.in > $TESTDIR/$name.out 2> /dev/null if test $? != 0; then $ECHO "FAILED with error condition!" $ECHO "Input: $name.in, Output: $name.out, Reference: $name.ref" $ECHO "Aborting" exit 1 fi # cd $TESTDIR ### if test -f $name.ref ; then # reference file exists if grep 'neb: convergence achieved' $name.ref > /dev/null; then # Specific test for NEB check_neb $name # fi # # extract wall time statistics # get_times $name # else $ECHO "not checked, reference file not available " fi # done $ECHO "Total wall time (s) spent in this run: " $totout $ECHO "Reference : " $totref NEB/examples/example01/run_example0000755000700200004540000001755512053145633016357 0ustar marsamoscm#!/bin/sh # run from directory where this script is cd `echo $0 | sed 's/\(.*\)\/.*/\1/'` # extract pathname EXAMPLE_DIR=`pwd` # check whether echo has the -e option if test "`echo -e`" = "-e" ; then ECHO=echo ; else ECHO="echo -e" ; fi $ECHO $ECHO "$EXAMPLE_DIR : starting" $ECHO $ECHO "This example shows how to use neb.x to calculate the" $ECHO "minimum energy path (MEP) of the collinear proton transfer reaction:" $ECHO " H2+H <==> H+H2, within the Born-Oppenheimer approximation." $ECHO $ECHO "!!! Beware: neb.x DOES NOT READ FROM STANDARD INPUT" $ECHO "!!! run as 'neb.x -inp input_file_name > output_file_name'" $ECHO # set the needed environment variables . ../../../environment_variables # required executables and pseudopotentials BIN_LIST="neb.x" PSEUDO_LIST="HUSPBE.RRKJ3" $ECHO $ECHO " executables directory: $BIN_DIR" $ECHO " pseudo directory: $PSEUDO_DIR" $ECHO " temporary directory: $TMP_DIR" $ECHO " checking that needed directories and files exist...\c" # check for directories for DIR in "$BIN_DIR" "$PSEUDO_DIR" ; do if test ! -d $DIR ; then $ECHO $ECHO "ERROR: $DIR not existent or not a directory" $ECHO "Aborting" exit 1 fi done for DIR in "$TMP_DIR" "$EXAMPLE_DIR/results" ; do if test ! -d $DIR ; then mkdir $DIR fi done cd $EXAMPLE_DIR/results # check for executables for FILE in $BIN_LIST ; do if test ! -x $BIN_DIR/$FILE ; then $ECHO $ECHO "ERROR: $BIN_DIR/$FILE not existent or not executable" $ECHO "Aborting" exit 1 fi done # check for pseudopotentials for FILE in $PSEUDO_LIST ; do if test ! -r $PSEUDO_DIR/$FILE ; then $ECHO $ECHO "Downloading $FILE to $PSEUDO_DIR...\c" $WGET $PSEUDO_DIR/$FILE $NETWORK_PSEUDO/$FILE 2> /dev/null fi if test $? != 0; then $ECHO $ECHO "ERROR: $PSEUDO_DIR/$FILE not existent or not readable" $ECHO "Aborting" exit 1 fi done $ECHO " done" # how to run executables NEB_COMMAND="$PARA_PREFIX $BIN_DIR/neb.x $PARA_POSTFIX" $ECHO $ECHO " running Born-Oppenheimer NEB as: $NEB_COMMAND" $ECHO # clean TMP_DIR $ECHO " cleaning $TMP_DIR...\c" rm -rf $TMP_DIR/* $ECHO " done" # NEB calculation. Automatic choice of the climbing image. cat > H2+H.in << EOF BEGIN BEGIN_PATH_INPUT &PATH restart_mode = 'from_scratch' string_method = 'neb', nstep_path = 20, ds = 2.D0, opt_scheme = "broyden", num_of_images = 7, k_max = 0.3D0, k_min = 0.2D0, CI_scheme = "auto", path_thr = 0.1D0, / END_PATH_INPUT BEGIN_ENGINE_INPUT &CONTROL prefix = "H2+H" outdir = "$TMP_DIR", pseudo_dir = "$PSEUDO_DIR", / &SYSTEM ibrav = 0, celldm(1) = 1.D0, nat = 3, ntyp = 1, ecutwfc = 20.0D0, ecutrho = 100.0D0, nspin = 2, starting_magnetization = 0.5D0, occupations = "smearing", degauss = 0.03D0, / &ELECTRONS conv_thr = 1.D-8, mixing_beta = 0.3D0, / &IONS / ATOMIC_SPECIES H 1.00794 HUSPBE.RRKJ3 BEGIN_POSITIONS FIRST_IMAGE ATOMIC_POSITIONS { bohr } H -4.56670009 0.00000000 0.00000000 1 0 0 H 0.00000000 0.00000000 0.00000000 0 0 0 H 1.55776676 0.00000000 0.00000000 1 0 0 LAST_IMAGE ATOMIC_POSITIONS { bohr } H -1.55776676 0.00000000 0.00000000 H 0.00000000 0.00000000 0.00000000 H 4.56670009 0.00000000 0.00000000 END_POSITIONS K_POINTS { gamma } CELL_PARAMETERS { cubic } 12.00000 0.00000 0.00000 0.00000 5.00000 0.00000 0.00000 0.00000 5.00000 END_ENGINE_INPUT END EOF $ECHO " running Born-Oppenheimer NEB calculation for H2+H => H+H2...\c" $NEB_COMMAND -inp H2+H.in > H2+H.out check_failure $? $ECHO " done" # clean TMP_DIR $ECHO " cleaning $TMP_DIR...\c" rm -rf $TMP_DIR/* $ECHO " done" # NEB calculation. Climbing image is not used cat > symmetric_H2+H.in << EOF BEGIN BEGIN_PATH_INPUT &PATH restart_mode = 'from_scratch' string_method = 'neb', nstep_path = 20, ds = 2.D0, opt_scheme = "broyden", num_of_images = 8, k_max = 0.3D0, k_min = 0.2D0, path_thr = 0.2D0, / END_PATH_INPUT BEGIN_ENGINE_INPUT &CONTROL prefix = "symmetric_H2+H" outdir = "$TMP_DIR", pseudo_dir = "$PSEUDO_DIR", / &SYSTEM ibrav = 0, celldm(1) = 1.D0, nat = 3, ntyp = 1, ecutwfc = 20.0D0, ecutrho = 100.0D0, nspin = 2, starting_magnetization = 0.5D0, occupations = "smearing", degauss = 0.03D0, / &ELECTRONS conv_thr = 1.D-8, mixing_beta = 0.3D0, / &IONS / ATOMIC_SPECIES H 1.00794 HUSPBE.RRKJ3 K_POINTS { gamma } CELL_PARAMETERS { cubic } 12.00000 0.00000 0.00000 0.00000 5.00000 0.00000 0.00000 0.00000 5.00000 BEGIN_POSITIONS FIRST_IMAGE ATOMIC_POSITIONS { bohr } H -4.56670009 0.00000000 0.00000000 1 0 0 H 0.00000000 0.00000000 0.00000000 0 0 0 H 1.55776676 0.00000000 0.00000000 1 0 0 LAST_IMAGE ATOMIC_POSITIONS { bohr } H -1.55776676 0.00000000 0.00000000 H 0.00000000 0.00000000 0.00000000 H 4.56670009 0.00000000 0.00000000 END_POSITIONS END_ENGINE_INPUT END EOF $ECHO " running Born-Oppenheimer NEB calculation for symmetric H2+H => H+H2...\c" $NEB_COMMAND -inp symmetric_H2+H.in > symmetric_H2+H.out check_failure $? $ECHO " done" # clean TMP_DIR $ECHO " cleaning $TMP_DIR...\c" rm -rf $TMP_DIR/* $ECHO " done" # the name of the restart file is changed in order to conform to the # prefix of the new run # the restart file asymmetric_H2+H.neb is modified (second row) # since a new simulation (from the old path) is started cat symmetric_H2+H.path | \ awk '{if(NR==2){printf" 0\n"}; if(NR!=2){print}}' > asymmetric_H2+H.path # NEB calculation. The image that has to climb is manually chosen cat > asymmetric_H2+H.in << EOF BEGIN BEGIN_PATH_INPUT &PATH restart_mode = 'restart' string_method = 'neb', nstep_path = 20, ds = 2.D0, opt_scheme = "broyden", num_of_images = 8, k_max = 0.3D0, k_min = 0.2D0, path_thr = 0.05D0, CI_scheme = "manual" / CLIMBING_IMAGES 5 END_PATH_INPUT BEGIN_ENGINE_INPUT &CONTROL prefix = "asymmetric_H2+H" outdir = "$TMP_DIR", pseudo_dir = "$PSEUDO_DIR", / &SYSTEM ibrav = 0, celldm(1) = 1.D0, nat = 3, ntyp = 1, ecutwfc = 20.0D0, ecutrho = 100.0D0, nspin = 2, starting_magnetization = 0.5D0, occupations = "smearing", degauss = 0.03D0, / &ELECTRONS conv_thr = 1.D-8, mixing_beta = 0.3D0, / &IONS / ATOMIC_SPECIES H 1.00794 HUSPBE.RRKJ3 K_POINTS { gamma } CELL_PARAMETERS { cubic } 12.00000 0.00000 0.00000 0.00000 5.00000 0.00000 0.00000 0.00000 5.00000 BEGIN_POSITIONS FIRST_IMAGE ATOMIC_POSITIONS { bohr } H -4.56670009 0.00000000 0.00000000 1 0 0 H 0.00000000 0.00000000 0.00000000 0 0 0 H 1.55776676 0.00000000 0.00000000 1 0 0 LAST_IMAGE ATOMIC_POSITIONS { bohr } H -1.55776676 0.00000000 0.00000000 H 0.00000000 0.00000000 0.00000000 H 4.56670009 0.00000000 0.00000000 END_POSITIONS END_ENGINE_INPUT END EOF $ECHO " running Born-Oppenheimer NEB calculation for asymmetric H2+H => H+H2...\c" $NEB_COMMAND -inp asymmetric_H2+H.in > asymmetric_H2+H.out check_failure $? $ECHO " done" # clean TMP_DIR $ECHO " cleaning $TMP_DIR...\c" rm -rf $TMP_DIR/* $ECHO " done" $ECHO $ECHO "$EXAMPLE_DIR: done" NEB/examples/example01/run_xml_example0000755000700200004540000004755212053145633017237 0ustar marsamoscm#!/bin/sh # run from directory where this script is cd `echo $0 | sed 's/\(.*\)\/.*/\1/'` # extract pathname EXAMPLE_DIR=`pwd` # check whether echo has the -e option if test "`echo -e`" = "-e" ; then ECHO=echo ; else ECHO="echo -e" ; fi $ECHO $ECHO "$EXAMPLE_DIR : starting" $ECHO $ECHO "This example shows how to use neb.x to calculate the" $ECHO "minimum energy path (MEP) of the collinear proton transfer reaction:" $ECHO " H2+H <==> H+H2, within the Born-Oppenheimer approximation." $ECHO $ECHO "!!!!!Atention for neb.x NO STANDARD INPUT is allowed," $ECHO "run with neb.x -inp input_file_name > output_file_name." $ECHO $ECHO "xml format is automatically detected." # set the needed environment variables . ../../../environment_variables # required executables and pseudopotentials BIN_LIST="neb.x" PSEUDO_LIST="HUSPBE.RRKJ3" $ECHO $ECHO " executables directory: $BIN_DIR" $ECHO " pseudo directory: $PSEUDO_DIR" $ECHO " temporary directory: $TMP_DIR" $ECHO " checking that needed directories and files exist...\c" # check for directories for DIR in "$BIN_DIR" "$PSEUDO_DIR" ; do if test ! -d $DIR ; then $ECHO $ECHO "ERROR: $DIR not existent or not a directory" $ECHO "Aborting" exit 1 fi done for DIR in "$TMP_DIR" "$EXAMPLE_DIR/results" ; do if test ! -d $DIR ; then mkdir $DIR fi done cd $EXAMPLE_DIR/results # check for executables for FILE in $BIN_LIST ; do if test ! -x $BIN_DIR/$FILE ; then $ECHO $ECHO "ERROR: $BIN_DIR/$FILE not existent or not executable" $ECHO "Aborting" exit 1 fi done # check for pseudopotentials for FILE in $PSEUDO_LIST ; do if test ! -r $PSEUDO_DIR/$FILE ; then $ECHO $ECHO "Downloading $FILE to $PSEUDO_DIR...\c" $WGET $PSEUDO_DIR/$FILE \ http://www.quantum-espresso.org/pseudo/1.3/UPF/$FILE 2> /dev/null fi if test $? != 0; then $ECHO $ECHO "ERROR: $PSEUDO_DIR/$FILE not existent or not readable" $ECHO "Aborting" exit 1 fi done $ECHO " done" # how to run executables NEB_COMMAND="$PARA_PREFIX $BIN_DIR/neb.x $PARA_POSTFIX" CP_COMMAND="$PARA_PREFIX $BIN_DIR/cp.x $PARA_POSTFIX" $ECHO $ECHO " running Born-Oppenheimer NEB as: $PW_COMMAND" $ECHO " running cp.x as: $CP_COMMAND" $ECHO # clean TMP_DIR $ECHO " cleaning $TMP_DIR...\c" rm -rf $TMP_DIR/* $ECHO " done" # NEB calculation. Automatic choice of the climbing image. cat > H2+H.in << EOF BEGIN EGIN_PATH_INPUT &PATH restart_mode = 'from_scratch' string_method = 'neb', nstep_path = 20, ds = 2.D0, opt_scheme = "broyden", num_of_images = 7, k_max = 0.3D0, k_min = 0.2D0, CI_scheme = "auto", path_thr = 0.1D0, / END_PATH_INPUT BEGIN_ENGINE_INPUT 12.0 0.0 0.0 0.0 5.0 0.0 0.0 0.0 5.0 1.00794 HUSPBE.RRKJ3 0.5 BEGIN_POSITIONS FIRST_IMAGE -4.56670009 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 1.55776676 0.00000000 0.00000000 LAST_IMAGE -1.55776676 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 4.56670009 0.00000000 0.00000000 END_POSITIONS from_scratch $PSEUDO_DIR $TMP_DIR/ 20.0 100.0 0.3 1.0d-8 smearing 0.01 2 END_ENGINE_INPUT END EOF $ECHO " running Born-Oppenheimer NEB calculation for H2+H => H+H2...\c" $NEB_COMMAND -inp H2+H.in > H2+H.out check_failure $? $ECHO " done" # clean TMP_DIR $ECHO " cleaning $TMP_DIR...\c" rm -rf $TMP_DIR/* $ECHO " done" # NEB calculation. Climbing image is not used cat > symmetric_H2+H.in << EOF BEGIN BEGIN_PATH_INPUT &PATH restart_mode = 'from_scratch' string_method = 'neb', nstep_path = 20, ds = 2.D0, opt_scheme = "broyden", num_of_images = 8, k_max = 0.3D0, k_min = 0.2D0, path_thr = 0.2D0, / END_PATH_INPUT BEGIN_ENGINE_INPUT 12.0 0.0 0.0 0.0 5.0 0.0 0.0 0.0 5.0 1.00794 HUSPBE.RRKJ3 0.5 BEGIN_POSITIONS FIRST_IMAGE -4.56670009 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 1.55776676 0.00000000 0.00000000 LAST_IMAGE -1.55776676 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 4.56670009 0.00000000 0.00000000 END_POSITIONS from_scratch $PSEUDO_DIR $TMP_DIR/ 20.0 100.0 0.3 1.0d-8 smearing 0.01 2 END_ENGINE_INPUT END EOF $ECHO " running Born-Oppenheimer NEB calculation for symmetric H2+H => H+H2...\c" $NEB_COMMAND -inp symmetric_H2+H.in > symmetric_H2+H.out check_failure $? $ECHO " done" # clean TMP_DIR $ECHO " cleaning $TMP_DIR...\c" rm -rf $TMP_DIR/* $ECHO " done" # the name of the restart file is changed in order to conform to the # prefix of the new run # the restart file asymmetric_H2+H.neb is modified (second row) # since a new simulation (from the old path) is started cat symmetric_H2+H.path | \ awk '{if(NR==2){printf" 0\n"}; if(NR!=2){print}}' > asymmetric_H2+H.path # NEB calculation. The image that has to climb is manually chosen cat > asymmetric_H2+H.in << EOF BEGIN BEGIN_PATH_INPUT &PATH restart_mode = 'restart' string_method = 'neb', nstep_path = 20, ds = 2.D0, opt_scheme = "broyden", num_of_images = 8, k_max = 0.3D0, k_min = 0.2D0, path_thr = 0.05D0, CI_scheme = "manual" / CLIMBING_IMAGES 5 END_PATH_INPUT BEGIN_ENGINE_INPUT 12.0 0.0 0.0 0.0 5.0 0.0 0.0 0.0 5.0 1.00794 HUSPBE.RRKJ3 0.5 BEGIN_POSITIONS FIRST_IMAGE -4.56670009 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 1.55776676 0.00000000 0.00000000 LAST_IMAGE -1.55776676 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 4.56670009 0.00000000 0.00000000 END_POSITIONS from_scratch $PSEUDO_DIR $TMP_DIR/ 20.0 100.0 0.3 1.0d-8 smearing 0.01 2 END_ENGINE_INPUT END EOF $ECHO " running Born-Oppenheimer NEB calculation for asymmetric H2+H => H+H2...\c" $NEB_COMMAND -inp asymmetric_H2+H.in > asymmetric_H2+H.out check_failure $? $ECHO " done" # clean TMP_DIR $ECHO " cleaning $TMP_DIR...\c" rm -rf $TMP_DIR/* $ECHO " done" $ECHO $ECHO "$EXAMPLE_DIR: done" NEB/examples/example01/README0000644000700200004540000000306412053145633014760 0ustar marsamoscm This example shows how to use neb.x to calculate the minimum energy path (MEP) of a simple activated reaction i.e. the collinear proton transfer reaction : H2 + H <==> H + H2 The MEP is obtained by means of the Climbing-Image Nudged Elastic Band (CI-NEB) method and two different climbing image algorithms are used ("auto" and "manual"). (for the meaning of the cited input variables see the Doc/INPUT_NEB* files) The symmetric reaction path H2 + H <==> H + H2 is calculated in three different ways. 1) The path connecting the initial and the final configurations is discretized with an odd number of images (7) so that the standard CI_scheme ("auto") will give rise to a symmetric MEP (3 images on the left of the saddle point and 3 images on the right). Note that in this system the use of the climbing image is not necessary. Indeed using CI_scheme = "no-CI" the result is the same. 2) The path connecting the initial and the final configurations is discretized with an even number of images (8) and no climbing image is used. The resulting path is symmetric, but no image is at the saddle point. 3) The path connecting the initial and the final configurations is again discretized with an even number of images (8), but the "manual" CI_scheme is used so that the resulting path is asymmetric. The image 5 now is at the saddle point. Given the low accuracy of these calculations (plane waves cut-off and thresholds) and the small box employed, these results should not be compared with experiments or with other "ab initio" calculations. NEB/Makefile0000644000700200004540000000126212053145633012124 0ustar marsamoscm# Makefile for NEB default: all all: if test -d src ; then \ ( cd src ; if test "$(MAKE)" = "" ; then make $(MFLAGS) $@; \ else $(MAKE) $(MFLAGS) $@ ; fi ) ; fi ; \ doc: if test -d Doc ; then \ ( cd Doc ; if test "$(MAKE)" = "" ; then make $(MFLAGS) $@; \ else $(MAKE) $(MFLAGS) $@ ; fi) ; fi ; \ clean : examples_clean if test -d src ; then \ ( cd src ; if test "$(MAKE)" = "" ; then make clean ; \ else $(MAKE) clean ; fi ) ; fi ;\ examples_clean: if test -d examples ; then \ ( cd examples ; ./clean_all ) ; fi doc_clean : if test -d Doc ; then \ ( cd Doc ; if test "$(MAKE)" = "" ; then make clean ; \ else $(MAKE) clean ; fi ) ; fi ;\ distclean: clean doc_clean NEB/src/0000755000700200004540000000000012053440276011253 5ustar marsamoscmNEB/src/path_gen_inputs.f900000644000700200004540000001217112053145633014763 0ustar marsamoscmsubroutine path_gen_inputs(parse_file_name,engine_prefix,nimage,root,comm) ! USE mp_global, only : mp_rank implicit none ! INTEGER, EXTERNAL :: find_free_unit ! character(len=*), intent(in) :: parse_file_name character(len=*), intent(in) :: engine_prefix integer, intent(out) :: nimage integer, intent(in) :: root integer, intent(in) :: comm ! character(len=512) :: dummy integer :: i, j integer :: parse_unit, neb_unit integer, allocatable :: unit_tmp(:) integer :: unit_tmp_i character(len=10) :: a_tmp integer :: myrank myrank = mp_rank(comm) parse_unit = find_free_unit() open(unit=parse_unit,file=trim(parse_file_name),status="old") ! --------------------------------------------------- ! NEB INPUT PART ! --------------------------------------------------- i=0 nimage = 0 neb_unit = find_free_unit() open(unit=neb_unit,file='neb.dat',status="unknown") dummy="" do while (LEN_TRIM(dummy)<1) read(parse_unit,fmt='(A512)',END=10) dummy enddo if(trim(dummy)=="BEGIN") then do while (trim(dummy)/="END") read(parse_unit,*) dummy if(trim(dummy)=="BEGIN_PATH_INPUT") then read(parse_unit,'(A512)') dummy do while (trim(dummy)/="END_PATH_INPUT") if(myrank==root) write(neb_unit,*) trim(dummy) read(parse_unit,'(A512)') dummy enddo endif if(trim(dummy)=="FIRST_IMAGE") then nimage = nimage + 1 endif if(trim(dummy)=="INTERMEDIATE_IMAGE") then nimage = nimage + 1 endif if(trim(dummy)=="LAST_IMAGE") then nimage=nimage+1 endif enddo else write(0,*) "key word BEGIN missing" endif close(neb_unit) !------------------------------------------------ ! ! ! ------------------------------------------------ ! ENGINE INPUT PART ! ------------------------------------------------ allocate(unit_tmp(1:nimage)) unit_tmp(:) = 0 do i=1,nimage unit_tmp(i) = find_free_unit() enddo do i=1,nimage if(i>=1.and.i<10) then write(a_tmp,'(i1)') i elseif(i>=10.and.i<100) then write(a_tmp,'(i2)') i elseif(i>=100.and.i<1000) then write(a_tmp,'(i3)') endif unit_tmp_i = unit_tmp(i) open(unit=unit_tmp_i,file=trim(engine_prefix)//trim(a_tmp)//".in") REWIND(parse_unit) dummy="" do while (LEN_TRIM(dummy)<1) read(parse_unit,fmt='(A512)',END=10) dummy enddo if(trim(dummy)=="BEGIN") then do while (trim(dummy)/="END") dummy="" do while (LEN_TRIM(dummy)<1) read(parse_unit,fmt='(A512)',END=10) dummy enddo if(trim(dummy)=="BEGIN_ENGINE_INPUT") then dummy="" do while (LEN_TRIM(dummy)<1) read(parse_unit,fmt='(A512)',END=10) dummy enddo do while (trim(dummy)/="BEGIN_POSITIONS") if(myrank==root) write(unit_tmp_i,'(A)') trim(dummy) read(parse_unit,'(A512)') dummy enddo if(i==1) then do while (trim(dummy)/="FIRST_IMAGE") read(parse_unit,'(A512)') dummy enddo if(trim(dummy)=="FIRST_IMAGE") then read(parse_unit,'(A512)') dummy do while (trim(dummy)/="INTERMEDIATE_IMAGE".and.(trim(dummy)/="LAST_IMAGE")) if(myrank==root) write(unit_tmp_i,'(A)') trim(dummy) read(parse_unit,'(A512)') dummy enddo do while (trim(dummy)/="END_POSITIONS") read(parse_unit,'(A512)') dummy enddo read(parse_unit,'(A512)') dummy do while (trim(dummy)/="END_ENGINE_INPUT") if(myrank==root) write(unit_tmp_i,'(A)') trim(dummy) read(parse_unit,'(A512)') dummy enddo endif endif ! if(i==nimage) then do while (trim(dummy)/="LAST_IMAGE") read(parse_unit,'(A512)') dummy enddo if(trim(dummy)=="LAST_IMAGE") then read(parse_unit,'(A512)') dummy do while (trim(dummy)/="END_POSITIONS") if(myrank==root) write(unit_tmp_i,'(A)') trim(dummy) read(parse_unit,'(A512)') dummy enddo read(parse_unit,'(A512)') dummy do while (trim(dummy)/="END_ENGINE_INPUT") if(myrank==root) write(unit_tmp_i,'(A)') trim(dummy) read(parse_unit,'(A512)') dummy enddo endif endif ! if(i/=nimage.and.i/=1) then do j=2,i dummy="" do while (trim(dummy)/="INTERMEDIATE_IMAGE") read(parse_unit,'(A512)') dummy write(0,*) i,j,trim(dummy) enddo enddo if(trim(dummy)=="INTERMEDIATE_IMAGE") then read(parse_unit,'(A512)') dummy do while ((trim(dummy)/="LAST_IMAGE").and.trim(dummy)/="INTERMEDIATE_IMAGE") if(myrank==root) write(unit_tmp_i,'(A)') trim(dummy) read(parse_unit,'(A512)') dummy enddo do while (trim(dummy)/="END_POSITIONS") read(parse_unit,'(A512)') dummy enddo read(parse_unit,'(A512)') dummy do while (trim(dummy)/="END_ENGINE_INPUT") if(myrank==root) write(unit_tmp_i,'(A)') trim(dummy) read(parse_unit,'(A512)') dummy enddo endif endif ! endif enddo endif close(unit_tmp_i) enddo deallocate(unit_tmp) close(parse_unit) ! 10 CONTINUE ! end subroutine path_gen_inputs NEB/src/path_io_units_module.f900000644000700200004540000000471712053145633016015 0ustar marsamoscm! ! Copyright (C) 2010 Quantum ESPRESSO group ! This file is distributed under the terms of the ! GNU General Public License. See the file `License' ! in the root directory of the present distribution, ! or http://www.gnu.org/copyleft/gpl.txt . ! !---------------------------------------------------------------------------- MODULE path_io_units_module !---------------------------------------------------------------------------- ! ! ... this module contains the I/O units and files used by "path"-routines ! IMPLICIT NONE ! ! SAVE ! INTEGER :: iunpath = 6 INTEGER :: stdinpath = 5 CHARACTER (LEN=256) :: & dat_file = 'os.dat', &! file containing the enegy profile int_file = 'os.int', &! file containing the interpolated energy profile crd_file = 'os.crd', &! file containing path coordinates in pw.x input format path_file = 'os.path', &! file containing information needed to restart a path simulation xyz_file = 'os.xyz', &! file containing coordinates of all images in xyz format axsf_file = 'os.axsf', &! file containing coordinates of all images in axsf format broy_file = 'os.broyden' ! file containing broyden's history ! INTEGER :: iunrestart = 2021 ! unit for saving the restart file ( neb_file ) INTEGER :: iundat = 2022 ! unit for saving the enegy profile INTEGER :: iunint = 2023 ! unit for saving the interpolated energy profile INTEGER :: iunxyz = 2024 ! unit for saving coordinates ( xyz format ) INTEGER :: iunaxsf = 2025 ! unit for saving coordinates ( axsf format ) INTEGER :: iunbroy = 2026 ! unit for saving broyden's history INTEGER :: iuncrd = 2027 ! unit for saving coordinates in pw.x input format INTEGER :: iunnewimage = 28 ! unit for parallelization among images ! INTEGER, EXTERNAL :: find_free_unit ! CONTAINS ! SUBROUTINE set_io_units() ! IMPLICIT NONE ! iunrestart = find_free_unit() iundat = find_free_unit() iunint = find_free_unit() iunxyz = find_free_unit() iunaxsf = find_free_unit() iunbroy = find_free_unit() iuncrd = find_free_unit() iunnewimage = find_free_unit() ! END SUBROUTINE set_io_units ! SUBROUTINE set_output_unit() ! IMPLICIT NONE ! iunpath = find_free_unit() ! END SUBROUTINE set_output_unit ! SUBROUTINE set_input_unit() ! IMPLICIT NONE ! stdinpath = find_free_unit() ! END SUBROUTINE set_input_unit ! END MODULE path_io_units_module NEB/src/path_io_tools.f900000644000700200004540000000661112053145633014441 0ustar marsamoscm ! Copyright (C) 2010 Quantum ESPRESSO group ! This file is distributed under the terms of the ! GNU General Public License. See the file `License' ! in the root directory of the present distribution, ! or http://www.gnu.org/copyleft/gpl.txt . ! ! !---------------------------------------------------------------------------- SUBROUTINE input_file_name_getarg(myname,lfound) !----------------------------------------------------------------------------- ! ! check for presence of command-line option "-inp myname" or "--inp myname" ! where "myname" is the name of the input file. Returns the name and if it ! has been found. ! USE kinds, ONLY : DP ! USE io_global, ONLY : stdout ! IMPLICIT NONE ! CHARACTER(len=256), intent(out) :: myname LOGICAL, intent(out) :: lfound ! INTEGER :: iiarg, nargs, iargc, i, i0 ! ! #if defined(__ABSOFT) # define getarg getarg_ # define iargc iargc_ #endif ! nargs = iargc() lfound = .false. ! DO iiarg = 1, nargs CALL getarg( iiarg, myname) ! IF ( TRIM( myname ) == '-input' .OR. & TRIM( myname ) == '-inp' .OR. & TRIM( myname ) == '-in' ) THEN ! CALL getarg( ( iiarg + 1 ) , myname ) ! lfound = .true. RETURN ! END IF ! ENDDO ! RETURN ! END SUBROUTINE input_file_name_getarg ! SUBROUTINE input_images_getarg(input_images,lfound) !----------------------------------------------------------------------------- ! ! check for presence of command-line option "-inp myname" or "--inp myname" ! where "myname" is the name of the input file. Returns the name and if it ! has been found. ! USE kinds, ONLY : DP ! USE io_global, ONLY : stdout ! IMPLICIT NONE ! INTEGER, intent(out) :: input_images LOGICAL, intent(out) :: lfound ! CHARACTER(len=256) :: myname INTEGER :: iiarg, nargs, iargc, i, i0 ! ! #if defined(__ABSOFT) # define getarg getarg_ # define iargc iargc_ #endif ! nargs = iargc() lfound = .false. input_images = 0 ! DO iiarg = 1, nargs CALL getarg( iiarg, myname) ! IF ( TRIM( myname ) == '-input_images' .OR. & TRIM( myname ) == '--input_images' ) THEN ! CALL getarg( ( iiarg + 1 ) , myname ) ! READ(myname,*) input_images ! lfound = .true. RETURN ! END IF ! ENDDO ! RETURN ! END SUBROUTINE input_images_getarg !---------------------------------------------------------------------------- SUBROUTINE close_io_units(myunit) !----------------------------------------------------------------------------- ! IMPLICIT NONE ! INTEGER, intent(in) :: myunit ! LOGICAL :: opnd ! INQUIRE( UNIT = myunit, OPENED = opnd ) IF ( opnd ) CLOSE( UNIT = myunit ) ! END SUBROUTINE close_io_units ! !---------------------------------------------------------------------------- SUBROUTINE open_io_units(myunit,file_name,lappend) !----------------------------------------------------------------------------- ! IMPLICIT NONE ! INTEGER, intent(in) :: myunit CHARACTER(LEN=256), intent(in) :: file_name LOGICAL, intent(in) :: lappend ! LOGICAL :: opnd ! INQUIRE( UNIT = myunit, OPENED = opnd ) IF ( opnd ) CLOSE( UNIT = myunit ) OPEN( UNIT = myunit, FILE = TRIM(file_name), & STATUS = 'UNKNOWN', POSITION = 'APPEND' ) ! END SUBROUTINE open_io_units NEB/src/path_base.f900000644000700200004540000010025312053145633013521 0ustar marsamoscm! ! Copyright (C) 2003-2007 Quantum ESPRESSO group ! This file is distributed under the terms of the ! GNU General Public License. See the file `License' ! in the root directory of the present distribution, ! or http://www.gnu.org/copyleft/gpl.txt . ! ! !--------------------------------------------------------------------------- MODULE path_base !--------------------------------------------------------------------------- ! ! ... This module contains most of the subroutines and functions needed by ! ... the implementation of "NEB" and "SMD" methods into Quantum ESPRESSO ! ! ... Other relevant files are: ! ! ... path_variables.f90 ! ... path_io_routines.f90 ! ... path_opt_routines.f90 ! ... path_reparametrisation.f90 ! ... path_formats.f90 ! ... compute_scf.f90 ! ! ... The code is based on the NEB algorithm described in : ! ! ... 1) G. Henkelman, B.P. Uberuaga, and H. Jonsson; ! ... J.Chem.Phys., 113, 9901, (2000) ! ... 2) G. Henkelman, and H. Jonsson; J.Chem.Phys., 113, 9978, (2000) ! ! ... More details about the implementation can be found at ! ! ... http://www.sissa.it/cm/thesis/2005/sbraccia.pdf ! ! ... Code written and maintained by Carlo Sbraccia ( 2003-2007 ) ! USE kinds, ONLY : DP USE constants, ONLY : eps32, pi, autoev, bohr_radius_angs, eV_to_kelvin USE path_io_units_module, ONLY : iunpath USE io_global, ONLY : meta_ionode, meta_ionode_id USE mp, ONLY : mp_bcast ! USE basic_algebra_routines ! PRIVATE ! PUBLIC :: initialize_path PUBLIC :: search_mep ! CONTAINS ! ! ... module procedures ! !----------------------------------------------------------------------- SUBROUTINE initialize_path() !----------------------------------------------------------------------- ! USE path_input_parameters_module, ONLY : pos_ => pos, & climbing_ => climbing, & input_images, nstep_path_ => nstep_path USE path_input_parameters_module, ONLY : restart_mode USE path_variables, ONLY : fix_atom_pos USE path_input_parameters_module, ONLY : nat USE control_flags, ONLY : conv_elec USE ions_base, ONLY : amass, ityp USE io_files, ONLY : prefix, tmp_dir USE path_io_units_module, ONLY : path_file, dat_file, crd_file, & int_file, xyz_file, axsf_file, broy_file USE path_variables, ONLY : climbing, pos, istep_path, nstep_path, & dim1, num_of_images, pes, grad_pes, mass, & use_masses, tangent, error, path_length, & deg_of_freedom, frozen, use_freezing, k, & k_min, tune_load_balance, grad, posold, & elastic_grad, pending_image, first_last_opt USE mp_image_global_module, ONLY : nimage USE path_io_routines, ONLY : read_restart USE path_variables, ONLY : path_allocation ! IMPLICIT NONE ! INTEGER :: i, fii, lii LOGICAL :: file_exists ! ! ... output files are set ! path_file = TRIM( prefix ) // ".path" dat_file = TRIM( prefix ) // ".dat" int_file = TRIM( prefix ) // ".int" crd_file = TRIM( prefix ) // ".crd" xyz_file = TRIM( prefix ) // ".xyz" axsf_file = TRIM( prefix ) // ".axsf" ! broy_file = TRIM( tmp_dir ) // TRIM( prefix ) // ".broyden" ! ! ... istep is initialised to zero ! istep_path = 0 pending_image = 0 conv_elec = .TRUE. ! ! ... the dimension of all "path" arrays (dim1) is set here ! ... ( it corresponds to the dimension of the configurational space ) ! ! dim1 = 3*nat ! ! IF ( nimage > 1 ) THEN ! ! ... the automatic tuning of the load balance in ! ... image-parallelisation is switched off by default ! tune_load_balance = .FALSE. ! ! ... in the case of image-parallelisation the number of images ! ... to be optimised must be larger than nimage ! IF ( first_last_opt ) THEN ! fii = 1 lii = num_of_images ! ELSE ! fii = 2 lii = num_of_images - 1 ! END IF ! IF ( nimage > ( lii - fii + 1 ) ) & CALL errore( 'initialize_path', 'nimage is ' // & & 'larger than the available number of images', 1 ) ! END IF ! ! ... dynamical allocation of arrays ! CALL path_allocation() ! IF ( use_masses ) THEN ! ! ... mass weighted coordinates are used ! DO i = 1, nat ! mass(3*i-2) = amass(ityp(i)) mass(3*i-1) = amass(ityp(i)) mass(3*i-0) = amass(ityp(i)) ! END DO ! ELSE ! mass = 1.0_DP ! END IF ! ! ... initialization of the allocatable arrays ! pos(:,1:input_images) = pos_(1:dim1,1:input_images) ! pes = 0.0_DP grad_pes = 0.0_DP elastic_grad = 0.0_DP tangent = 0.0_DP grad = 0.0_DP error = 0.0_DP frozen = .FALSE. ! k = k_min ! IF ( ALLOCATED( climbing_ ) ) THEN ! climbing = climbing_ ! ELSE ! climbing = .FALSE. ! END IF ! ! ... initial path is read from file ( restart_mode == "restart" ) or ! ... generated from the input images ( restart_mode = "from_scratch" ) ! ... It is always read from file in the case of "free-energy" ! ... calculations ! IF ( restart_mode == "restart" ) THEN ! IF ( meta_ionode ) THEN ! INQUIRE( FILE = path_file, EXIST = file_exists ) ! IF ( .NOT. file_exists ) THEN ! WRITE( iunpath, & & '(/,5X,"restart file ''",A,"'' not found: ", & & /,5X,"starting from scratch")' ) TRIM( path_file ) ! restart_mode = "from_scratch" ! END IF ! END IF ! CALL mp_bcast( restart_mode, meta_ionode_id ) ! END IF ! IF ( restart_mode == "restart" ) THEN ! CALL read_restart() ! ! ... consistency between the input value of nstep and the value ! ... of nstep_path read from the restart_file is checked ! IF ( nstep_path_ == 0 ) THEN ! istep_path = 0 nstep_path = nstep_path_ ! END IF ! IF ( nstep_path_ > nstep_path ) nstep_path = nstep_path_ ! ! ... in case first_last_opt has been set to true, reset the frozen ! ... array to false (all the images have to be optimized, at least ! ... on the first iteration) ! IF ( first_last_opt ) frozen = .FALSE. ! ! ... path length is computed here ! path_length = 0.0_DP ! DO i = 1, ( num_of_images - 1 ) ! path_length = path_length + norm( pos(:,i+1) - pos(:,i) ) ! END DO ! ELSE ! CALL initial_guess() ! posold(:,:) = pos(:,:) ! END IF ! ! ... the actual number of degrees of freedom is computed ! deg_of_freedom = 0 ! DO i = 1, nat ! IF ( fix_atom_pos(1,i) == 1 ) deg_of_freedom = deg_of_freedom + 1 IF ( fix_atom_pos(2,i) == 1 ) deg_of_freedom = deg_of_freedom + 1 IF ( fix_atom_pos(3,i) == 1 ) deg_of_freedom = deg_of_freedom + 1 ! END DO ! RETURN ! END SUBROUTINE initialize_path ! !-------------------------------------------------------------------- SUBROUTINE initial_guess() !-------------------------------------------------------------------- ! ! ... linear interpolation ! USE path_input_parameters_module, ONLY : input_images USE path_variables, ONLY : pos, dim1, num_of_images, path_length ! USE path_formats, ONLY : summary_fmt USE path_io_units_module, ONLY : iunpath ! IMPLICIT NONE ! REAL(DP) :: s INTEGER :: i, j ! REAL(DP), ALLOCATABLE :: pos_n(:,:), dr(:,:), image_spacing(:) ! ! IF ( meta_ionode ) THEN ! ALLOCATE( pos_n( dim1, num_of_images ) ) ALLOCATE( dr( dim1, input_images - 1 ) ) ALLOCATE( image_spacing( input_images - 1 ) ) ! DO i = 1, input_images - 1 ! dr(:,i) = ( pos(:,i+1) - pos(:,i) ) ! image_spacing(i) = norm( dr(:,i) ) ! END DO ! path_length = SUM( image_spacing(:) ) ! DO i = 1, input_images - 1 ! dr(:,i) = dr(:,i) / image_spacing(i) ! END DO ! pos_n(:,1) = pos(:,1) ! i = 1 s = 0.0_DP ! DO j = 2, num_of_images - 1 ! s = s + path_length / DBLE( num_of_images - 1 ) ! IF ( s > image_spacing(i) ) THEN ! s = s - image_spacing(i) ! i = i + 1 ! END IF ! IF ( i >= input_images ) & CALL errore( 'initialize_path', 'i >= input_images', i ) ! pos_n(:,j) = pos(:,i) + s * dr(:,i) ! END DO ! pos_n(:,num_of_images) = pos(:,input_images) ! pos(:,:) = pos_n(:,:) ! path_length = 0.0_DP ! DO i = 1, num_of_images - 1 ! path_length = path_length + norm( pos(:,i+1) - pos(:,i) ) ! END DO ! WRITE( UNIT = iunpath, & FMT = '(/,5X,"initial path length",& & T35," = ",F7.4," bohr")' ) path_length ! WRITE( UNIT = iunpath, & FMT = '(5X,"initial inter-image distance",T35," = ",F7.4, & &" bohr")' ) path_length / DBLE( num_of_images - 1 ) ! DEALLOCATE( image_spacing, dr, pos_n ) ! END IF ! CALL mp_bcast( pos, meta_ionode_id ) CALL mp_bcast( path_length, meta_ionode_id ) ! RETURN ! END SUBROUTINE initial_guess ! !----------------------------------------------------------------------- FUNCTION real_space_tangent( i ) RESULT( rtan ) !----------------------------------------------------------------------- ! ! ... improved definition of the tangent (see JCP 113, 9978) ! USE path_variables, ONLY : dim1, pos, num_of_images, pes ! IMPLICIT NONE ! INTEGER, INTENT(IN) :: i REAL(DP) :: rtan( dim1 ) ! REAL(DP) :: V_previous, V_actual, V_next REAL(DP) :: abs_next, abs_previous REAL(DP) :: delta_V_max, delta_V_min ! ! IF ( i == 1 ) THEN ! rtan(:) = pos(:,i+1) - pos(:,i) ! RETURN ! ELSE IF ( i == num_of_images ) THEN ! rtan(:) = pos(:,i) - pos(:,i-1) ! RETURN ! END IF ! V_previous = pes( i - 1 ) V_actual = pes( i ) V_next = pes( i + 1 ) ! IF ( ( V_next > V_actual ) .AND. ( V_actual > V_previous ) ) THEN ! rtan(:) = pos(:,i+1) - pos(:,i) ! ELSE IF ( ( V_next < V_actual ) .AND. ( V_actual < V_previous ) ) THEN ! rtan(:) = pos(:,i) - pos(:,i-1) ! ELSE ! abs_next = ABS( V_next - V_actual ) abs_previous = ABS( V_previous - V_actual ) ! delta_V_max = MAX( abs_next, abs_previous ) delta_V_min = MIN( abs_next, abs_previous ) ! IF ( V_next > V_previous ) THEN ! rtan(:) = ( pos(:,i+1) - pos(:,i) ) * delta_V_max + & ( pos(:,i) - pos(:,i-1) ) * delta_V_min ! ELSE IF ( V_next < V_previous ) THEN ! rtan(:) = ( pos(:,i+1) - pos(:,i) ) * delta_V_min + & ( pos(:,i) - pos(:,i-1) ) * delta_V_max ! ELSE ! rtan(:) = pos(:,i+1) - pos(:,i-1) ! END IF ! END IF ! rtan(:) = rtan(:) / norm( rtan(:) ) ! RETURN ! END FUNCTION real_space_tangent ! !------------------------------------------------------------------------ SUBROUTINE elastic_constants() !------------------------------------------------------------------------ ! USE path_variables, ONLY : num_of_images, Emax, Emin, & k_max, k_min, k, pes ! IMPLICIT NONE ! INTEGER :: i REAL(DP) :: delta_E REAL(DP) :: k_sum, k_diff ! ! ! ... standard neb ( with springs ) ! k_sum = k_max + k_min k_diff = k_max - k_min ! k(:) = k_min ! delta_E = Emax - Emin ! IF ( delta_E > eps32 ) THEN ! DO i = 1, num_of_images ! k(i) = 0.5_DP*( k_sum - k_diff * & COS( pi * ( pes(i) - Emin ) / delta_E ) ) ! END DO ! END IF ! k(:) = 0.5_DP*k(:) ! RETURN ! END SUBROUTINE elastic_constants ! !------------------------------------------------------------------------ SUBROUTINE neb_gradient() !------------------------------------------------------------------------ ! USE path_variables, ONLY : pos, grad, elastic_grad, grad_pes, k, & num_of_images, climbing, mass, tangent ! IMPLICIT NONE ! INTEGER :: i ! ! IF ( meta_ionode ) THEN ! CALL elastic_constants() ! gradient_loop: DO i = 1, num_of_images ! IF ( i > 1 .AND. i < num_of_images ) THEN ! ! ... elastic gradient only along the path ( variable elastic ! ... consatnt is used ) NEB recipe ! elastic_grad = tangent(:,i) * 0.5_DP * & ( ( k(i) + k(i-1) ) * norm( pos(:,i) - pos(:,(i-1)) ) - & ( k(i) + k(i+1) ) * norm( pos(:,(i+1)) - pos(:,i) ) ) ! END IF ! ! ... total gradient on each image ( climbing image is used if ! ... required ) only the component of the pes gradient orthogonal ! ... to the path is used ! grad(:,i) = grad_pes(:,i) / SQRT( mass(:) ) ! IF ( climbing(i) ) THEN ! grad(:,i) = grad(:,i) - & 2.0_DP*tangent(:,i)*( grad(:,i) .dot. tangent(:,i) ) ! ELSE IF ( i > 1 .AND. i < num_of_images ) THEN ! grad(:,i) = elastic_grad + grad(:,i) - & tangent(:,i)*( grad(:,i) .dot. tangent(:,i) ) ! END IF ! END DO gradient_loop ! END IF ! CALL mp_bcast( grad, meta_ionode_id ) ! RETURN ! END SUBROUTINE neb_gradient ! !----------------------------------------------------------------------- SUBROUTINE smd_gradient() !----------------------------------------------------------------------- ! USE ions_base, ONLY : if_pos USE path_variables, ONLY : dim1, mass, num_of_images, grad_pes, & tangent, llangevin, lang, grad, ds, & temp_req USE path_variables, ONLY : climbing USE random_numbers, ONLY : gauss_dist ! IMPLICIT NONE ! INTEGER :: i ! ! IF ( meta_ionode ) THEN ! grad(:,:) = 0.0_DP lang(:,:) = 0.0_DP ! ! ... we project pes gradients and gaussian noise ! DO i = 1, num_of_images ! IF ( llangevin ) THEN ! ! ... the random term used in langevin dynamics is generated here ! lang(:,i) = gauss_dist( 0.0_DP, SQRT( 2.0_DP*temp_req*ds ), dim1 ) ! lang(:,i) = lang(:,i)*DBLE( RESHAPE( if_pos, (/ dim1 /) ) ) ! END IF ! grad(:,i) = grad_pes(:,i) / SQRT( mass(:) ) ! IF ( climbing(i) ) THEN ! grad(:,i) = grad(:,i) - & 2.0_DP*tangent(:,i)*( grad(:,i) .dot. tangent(:,i) ) ! ELSE IF ( i > 1 .AND. i < num_of_images ) THEN ! ! ... projection of the pes gradients ! grad(:,i) = grad(:,i) - & tangent(:,i)*( grad(:,i) .dot. tangent(:,i) ) ! IF ( llangevin ) THEN ! lang(:,i) = lang(:,i) - & tangent(:,i)*( lang(:,i) .dot. tangent(:,i) ) ! END IF ! END IF ! END DO ! END IF ! CALL mp_bcast( grad, meta_ionode_id ) CALL mp_bcast( lang, meta_ionode_id ) ! RETURN ! END SUBROUTINE smd_gradient ! ! ... shared routines ! !----------------------------------------------------------------------- FUNCTION new_tangent() RESULT( ntan ) !----------------------------------------------------------------------- ! USE path_variables, ONLY : dim1, num_of_images ! IMPLICIT NONE ! REAL(DP) :: ntan( dim1, num_of_images ) ! INTEGER :: i ! ! IF ( meta_ionode ) THEN ! DO i = 1, num_of_images ! ntan(:,i) = real_space_tangent( i ) ! END DO ! END IF ! CALL mp_bcast( ntan, meta_ionode_id ) ! RETURN ! END FUNCTION new_tangent ! !----------------------------------------------------------------------- SUBROUTINE compute_error( err_out ) !----------------------------------------------------------------------- ! USE path_variables, ONLY : pos, posold, num_of_images, grad, & use_freezing, first_last_opt, path_thr, & error, frozen, lquick_min USE mp_image_global_module, ONLY : nimage ! IMPLICIT NONE ! REAL(DP), OPTIONAL, INTENT(OUT) :: err_out ! INTEGER :: i INTEGER :: fii, lii, freed, num_of_scf_images REAL(DP) :: err_max LOGICAL :: first ! ! IF ( first_last_opt ) THEN ! fii = 1 lii = num_of_images ! frozen = .FALSE. ! ELSE ! fii = 2 lii = num_of_images - 1 ! frozen = .FALSE. ! ! ... the first and the last images are always frozen ! frozen(fii-1) = .TRUE. frozen(lii+1) = .TRUE. ! END IF ! IF ( meta_ionode ) THEN ! DO i = 1, num_of_images ! ! ... the error is given by the largest component of the gradient ! ... vector ( PES + SPRINGS in the neb case ) ! error(i) = MAXVAL( ABS( grad(:,i) ) ) / bohr_radius_angs * autoev ! END DO ! err_max = MAXVAL( error(fii:lii), 1 ) ! IF ( use_freezing ) THEN ! frozen(fii:lii) = ( error(fii:lii) < & MAX( 0.5_DP*err_max, path_thr ) ) ! END IF ! IF ( nimage > 1 .AND. use_freezing ) THEN ! find_scf_images: DO ! num_of_scf_images = COUNT( .NOT.frozen(fii:lii) ) ! IF ( num_of_scf_images >= nimage ) EXIT find_scf_images ! first = .TRUE. ! search: DO i = fii, lii ! IF ( .NOT.frozen(i) ) CYCLE search ! IF ( first ) THEN ! first = .FALSE. freed = i ! CYCLE search ! END IF ! IF ( error(i) > error(freed) ) freed = i ! END DO search ! frozen(freed) = .FALSE. ! END DO find_scf_images ! END IF ! IF ( use_freezing .AND. lquick_min ) THEN ! ! ... the old positions of the frozen images are set to the ! ... present position (equivalent to resetting the velocity) ! FORALL( i = fii:lii, frozen(i) ) posold(:,i) = pos(:,i) ! END IF ! END IF ! CALL mp_bcast( error, meta_ionode_id ) CALL mp_bcast( err_max, meta_ionode_id ) CALL mp_bcast( frozen, meta_ionode_id ) CALL mp_bcast( posold, meta_ionode_id ) ! IF ( PRESENT( err_out ) ) err_out = err_max ! RETURN ! END SUBROUTINE compute_error ! !------------------------------------------------------------------------ SUBROUTINE born_oppenheimer_pes( stat ) !------------------------------------------------------------------------ ! USE path_variables, ONLY : nim => num_of_images, & pending_image, istep_path, pes, & first_last_opt, Emin, Emax, Emax_index ! IMPLICIT NONE ! LOGICAL, INTENT(OUT) :: stat ! INTEGER :: fii, lii ! ! IF ( istep_path == 0 .OR. first_last_opt ) THEN ! fii = 1 lii = nim ! ELSE ! fii = 2 lii = nim - 1 ! END IF ! IF ( pending_image /= 0 ) fii = pending_image ! CALL compute_scf( fii, lii, stat ) ! IF ( .NOT. stat ) RETURN ! Emin = MINVAL( pes(1:nim) ) Emax = MAXVAL( pes(1:nim) ) Emax_index = MAXLOC( pes(1:nim), 1 ) ! RETURN ! END SUBROUTINE born_oppenheimer_pes ! !------------------------------------------------------------------------ SUBROUTINE fe_profile() !------------------------------------------------------------------------ ! USE path_variables, ONLY : nim => num_of_images USE path_variables, ONLY : pos, pes, grad_pes, & Emin, Emax, Emax_index ! IMPLICIT NONE ! INTEGER :: i ! ! pes(:) = 0.0_DP ! DO i = 2, nim ! pes(i) = pes(i-1) + 0.5_DP*( ( pos(:,i) - pos(:,i-1) ) .dot. & ( grad_pes(:,i) + grad_pes(:,i-1) ) ) ! END DO ! Emin = MINVAL( pes(1:nim) ) Emax = MAXVAL( pes(1:nim) ) Emax_index = MAXLOC( pes(1:nim), 1 ) ! RETURN ! END SUBROUTINE fe_profile ! !----------------------------------------------------------------------- SUBROUTINE search_mep() !----------------------------------------------------------------------- ! USE path_variables, ONLY : lneb, lsmd USE path_variables, ONLY : conv_path, istep_path, nstep_path, & pending_image, activation_energy, & err_max, pes, climbing, CI_scheme, & Emax_index, fixed_tan, tangent USE path_io_routines, ONLY : write_restart, write_dat_files, write_output USE path_formats, ONLY : scf_iter_fmt ! USE path_reparametrisation ! IMPLICIT NONE ! LOGICAL :: stat ! REAL(DP), EXTERNAL :: get_clock ! ! conv_path = .FALSE. ! CALL search_mep_init() ! IF ( istep_path == nstep_path ) THEN ! CALL write_dat_files() ! CALL write_output() ! pending_image = 0 ! CALL write_restart() ! RETURN ! END IF ! ! ... path optimisation loop ! optimisation: DO ! ! ... new positions are saved on file: it has to be done here ! ... because, in the event of an unexpected crash the new positions ! ... would be lost. At this stage the forces and the energies are ! ... not yet known (but are not necessary for restarting); the ! ... restart file is written again as soon as the energies and ! ... forces have been computed. ! CALL write_restart() ! IF ( meta_ionode ) & WRITE( UNIT = iunpath, FMT = scf_iter_fmt ) istep_path + 1 ! ! ... energies and gradients acting on each image of the path (in real ! ... space) are computed calling a driver for the scf calculations ! ! CALL born_oppenheimer_pes( stat ) ! ! IF ( .NOT. stat ) THEN ! conv_path = .FALSE. ! EXIT optimisation ! END IF ! ! ... istep_path is updated after a self-consistency step has been ! ... completed ! istep_path = istep_path + 1 ! ! ... the new tangent is computed here : ! ... the improved definition of tangent requires the energies ! IF ( .NOT. fixed_tan ) tangent(:,:) = new_tangent() ! IF ( CI_scheme == "auto" ) THEN ! climbing = .FALSE. ! climbing(Emax_index) = .TRUE. ! END IF ! IF ( lneb ) CALL neb_gradient() IF ( lsmd ) CALL smd_gradient() ! ! ... the forward activation energy is computed here ! activation_energy = ( pes(Emax_index) - pes(1) )*autoev ! ! ... the error is computed here (frozen images are also set here) ! CALL compute_error( err_max ) ! ! ... information is written on the files ! CALL write_dat_files() ! ! ... information is written on the standard output ! CALL write_output() ! ! ... the restart file is written ! CALL write_restart() ! ! ... exit conditions ! IF ( check_exit( err_max ) ) EXIT optimisation ! ! ... if convergence is not yet achieved, the path is optimised ! CALL optimisation_step() ! IF ( lsmd ) CALL reparametrise() ! END DO optimisation ! ! ... the restart file is written before the exit ! CALL write_restart() ! RETURN ! END SUBROUTINE search_mep ! !------------------------------------------------------------------------ SUBROUTINE search_mep_init() !------------------------------------------------------------------------ ! USE path_variables, ONLY : lsmd USE path_variables, ONLY : pending_image, tangent ! USE path_reparametrisation ! IMPLICIT NONE ! ! IF ( pending_image /= 0 ) RETURN ! IF ( lsmd ) CALL reparametrise() ! tangent(:,:) = new_tangent() ! RETURN ! END SUBROUTINE search_mep_init ! !------------------------------------------------------------------------ FUNCTION check_exit( err_max ) !------------------------------------------------------------------------ ! USE path_input_parameters_module, ONLY : num_of_images_inp => num_of_images USE path_variables, ONLY : lneb, lsmd USE path_variables, ONLY : path_thr, istep_path, nstep_path, & conv_path, pending_image, & num_of_images, llangevin USE path_formats, ONLY : final_fmt ! IMPLICIT NONE ! LOGICAL :: check_exit REAL(DP), INTENT(IN) :: err_max LOGICAL :: exit_condition ! ! check_exit = .FALSE. ! ! ... the program checks if the convergence has been achieved ! exit_condition = ( .NOT.llangevin .AND. & ( num_of_images == num_of_images_inp ) .AND. & ( err_max <= path_thr ) ) ! IF ( exit_condition ) THEN ! IF ( meta_ionode ) THEN ! WRITE( UNIT = iunpath, FMT = final_fmt ) ! IF ( lneb ) & WRITE( UNIT = iunpath, & FMT = '(/,5X,"neb: convergence achieved in ",I3, & & " iterations" )' ) istep_path IF ( lsmd ) & WRITE( UNIT = iunpath, & FMT = '(/,5X,"smd: convergence achieved in ",I3, & & " iterations" )' ) istep_path ! END IF ! pending_image = 0 ! conv_path = .TRUE. check_exit = .TRUE. ! RETURN ! END IF ! ! ... the program checks if the maximum number of iterations has ! ... been reached ! IF ( istep_path >= nstep_path ) THEN ! IF ( meta_ionode ) THEN ! WRITE( UNIT = iunpath, FMT = final_fmt ) ! IF ( lneb ) & WRITE( UNIT = iunpath, & FMT = '(/,5X,"neb: reached the maximum number of ", & & "steps")' ) IF ( lsmd ) & WRITE( UNIT = iunpath, & FMT = '(/,5X,"smd: reached the maximum number of ", & & "steps")' ) ! END IF ! pending_image = 0 ! check_exit = .TRUE. ! RETURN ! END IF ! RETURN ! END FUNCTION check_exit ! !------------------------------------------------------------------------ SUBROUTINE optimisation_step() !------------------------------------------------------------------------ ! USE path_variables, ONLY : num_of_images, frozen, lsteep_des, & lquick_min, lbroyden, lbroyden2, & llangevin, istep_path USE path_opt_routines, ONLY : quick_min, broyden, broyden2, & steepest_descent, langevin ! IMPLICIT NONE ! INTEGER :: image ! ! IF ( lbroyden ) THEN ! CALL broyden() ! ELSE IF (lbroyden2 ) THEN ! CALL broyden2() ! ELSE ! DO image = 1, num_of_images ! IF ( frozen(image) ) CYCLE ! IF ( lsteep_des ) THEN ! CALL steepest_descent( image ) ! ELSE IF ( llangevin ) THEN ! CALL langevin( image ) ! ELSE IF ( lquick_min ) THEN ! CALL quick_min( image, istep_path ) ! END IF ! END DO ! END IF ! RETURN ! END SUBROUTINE optimisation_step ! END MODULE path_base NEB/src/engine_to_path_fix_atom_pos.f900000644000700200004540000000151312053145633017324 0ustar marsamoscm! ! Copyright (C) 2011 Quantum ESPRESSO group ! This file is distributed under the terms of the ! GNU General Public License. See the file `License' ! in the root directory of the present distribution, ! or http://www.gnu.org/copyleft/gpl.txt . ! ! !---------------------------------------------------------------------------- SUBROUTINE engine_to_path_fix_atom_pos() !----------------------------------------------------------------------------- ! ! USE kinds, ONLY : DP ! USE ions_base, ONLY : if_pos USE path_variables, ONLY : fix_atom_pos USE path_input_parameters_module, ONLY : nat ! ! ... "path" specific ! ! IMPLICIT NONE ! ! set_my_if_pos ! allocate(fix_atom_pos(3,nat)) fix_atom_pos(:,:) = 1 fix_atom_pos(:,:) = if_pos(:,:) ! RETURN ! END SUBROUTINE engine_to_path_fix_atom_pos ! NEB/src/path_io_routines.f900000644000700200004540000010100712053145633015144 0ustar marsamoscm! ! Copyright (C) 2002-2006 Quantum ESPRESSO group ! This file is distributed under the terms of the ! GNU General Public License. See the file `License' ! in the root directory of the present distribution, ! or http://www.gnu.org/copyleft/gpl.txt . ! ! !---------------------------------------------------------------------------- MODULE path_io_routines !---------------------------------------------------------------------------- ! ! ... This module contains all subroutines used for I/O in path ! ... optimisations ! ! ... Written by Carlo Sbraccia ( 2003-2006 ) ! USE kinds, ONLY : DP USE constants, ONLY : pi, autoev, bohr_radius_angs, eV_to_kelvin USE io_global, ONLY : meta_ionode, meta_ionode_id USE mp, ONLY : mp_bcast ! USE basic_algebra_routines ! IMPLICIT NONE ! PRIVATE ! PUBLIC :: path_summary PUBLIC :: read_restart PUBLIC :: write_restart, write_dat_files, write_output PUBLIC :: new_image_init, get_new_image, stop_other_images ! CONTAINS ! !----------------------------------------------------------------------- SUBROUTINE path_summary() !----------------------------------------------------------------------- ! USE path_input_parameters_module, ONLY : string_method, opt_scheme USE path_input_parameters_module, ONLY : restart_mode USE path_variables, ONLY : lneb, lsmd USE path_variables, ONLY : climbing, nstep_path, num_of_images, & path_length, path_thr, ds, use_masses, & first_last_opt, temp_req, use_freezing, & k_min, k_max, CI_scheme, fixed_tan, & llangevin USE path_formats, ONLY : summary_fmt USE path_io_units_module, ONLY : iunpath ! IMPLICIT NONE ! INTEGER :: i REAL(DP) :: k_ratio CHARACTER(LEN=256) :: outline CHARACTER(LEN=20) :: nim_char, nstep_path_char ! CHARACTER(LEN=6), EXTERNAL :: int_to_char ! ! IF ( .NOT. meta_ionode ) RETURN ! ! ... details of the calculation are written on output ! nstep_path_char = int_to_char( nstep_path ) nim_char = int_to_char( num_of_images ) ! WRITE( iunpath, * ) WRITE( iunpath, summary_fmt ) "string_method", TRIM( string_method ) WRITE( iunpath, summary_fmt ) "restart_mode", TRIM( restart_mode ) WRITE( iunpath, summary_fmt ) "opt_scheme", TRIM( opt_scheme ) WRITE( iunpath, summary_fmt ) "num_of_images", TRIM( nim_char ) WRITE( iunpath, summary_fmt ) "nstep_path", TRIM( nstep_path_char ) WRITE( iunpath, summary_fmt ) "CI_scheme", TRIM( CI_scheme ) ! WRITE( UNIT = iunpath, & FMT = '(5X,"first_last_opt",T35," = ",L4)' ) first_last_opt ! ! WRITE( UNIT = iunpath, & FMT = '(5X,"use_freezing",T35," = ",L4)' ) use_freezing ! WRITE( UNIT = iunpath, & FMT = '(5X,"ds",T35," = ",F9.4," a.u.")' ) ds ! IF ( lneb ) THEN ! WRITE( UNIT = iunpath, & FMT = '(5X,"k_max",T35," = ",F9.4," a.u.")' ) k_max WRITE( UNIT = iunpath, & FMT = '(5X,"k_min",T35," = ",F9.4," a.u.")' ) k_min ! k_ratio = k_min / k_max ! WRITE( UNIT = iunpath, FMT = '(5X,"suggested k_max",T35, & & " = ",F9.4," a.u.")' ) ( pi / ds )**2 / 16.0_DP ! WRITE( UNIT = iunpath, FMT = '(5X,"suggested k_min",T35, & & " = ",F9.4," a.u.")' ) ( pi / ds )**2 / 16.0_DP * k_ratio ! END IF ! IF ( lsmd ) THEN ! WRITE( UNIT = iunpath, & FMT = '(5X,"fixed_tan",T35," = ",L4)' ) fixed_tan ! IF ( llangevin ) & WRITE( UNIT = iunpath, & FMT = '(5X,"required temperature",T35, & &" = ",F9.4," K")' ) temp_req * eV_to_kelvin*autoev ! END IF ! WRITE( UNIT = iunpath, & FMT = '(5X,"path_thr",T35," = ",F9.4," eV / A")' ) path_thr ! IF ( CI_scheme == "manual" ) THEN ! outline = ' ' ! DO i = 2, num_of_images ! IF ( climbing(i) ) outline = TRIM( outline ) // ' ' // & & TRIM( int_to_char( i ) ) // ',' ! END DO ! WRITE( UNIT = iunpath, & FMT = '(/,5X,"list of climbing images :",2X,A)' ) & TRIM( outline ) ! END IF ! RETURN ! END SUBROUTINE path_summary ! !----------------------------------------------------------------------- SUBROUTINE read_restart() !----------------------------------------------------------------------- ! USE path_variables, ONLY : lsmd USE path_io_units_module, ONLY : iunpath USE path_io_units_module, ONLY : iunrestart, path_file USE path_variables, ONLY : fix_atom_pos USE path_variables, ONLY : nim => num_of_images USE path_variables, ONLY : istep_path, nstep_path, frozen, dim1,& pending_image, pos, pes, grad_pes, & lquick_min, posold, Emax, Emin, & Emax_index USE path_reparametrisation, ONLY : spline_interpolation ! IMPLICIT NONE ! INTEGER :: i, j, ia, ierr INTEGER :: nim_inp CHARACTER(LEN=256) :: input_line LOGICAL :: exists LOGICAL, EXTERNAL :: matches ! ! IF ( meta_ionode ) THEN ! WRITE( UNIT = iunpath, & FMT = '(/,5X,"reading file ''",A,"''",/)') TRIM( path_file ) ! INQUIRE( FILE = TRIM( path_file ), EXIST = exists ) ! IF ( .NOT. exists ) & CALL errore( 'read_restart', 'restart file not found', 1 ) ! OPEN( UNIT = iunrestart, FILE = path_file, STATUS = "OLD", & ACTION = "READ" ) ! READ( UNIT = iunrestart, FMT = '(256A)' ) input_line ! IF ( matches( "RESTART INFORMATION", input_line ) ) THEN ! READ( UNIT = iunrestart, FMT = * ) istep_path READ( UNIT = iunrestart, FMT = * ) nstep_path READ( UNIT = iunrestart, FMT = * ) pending_image ! ELSE ! ! ... mandatory fields ! CALL errore( 'read_restart', 'RESTART INFORMATION missing', 1 ) ! END IF ! READ( UNIT = iunrestart, FMT = '(256A)' ) input_line ! IF ( matches( "NUMBER OF IMAGES", input_line ) ) THEN ! ! ... optional field ! READ( UNIT = iunrestart, FMT = * ) nim_inp ! IF ( nim_inp > nim ) & CALL errore( 'read_restart', & 'wrong number of images in the restart file', 1 ) ! READ( UNIT = iunrestart, FMT = '(256A)' ) input_line ! ELSE ! nim_inp = nim ! END IF ! IF ( .NOT. ( matches( "ENERGIES, POSITIONS AND GRADIENTS", & input_line ) ) ) THEN ! ! ... mandatory fields ! CALL errore( 'read_restart', & 'ENERGIES, POSITIONS AND GRADIENTS missing', 1 ) ! END IF ! ! READ( UNIT = iunrestart, FMT = * ) READ( UNIT = iunrestart, FMT = * ) pes(1) ! ia = 0 ! ! the default is not the same as in pw .... all atoms are fixed by default .... fix_atom_pos = 0 ! DO j = 1, dim1, 3 ! ia = ia + 1 ! READ( UNIT = iunrestart, FMT = * ) & pos(j+0,1), & pos(j+1,1), & pos(j+2,1), & grad_pes(j+0,1), & grad_pes(j+1,1), & grad_pes(j+2,1), & fix_atom_pos(1,ia), & fix_atom_pos(2,ia), & fix_atom_pos(3,ia) ! grad_pes(:,1) = grad_pes(:,1) * & DBLE( RESHAPE( fix_atom_pos, (/ dim1 /) ) ) ! END DO ! DO i = 2, nim_inp ! READ( UNIT = iunrestart, FMT = * ) READ( UNIT = iunrestart, FMT = * ) pes(i) ! DO j = 1, dim1, 3 ! READ( UNIT = iunrestart, FMT = * ) & pos(j+0,i), & pos(j+1,i), & pos(j+2,i), & grad_pes(j+0,i), & grad_pes(j+1,i), & grad_pes(j+2,i) ! END DO ! grad_pes(:,i) = grad_pes(:,i) * & DBLE( RESHAPE( fix_atom_pos, (/ dim1 /) ) ) ! END DO ! READ( UNIT = iunrestart, FMT = '(256A)', IOSTAT = ierr ) input_line ! IF ( ( ierr == 0 ) .AND. lquick_min ) THEN ! IF ( matches( "QUICK-MIN FIELDS", input_line ) ) THEN ! ! ... optional fields ! ! DO i = 1, nim_inp ! READ( UNIT = iunrestart, FMT = * ) READ( UNIT = iunrestart, FMT = * ) frozen(i) ! DO j = 1, dim1, 3 ! READ( UNIT = iunrestart, FMT = * ) & posold(j+0,i), & posold(j+1,i), & posold(j+2,i) ! END DO ! posold(:,i) = posold(:,i) * & DBLE( RESHAPE( fix_atom_pos, (/ dim1 /) ) ) ! END DO ! END IF ! END IF ! CLOSE( iunrestart ) ! IF ( nim_inp /= nim ) THEN ! ! ... the input path is reinterpolated to have the required ! ... number of images ! CALL spline_interpolation( pos, 1, nim, nim_inp ) CALL spline_interpolation( pes, 1, nim, nim_inp ) CALL spline_interpolation( grad_pes, 1, nim, nim_inp ) ! IF ( lquick_min ) THEN ! CALL spline_interpolation( posold, 1, nim, nim_inp ) ! frozen(:) = .FALSE. ! END IF ! END IF ! IF ( pending_image == 0 ) THEN ! Emin = MINVAL( pes(:) ) Emax = MAXVAL( pes(:) ) Emax_index = MAXLOC( pes(:), 1 ) ! END IF ! END IF ! ! ... broadcast to all nodes ! CALL mp_bcast( istep_path, meta_ionode_id ) CALL mp_bcast( nstep_path, meta_ionode_id ) CALL mp_bcast( pending_image, meta_ionode_id ) ! CALL mp_bcast( pos, meta_ionode_id ) CALL mp_bcast( fix_atom_pos, meta_ionode_id ) CALL mp_bcast( pes, meta_ionode_id ) CALL mp_bcast( grad_pes, meta_ionode_id ) ! CALL mp_bcast( Emax, meta_ionode_id ) CALL mp_bcast( Emin, meta_ionode_id ) CALL mp_bcast( Emax_index, meta_ionode_id ) ! IF ( lquick_min ) THEN ! CALL mp_bcast( frozen, meta_ionode_id ) CALL mp_bcast( posold, meta_ionode_id ) ! END IF ! RETURN ! END SUBROUTINE read_restart ! !----------------------------------------------------------------------- SUBROUTINE write_restart() !----------------------------------------------------------------------- ! USE path_variables, ONLY : fix_atom_pos USE path_io_units_module, ONLY : iunrestart, path_file USE io_files, ONLY : tmp_dir USE control_flags, ONLY : conv_elec USE path_variables, ONLY : istep_path, nstep_path, pending_image, & dim1, num_of_images, pos, pes, grad_pes, & posold, frozen, lquick_min USE path_formats, ONLY : energy, restart_first, restart_others, & quick_min ! IMPLICIT NONE ! INTEGER :: i, j, ia CHARACTER(LEN=256) :: file ! CHARACTER(LEN=6), EXTERNAL :: int_to_char ! IF ( meta_ionode ) THEN ! ! ... first the restart file is written in the working directory ! OPEN( UNIT = iunrestart, FILE = path_file, STATUS = "UNKNOWN", & ACTION = "WRITE" ) ! CALL write_common_fields( iunrestart ) ! IF ( lquick_min ) THEN ! CALL write_quick_min_fields( iunrestart ) ! END IF ! CLOSE( iunrestart ) ! ! ... then, if pending_image == 0, it is also written on the ! ... scratch direcoty (a backup copy at each iteration) ! IF ( pending_image == 0 ) THEN ! file = TRIM( tmp_dir ) // & TRIM( path_file ) // TRIM( int_to_char( istep_path ) ) ! OPEN( UNIT = iunrestart, FILE = TRIM( file ), & STATUS = "UNKNOWN", ACTION = "WRITE" ) ! CALL write_common_fields( iunrestart ) ! IF ( lquick_min ) THEN ! CALL write_quick_min_fields( iunrestart ) ! END IF ! CLOSE( iunrestart ) ! END IF ! END IF ! CONTAINS ! !------------------------------------------------------------------- SUBROUTINE write_common_fields( in_unit ) !------------------------------------------------------------------- ! IMPLICIT NONE ! INTEGER, INTENT(IN) :: in_unit ! ! WRITE( UNIT = in_unit, FMT = '("RESTART INFORMATION")' ) ! WRITE( UNIT = in_unit, FMT = '(I8)' ) istep_path WRITE( UNIT = in_unit, FMT = '(I8)' ) nstep_path WRITE( UNIT = in_unit, FMT = '(I8)' ) pending_image ! WRITE( UNIT = in_unit, FMT = '("NUMBER OF IMAGES")' ) ! WRITE( UNIT = in_unit, FMT = '(I4)' ) num_of_images ! WRITE( UNIT = in_unit, & FMT = '("ENERGIES, POSITIONS AND GRADIENTS")' ) ! DO i = 1, num_of_images ! WRITE( UNIT = in_unit, FMT = '("Image: ",I4)' ) i ! ! WRITE( UNIT = in_unit, FMT = energy ) pes(i) ! ia = 0 ! DO j = 1, dim1, 3 ! ia = ia + 1 ! IF ( i == 1 ) THEN ! WRITE( UNIT = in_unit, FMT = restart_first ) & pos(j+0,i), & pos(j+1,i), & pos(j+2,i), & grad_pes(j+0,i), & grad_pes(j+1,i), & grad_pes(j+2,i), & fix_atom_pos(1,ia), & fix_atom_pos(2,ia), & fix_atom_pos(3,ia) ! ELSE ! WRITE( UNIT = in_unit, FMT = restart_others ) & pos(j+0,i), & pos(j+1,i), & pos(j+2,i), & grad_pes(j+0,i), & grad_pes(j+1,i), & grad_pes(j+2,i) ! END IF ! END DO ! END DO ! RETURN ! END SUBROUTINE write_common_fields ! !------------------------------------------------------------------- SUBROUTINE write_quick_min_fields( in_unit ) !------------------------------------------------------------------- ! IMPLICIT NONE ! INTEGER, INTENT(IN) :: in_unit ! ! WRITE( UNIT = in_unit, FMT = '("QUICK-MIN FIELDS")' ) ! DO i = 1, num_of_images ! WRITE( UNIT = in_unit, FMT = '("Image: ",I4)' ) i WRITE( UNIT = in_unit, & FMT = '(2(L1,1X))' ) frozen(i) ! DO j = 1, dim1, 3 ! WRITE( UNIT = in_unit, FMT = quick_min ) & posold(j+0,i), & posold(j+1,i), & posold(j+2,i) ! END DO ! ! END DO ! RETURN ! END SUBROUTINE write_quick_min_fields ! END SUBROUTINE write_restart ! !----------------------------------------------------------------------- SUBROUTINE write_dat_files() !----------------------------------------------------------------------- ! USE constants, ONLY : pi USE cell_base, ONLY : alat, at, bg USE ions_base, ONLY : ityp, nat, atm, tau_format USE path_formats, ONLY : dat_fmt, int_fmt, xyz_fmt, axsf_fmt USE path_variables, ONLY : fix_atom_pos USE path_variables, ONLY : pos, grad_pes, pes, num_of_images, & tangent, dim1, error USE path_io_units_module, ONLY : iundat, iunint, iunxyz, iuncrd, iunaxsf, & dat_file, int_file, xyz_file, axsf_file, & crd_file ! IMPLICIT NONE ! REAL(DP) :: r, delta, x REAL(DP), ALLOCATABLE :: a(:), b(:), c(:), d(:), f(:), s(:), tau_out(:,:,:) REAL(DP) :: ener, ener_0 INTEGER :: i, j, ia INTEGER, PARAMETER :: max_i = 250 CHARACTER(LEN=256) :: strcrd ! ! IF ( .NOT. meta_ionode ) RETURN ! ! ... the *.dat and *.int files are written here ! OPEN( UNIT = iundat, FILE = dat_file, STATUS = "UNKNOWN", & ACTION = "WRITE" ) OPEN( UNIT = iunint, FILE = int_file, STATUS = "UNKNOWN", & ACTION = "WRITE" ) ! ALLOCATE( a( num_of_images - 1 ) ) ALLOCATE( b( num_of_images - 1 ) ) ALLOCATE( c( num_of_images - 1 ) ) ALLOCATE( d( num_of_images - 1 ) ) ALLOCATE( f( num_of_images ) ) ALLOCATE( s( num_of_images ) ) ! f(:) = 0.0_DP ! DO i = 2, num_of_images - 1 ! f(i) = - ( grad_pes(:,i) .dot. tangent(:,i) ) ! END DO ! s(1) = 0.0_DP ! DO i = 1, num_of_images - 1 ! r = norm( pos(:,i+1) - pos(:,i) ) ! s(i+1) = s(i) + r ! ! ... cubic interpolation ! a(i) = 2.0_DP*( pes(i) - pes(i+1) ) / r**3 - ( f(i) + f(i+1) ) / r**2 ! b(i) = 3.0_DP*( pes(i+1) - pes(i) ) / r**2 + ( 2.0_DP*f(i) + f(i+1) ) / r ! c(i) = - f(i) ! d(i) = pes(i) ! END DO ! DO i = 1, num_of_images ! WRITE( UNIT = iundat, FMT = dat_fmt ) & ( s(i) / s(num_of_images) ), ( pes(i) - pes(1) )*autoev, error(i) ! END DO ! i = 1 ! delta = s(num_of_images) / DBLE( max_i ) ! DO j = 0, max_i ! r = DBLE( j ) * delta ! IF ( r >= s(i+1) .AND. i < num_of_images - 1 ) i = i + 1 ! x = r - s(i) ! ener = a(i)*x**3 + b(i)*x**2 + c(i)*x + d(i) ! IF ( j == 0 ) ener_0 = ener ! WRITE( UNIT = iunint, FMT = int_fmt ) & ( r / s(num_of_images) ), ( ener - ener_0 )*autoev ! END DO ! DEALLOCATE( a, b, c, d, f, s ) ! CLOSE( UNIT = iundat ) CLOSE( UNIT = iunint ) ! ! ... the *.xyz file is written here ! OPEN( UNIT = iunxyz, FILE = xyz_file, & STATUS = "UNKNOWN", ACTION = "WRITE" ) ! DO i = 1, num_of_images ! WRITE( UNIT = iunxyz, FMT = '(I5,/)' ) nat ! DO ia = 1, nat ! WRITE( UNIT = iunxyz, FMT = xyz_fmt ) & TRIM( atm( ityp( ia ) ) ), & pos(3*ia-2,i) * bohr_radius_angs, & pos(3*ia-1,i) * bohr_radius_angs, & pos(3*ia-0,i) * bohr_radius_angs ! END DO ! END DO ! CLOSE( UNIT = iunxyz ) ! ! ... the *.crd file is written here ! OPEN( UNIT = iuncrd, FILE = crd_file, STATUS = "UNKNOWN", & ACTION = "WRITE" ) ALLOCATE( tau_out(3,nat,num_of_images) ) ! DO i = 1, num_of_images DO ia = 1,nat tau_out(1,ia,i) = pos(3*ia-2,i) tau_out(2,ia,i) = pos(3*ia-1,i) tau_out(3,ia,i) = pos(3*ia-0,i) ENDDO ENDDO ! SELECT CASE( tau_format ) ! ! ... convert output atomic positions from internally used format ! ... (bohr units, for path) to the same format used in input ! CASE( 'alat' ) strcrd = "ATOMIC_POSITIONS (alat)" tau_out(:,:,:) = tau_out(:,:,:) / alat CASE( 'bohr' ) strcrd = "ATOMIC_POSITIONS (bohr)" CASE( 'crystal' ) strcrd = "ATOMIC_POSITIONS (crystal)" tau_out(:,:,:) = tau_out(:,:,:) / alat DO i = 1, num_of_images call cryst_to_cart( nat, tau_out(1,1,i), bg, -1 ) ENDDO CASE( 'angstrom' ) strcrd = "ATOMIC_POSITIONS (angstrom)" tau_out(:,:,:) = tau_out(:,:,:) * bohr_radius_angs CASE DEFAULT strcrd = "ATOMIC_POSITIONS" END SELECT DO i = 1, num_of_images ! Add the image label and atomic position card header IF ( i == 1) THEN WRITE( UNIT = iuncrd, FMT='(A,/,A)') "FIRST_IMAGE", TRIM(strcrd) ELSEIF ( i == num_of_images) THEN WRITE( UNIT = iuncrd, FMT='(A,/,A)') "LAST_IMAGE", TRIM(strcrd) ELSE WRITE( UNIT = iuncrd, FMT='(A,/,A)') & "INTERMEDIATE_IMAGE", TRIM(strcrd) ENDIF ! DO ia = 1, nat ! IF ( i == 1 .and. ANY(fix_atom_pos(:,ia) /= 1) ) THEN WRITE( UNIT = iuncrd, FMT = '(1x,a4,3f18.10,3i2)' ) & TRIM( atm( ityp( ia ) ) ), & tau_out(1:3,ia,i), fix_atom_pos(1:3,ia) ELSE WRITE( UNIT = iuncrd, FMT = '(1x,a4,3f18.10)' ) & TRIM( atm( ityp( ia ) ) ), & tau_out(1:3,ia,i) ENDIF ! END DO ! END DO ! DEALLOCATE ( tau_out ) CLOSE( UNIT = iuncrd ) ! ! ... the *.axsf file is written here ! OPEN( UNIT = iunaxsf, FILE = axsf_file, STATUS = "UNKNOWN", & ACTION = "WRITE" ) ! WRITE( UNIT = iunaxsf, FMT = '(" ANIMSTEPS ",I3)' ) num_of_images WRITE( UNIT = iunaxsf, FMT = '(" CRYSTAL ")' ) WRITE( UNIT = iunaxsf, FMT = '(" PRIMVEC ")' ) WRITE( UNIT = iunaxsf, FMT = '(3F14.10)' ) & at(1,1) * alat * bohr_radius_angs, & at(2,1) * alat * bohr_radius_angs, & at(3,1) * alat * bohr_radius_angs WRITE( UNIT = iunaxsf, FMT = '(3F14.10)' ) & at(1,2) * alat * bohr_radius_angs, & at(2,2) * alat * bohr_radius_angs, & at(3,2) * alat * bohr_radius_angs WRITE( UNIT = iunaxsf, FMT = '(3F14.10)' ) & at(1,3) * alat * bohr_radius_angs, & at(2,3) * alat * bohr_radius_angs, & at(3,3) * alat * bohr_radius_angs ! DO i = 1, num_of_images ! WRITE( UNIT = iunaxsf, FMT = '(" PRIMCOORD ",I3)' ) i WRITE( UNIT = iunaxsf, FMT = '(I5," 1")' ) nat ! DO ia = 1, nat ! WRITE( UNIT = iunaxsf, FMT = axsf_fmt ) & TRIM( atm(ityp(ia)) ), & pos(3*ia-2,i) * bohr_radius_angs, & pos(3*ia-1,i) * bohr_radius_angs, & pos(3*ia-0,i) * bohr_radius_angs, & - grad_pes(3*ia-2,i) / bohr_radius_angs, & - grad_pes(3*ia-1,i) / bohr_radius_angs, & - grad_pes(3*ia-0,i) / bohr_radius_angs ! END DO ! END DO ! CLOSE( UNIT = iunaxsf ) ! END SUBROUTINE write_dat_files ! !----------------------------------------------------------------------- SUBROUTINE write_output() !----------------------------------------------------------------------- ! USE path_io_units_module, ONLY : iunpath USE path_variables, ONLY : num_of_images, error, path_length, & activation_energy, pes, pos, frozen, & CI_scheme, Emax_index USE path_formats, ONLY : run_info, run_output ! IMPLICIT NONE ! ! ... local variables ! INTEGER :: image REAL (DP) :: inter_image_distance ! ! IF ( .NOT. meta_ionode ) RETURN ! WRITE( UNIT = iunpath, & FMT = '(/,5X,"activation energy (->) = ",F10.6," eV")' ) & activation_energy WRITE( UNIT = iunpath, & FMT = '(5X,"activation energy (<-) = ",F10.6," eV",/)' ) & activation_energy + ( pes(1) - pes(num_of_images) ) * autoev ! WRITE( UNIT = iunpath, FMT = run_info ) ! path_length = 0.0_DP ! DO image = 1, num_of_images ! IF ( image > 1 ) & path_length = path_length + & norm( pos(:,image) - pos(:,image-1) ) ! WRITE( UNIT = iunpath, FMT = run_output ) & image, pes(image) * autoev, error(image), frozen(image) ! END DO ! inter_image_distance = path_length / DBLE( num_of_images - 1 ) ! IF ( CI_scheme == "auto" ) & WRITE( UNIT = iunpath, & FMT = '(/,5X,"climbing image = ",I2)' ) Emax_index ! WRITE( UNIT = iunpath, & FMT = '(/,5X,"path length",& & T26," = ",F6.3," bohr")' ) path_length WRITE( UNIT = iunpath, & FMT = '(5X,"inter-image distance", & & T26," = ",F6.3," bohr")' ) inter_image_distance ! END SUBROUTINE write_output ! !----------------------------------------------------------------------- SUBROUTINE new_image_init( fii, outdir ) !----------------------------------------------------------------------- ! ! ... this subroutine initializes the file needed for the ! ... parallelization among images ! USE path_io_units_module, ONLY : iunnewimage USE io_files, ONLY : prefix USE path_variables, ONLY : tune_load_balance USE mp_image_global_module, ONLY : nimage ! IMPLICIT NONE ! INTEGER, INTENT(IN) :: fii CHARACTER(LEN=*), INTENT(IN) :: outdir ! ! IF ( nimage == 1 .OR. .NOT.tune_load_balance ) RETURN ! OPEN( UNIT = iunnewimage, FILE = TRIM( outdir ) // & & TRIM( prefix ) // '.newimage' , STATUS = 'UNKNOWN' ) ! WRITE( iunnewimage, * ) fii + nimage ! CLOSE( UNIT = iunnewimage, STATUS = 'KEEP' ) ! RETURN ! END SUBROUTINE new_image_init ! !----------------------------------------------------------------------- SUBROUTINE get_new_image( image, outdir ) !----------------------------------------------------------------------- ! ! ... this subroutine is used to get the new image to work on ! ... the "prefix.LOCK" file is needed to avoid (when present) that ! ... other jobs try to read/write on file "prefix.newimage" ! USE io_files, ONLY : iunnewimage, iunlock, prefix USE io_global, ONLY : ionode USE path_variables, ONLY : tune_load_balance USE mp_image_global_module, ONLY : nimage ! IMPLICIT NONE ! INTEGER, INTENT(INOUT) :: image CHARACTER(LEN=*), INTENT(IN) :: outdir ! INTEGER :: ioerr CHARACTER(LEN=256) :: filename LOGICAL :: opened ! ! IF ( .NOT.ionode ) RETURN ! IF ( nimage > 1 ) THEN ! IF ( tune_load_balance ) THEN ! filename = TRIM( outdir ) // TRIM( prefix ) // '.LOCK' ! open_loop: DO ! OPEN( UNIT = iunlock, FILE = TRIM( filename ), & & IOSTAT = ioerr, STATUS = 'NEW' ) ! IF ( ioerr > 0 ) CYCLE open_loop ! INQUIRE( UNIT = iunnewimage, OPENED = opened ) ! IF ( .NOT. opened ) THEN ! OPEN( UNIT = iunnewimage, FILE = TRIM( outdir ) // & & TRIM( prefix ) // '.newimage' , STATUS = 'OLD' ) ! READ( iunnewimage, * ) image ! CLOSE( UNIT = iunnewimage, STATUS = 'DELETE' ) ! OPEN( UNIT = iunnewimage, FILE = TRIM( outdir ) // & & TRIM( prefix ) // '.newimage' , STATUS = 'NEW' ) ! WRITE( iunnewimage, * ) image + 1 ! CLOSE( UNIT = iunnewimage, STATUS = 'KEEP' ) ! EXIT open_loop ! END IF ! END DO open_loop ! CLOSE( UNIT = iunlock, STATUS = 'DELETE' ) ! ELSE ! image = image + nimage ! END IF ! ELSE ! image = image + 1 ! END IF ! RETURN ! END SUBROUTINE get_new_image ! !----------------------------------------------------------------------- SUBROUTINE stop_other_images() !----------------------------------------------------------------------- ! ! ... this subroutine is used to send a stop signal to other images ! ... this is done by creating the exit_file on the working directory ! USE io_files, ONLY : iunexit, exit_file USE io_global, ONLY : ionode ! IMPLICIT NONE ! ! IF ( .NOT. ionode ) RETURN ! OPEN( UNIT = iunexit, FILE = TRIM( exit_file ) ) CLOSE( UNIT = iunexit, STATUS = 'KEEP' ) ! RETURN ! END SUBROUTINE stop_other_images ! END MODULE path_io_routines NEB/src/neb.f900000644000700200004540000001266512053145633012350 0ustar marsamoscm! ! Copyright (C) 2011 Quantum ESPRESSO group ! This file is distributed under the terms of the ! GNU General Public License. See the file `License' ! in the root directory of the present distribution, ! or http://www.gnu.org/copyleft/gpl.txt . ! !---------------------------------------------------------------------------- PROGRAM neb !---------------------------------------------------------------------------- ! ! ... Nudged Elastic Band / Strings Method algorithm ! USE io_global, ONLY : meta_ionode_id, xmlinputunit USE parameters, ONLY : ntypx, npk, lmaxx USE control_flags, ONLY : conv_elec, conv_ions, lpath, gamma_only USE environment, ONLY : environment_start, environment_end USE path_variables, ONLY : conv_path USE check_stop, ONLY : check_stop_init USE path_base, ONLY : initialize_path, search_mep USE path_io_routines, ONLY : path_summary USE image_io_routines, ONLY : io_image_start USE mp_global, ONLY : mp_bcast, mp_rank ! USE mp_image_global_module, ONLY : mp_image_startup, world_comm USE mp_image_global_module, ONLY : me_image, nimage USE mp_global, ONLY : mp_start USE iotk_module, ONLY : iotk_attlenx USE open_close_input_file, ONLY : open_input_file, close_input_file USE read_xml_module, ONLY : read_xml USE read_cards_module, ONLY : read_cards USE read_namelists_module, ONLY : read_namelists USE path_read_namelists_module, ONLY : path_read_namelist USE path_read_cards_module, ONLY : path_read_cards ! USE path_io_units_module, ONLY : stdinpath, set_input_unit ! USE path_input_parameters_module, ONLY : nstep_path ! USE path_input_parameters_module, ONLY : input_images ! USE path_input_parameters_module, ONLY : allocate_path_input_ions, & deallocate_path_input_ions ! USE iotk_module, ONLY : iotk_open_read, iotk_close_read,iotk_attlenx ! IMPLICIT NONE ! ! CHARACTER (len=iotk_attlenx) :: attr ! CHARACTER(len=256) :: engine_prefix ! INTEGER :: unit_tmp ! INTEGER :: i, iimage CHARACTER(len=10) :: a_tmp ! INTEGER :: mpime = 0, nproc = 1, neb_comm = 0 INTEGER :: root = 0 ! CHARACTER(len=256) :: parsing_file_name LOGICAL :: lfound_parsing_file, lfound_input_images ! LOGICAL :: lxml ! CHARACTER(LEN=6), EXTERNAL :: int_to_char ! unit_tmp = 45 xmlinputunit = 45 ! #ifdef __MPI CALL mp_start(nproc,mpime,neb_comm) CALL mp_image_startup (root,neb_comm) CALL engine_mp_start() #endif CALL environment_start ( 'NEB' ) ! ! ! INPUT RELATED ! ! ... open input file ! if(mpime==root) CALL input_file_name_getarg(parsing_file_name,lfound_parsing_file) ! engine_prefix = "pw_" ! CALL mp_bcast(parsing_file_name,root,neb_comm) CALL mp_bcast(lfound_parsing_file,root,neb_comm) ! ! if(lfound_parsing_file) then write(0,*) "" write(0,*) "parsing_file_name: ", trim(parsing_file_name) call path_gen_inputs(trim(parsing_file_name),engine_prefix,input_images,root,neb_comm) ! else ! write(0,*) "" write(0,*) "NO input file found, assuming nothing to parse." write(0,*) "Searching argument -input_images or --input_images" if(mpime==root) CALL input_images_getarg(input_images,lfound_input_images) CALL mp_bcast(input_images,root,neb_comm) CALL mp_bcast(lfound_input_images,root,neb_comm) ! IF(.not.lfound_input_images) CALL errore('string_methods', & 'Neither a file to parse nor input files for each image found',1) ! endif ! call set_input_unit() ! open(unit=stdinpath,file="neb.dat",status="old") CALL path_read_namelist(stdinpath) CALL path_read_cards(stdinpath) close(stdinpath) ! ! OPEN(unit_tmp, file=trim(engine_prefix)//"1.in") CALL test_input_xml(unit_tmp,lxml) CLOSE(unit_tmp) if(.not.lxml) then OPEN(unit_tmp, file=trim(engine_prefix)//"1.in") CALL read_namelists( prog='PW', unit=unit_tmp ) CALL read_cards( prog='PW', unit=unit_tmp ) CLOSE(unit_tmp) else CALL iotk_open_read( unit_tmp, trim(engine_prefix)//"1.in", & attr = attr, qe_syntax = .true.) CALL read_xml('PW', attr = attr ) CALL iotk_close_read(unit_tmp) endif CALL iosys() CALL engine_to_path_nat() CALL engine_to_path_alat() CALL allocate_path_input_ions(input_images) CALL engine_to_path_pos(1) CALL engine_to_path_fix_atom_pos() do i=2,input_images CALL set_engine_input_defaults() CALL clean_pw(.true.) a_tmp=trim(int_to_char(i)) OPEN(unit_tmp,file=trim(engine_prefix)//trim(a_tmp)//".in") CALL test_input_xml(unit_tmp,lxml) CLOSE(unit_tmp) if(.not.lxml) then OPEN(unit_tmp,file=trim(engine_prefix)//trim(a_tmp)//".in") CALL read_namelists( prog='PW', unit=unit_tmp ) CALL read_cards( prog='PW', unit=unit_tmp ) CLOSE(unit_tmp) else CALL iotk_open_read( unit_tmp, trim(engine_prefix)//trim(a_tmp)//".in", & attr = attr, qe_syntax = .true. ) CALL read_xml('PW', attr = attr ) CALL iotk_close_read(unit_tmp) endif CALL iosys() CALL engine_to_path_pos(i) enddo ! CALL path_to_engine_fix_atom_pos() ! CALL ioneb() ! CALL set_engine_io_units() ! ! END INPUT RELATED ! CALL check_stop_init() ! CALL io_image_start() ! CALL initialize_path() ! CALL deallocate_path_input_ions() ! CALL path_summary() ! CALL search_mep() ! CALL stop_run_path( conv_path ) ! ! STOP ! END PROGRAM neb NEB/src/set_defaults.f900000644000700200004540000000247312053145633014262 0ustar marsamoscm ! Copyright (C) 2010 Quantum ESPRESSO group ! This file is distributed under the terms of the ! GNU General Public License. See the file `License' ! in the root directory of the present distribution, ! or http://www.gnu.org/copyleft/gpl.txt . ! ! !---------------------------------------------------------------------------- SUBROUTINE set_engine_input_defaults() !----------------------------------------------------------------------------- ! USE input_parameters, ONLY : & tapos, tkpoints, taspc, twannier, & tconstr, tforces, tocc, tksout, & tionvel, tesr, tdipole, tcell ! tapos = .false. tkpoints = .false. taspc = .false. twannier = .false. tconstr = .false. tforces = .false. tocc = .false. tksout = .false. tionvel = .false. tesr = .false. tdipole = .false. tcell = .false. ! END SUBROUTINE set_engine_input_defaults ! !---------------------------------------------------------------------------- SUBROUTINE set_engine_io_units() !----------------------------------------------------------------------------- ! USE io_global, ONLY : stdout, xmlinputunit, ionode INTEGER, EXTERNAL :: find_free_unit ! if(ionode) stdout = find_free_unit() ! ! END SUBROUTINE set_engine_io_units ! NEB/src/engine_to_path_pos.f900000644000700200004540000000517412053145633015445 0ustar marsamoscm! ! Copyright (C) 2002-2009 Quantum ESPRESSO group ! This file is distributed under the terms of the ! GNU General Public License. See the file `License' ! in the root directory of the present distribution, ! or http://www.gnu.org/copyleft/gpl.txt . ! ! !---------------------------------------------------------------------------- SUBROUTINE engine_to_path_pos(idx) !----------------------------------------------------------------------------- ! ! USE kinds, ONLY : DP ! USE path_input_parameters_module, ONLY : input_images ! USE path_input_parameters_module, ONLY : nat, alat ! ! USE path_input_parameters_module, ONLY : pos, typ USE ions_base, ONLY : tau, ityp USE cell_base, ONLY : bg, at ! ! IMPLICIT NONE ! INTEGER, INTENT(IN) :: idx ! ! internal variables INTEGER :: iat ! counter on atoms REAL(DP), ALLOCATABLE :: pos0(:,:), pos1(:,:) ! atomic positions (in crystal units) of the previous and current image ! ! set_my_tau ! il tau e gia in units di pw ! ! is this really necessary? (GS) if(.not.allocated(pos)) allocate(pos(3*nat,input_images)) pos(:,idx) = 0.0_dp ! ! ... note that this positions array is in Bohr ! pos(1:3*nat,idx) = reshape( tau, (/ 3 * nat /) ) * alat ! ! Use the translational periodicity of the unit cell to ensure that the path ! is smooth (.i.e., to avoid "jumps" between periodic replicas of atoms). ! IF ( idx > 1 ) THEN ! ALLOCATE( pos0(3,nat), pos1(3,nat) ) pos0 = reshape( pos(:,idx-1), (/ 3, nat /) ) / alat pos1 = reshape( pos(:,idx), (/ 3, nat /) ) / alat CALL cryst_to_cart( nat, pos0(1,1), bg, -1 ) CALL cryst_to_cart( nat, pos1(1,1), bg, -1 ) ! DO iat = 1,nat ! ! translate atom by a lattice vector if needed ! N.B.: this solves the problem only when |p1-p0|<1.0 ! WHERE( (pos1(:,iat) - pos0(:,iat)) > 0.5_DP ) pos1(:,iat) = pos1(:,iat) - 1.0_DP ENDWHERE ! WHERE( (pos1(:,iat) - pos0(:,iat)) < -0.5_DP ) pos1(:,iat) = pos1(:,iat) + 1.0_DP ENDWHERE ENDDO ! CALL cryst_to_cart( nat, pos1(1,1), at, 1 ) pos(1:3*nat,idx) = reshape( pos1, (/ 3 * nat /) ) * alat ! DEALLOCATE( pos0, pos1 ) ! ENDIF ! ! consistency check on atomic type, just to be sure... (GS) ! IF ( idx == 1 ) THEN ! is this really necessary? (GS) if(.not.allocated(typ)) allocate(typ(nat)) typ = ityp(:) ELSE IF ( ANY( typ .NE. ityp ) ) CALL errore("engine_to_path_pos", & "inconsistency of atomic species", idx ) ENDIF ! RETURN ! END SUBROUTINE engine_to_path_pos ! NEB/src/path_to_engine_mp.f900000644000700200004540000000277312053145633015262 0ustar marsamoscm! ! Copyright (C) 2011 Quantum ESPRESSO group ! This file is distributed under the terms of the ! GNU General Public License. See the file `License' ! in the root directory of the present distribution, ! or http://www.gnu.org/copyleft/gpl.txt . ! ! !---------------------------------------------------------------------------- SUBROUTINE engine_mp_start() !----------------------------------------------------------------------------- ! ! fill engine modules for parallel calculations ! USE kinds, ONLY : DP ! USE mp_image_global_module, ONLY : intra_image_comm USE mp_image_global_module, ONLY : root_image, me_image, nproc_image_file, & nproc_image, my_image_id, nimage ! USE mp_global, ONLY : mp_startup_new, & intra_image_comm_ => intra_image_comm, & me_image_ => me_image, & root_image_ => root_image, & nproc_image_file_ => nproc_image_file, & nproc_image_ => nproc_image, & my_image_id_ => my_image_id, & nimage_ => nimage ! ! ... "path" specific ! IMPLICIT NONE ! intra_image_comm_ = intra_image_comm me_image_ = me_image root_image_ = root_image nproc_image_ = nproc_image nproc_image_file = nproc_image_file my_image_id_ = my_image_id nimage_ = nimage ! CALL mp_startup_new(root_image, intra_image_comm) ! ! RETURN ! END SUBROUTINE engine_mp_start ! NEB/src/input.f900000644000700200004540000002063412053145633012736 0ustar marsamoscm! ! Copyright (C) 2002-2009 Quantum ESPRESSO group ! This file is distributed under the terms of the ! GNU General Public License. See the file `License' ! in the root directory of the present distribution, ! or http://www.gnu.org/copyleft/gpl.txt . ! ! !---------------------------------------------------------------------------- SUBROUTINE ioneb() !----------------------------------------------------------------------------- ! ! ... this subroutine reads input data from standard input ( unit 5 ) ! ... Use "-input filename" to read input from file "filename": ! ... may be useful if you have trouble reading from standard input ! ... --------------------------------------------------------------- ! ! ... access the modules renaming the variables that have the same name ! ... as the input parameters, this is required in order to use a code ! ... independent input parser ! ! USE kinds, ONLY : DP USE constants, ONLY : autoev, eV_to_kelvin USE io_global, ONLY : stdout USE io_files, ONLY : tmp_dir USE path_variables, ONLY : lsteep_des, lquick_min, & lbroyden, lbroyden2, & llangevin, & nstep_path_ => nstep_path, & ds_ => ds, & use_masses_ => use_masses, & CI_scheme_ => CI_scheme, & fixed_tan_ => fixed_tan, & use_freezing_ => use_freezing, & k_max_ => k_max, & k_min_ => k_min, & num_of_images_ => num_of_images, & first_last_opt_ => first_last_opt, & temp_req_ => temp_req, & path_thr_ => path_thr ! ! USE path_variables, ONLY : lneb, lsmd ! USE path_input_parameters_module, ONLY : restart_mode ! USE path_variables, ONLY : restart ! USE path_input_parameters_module, ONLY : nstep_path, string_method, & num_of_images, path_thr, CI_scheme, opt_scheme, & use_masses, first_last_opt, temp_req, k_max, & k_min, ds, use_freezing, fixed_tan ! ! ! ... "path" specific ! ! IMPLICIT NONE ! INTEGER :: ia, image, nt REAL(DP) :: theta, phi INTEGER :: iiarg, nargs, iargc, ierr CHARACTER (len=50) :: arg ! ! SELECT CASE(trim( string_method )) ! CASE( 'neb' ) ! lneb = .true. ! CASE( 'smd' ) ! lsmd = .true. ! CASE DEFAULT ! CALL errore( 'ioneb', 'string_method ' // & & trim( string_method ) // ' not implemented', 1 ) ! END SELECT ! SELECT CASE( trim( restart_mode ) ) CASE( 'from_scratch' ) ! restart = .false. ! CASE( 'restart' ) ! IF ( lneb .or. lsmd ) THEN ! ! ... "path" specific ! restart = .true. ! ENDIF ! CASE DEFAULT ! CALL errore( 'ioneb', & & 'unknown restart_mode ' // trim( restart_mode ), 1 ) ! END SELECT ! ! ! ! check da mettere dopo iosys del pw ! ! IF( io_level < 0) CALL errore ( 'ioneb', & ! 'NEB, SMD do not work with "disk_io" set to "none"', 1) ! ! IF ( num_of_images < 2 ) & CALL errore( 'ioneb', 'string_method=' // trim( string_method ) // & & ': num_of_images must be at least 2', 1 ) ! IF ( ( CI_scheme /= "no-CI" ) .and. & ( CI_scheme /= "auto" ) .and. & ( CI_scheme /= "manual" ) ) THEN ! CALL errore( 'ioneb', 'string_method=' // trim( string_method ) // & & ': unknown CI_scheme', 1 ) ! ENDIF ! ! ... initialization of logical variables ! lsteep_des = .false. lquick_min = .false. lbroyden = .false. lbroyden2 = .false. ! SELECT CASE( opt_scheme ) CASE( "sd" ) ! lsteep_des = .true. ! CASE( "quick-min" ) ! lquick_min = .true. ! CASE( "broyden" ) ! lbroyden = .true. ! CASE( "broyden2" ) ! lbroyden2 = .true. ! CASE( "langevin" ) ! llangevin = .true. ! IF ( lneb ) & CALL errore( 'iosys','string_method=' // trim( string_method ) // & & ': langevin dynamics not implemented', 1 ) ! temp_req = temp_req / ( eV_to_kelvin * autoev ) ! IF ( temp_req <= 0.D0 ) & CALL errore( 'iosys','string_method=' // trim( string_method ) // & & ': tepm_req has not been set', 1 ) ! IF ( use_freezing ) & WRITE( UNIT = stdout, & FMT = '(5X,"warning: freezing cannot be used in langevin")' ) ! use_freezing = .false. ! CASE DEFAULT ! CALL errore( 'iosys','string_method=' // trim( string_method ) // & & ': unknown opt_scheme', 1 ) ! END SELECT ! ! ! ... "path"-optimization variables ! nstep_path_ = nstep_path ds_ = ds num_of_images_ = num_of_images first_last_opt_ = first_last_opt use_masses_ = use_masses use_freezing_ = use_freezing temp_req_ = temp_req path_thr_ = path_thr CI_scheme_ = CI_scheme k_max_ = k_max k_min_ = k_min fixed_tan_ = fixed_tan ! ! ! CALL verify_neb_tmpdir( tmp_dir ) ! ! RETURN ! END SUBROUTINE ioneb ! !----------------------------------------------------------------------- SUBROUTINE verify_neb_tmpdir( tmp_dir ) !----------------------------------------------------------------------- ! USE wrappers, ONLY : f_mkdir USE path_input_parameters_module, ONLY : restart_mode USE io_files, ONLY : prefix, xmlpun, & delete_if_present USE path_variables, ONLY : num_of_images USE mp_image_global_module, ONLY : mpime, nproc, nimage USE io_global, ONLY : meta_ionode USE mp, ONLY : mp_barrier USE xml_io_base, ONLY : copy_file ! IMPLICIT NONE ! CHARACTER(len=*), INTENT(inout) :: tmp_dir ! INTEGER :: ios, image, proc, nofi LOGICAL :: exst CHARACTER (len=256) :: file_path, filename CHARACTER(len=6), EXTERNAL :: int_to_char ! ! file_path = trim( tmp_dir ) // trim( prefix ) ! ! IF ( restart_mode == 'from_scratch' ) THEN ! ! ... let us try to create the scratch directory ! CALL parallel_mkdir ( tmp_dir ) ! ENDIF ! ! ! ... if starting from scratch all temporary files are removed ! ... from tmp_dir ( only by the master node ) ! IF ( meta_ionode ) THEN ! ! ... files needed by parallelization among images are removed ! CALL delete_if_present( trim( file_path ) // '.newimage' ) ! ! ... file containing the broyden's history ! IF ( restart_mode == 'from_scratch' ) THEN ! CALL delete_if_present( trim( file_path ) // '.broyden' ) ! ENDIF ! ENDIF ! end if ionode ! nofi = num_of_images ! DO image = 1, nofi ! file_path = trim( tmp_dir ) // trim( prefix ) //"_" // & trim( int_to_char( image ) ) // '/' ! CALL parallel_mkdir ( file_path ) ! ! ... if starting from scratch all temporary files are removed ! ... from tmp_dir ( by all the cpus in sequence ) ! IF ( restart_mode == 'from_scratch' ) THEN ! DO proc = 0, nproc - 1 ! IF ( proc == mpime ) THEN ! ! ... extrapolation file is removed ! CALL delete_if_present( trim( file_path ) // & & trim( prefix ) // '.update' ) ! ! ... standard output of the self-consistency is removed ! CALL delete_if_present( trim( file_path ) // 'PW.out' ) ! ENDIF ! CALL mp_barrier() ! ENDDO ! ENDIF ! end restart_mode ! ENDDO ! end do image ! RETURN ! END SUBROUTINE verify_neb_tmpdir NEB/src/Makefile0000644000700200004540000000323512053145633012715 0ustar marsamoscm# Makefile for NEB include ../../make.sys # location of needed modules MODFLAGS= $(MOD_FLAG)../../iotk/src \ $(MOD_FLAG)../../Modules \ $(MOD_FLAG)../../PW/src $(MOD_FLAG). #location of needed libraries LIBOBJS= ../../iotk/src/libiotk.a ../../flib/flib.a \ ../../clib/clib.a ../../flib/ptools.a NEBOBJS = \ neb.o \ NEBLIBS = \ compute_scf.o \ engine_to_path_pos.o \ engine_to_path_alat.o \ engine_to_path_nat.o \ engine_to_path_fix_atom_pos.o \ input.o \ path_base.o \ path_formats.o \ path_gen_inputs.o \ path_input_parameters_module.o \ path_io_routines.o \ path_io_tools.o \ path_io_units_module.o \ path_opt_routines.o \ path_reparametrisation.o \ path_read_cards_module.o \ path_read_namelists_module.o \ path_to_engine_fix_atom_pos.o \ path_to_engine_mp.o \ path_variables.o \ set_defaults.o \ stop_run_path.o QEMODS=../../Modules/libqemod.a PWOBJS= ../../PW/src/libpw.a TLDEPS=bindir mods libs liblapack libblas pw all : tldeps neb.x path_interpolation.x neb.x : $(NEBOBJS) libneb.a $(LIBOBJS) $(PWOBJS) $(QEMODS) $(LD) $(LDFLAGS) -o $@ \ $(NEBOBJS) libneb.a $(PWOBJS) $(QEMODS) $(LIBOBJS) $(LIBS) - ( cd ../../bin; ln -fs ../NEB/src/$@ . ) path_interpolation.x : path_interpolation.o $(PWOBJS) $(QEMODS) $(LIBOBJS) $(LD) $(LDFLAGS) -o $@ \ path_interpolation.o $(PWOBJS) $(QEMODS) $(LIBOBJS) $(LIBS) - ( cd ../../bin ; ln -fs ../NEB/src/$@ . ) libneb.a : $(NEBLIBS) $(AR) $(ARFLAGS) $@ $? $(RANLIB) $@ tldeps: test -n "$(TLDEPS)" && ( cd ../.. ; $(MAKE) $(MFLAGS) $(TLDEPS) || exit 1) || : clean : - /bin/rm -f *.x *.o *.a *~ *.F90 *.d *.mod *.i *.L - /bin/rm -f ../../bin/neb.x - /bin/rm -f ../../bin/path_interpolation.x include make.depend NEB/src/path_to_engine_fix_atom_pos.f900000644000700200004540000000153212053145633017325 0ustar marsamoscm! ! Copyright (C) 2011 Quantum ESPRESSO group ! This file is distributed under the terms of the ! GNU General Public License. See the file `License' ! in the root directory of the present distribution, ! or http://www.gnu.org/copyleft/gpl.txt . ! ! !---------------------------------------------------------------------------- SUBROUTINE path_to_engine_fix_atom_pos() !----------------------------------------------------------------------------- ! ! USE kinds, ONLY : DP ! USE ions_base, ONLY : if_pos USE path_variables, ONLY : fix_atom_pos USE path_input_parameters_module, ONLY : nat ! ! ... "path" specific ! IMPLICIT NONE ! ! set_my_if_pos ! if(.not.allocated(if_pos)) allocate(if_pos(3,nat)) if_pos(:,:) = 1 if_pos(:,:) = fix_atom_pos(:,:) ! ! RETURN ! END SUBROUTINE path_to_engine_fix_atom_pos ! NEB/src/engine_to_path_alat.f900000644000700200004540000000124512053145633015560 0ustar marsamoscm! ! Copyright (C) 2002-2009 Quantum ESPRESSO group ! This file is distributed under the terms of the ! GNU General Public License. See the file `License' ! in the root directory of the present distribution, ! or http://www.gnu.org/copyleft/gpl.txt . ! ! !---------------------------------------------------------------------------- SUBROUTINE engine_to_path_alat() !----------------------------------------------------------------------------- ! ! USE kinds, ONLY : DP ! USE cell_base, ONLY : alat USE path_input_parameters_module, ONLY : alat_ => alat ! ! IMPLICIT NONE ! alat_ = alat ! ! RETURN ! END SUBROUTINE engine_to_path_alat ! NEB/src/stop_run_path.f900000644000700200004540000000321512053145633014460 0ustar marsamoscm! ! Copyright (C) 2001-2009 Quantum ESPRESSO group ! This file is distributed under the terms of the ! GNU General Public License. See the file `License' ! in the root directory of the present distribution, ! or http://www.gnu.org/copyleft/gpl.txt . ! !---------------------------------------------------------------------------- SUBROUTINE stop_run_path( lflag ) !---------------------------------------------------------------------------- ! ! ... Close all files and synchronize processes before stopping. ! ... Called at the end of the run with flag = .TRUE. (removes 'restart') ! ... or during execution with flag = .FALSE. (does not remove 'restart') ! USE io_global, ONLY : ionode, stdout USE mp_global, ONLY : mp_global_end USE mp_image_global_module, ONLY : nimage USE environment, ONLY : environment_end USE path_variables, ONLY : path_deallocation USE image_io_routines, ONLY : io_image_stop USE path_io_units_module, ONLY : iunpath ! IMPLICIT NONE ! LOGICAL, INTENT(IN) :: lflag LOGICAL :: exst, opnd, flag2 ! ! ! ! CALL io_image_stop() ! ! call pwscf stop run routine, close files and deallocate arrays ! CALL close_files(lflag) ! ! as environment_end writes final info on stdout ! stdout has to be redirected to iunpath (neb output) ! stdout=iunpath ! CALL environment_end( 'NEB' ) ! CALL clean_pw( .TRUE. ) ! CALL path_deallocation() ! CALL mp_global_end() ! IF ( .not. lflag ) THEN ! STOP 1 ! END IF ! END SUBROUTINE stop_run_path ! !---------------------------------------------------------------------------- NEB/src/path_opt_routines.f900000644000700200004540000003556412053145633015355 0ustar marsamoscm! ! Copyright (C) 2003-2006 Quantum ESPRESSO group ! This file is distributed under the terms of the ! GNU General Public License. See the file `License' ! in the root directory of the present distribution, ! or http://www.gnu.org/copyleft/gpl.txt . ! !-------------------------------------------------------------------------- MODULE path_opt_routines !--------------------------------------------------------------------------- ! ! ... This module contains all subroutines and functions needed for ! ... the optimisation of the reaction path (NEB and SMD calculations) ! ! ... Written by Carlo Sbraccia ( 2003-2006 ) ! USE kinds, ONLY : DP USE constants, ONLY : eps8, eps16 USE path_variables, ONLY : ds, pos, grad USE io_global, ONLY : meta_ionode, meta_ionode_id USE mp, ONLY : mp_bcast ! USE basic_algebra_routines ! IMPLICIT NONE ! PRIVATE ! PUBLIC :: langevin, steepest_descent, quick_min, broyden, broyden2 ! CONTAINS ! !---------------------------------------------------------------------- SUBROUTINE langevin( idx ) !---------------------------------------------------------------------- ! USE path_variables, ONLY : lang ! IMPLICIT NONE ! INTEGER, INTENT(IN) :: idx ! IF ( meta_ionode ) THEN ! pos(:,idx) = pos(:,idx) - ds*grad(:,idx) + lang(:,idx) ! END IF ! CALL mp_bcast( pos, meta_ionode_id ) ! RETURN ! END SUBROUTINE langevin ! !---------------------------------------------------------------------- SUBROUTINE steepest_descent( idx ) !---------------------------------------------------------------------- ! IMPLICIT NONE ! INTEGER, INTENT(IN) :: idx ! IF ( meta_ionode ) THEN ! pos(:,idx) = pos(:,idx) - ds*ds*grad(:,idx) ! END IF ! CALL mp_bcast( pos, meta_ionode_id ) ! RETURN ! END SUBROUTINE steepest_descent ! !---------------------------------------------------------------------- SUBROUTINE quick_min( idx, istep ) !---------------------------------------------------------------------- ! ! ... projected Verlet algorithm ! USE path_variables, ONLY : dim1, posold ! IMPLICIT NONE ! INTEGER, INTENT(IN) :: idx, istep ! REAL(DP), ALLOCATABLE :: vel(:), force_versor(:), step(:) REAL(DP) :: projection, norm_grad, norm_vel, norm_step ! REAL(DP), PARAMETER :: max_step = 0.6_DP ! in bohr ! ! IF ( meta_ionode ) THEN ! ALLOCATE( vel( dim1 ), force_versor( dim1 ), step( dim1 ) ) ! vel(:) = pos(:,idx) - posold(:,idx) ! norm_grad = norm( grad(:,idx) ) ! norm_vel = norm( vel(:) ) ! IF ( norm_grad > eps16 .AND. norm_vel > eps16 ) THEN ! force_versor(:) = - grad(:,idx) / norm_grad ! projection = ( vel(:) .dot. force_versor(:) ) ! vel(:) = MAX( 0.0_DP, projection ) * force_versor(:) ! ELSE ! vel(:) = 0.0_DP ! END IF ! posold(:,idx) = pos(:,idx) ! step(:) = vel(:) - ds*ds*grad(:,idx) ! norm_step = norm( step(:) ) ! step(:) = step(:) / norm_step ! pos(:,idx) = pos(:,idx) + step(:) * MIN( norm_step, max_step ) ! DEALLOCATE( vel, force_versor, step ) ! END IF ! CALL mp_bcast( pos, meta_ionode_id ) CALL mp_bcast( posold, meta_ionode_id ) ! RETURN ! END SUBROUTINE quick_min ! ! ... Broyden (rank one) optimisation ! !----------------------------------------------------------------------- SUBROUTINE broyden() !----------------------------------------------------------------------- ! USE path_variables, ONLY : lsmd USE path_io_units_module, ONLY : broy_file, iunbroy, iunpath USE path_variables, ONLY : dim1, frozen, tangent, nim => num_of_images ! IMPLICIT NONE ! REAL(DP), ALLOCATABLE :: t(:), g(:), s(:,:) INTEGER :: k, i, j, I_in, I_fin REAL(DP) :: s_norm, coeff, norm_g REAL(DP) :: J0 LOGICAL :: exists ! REAL(DP), PARAMETER :: step_max = 0.6_DP INTEGER, PARAMETER :: broyden_ndim = 5 ! ! ! ... starting guess for the inverse Jacobian ! J0 = ds*ds ! ALLOCATE( g( dim1*nim ) ) ALLOCATE( s( dim1*nim, broyden_ndim ) ) ALLOCATE( t( dim1*nim ) ) ! g(:) = 0.0_DP t(:) = 0.0_DP ! DO i = 1, nim ! I_in = ( i - 1 )*dim1 + 1 I_fin = i * dim1 ! IF ( frozen(i) ) CYCLE ! IF ( lsmd ) t(I_in:I_fin) = tangent(:,i) ! g(I_in:I_fin) = grad(:,i) ! END DO ! norm_g = MAXVAL( ABS( g ) ) ! IF ( norm_g == 0.0_DP ) RETURN ! IF ( meta_ionode ) THEN ! ! ... open the file containing the broyden's history ! INQUIRE( FILE = broy_file, EXIST = exists ) ! IF ( exists ) THEN ! OPEN( UNIT = iunbroy, FILE = broy_file, STATUS = "OLD" ) ! READ( UNIT = iunbroy , FMT = * ) i ! ! ... if the number of images is changed the broyden history is ! ... reset and the algorithm starts from scratch ! exists = ( i == nim ) ! END IF ! IF ( exists ) THEN ! READ( UNIT = iunbroy , FMT = * ) k READ( UNIT = iunbroy , FMT = * ) s(:,:) ! k = k + 1 ! ELSE ! s(:,:) = 0.0_DP ! k = 1 ! END IF ! CLOSE( UNIT = iunbroy ) ! ! ... Broyden's update ! IF ( k > broyden_ndim ) THEN ! ! ... the Broyden's subspace is swapped and the projection of ! ... s along the current tangent is removed (this last thing ! ... in the smd case only, otherwise t = 0.0_DP) ! k = broyden_ndim ! DO j = 1, k - 1 ! s(:,j) = s(:,j+1) - t(:) * ( s(:,j+1) .dot. t(:) ) ! END DO ! END IF ! s(:,k) = - J0 * g(:) ! IF ( k > 1 ) THEN ! DO j = 1, k - 2 ! s(:,k) = s(:,k) + ( s(:,j) .dot. s(:,k) ) / & ( s(:,j) .dot. s(:,j) ) * s(:,j+1) ! END DO ! coeff = ( s(:,k-1) .dot. ( s(:,k-1) - s(:,k) ) ) ! IF ( coeff > eps8 ) THEN ! s(:,k) = ( s(:,k-1) .dot. s(:,k-1) ) / coeff * s(:,k) ! END IF ! END IF ! IF ( ( s(:,k) .dot. g(:) ) > 0.0_DP ) THEN ! ! ... uphill step : history reset ! WRITE( UNIT = iunpath, & FMT = '(/,5X,"broyden uphill step : history is reset",/)' ) ! k = 1 ! s(:,:) = 0.0_DP s(:,k) = - J0 * g(:) ! END IF ! s_norm = norm( s(:,k) ) ! s(:,k) = s(:,k) / s_norm * MIN( s_norm, step_max ) ! ! ... save the file containing the history ! OPEN( UNIT = iunbroy, FILE = broy_file ) ! WRITE( UNIT = iunbroy, FMT = * ) nim WRITE( UNIT = iunbroy, FMT = * ) k WRITE( UNIT = iunbroy, FMT = * ) s ! CLOSE( UNIT = iunbroy ) ! ! ... broyden's step ! pos(:,1:nim) = pos(:,1:nim) + RESHAPE( s(:,k), (/ dim1, nim /) ) ! END IF ! CALL mp_bcast( pos, meta_ionode_id ) ! DEALLOCATE( t ) DEALLOCATE( g ) DEALLOCATE( s ) ! RETURN ! END SUBROUTINE broyden ! ! ... Broyden (rank one) optimisation - second attempt ! !----------------------------------------------------------------------- SUBROUTINE broyden2() !----------------------------------------------------------------------- #define DEBUG ! USE path_variables, ONLY : lsmd USE path_io_units_module, ONLY : broy_file, iunbroy, iunpath USE path_variables, ONLY : dim1, frozen, tangent, nim => num_of_images ! IMPLICIT NONE ! REAL(DP), PARAMETER :: step_max = 0.6_DP INTEGER, PARAMETER :: broyden_ndim = 5 ! REAL(DP), ALLOCATABLE :: dx(:,:), df(:,:), x(:), f(:) REAL(DP), ALLOCATABLE :: x_last(:), f_last(:), mask(:) REAL(DP), ALLOCATABLE :: b(:,:), c(:), work(:) INTEGER, ALLOCATABLE :: iwork(:) ! REAL(DP) :: x_norm, gamma0, J0, d2, d2_estimate LOGICAL :: exists INTEGER :: i, I_in, I_fin, info, j, niter ! ! ... starting guess for the inverse Jacobian ! J0 = ds*ds ! ALLOCATE( dx( dim1*nim, broyden_ndim ), df( dim1*nim, broyden_ndim ) ) ALLOCATE( x( dim1*nim ), f( dim1*nim ) ) ALLOCATE( x_last( dim1*nim ), f_last( dim1*nim ), mask( dim1*nim ) ) ! ! define mask to skip frozen images ! mask(:) = 0.0_DP DO i = 1, nim I_in = ( i - 1 )*dim1 + 1 I_fin = i * dim1 IF ( frozen(i) ) CYCLE mask(I_in:I_fin) = 1.0_DP END DO ! ! copy current positions and gradients in local arrays ! DO i = 1, nim I_in = ( i - 1 )*dim1 + 1 I_fin = i * dim1 f(I_in:I_fin) =-grad(:,i) x(I_in:I_fin) = pos(:,i) END DO ! ! only meta_ionode execute this part ! IF ( meta_ionode ) THEN d2 = DOT_PRODUCT( f(:),mask(:)*f(:) ) #ifdef DEBUG WRITE (*,*) " CURRENT ACTUAL D2 = ", d2 #endif ! ! ... open the file containing the broyden's history ! INQUIRE( FILE = broy_file, EXIST = exists ) ! IF ( exists ) THEN ! OPEN( UNIT = iunbroy, FILE = broy_file, STATUS = "OLD" ) ! READ( UNIT = iunbroy , FMT = * ) i ! ! ... if the number of images is changed the broyden history is ! ... reset and the algorithm starts from scratch ! exists = ( i == nim ) ! END IF ! IF ( exists ) THEN ! READ( UNIT = iunbroy , FMT = * ) niter, d2_estimate READ( UNIT = iunbroy , FMT = * ) df(:,:), dx(:,:) READ( UNIT = iunbroy , FMT = * ) f_last(:), x_last(:) niter = min(broyden_ndim, niter + 1) ! if (d2 > 2.0_DP * d2_estimate ) then #ifdef DEBUG write (*,*) " bad D2 estimate ... reset history " #endif niter = 1 df(:,:) = 0.0_DP dx(:,:) = 0.0_DP end if ELSE ! df(:,:) = 0.0_DP dx(:,:) = 0.0_DP niter = 0 ! END IF CLOSE( UNIT = iunbroy ) ! ! ... Broyden's update ! ! shift previous history, automatically discarding oldest iterations ! DO i = broyden_ndim, 2, -1 df(:,i) = df(:,i-1) dx(:,i) = dx(:,i-1) END DO ! ! and update it with last increment ! IF (niter > 0 ) THEN df(:,1) = f(:) - f_last(:) dx(:,1) = x(:) - x_last(:) END IF ! save for later use f_last(:) = f(:) x_last(:) = x(:) ! x(:) = 0.0_DP IF ( niter > 0 ) THEN ! ALLOCATE (b(niter,niter), c(niter), work(niter), iwork(niter)) ! ! create the matrix and the right-hand side of the liner system ! b(:,:) = 0.0_DP c(:) = 0.0_DP DO i = 1,niter DO j = 1,niter b(i,j) = DOT_PRODUCT(df(:,i),mask(:)*df(:,j)) END DO c(i) = DOT_PRODUCT(f(:),mask(:)*df(:,i)) END DO ! ! solve the linear system ! CALL DSYTRF( 'U', niter, b, niter, iwork, work, niter, info ) CALL errore( 'broyden', 'factorization', abs(info) ) CALL DSYTRI( 'U', niter, b, niter, iwork, work, info ) CALL errore( 'broyden', 'DSYTRI', abs(info) ) FORALL( i = 1:niter, j = 1:niter, j > i ) b(j,i) = b(i,j) ! ! set the best correction vector and gradient ! DO i = 1, niter gamma0 = DOT_PRODUCT( b(1:niter,i), c(1:niter) ) call DAXPY(dim1*nim, -gamma0, dx(:,i),1, x,1) call DAXPY(dim1*nim, -gamma0, df(:,i),1, f,1) END DO ! DEALLOCATE (b,c,work,iwork) ! END IF d2 = DOT_PRODUCT( f(:), mask(:)*f(:) ) x(:) = mask(:) * ( x(:) + J0 * f(:) ) x_norm = norm(x) x(:) = x_last(:) + x(:) * min ( 1.0_DP, step_max/x_norm) #ifdef DEBUG WRITE (*,*) " ESTIMATED NEXT D2 = ", d2 IF (x_norm > step_max) & WRITE (*,*) " x_norm = ", x_norm, step_max #endif ! ! ... save the file containing the history ! OPEN( UNIT = iunbroy, FILE = broy_file ) ! WRITE( UNIT = iunbroy, FMT = * ) nim WRITE( UNIT = iunbroy, FMT = * ) niter, d2 WRITE( UNIT = iunbroy, FMT = * ) df(:,:), dx(:,:) WRITE( UNIT = iunbroy, FMT = * ) f_last(:), x_last(:) ! CLOSE( UNIT = iunbroy ) ! ! ... copy broyden's step on the position array ... ! pos(:,1:nim) = RESHAPE( x, (/ dim1, nim /) ) ! END IF ! ! ... and distribute it ! CALL mp_bcast( pos, meta_ionode_id ) ! DEALLOCATE( df, dx, f, x, f_last, x_last, mask ) ! RETURN ! END SUBROUTINE broyden2 ! END MODULE path_opt_routines NEB/src/path_input_parameters_module.f900000644000700200004540000001270412053145633017541 0ustar marsamoscm! ! Copyright (C) 2002-2008 Quantum ESPRESSO group ! This file is distributed under the terms of the ! GNU General Public License. See the file `License' ! in the root directory of the present distribution, ! or http://www.gnu.org/copyleft/gpl.txt . ! ! !=----------------------------------------------------------------------------=! ! MODULE path_input_parameters_module ! !=----------------------------------------------------------------------------=! ! ! this module contains ! 1) the definitions of all input parameters ! (both those read from namelists and those read from cards) ! 2) the definitions of all namelists ! 3) routines that allocate data needed in input ! Note that all values are initialized, but the default values should be ! set in the appropriate routines contained in module "read_namelists" ! The documentation of input variables can be found in Doc/INPUT_PW.* ! (for pw.x) or in Doc/INPUT_CP (for cp.x) ! Originally written by Carlo Cavazzoni for FPMD ! !=----------------------------------------------------------------------------=! ! USE kinds, ONLY : DP USE parameters, ONLY : nsx ! IMPLICIT NONE ! SAVE ! !=----------------------------------------------------------------------------=! ! BEGIN manual ! ! ! * DESCRIPTION OF THE INPUT FILE ! (to be given as standard input) ! ! The input file has the following layout: ! ! &PATH ! path_parameter_1, ! path_parameter_2, ! ....... ! path_parameter_Lastone ! / ! ATOMIC_SPECIES ! slabel_1 mass_1 pseudo_file_1 ! slabel_2 mass_2 pseudo_file_2 ! ..... ! PATH_ATOMIC_POSITIONS ! alabel_1 px_1 py_1 pz_1 ! alabel_2 px_2 py_2 pz_2 ! ..... ! CARD_3 ! .... ! CARD_N ! ! -- end of input file -- ! ! ... variables added for "path" calculations ! ! ! ... these are two auxiliary variables used in read_cards to ! ... distinguish among neb and smd done in the full phase-space ! ... or in the coarse-grained phase-space ! ! INTEGER :: n_inp_images INTEGER :: nat = 1 REAL(DP) :: alat ! CHARACTER(len=80) :: restart_mode ! specify how to start/restart the simulation CHARACTER(len=80) :: restart_mode_allowed(3) DATA restart_mode_allowed / 'from_scratch', 'restart', 'reset_counters' / ! LOGICAL :: full_phs_path_flag = .false. LOGICAL :: cg_phs_path_flag = .false. ! INTEGER :: nstep_path ! CHARACTER(len=80) :: string_method = 'neb' ! 'neb' traditional neb as described by Jonsson ! 'sm' something else CHARACTER(len=80) :: string_method_scheme_allowed(2) DATA string_method_scheme_allowed / 'neb', 'sm' / ! INTEGER :: input_images = 0 ! INTEGER :: num_of_images = 0 ! CHARACTER(len=80) :: CI_scheme = 'no-CI' ! CI_scheme = 'no-CI' | 'auto' | 'manual' ! set the Climbing Image scheme ! 'no-CI' Climbing Image is not used ! 'auto' Standard Climbing Image ! 'manual' the image is selected by hand ! CHARACTER(len=80) :: CI_scheme_allowed(3) DATA CI_scheme_allowed / 'no-CI', 'auto', 'manual' / ! LOGICAL :: first_last_opt = .false. LOGICAL :: use_masses = .false. LOGICAL :: use_freezing = .false. LOGICAL :: fixed_tan = .false. ! CHARACTER(len=80) :: opt_scheme = 'quick-min' ! minimization_scheme = 'quick-min' | 'damped-dyn' | ! 'mol-dyn' | 'sd' ! set the minimization algorithm ! 'quick-min' projected molecular dynamics ! 'sd' steepest descent ! 'broyden' broyden acceleration ! 'broyden2' broyden acceleration - better ? ! 'langevin' langevin dynamics ! CHARACTER(len=80) :: opt_scheme_allowed(5) DATA opt_scheme_allowed / 'quick-min', 'broyden', 'broyden2', 'sd', 'langevin' / ! REAL (DP) :: temp_req = 0.0_DP ! meaningful only when minimization_scheme = 'sim-annealing' REAL (DP) :: ds = 1.0_DP ! REAL (DP) :: k_max = 0.1_DP, k_min = 0.1_DP ! REAL (DP) :: path_thr = 0.05_DP ! ! NAMELIST / PATH / & restart_mode, & string_method, nstep_path, num_of_images, & CI_scheme, opt_scheme, use_masses, & first_last_opt, ds, k_max, k_min, temp_req, & path_thr, fixed_tan, use_freezing ! ! ATOMIC_POSITIONS ! ! ! ... variable added for NEB ( C.S. 17/10/2003 ) ! REAL(DP), ALLOCATABLE :: pos(:,:) ! INTEGER, ALLOCATABLE :: typ(:) ! ! ! CLIMBING_IMAGES ! ! ! ... variable added for NEB ( C.S. 20/11/2003 ) ! LOGICAL, ALLOCATABLE :: climbing( : ) ! ---------------------------------------------------------------------- CONTAINS SUBROUTINE allocate_path_input_ions( num_of_images ) ! INTEGER, INTENT(in) :: num_of_images ! IF ( allocated( pos ) ) DEALLOCATE( pos ) IF ( allocated( typ ) ) DEALLOCATE( typ ) ! ALLOCATE( pos( 3*nat, num_of_images ) ) ALLOCATE( typ( nat ) ) ! pos(:,:) = 0.0 ! RETURN ! END SUBROUTINE allocate_path_input_ions ! SUBROUTINE deallocate_path_input_ions() ! IF ( allocated( pos ) ) DEALLOCATE( pos ) IF ( allocated( typ ) ) DEALLOCATE( typ ) ! IF ( allocated( climbing ) ) DEALLOCATE( climbing ) ! RETURN ! END SUBROUTINE deallocate_path_input_ions ! !=----------------------------------------------------------------------------=! ! END MODULE path_input_parameters_module ! !=----------------------------------------------------------------------------=! NEB/src/path_read_namelists_module.f900000644000700200004540000001612512053145633017152 0ustar marsamoscm! ! Copyright (C) 2002-2008 Quantum ESPRESSO group ! This file is distributed under the terms of the ! GNU General Public License. See the file `License' ! in the root directory of the present distribution, ! or http://www.gnu.org/copyleft/gpl.txt . ! !---------------------------------------------------------------------------- MODULE path_read_namelists_module !---------------------------------------------------------------------------- ! ! ... this module handles the reading of input namelists ! ... written by: Carlo Cavazzoni ! -------------------------------------------------- ! USE kinds, ONLY : DP USE path_input_parameters_module ! IMPLICIT NONE ! SAVE ! PRIVATE ! PUBLIC :: path_read_namelist ! ! ... modules needed by read_xml.f90 ! ! ---------------------------------------------- ! CONTAINS ! !=----------------------------------------------------------------------=! ! ! Variables initialization for Namelist PATH ! !=----------------------------------------------------------------------=! ! !----------------------------------------------------------------------- SUBROUTINE path_defaults( ) !----------------------------------------------------------------------- ! USE path_input_parameters_module ! IMPLICIT NONE ! ! ! ... ( 'full' | 'coarse-grained' ) ! ! ... defaults for "path" optimisations variables ! restart_mode = 'from_scratch' string_method = 'neb' num_of_images = 0 first_last_opt = .FALSE. use_masses = .FALSE. use_freezing = .FALSE. opt_scheme = 'quick-min' temp_req = 0.0_DP ds = 1.0_DP path_thr = 0.05_DP CI_scheme = 'no-CI' k_max = 0.1_DP k_min = 0.1_DP fixed_tan = .FALSE. nstep_path = 1 ! ! for reading ions namelist we need to set calculation=relax ! RETURN ! END SUBROUTINE ! !=----------------------------------------------------------------------=! ! ! Broadcast variables values for Namelist NEB ! !=----------------------------------------------------------------------=! ! !----------------------------------------------------------------------- SUBROUTINE path_bcast() !----------------------------------------------------------------------- ! USE io_global, ONLY: ionode_id USE mp, ONLY: mp_bcast USE path_input_parameters_module ! IMPLICIT NONE ! ! ... "path" variables broadcast ! CALL mp_bcast ( restart_mode, ionode_id ) CALL mp_bcast ( string_method, ionode_id ) CALL mp_bcast( num_of_images, ionode_id ) CALL mp_bcast( first_last_opt, ionode_id ) CALL mp_bcast( use_masses, ionode_id ) CALL mp_bcast( use_freezing, ionode_id ) CALL mp_bcast( fixed_tan, ionode_id ) CALL mp_bcast( CI_scheme, ionode_id ) CALL mp_bcast( opt_scheme, ionode_id ) CALL mp_bcast( temp_req, ionode_id ) CALL mp_bcast( ds, ionode_id ) CALL mp_bcast( k_max, ionode_id ) CALL mp_bcast( k_min, ionode_id ) CALL mp_bcast( path_thr, ionode_id ) CALL mp_bcast( nstep_path, ionode_id ) ! RETURN ! END SUBROUTINE ! ! !----------------------------------------------------------------------- SUBROUTINE path_checkin( ) !----------------------------------------------------------------------- ! USE path_input_parameters_module ! IMPLICIT NONE ! CHARACTER(LEN=20) :: sub_name = ' path_checkin ' INTEGER :: i LOGICAL :: allowed = .FALSE. ! ! ! ... general "path" variables checkin IF ( ds < 0.0_DP ) & CALL errore( sub_name,' ds out of range ',1) IF ( temp_req < 0.0_DP ) & CALL errore( sub_name,' temp_req out of range ',1) ! allowed = .FALSE. DO i = 1, SIZE( opt_scheme_allowed ) IF ( TRIM( opt_scheme ) == & opt_scheme_allowed(i) ) allowed = .TRUE. END DO IF ( .NOT. allowed ) & CALL errore( sub_name, ' opt_scheme '''// & & TRIM( opt_scheme )//''' not allowed ', 1 ) ! ! ! ... NEB(SM) specific checkin ! IF ( k_max < 0.0_DP ) CALL errore( sub_name, 'k_max out of range', 1 ) IF ( k_min < 0.0_DP ) CALL errore( sub_name, 'k_min out of range', 1 ) IF ( k_max < k_min ) CALL errore( sub_name, 'k_max < k_min', 1 ) ! ! IF ( nstep_path < 1 ) CALL errore ( sub_name, 'step_path out of range', 1 ) ! allowed = .FALSE. DO i = 1, SIZE( CI_scheme_allowed ) IF ( TRIM( CI_scheme ) == CI_scheme_allowed(i) ) allowed = .TRUE. END DO ! IF ( .NOT. allowed ) & CALL errore( sub_name, ' CI_scheme ''' // & & TRIM( CI_scheme ) //''' not allowed ', 1 ) ! RETURN ! END SUBROUTINE ! !=----------------------------------------------------------------------=! ! ! Namelist parsing main routine ! !=----------------------------------------------------------------------=! ! !----------------------------------------------------------------------- SUBROUTINE path_read_namelist(unit) !----------------------------------------------------------------------- ! ! this routine reads data from standard input and puts them into ! module-scope variables (accessible from other routines by including ! this module, or the one that contains them) ! ---------------------------------------------- ! ! ... declare modules ! USE io_global, ONLY : ionode, ionode_id USE mp, ONLY : mp_bcast ! IMPLICIT NONE ! ! ... declare variables ! INTEGER, intent(in) :: unit ! ! ! ... declare other variables ! INTEGER :: ios ! ! ... end of declarations ! ! ---------------------------------------------- ! ! ! ... default settings for all namelists ! CALL path_defaults( ) ! ! ... Here start reading standard input file ! ! ... PATH namelist ! ios = 0 IF ( ionode ) THEN ! READ( unit, path, iostat = ios ) ! END IF CALL mp_bcast( ios, ionode_id ) IF( ios /= 0 ) THEN CALL errore( ' path_read_namelists ', & & ' reading namelist path ', ABS(ios) ) END IF ! CALL path_bcast( ) CALL path_checkin( ) ! RETURN ! END SUBROUTINE path_read_namelist ! END MODULE path_read_namelists_module NEB/src/path_variables.f900000644000700200004540000001474212053145633014566 0ustar marsamoscm! ! Copyright (C) 2003-2006 Quantum ESPRESSO group ! This file is distributed under the terms of the ! GNU General Public License. See the file `License' ! in the root directory of the present distribution, ! or http://www.gnu.org/copyleft/gpl.txt . ! !-------------------------------------------------------------------------- MODULE path_variables !--------------------------------------------------------------------------- ! ! ... This module contains all variables needed by path optimisations ! ! ... Written by Carlo Sbraccia ( 2003-2006 ) ! USE kinds, ONLY : DP ! IMPLICIT NONE ! SAVE ! ! ... "general" variables : ! LOGICAL :: lneb, lsmd ! LOGICAL :: restart ! LOGICAL :: & conv_path ! .TRUE. when "path" convergence has been ! achieved LOGICAL :: & first_last_opt, &! if .TRUE. the first and the last image ! are optimised too. use_masses, &! if .TRUE. mass weighted coordinates are ! used fixed_tan, &! if. TRUE. the projection is done using the ! tangent of the average path use_freezing, &! if .TRUE. images are optimised according ! to their error (see frozen array) tune_load_balance ! if .TRUE. the load balance for image ! parallelisation is tuned at ! runtime INTEGER :: & dim1, &! dimension of the configuration space num_of_images, &! number of images deg_of_freedom, &! number of degrees of freedom ! ( dim1 - #( of fixed coordinates ) ) pending_image ! last image for which scf has not been ! achieved REAL(DP) :: & ds, &! the optimization step path_thr, &! convergence threshold temp_req, &! required temperature activation_energy, &! forward activatation energy err_max, &! the largest error path_length ! length of the path LOGICAL :: & lsteep_des = .FALSE., &! .TRUE. if opt_scheme = "sd" lquick_min = .FALSE., &! .TRUE. if opt_scheme = "quick-min" lbroyden = .FALSE., &! .TRUE. if opt_scheme = "broyden" lbroyden2 = .FALSE., &! .TRUE. if opt_scheme = "broyden2" llangevin = .FALSE. ! .TRUE. if opt_scheme = "langevin" INTEGER :: & istep_path, &! iteration in the optimization procedure nstep_path ! maximum number of iterations ! ! ... "general" real space arrays ! REAL(DP), ALLOCATABLE :: & pes(:), &! the potential enrgy along the path error(:) ! the error from the true MEP REAL(DP), ALLOCATABLE :: & pos(:,:), &! reaction path grad_pes(:,:), &! gradients acting on the path tangent(:,:) ! tangent to the path INTEGER, ALLOCATABLE :: & fix_atom_pos(:,:) ! 0 or 1, if 0 fixed atom LOGICAL, ALLOCATABLE :: & frozen(:) ! .TRUE. if the image or mode has not ! to be optimized ! ! ... "neb specific" variables : ! LOGICAL, ALLOCATABLE :: & climbing(:) ! .TRUE. if the image is required to climb CHARACTER(LEN=20) :: & CI_scheme ! Climbing Image scheme INTEGER :: & Emax_index ! index of the image with the highest energy ! REAL (DP) :: & k_max, &! k_min, &! Emax, &! Emin ! ! ! ... real space arrays ! REAL(DP), ALLOCATABLE :: & elastic_grad(:), &! elastic part of the gradients mass(:), &! atomic masses k(:) ! elastic constants REAL(DP), ALLOCATABLE :: & posold(:,:), &! old positions (for the quick-min) grad(:,:), &! lang(:,:) ! langevin random force ! CONTAINS ! !---------------------------------------------------------------------- SUBROUTINE path_allocation() !---------------------------------------------------------------------- ! IMPLICIT NONE ! ALLOCATE( pos( dim1, num_of_images ) ) ! ALLOCATE( posold( dim1, num_of_images ) ) ALLOCATE( grad( dim1, num_of_images ) ) ALLOCATE( grad_pes( dim1, num_of_images ) ) ALLOCATE( tangent( dim1, num_of_images ) ) ! ALLOCATE( pes( num_of_images ) ) ALLOCATE( k( num_of_images ) ) ALLOCATE( error( num_of_images ) ) ALLOCATE( climbing( num_of_images ) ) ALLOCATE( frozen( num_of_images ) ) ! ALLOCATE( mass( dim1 ) ) ALLOCATE( elastic_grad( dim1 ) ) ! ALLOCATE( lang( dim1, num_of_images ) ) ! END SUBROUTINE path_allocation ! ! !---------------------------------------------------------------------- SUBROUTINE path_deallocation() !---------------------------------------------------------------------- ! IMPLICIT NONE ! IF ( ALLOCATED( pos ) ) DEALLOCATE( pos ) IF ( ALLOCATED( posold ) ) DEALLOCATE( posold ) IF ( ALLOCATED( grad ) ) DEALLOCATE( grad ) IF ( ALLOCATED( pes ) ) DEALLOCATE( pes ) IF ( ALLOCATED( grad_pes ) ) DEALLOCATE( grad_pes ) IF ( ALLOCATED( k ) ) DEALLOCATE( k ) IF ( ALLOCATED( mass ) ) DEALLOCATE( mass ) IF ( ALLOCATED( elastic_grad ) ) DEALLOCATE( elastic_grad ) IF ( ALLOCATED( tangent ) ) DEALLOCATE( tangent ) IF ( ALLOCATED( error ) ) DEALLOCATE( error ) IF ( ALLOCATED( climbing ) ) DEALLOCATE( climbing ) IF ( ALLOCATED( frozen ) ) DEALLOCATE( frozen ) IF ( ALLOCATED( lang ) ) DEALLOCATE( lang ) ! IF ( ALLOCATED( fix_atom_pos ) ) DEALLOCATE( fix_atom_pos ) ! END SUBROUTINE path_deallocation ! END MODULE path_variables NEB/src/path_read_cards_module.f900000644000700200004540000001030412053145633016240 0ustar marsamoscm! ! Copyright (C) 2010 Quantum ESPRESSO group ! This file is distributed under the terms of the ! GNU General Public License. See the file `License' ! in the root directory of the present distribution, ! or http://www.gnu.org/copyleft/gpl.txt . ! !--------------------------------------------------------------------------- MODULE path_read_cards_module !--------------------------------------------------------------------------- ! ! ... This module handles the reading of cards from standard input ! ... Written by Carlo Cavazzoni and modified for "path" implementation ! ... by Carlo Sbraccia ! USE kinds, ONLY : DP USE constants, ONLY : angstrom_au USE parser, ONLY : parse_unit,field_count, read_line, get_field USE io_global, ONLY : meta_ionode ! USE path_input_parameters_module ! IMPLICIT NONE ! SAVE ! PRIVATE ! PUBLIC :: path_read_cards ! ! ... end of module-scope declarations ! ! ---------------------------------------------- ! CONTAINS ! ! ... Read CARDS .... ! ! ... subroutines ! !---------------------------------------------------------------------- ! !---------------------------------------------------------------------- SUBROUTINE path_read_cards(unit) !---------------------------------------------------------------------- ! IMPLICIT NONE ! INTEGER, INTENT(IN) :: unit ! CHARACTER(len=256) :: input_line CHARACTER(len=80) :: card CHARACTER(len=1), EXTERNAL :: capital LOGICAL :: tend INTEGER :: i ! ! parse_unit = unit ! 100 CALL read_line( input_line, end_of_file=tend ) ! IF( tend ) GOTO 120 IF( input_line == ' ' .or. input_line(1:1) == '#' ) GOTO 100 ! READ (input_line, *) card ! DO i = 1, len_trim( input_line ) input_line( i : i ) = capital( input_line( i : i ) ) ENDDO ! IF( trim(card) =='CLIMBING_IMAGES' ) THEN ! CALL card_climbing_images( input_line ) ! ELSE ! IF ( meta_ionode ) & WRITE( 0,'(A)') 'Warning: card '//trim(input_line)//' ignored' ! ENDIF ! ! ... END OF LOOP ... ! ! GOTO 100 ! 120 CONTINUE ! RETURN ! END SUBROUTINE path_read_cards ! ! ... Description of the allowed input CARDS ! ! !------------------------------------------------------------------------ ! BEGIN manual !---------------------------------------------------------------------- ! ! CLIMBING_IMAGES ! ! Needed to explicitly specify which images have to climb ! ! Syntax: ! ! CLIMBING_IMAGES ! index1, ..., indexN ! ! Where: ! ! index1, ..., indexN are indices of the images that have to climb ! !---------------------------------------------------------------------- ! END manual !------------------------------------------------------------------------ ! SUBROUTINE card_climbing_images( input_line ) ! IMPLICIT NONE ! CHARACTER(len=256) :: input_line LOGICAL, SAVE :: tread = .false. LOGICAL, EXTERNAL :: matches ! INTEGER :: i CHARACTER(len=5) :: i_char ! CHARACTER(len=6), EXTERNAL :: int_to_char ! ! IF ( tread ) & CALL errore( ' card_climbing_images ', ' two occurrences', 2 ) ! IF ( CI_scheme == 'manual' ) THEN ! IF ( allocated( climbing ) ) DEALLOCATE( climbing ) ! ALLOCATE( climbing( num_of_images ) ) ! climbing(:) = .false. ! CALL read_line( input_line ) ! DO i = 1, num_of_images ! i_char = int_to_char( i ) ! IF ( matches( ' ' // trim( i_char ) // ',' , & ' ' // trim( input_line ) // ',' ) ) & climbing(i) = .true. ! ENDDO ! ENDIF ! tread = .true. ! RETURN ! END SUBROUTINE card_climbing_images ! END MODULE path_read_cards_module NEB/src/engine_to_path_nat.f900000644000700200004540000000124612053145633015422 0ustar marsamoscm! ! Copyright (C) 2002-2009 Quantum ESPRESSO group ! This file is distributed under the terms of the ! GNU General Public License. See the file `License' ! in the root directory of the present distribution, ! or http://www.gnu.org/copyleft/gpl.txt . ! ! !---------------------------------------------------------------------------- SUBROUTINE engine_to_path_nat() !----------------------------------------------------------------------------- ! ! USE kinds, ONLY : DP ! USE input_parameters, ONLY : nat USE path_input_parameters_module, ONLY : nat_ => nat ! ! IMPLICIT NONE ! nat_ = nat ! ! RETURN ! END SUBROUTINE engine_to_path_nat ! NEB/src/compute_scf.f900000644000700200004540000002673212053145633014113 0ustar marsamoscm! ! Copyright (C) 2002-2009 Quantum ESPRESSO group ! This file is distributed under the terms of the ! GNU General Public License. See the file `License' ! in the root directory of the present distribution, ! or http://www.gnu.org/copyleft/gpl.txt . ! ! !---------------------------------------------------------------------------- SUBROUTINE compute_scf( fii, lii, stat ) !---------------------------------------------------------------------------- ! ! ... this subroutine is the main scf-driver for all "path" calculations ! ... ( called by Modules/path_base.f90/born_oppenheimer() subroutine ) ! ! ... for each image in the path, it performs the self-consistent loop ! ... computing the energy and the forces ! ! ... Written by Carlo Sbraccia (2003-2006) ! USE basis, ONLY : starting_wfc, starting_pot USE kinds, ONLY : DP USE constants, ONLY : e2 USE control_flags, ONLY : conv_elec, istep, history, pot_order USE vlocal, ONLY : strf USE cell_base, ONLY : bg, alat USE gvect, ONLY : ngm, g, eigts1, eigts2, eigts3 USE fft_base, ONLY : dfftp USE ions_base, ONLY : tau, nat, nsp, ityp USE ener, ONLY : etot USE force_mod, ONLY : force USE io_files, ONLY : prefix, tmp_dir, iunupdate, seqopn, & exit_file, iunexit, delete_if_present USE path_io_units_module, ONLY : iunpath USE path_formats, ONLY : scf_fmt, scf_fmt_para USE path_variables, ONLY : pos, pes, grad_pes, dim1, pending_image, & istep_path, frozen, num_of_images, & first_last_opt USE io_global, ONLY : stdout, ionode, ionode_id, meta_ionode USE mp_image_global_module, ONLY : inter_image_comm, intra_image_comm, & my_image_id, nimage, root_image USE mp, ONLY : mp_bcast, mp_barrier, mp_sum, mp_min USE path_io_routines, ONLY : new_image_init, get_new_image, & stop_other_images ! IMPLICIT NONE ! INTEGER, INTENT(IN) :: fii, lii ! indexes to first and last images LOGICAL, INTENT(OUT) :: stat ! INTEGER :: fii_, lii_ ! local copies of fii and lii INTEGER :: image, istat REAL(DP) :: tcpu CHARACTER (LEN=256) :: tmp_dir_saved LOGICAL :: file_exists, opnd REAL(DP), ALLOCATABLE :: tauold(:,:,:) ! previous positions of atoms (needed by extrapolation) ! CHARACTER(LEN=6), EXTERNAL :: int_to_char ! ! fii_ = fii lii_ = lii ! istep = istep_path istat = 0 ! CALL flush_unit( iunpath ) ! ALLOCATE( tauold( 3, nat, 3 ) ) ! tmp_dir_saved = tmp_dir ! IF ( nimage > 1 ) THEN ! ! ... vectors pes and grad_pes are initalized to zero for all images on ! ... all nodes: this is needed for the final mp_sum() ! IF ( my_image_id == root_image ) THEN ! FORALL( image = fii:lii, .NOT.frozen(image) ) ! pes(image) = 0.D0 grad_pes(:,image) = 0.D0 ! END FORALL ! ELSE ! pes(fii:lii) = 0.D0 grad_pes(:,fii:lii) = 0.D0 ! END IF ! END IF ! ! ... all processes are syncronized (needed to have a readable output) ! CALL mp_barrier() ! IF ( nimage > 1 .AND. .NOT.first_last_opt ) THEN ! ! ... self-consistency on the first and last images is done separately ! IF ( fii == 1 ) THEN ! IF ( my_image_id == root_image ) THEN ! CALL do_scf( 1, istat ) ! IF ( istat /= 0 ) GOTO 1 ! END IF ! fii_ = 2 ! END IF IF ( lii == num_of_images ) THEN ! IF ( my_image_id == root_image + 1 ) THEN ! CALL do_scf( num_of_images, istat ) ! IF ( istat /= 0 ) GOTO 1 ! END IF ! lii_ = lii - 1 ! END IF ! END IF ! ! ... only the first cpu initializes the file needed by parallelization ! ... among images ! IF ( meta_ionode ) CALL new_image_init( fii_, tmp_dir_saved ) ! image = fii_ + my_image_id ! scf_loop: DO ! ! ... exit if available images are finished ! IF ( image > lii_ ) EXIT scf_loop ! pending_image = image ! CALL do_scf( image, istat ) ! IF ( istat /= 0 ) GOTO 1 ! ! ... the new image is obtained (by ionode only) ! CALL get_new_image( image, tmp_dir_saved ) ! CALL mp_bcast( image, ionode_id, intra_image_comm ) ! END DO scf_loop ! ! ... after the first call to compute_scf the input values of startingpot ! ... and startingwfc are both set to 'file' ! starting_pot = 'file' starting_wfc = 'file' ! ! ... finalization of the job (this point is also reached in case of error ! ... condition) ! 1 CALL mp_barrier() ! DEALLOCATE( tauold ) ! IF ( nimage > 1 ) THEN ! ! ... pes and grad_pes are communicated among "image" pools ! CALL mp_sum( pes(fii:lii), inter_image_comm ) CALL mp_sum( grad_pes(:,fii:lii), inter_image_comm ) CALL mp_sum( istat, inter_image_comm ) ! END IF ! ! ... global status is computed here ! IF ( istat == 0 ) THEN ! stat = .TRUE. ! pending_image = 0 ! ELSE ! stat = .FALSE. ! IF ( nimage > 1 ) THEN ! CALL mp_min( pending_image, inter_image_comm ) ! IF ( meta_ionode ) CALL delete_if_present( exit_file ) ! END IF ! IF ( meta_ionode ) THEN ! ! ... some image didn't converge: extrapolation is no longer ! ... possible, files are removed ! WRITE( UNIT = iunpath, & FMT = '(/,5X,"cleaning-up extrapolation files"/)' ) ! DO image = pending_image, lii ! tmp_dir = TRIM( tmp_dir_saved ) // TRIM( prefix ) // "_" // & TRIM( int_to_char( image ) ) // "/" ! CALL delete_if_present( TRIM( tmp_dir ) // & TRIM( prefix ) // '.update' ) ! END DO ! END IF ! END IF ! tmp_dir = tmp_dir_saved ! RETURN ! CONTAINS ! !----------------------------------------------------------------------- SUBROUTINE do_scf( image, istat ) !----------------------------------------------------------------------- ! USE input_parameters, ONLY : diago_thr_init USE control_flags, ONLY : ethr ! IMPLICIT NONE ! INTEGER, INTENT(IN) :: image INTEGER, INTENT(INOUT) :: istat ! REAL(DP), EXTERNAL :: get_clock ! ! ... self-consistency ( for non-frozen images only ) ! IF ( frozen(image) ) RETURN ! CALL clean_pw( .FALSE. ) ! tcpu = get_clock( 'NEB' ) ! IF ( nimage > 1 ) THEN ! WRITE( UNIT = iunpath, FMT = scf_fmt_para ) my_image_id, tcpu, image ! ELSE ! WRITE( UNIT = iunpath, FMT = scf_fmt ) tcpu, image ! END IF ! tmp_dir = TRIM( tmp_dir_saved ) // TRIM( prefix ) // "_" // & TRIM( int_to_char( image ) ) // "/" ! ! ... unit stdout is connected to the appropriate file ! IF ( ionode ) THEN ! INQUIRE( UNIT = stdout, OPENED = opnd ) IF ( opnd ) CLOSE( UNIT = stdout ) OPEN( UNIT = stdout, FILE = TRIM( tmp_dir ) // 'PW.out', & STATUS = 'UNKNOWN', POSITION = 'APPEND' ) ! END IF ! ! ... tau is in alat units ( pos is in bohr ) ! tau = RESHAPE( pos(:,image), SHAPE( tau ) ) / alat ! WRITE( stdout, '(/,5X,"coordinates at iteration ",I3,/)' ) istep ! CALL output_tau( .FALSE., .FALSE. ) ! ! ... initialization of the scf calculation ! CALL start_clock('PWSCF') CALL setup () CALL init_run() ! IF ( ionode ) THEN ! ! ... the file containing old positions is opened ! ... ( needed for extrapolation ) ! CALL seqopn( iunupdate, 'update', 'FORMATTED', file_exists ) ! IF ( file_exists ) THEN ! READ( UNIT = iunupdate, FMT = * ) history READ( UNIT = iunupdate, FMT = * ) tauold ! ELSE ! history = 0 tauold = 0.D0 ! WRITE( UNIT = iunupdate, FMT = * ) history WRITE( UNIT = iunupdate, FMT = * ) tauold ! END IF ! CLOSE( UNIT = iunupdate, STATUS = 'KEEP' ) ! END IF ! CALL mp_bcast( history, ionode_id, intra_image_comm ) CALL mp_bcast( tauold, ionode_id, intra_image_comm ) ! IF ( history > 0 ) THEN ! ! ... potential and wavefunctions are extrapolated only if ! ... we are starting a new self-consistency ( scf on the ! ... previous image was achieved ) ! IF ( pot_order > 0 ) THEN ! ! ... structure factors of the old positions are computed ! ... (needed for the old atomic charge) ! CALL struc_fact( nat, tauold(:,:,1), nsp, ityp, ngm, g, bg, & dfftp%nr1, dfftp%nr2, dfftp%nr3, strf, eigts1, eigts2, eigts3 ) ! END IF ! CALL update_pot() ! END IF ! ! ... self-consistency loop ! CALL electrons() ! CALL punch( 'all' ) ! ! ... scf convergence is checked here ! IF ( .NOT.conv_elec ) THEN ! istat = 1 ! WRITE( UNIT = iunpath, & FMT = '(/,5X,"WARNING : scf convergence ", & & "NOT achieved on image ",I3)' ) image ! ! ... in case of parallelization on images a stop signal ! ... is sent via the "EXIT" file ! IF ( nimage > 1 ) CALL stop_other_images() ! RETURN ! END IF ! ! ... self-consistent forces ! CALL forces() ! ! ... energy is converted from rydberg to hartree ! pes(image) = etot / e2 ! ! ... gradients are converted from rydberg/bohr to hartree/bohr ! grad_pes(:,image) = - RESHAPE( force, (/ dim1 /) ) / e2 ! IF ( ionode ) THEN ! ! ... save the previous two steps ! ... ( a total of three ionic steps is saved ) ! tauold(:,:,3) = tauold(:,:,2) tauold(:,:,2) = tauold(:,:,1) tauold(:,:,1) = tau(:,:) ! history = MIN( 3, ( history + 1 ) ) ! CALL seqopn( iunupdate, 'update', 'FORMATTED', file_exists ) ! WRITE( UNIT = iunupdate, FMT = * ) history WRITE( UNIT = iunupdate, FMT = * ) tauold ! CLOSE( UNIT = iunupdate, STATUS = 'KEEP' ) ! END IF ! ! ... input values are restored at the end of each iteration ! ... ( they are modified by init_run ) - OBSOLETE? ! ! starting_pot = 'atomic' ! starting_wfc = 'file' ! ethr = diago_thr_init ! CALL close_files(.FALSE.) ! RETURN ! END SUBROUTINE do_scf ! END SUBROUTINE compute_scf NEB/src/make.depend0000644000700200004540000001434312053145633013355 0ustar marsamoscmcompute_scf.o : ../../Modules/cell_base.o compute_scf.o : ../../Modules/constants.o compute_scf.o : ../../Modules/control_flags.o compute_scf.o : ../../Modules/fft_base.o compute_scf.o : ../../Modules/input_parameters.o compute_scf.o : ../../Modules/io_files.o compute_scf.o : ../../Modules/io_global.o compute_scf.o : ../../Modules/ions_base.o compute_scf.o : ../../Modules/kind.o compute_scf.o : ../../Modules/mp.o compute_scf.o : ../../Modules/mp_image_global_module.o compute_scf.o : ../../Modules/recvec.o compute_scf.o : ../../PW/src/pwcom.o compute_scf.o : path_formats.o compute_scf.o : path_io_routines.o compute_scf.o : path_io_units_module.o compute_scf.o : path_variables.o engine_to_path_alat.o : ../../Modules/cell_base.o engine_to_path_alat.o : ../../Modules/kind.o engine_to_path_alat.o : path_input_parameters_module.o engine_to_path_fix_atom_pos.o : ../../Modules/ions_base.o engine_to_path_fix_atom_pos.o : ../../Modules/kind.o engine_to_path_fix_atom_pos.o : path_input_parameters_module.o engine_to_path_fix_atom_pos.o : path_variables.o engine_to_path_nat.o : ../../Modules/input_parameters.o engine_to_path_nat.o : ../../Modules/kind.o engine_to_path_nat.o : path_input_parameters_module.o engine_to_path_pos.o : ../../Modules/cell_base.o engine_to_path_pos.o : ../../Modules/ions_base.o engine_to_path_pos.o : ../../Modules/kind.o engine_to_path_pos.o : path_input_parameters_module.o input.o : ../../Modules/constants.o input.o : ../../Modules/io_files.o input.o : ../../Modules/io_global.o input.o : ../../Modules/kind.o input.o : ../../Modules/mp.o input.o : ../../Modules/mp_image_global_module.o input.o : ../../Modules/wrappers.o input.o : ../../Modules/xml_io_base.o input.o : path_input_parameters_module.o input.o : path_variables.o neb.o : ../../Modules/check_stop.o neb.o : ../../Modules/control_flags.o neb.o : ../../Modules/environment.o neb.o : ../../Modules/image_io_routines.o neb.o : ../../Modules/io_global.o neb.o : ../../Modules/mp_global.o neb.o : ../../Modules/mp_image_global_module.o neb.o : ../../Modules/open_close_input_file.o neb.o : ../../Modules/parameters.o neb.o : ../../Modules/read_cards.o neb.o : ../../Modules/read_namelists.o neb.o : ../../Modules/read_xml.o neb.o : ../../iotk/src/iotk_module.o neb.o : path_base.o neb.o : path_input_parameters_module.o neb.o : path_io_routines.o neb.o : path_io_units_module.o neb.o : path_read_cards_module.o neb.o : path_read_namelists_module.o neb.o : path_variables.o path_base.o : ../../Modules/basic_algebra_routines.o path_base.o : ../../Modules/constants.o path_base.o : ../../Modules/control_flags.o path_base.o : ../../Modules/io_files.o path_base.o : ../../Modules/io_global.o path_base.o : ../../Modules/ions_base.o path_base.o : ../../Modules/kind.o path_base.o : ../../Modules/mp.o path_base.o : ../../Modules/mp_image_global_module.o path_base.o : ../../Modules/random_numbers.o path_base.o : path_formats.o path_base.o : path_input_parameters_module.o path_base.o : path_io_routines.o path_base.o : path_io_units_module.o path_base.o : path_opt_routines.o path_base.o : path_reparametrisation.o path_base.o : path_variables.o path_gen_inputs.o : ../../Modules/mp_global.o path_input_parameters_module.o : ../../Modules/kind.o path_input_parameters_module.o : ../../Modules/parameters.o path_interpolation.o : ../../Modules/basic_algebra_routines.o path_interpolation.o : ../../Modules/cell_base.o path_interpolation.o : ../../Modules/constants.o path_interpolation.o : ../../Modules/kind.o path_interpolation.o : ../../Modules/splinelib.o path_interpolation.o : path_formats.o path_io_routines.o : ../../Modules/basic_algebra_routines.o path_io_routines.o : ../../Modules/cell_base.o path_io_routines.o : ../../Modules/constants.o path_io_routines.o : ../../Modules/control_flags.o path_io_routines.o : ../../Modules/io_files.o path_io_routines.o : ../../Modules/io_global.o path_io_routines.o : ../../Modules/ions_base.o path_io_routines.o : ../../Modules/kind.o path_io_routines.o : ../../Modules/mp.o path_io_routines.o : ../../Modules/mp_image_global_module.o path_io_routines.o : path_formats.o path_io_routines.o : path_input_parameters_module.o path_io_routines.o : path_io_units_module.o path_io_routines.o : path_reparametrisation.o path_io_routines.o : path_variables.o path_io_tools.o : ../../Modules/io_global.o path_io_tools.o : ../../Modules/kind.o path_opt_routines.o : ../../Modules/basic_algebra_routines.o path_opt_routines.o : ../../Modules/constants.o path_opt_routines.o : ../../Modules/io_global.o path_opt_routines.o : ../../Modules/kind.o path_opt_routines.o : ../../Modules/mp.o path_opt_routines.o : path_io_units_module.o path_opt_routines.o : path_variables.o path_read_cards_module.o : ../../Modules/constants.o path_read_cards_module.o : ../../Modules/io_global.o path_read_cards_module.o : ../../Modules/kind.o path_read_cards_module.o : ../../Modules/parser.o path_read_cards_module.o : path_input_parameters_module.o path_read_namelists_module.o : ../../Modules/io_global.o path_read_namelists_module.o : ../../Modules/kind.o path_read_namelists_module.o : ../../Modules/mp.o path_read_namelists_module.o : path_input_parameters_module.o path_reparametrisation.o : ../../Modules/basic_algebra_routines.o path_reparametrisation.o : ../../Modules/io_global.o path_reparametrisation.o : ../../Modules/kind.o path_reparametrisation.o : ../../Modules/mp.o path_reparametrisation.o : ../../Modules/splinelib.o path_reparametrisation.o : path_io_units_module.o path_reparametrisation.o : path_variables.o path_to_engine_fix_atom_pos.o : ../../Modules/ions_base.o path_to_engine_fix_atom_pos.o : ../../Modules/kind.o path_to_engine_fix_atom_pos.o : path_input_parameters_module.o path_to_engine_fix_atom_pos.o : path_variables.o path_to_engine_mp.o : ../../Modules/kind.o path_to_engine_mp.o : ../../Modules/mp_global.o path_to_engine_mp.o : ../../Modules/mp_image_global_module.o path_variables.o : ../../Modules/kind.o set_defaults.o : ../../Modules/input_parameters.o set_defaults.o : ../../Modules/io_global.o stop_run_path.o : ../../Modules/environment.o stop_run_path.o : ../../Modules/image_io_routines.o stop_run_path.o : ../../Modules/io_global.o stop_run_path.o : ../../Modules/mp_global.o stop_run_path.o : ../../Modules/mp_image_global_module.o stop_run_path.o : path_io_units_module.o stop_run_path.o : path_variables.o NEB/src/path_reparametrisation.f900000644000700200004540000001736112053145633016347 0ustar marsamoscm! ! Copyright (C) 2003-2006 Quantum ESPRESSO group ! This file is distributed under the terms of the ! GNU General Public License. See the file `License' ! in the root directory of the present distribution, ! or http://www.gnu.org/copyleft/gpl.txt . ! ! !--------------------------------------------------------------------------- MODULE path_reparametrisation !--------------------------------------------------------------------------- ! ! ... This module contains all subroutines and functions needed for ! ... the reparametrisation of the path in the string method ! ! ... Written by Carlo Sbraccia ( 2003-2006 ) ! USE kinds, ONLY : DP USE path_io_units_module, ONLY : iunpath USE io_global, ONLY : meta_ionode, meta_ionode_id USE mp, ONLY : mp_bcast ! USE basic_algebra_routines ! PRIVATE ! PUBLIC :: reparametrise, spline_interpolation ! INTERFACE spline_interpolation ! MODULE PROCEDURE spline_interpolation_1D, spline_interpolation_2D ! END INTERFACE ! CONTAINS ! ! ... reparametrisation routines in real space ! !------------------------------------------------------------------------ SUBROUTINE reparametrise() !------------------------------------------------------------------------ ! USE path_variables, ONLY : pos USE path_variables, ONLY : nim => num_of_images USE path_variables, ONLY : climbing ! IMPLICIT NONE ! INTEGER :: i, ni, nf ! ! IF ( meta_ionode ) THEN ! IF ( ANY( climbing(:) ) ) THEN ! ni = 1 ! DO i = 2, nim ! IF ( .NOT. climbing(i) ) CYCLE ! nf = i ! CALL spline_interpolation( pos, ni, nf ) ! ni = nf ! END DO ! nf = nim ! CALL spline_interpolation( pos, ni, nf ) ! ELSE ! ni = 1 nf = nim ! CALL spline_interpolation( pos, ni, nf ) ! END IF ! END IF ! CALL mp_bcast( pos, meta_ionode_id ) ! RETURN ! END SUBROUTINE reparametrise ! !-------------------------------------------------------------------- SUBROUTINE spline_interpolation_1D( vec, ni, nf, nim ) !-------------------------------------------------------------------- ! USE splinelib, ONLY : dosplineint ! IMPLICIT NONE ! REAL(DP), INTENT(INOUT) :: vec(:) INTEGER, INTENT(IN) :: ni, nf INTEGER, INTENT(IN), OPTIONAL :: nim ! INTEGER :: i, j INTEGER :: nio, nfo REAL(DP) :: delta, length REAL(DP), ALLOCATABLE :: new_vec(:) REAL(DP), ALLOCATABLE :: old_mesh(:), new_mesh(:) ! ! IF ( PRESENT( nim ) ) THEN ! nio = 1 nfo = nim ! ELSE ! nio = ni nfo = nf ! END IF ! ! ... cubic spline interpolation ! ALLOCATE( new_vec( ni:nf ) ) ! ALLOCATE( old_mesh( nio:nfo ) ) ALLOCATE( new_mesh( ni:nf ) ) ! old_mesh(:) = 0.0_DP new_mesh(:) = 0.0_DP ! DO i = nio, nfo - 1 ! old_mesh(i+1) = old_mesh(i) + ABS( vec(i+1) - vec(i) ) ! END DO ! length = old_mesh(nfo) ! delta = length / DBLE( nf - ni ) ! DO j = 0, nf - ni ! new_mesh(j+ni) = DBLE(j) * delta ! END DO ! old_mesh(:) = old_mesh(:) / length new_mesh(:) = new_mesh(:) / length ! CALL dosplineint( old_mesh(:), vec(nio:nfo), new_mesh(:), new_vec(:) ) ! vec(ni:nf) = new_vec(:) ! DEALLOCATE( new_vec, old_mesh, new_mesh ) ! RETURN ! END SUBROUTINE spline_interpolation_1D ! !-------------------------------------------------------------------- SUBROUTINE spline_interpolation_2D( vec, ni, nf, nim ) !-------------------------------------------------------------------- ! USE splinelib, ONLY : dosplineint ! IMPLICIT NONE ! REAL(DP), INTENT(INOUT) :: vec(:,:) INTEGER, INTENT(IN) :: ni, nf INTEGER, INTENT(IN), OPTIONAL :: nim ! INTEGER :: i, j INTEGER :: nio, nfo INTEGER :: dim1 REAL(DP) :: delta, length REAL(DP), ALLOCATABLE :: new_vec(:,:) REAL(DP), ALLOCATABLE :: old_mesh(:), new_mesh(:) ! ! dim1 = SIZE( vec, 1 ) ! IF ( PRESENT( nim ) ) THEN ! nio = 1 nfo = nim ! ELSE ! nio = ni nfo = nf ! END IF ! ! ... cubic spline interpolation ! ALLOCATE( new_vec( dim1, ni:nf ) ) ! ALLOCATE( old_mesh( nio:nfo ) ) ALLOCATE( new_mesh( ni:nf ) ) ! old_mesh(:) = 0.0_DP new_mesh(:) = 0.0_DP ! DO i = nio, nfo - 1 ! old_mesh(i+1) = old_mesh(i) + norm( vec(:,i+1) - vec(:,i) ) ! END DO ! length = old_mesh(nfo) ! delta = length / DBLE( nf - ni ) ! DO j = 0, nf - ni ! new_mesh(j+ni) = DBLE(j) * delta ! END DO ! old_mesh(:) = old_mesh(:) / length new_mesh(:) = new_mesh(:) / length ! CALL dosplineint( old_mesh(:), vec(:,nio:nfo), new_mesh(:), new_vec(:,:) ) ! vec(:,ni:nf) = new_vec(:,:) ! DEALLOCATE( new_vec, old_mesh, new_mesh ) ! RETURN ! END SUBROUTINE spline_interpolation_2D ! !-------------------------------------------------------------------- SUBROUTINE cubic_interpolation( ni, nf ) !-------------------------------------------------------------------- ! USE path_variables, ONLY : dim1, pos ! IMPLICIT NONE ! INTEGER, INTENT(IN) :: ni, nf ! INTEGER :: i, j REAL(DP) :: r, delta, x REAL(DP), ALLOCATABLE :: a(:,:), b(:,:), c(:,:), d(:,:), t(:,:), s(:) ! ALLOCATE( a( dim1, ni:nf-1 ) ) ALLOCATE( b( dim1, ni:nf-1 ) ) ALLOCATE( c( dim1, ni:nf-1 ) ) ALLOCATE( d( dim1, ni:nf-1 ) ) ALLOCATE( t( dim1, ni:nf ) ) ALLOCATE( s( ni:nf ) ) ! t(:,ni) = pos(:,ni+1) - pos(:,ni) t(:,nf) = pos(:,nf) - pos(:,nf-1) ! DO i = ni+1, nf - 1 ! t(:,i) = ( pos(:,i+1) - pos(:,i-1) ) / 2.0_DP ! END DO ! s(ni) = 0.0_DP ! DO i = ni, nf - 1 ! r = norm( pos(:,i+1) - pos(:,i) ) ! s(i+1) = s(i) + r ! ! ... cubic interpolation ! a(:,i) = 2.0_DP *( pos(:,i) - pos(:,i+1) ) / r**3 + & ( t(:,i) + t(:,i+1) ) / r**2 ! b(:,i) = 3.0_DP *( pos(:,i+1) - pos(:,i) ) / r**2 - & ( 2.0_DP*t(:,i) + t(:,i+1) ) / r ! c(:,i) = t(:,i) ! d(:,i) = pos(:,i) ! END DO ! i = ni ! delta = s(nf) / DBLE( nf - ni ) ! DO j = ni, nf ! r = DBLE( j - ni ) * delta ! IF ( r >= s(i+1) .AND. i < nf - 1 ) i = i + 1 ! x = r - s(i) ! pos(:,j) = a(:,i)*x**3 + b(:,i)*x**2 + c(:,i)*x + d(:,i) ! END DO ! DEALLOCATE( a, b, c, d, t, s ) ! RETURN ! END SUBROUTINE cubic_interpolation ! END MODULE path_reparametrisation NEB/src/path_interpolation.f900000644000700200004540000002500312053145633015475 0ustar marsamoscm! ! Copyright (C) 2004 PWSCF group ! This file is distributed under the terms of the ! GNU General Public License. See the file `License' ! in the root directory of the present distribution, ! or http://www.gnu.org/copyleft/gpl.txt . ! ! MODULE int_global_variables ! USE kinds, ONLY : DP ! IMPLICIT NONE ! INTEGER :: N, dim INTEGER :: old_num_of_images, new_num_of_images INTEGER :: first_image, last_image REAL (DP), ALLOCATABLE :: old_pos(:,:), new_pos(:,:) REAL (DP), ALLOCATABLE :: old_PES_gradient(:,:), new_PES_gradient(:,:) INTEGER, ALLOCATABLE :: fix_atom(:) REAL (DP), ALLOCATABLE :: old_V(:), new_V(:) REAL (DP), ALLOCATABLE :: d_R(:) REAL (DP), ALLOCATABLE :: a(:), b(:), c(:), d(:), F(:) REAL (DP), ALLOCATABLE :: old_mesh(:), new_mesh(:) REAL (DP), ALLOCATABLE :: tangent(:) CHARACTER(LEN=256) :: old_restart_file, new_restart_file ! END MODULE int_global_variables ! ! PROGRAM images_interpolator ! USE kinds, ONLY : DP USE constants, ONLY : eps16 USE path_formats USE basic_algebra_routines, ONLY : norm USE cell_base, ONLY : at, alat USE int_global_variables USE splinelib ! IMPLICIT NONE ! INTEGER :: i, j, ia INTEGER :: istep, nstep, suspended_image INTEGER :: ierr REAL (DP) :: R, delta_R, x LOGICAL :: no_interpolation LOGICAL, EXTERNAL :: matches CHARACTER (LEN=20) :: cell_parameters CHARACTER (LEN=256) :: input_line ! INTEGER :: iunrestart ! iunrestart = 28 ! ! ! ... the input file is read ! READ(*,*) N READ(*,*) old_num_of_images READ(*,*) new_num_of_images READ(*,*) first_image READ(*,*) last_image READ(*,'(A)') old_restart_file READ(*,'(A)') new_restart_file READ(*,*) alat ! READ( UNIT = *, FMT = '(A)', IOSTAT = ierr ) cell_parameters ! IF ( ierr < 0 ) THEN ! WRITE(*,'(T2,"read_input: the card CELL_PARAMETERS not found")') STOP ! ELSE IF ( ierr > 0 ) THEN ! WRITE(*,'(T2,"read_input: an error occured reading CELL_PARAMETERS")') STOP ! END IF ! IF ( .NOT. matches( "CELL_PARAMETERS" , TRIM( cell_parameters ) ) ) THEN ! WRITE(*,'(T2,"read_input: ",A," is not a valid card")') cell_parameters STOP ! END IF ! READ( UNIT = *, FMT = *, IOSTAT = ierr ) at ! IF ( ierr < 0 ) THEN ! WRITE(*,'(T2,"read_input: lattice vectors not found")') STOP ! ELSE IF ( ierr > 0 ) THEN ! WRITE(*,'(T2,"read_input: an error occured reading laccice vectors")') WRITE(*, FMT = lattice_vectors ) at STOP ! END IF ! dim = 3 * N ! ALLOCATE( old_pos( dim, old_num_of_images ) ) ALLOCATE( old_PES_gradient( dim, old_num_of_images ) ) ALLOCATE( old_V( old_num_of_images ) ) ALLOCATE( new_pos( dim, new_num_of_images ) ) ALLOCATE( new_PES_gradient( dim, new_num_of_images ) ) ALLOCATE( new_V( new_num_of_images ) ) ALLOCATE( fix_atom( dim ) ) ALLOCATE( d_R( dim ) ) ALLOCATE( tangent( dim ) ) ALLOCATE( a( old_num_of_images - 1 ) ) ALLOCATE( b( old_num_of_images - 1 ) ) ALLOCATE( c( old_num_of_images - 1 ) ) ALLOCATE( d( old_num_of_images - 1 ) ) ALLOCATE( F( old_num_of_images ) ) ALLOCATE( old_mesh( old_num_of_images ) ) ALLOCATE( new_mesh( new_num_of_images ) ) ! ! ... the old restart file is read ! OPEN( UNIT = iunrestart, FILE = old_restart_file, STATUS = "OLD", & ACTION = "READ" ) ! no_interpolation = .FALSE. ! READ( UNIT = iunrestart, FMT = * ) ! RESTART INFORMATION READ( UNIT = iunrestart, FMT = * ) istep READ( UNIT = iunrestart, FMT = * ) nstep READ( UNIT = iunrestart, FMT = * ) suspended_image READ( UNIT = iunrestart, FMT = * ) ! conv_elec ! ! ... read either "ENERGIES, POSITIONS AND GRADIENTS" ! repeat_loop: DO ! READ( UNIT = iunrestart, FMT = '(256A)', IOSTAT = ierr ) input_line ! IF ( matches( input_line, & "ENERGIES, POSITIONS AND GRADIENTS" ) ) EXIT repeat_loop ! IF ( ierr /= 0 ) THEN ! WRITE( *, '(/,5X,"an error occured reading",A)' ) old_restart_file ! STOP ! END IF ! END DO repeat_loop ! READ( UNIT = iunrestart, FMT = * ) ! Image: READ( UNIT = iunrestart, FMT = * ) old_V(1) ! ia = 0 ! DO j = 1, dim, 3 ! ia = ia + 1 ! READ( UNIT = iunrestart, FMT = * ) & old_pos(j,1), & old_pos((j+1),1), & old_pos((j+2),1), & old_PES_gradient(j,1), & old_PES_gradient((j+1),1), & old_PES_gradient((j+2),1), & fix_atom(j), & fix_atom((j+1)), & fix_atom((j+2)) ! old_PES_gradient(:,1) = old_PES_gradient(:,1) * fix_atom ! END DO ! DO i = 2, old_num_of_images ! READ( UNIT = iunrestart, FMT = * ) ! Image: READ( UNIT = iunrestart, FMT = * ) old_V(i) ! DO j = 1, dim, 3 ! READ( UNIT = iunrestart, FMT = * ) & old_pos(j,i), & old_pos((j+1),i), & old_pos((j+2),i), & old_PES_gradient(j,i), & old_PES_gradient((j+1),i), & old_PES_gradient((j+2),i) ! END DO ! old_PES_gradient(:,i) = old_PES_gradient(:,i) * fix_atom ! END DO ! CLOSE( UNIT = iunrestart ) ! F = 0.D0 ! DO i = 2, ( old_num_of_images - 1 ) ! ! ... tangent to the path ( normalized ) ! tangent(:) = 0.5D0 * ( ( old_pos(:,i+1) - old_pos(:,i) ) / & norm( old_pos(:,i+1) - old_pos(:,i) ) + & ( old_pos(:,i) - old_pos(:,i-1) ) / & norm( old_pos(:,i) - old_pos(:,i-1) ) ) ! tangent = tangent / norm( tangent ) ! F(i) = DOT_PRODUCT( - old_PES_gradient(:,i) , tangent ) ! END DO ! old_mesh(1) = 0.D0 ! DO i = 1, ( old_num_of_images - 1 ) ! d_R = old_pos(:,(i+1)) - old_pos(:,i) ! R = norm( d_R ) ! old_mesh(i+1) = old_mesh(i) + R ! a(i) = 2.D0 * ( old_V(i) - old_V(i+1) ) / R**(3) - & ( F(i) + F(i+1) ) / R**(2) ! b(i) = 3.D0 * ( old_V(i+1) - old_V(i) ) / R**(2) + & ( 2.D0 * F(i) + F(i+1) ) / R ! c(i) = - F(i) ! d(i) = old_V(i) ! END DO ! i = first_image ! delta_R = ( old_mesh(last_image) - & old_mesh(first_image) ) / DBLE( new_num_of_images - 1 ) ! DO j = 0, ( new_num_of_images - 1 ) ! R = old_mesh( first_image ) + DBLE(j) * delta_R ! new_mesh(j+1) = R ! check_index: DO ! IF ( ( R > old_mesh(i+1) ) .AND. & ( i < ( old_num_of_images - 1 ) ) ) THEN ! i = i + 1 ! ELSE ! EXIT check_index ! END IF ! END DO check_index ! x = R - old_mesh( i ) ! new_V(j+1) = a(i)*(x**3) + b(i)*(x**2) + c(i)*x + d(i) ! END DO ! new_mesh = new_mesh / old_mesh(old_num_of_images) old_mesh = old_mesh / old_mesh(old_num_of_images) ! CALL dosplineint( old_mesh , old_pos , new_mesh , new_pos ) ! new_PES_gradient = 0.D0 ! new_PES_gradient(:,1) = old_PES_gradient(:,1) ! new_PES_gradient(:,new_num_of_images) = old_PES_gradient(:,old_num_of_images) ! ! ... the new restart file is written ! OPEN( UNIT = iunrestart, FILE = new_restart_file, STATUS = "UNKNOWN", & ACTION = "WRITE" ) ! WRITE( UNIT = iunrestart, FMT = '("RESTART INFORMATION")' ) ! ! ... by default istep and nstep are set to zero ! WRITE( UNIT = iunrestart, FMT = '(I4)' ) 0 WRITE( UNIT = iunrestart, FMT = '(I4)' ) 0 WRITE( UNIT = iunrestart, FMT = '(I4)' ) 0 WRITE( UNIT = iunrestart, FMT = '(A4)' ) 'F' ! WRITE( UNIT = iunrestart, FMT = '("ENERGIES, POSITIONS AND GRADIENTS")' ) ! DO i = 1, new_num_of_images ! WRITE( UNIT = iunrestart, FMT = '("Image: ",I4)' ) i WRITE( UNIT = iunrestart, FMT = energy ) new_V(i) ! ia = 0 ! DO j = 1, dim, 3 ! ia = ia + 1 ! IF ( i == 1 ) THEN ! WRITE( UNIT = iunrestart, FMT = restart_first ) & new_pos(j,i), & new_pos((j+1),i), & new_pos((j+2),i), & new_PES_gradient(j,i), & new_PES_gradient((j+1),i), & new_PES_gradient((j+2),i), & fix_atom(j), & fix_atom((j+1)), & fix_atom((j+2)) ! ELSE ! WRITE( UNIT = iunrestart, FMT = restart_others ) & new_pos(j,i), & new_pos((j+1),i), & new_pos((j+2),i), & new_PES_gradient(j,i), & new_PES_gradient((j+1),i), & new_PES_gradient((j+2),i) ! END IF ! END DO ! END DO ! WRITE( UNIT = iunrestart, FMT = '("END")' ) ! CLOSE( UNIT = iunrestart ) ! IF ( ALLOCATED( old_pos ) ) DEALLOCATE( old_pos ) IF ( ALLOCATED( old_PES_gradient ) ) DEALLOCATE( old_PES_gradient ) IF ( ALLOCATED( old_V ) ) DEALLOCATE( old_V ) IF ( ALLOCATED( new_pos ) ) DEALLOCATE( new_pos ) IF ( ALLOCATED( new_PES_gradient ) ) DEALLOCATE( new_PES_gradient ) IF ( ALLOCATED( new_V ) ) DEALLOCATE( new_V ) IF ( ALLOCATED( fix_atom ) ) DEALLOCATE( fix_atom ) IF ( ALLOCATED( d_R ) ) DEALLOCATE( d_R ) IF ( ALLOCATED( tangent ) ) DEALLOCATE( tangent ) IF ( ALLOCATED( a ) ) DEALLOCATE( a ) IF ( ALLOCATED( b ) ) DEALLOCATE( b ) IF ( ALLOCATED( c ) ) DEALLOCATE( c ) IF ( ALLOCATED( d ) ) DEALLOCATE( d ) IF ( ALLOCATED( F ) ) DEALLOCATE( F ) IF ( ALLOCATED( old_mesh ) ) DEALLOCATE( old_mesh ) IF ( ALLOCATED( new_mesh ) ) DEALLOCATE( new_mesh ) ! END PROGRAM images_interpolator NEB/src/path_formats.f900000644000700200004540000000352012053145633014261 0ustar marsamoscm! ! Copyright (C) 2003-2005 Quantum ESPRESSO group ! This file is distributed under the terms of the ! GNU General Public License. See the file `License' ! in the root directory of the present distribution, ! or http://www.gnu.org/copyleft/gpl.txt . ! !---------------------------------------------------------------------------- MODULE path_formats !---------------------------------------------------------------------------- ! ! ... this module contains the I/O formats used by all "path"-routines ! ! ... Written by Carlo Sbraccia ( 2003-2005 ) ! CHARACTER (LEN=*), PARAMETER :: & lattice_vectors = "(3(2X,F14.10),/,3(2X,F14.10),/,3(2X,F14.10))" ! CHARACTER (LEN=*), PARAMETER :: & restart_first = "(3(2X,F18.12),3(2X,F18.12),3(2X,I1))", & restart_others = "(3(2X,F18.12),3(2X,F18.12))" ! CHARACTER (LEN=*), PARAMETER :: & quick_min = "(9(2X,F18.12))", & energy = "(2X,F18.10)" ! CHARACTER (LEN=*), PARAMETER :: & dat_fmt = "(3(2X,F16.10))", & int_fmt = "(2(2X,F16.10))", & xyz_fmt = "(A2,3(2X,F14.10))", & axsf_fmt = "(A2,6(2X,F14.10))" ! CHARACTER (LEN=*), PARAMETER :: & scf_iter_fmt = "(/,5X,30('-'),(1X,'iteration ',I3,1X),30('-'),/)", & scf_fmt = "(5X,'tcpu = ',F8.1," // & & "' self-consistency for image ', I3)", & scf_fmt_para = "(5X,'cpu = ',I2,' tcpu = ',F8.1," // & & "' self-consistency for image ', I3)" ! CHARACTER (LEN=*), PARAMETER :: & run_info = "(5X,'image',8X,'energy (eV)',8X,'error (eV/A)',8X,'frozen',/)" ! CHARACTER (LEN=*), PARAMETER :: & run_output = "(5X,I5,4X,F15.7,10X,F10.6,12X,L1)" ! CHARACTER (LEN=*), PARAMETER :: & summary_fmt = "(5X,A,T35,' = ',3X,A)" ! CHARACTER (LEN=*), PARAMETER :: & final_fmt = "(/,5X,75('-'),/)" ! END MODULE path_formats NEB/Doc/0000755000700200004540000000000012053440276011171 5ustar marsamoscmNEB/Doc/user_guide/0000755000700200004540000000000012053147432013322 5ustar marsamoscmNEB/Doc/user_guide/prev.png0000644000700200004540000000042712053147432015007 0ustar marsamoscmPNG  IHDR?GT PLTEooo[tRNS@fIDATx= 0 _pFD5K t tޡC)ät-}Y#% 4ҁͥd/v`3 v3tE$S5s}jf/hQ!ە=KV_N8K8!)x'D^K -sNH!%IENDB`NEB/Doc/user_guide/node7.html0000644000700200004540000001044212053147432015225 0ustar marsamoscm 4.1 Running on parallel machines next up previous contents
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4.1 Running on parallel machines

Parallel execution is strongly system- and installation-dependent. Typically one has to specify:

  1. a launcher program (not always needed), such as poe, mpirun, mpiexec, with the appropriate options (if any);
  2. the number of processors, typically as an option to the launcher program, but in some cases to be specified after the name of the program to be executed;
  3. the program to be executed, with the proper path if needed: for instance, ./neb.x, or $HOME/bin/neb.x, or whatever applies;
  4. other PWscf-specific parallelization options, to be read and interpreted by the running code;
  5. the number of image groups used by NEB (see next subsection).
Items 1) and 2) are machine- and installation-dependent, and may be different for interactive and batch execution. Note that large parallel machines are often configured so as to disallow interactive execution: if in doubt, ask your system administrator. Item 3) also depend on your specific configuration (shell, execution path, etc). Item 4) is optional but may be important: see the following section for the meaning of the various options.

For illustration, here is how to run neb.x on 16 processors partitioned into 4 image groups (4 processors each), for a path containing at least 4 images with POE: 

   poe neb.x -procs 16 -nimage 4 -inp input

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6 Performances

PWneb requires roughly the time and memory needed for a single SCF calculation, times num_of_images, times the number of NEB iterations needed to reach convergence. We refer the reader to the PW user_guide for more information.


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1 Introduction

This guide covers the usage of PWneb, version 5.0.2: an open-source package for the calculation of energy barriers and reaction pathway using the Nudged Elastic Band (NEB) method.

This guide assumes that you know the physics that PWneb describes and the methods it implements. It also assumes that you have already installed, or know how to install, QUANTUM ESPRESSO. If not, please read the general User's Guide for QUANTUM ESPRESSO, found in directory Doc/ two levels above the one containing this guide; or consult the web site:
http://www.quantum-espresso.org.

PWneb is part of the QUANTUM ESPRESSO distribution and uses the PWscf package as electronic-structure computing tools (``engine''). It is however written in a modular way and could be adapted to use other codes as ``engine''. Note that since v.4.3 PWscf no longer performs NEB calculations. Also note that NEB with Car-Parrinello molecular dynamics is not implemented anymore since v.4.3.


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7 Troubleshooting

Almost all problems in PWneb arise from incorrect input data and result in error stops. Error messages should be self-explanatory, but unfortunately this is not always true. If the code issues a warning messages and continues, pay attention to it but do not assume that something is necessarily wrong in your calculation: most warning messages signal harmless problems.


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Image quantum_espresso Image democritos
User's Guide for PWneb (version 5.0.2)



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5 Using PWneb

NEB calculations with neb.x can be started in two different ways:

  1. by reading a single input file, specified with the command line option -inp (or -input);
  2. by specifying the number N of images with the command line option -input_images N, and providing the input data for PWneb in a file named neb.dat and for the PWscf engine in the files pw_X.in (X = 1,..., N , see also below).

In the first case, the input file contains keywords (described here below) that enable the code to distinguish between parts of the input containing NEB-specific parameters and parts containing instructions for the computational engine (only PW is currently supported).

N.B.: the neb.x code does not read from standard input, so that input redirection (e.g., neb.x < neb.in ...) cannot be used.

The general structure of the file to be parsed should be as follows: 

BEGIN
BEGIN_PATH_INPUT
~... neb specific namelists and cards
END_PATH_INPUT
BEGIN_ENGINE_INPUT
~...pw specific namelists and cards
BEGIN_POSITIONS
FIRST_IMAGE
~...pw ATOMIC_POSITIONS card
INTERMEDIATE_IMAGE
~...pw ATOMIC_POSITIONS card
LAST_IMAGE
~...pw ATOMIC_POSITIONS card
END_POSITIONS
~... other pw specific cards
END_ENGINE_INPUT
END

After the parsing is completed, several files are generated by PWneb, more specifically: neb.dat, with NEB-related input data, and a set of input files in the PWscf format, pw_1.in, ..., pw_N.in, one for each set of atomic position (image) found in the original input file. For the second case, the neb.dat file and all pw_X.in should be already present in the directory where the code is started. A detailed description of all NEB-specific input variables is contained in the input description files Doc/INPUT_NEB.*, while for the PWscf engine all the options of a scf calculation apply (see PW/Doc/INPUT_PW.* and example01 in the NEB/examples directory).

A NEB calculation will produce a number of output files containing additional information on the minimum-energy path. The following files are created in the directory were the code is started:

prefix.dat
is a three-column file containing the position of each image on the reaction coordinate (arb. units), its energy in eV relative to the energy of the first image and the residual error for the image in eV/a0 .
prefix.int
contains an interpolation of the path energy profile that pass exactly through each image; it is computed using both the image energies and their derivatives
prefix.path
information used by QUANTUM ESPRESSO to restart a path calculation, its format depends on the input details and is undocumented
prefix.axsf
atomic positions of all path images in the XCrySDen animation format: to visualize it, use xcrysden -axsf prefix.axsf
prefix.xyz
atomic positions of all path images in the generic xyz format, used by many quantum-chemistry softwares
prefix.crd
path information in the input format used by pw.x, suitable for a manual restart of the calculation
where prefix is the PWscf variable specified in the input. The more verbose output from the PWscf engine is not printed on the standard output, but is redirected into a file stored in the image-specific temporary directories (e.g. outdir/prefix_1/PW.out for the first image, etc.).

NEB calculations are a bit tricky in general and require extreme care to be setup correctly. Sometimes it can easily take hundreds of iterations for them to converge, depending on the number of atoms and of images. Here you can find some advice (courtesy of Lorenzo Paulatto):

  1. Don't use Climbing Image (CI) from the beginning. It makes convergence slower, especially if the special image changes during the convergence process (this may happen if CI_scheme='auto' and if it does it may mess up everything). Converge your calculation, then restart from the last configuration with CI option enabled (note that this will increase the barrier).
  2. Carefully choose the initial path. If you ask the code to use more images than those you have supplied on input, the code will make a linear interpolation of the atomic positions between consecutive input images. You can visualize the .axsf file with XCrySDen as an animation: take some time to check if any atoms overlap or get very close in some of the new images (in that case you will have to supply intermediate images).
  3. Try to start the NEB process with most atomic positions fixed, in order to converge the more "problematic" ones, before leaving all atoms move.
  4. Especially for larger systems, you can start NEB with lower accuracy (less k-points, lower cutoff) and then increase it when it has converged to refine your calculation.
  5. Use the Broyden algorithm instead of the default one: it is a bit more fragile, but it removes the problem of "oscillations" in the calculated activation energies. If these oscillations persist, and you cannot afford more images, focus to a smaller problem, decompose it into pieces.
  6. A gross estimate of the required number of iterations is (number of images) * (number of atoms) * 3. Atoms that do not move should not be counted. It may take half that many iterations, or twice as many, but more or less that's the order of magnitude, unless one starts from a very good or very bad initial guess.

The code path_int.x is is a tool to generate a new path (what is actually generated is the restart file) starting from an old one through interpolation (cubic splines). The new path can be discretized with a different number of images (this is its main purpose), images are equispaced and the interpolation can be also performed on a subsection of the old path. The input file needed by path_int.x can be easily set up with the help of the self-explanatory path_interpolation.sh shell script in the NEB/tools folder.

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3 Compilation

PWneb is a package tightly bound to QUANTUM ESPRESSO. For instruction on how to download and compile QUANTUM ESPRESSO, please refer to the general Users' Guide, available in file Doc/user_guide.pdf under the main QUANTUM ESPRESSO directory, or in web site http://www.quantum-espresso.org.

Once QUANTUM ESPRESSO is correctly configured, PWneb can be automatically downloaded, unpacked and compiled by just typing make neb, from the main QUANTUM ESPRESSO directory. make neb will produce the following codes in NEB/src:

Symlinks to executable programs will be placed in the bin/ subdirectory of the main QUANTUM ESPRESSO directory.


Subsections
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Contents


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Next: 3 Compilation Up: User's Guide for The Previous: 1 Introduction   Contents

2 People and terms of use

The current maintainers of PWneb are Layla Martin-Samos, Paolo Giannozzi, Stefano de Gironcoli. The original QUANTUM ESPRESSO implementation of NEB was written by Carlo Sbraccia.

PWneb is free software, released under the GNU General Public License.
See http://www.gnu.org/licenses/old-licenses/gpl-2.0.txt, or the file License in the distribution).

We shall greatly appreciate if scientific work done using this code will contain an explicit acknowledgment and the following reference:

P. Giannozzi, S. Baroni, N. Bonini, M. Calandra, R. Car, C. Cavazzoni, D. Ceresoli, G. L. Chiarotti, M. Cococcioni, I. Dabo, A. Dal Corso, S. Fabris, G. Fratesi, S. de Gironcoli, R. Gebauer, U. Gerstmann, C. Gougoussis, A. Kokalj, M. Lazzeri, L. Martin-Samos, N. Marzari, F. Mauri, R. Mazzarello, S. Paolini, A. Pasquarello, L. Paulatto, C. Sbraccia, S. Scandolo, G. Sclauzero, A. P. Seitsonen, A. Smogunov, P. Umari, R. M. Wentzcovitch, J.Phys.:Condens.Matter 21, 395502 (2009), http://arxiv.org/abs/0906.2569


Layla Martin-Samos Colomer 2012-11-21
NEB/Doc/user_guide/node6.html0000644000700200004540000000607012053147432015226 0ustar marsamoscm 4 Parallelism next up previous contents
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4 Parallelism

The PWneb code is interfaced to PWscf, which is used as computational engine for total energies and forces. It can therefore take advantage from the two parallelization paradigms currently implemented in QUANTUM ESPRESSO, namely Message Passing Interface (MPI) and OpenMP threads, and exploit all PWscf-specific parallelization options. For a detailed information about parallelization in QUANTUM ESPRESSO, please refer to the general documentation.

As PWneb makes several independent evaluations of energy and forces at each step of the path optimization (one for each point in the configurational space, called ``image'', consituting the path) it is possible to distribute them among processors using an additional level of parallelization (see later).


Subsections
Layla Martin-Samos Colomer 2012-11-21
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About this document ...

Image quantum_espresso Image democritos
User's Guide for PWneb (version 5.0.2)

This document was generated using the LaTeX2HTML translator Version 2002-2-1 (1.71)

Copyright © 1993, 1994, 1995, 1996, Nikos Drakos, Computer Based Learning Unit, University of Leeds.
Copyright © 1997, 1998, 1999, Ross Moore, Mathematics Department, Macquarie University, Sydney.

The command line arguments were:
latex2html -t 'User's Guide for The Quantum ESPRESSO Nudged Elastic Band' -html_version 3.2,math -toc_depth 5 -split 5 -toc_stars -show_section_numbers -local_icons -image_type png user_guide.tex

The translation was initiated by Layla Martin-Samos Colomer on 2012-11-21

Layla Martin-Samos Colomer 2012-11-21
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Next: 4 Parallelism Up: 3 Compilation Previous: 3 Compilation   Contents


3.1 Running examples

As a final check that compilation was successful, you may want to run some or all of the examples (presently only one). To run the examples, you should follow this procedure:
  1. Edit the environment_variables file in the main QUANTUM ESPRESSO directory, setting the following variables as needed:
    BIN_DIR: directory where executables reside
    PSEUDO_DIR: directory where pseudopotential files reside
    TMP_DIR: directory to be used as temporary storage area
The default values of BIN_DIR and PSEUDO_DIR should be fine, unless you have installed things in nonstandard places. The TMP_DIR variable must point to a directory where you have read and write permissions, with enough available space to host the temporary files produced by the example runs, and possibly offering good I/O performance (i.e., don't use an NFS-mounted directory). N.B. Use a dedicated directory, because the example script will automatically delete all data inside TMP_DIR. If you have compiled the parallel version of QUANTUM ESPRESSO (this is the default if parallel libraries are detected), you will usually have to specify a driver program (such as mpirun or mpiexec) and the number of processors: see Sec.4.1 for details. In order to do that, edit again the environment_variables file and set the PARA_PREFIX and PARA_POSTFIX variables as needed. Parallel executables will be started with a command line like this: 
      $PARA_PREFIX neb.x $PARA_POSTFIX -inp file.in > file.out
For example, the command for IBM's POE looks like this: 
      poe neb.x -procs 4 -inp file.in > file.out
therefore you will need to set PARA_PREFIX="poe", PARA_POSTFIX="-procs 4". Furthermore, if your machine does not support interactive use, you must run the commands specified below through the batch queuing system installed on that machine. Ask your system administrator for instructions.

Go to NEB/examples and execute: 

      ./run_example
This will create a subdirectory results/ containing the input and output files generated by the calculation.

The reference/ subdirectory contains verified output files, that you can check your results against. They were generated on a Linux PC using the Intel compiler. On different architectures the precise numbers could be slightly different, in particular if different FFT dimensions are automatically selected. For this reason, a plain diff of your results against the reference data doesn't work, or at least, it requires human inspection of the results.

next up previous contents
Next: 4 Parallelism Up: 3 Compilation Previous: 3 Compilation   Contents
Layla Martin-Samos Colomer 2012-11-21
NEB/Doc/user_guide/node8.html0000644000700200004540000000545112053147432015232 0ustar marsamoscm 4.2 Parallelization levels next up previous contents
Next: 5 Using PWneb Up: 4 Parallelism Previous: 4.1 Running on parallel   Contents

4.2 Parallelization levels

Data structures are distributed across processors. Processors are organized in a hierarchy of groups, which are identified by different MPI communicators level. The groups hierarchy is as follow: 

  world - image_group - PWscf hierarchy

world: is the group of all processors (MPI_COMM_WORLD).

image_group: Processors can then be divided into different image groups, each of them taking care of one or more NEB images.

Image parallelization is of loosely coupled type, so that processors belonging to different image groups communicate only once in a while, whereas processors within the same image group are tightly coupled and communications are more significant (please refer to the user guide of PWscf).

The default number of image groups is one, corresponding to the option -nimage 1 (or, equivalently, -nimages 1).


Layla Martin-Samos Colomer 2012-11-21
NEB/Doc/user_guide.out0000644000700200004540000000101312053147431014045 0ustar marsamoscm\BOOKMARK [1][-]{section.1}{Introduction}{} \BOOKMARK [1][-]{section.2}{People and terms of use}{} \BOOKMARK [1][-]{section.3}{Compilation}{} \BOOKMARK [2][-]{subsection.3.1}{Running examples}{section.3} \BOOKMARK [1][-]{section.4}{Parallelism}{} \BOOKMARK [2][-]{subsection.4.1}{Running on parallel machines}{section.4} \BOOKMARK [2][-]{subsection.4.2}{Parallelization levels}{section.4} \BOOKMARK [1][-]{section.5}{Using PWneb}{} \BOOKMARK [1][-]{section.6}{Performances}{} \BOOKMARK [1][-]{section.7}{Troubleshooting}{} NEB/Doc/INPUT_NEB.html0000644000700200004540000004533312053147432013450 0ustar marsamoscm

Input File Description

Program: neb.x / NEB / Quantum Espresso

TABLE OF CONTENTS

INTRODUCTION

&PATH

string_method | restart_mode | nstep_path | num_of_images | opt_scheme | CI_scheme | first_last_opt | temp_req | ds | k_max | k_min | path_thr | use_masses | use_freezing

CLIMBING_IMAGES

index1, index2, ... indexN

INTRODUCTION

Input data format: { } = optional, [ ] = it depends, | = or

All quantities whose dimensions are not explicitly specified are in
RYDBERG ATOMIC UNITS

BEWARE: TABS, DOS <CR><LF> CHARACTERS ARE POTENTIAL SOURCES OF TROUBLE

General input file structure:
===============================================================================

neb.x DOES NOT READ FROM STANDARD INPUT
There are two ways for running a calculation with neb.x:
1) specifying a file to parse with the ./neb.x -inp or
 neb.x -input command line option.
2) or specifying the number of copies of PWscf input ./neb.x -input\_images.

For case 1) a file containing KEYWORDS has to be written (see below).
These KEYWORDS tells the parser which part of the file regards neb specifics
and which part regards the energy/force engine (at the moment only PW).
After the parsing different files are generated: neb.dat, with
neb specific variables and a set of pw_*.in PWscf input files like
one for each input position. All options for a single SCF calculation apply.

The general structure of the file to be parsed is:

BEGIN
BEGIN_PATH_INPUT
... neb specific namelists and cards
END_PATH_INPUT
BEGIN_ENGINE_INPUT
...pw specific namelists and cards
BEGIN_POSITIONS
FIRST_IMAGE
...pw ATOMIC_POSITIONS card
INTERMEDIATE_IMAGE
...pw ATOMIC_POSITIONS card
LAST_IMAGE
...pw ATOMIC_POSITIONS card
END_POSITIONS
... other pw specific cards
END_ENGINE_INPUT
END

For case 2) neb.dat and all pw_1.in, pw_2.in ... should be already present.

Structure of the input data (file neb.dat) :
===============================================================================

&PATH
  ...
/

[ CLIMBING_IMAGES
   list of images, separated by a comma ]

Namelist: PATH

string_method CHARACTER
Default: 'neb' 
a string describing the task to be performed:
   'neb',
   'smd'
restart_mode CHARACTER
Default: 'from_scratch' 
'from_scratch'  : from scratch

'restart'       : from previous interrupted run
nstep_path INTEGER
Default: 1 
number of ionic + electronic steps
num_of_images INTEGER
Default: 0 
Number of points used to discretize the path
(it must be larger than 3).
opt_scheme CHARACTER
Default: 'quick-min' 
Specify the type of optimization scheme:

'sd'         : steepest descent

'broyden'    : quasi-Newton Broyden's second method (suggested)

'broyden2'   : another variant of the quasi-Newton Broyden's
               second method to be tested and compared with the
               previous one.

'quick-min'  : an optimisation algorithm based on the
               projected velocity Verlet scheme

'langevin'   : finite temperature langevin dynamics of the
               string (smd only). It is used to compute the
               average path and the free-energy profile.
CI_scheme CHARACTER
Default: 'no-CI' 
Specify the type of Climbing Image scheme:

'no-CI'      : climbing image is not used

'auto'       : original CI scheme. The image highest in energy
               does not feel the effect of springs and is
               allowed to climb along the path

'manual'     : images that have to climb are manually selected.
               See also CLIMBING_IMAGES card
first_last_opt LOGICAL
Default: .FALSE. 
Also the first and the last configurations are optimized
"on the fly" (these images do not feel the effect of the springs).
temp_req REAL
Default: 0.D0 Kelvin 
Temperature used for the langevin dynamics of the string.
ds REAL
Default: 1.D0 
Optimisation step length ( Hartree atomic units ).
If opt_scheme="broyden", ds is used as a guess for the
diagonal part of the Jacobian matrix.
k_max, k_min REAL
Default: 0.1D0 Hartree atomic units 
Set them to use a Variable Elastic Constants scheme
elastic constants are in the range [ k_min, k_max ]
this is useful to rise the resolution around the saddle point.
path_thr REAL
Default: 0.05D0 eV / Angstrom 
The simulation stops when the error ( the norm of the force
orthogonal to the path in eV/A ) is less than path_thr.
use_masses LOGICAL
Default: .FALSE. 
If. TRUE. the optimisation of the path is performed using
mass-weighted coordinates. Useful together with quick-min
optimization scheme, if some bonds are much stiffer than
others. By assigning a larger (fictitious) mass to atoms
with stiff bonds, one may use a longer time step "ds"
use_freezing LOGICAL
Default: .FALSE. 
If. TRUE. the images are optimised according to their error:
only those images with an error larger than half of the largest
are optimised. The other images are kept frozen.

Card: CLIMBING_IMAGES

Optional card, needed only if CI_scheme = 'manual', ignored otherwise !

Syntax:

CLIMBING_IMAGES
index1, index2, ... indexN   

Description of items:






 index1, index2, ... indexN
            
INTEGER



index1, index2, ..., indexN are indices of the images to which the
Climbing-Image procedure apply. If more than one image is specified
they must be separated by a comma.
            


















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Output written on user_guide.pdf (7 pages, 145699 bytes).
NEB/Doc/input_xx.xsl0000777000700200004540000000000012053147432020542 2../../dev-tools/input_xx.xslustar  marsamoscmNEB/Doc/Makefile0000644000700200004540000000334112053145633012631 0ustar  marsamoscmHELPDOC=../../dev-tools/helpdoc

LATEX   = pdflatex
LATEX2HTML = latex2html

PDFS = user_guide.pdf
AUXS = $(PDFS:.pdf=.aux)
LOGS = $(PDFS:.pdf=.log)
OUTS = $(PDFS:.pdf=.out)
TOCS = $(PDFS:.pdf=.toc)

doc:  all
all:  pdf html defs
pdf:  $(PDFS)
html: user_guide

$(PDFS): %.pdf: %.tex
	$(LATEX)  $<
	$(LATEX)  $<

clean:
	- rm -f $(PDFS) $(AUXS) $(LOGS) $(OUTS) $(TOCS) *~
	- rm -rf user_guide/
	- rm -f INPUT_*.html INPUT_*.txt INPUT_*.xml
	- rm -rf input_xx.xsl
	- rm -rf ../../Doc/INPUT_NEB.*

user_guide: user_guide.pdf
	 rm -rf user_guide/
	 latex2html \
                -t "User's Guide for The Quantum ESPRESSO Nudged Elastic Band" \
                -html_version 3.2,math \
                -toc_depth 5 -split 5 -toc_stars -show_section_numbers \
                -local_icons -image_type png \
                user_guide.tex
	cd user_guide; \
        for file in *.html; do \
                cp $$file /tmp/$$file; \
                cat /tmp/$$file | sed 's/HREF="http/NAME="http/g' | sed 's/mathend000#//g' - > $$file; \
                rm -f /tmp/$$file; \
        done
	@echo ""
	@echo "***"
	@echo "*** User's Guide created in user_guide/user_guide.html"
	@echo "***"
	@echo ""

defs: link_input_xx INPUT_NEB.html INPUT_NEB.txt link_on_main_doc
link_input_xx:
	@(if test ! -f input_xx.xsl; then \
	(if test -f ../../dev-tools/input_xx.xsl; then \
	(ln -sf ../../dev-tools/input_xx.xsl input_xx.xsl) ; \
	else \
	echo ; \
	echo "  Sorry, can not find input_xx.xsl html style file !!!" ; \
	echo ; \
	fi) ; fi)

INPUT_NEB.html: %.html: %.def
	$(HELPDOC) $<
INPUT_NEB.txt: %.txt: %.def
	$(HELPDOC) $<
link_on_main_doc:
	-@( cd ../../Doc ; ln -fs ../NEB/Doc/INPUT_NEB.html . ; \
	ln -fs ../NEB/Doc/INPUT_NEB.xml . ; \
	ln -fs ../NEB/Doc/INPUT_NEB.txt .)
NEB/Doc/user_guide.toc0000644000700200004540000000135712053147431014036 0ustar  marsamoscm\contentsline {section}{\numberline {1}Introduction}{1}{section.1}
\contentsline {section}{\numberline {2}People and terms of use}{2}{section.2}
\contentsline {section}{\numberline {3}Compilation}{2}{section.3}
\contentsline {subsection}{\numberline {3.1}Running examples}{2}{subsection.3.1}
\contentsline {section}{\numberline {4}Parallelism}{3}{section.4}
\contentsline {subsection}{\numberline {4.1}Running on parallel machines}{4}{subsection.4.1}
\contentsline {subsection}{\numberline {4.2}Parallelization levels}{4}{subsection.4.2}
\contentsline {section}{\numberline {5}Using \texttt {PWneb}}{5}{section.5}
\contentsline {section}{\numberline {6}Performances}{7}{section.6}
\contentsline {section}{\numberline {7}Troubleshooting}{7}{section.7}
NEB/Doc/INPUT_NEB.xml0000644000700200004540000001551412053147432013302 0ustar  marsamoscm


    

   
   
   
Input data format: { } = optional, [ ] = it depends, | = or

All quantities whose dimensions are not explicitly specified are in
RYDBERG ATOMIC UNITS

BEWARE: TABS, DOS <CR><LF> CHARACTERS ARE POTENTIAL SOURCES OF TROUBLE

General input file structure:
===============================================================================

neb.x DOES NOT READ FROM STANDARD INPUT
There are two ways for running a calculation with neb.x:
1) specifying a file to parse with the ./neb.x -inp or
 neb.x -input command line option.
2) or specifying the number of copies of PWscf input ./neb.x -input\_images.

For case 1) a file containing KEYWORDS has to be written (see below).
These KEYWORDS tells the parser which part of the file regards neb specifics
and which part regards the energy/force engine (at the moment only PW).
After the parsing different files are generated: neb.dat, with
neb specific variables and a set of pw_*.in PWscf input files like
one for each input position. All options for a single SCF calculation apply.

The general structure of the file to be parsed is:

BEGIN
BEGIN_PATH_INPUT
... neb specific namelists and cards
END_PATH_INPUT
BEGIN_ENGINE_INPUT
...pw specific namelists and cards
BEGIN_POSITIONS
FIRST_IMAGE
...pw ATOMIC_POSITIONS card
INTERMEDIATE_IMAGE
...pw ATOMIC_POSITIONS card
LAST_IMAGE
...pw ATOMIC_POSITIONS card
END_POSITIONS
... other pw specific cards
END_ENGINE_INPUT
END

For case 2) neb.dat and all pw_1.in, pw_2.in ... should be already present.

Structure of the input data (file neb.dat) :
===============================================================================

&PATH
  ...
/

[ CLIMBING_IMAGES
   list of images, separated by a comma ]
   
   
      
          'neb'
         
         
a string describing the task to be performed:
   'neb',
   'smd'
         
      
      
          'from_scratch'
         
         
'from_scratch'  : from scratch

'restart'       : from previous interrupted run
         
      
      
         
number of ionic + electronic steps
         
         
1
         
      
      
          0
         
         
Number of points used to discretize the path
(it must be larger than 3).
         
      
      
          'quick-min'
         
         
Specify the type of optimization scheme:

'sd'         : steepest descent

'broyden'    : quasi-Newton Broyden's second method (suggested)

'broyden2'   : another variant of the quasi-Newton Broyden's
               second method to be tested and compared with the
               previous one.

'quick-min'  : an optimisation algorithm based on the
               projected velocity Verlet scheme

'langevin'   : finite temperature langevin dynamics of the
               string (smd only). It is used to compute the
               average path and the free-energy profile.
         
      
      
          'no-CI'
         
         
Specify the type of Climbing Image scheme:

'no-CI'      : climbing image is not used

'auto'       : original CI scheme. The image highest in energy
               does not feel the effect of springs and is
               allowed to climb along the path

'manual'     : images that have to climb are manually selected.
               See also CLIMBING_IMAGES card
         
      
      
          .FALSE.
         
         
Also the first and the last configurations are optimized
"on the fly" (these images do not feel the effect of the springs).
         
      
      
          0.D0 Kelvin
         
         
Temperature used for the langevin dynamics of the string.
         
      
      
          1.D0
         
         
Optimisation step length ( Hartree atomic units ).
If opt_scheme="broyden", ds is used as a guess for the
diagonal part of the Jacobian matrix.
         
      
      
         
         
         
         
          0.1D0 Hartree atomic units
         
         
Set them to use a Variable Elastic Constants scheme
elastic constants are in the range [ k_min, k_max ]
this is useful to rise the resolution around the saddle point.
         
      
      
          0.05D0 eV / Angstrom
         
         
The simulation stops when the error ( the norm of the force
orthogonal to the path in eV/A ) is less than path_thr.
         
      
      
          .FALSE.
         
         
If. TRUE. the optimisation of the path is performed using
mass-weighted coordinates. Useful together with quick-min
optimization scheme, if some bonds are much stiffer than
others. By assigning a larger (fictitious) mass to atoms
with stiff bonds, one may use a longer time step "ds"
         
      
      
          .FALSE.
         
         
If. TRUE. the images are optimised according to their error:
only those images with an error larger than half of the largest
are optimised. The other images are kept frozen.
         
      
   
   
      
      
         
             index1, index2, ... indexN
            
            
index1, index2, ..., indexN are indices of the images to which the
Climbing-Image procedure apply. If more than one image is specified
they must be separated by a comma.
            
         
      
   

NEB/Doc/user_guide.aux0000644000700200004540000000302012053147431014033 0ustar  marsamoscm\relax 
\ifx\hyper@anchor\@undefined
\global \let \oldcontentsline\contentsline
\gdef \contentsline#1#2#3#4{\oldcontentsline{#1}{#2}{#3}}
\global \let \oldnewlabel\newlabel
\gdef \newlabel#1#2{\newlabelxx{#1}#2}
\gdef \newlabelxx#1#2#3#4#5#6{\oldnewlabel{#1}{{#2}{#3}}}
\AtEndDocument{\let \contentsline\oldcontentsline
\let \newlabel\oldnewlabel}
\else
\global \let \hyper@last\relax 
\fi

\@writefile{toc}{\contentsline {section}{\numberline {1}Introduction}{1}{section.1}}
\@writefile{toc}{\contentsline {section}{\numberline {2}People and terms of use}{2}{section.2}}
\@writefile{toc}{\contentsline {section}{\numberline {3}Compilation}{2}{section.3}}
\@writefile{toc}{\contentsline {subsection}{\numberline {3.1}Running examples}{2}{subsection.3.1}}
\newlabel{SubSec:Examples}{{3.1}{2}{Running examples\relax }{subsection.3.1}{}}
\@writefile{toc}{\contentsline {section}{\numberline {4}Parallelism}{3}{section.4}}
\newlabel{Sec:para}{{4}{3}{Parallelism\relax }{section.4}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {4.1}Running on parallel machines}{4}{subsection.4.1}}
\newlabel{SubSec:para}{{4.1}{4}{Running on parallel machines\relax }{subsection.4.1}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {4.2}Parallelization levels}{4}{subsection.4.2}}
\@writefile{toc}{\contentsline {section}{\numberline {5}Using \texttt  {PWneb}}{5}{section.5}}
\@writefile{toc}{\contentsline {section}{\numberline {6}Performances}{7}{section.6}}
\@writefile{toc}{\contentsline {section}{\numberline {7}Troubleshooting}{7}{section.7}}
NEB/Doc/user_guide.tex0000644000700200004540000004265112053145633014055 0ustar  marsamoscm\documentclass[12pt,a4paper]{article}
\def\version{5.0.2}
\def\qe{{\sc Quantum ESPRESSO}}
\def\NEB{\texttt{PWneb}} % to be decided
\usepackage{html}

% BEWARE: don't revert from graphicx for epsfig, because latex2html
% doesn't handle epsfig commands !!!
\usepackage{graphicx}

\textwidth = 17cm
\textheight = 24cm
\topmargin =-1 cm
\oddsidemargin = 0 cm

\def\pwx{\texttt{pw.x}}
\def\cpx{\texttt{cp.x}}
\def\phx{\texttt{ph.x}}
\def\nebx{\texttt{neb.x}}
\def\configure{\texttt{configure}}
\def\PWscf{\texttt{PWscf}}
\def\PHonon{\texttt{PHonon}}
\def\CP{\texttt{CP}}
\def\PostProc{\texttt{PostProc}}
\def\make{\texttt{make}}

\begin{document} 
\author{}
\date{}

\def\qeImage{../../Doc/quantum_espresso.pdf}
\def\democritosImage{../../Doc/democritos.pdf}

\begin{htmlonly}
\def\qeImage{../../Doc/quantum_espresso.png}
\def\democritosImage{../../Doc/democritos.png}
\end{htmlonly}

\title{
  \includegraphics[width=5cm]{\qeImage} \hskip 2cm
  \includegraphics[width=6cm]{\democritosImage}\\
  \vskip 1cm
  % title
  \Huge User's Guide for \NEB\
  \Large (version \version)
}
%\endhtmlonly

\maketitle

\tableofcontents

\section{Introduction}

This guide covers the usage of \NEB, version \version: 
an open-source package for the calculation of energy barriers 
and reaction pathway using the Nudged Elastic Band (NEB) method.

This guide assumes that you know the physics 
that \NEB\ describes and the methods it implements.
It also assumes  that you have already installed,
or know how to install, \qe. If not, please read
the general User's Guide for \qe, found in 
directory \texttt{Doc/} two levels above the 
one containing this guide; or consult the web site:\\
\texttt{http://www.quantum-espresso.org}.

\NEB \ is part of the \qe \ distribution and uses the \PWscf\
package as electronic-structure computing tools (``engine''). 
It is however written in a modular way and could be adapted 
to use other codes as ``engine''. Note that since v.4.3 \PWscf\ no 
longer performs NEB calculations. Also note that NEB with 
Car-Parrinello molecular dynamics is not implemented anymore since v.4.3.

\section{People and terms of use}
The current maintainers of \NEB\ are Layla Martin-Samos,
Paolo Giannozzi, Stefano de Gironcoli.
The original \qe \ implementation of NEB was written 
by Carlo Sbraccia.

\NEB\ is free software, released under the 
GNU General Public License. \\ See
\texttt{http://www.gnu.org/licenses/old-licenses/gpl-2.0.txt}, 
or the file License in the distribution).
    
We shall greatly appreciate if scientific work done using this code will 
contain an explicit acknowledgment and the following reference:
\begin{quote}
P. Giannozzi, S. Baroni, N. Bonini, M. Calandra, R. Car, C. Cavazzoni,
D. Ceresoli, G. L. Chiarotti, M. Cococcioni, I. Dabo, A. Dal Corso,
S. Fabris, G. Fratesi, S. de Gironcoli, R. Gebauer, U. Gerstmann,
C. Gougoussis, A. Kokalj, M. Lazzeri, L. Martin-Samos, N. Marzari,
F. Mauri, R. Mazzarello, S. Paolini, A. Pasquarello, L. Paulatto,
C. Sbraccia, S. Scandolo, G. Sclauzero, A. P. Seitsonen, A. Smogunov,
P. Umari, R. M. Wentzcovitch, J.Phys.:Condens.Matter 21, 395502 (2009),
http://arxiv.org/abs/0906.2569
\end{quote}

\section{Compilation}

\NEB\ is a package tightly bound to \qe.
For instruction on how to download and compile \qe, please refer 
to the general Users' Guide, available in file \texttt{Doc/user\_guide.pdf}
under the main \qe\ directory, or in web site 
\texttt{http://www.quantum-espresso.org}.

Once \qe\ is correctly configured, \NEB\ can be automatically 
downloaded, unpacked and compiled by
just typing \texttt{make neb}, from the main \qe\ directory.
\texttt{make neb} will produce 
the following codes in \texttt{NEB/src}:
\begin{itemize}
\item \nebx: calculates reaction barriers and pathways using NEB.
\item \texttt{path\_int.x}: generates a reaction path (a set of points
in the configuration space of the atomic system, called ``images''), by
 interpolating the supplied path. The new path can have a 
 different number of images than the old one and the initial and final 
 images of the new path can differ from the original ones.
 The utility \texttt{path\_interpolation.sh} in the \texttt{tools/}
 directory shows how to use the code.
\end{itemize}

Symlinks to executable programs will be placed in the
\texttt{bin/} subdirectory of the main \qe\  directory.

\subsection{Running examples}
\label{SubSec:Examples}
As a final check that compilation was successful, you may want to run some or
all of the examples (presently only one). To run the examples, you should follow this procedure:
\begin{enumerate}   
\item Edit the \texttt{environment\_variables} file in the main \qe \ directory,
 setting the following variables as needed: 
\begin{quote}
   BIN\_DIR: directory where executables reside\\
   PSEUDO\_DIR: directory where pseudopotential files reside\\
   TMP\_DIR: directory to be used as temporary storage area
\end{quote}
\end{enumerate}
The default values of BIN\_DIR and PSEUDO\_DIR should be fine, 
unless you have installed things in nonstandard places. The TMP\_DIR 
variable must point to a directory where you have read and write permissions, 
with enough available space to host the temporary files produced by the 
example runs, and possibly offering good I/O performance (i.e., don't 
use an NFS-mounted directory). \textbf{N.B.} Use a dedicated directory,
because the example script will automatically delete all data inside TMP\_DIR.
If you have compiled the parallel version of \qe\ (this
is the default if parallel libraries are detected), you will usually
have to specify a driver program (such as \texttt{mpirun} or \texttt{mpiexec}) 
and the number of processors: see Sec.\ref{SubSec:para} for
details. In order to do that, edit again the \texttt{environment\_variables} 
file
and set the PARA\_PREFIX and PARA\_POSTFIX variables as needed. 
Parallel executables will be started with a command line like this: 
\begin{verbatim}
      $PARA_PREFIX neb.x $PARA_POSTFIX -inp file.in > file.out
\end{verbatim}
For example, the command for IBM's POE looks like this:
\begin{verbatim}
      poe neb.x -procs 4 -inp file.in > file.out
\end{verbatim}
therefore you will need to set PARA\_PREFIX="poe", PARA\_POSTFIX="-procs 4". 
Furthermore, if your machine does not support interactive use, you
must run the commands specified below through the batch queuing
system installed on that machine. Ask your system administrator for
instructions. 

Go to NEB/examples and execute:
\begin{verbatim}
      ./run_example
\end{verbatim}
This will create a subdirectory \texttt{results/} containing the input and
output files generated by the calculation.

The \texttt{reference/} subdirectory contains
verified output files, that you can check your results against. They
were generated on a Linux PC using the Intel compiler. On different
architectures the precise numbers could be slightly different, in
particular if different FFT dimensions are automatically selected. For
this reason, a plain diff of your results against the reference data
doesn't work, or at least, it requires human inspection of the
results. 

\section{Parallelism}
\label{Sec:para}

The \NEB\ code is interfaced to \PWscf, which is used as computational engine 
for total energies and forces. It can therefore take advantage from the two 
parallelization paradigms currently implemented in \qe, namely
  Message Passing Interface (MPI) and OpenMP threads, and exploit
all \PWscf-specific parallelization options.
For a detailed information about parallelization in \qe, 
please refer to the general documentation.

As \NEB \ makes several independent evaluations of energy and forces at each step of
the path optimization (one for each point in the configurational space,
 called ``image'', consituting the path)
 it is possible to distribute them among processors using an additional level of 
parallelization (see later).
%corresponding to a point in configuration space (i.e. to
%a different set of atomic positions).

\subsection{Running on parallel machines}
\label{SubSec:para}

Parallel execution is strongly system- and installation-dependent. 
Typically one has to specify:
\begin{enumerate}
\item a launcher program (not always needed), 
such as \texttt{poe}, \texttt{mpirun}, \texttt{mpiexec},
  with the  appropriate options (if any);
\item the number of processors, typically as an option to the launcher
  program, but in some cases to be specified after the name of the
  program to be
  executed; 
\item the program to be executed, with the proper path if needed: for
  instance, \texttt{./neb.x}, or \texttt{\$HOME/bin/neb.x}, or
  whatever applies; 
\item other \texttt{PWscf}-specific parallelization options, to be
  read and interpreted by the running code; 
\item the number of image groups used by NEB (see next subsection).
\end{enumerate}
Items 1) and 2) are machine- and installation-dependent, and may be 
different for interactive and batch execution. Note that large
parallel machines are  often configured so as to disallow interactive
execution: if in doubt, ask your system administrator.
Item 3) also depend on your specific configuration (shell, execution
path, etc). 
Item 4) is optional but may be important: see the following section
for the meaning of the various options.

For illustration, here is how to run \texttt{neb.x} \ on 16 processors partitioned into
4 image groups (4 processors each), for a path containing at least 4 images with POE:
\begin{verbatim}
   poe neb.x -procs 16 -nimage 4 -inp input
\end{verbatim}


\subsection{Parallelization levels}

Data structures are distributed across processors.
Processors are organized in a hierarchy of groups, 
which are identified by different MPI communicators level.
The groups hierarchy is as follow:
\begin{verbatim}
  world - image_group - PWscf hierarchy
\end{verbatim}

\texttt{world}: is the group of all processors (MPI\_COMM\_WORLD).

\texttt{image\_group}: Processors can then be divided into different image groups,
each of them taking care of one or more NEB images.

%{\bf Communications}:
Image parallelization is of loosely coupled type, so that processors belonging to
different image groups communicate only once in a while, 
whereas processors within the same image group are tightly coupled and 
communications are more significant (please refer to the user guide of \PWscf).

The default number of image groups is one, corresponding to the option
 \texttt{-nimage 1} (or, equivalently,  \texttt{-nimages 1}).

\newpage

\section{Using \NEB}

NEB calculations with \texttt{neb.x} can be started in two different ways:
\begin{enumerate}
\item by reading a single input file, specified with the command line 
option \texttt{-inp} (or \texttt{-input});
\item by specifying the number $N$ of images with the command line option 
\texttt{-input\_images N}, and providing the input data for \NEB\ in
a file named \texttt{neb.dat} and for the \PWscf\ engine in the files
 \texttt{pw\_X.in} ($X=1,...,N$, see also below).
\end{enumerate}

In the first case, the input file contains keywords (described here below) 
that enable the code to distinguish between parts of the input containing 
NEB-specific parameters and parts containing instructions for the 
computational engine (only PW is currently supported).

\noindent\textbf{N.B.:} the \nebx\ code does not read from standard input,
so that input redirection (e.g., \texttt{neb.x < neb.in ...}) cannot be used.

The general structure of the file to be parsed should be as follows:
\begin{verbatim}
BEGIN
BEGIN_PATH_INPUT
~... neb specific namelists and cards
END_PATH_INPUT
BEGIN_ENGINE_INPUT
~...pw specific namelists and cards
BEGIN_POSITIONS
FIRST_IMAGE
~...pw ATOMIC_POSITIONS card
INTERMEDIATE_IMAGE
~...pw ATOMIC_POSITIONS card
LAST_IMAGE
~...pw ATOMIC_POSITIONS card
END_POSITIONS
~... other pw specific cards
END_ENGINE_INPUT
END
\end{verbatim}

After the parsing is completed, several files are generated by \NEB, more 
specifically: \texttt{neb.dat}, with NEB-related input data, 
and a set of input files in the \PWscf\ format, \texttt{pw\_1.in}, \ldots,
\texttt{pw\_N.in}, one for each set of atomic position (image) found in 
the original input file.
For the second case, the \texttt{neb.dat} file and all \texttt{pw\_X.in} 
should be already present in the directory where the code is started.
A detailed description of all NEB-specific input variables is contained 
in the input description files \texttt{Doc/INPUT\_NEB.*}, while for the
\PWscf\ engine all the options of a \texttt{scf} calculation apply (see
\texttt{PW/Doc/INPUT\_PW.*} and \texttt{example01} in the 
\texttt{NEB/examples} directory). 

A NEB calculation will produce a number of output files containing additional 
information on the minimum-energy path. The following files are created in the
directory were the code is started:
\begin{description}
\item[\texttt{prefix.dat}]
is a three-column file containing the position of each image on the reaction
coordinate (arb. units), its energy in eV relative to the energy of the first image
and the residual error for the image in eV/$a_0$.
\item[\texttt{prefix.int}]
contains an interpolation of the path energy profile that pass exactly through each
image; it is computed using both the image energies and their derivatives
\item[\texttt{prefix.path}]
information used by \qe\ 
to restart a path calculation, its format depends on the input
details and is undocumented
\item[\texttt{prefix.axsf}]
atomic positions of all path images in the XCrySDen animation format:
to visualize it, use \texttt{xcrysden -\--axsf prefix.axsf}
\item[\texttt{prefix.xyz}]
atomic positions of all path images in the generic xyz format, used by
many quantum-chemistry softwares
\item[\texttt{prefix.crd}]
path information in the input format used by \pwx, suitable for a manual
restart of the calculation
\end{description}
where \texttt{prefix} is the \PWscf\ variable specified in the input.
The more verbose output from the \PWscf\ engine is not printed on the standard
output, but is redirected into a file stored in the image-specific temporary 
directories (e.g. \texttt{outdir/prefix\_1/PW.out} for the first image, etc.).

NEB calculations are a bit tricky in general and require extreme care to be
setup correctly. Sometimes it can easily take hundreds of iterations for them
 to converge, depending on the number of atoms and of images. 
Here you can find some advice (courtesy of Lorenzo Paulatto):
\begin{enumerate}
\item 
Don't use Climbing Image (CI) from the beginning. It makes convergence slower, 
especially if the special image changes during the convergence process (this 
may happen if \texttt{CI\_scheme='auto'} and if it does it may mess up everything).
Converge your calculation, then restart from the last configuration with
CI option enabled (note that this will {\em increase} the barrier).
\item
Carefully choose the initial path. 
If you ask the code to use more images than those you have supplied on input,
the code will make a linear interpolation of the atomic positions between
consecutive input images.
You can visualize the \texttt{.axsf} file with XCrySDen as an animation:
 take some time to check if any atoms overlap or get very close in some
of the new images (in that case you will have to supply intermediate images).
%% the following should have been fixed (GS)
%Remember that \qe\ assumes continuity
%between the first and the last image at the initial condition. In other 
%words, periodic images are NOT used; you may have to manually translate
%an atom by one or more unit cell base vectors in order to have a meaningful
%initial path. 
\item
Try to start the NEB process with most atomic positions fixed, 
in order to converge the more "problematic" ones, before leaving
all atoms move.
\item
Especially for larger systems, you can start NEB with lower accuracy 
(less k-points, lower cutoff) and then increase it when it has
converged to refine your calculation.
\item
Use the Broyden algorithm instead of the default one: it is a bit more
fragile, but it removes the problem of "oscillations" in the calculated
activation energies. If these oscillations persist, and you cannot afford 
more images, focus to a smaller problem, decompose it into pieces.
\item
A gross estimate of the required number of iterations is
(number of images) * (number of atoms) * 3. Atoms that do not
move should not be counted. It may take half that many iterations, 
or twice as many, but more or less that's the order of magnitude, 
unless one starts from a very good or very bad initial guess.
\end{enumerate}

The code \texttt{path\_int.x} is
is a tool to generate a new path (what is actually
generated is the restart file) starting from an old one through
interpolation (cubic splines). The new path can be discretized with a
different number of images (this is its main purpose), images are
equispaced and the interpolation can be also
performed on a subsection of the old path. The input file needed by
\texttt{path\_int.x} can be easily set up  with the help of the self-explanatory
\texttt{path\_interpolation.sh} shell script in the \texttt{NEB/tools} folder.


\section{Performances}

\NEB \ requires roughly the time and memory 
needed for a single SCF calculation, times
\texttt{num\_of\_images}, times the number 
of NEB iterations needed to reach convergence.
We
refer the reader to the PW user\_guide for more information.

\section{Troubleshooting}

Almost all problems in \NEB \ arise from incorrect input data 
and result in
error stops. Error messages should be self-explanatory, but unfortunately
this is not always true. If the code issues a warning messages and continues,
pay attention to it but do not assume that something is necessarily wrong in
your calculation: most warning messages signal harmless problems.

\end{document}
NEB/Doc/INPUT_NEB.txt0000644000700200004540000002254112053147432013317 0ustar  marsamoscm*** FILE AUTOMATICALLY CREATED: DO NOT EDIT, CHANGES WILL BE LOST ***

------------------------------------------------------------------------
INPUT FILE DESCRIPTION

Program: neb.x / NEB / Quantum Espresso
------------------------------------------------------------------------


Input data format: { } = optional, [ ] = it depends, | = or

All quantities whose dimensions are not explicitly specified are in
RYDBERG ATOMIC UNITS

BEWARE: TABS, DOS  CHARACTERS ARE POTENTIAL SOURCES OF TROUBLE

General input file structure:
===============================================================================

neb.x DOES NOT READ FROM STANDARD INPUT
There are two ways for running a calculation with neb.x:
1) specifying a file to parse with the ./neb.x -inp or
 neb.x -input command line option.
2) or specifying the number of copies of PWscf input ./neb.x -input\_images.

For case 1) a file containing KEYWORDS has to be written (see below).
These KEYWORDS tells the parser which part of the file regards neb specifics
and which part regards the energy/force engine (at the moment only PW).
After the parsing different files are generated: neb.dat, with
neb specific variables and a set of pw_*.in PWscf input files like
one for each input position. All options for a single SCF calculation apply.

The general structure of the file to be parsed is:

BEGIN
BEGIN_PATH_INPUT
... neb specific namelists and cards
END_PATH_INPUT
BEGIN_ENGINE_INPUT
...pw specific namelists and cards
BEGIN_POSITIONS
FIRST_IMAGE
...pw ATOMIC_POSITIONS card
INTERMEDIATE_IMAGE
...pw ATOMIC_POSITIONS card
LAST_IMAGE
...pw ATOMIC_POSITIONS card
END_POSITIONS
... other pw specific cards
END_ENGINE_INPUT
END

For case 2) neb.dat and all pw_1.in, pw_2.in ... should be already present.

Structure of the input data (file neb.dat) :
===============================================================================

&PATH
  ...
/

[ CLIMBING_IMAGES
   list of images, separated by a comma ]



========================================================================
NAMELIST: &PATH

   +--------------------------------------------------------------------
   Variable:       string_method
   
   Type:           CHARACTER
   Default:        'neb'
   Description:    a string describing the task to be performed:
                      'neb',
                      'smd'
   +--------------------------------------------------------------------
   
   +--------------------------------------------------------------------
   Variable:       restart_mode
   
   Type:           CHARACTER
   Default:        'from_scratch'
   Description:    'from_scratch'  : from scratch
                   
                   'restart'       : from previous interrupted run
   +--------------------------------------------------------------------
   
   +--------------------------------------------------------------------
   Variable:       nstep_path
   
   Type:           INTEGER
   Description:    number of ionic + electronic steps
   Default:        1
   +--------------------------------------------------------------------
   
   +--------------------------------------------------------------------
   Variable:       num_of_images
   
   Type:           INTEGER
   Default:        0
   Description:    Number of points used to discretize the path
                   (it must be larger than 3).
   +--------------------------------------------------------------------
   
   +--------------------------------------------------------------------
   Variable:       opt_scheme
   
   Type:           CHARACTER
   Default:        'quick-min'
   Description:    Specify the type of optimization scheme:
                   
                   'sd'         : steepest descent
                   
                   'broyden'    : quasi-Newton Broyden's second method (suggested)
                   
                   'broyden2'   : another variant of the quasi-Newton Broyden's
                                  second method to be tested and compared with the
                                  previous one.
                   
                   'quick-min'  : an optimisation algorithm based on the
                                  projected velocity Verlet scheme
                   
                   'langevin'   : finite temperature langevin dynamics of the
                                  string (smd only). It is used to compute the
                                  average path and the free-energy profile.
   +--------------------------------------------------------------------
   
   +--------------------------------------------------------------------
   Variable:       CI_scheme
   
   Type:           CHARACTER
   Default:        'no-CI'
   Description:    Specify the type of Climbing Image scheme:
                   
                   'no-CI'      : climbing image is not used
                   
                   'auto'       : original CI scheme. The image highest in energy
                                  does not feel the effect of springs and is
                                  allowed to climb along the path
                   
                   'manual'     : images that have to climb are manually selected.
                                  See also CLIMBING_IMAGES card
   +--------------------------------------------------------------------
   
   +--------------------------------------------------------------------
   Variable:       first_last_opt
   
   Type:           LOGICAL
   Default:        .FALSE.
   Description:    Also the first and the last configurations are optimized
                   "on the fly" (these images do not feel the effect of the springs).
   +--------------------------------------------------------------------
   
   +--------------------------------------------------------------------
   Variable:       temp_req
   
   Type:           REAL
   Default:        0.D0 Kelvin
   Description:    Temperature used for the langevin dynamics of the string.
   +--------------------------------------------------------------------
   
   +--------------------------------------------------------------------
   Variable:       ds
   
   Type:           REAL
   Default:        1.D0
   Description:    Optimisation step length ( Hartree atomic units ).
                   If opt_scheme="broyden", ds is used as a guess for the
                   diagonal part of the Jacobian matrix.
   +--------------------------------------------------------------------
   
   +--------------------------------------------------------------------
   Variables:      k_max, k_min
   
   Type:           REAL
   Default:        0.1D0 Hartree atomic units
   Description:    Set them to use a Variable Elastic Constants scheme
                   elastic constants are in the range [ k_min, k_max ]
                   this is useful to rise the resolution around the saddle point.
   +--------------------------------------------------------------------
   
   +--------------------------------------------------------------------
   Variable:       path_thr
   
   Type:           REAL
   Default:        0.05D0 eV / Angstrom
   Description:    The simulation stops when the error ( the norm of the force
                   orthogonal to the path in eV/A ) is less than path_thr.
   +--------------------------------------------------------------------
   
   +--------------------------------------------------------------------
   Variable:       use_masses
   
   Type:           LOGICAL
   Default:        .FALSE.
   Description:    If. TRUE. the optimisation of the path is performed using
                   mass-weighted coordinates. Useful together with quick-min
                   optimization scheme, if some bonds are much stiffer than
                   others. By assigning a larger (fictitious) mass to atoms
                   with stiff bonds, one may use a longer time step "ds"
   +--------------------------------------------------------------------
   
   +--------------------------------------------------------------------
   Variable:       use_freezing
   
   Type:           LOGICAL
   Default:        .FALSE.
   Description:    If. TRUE. the images are optimised according to their error:
                   only those images with an error larger than half of the largest
                   are optimised. The other images are kept frozen.
   +--------------------------------------------------------------------
   
===END OF NAMELIST======================================================


========================================================================
CARD: CLIMBING_IMAGES 

   OPTIONAL CARD, NEEDED ONLY IF CI_SCHEME = 'MANUAL', IGNORED OTHERWISE !
   
   /////////////////////////////////////////
   // Syntax:                             //
   /////////////////////////////////////////
   
      CLIMBING_IMAGES 
         index1, index2, ... indexN
   
   /////////////////////////////////////////
   
   DESCRIPTION OF ITEMS:
   
      +--------------------------------------------------------------------
      Variables:      index1, index2, ... indexN
      
      Type:           INTEGER
      Description:    index1, index2, ..., indexN are indices of the images to which the
                      Climbing-Image procedure apply. If more than one image is specified
                      they must be separated by a comma.
      +--------------------------------------------------------------------
      
      
===END OF CARD==========================================================


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trailer
<<
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/Root 170 0 R
/Info 171 0 R
/ID [<9EF5C17A21093D93AB806E74EFADC7A7> <9EF5C17A21093D93AB806E74EFADC7A7>]
>>
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142097
%%EOF
NEB/Doc/INPUT_NEB.def0000644000700200004540000001435012053145633013236 0ustar  marsamoscminput_description -distribution {Quantum Espresso} -package NEB -program neb.x {

    toc {}

    intro {
	Input data format: { } = optional, [ ] = it depends, | = or
	
	All quantities whose dimensions are not explicitly specified are in
	RYDBERG ATOMIC UNITS

        BEWARE: TABS, DOS  CHARACTERS ARE POTENTIAL SOURCES OF TROUBLE 

	General input file structure:
	===============================================================================
        
        neb.x DOES NOT READ FROM STANDARD INPUT
        There are two ways for running a calculation with neb.x:
        1) specifying a file to parse with the ./neb.x -inp or
         neb.x -input command line option.
        2) or specifying the number of copies of PWscf input ./neb.x -input\_images. 

        For case 1) a file containing KEYWORDS has to be written (see below).
        These KEYWORDS tells the parser which part of the file regards neb specifics
        and which part regards the energy/force engine (at the moment only PW).
        After the parsing different files are generated: neb.dat, with
        neb specific variables and a set of pw_*.in PWscf input files like
        one for each input position. All options for a single SCF calculation apply.

        The general structure of the file to be parsed is:

        BEGIN
        BEGIN_PATH_INPUT
        ... neb specific namelists and cards
        END_PATH_INPUT
        BEGIN_ENGINE_INPUT
        ...pw specific namelists and cards
        BEGIN_POSITIONS
        FIRST_IMAGE
        ...pw ATOMIC_POSITIONS card
        INTERMEDIATE_IMAGE
        ...pw ATOMIC_POSITIONS card
        LAST_IMAGE
        ...pw ATOMIC_POSITIONS card
        END_POSITIONS
        ... other pw specific cards
        END_ENGINE_INPUT
        END

        For case 2) neb.dat and all pw_1.in, pw_2.in ... should be already present. 

	Structure of the input data (file neb.dat) :
	===============================================================================

	&PATH
	  ...
	/

	[ CLIMBING_IMAGES
	   list of images, separated by a comma ]
    }


    namelist PATH {

	var string_method -type CHARACTER {
	    default { 'neb' }
	    info {
	     a string describing the task to be performed:
                'neb', 
                'smd'

	    }
	}
	
	var restart_mode -type CHARACTER {
	    default { 'from_scratch' }
	    info {
		'from_scratch'  : from scratch
	    
		'restart'       : from previous interrupted run
	    }
	}
	
	var nstep_path -type INTEGER {
	    info {
		number of ionic + electronic steps
	    }
	    default {
		1 
	    }
	}
	
	    var num_of_images -type INTEGER { 
		default { 0 }
		info {
		    Number of points used to discretize the path
		    (it must be larger than 3).
		}
	    }

	    var opt_scheme -type CHARACTER { 
		default { 'quick-min' }
		info {
		    Specify the type of optimization scheme:

		    'sd'         : steepest descent

		    'broyden'    : quasi-Newton Broyden's second method (suggested)

		    'broyden2'   : another variant of the quasi-Newton Broyden's 
                                   second method to be tested and compared with the
                                   previous one.

		    'quick-min'  : an optimisation algorithm based on the
		                   projected velocity Verlet scheme

		    'langevin'   : finite temperature langevin dynamics of the
                                   string (smd only). It is used to compute the
                                   average path and the free-energy profile.
		}
	    }

	    var CI_scheme -type CHARACTER {
		default { 'no-CI' }
		info {
		    Specify the type of Climbing Image scheme:

		    'no-CI'      : climbing image is not used

		    'auto'       : original CI scheme. The image highest in energy
	                           does not feel the effect of springs and is
			           allowed to climb along the path

		    'manual'     : images that have to climb are manually selected.
		                   See also CLIMBING_IMAGES card
		}
	    }

	    var first_last_opt -type LOGICAL { 
		default { .FALSE. }
		info {
		    Also the first and the last configurations are optimized
		    "on the fly" (these images do not feel the effect of the springs).
		}
	    }

	    var temp_req -type REAL { 
		default { 0.D0 Kelvin }
		info {
		    Temperature used for the langevin dynamics of the string.
		}
	    }

	    var ds -type REAL { 
		default { 1.D0 }
		info {
		    Optimisation step length ( Hartree atomic units ).
		    If opt_scheme="broyden", ds is used as a guess for the
                    diagonal part of the Jacobian matrix.
		}
	    }

	    vargroup -type REAL {
		var k_max
		var k_min
		default { 0.1D0 Hartree atomic units }
		info {
		    Set them to use a Variable Elastic Constants scheme
		    elastic constants are in the range [ k_min, k_max ]
		    this is useful to rise the resolution around the saddle point.
		}
	    }

	    var path_thr -type REAL { 
		default { 0.05D0 eV / Angstrom }
		info {
		    The simulation stops when the error ( the norm of the force
	            orthogonal to the path in eV/A ) is less than path_thr.
		}
	    }

	    var use_masses -type LOGICAL { 
		default { .FALSE. }
		info {
		    If. TRUE. the optimisation of the path is performed using
		    mass-weighted coordinates. Useful together with quick-min
                    optimization scheme, if some bonds are much stiffer than
                    others. By assigning a larger (fictitious) mass to atoms
                    with stiff bonds, one may use a longer time step "ds"
		}
	    }

	    var use_freezing -type LOGICAL { 
		default { .FALSE. }
		info {
		    If. TRUE. the images are optimised according to their error:
		    only those images with an error larger than half of the largest
		    are optimised. The other images are kept frozen.
		}
	    }
	}


    #
    # CLIMBING_IMAGES
    #

    card CLIMBING_IMAGES {
	label { 
    	    Optional card, needed only if CI_scheme = 'manual', ignored otherwise ! 
    	}

    	syntax {
    	    list climbing_images_list -type INTEGER {
    		format { index1, index2, ... indexN }
    		info {		
    		    index1, index2, ..., indexN are indices of the images to which the 
    		    Climbing-Image procedure apply. If more than one image is specified 
    		    they must be separated by a comma.
    		}
    	    }
    	}
    }
}
NEB/tools/0000755000700200004540000000000012053440276011624 5ustar  marsamoscmNEB/tools/path_interpolation.sh0000755000700200004540000001545312053145633016075 0ustar  marsamoscm#!/bin/bash --noprofile
#
################################################################################
##                    Copyright (C) 2004 Carlo Sbraccia.                      ##
##                 This file is distributed under the terms                   ##
##                 of the GNU General Public License.                         ##
##                 See http://www.gnu.org/copyleft/gpl.txt .                  ##
##                                                                            ##
##    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,         ##
##    EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF      ##
##    MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND                   ##
##    NONINFRINGEMENT.  IN NO EVENT SHALL CARLO SBRACCIA BE LIABLE FOR ANY    ##
##    CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,    ##
##    TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE       ##
##    SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.                  ##
################################################################################
# make sure there is no locale setting creating unneeded differences.
LC_ALL=C
export LC_ALL
#
################################################################################
##                Set these variables according to your needs                 ##
################################################################################
#
# ... root directory of the PWscf package
#
ROOT_DIR=""
#
# ... old and new restart file name 
# ... ( usually old_prefix.neb and new_prefix.neb )
#
old_restart_file=""
new_restart_file=""
#
# ... number of images of the old and of the new path
#
old_num_of_images=
new_num_of_images=
#
# ... interpolation is performed between the first_image and the last_image
# ... of the old path
#
first_image=
last_image=  
#
# ... the number of atoms
#
nat=
#
# ... lattice parameter ( celldm(1) in the pw input file )
#
alat=1.D0
#
# ... interpolation is possible only in the ibrav=0 case
# ... this card is the same used in the pw input file
#
cat > CELL_PARAMETERS << EOF
CELL_PARAMETERS
   0.00000  0.00000  0.00000
   0.00000  0.00000  0.00000
   0.00000  0.00000  0.00000
EOF
#
# ... optional informations:
# ... needed to gereate visualization files ( xyz and axsf formats ) 
#
# ... put a symbol for each atomic specie that compose the system
#
list_of_atoms=""
#
# ... number of atoms of each specie 
# ... (the sum of all N[i] must be equal to nat)
#
N[1]=
#
################################################################################
################################################################################
######             DO NOT MODIFY THE SCRIPT UNDER THESE LINES             ######
################################################################################
################################################################################
#
GAWK=$( which gawk )
#
################################################################################
##                     lattice vectors for gawk scripts                       ##
################################################################################
a11=$( cat CELL_PARAMETERS | $GAWK '{ if (NR==2) {printf "%12.8f", $1} }' )
a12=$( cat CELL_PARAMETERS | $GAWK '{ if (NR==2) {printf "%12.8f", $2} }' )
a13=$( cat CELL_PARAMETERS | $GAWK '{ if (NR==2) {printf "%12.8f", $3} }' )
a21=$( cat CELL_PARAMETERS | $GAWK '{ if (NR==3) {printf "%12.8f", $1} }' )
a22=$( cat CELL_PARAMETERS | $GAWK '{ if (NR==3) {printf "%12.8f", $2} }' )
a23=$( cat CELL_PARAMETERS | $GAWK '{ if (NR==3) {printf "%12.8f", $3} }' )
a31=$( cat CELL_PARAMETERS | $GAWK '{ if (NR==4) {printf "%12.8f", $1} }' )
a32=$( cat CELL_PARAMETERS | $GAWK '{ if (NR==4) {printf "%12.8f", $2} }' )
a33=$( cat CELL_PARAMETERS | $GAWK '{ if (NR==4) {printf "%12.8f", $3} }' )
#
################################################################################
##            the input file for the iterpolator code is generated            ##
################################################################################
#
if [ ! -f ${old_restart_file} ]; then
  echo "Error: file ${old_restart_file} not fount"; exit
fi
#
cat > input << EOF
${nat}
${old_num_of_images}
${new_num_of_images}
${first_image}
${last_image}
${old_restart_file}
${new_restart_file}
${alat}
EOF
#
cat CELL_PARAMETERS | $GAWK '{ if ( NR == 1 ) { print }; if ( NR > 1 ) \
{ printf "  %12.8f  %12.8f  %12.8f\n", $1, $2, $3} }' >> input
#
#
$ROOT_DIR/bin/path_int.x < input
#
if [[ "${list_of_atoms}" != "" ]]; then
  #
  ##############################################################################
  ##      dynamical generation of the "from_restart_to_axfs.gawk" script      ##
  ##############################################################################
  file="from_restart_to_axsf.gawk"
cat > ${file} << EOF
BEGIN{ 
  a_0  = 0.529177 ; count = -10000;
  printf " ANIMSTEPS %3i \n", ${new_num_of_images} ;
  printf " CRYSTAL       \n" ;
  printf " PRIMVEC       \n" ;
  printf "  %16.10f  %16.10f  %16.10f \n", ${a11}*a_0, ${a12}*a_0, ${a13}*a_0;
  printf "  %16.10f  %16.10f  %16.10f \n", ${a21}*a_0, ${a22}*a_0, ${a23}*a_0;
  printf "  %16.10f  %16.10f  %16.10f \n", ${a31}*a_0, ${a32}*a_0, ${a33}*a_0;
}
{
if ( \$0 == "RESTART INFORMATIONS" ) { next; next; next }
if ( \$0 == "ENERGY, POSITIONS AND GRADIENTS" ) { next }
if ( \$0 == "VELOCITIES" ) { exit }
if ( \$1 == "Image:" ) {
  count = -1 ;
  printf " PRIMCOORD %3i \n", \$2 ;
  printf "%4i  1 \n", ${nat} ;
  }
else {
    count++;
EOF
  #
  ref1=0
  ref2=0
  #
  index=0
  #
  for atom in ${list_of_atoms}; do
    #
    index=$(( ${index} + 1 ))
    #
    ref1=$(( ${ref2} + 1 ))
    ref2=$(( ${ref2} + ${N[${index}]} ))
    #
    echo "  if ( count >= ${ref1} && count <= ${ref2} ) { " >> ${file}
    echo "    printf \"${atom}  \";                       " >> ${file}
    echo "    printf \" %16.10f   \", \$1 * a_0 ;         " >> ${file}
    echo "    printf \" %16.10f   \", \$2 * a_0 ;         " >> ${file}
    echo "    printf \" %16.10f   \", \$3 * a_0 ;         " >> ${file}
    echo "    printf \" %16.10f   \", \$4 / a_0 ;         " >> ${file}
    echo "    printf \" %16.10f   \", \$5 / a_0 ;         " >> ${file}
    echo "    printf \" %16.10f   \", \$6 / a_0 ;         " >> ${file}  
    echo "    printf \" \\n\";                            " >> ${file}
    echo "    }                                           " >> ${file}
    #
  done
  #
  echo "  }                                               " >> ${file}
  echo "}                                                 " >> ${file}
  #
  ##############################################################################
  #
  $GAWK -f from_restart_to_axsf.gawk ${new_restart_file} > \
  ${new_restart_file}.axsf
  #
  rm -f from_restart_to_axsf.gawk
  #
fi
#
echo "done"
#
rm -f input 
rm -f CELL_PARAMETERS
NEB/tools/path_merge.sh0000755000700200004540000001031712053145633014277 0ustar  marsamoscm#!/bin/bash
################################################################################
##                    Copyright (C) 2007 Guido Fratesi.                       ##
##                 This file is distributed under the terms                   ##
##                 of the GNU General Public License.                         ##
##                 See http://www.gnu.org/copyleft/gpl.txt .                  ##
##                                                                            ##
##    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,         ##
##    EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF      ##
##    MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND                   ##
##    NONINFRINGEMENT.  IN NO EVENT SHALL GUIDO FRATESI BE LIABLE FOR ANY     ##
##    CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,    ##
##    TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE       ##
##    SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.                  ##
################################################################################
#                                                                              #
# Suitable for PWSCF v. 4.0, might require revisions for future releases.      #
# Execute with no arguments for help.                                          #
#                                                                              #
################################################################################

function showhelp () {
cat < /dev/stderr

  USAGE:  path_merge.bash  file0.path n0 m0  file1.path n1 m1

    merges the two path files file0.path and file1.path by taking the
    images n0 to m0 from file0.path and images n1 to m1 from file file1.path.
    Merged file is written to standard output.

EOF

if [ "$err" ]; then cat << EOF > /dev/stderr

* ERROR:  $err

EOF
fi
exit
}

awk=`which awk`

#
# ... Parse and check input parameters
#
inpf[0]=$1   # first path file (file0.path)
imlw[0]=$2   # from this image index (n0)
imup[0]=$3   # to this image index (m0)
inpf[1]=$4   # second path file (file1.path)
imlw[1]=$5   # from this image index (n1)
imup[1]=$6   # to this image index (m1)
#
if (($#==0)); then err=""; showhelp; fi
if (($#<6)); then err="Too few arguments!"; showhelp; fi
if (($#>6)); then err="Too many arguments!"; showhelp; fi
for i in 0 1; do
    if [ ! -f ${inpf[$i]} ]; then
	err="File n.$i \"${inpf[$i]}\" not found!"
	showhelp
    fi
    #
    # ... Extract number of atoms
    #
    nat[$i]=`$awk '
      ($1=="Image:")&&($2==1) {n=NR};
      ($1=="Image:")&&($2==2) {printf NR-n-2; exit};
    ' ${inpf[$i]}`
    #
    # ... Read number of images
    #
    nim[$i]=`$awk '/NUMBER OF IMAGES/ {getline; printf $1; exit}' ${inpf[$i]}`
    #
    if  ((${imlw[$i]}<1)) || ((${imlw[$i]}>${nim[$i]})) ||
	((${imup[$i]}<1)) || ((${imup[$i]}>${nim[$i]})) ||
	((${imup[$i]}<${imlw[$i]})) ; then
	err="Check the images requested from file n.$((i+1))"
	showhelp
    fi
    #
done
#
if ((${nat[0]}!=${nat[1]})); then
    err="The number of atoms in the two path files is not the same!"
    showhelp
fi


#
# ... Write the header
#
cat <=nfix+1)&&(NR<=nfix+nat) {fix[NR-nfix]=sprintf("%3i%3i%3i",$7,$8,$9)};
      #
      # ... Write images in the range requested
      #
      ($1=="Image:")&&($2>=imlw)&&($2<=imup) { n=NR+1;
                                               printf("Image:%5i\n",iim); }
      (NR==n)
      (NR>=n+1)&&(NR<=n+nat) { for(i=1;i<=6;i++) printf("%20.12f",$i);
                               if(iim==1) printf("%9s",fix[NR-n]);
                               printf("\n"); };
      (NR==n+nat)            { iim++; };
    ' ${inpf[$i]}
    #
    iim=$(($iim+${imup[$i]}-${imlw[$i]}+1))
    #
done