pax_global_header00006660000000000000000000000064136062054210014511gustar00rootroot0000000000000052 comment=c3a1f4ae1dca06a9891f6864f02528ea9727c38d packmol-20.010/000077500000000000000000000000001360620542100132215ustar00rootroot00000000000000packmol-20.010/.gitignore000066400000000000000000000000371360620542100152110ustar00rootroot00000000000000build/ *.mod *.o *.swp packmol packmol-20.010/AUTHORS000066400000000000000000000007271360620542100142770ustar00rootroot00000000000000L. Martinez, R. Andrade, E. G. Birgin, J. M. Martinez. Packmol: A package for building initial configurations for molecular dynamics simulations. Journal of Computational Chemistry, 30(13):2157-2164, 2009. J. M. Martinez and L. Martinez. Packing optimization for automated generation of complex system's initial configurations for molecular dynamics and docking. Journal of Computational Chemistry, 24(7):819-825, 2003. Home-Page: http://m3g.iqm.unicamp.br/packmol packmol-20.010/CMakeLists.txt000066400000000000000000000021361360620542100157630ustar00rootroot00000000000000cmake_minimum_required(VERSION 2.6) project(packmol Fortran) if(NOT CMAKE_BUILD_TYPE) set(CMAKE_BUILD_TYPE Release) endif(NOT CMAKE_BUILD_TYPE) if(CMAKE_Fortran_COMPILER_ID MATCHES GNU) add_compile_options( -Wall "$<$:-Werror>" ) endif() # Build the executable add_executable(packmol cenmass.f90 gencan.f pgencan.f90 initial.f90 title.f90 setsizes.f90 getinp.f90 strlength.f90 output.f90 checkpoint.f90 writesuccess.f90 fparc.f90 gparc.f90 gwalls.f90 comprest.f90 comparegrad.f90 packmol.f90 polartocart.f90 resetboxes.f90 tobar.f90 setijk.f90 setibox.f90 restmol.f90 swaptype.f90 swaptypemod.f90 ahestetic.f90 heuristics.f90 flashsort.f90 jacobi.f90 random.f90 sizes.f90 usegencan.f90 compute_data.f90 flashmod.f90 computef.f90 computeg.f90 input.f90 ) # Installation directive install(TARGETS packmol DESTINATION bin) packmol-20.010/LICENSE000066400000000000000000000021361360620542100142300ustar00rootroot00000000000000MIT License Copyright (c) 2009-2018 Leandro Martínez, José Mario Martínez, Ernesto Birgin Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. 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 THE AUTHORS OR COPYRIGHT HOLDERS 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. packmol-20.010/Makefile000066400000000000000000000135621360620542100146700ustar00rootroot00000000000000# # Makefile for Packmol: Read the comments if you have some # problem while compiling. # # You may use the ./configure script to search automatically for # some fortran compiler. # # This make file will try to compile packmol with the default # fortran compiler, defined by the FC directive. For doing this, # just type # # make # # If you want to compile with some specific fortran compiler, you must # change the line below to the path of your fortran compiler. # FORTRAN=/usr/bin/gfortran # # Change the flags of the compilation if you want: # FLAGS= -O3 --fast-math ################################################################### # # # Generally no modifications are required after this. # # # ################################################################### # # Flags for compiling development version # GENCANFLAGS := $(FLAGS) ifeq ($(MAKECMDGOALS),devel) FLAGS = -Wall -fcheck=bounds -g -fbacktrace -ffpe-trap=zero,overflow,underflow GENCANFLAGS = -fcheck=bounds -g -fbacktrace -ffpe-trap=zero,overflow,underflow endif ifeq ($(MAKECMDGOALS),perf) FLAGS = -g -pg GENCANFLAGS = -g -pg endif # # Files required # oall = cenmass.o \ gencan.o \ pgencan.o \ initial.o \ title.o \ setsizes.o \ getinp.o \ strlength.o \ output.o \ checkpoint.o \ writesuccess.o \ fparc.o \ gparc.o \ gwalls.o \ comprest.o \ comparegrad.o \ packmol.o \ polartocart.o \ resetboxes.o \ tobar.o \ setijk.o \ setibox.o \ restmol.o \ swaptype.o \ swaptypemod.o \ ahestetic.o \ heuristics.o \ flashsort.o \ jacobi.o \ random.o \ sizes.o \ usegencan.o \ compute_data.o \ flashmod.o \ computef.o \ computeg.o \ input.o # # Linking # all : $(oall) @echo " ------------------------------------------------------ " @echo " Compiling packmol with $(FORTRAN) " @echo " Flags: $(FLAGS) " @echo " ------------------------------------------------------ " @$(FORTRAN) -o packmol $(oall) $(FLAGS) @\rm -f *.mod *.o @echo " ------------------------------------------------------ " @echo " Packmol succesfully built." @echo " ------------------------------------------------------ " # # Compiling with flags for development # perf : devel devel : $(oall) @echo " ------------------------------------------------------ " @echo " Compiling packmol with $(FORTRAN) " @echo " Flags: $(FLAGS)" @echo " ------------------------------------------------------ " @$(FORTRAN) -o packmol $(oall) $(FLAGS) @echo " ------------------------------------------------------ " @echo " Packmol succesfully built. " @echo " ------------------------------------------------------ " # # Modules # modules = sizes.o compute_data.o usegencan.o input.o flashmod.o swaptypemod.o ahestetic.o sizes.o : sizes.f90 @$(FORTRAN) $(FLAGS) -c sizes.f90 compute_data.o : compute_data.f90 sizes.o @$(FORTRAN) $(FLAGS) -c compute_data.f90 input.o : input.f90 sizes.o @$(FORTRAN) $(FLAGS) -c input.f90 flashmod.o : flashmod.f90 sizes.o @$(FORTRAN) $(FLAGS) -c flashmod.f90 usegencan.o : usegencan.f90 sizes.o @$(FORTRAN) $(FLAGS) -c usegencan.f90 swaptypemod.o : swaptypemod.f90 @$(FORTRAN) $(FLAGS) -c swaptypemod.f90 ahestetic.o : ahestetic.f90 @$(FORTRAN) $(FLAGS) -c ahestetic.f90 # # Code compiled only for all versions # cenmass.o : cenmass.f90 $(modules) @$(FORTRAN) $(FLAGS) -c cenmass.f90 initial.o : initial.f90 $(modules) @$(FORTRAN) $(FLAGS) -c initial.f90 title.o : title.f90 $(modules) @$(FORTRAN) $(FLAGS) -c title.f90 setsizes.o : setsizes.f90 $(modules) @$(FORTRAN) $(FLAGS) -c setsizes.f90 getinp.o : getinp.f90 $(modules) @$(FORTRAN) $(FLAGS) -c getinp.f90 strlength.o : strlength.f90 @$(FORTRAN) $(FLAGS) -c strlength.f90 output.o : output.f90 $(modules) @$(FORTRAN) $(FLAGS) -c output.f90 checkpoint.o : checkpoint.f90 $(modules) @$(FORTRAN) $(FLAGS) -c checkpoint.f90 writesuccess.o : writesuccess.f90 $(modules) @$(FORTRAN) $(FLAGS) -c writesuccess.f90 fparc.o : fparc.f90 $(modules) @$(FORTRAN) $(FLAGS) -c fparc.f90 gparc.o : gparc.f90 $(modules) @$(FORTRAN) $(FLAGS) -c gparc.f90 gwalls.o : gwalls.f90 $(modules) @$(FORTRAN) $(FLAGS) -c gwalls.f90 comprest.o : comprest.f90 $(modules) @$(FORTRAN) $(FLAGS) -c comprest.f90 comparegrad.o : comparegrad.f90 $(modules) @$(FORTRAN) $(FLAGS) -c comparegrad.f90 packmol.o : packmol.f90 $(modules) @$(FORTRAN) $(FLAGS) -c packmol.f90 polartocart.o : polartocart.f90 $(modules) @$(FORTRAN) $(FLAGS) -c polartocart.f90 resetboxes.o : resetboxes.f90 $(modules) @$(FORTRAN) $(FLAGS) -c resetboxes.f90 tobar.o : tobar.f90 $(modules) @$(FORTRAN) $(FLAGS) -c tobar.f90 setijk.o : setijk.f90 $(modules) @$(FORTRAN) $(FLAGS) -c setijk.f90 setibox.o : setibox.f90 $(modules) @$(FORTRAN) $(FLAGS) -c setibox.f90 restmol.o : restmol.f90 $(modules) @$(FORTRAN) $(FLAGS) -c restmol.f90 swaptype.o : swaptype.f90 $(modules) @$(FORTRAN) $(FLAGS) -c swaptype.f90 heuristics.o : heuristics.f90 $(modules) @$(FORTRAN) $(FLAGS) -c heuristics.f90 flashsort.o : flashsort.f90 $(modules) @$(FORTRAN) $(FLAGS) -c flashsort.f90 jacobi.o : jacobi.f90 @$(FORTRAN) $(FLAGS) -c jacobi.f90 pgencan.o : pgencan.f90 $(modules) @$(FORTRAN) $(FLAGS) -c pgencan.f90 gencan.o : gencan.f @$(FORTRAN) $(GENCANFLAGS) -c gencan.f random.o : random.f90 @$(FORTRAN) $(FLAGS) -c random.f90 computef.o : computef.f90 $(modules) @$(FORTRAN) $(FLAGS) -c computef.f90 computeg.o : computeg.f90 $(modules) @$(FORTRAN) $(FLAGS) -c computeg.f90 # # Clean build files # clean: @\rm -f ./*.o ./*.mod # # Remove all build and executable files to upload to git # cleanall: @\rm -f ./packmol ./*.o ./*.mod packmol-20.010/README.md000066400000000000000000000032671360620542100145100ustar00rootroot00000000000000Packmol ======= Packmol - Creates Initial Configurations for Molecular Dynamics Simulations This page contains the version history of Packmol. You can download packmol from this page, but give preference to the official Packmol page, for which the link is provided here. What is Packmol --------------- Packmol creates an initial point for molecular dynamics simulations by packing molecules in defined regions of space. The packing guarantees that short range repulsive interactions do not disrupt the simulations. The great variety of types of spatial constraints that can be attributed to the molecules, or atoms within the molecules, makes it easy to create ordered systems, such as lamellar, spherical or tubular lipid layers. The user must provide only the coordinates of one molecule of each type, the number of molecules of each type and the spatial constraints that each type of molecule must satisfy. The package is compatible with input files of PDB, TINKER, XYZ and MOLDY formats. See http://m3g.iqm.unicamp.br/packmol for more information. References ---------- Please always cite one of the following references in publications for which Packmol was useful: L Martinez, R Andrade, EG Birgin, JM Martinez, Packmol: A package for building initial configurations for molecular dynamics simulations. Journal of Computational Chemistry, 30, 2157-2164, 2009. (http://www3.interscience.wiley.com/journal/122210103/abstract) JM Martinez, L Martinez, Packing optimization for the automated generation of complex system's initial configurations for molecular dynamics and docking. Journal of Computational Chemistry, 24, 819-825, 2003. (http://www3.interscience.wiley.com/journal/104086246/abstract) packmol-20.010/ahestetic.f90000066400000000000000000000014301360620542100155100ustar00rootroot00000000000000! ! Written by Leandro Martínez, 2009-2011. ! Copyright (c) 2009-2018, Leandro Martínez, Jose Mario Martinez, ! Ernesto G. Birgin. ! ! Module that contains some ahestetic output definitions ! module ahestetic character(len=13), parameter :: dash1_line = "( 80('-') )",& dash2_line = "(/,80('-') )",& dash3_line = "(/,80('-'),/)" character(len=13), parameter :: hash1_line = "( 80('#') )",& hash2_line = "(/,80('#') )",& hash3_line = "(/,80('#'),/)" character(len=31), parameter :: prog1_line = "(' Packing:|0 ',tr60,'100%|' )",& prog2_line = "(' Moving:|0 ',tr60,'100%|' )" end module ahestetic packmol-20.010/cenmass.f90000066400000000000000000000045511360620542100151770ustar00rootroot00000000000000! ! Written by Leandro Martínez, 2009-2011. ! Copyright (c) 2009-2018, Leandro Martínez, Jose Mario Martinez, ! Ernesto G. Birgin. ! ! Subroutine cenmass ! ! Computes the center of mass of free molecules and ! for fixed molecules, if required. ! subroutine cenmass() use sizes use compute_data, only : ntype, coor, idfirst, natoms use input, only : keyword, amass, nlines, linestrut implicit none integer :: k, iline integer :: itype, iatom, idatom double precision, allocatable :: cm(:,:), totm(:) logical, allocatable :: domass(:) ! Allocate local vectors allocate(cm(ntype,3),totm(ntype),domass(ntype)) ! Setting the molecules for which the center of mass is computed do itype = 1, ntype domass(itype) = .true. end do do iline = 1, nlines if(keyword(iline,1).eq.'fixed') then do itype = 1, ntype if(iline.gt.linestrut(itype,1).and. & iline.lt.linestrut(itype,2)) then domass(itype) = .false. end if end do end if end do do iline = 1, nlines if(keyword(iline,1).eq.'centerofmass'.or. & keyword(iline,1).eq.'center') then do itype = 1, ntype if(iline.gt.linestrut(itype,1).and. & iline.lt.linestrut(itype,2)) then domass(itype) = .true. end if end do end if end do ! Computing the center of mass do itype = 1, ntype do k = 1, 3 cm(itype, k) = 0.d0 end do end do do itype = 1, ntype totm(itype) = 0.d0 idatom = idfirst(itype) - 1 do iatom = 1, natoms(itype) idatom = idatom + 1 totm(itype) = totm(itype) + amass(idatom) end do end do do itype = 1, ntype idatom = idfirst(itype) - 1 do iatom = 1, natoms(itype) idatom = idatom + 1 do k = 1, 3 cm(itype, k) = cm(itype, k) + coor(idatom, k)*amass(idatom) end do end do do k = 1, 3 cm(itype, k) = cm(itype, k) / totm(itype) end do end do ! Putting molecules in their center of mass do itype = 1, ntype if(domass(itype)) then idatom = idfirst(itype) - 1 do iatom = 1, natoms(itype) idatom = idatom + 1 do k = 1, 3 coor(idatom, k) = coor(idatom, k) - cm(itype, k) end do end do end if end do deallocate(cm,totm,domass) return end subroutine cenmass packmol-20.010/checkpoint.f90000066400000000000000000000067771360620542100157110ustar00rootroot00000000000000! ! Written by Leandro Martínez, 2009-2011. ! Copyright (c) 2009-2018, Leandro Martínez, Jose Mario Martinez, ! Ernesto G. Birgin. ! ! ! Subroutine that writes the last point obtained when ! a solution was not found ! subroutine checkpoint(n,x) use sizes use compute_data use input use usegencan use ahestetic implicit none integer :: i, strlength integer :: n double precision :: x(n) double precision :: fx logical :: movebadprint ! All molecules are important do i = 1, ntfix comptype(i) = .true. end do ! Call the subroutine that computes de function value call computef(n,x,fx) write(*,dash3_line) write(*,"(& &' Packmol was not able to find a solution to your',/,& &' packing problem with the desired distance tolerance.',/,/,& &' First of all, be sure if the molecules fit in the',/,& &' regions specified and if the constraints were set',/,& &' correctly. ',/,/,& &' Secondly, try simply running it again with a different ',/,& &' seed for the random number generator of the initial ',/,& &' point. This is done by adding the keyword seed to the',/,& &' input file, as in: ',/,/,& &' seed 192911 ',/,/,& &' The best configuration found has a function value of',/,& &' f = ', e14.7,/,/,& &' IMPORTANT: ',/,& &' If the number of molecules and the restraints are',/,& &' correct, it is still very likely that the current point',/,& &' fits your needs if your purpose is to run a MD',/,& &' simulation.',/,& &' Therefore, we recommend to minimize the energy of the',/,& &' solution found, equilibrate it and run with it as well.',/& &)") fx write(*,dash3_line) call output(n,x) write(*,*) ' The solution with the best function value was ' write(*,*) ' written to the output file: ', xyzout(1:strlength(xyzout)) if ( crd ) write(*,*) ' ... and to CRD file: ', trim(adjustl(crdfile)) write(*,dash1_line) write(*,*) ' Forcing the solution to fit the constraints...' ! CALL GENCAN init1 = .true. do i = 1, nloop iprint1 = 0 iprint2 = 0 call pgencan(n,x,fx) movebadprint = .false. call movebad(n,x,fx,movebadprint) end do init1 = .false. write(*,*) write(*,dash1_line) xyzout = xyzout(1:strlength(xyzout))//'_FORCED' call output(n,x) write(*,*) ' The forced point was writen to the ' write(*,*) ' output file: ', xyzout(1:strlength(xyzout)+7) if ( crd ) write(*,*) ' ... and to CRD file: ', trim(adjustl(crdfile)) write(*,*) write(*,*) ' If you want that the packing procedure continues' write(*,*) ' for a longer time, add the following keyword ' write(*,*) ' to the input file: ' write(*,*) write(*,*) ' nloop [integer] (ex: nloop 200) ' write(*,*) write(*,*) ' The default nloop value is 50 for each molecule.' write(*,*) write(*,hash1_line) write(*,*) ' ENDED WITHOUT PERFECT PACKING: ' write(*,*) ' The output file:' write(*,*) write(*,*) ' ',xyzout(1:strlength(xyzout)-7) if ( crd ) write(*,*) ' (... and to CRD file: ', trim(adjustl(crdfile)), ')' write(*,*) write(*,*) ' contains the best solution found. ' write(*,*) write(*,*) ' Very likely, if the input data was correct, ' write(*,*) ' it is a reasonable starting configuration.' write(*,*) ' Check commentaries above for more details. ' write(*,hash1_line) return end subroutine checkpoint packmol-20.010/comparegrad.f90000066400000000000000000000050701360620542100160270ustar00rootroot00000000000000! ! Written by Leandro Martínez, 2009-2011. ! Copyright (c) 2009-2018, Leandro Martínez, Jose Mario Martinez, ! Ernesto G. Birgin. ! ! ! Subroutine that performs finite difference and analytical gradient ! comparision. Used only for test purpouses ! subroutine comparegrad(n,x) use sizes implicit none integer :: n, i, iworst double precision :: x(n), fx, step, gcomp, gbest, eworst, & error, steperror, stepbest double precision, allocatable :: g(:) real :: time0, tarray(2), etime ! Allocate local array allocate(g(nn)) write(*,*) write(*,*) ' Comparing analytical and finite-difference ' write(*,*) ' gradients... may take a while. ' write(*,*) write(*,*) ' Five first center of masses and angles of tested point: ' do i = 1, 15, 3 write(*,"( i4,6(tr2,f8.3) )") (i+2)/3, x(i), x(i+1), x(i+2), x(n/2+i),& x(n/2+i+1),x(n/2+i+2) end do write(*,*) write(*,*) ' Computing gradient ... ' call computef(n,x,fx) write(*,*) ' Function value on test point: ', fx open(98, file = 'chkgrad.log',status='unknown') write(98, *)'Function Value = ', fx call computeg(n,x,g) write(98,"( t2,'Component',t16,'Analytical',t33,'Discrete', & &t51,'Error',t62,'Best step' )") time0 = etime(tarray) eworst = 0.d0 do i = 1, n if(etime(tarray)-time0.gt.10.) then time0 = etime(tarray) write(*,*) ' Computing the ',i,'th of ',n,' components. Worst error: ', eworst end if error = 1.d20 step = 1.d-2 do while(error.gt.1.d-6.and.step.ge.1.d-20) call discret(i,n,x,gcomp,step) if(dmin1(abs(g(i)),abs(gcomp)).gt.1.d-10) then steperror = abs( ( gcomp - g(i) ) / g(i) ) else steperror = abs( gcomp - g(i) ) end if if( steperror .lt. error ) then error = steperror gbest = gcomp stepbest = step end if step = step / 10.d0 end do write(98,"(i10,5(tr2,d13.7))") i, g(i), gbest, error, stepbest if(error.gt.eworst) then iworst = i eworst = error end if end do write(98,*) 'Maximum difference = ', iworst,' Error= ', eworst write(*,*) ' Done. ' stop end subroutine comparegrad subroutine discret(icomp,n,x,gcomp,step) implicit none integer :: n, icomp double precision :: save, step, x(n), fplus, fminus, gcomp save = x(icomp) x(icomp) = save + step call computef(n,x,fplus) x(icomp) = save - step call computef(n,x,fminus) gcomp = (fplus - fminus) / (2.d0 * step) x(icomp) = save return end subroutine discret packmol-20.010/compile_cmake.sh000066400000000000000000000012061360620542100163440ustar00rootroot00000000000000#!/bin/bash # Fortran compiler to use export FC=gfortran # Compiler flags to use export FFLAGS="-g -O2 -Wall" #export FFLAGS="-g -O2 -Wall -fbounds-check" #export FFLAGS="-g -O0 -Wall -fbounds-check" # Installation directory export target=$(pwd) # this installs packmol under bin/ in the present directory # Number of parallel processes in build export npar=4 # No changes should be necessary hereafter. if [[ ! -d objdir ]]; then mkdir objdir fi cd objdir cmake .. \ -DCMAKE_INSTALL_PREFIX=${target} \ -DCMAKE_BUILD_TYPE=Release \ -DCMAKE_Fortran_FLAGS_RELEASE:STRING="-DNDEBUG" make -j ${npar} install VERBOSE=1 cd .. packmol-20.010/comprest.f90000066400000000000000000000143511360620542100154010ustar00rootroot00000000000000! ! Written by Leandro Martínez, 2009-2011. ! Copyright (c) 2009-2018, Leandro Martínez, Jose Mario Martinez, ! Ernesto G. Birgin. ! ! ! Subroutine comprest: Compute the function value relative to ! to the restrictions for one atom ! subroutine comprest(icart,f) use sizes use compute_data, only : xcart, restpars, scale, scale2, nratom, ityperest, iratom implicit none integer :: iratcount, irest, icart double precision :: xmin, ymin, zmin, clength, a1, a2, a3, a4, w, b1, b2, b3, d, a5, a6 double precision :: f double precision :: xmax, ymax, zmax double precision :: v1, v2, v3 double precision :: vnorm f = 0.d0 do iratcount = 1, nratom(icart) irest = iratom(icart,iratcount) if(ityperest(irest).eq.2) then clength = restpars(irest,4) xmin = restpars(irest,1) ymin = restpars(irest,2) zmin = restpars(irest,3) xmax = restpars(irest,1) + clength ymax = restpars(irest,2) + clength zmax = restpars(irest,3) + clength a1 = dmin1(xcart(icart,1) - xmin, 0.d0) a2 = dmin1(xcart(icart,2) - ymin, 0.d0) a3 = dmin1(xcart(icart,3) - zmin, 0.d0) f = f + scale*(a1 * a1 + a2 * a2 + a3 * a3) a1 = dmax1(xcart(icart,1) - xmax, 0.d0) a2 = dmax1(xcart(icart,2) - ymax, 0.d0) a3 = dmax1(xcart(icart,3) - zmax, 0.d0) f = f + scale*(a1 * a1 + a2 * a2 + a3 * a3) else if(ityperest(irest).eq.3) then xmin = restpars(irest,1) ymin = restpars(irest,2) zmin = restpars(irest,3) xmax = restpars(irest,4) ymax = restpars(irest,5) zmax = restpars(irest,6) a1 = dmin1(xcart(icart,1) - xmin, 0.d0) a2 = dmin1(xcart(icart,2) - ymin, 0.d0) a3 = dmin1(xcart(icart,3) - zmin, 0.d0) f = f + scale*(a1 * a1 + a2 * a2 + a3 * a3) a1 = dmax1(xcart(icart,1) - xmax, 0.d0) a2 = dmax1(xcart(icart,2) - ymax, 0.d0) a3 = dmax1(xcart(icart,3) - zmax, 0.d0) f = f + scale*(a1 * a1 + a2 * a2 + a3 * a3) else if(ityperest(irest).eq.4) then w = (xcart(icart,1)-restpars(irest,1))**2 + & (xcart(icart,2)-restpars(irest,2))**2 + & (xcart(icart,3)-restpars(irest,3))**2 - & restpars(irest,4)**2 a1 = dmax1(w,0.d0) f = f + scale2*a1*a1 else if(ityperest(irest).eq.5) then a1 = (xcart(icart,1)-restpars(irest,1))**2 / restpars(irest,4)**2 a2 = (xcart(icart,2)-restpars(irest,2))**2 / restpars(irest,5)**2 a3 = (xcart(icart,3)-restpars(irest,3))**2 / restpars(irest,6)**2 a4 = restpars(irest,7)**2 w = a1 + a2 + a3 - a4 a1 = dmax1(w,0.d0) f = f + scale2*a1*a1 else if(ityperest(irest).eq.6) then xmin = restpars(irest,1) ymin = restpars(irest,2) zmin = restpars(irest,3) xmax = restpars(irest,1) + restpars(irest,4) ymax = restpars(irest,2) + restpars(irest,4) zmax = restpars(irest,3) + restpars(irest,4) a1 = dmax1(xcart(icart,1) - xmin,0.d0) a2 = dmax1(xcart(icart,2) - ymin,0.d0) a3 = dmax1(xcart(icart,3) - zmin,0.d0) a4 = dmax1(xmax - xcart(icart,1),0.d0) a5 = dmax1(ymax - xcart(icart,2),0.d0) a6 = dmax1(zmax - xcart(icart,3),0.d0) f = f + a1*a2*a3*a4*a5*a6 else if(ityperest(irest).eq.7) then xmin = restpars(irest,1) ymin = restpars(irest,2) zmin = restpars(irest,3) xmax = restpars(irest,4) ymax = restpars(irest,5) zmax = restpars(irest,6) a1 = dmax1(xcart(icart,1) - xmin,0.d0) a2 = dmax1(xcart(icart,2) - ymin,0.d0) a3 = dmax1(xcart(icart,3) - zmin,0.d0) a4 = dmax1(xmax - xcart(icart,1),0.d0) a5 = dmax1(ymax - xcart(icart,2),0.d0) a6 = dmax1(zmax - xcart(icart,3),0.d0) f = f + a1*a2*a3*a4*a5*a6 else if(ityperest(irest).eq.8) then w = (xcart(icart,1)-restpars(irest,1))**2 + & (xcart(icart,2)-restpars(irest,2))**2 + & (xcart(icart,3)-restpars(irest,3))**2 - & restpars(irest,4)**2 a1 = dmin1(w,0.d0) f = f + scale2*a1*a1 else if(ityperest(irest).eq.9) then a1 = (xcart(icart,1)-restpars(irest,1))**2 / restpars(irest,4)**2 a2 = (xcart(icart,2)-restpars(irest,2))**2 / restpars(irest,5)**2 a3 = (xcart(icart,3)-restpars(irest,3))**2 / restpars(irest,6)**2 a4 = restpars(irest,7)**2 w = a1 + a2 + a3 - a4 a1 = dmin1(w,0.d0) f = f + a1*a1 else if(ityperest(irest).eq.10) then w = restpars(irest,1)*xcart(icart,1) + & restpars(irest,2)*xcart(icart,2) + & restpars(irest,3)*xcart(icart,3) - & restpars(irest,4) a1 = dmin1(w,0.d0) f = f + scale * a1*a1 else if(ityperest(irest).eq.11) then w = restpars(irest,1)*xcart(icart,1) + & restpars(irest,2)*xcart(icart,2) + & restpars(irest,3)*xcart(icart,3) - & restpars(irest,4) a1 = dmax1(w,0.d0) f = f + scale * a1*a1 else if(ityperest(irest).eq.12) then a1 = xcart(icart,1) - restpars(irest,1) a2 = xcart(icart,2) - restpars(irest,2) a3 = xcart(icart,3) - restpars(irest,3) vnorm = sqrt(restpars(irest,4)**2 + restpars(irest,5)**2 + restpars(irest,6)**2) v1 = restpars(irest,4)/vnorm v2 = restpars(irest,5)/vnorm v3 = restpars(irest,6)/vnorm b1 = v1 * a1 b2 = v2 * a2 b3 = v3 * a3 w = b1 + b2 + b3 d = ( a1 - v1*w )**2 + ( a2 - v2*w )**2 + ( a3 - v3*w )**2 f = f + scale2 * ( & dmax1(-w , 0.d0)**2 + & dmax1(w - restpars(irest,9), 0.d0)**2 + & dmax1(d - restpars(irest,7)**2 , 0.d0 )**2 ) else if(ityperest(irest).eq.13) then a1 = xcart(icart,1) - restpars(irest,1) a2 = xcart(icart,2) - restpars(irest,2) a3 = xcart(icart,3) - restpars(irest,3) vnorm = sqrt(restpars(irest,4)**2 + restpars(irest,5)**2 + restpars(irest,6)**2) v1 = restpars(irest,4)/vnorm v2 = restpars(irest,5)/vnorm v3 = restpars(irest,6)/vnorm b1 = v1 * a1 b2 = v2 * a2 b3 = v3 * a3 w = b1 + b2 + b3 d = ( a1 - v1*w )**2 +( a2 - v2*w )**2 + ( a3 - v3*w )**2 f = f + scale2 * ( & dmin1(-w , 0.d0)**2 * & dmin1(w - restpars(irest,9), 0.d0)**2 * & dmin1(d - restpars(irest,7)**2 , 0.d0 )**2 ) end if end do return end subroutine comprest packmol-20.010/compute_data.f90000066400000000000000000000045451360620542100162160ustar00rootroot00000000000000! ! Written by Leandro Martínez, 2009-2011. ! Copyright (c) 2009-2018, Leandro Martínez, Jose Mario Martinez, ! Ernesto G. Birgin. ! module compute_data use sizes integer :: ntotmol, ntype, natfix, ntotat integer :: nboxes(3), nb2(3) integer, allocatable :: nmols(:) ! (ntype) integer, allocatable :: natoms(:) ! (ntype) integer, allocatable :: idfirst(:) ! (ntype) integer, allocatable :: nratom(:) ! (ntotat) integer, allocatable :: iratom(:,:) ! (ntotat,mrperatom) integer, allocatable :: ityperest(:) ! (maxrest) integer, allocatable :: ibmol(:) ! (ntotat) integer, allocatable :: ibtype(:) ! (ntotat) double precision :: scale, scale2 double precision :: fdist, frest double precision :: sizemin(3), sizemax(3) double precision :: boxl(3) double precision, allocatable :: xcart(:,:) ! (ntotat,3) double precision, allocatable :: coor(:,:) ! (ntotat,3) double precision, allocatable :: restpars(:,:) ! (maxrest,9) double precision, allocatable :: rot_bound(:,:,:) ! (ntype,3,2) double precision, allocatable :: radius(:), radius_ini(:), fscale(:) ! (ntotat) double precision, allocatable :: short_radius(:), short_radius_scale(:) ! ntotat double precision, allocatable :: gxcar(:,:) ! (ntotat,3) double precision, allocatable :: fdist_atom(:), frest_atom(:) ! (ntotat) double precision, allocatable :: dmax(:) ! (ntype) double precision, allocatable :: cmxmin(:), cmymin(:), cmzmin(:) ! (ntype) double precision, allocatable :: cmxmax(:), cmymax(:), cmzmax(:) ! (ntype) logical, allocatable :: constrain_rot(:,:) ! (ntype,3) logical, allocatable :: comptype(:) ! (ntype) logical, allocatable :: fixedatom(:) ! (ntotat) logical, allocatable :: use_short_radius(:) ! ntotat logical :: init1, move ! For linked lists integer, allocatable :: latomnext(:) ! (ntotat) integer, allocatable :: latomfirst(:,:,:) ! (0:nbp+1,0:nbp+1,0:nbp+1) integer, allocatable :: latomfix(:,:,:) ! (0:nbp+1,0:nbp+1,0:nbp+1) ! For movebad double precision, allocatable :: fmol(:), radiuswork(:) ! (ntotat) ! For restmol double precision, allocatable :: xmol(:) ! (nn) logical, allocatable :: compsafe(:) ! (ntype) ! For boxes with atoms linked lists integer :: lboxfirst integer, allocatable :: lboxnext(:) ! ((nbp+2)**3) logical, allocatable :: hasfree(:,:,:) ! (0:nbp+1,0:nbp+1,0:nbp+1) end module compute_data packmol-20.010/computef.f90000066400000000000000000000130301360620542100153600ustar00rootroot00000000000000! ! Written by Leandro Martínez, 2009-2011. ! Copyright (c) 2009-2018, Leandro Martínez, Jose Mario Martinez, ! Ernesto G. Birgin. ! ! Subroutine that computes the function value ! subroutine computef(n,x,f) use sizes use compute_data use input, only : fix implicit none integer :: n, i, j, k, ibox integer :: ilugan, ilubar, icart, itype, imol, iatom, idatom, & iboxx, iboxy, iboxz double precision :: v1(3), v2(3), v3(3) double precision :: x(n) double precision :: f,fparc,fplus double precision :: xtemp, ytemp, ztemp double precision :: xbar, ybar, zbar double precision :: beta, gama, teta ! Reset function value f = 0.d0 frest = 0.d0 fdist = 0.d0 ! Reset boxes if(.not.init1) call resetboxes() ! Transform baricenter and angles into cartesian coordinates ! Computes cartesian coordinates from vector x and coor ilubar = 0 ilugan = ntotmol*3 icart = 0 do itype = 1, ntype if(.not.comptype(itype)) then icart = icart + nmols(itype)*natoms(itype) else do imol = 1, nmols(itype) xbar = x(ilubar+1) ybar = x(ilubar+2) zbar = x(ilubar+3) ! Computing the rotation matrix beta = x(ilugan+1) gama = x(ilugan+2) teta = x(ilugan+3) call eulerrmat(beta,gama,teta,v1,v2,v3) ! Looping over the atoms of this molecule idatom = idfirst(itype) - 1 do iatom = 1, natoms(itype) icart = icart + 1 idatom = idatom + 1 ! Computing the cartesian coordinates for this atom call compcart(icart,xbar,ybar,zbar, & coor(idatom,1),coor(idatom,2),coor(idatom,3), & v1,v2,v3) ! Adding to f the value relative to constraints for this atom call comprest(icart,fplus) f = f + fplus frest = dmax1(frest,fplus) if(move) frest_atom(icart) = frest_atom(icart) + fplus ! Putting atoms in their boxes if(.not.init1) then xtemp = xcart(icart,1) - sizemin(1) ytemp = xcart(icart,2) - sizemin(2) ztemp = xcart(icart,3) - sizemin(3) iboxx = int(xtemp/boxl(1)) + 1 iboxy = int(ytemp/boxl(2)) + 1 iboxz = int(ztemp/boxl(3)) + 1 if(xtemp.le.0) iboxx = 1 if(ytemp.le.0) iboxy = 1 if(ztemp.le.0) iboxz = 1 if(iboxx.gt.nboxes(1)) iboxx = nboxes(1) if(iboxy.gt.nboxes(2)) iboxy = nboxes(2) if(iboxz.gt.nboxes(3)) iboxz = nboxes(3) ! Atom linked list latomnext(icart) = latomfirst(iboxx,iboxy,iboxz) latomfirst(iboxx,iboxy,iboxz) = icart ! Box with atoms linked list if ( .not. hasfree(iboxx,iboxy,iboxz) ) then hasfree(iboxx,iboxy,iboxz) = .true. call ijk_to_ibox(iboxx,iboxy,iboxz,ibox) lboxnext(ibox) = lboxfirst lboxfirst = ibox ! Add boxes with fixed atoms which are vicinal to this box, and ! are behind if ( fix ) then call add_box_behind(iboxx-1,iboxy,iboxz) call add_box_behind(iboxx,iboxy-1,iboxz) call add_box_behind(iboxx,iboxy,iboxz-1) call add_box_behind(iboxx,iboxy-1,iboxz+1) call add_box_behind(iboxx,iboxy-1,iboxz-1) call add_box_behind(iboxx-1,iboxy+1,iboxz) call add_box_behind(iboxx-1,iboxy,iboxz+1) call add_box_behind(iboxx-1,iboxy-1,iboxz) call add_box_behind(iboxx-1,iboxy,iboxz-1) call add_box_behind(iboxx-1,iboxy+1,iboxz+1) call add_box_behind(iboxx-1,iboxy+1,iboxz-1) call add_box_behind(iboxx-1,iboxy-1,iboxz+1) call add_box_behind(iboxx-1,iboxy-1,iboxz-1) end if end if ibtype(icart) = itype ibmol(icart) = imol end if end do ilugan = ilugan + 3 ilubar = ilubar + 3 end do end if end do if(init1) return ! Minimum distance function evaluation ibox = lboxfirst do while( ibox > 0 ) call ibox_to_ijk(ibox,i,j,k) icart = latomfirst(i,j,k) do while( icart > 0 ) if(comptype(ibtype(icart))) then ! Interactions inside box f = f + fparc(icart,latomnext(icart)) ! Interactions of boxes that share faces f = f + fparc(icart,latomfirst(i+1,j,k)) f = f + fparc(icart,latomfirst(i,j+1,k)) f = f + fparc(icart,latomfirst(i,j,k+1)) ! Interactions of boxes that share axes f = f + fparc(icart,latomfirst(i+1,j+1,k)) f = f + fparc(icart,latomfirst(i+1,j,k+1)) f = f + fparc(icart,latomfirst(i+1,j-1,k)) f = f + fparc(icart,latomfirst(i+1,j,k-1)) f = f + fparc(icart,latomfirst(i,j+1,k+1)) f = f + fparc(icart,latomfirst(i,j+1,k-1)) ! Interactions of boxes that share vertices f = f + fparc(icart,latomfirst(i+1,j+1,k+1)) f = f + fparc(icart,latomfirst(i+1,j+1,k-1)) f = f + fparc(icart,latomfirst(i+1,j-1,k+1)) f = f + fparc(icart,latomfirst(i+1,j-1,k-1)) end if icart = latomnext(icart) end do ibox = lboxnext(ibox) end do return end subroutine computef subroutine add_box_behind(i,j,k) use sizes use compute_data implicit none integer :: ibox, i, j, k if ( .not. hasfree(i,j,k) .and. latomfix(i,j,k) /= 0 ) then hasfree(i,j,k) = .true. call ijk_to_ibox(i,j,k,ibox) lboxnext(ibox) = lboxfirst lboxfirst = ibox end if end subroutine add_box_behind packmol-20.010/computeg.f90000066400000000000000000000175231360620542100153740ustar00rootroot00000000000000! ! Written by Leandro Martínez, 2009-2011. ! Copyright (c) 2009-2018, Leandro Martínez, Jose Mario Martinez, ! Ernesto G. Birgin. ! ! Subroutine that computes the analytical derivatives ! subroutine computeg(n,x,g) use sizes use compute_data use input, only : fix implicit none integer :: n integer :: idatom, iatom, irest integer :: i, j, k, ilubar, ilugan, icart, itype, imol integer :: ibox, iboxx, iboxy, iboxz integer :: k1, k2 integer :: iratcount double precision :: x(n), g(n) double precision :: dv1beta(3), dv1gama(3), dv1teta(3),& dv2beta(3), dv2gama(3), dv2teta(3),& dv3beta(3), dv3gama(3), dv3teta(3) double precision :: v1(3), v2(3), v3(3) double precision :: xbar, ybar, zbar double precision :: xtemp, ytemp, ztemp double precision :: beta, gama, teta, cb, sb, cg, sg, ct, st ! Reset gradients do i = 1, ntotat do j = 1, 3 gxcar(i,j) = 0.d0 end do end do ! Reset boxes if(.not.init1) call resetboxes() ! Transform baricenter and angles into cartesian coordinates ! Computes cartesian coordinates from vector x and coor ilubar = 0 ilugan = ntotmol*3 icart = 0 do itype = 1, ntype if(.not.comptype(itype)) then icart = icart + nmols(itype)*natoms(itype) else do imol = 1, nmols(itype) xbar = x(ilubar + 1) ybar = x(ilubar + 2) zbar = x(ilubar + 3) ! Compute the rotation matrix beta = x(ilugan + 1) gama = x(ilugan + 2) teta = x(ilugan + 3) call eulerrmat(beta,gama,teta,v1,v2,v3) idatom = idfirst(itype) - 1 do iatom = 1, natoms(itype) icart = icart + 1 idatom = idatom + 1 call compcart(icart,xbar,ybar,zbar, & coor(idatom,1),coor(idatom,2),coor(idatom,3), & v1,v2,v3) ! Gradient relative to the wall distace do iratcount = 1, nratom(icart) irest = iratom(icart,iratcount) call gwalls(icart,irest) end do if(.not.init1) then xtemp = xcart(icart,1) - sizemin(1) ytemp = xcart(icart,2) - sizemin(2) ztemp = xcart(icart,3) - sizemin(3) iboxx = int(xtemp/boxl(1)) + 1 iboxy = int(ytemp/boxl(2)) + 1 iboxz = int(ztemp/boxl(3)) + 1 if(xtemp.le.0) iboxx = 1 if(ytemp.le.0) iboxy = 1 if(ztemp.le.0) iboxz = 1 if(iboxx.gt.nboxes(1)) iboxx = nboxes(1) if(iboxy.gt.nboxes(2)) iboxy = nboxes(2) if(iboxz.gt.nboxes(3)) iboxz = nboxes(3) ! Atom linked list latomnext(icart) = latomfirst(iboxx,iboxy,iboxz) latomfirst(iboxx,iboxy,iboxz) = icart ! Box with atoms linked list if ( .not. hasfree(iboxx,iboxy,iboxz) ) then hasfree(iboxx,iboxy,iboxz) = .true. call ijk_to_ibox(iboxx,iboxy,iboxz,ibox) lboxnext(ibox) = lboxfirst lboxfirst = ibox ! Add boxes with fixed atoms which are vicinal to this box, and ! are behind if ( fix ) then call add_box_behind(iboxx-1,iboxy,iboxz) call add_box_behind(iboxx,iboxy-1,iboxz) call add_box_behind(iboxx,iboxy,iboxz-1) call add_box_behind(iboxx,iboxy-1,iboxz+1) call add_box_behind(iboxx,iboxy-1,iboxz-1) call add_box_behind(iboxx-1,iboxy+1,iboxz) call add_box_behind(iboxx-1,iboxy,iboxz+1) call add_box_behind(iboxx-1,iboxy-1,iboxz) call add_box_behind(iboxx-1,iboxy,iboxz-1) call add_box_behind(iboxx-1,iboxy+1,iboxz+1) call add_box_behind(iboxx-1,iboxy+1,iboxz-1) call add_box_behind(iboxx-1,iboxy-1,iboxz+1) call add_box_behind(iboxx-1,iboxy-1,iboxz-1) end if end if ibtype(icart) = itype ibmol(icart) = imol end if end do ilugan = ilugan + 3 ilubar = ilubar + 3 end do end if end do if( .not. init1 ) then ! ! Gradient relative to minimum distance ! ibox = lboxfirst do while( ibox > 0 ) call ibox_to_ijk(ibox,i,j,k) icart = latomfirst(i,j,k) do while ( icart .ne. 0 ) if(comptype(ibtype(icart))) then ! Interactions inside box call gparc(icart,latomnext(icart)) ! Interactions of boxes that share faces call gparc(icart,latomfirst(i+1,j,k)) call gparc(icart,latomfirst(i,j+1,k)) call gparc(icart,latomfirst(i,j,k+1)) ! Interactions of boxes that share axes call gparc(icart,latomfirst(i+1,j+1,k)) call gparc(icart,latomfirst(i+1,j,k+1)) call gparc(icart,latomfirst(i+1,j-1,k)) call gparc(icart,latomfirst(i+1,j,k-1)) call gparc(icart,latomfirst(i,j+1,k+1)) call gparc(icart,latomfirst(i,j+1,k-1)) ! Interactions of boxes that share vertices call gparc(icart,latomfirst(i+1,j+1,k+1)) call gparc(icart,latomfirst(i+1,j+1,k-1)) call gparc(icart,latomfirst(i+1,j-1,k+1)) call gparc(icart,latomfirst(i+1,j-1,k-1)) end if icart = latomnext(icart) end do ibox = lboxnext(ibox) end do end if ! Computing the gradient using chain rule do i = 1, n g(i) = 0.d0 end do k1 = 0 k2 = ntotmol * 3 icart = 0 do itype = 1, ntype if(.not.comptype(itype)) then icart = icart + nmols(itype)*natoms(itype) else do imol = 1, nmols(itype) beta = x(k2 + 1) gama = x(k2 + 2) teta = x(k2 + 3) cb = dcos(beta) sb = dsin(beta) cg = dcos(gama) sg = dsin(gama) ct = dcos(teta) st = dsin(teta) dv1beta(1) = - cb * sg * ct - sb * cg dv2beta(1) = - sb * sg * ct + cb * cg dv3beta(1) = 0.d0 dv1gama(1) = - sb * cg * ct - cb * sg dv2gama(1) = cb * cg * ct - sb * sg dv3gama(1) = cg * st dv1teta(1) = sb * sg * st dv2teta(1) = - cb * sg * st dv3teta(1) = sg * ct dv1beta(2) = - cb * cg * ct + sb * sg dv2beta(2) = - sb * cg * ct - cb * sg dv3beta(2) = 0.d0 dv1gama(2) = sb * sg * ct - cb * cg dv2gama(2) = - sg * cb * ct - cg * sb dv3gama(2) = - sg * st dv1teta(2) = sb * cg * st dv2teta(2) = - cb * cg * st dv3teta(2) = cg * ct dv1beta(3) = cb * st dv2beta(3) = sb * st dv3beta(3) = 0.d0 dv1gama(3) = 0.d0 dv2gama(3) = 0.d0 dv3gama(3) = 0.d0 dv1teta(3) = sb * ct dv2teta(3) = - cb * ct dv3teta(3) = - st idatom = idfirst(itype) - 1 do iatom = 1, natoms(itype) icart = icart + 1 idatom = idatom + 1 do k = 1, 3 g(k1+k) = g(k1+k) + gxcar(icart, k) end do do k = 1, 3 g(k2 + 1) = g(k2 + 1) & + (coor(idatom,1) * dv1beta(k) & + coor(idatom, 2) * dv2beta(k) & + coor(idatom, 3) * dv3beta(k)) & * gxcar(icart, k) g(k2 + 2) = g(k2 + 2) & + (coor(idatom,1) * dv1gama(k) & + coor(idatom, 2) * dv2gama(k) & + coor(idatom, 3) * dv3gama(k)) & * gxcar(icart, k) g(k2 + 3) = g(k2 + 3) & + (coor(idatom,1) * dv1teta(k) & + coor(idatom, 2) * dv2teta(k) & + coor(idatom, 3) * dv3teta(k)) & * gxcar(icart, k) end do end do k2 = k2 + 3 k1 = k1 + 3 end do end if end do return end subroutine computeg packmol-20.010/configure000077500000000000000000000021041360620542100151250ustar00rootroot00000000000000#!/bin/bash # # Configure file for packmol # # If you want to set your own compiler, run the script with: # # ./configure gfortran # # where "gfortran" can be substituted by the compiler you use, # put the path if it is not in the path, for example, # /usr/bin/gfortran # # # List of possible compilers: compilerlist=" $1 gfortran f77 fort77 ifc ifort " # # IFS=$'\n' for searchcompiler in $compilerlist; do compiler=`which $searchcompiler` if [ "$compiler" \> " " ]; then echo "Setting compiler to $compiler" makefile=`cat Makefile` \rm -f Makefile for line in $makefile; do echo ${line//"FORTRAN="*/"FORTRAN=$compiler"} >> Makefile done exit fi done echo " " echo " ERROR: Could not find any fortran compiler." echo " " echo " To use your own compiler, run this script with: " echo " " echo " ./configure /path/to/compiler/yourcompiler " echo " " echo " Otherwise, install one of the following compilers" echo " and run this configure script again:" echo " " echo " gfortran, f77, fort77, ifc, ifort" echo " " packmol-20.010/data_types.f90000066400000000000000000000002771360620542100157040ustar00rootroot00000000000000 type input_file logical :: tinker, pdb, xyz, moldy integer :: nlines character(len=200), allocatable :: line(:) character(len=200), allocatable :: keyword(:,:) end type input_file packmol-20.010/docs/000077500000000000000000000000001360620542100141515ustar00rootroot00000000000000packmol-20.010/docs/README.md000077500000000000000000001040371360620542100154400ustar00rootroot00000000000000{::nomarkdown}

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Contents
1. What do you need?
2. How to compile Packmol.
3. Running Packmol.
4. Basic input structure.
5. More types of molecules.
6. Atom selections.
7. Types of constraints.
8. Periodic boundary conditions.
9. Different radii for different atoms.
10. Controlling residue numbering in PDB files.
11. Building very large systems: using restart files.
12. Convergence problems: what to try.
13. Additional input options and keywords.

What do you need?

You need coordinate files for each type of molecule you want your simulation to have. For example, if you are going to simulate a solution of water and ions, you will need a coordinate file for one water molecule, and independent coordinates files for each of the ions. This coordinate files may be in the PDB, TINKER, MOLDEN or MOLDY format.

Of course, you also need the Packmol package, which you can get from 
  http://www.ime.unicamp.br/~martinez/packmol
or by clicking on the [Latest Release] link. By following this link you will download the file packmol.tar.gz which contains the whole source code of Packmol.

How to compile Packmol

Once you have downloaded the packmol.tar.gz file from the home-page, you need to expand the files and compile the package. This is done by:

Expanding the files: 
tar -xvzf packmol.tar.gz
This will create a directory called packmol inside which you can find the source code. You can build the executable by: 
  cd packmol
  make

That's it, if no error was reported the packmol executable was built.

-----

If you have problems, let the configure script find a suitable compiler for you:

chmod +x ./configure (this makes the script executable)

./configure (this executes the script)

If the script was not able to find a suitable compiler, then you can manually set the compiler by:

./configure /path/to/your/compiler/yourcompiler

Then, run the "make" command again:

make

If no error was detected, an executable called packmol is now ready.

Running Packmol

Once you have compiled and built your input file, run Packmol with 
packmol < packmol.inp

Where packmol.inp is the input file (you can obtain example files by clicking at the 'Input examples' link on the left).

A successful packing will end with something like 
-------------------------------------------------
                Success!
Final objective function value: .22503E-01
Maximum violation of target distance:   0.000000
Maximum violation of the constraints: .78985E-02
-------------------------------------------------

Where the maximum violation of the target distance indicates the difference between the minimum distance between atoms required by the user and that of the solution. It will not be greater than 10-2 The maximum violation of the constrains must not be greater than 10-2.

A good idea is to check if your constraints are correct by using the "check" keyword in the input file. With this option a rough initial approximation will be built but no actual packing will be performed. You can look at the output to see if the molecules are within the desired regions (but do not expect a good structure at this point!). Just add the word "check" to any line of your input file (available since 28 Feb 2008).


Common issues:

- If you get "Command not found" when running Packmol, use 
./packmol < packmol.inp
(with a "./" before "packmol") or add the directory where the packmol executable is located to your path.

- If you run packmol and get the message "Killed", this is because the package is trying to allocate more memory than available for static storage. Open the "sizes.i" file and decrease the "maxatom" parameter to the number of atoms of your system, compile the package again, and try again.

Basic input structure

The minimal input file must contain the distance tolerance required (for systems at room temperature and pressure and coordinates in Angstroms, 2.0 Å is a good value. This is specified with

tolerance 2.0

The file must contain also the name of the output file to be created, specified with

output test.pdb

and the file type (pdb, tinker, xyz or moldy, pdb is the default value),

filetype pdb

At least one type of molecule must be present. This is set by the structure ... end structure section, for example, if water.pdb is the file containing the coordinates of a single water molecule, you could add to your input file something like 
structure water.pdb
  number 2000
  inside cube 0. 0. 0. 40. 
end structure

This section specifies that 2000 molecules of the water.pdb type, will be placed inside a cube with minimum coordinates (x,y,z) = (0,0,0) and maximum coordinates (40,40,40). Therefore, this minimum input file must be: 
tolerance 2.0
output test.pdb
filetype pdb
structure water.pdb
  number 2000 
  inside cube 0. 0. 0. 40. 
end structure

Running Packmol with this input file will fill a cube of side 40.0 Å with 2000 water molecules. Every pair of atoms of different molecules will be separated by, at least, 2.0 Å and the molecules will be randomly distributed inside de cube.

More types of molecules

You can add more types of molecules to the same region, or to different regions of the space, simply adding other structure ... end structure section to the input file.

Atom selections

The coordinate file of a single molecule contains, for example, 10 atoms. You can restrain a part of the molecule to be in a specified region of the space. This is useful for building vesicles where the hydrophilic part of the surfactants must be pointing to the aqueous environment, for example. For the 10 atoms molecule, this is done by using the keyword atoms, as in 
structure molecule.pdb     
  inside cube 0. 0. 0. 20.
  atoms 9 10              
    inside box 0. 0. 15. 20. 20. 20.
  end atoms 
end structure

In this case, all the atoms of the molecule will be put inside the defined cube, but atoms 9 and 10 will be restrained to be inside the box.

Types of constraints

There are several types of constraints that can be applied both to whole molecules or to parts of the molecule. These constraints define the region of the space in which the molecules must be at the solution. Very ordered systems can be built in such a way. The constraints are:

1. fixed
Usage: fixed x y z a b g

This options holds the molecule fixed in the position specified by the parameters. x, y, z, a, b, g, which are six real numbers. The first three determine the translation of the molecule relative to its position in the coordinate file. The former three parameters are rotation angles (in radians). For this option it is required that only one molecule is set. It may be accompanied by the keyword center. If this keyword is present the first three numbers are the position of the baricenter (not really the center of mass, because we suppose that all atoms have the same mass). Therefore this keyword must be used in the following context: 

structure molecule.pdb
  number 1  
  center    
  fixed 0. 0. 0. 0. 0. 0.
end structure


In this example, the molecule will be fixed with its center the origin and no rotation.

2. inside cube
Usage: inside cube xmin  ymin  zmin  d

xmin , ymin , zmin and d are four real numbers. The coordinates (x,y,z) of the atoms restrained by this option will satisfy, at the solution:


xmin < x < xmin + d
ymin < y < ymin + d
zmin < z < zmin + d


3. outside cube
Usage: outside cube xmin  ymin  zmin  d

xmin , ymin , zmin and d are four real numbers. The coordinates (x,y,z) of the atoms restrained by this option will satisfy, at the solution:


x < xmin or x > xmin + d
y < ymin or y > ymin + d
z < zmin or z > zmin + d


4. inside box
Usage: inside box  xmin  ymin  zmin  xmax  ymax  zmax

xmin , ymin , zmin , xmax , ymax  and zmax are six real numbers. The coordinates (x,y,z) of the atoms restrained by this option will satisfy, at the solution:

xmin < x < xmax
ymin < y < ymax
zmin < z < zmax


5. outside box
Usage: outside box  xmin  ymin  zmin  xmax  ymax  zmax

xmin , ymin , zmin , xmax , ymax  and zmax are six real numbers. The coordinates (x,y,z) of the atoms restrained by this option will satisfy, at the solution:

x < xmin or x > xmax
y < ymin or y > ymax
z < zmin or z > zmax


6. inside (or outside) sphere
Spheres are defined by equations of the general form


and, therefore, you must provide four real parameters a, b, c and d in order to define it. The input syntax is, for example,

inside sphere 2.30 3.40 4.50 8.0

and therefore the coordinates of the atoms will satisfy the equation


Other input alternative would be:

outside sphere 2.30 3.40 4.50 8.0

The outside parameter is similar to the inside parameter, but the equation above uses instead of and, therefore, the atoms will be placed outside the defined sphere.

7. inside (or outside) ellipsoid
Ellipsoids are defined by the general equation


The parameters must be given as in the sphere example, but now they are 7, and must be entered in the following order:

inside ellipsoid   a1  b1  c1  a2  b2  c2  d

The coordinates (a1,b1,c1) will define the center of the ellipsoid, the coordinates (a2,b2,c2) will define the relative size of the axes and d will define the volume of the ellipsoid. Of course, the commands

outside ellipsoid   a1  b1  c1  a2  b2  c2  d

can also be used in the same manner as the parameters for spheres. Note that the case a2 = b2 = c2 = 1.0 provides the exactly the same as the sphere parameter. The parameters for the ellipsoid are not normalized. Therefore, if a2, b2 and c2 are large, the ellipsoid will be large, even for a small d.

8. over (or below) plane
The planes are defined by the general equation

ax + by + cz - d = 0

And it is possible to restrict atoms to be over or below the plane. The syntax is 
over plane 2.5 3.2 1.2 6.2

below plane 2.5 3.2 1.2 6.2

where the over keyword will make the atoms satisfy the condition
2.5x + 3.2y + 1.2z - 6.2 0


the below keyword will make the atoms satisfy

2.5x + 3.2y + 1.2z - 6.2 0



9. inside (or outside) cylinder
In order to define a cylinder, it is necessary first to define a line oriented in space. This line is defined in Packmol by the parametric equation

p = ( a1 , b1 , c1 ) + t ( a2 , b2 , c2)

where t is the independent parameter. The vector (a2 , b2 , c2) defines the direction of the line. The cylinder is therefore defined by the distance to this line, d, and a length l. Therefore, the usage must be:

inside cylinder  a1  b1  c1  a2  b2  c2  d  l

outside cylinder  a1  b1  c1  a2  b2  c2  d  l

Here, the first three parameters define the point where the cylinder starts, and l defines the length of the cylinder. d defines de radius of the cylinder. The simpler example is a cylinder oriented in the x axis and starting at the origin, such as 

inside cylinder 0. 0. 0. 1. 0. 0. 10. 20.


This cylinder is specified by the points that have a distance of 10. to the x axis (the cylinder has a radius of 10.). Furthermore, it starts at the origin, therefore no atom restricted by this cylinder will have an x coordinate less than 0. Furthermore, it has a length of 20. and, as such, no atom will have an x coordinate greater than 20. The orientation of the cylinder, parallel to the x axis is defined by the director vector (1,0,0), the fourth, fifth and sixth parameters. Cylinders can be oriented in space in anyway.

10. Constrain rotations
It is possible to constrain rotations of all molecules of each type, so that they have some average orientation in space.

The keywords to be used are, within a structure...end structure section: 

constrain_rotation x 180. 20. 
constrain_rotation y 180. 20. 
constrain_rotation z 180. 20.


Each of these keywords restricts the possible rotation angles around each axis to be within 180±20 degrees (or any other value). For a technical reason the rotation around the z axis will, alone, be identical to the rotation around the y axis (we hope to fix this some day). Constraining the three rotations will constrain completely the rotations. Note that to have your molecules oriented parallel to an axis, you need to constrain the rotations relative to the other two.

For example, to constrain the rotation of your molecule along the z axis, use something like: 

constrain_rotation x 0. 20. 
constrain_rotation y 0. 20.

Note that these rotations are defined relative to the molecule in the orientation which was provided by the user, in the input PDB file. Therefore, it is a good idea to orient the molecule in a reasonable way in order to understand the rotations. For example, if the molecule is elongated in one direction, a good idea is to provide the molecule with the larger dimension oriented along the z axis.





Periodic Boundary Conditions

Periodic Boundary Conditions for cubic and rectangular boxes are often requested by users. We aim to implement that in the future. At the same time, there is a simple workaround we suggest: If your system will be simulated in a, for example, 100. Angs box, define your cubic constraints such that the packing is done in a 98. Angs box. That way, when the actual simulation box with PBC is built, images will be 2. Angs apart from each other, as illustrated in the figure below. There will be an empty space at the boundary, but that will readily disappear with energy minimization and equilibration.



Different radii for different atoms

It is possible (from version 15.133 on) to attribute different radii to different atoms during the packing procedure. The default behavior is that all atoms will be distant to each other at the final structure at least the distance defined by the tolerance parameter. In this case it is possible to think that the radius of every atom is half the distance tolerance. A tolerance of 2.0 Angs is usually fine for simulation of molecular systems using all-atom models.

Most times, therefore, you won't need this option. This was requested by users that want to pack multiscale models, in which all-atom and coarse-grained representations are combined in the same system.

It is easy to define different radii to different molecules, or to atoms within a molecule. Just add the "radius" keyword within the structure ... end structure section of a molecule type, or within atoms ... end atoms section of an atom selection.

For example, in this case:

tolerance 2.0
structure water.pdb
  number 500
  inside box 0. 0. 0. 30. 30. 30.
  radius 1.5
end structure
the radius of the atoms of the water molecules will be 1.5. Note that this implies a distance tolerance of 3.0 within water molecules.

In this case, on the other side:

tolerance 2.0
structure water.pdb
  number 500
  inside box 0. 0. 0. 30. 30. 30.
  atoms 1 2
    radius 1.5
  end atoms
end structure
only atoms 1 and 2 of the water molecule (as listed in the water.pdb file) will have a radius of 1.5, while atom 3 will have a radius of 1.0, as defined by the tolerance of 2.0

Always remember that the distance tolerance is the sum of the radii of each pair of atoms, and that the greatest the radii the harder the packing. Also, keep in mind that your minimization and equilibration will take care of the actual atom radii, and Packmol is designed only to give a first coordinate file.

Finally, currently the restrictions are set to be fulfilled by the center of the atoms. Therefore, if you are using large radii, you might want to adjust the sizes of the boxes, spheres, etc., so that the whole atoms are within the desired regions. For standard all-atom simulations this is not usually an issue because the radii are small.

Controlling residue numbering in PDB files.

Since Packmol will create one or more copies of your molecules in a new PDB file, there are some options on how residue numbers are set to these new molecules. There are four options, which are set with the resnumbers keyword. This keyword may assume three values, 0, 1, 2 or 3, and may be inserted within the structure ... end structure section of each type of molecule. The options are:

resnumbers 0

In this case the residue numbers of all residues will correspond to the molecule of each type, independently of the residue numbering of the original pdb file. This means that if you pack 10 water molecules and 10 ethanol molecules, the water molecules will be numbered 1 to 10, and the ethanol molecules will be numbered 1 to 10.

resnumbers 1

In this case, the residue numbers of the original pdb files are kept unmodified. This means that if you pack 10 proteins of 5 residues, the residue numbers will be preserved and, therefore, they will be repeated for equivalent residues in each molecule of the same protein.

resnumbers 2

In this case, the residue numbers of all residues for this structure will be numbered sequentially according to the number of residues that are printed previously in the same file. This means that if you pack 10 proteins of 5 residues, there will be residue numbers ranging from 1 to 50.

resnumbers 3

In this case, the numbering of the residues will correspond to the sequential numbering of all residues in the file. That is, if you pack a protein with 150 residues followed by 10 water molecules, the water molecules will be numbered from 151 to 161.

For example, this keyword may be used as in: 
structure peptide.pdb  
  number 10               
  resnumbers 1            
  inside box 0. 0. 0. 20. 20. 20.
end structure
Default: The default behavior is to use 0 for structures with only one residue and 1 for structures with more than one residue.

Chain identifier:
It is also possible to modify the "chain" identifiers of PDB files. By default, each type of molecule is set to a "chain". On the otherside, using the

changechains

whithin the structure...end structure section of a type of molecule, the chains will alternate between two values ("A" and "B" for example). This might be useful if the molecules are peptides, and topology builders sometimes think that the peptides of the same chain must be join by covalent bonds. This is avoided by alternating the chain from molecule to molecule.

Additionally each structure can have a specific chain identifier, set by the user with the option:

chain D

where "D" is the desired identifier (Do not use "#").

Building very large systems: using restart files

From version 16.143 on, it is possible to build the system from multiple and independent executions of Packmol by the use of restart files. In order to write a restart file, the following keyword must be used: restart_to restart.pack where restart.pack is the name of the restart file to be created. It is possible to write restart files for the whole system, if the keyword is put outside structure...end structure sections, or to write a restart file for a specific part of the system, using, for instance: 
structure water.pdb
  number 1000
  inside cube 0. 0. 0. 40.
  restart_to water1.pack
end structure
This will generate a restart file for the water molecules only.

These restart files can be used to start a new execution of Packmol with more molecules. The restart_from keyword must then be used. For example: 
structure water.pdb
  number 1000
  inside cube 0. 0. 0. 40.
  restart_from water1.pack
end structure
The new input file might contain other molecules, as a regular Packmol input file, and these water molecules will be packed together with the new molecules, but starting from the previous runs. This can be used, for example, to build solvated bilayers by parts. For instance, the bilayers could be built and, later, different solvents can be added to the bilayer, without having to restart the whole system construction from scratch every time. This could also be used to add some molecule to the bilayer.

Tip: the restart file can be used to restart the position of a smaller number of molecules of the same type. For instance, if a new molecule is introduced inside a previous set of molecules (a lipid bilayer, for instance), you can tell Packmol to pack less molecules of the original set, in order to provide space for the new structure, while using the original restart file of more molecules. That is, a restart_from water1.pack similar to the ones of the example above could be used to restart the positions of 800 molecules.

Convergence problems: what to try

Sometimes Packmol is not able to find an adequate packing solution. Here are some tips to try to overcome these difficulties:

• Look at the best solution obtained, many times it is good enough to be used.
• Simulate the same problem with only a few molecules of each type. For example, instead of using 20 thousand water molecules, put 300, and see if they are in the correct regions.
• If you have large molecules, try running the program twice, one to pack these molecules, and then use the solution as fixed molecule for the next packing, in which solvation is included. This may be particularly useful for building solvated membranes. Build the membrane first and then use it as a fixed molecule for a solvation run.
• You can change some options of the packing procedure to try improve the optimization:
1. discale [real]
This option controls the distance tolerance actually used in the local optimization method. It was found that using larger distances helps sometimes. Try setting discale to 1.5, for example.
2. maxit [integer]
This is the maximum number of iterations of the local optimizer (GENCAN) per loop. The default value is currently 20, changing it may improve (or worse) the convergence.
2. movebadrandom
One of the convergence heuristics of Packmol consists in moving molecules that are badly placed. If this option is set, the molecules will be placed in new random position in the box. If not (default), the molecules are moved to positions nearby molecules that are well packed. Using this option can help when the restraints are complex, but will probably be bad if there are large structures, because the new random position might overlap with those.


Additional input options and keywords

There are some input options which are probably not of interest of the general user, but may be useful in specific contexts. These keywords may be added in the input file in any position.

Add the TER flag betwen every molecule (AMBER uses this):
Usage: add_amber_ter

Add box side information to output PDB File (GROMACS uses this):
Usage: add_box_sides 1.0
Where the "1.0" is an optional real number that will be added to the length of each side, if the actual sides of your simulation box will not be exactly the same as the maximum and minimum coordinates of the molecules of the system (usually, if you are using periodic boundary conditions, you may want to add "1.0" to avoid clashes at the boundary).

Increase maximum system dimensions:
Usage: sidemax [real] (ex: sidemax 2000.d0)
"sidemax" is used to build an initial approximation of the molecular distribution. Increase "sidemax" if your system is very large, or your system may look cut out by this maximum dimension. All system coordinates must fit within -sidemax and +sidemax, and using a sidemax that approximately fits your system may accelerate a little bit the packing calculation. The default value is 1000.d0.

Change random number generator seed:
Usage: seed [integer] (ex: seed 191917)
Use seed -1 to generate a seed automatically from the computer time.

Use a truly random initial point for the minimization (the default option is to generate an homogeneous-density initial):
Usage: randominitialpoint

Avoid, or not, overlap with fixed molecules at initial point (avoiding this overlaps is generally recommended, but sometimes generates gaps that are too large):
Usage: avoid_overlap yes/no

Change the maximum number of Gencan iterations per loop:
Usage: maxit [integer]

Change the maximum number of loops:
Usage: nloop [integer]

Change the frequency of output file writing:
Usage: writeout [integer]

Write the current point to output file even if it is worst than the the best point so far (used for checking purposes only):
Usage: writebad

Check the initial point: This is only for testing purposes, just build the initial approximation, writes it to the output file and exits.
Usage: check

Change the optimization subroutine printing output:
Usage: iprint1 [integer] and/or iprint2 [integer]
where the integer must be 0, 1, 2 or 3.

Change the number of bins of the linked-cell method (technical):
Usage: fbins [real]
The default value is the square root of three.

Compare analytical and finite-difference gradients: This is only for testing purposes. Writes chkgrad.log file containing the comparison.
Usage: chkgrad

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( GN70󁂞 a xXh'?odYV;"CmUe'z+NlRWZe xcy@:QYw\I?ϝp1$G=7 f`}\3kQգPI!S0րY ,}'EeGԇi\kuG2Ѱ*=#i!4=r7m0L `dd9/jW.km55H|B{h |AfUBpNz4UN9#&v[j +* zت-{HX*x>EY,u,)enET 'T~VL?P% Yl<2=w]d(,O-T349?8ti{CIFBlw>A8 1\ (5LO);}ֶH)᭖Hi)+p +#B\¶s]=y7YLY$A,vp 9릅9u5@LUu07(+^ST[Х5M}Vx<̄f~Q k'Ꮽ\w+@DI3~uA `0EMrD'YHRˀVTmn\=Fݿ^ҚMiGJz7a™1=ܚI|FиCpr5־usڨDM"),ۘ~8Z4C߭+J@ 3'_packmol-20.010/flashmod.f90000066400000000000000000000007011360620542100153340ustar00rootroot00000000000000! ! Written by Leandro Martínez, 2009-2011. ! Copyright (c) 2009-2018, Leandro Martínez, Jose Mario Martinez, ! Ernesto G. Birgin. ! ! ! Arrays required by the flashsort package. Used only in heuristics, but ! defined here to be allocated dynamically ! module flashsort use sizes implicit none integer, allocatable :: indflash(:) ! (ntotat) integer, allocatable :: lflash(:) ! (ntotat) integer :: mflash end module flashsort packmol-20.010/flashsort.f90000066400000000000000000000047371360620542100155610ustar00rootroot00000000000000!cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc ! c ! Subroutine Flash1 c ! SORTS ARRAY A WITH N ELEMENTS BY USE OF INDEX VECTOR L c ! OF DIMENSION M WITH M ABOUT 0.1 N. c ! Karl-Dietrich Neubert, FlashSort1 Algorithm c ! in Dr. Dobb's Journal Feb.1998,p.123 c ! c !cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc subroutine flash1 (A, N, L, M, ind) implicit none double precision :: a(*), anmin, c1, hold, flash integer :: L(*), ind(*), i, n, nmax, m, k, ihold, nmove, j, iflash ! ============================ CLASS FORMATION ===== do i = 1, n ind(i) = i end do ANMIN=A(1) NMAX=1 DO I=1,N IF( A(I).LT.ANMIN) ANMIN=A(I) IF( A(I).GT.A(NMAX)) NMAX=I END DO IF (ANMIN.EQ.A(NMAX)) RETURN C1=(M - 1) / (A(NMAX) - ANMIN) DO K=1,M L(K)=0 END DO DO I=1,N K=1 + INT(C1 * (A(I) - ANMIN)) L(K)=L(K) + 1 END DO DO K=2,M L(K)=L(K) + L(K - 1) END DO HOLD=A(NMAX) A(NMAX)=A(1) A(1)=HOLD ihold = ind(nmax) ind(nmax) = ind(1) ind(1) = ihold ! =============================== PERMUTATION ===== NMOVE=0 J=1 K=M DO WHILE (NMOVE.LT.N - 1) DO WHILE (J.GT.L(K)) J=J + 1 K=1 + INT(C1 * (A(J) - ANMIN)) END DO FLASH=A(J) iflash=ind(j) DO WHILE (.NOT.(J.EQ.L(K) + 1)) K=1 + INT(C1 * (FLASH - ANMIN)) HOLD=A(L(K)) ihold = ind(L(k)) A(L(K))=FLASH ind(L(k)) = iflash iflash = ihold FLASH=HOLD L(K)=L(K) - 1 NMOVE=NMOVE + 1 END DO END DO ! ========================= STRAIGHT INSERTION ===== DO I=N-2,1,-1 IF (A(I + 1).LT.A(I)) THEN HOLD=A(I) ihold = ind(i) J=I DO WHILE (A(J + 1).LT.HOLD) A(J)=A(J + 1) ind(j) = ind(j+1) J=J + 1 END DO A(J)=HOLD ind(j) = ihold ENDIF END DO ! =========================== RETURN,END FLASH1 ===== RETURN END packmol-20.010/fparc.f90000066400000000000000000000043421360620542100146370ustar00rootroot00000000000000! ! Written by Leandro Martínez, 2009-2011. ! Copyright (c) 2009-2018, Leandro Martínez, Jose Mario Martinez, ! Ernesto G. Birgin. ! ! Function that computes the atom-to-atom component of the objective ! function ! double precision function fparc(icart,firstjcart) use sizes use compute_data implicit none ! SCALAR ARGUMENTS integer :: icart,firstjcart ! LOCAL SCALARS integer :: jcart double precision :: datom, tol, short_tol, short_tol_penalty, short_tol_scale fparc = 0.0d0 jcart = firstjcart do while ( jcart > 0 ) ! ! Cycle if this type is not to be computed ! if ( .not. comptype(ibtype(jcart))) then jcart = latomnext(jcart) cycle end if ! ! Cycle if the atoms are from the same molecule ! if ( ibmol(icart) == ibmol(jcart) .and. & ibtype(icart) == ibtype(jcart) ) then jcart = latomnext(jcart) cycle end if ! ! Cycle if both atoms are from fixed molecules ! if ( fixedatom(icart) .and. fixedatom(jcart) ) then jcart = latomnext(jcart) cycle end if ! ! Otherwise, compute distance and evaluate function for this pair ! datom = ( xcart(icart,1)-xcart(jcart,1) )**2 + & ( xcart(icart,2)-xcart(jcart,2) )**2 + & ( xcart(icart,3)-xcart(jcart,3) )**2 tol = (radius(icart)+radius(jcart))**2 if ( datom < tol ) then fparc = fparc + fscale(icart)*fscale(jcart)*(datom-tol)**2 if ( use_short_radius(icart) .or. use_short_radius(jcart) ) then short_tol = (short_radius(icart)+short_radius(jcart))**2 if ( datom < short_tol ) then short_tol_penalty = datom-short_tol short_tol_scale = dsqrt(short_radius_scale(icart)*short_radius_scale(jcart)) short_tol_scale = short_tol_scale*(tol**2/short_tol**2) fparc = fparc + fscale(icart)*fscale(jcart)*short_tol_scale*short_tol_penalty**2 end if end if end if tol = (radius_ini(icart)+radius_ini(jcart))**2 fdist = dmax1(tol-datom,fdist) if ( move ) then fdist_atom(icart) = dmax1(tol-datom,fdist_atom(icart)) fdist_atom(jcart) = dmax1(tol-datom,fdist_atom(jcart)) end if jcart = latomnext(jcart) end do end function fparc packmol-20.010/gencan.f000066400000000000000000006134261360620542100146370ustar00rootroot00000000000000C ***************************************************************** C ***************************************************************** subroutine evalal(n,x,m,lambda,rho,f,flag) C This subroutine computes the objective function when GENCAN is C being used stand-alone to solve a unique bound-constrained problem. C When GENCAN is being used in an Augmented Lagrangian framework, C this subroutine must compute the Augmented Lagrangian function. C C On Entry: C C n integer, C number of variables, C C x double precision x(n), C current point, C C m integer, C number of constraints (equalities plus inequalities), C C lambda double precision lambdae(m), C current estimation of the Lagrange multipliers, C C rho double precision rho(m) C penalty parameters, C C NOTE: arguments m, lambda and rho are useful when GENCAN is being used C for solving the box-constrained subproblems of an Augmented Lagrangian C framework. When GENCAN is being used stand-alone for solving a bound- C constrained problem, these arguments are dummy arguments. C C On Return C C f double precision, C objective function value at x, C C flag integer C 0 means "no errors", C 1 means "some error occurs in the objective funtion evaluation". implicit none C SCALAR ARGUMENTS integer flag,m,n double precision f C ARRAY ARGUMENTS double precision lambda(m),rho(m),x(n) C LOCAL SCALARS flag = 0 call computef(n,x,f) end C ***************************************************************** C ***************************************************************** subroutine evalnal(n,x,m,lambda,rho,g,flag) C This subroutine computes the gradient of the objective function C when GENCAN is being used stand-alone to solve a unique bound- C constrained problem. When GENCAN is being used in an Augmented C Lagrangian framework, this subroutine must compute the gradient of C Augmented Lagrangian. C C On Entry: C C n integer, C number of variables, C C x double precision x(n), C current point, C C m integer, C number of constraints (equalities plus inequalities), C C lambda double precision lambdae(m), C current estimation of the Lagrange multipliers, C C rho double precision rho(m) C penalty parameters, C C NOTE: arguments m, lambda and rho are useful when GENCAN is being used C for solving the box-constrained subproblems of an Augmented Lagrangian C framework. When GENCAN is being used stand-alone for solving a bound- C constrained problem, these arguments are dummy arguments. C C On Return C C g double precision g(n), C gradient of the objective function at x, C C flag integer C 0 means "no errors", C 1 means "some error occurs in the gradient evaluation". implicit none C SCALAR ARGUMENTS integer flag,m,n C ARRAY ARGUMENTS double precision g(n),lambda(m),rho(m),x(n) C LOCAL SCALARS flag = 0 call computeg(n,x,g) end C ***************************************************************** C ***************************************************************** c Modified by L. Martinez (there was an error on the number of c parameters when calling this subroutine). This subroutine does c nothing. c subroutine evalhd(nind,ind,n,x,m,lambda,rho,d,hd,flag) subroutine evalhd(n) C This subroutine computes the product of the Hessian matrix times C the input vector argument d. If GENCAN is being used stand-alone C to solve a bound-constrained problem, the ''Hessian matrix'' must C be the Hessian matrix of the objective function. On the other hand, C if GENCAN is being used to solve the bound-constrained subproblems C in an Augmented Lagrangian framework, the Hessian matrix must be C the Hessian of the Augmented Lagrangian function. C C IMPORTANT: This subroutine does not need to be coded if the user C prefers to approximate the Hessian-vector product by incremental C quotients. In this case, it is enough to set the GENCAN input C argument htvtype equal to 1 and an internal GENCAN subroutine will C be used to compute the approximation. In fact, this is the default C GENCAN option. See the GENCAN and EASYGENCAN arguments descriptions C for details. C C On Entry: C C nind integer C number of component of the Hessian-vector product that C must be computed, C C ind integer ind(nind) C the component that must be computed are ind(1)-th ... ind(nind)-th, C C n integer, C number of variables, C C x double precision x(n), C current point, C C m integer, C number of constraints (equalities plus inequalities), C C lambda double precision lambdae(m), C current estimation of the Lagrange multipliers, C C rho double precision rho(m) C penalty parameters, C C d double precision d(n) C vector of the Hessian-vector product. C C NOTE: arguments m, lambda and rho are useful when GENCAN is being used C for solving the box-constrained subproblems of an Augmented Lagrangian C framework. When GENCAN is being used stand-alone for solving a bound- C constrained problem, these arguments are dummy arguments. C C On Return C C hd double precision g(n), C Hessian-vector product, C C flag integer C 0 means "no errors", C 1 means "some error occurs in the gradient evaluation". implicit none C SCALAR ARGUMENTS c integer flag,m,n,nind integer n C ARRAY ARGUMENTS c integer ind(nind) c double precision d(n),hd(n),lambda(m),rho(m),x(n) c flag = - 1 end C************************************************************************** C Last update of EASYGENCAN: February 18th, 2005. subroutine easygencan(n,x,l,u,m,lambda,rho,epsgpsn,maxit,maxfc, +trtype,iprint,ncomp,f,g,gpsupn,iter,fcnt,gcnt,cgcnt,inform,wi,wd, +delmin) implicit none C SCALAR ARGUMENTS integer cgcnt,fcnt,gcnt,m,maxfc,maxit,n,ncomp,inform,iprint,iter double precision epsgpsn,f,gpsupn C ARRAY ARGUMENTS integer wi(n) double precision g(n),l(n),lambda(m),rho(m),u(n),wd(8*n),x(n) C This subroutine aims to simplify the use of GENCAN. For this C purpose it gives values to most of the GENCAN arguments and C leaves to the user those arguments which he/she may would like to C set by him/herself. C C The arguments of EASYGENCAN are the input and output arguments of C GENCAN that are supposed to be useful for a common user. The input C arguments are mostly related to basic problem information, like C dimension and bounds, and the initial point. There are also input C arguments related to simple stopping criteria (like norm of the C projected gradient, and maximum number of iterations and C functional evaluations). There are also two input arguments C related to control the amount of information written into the C screen. The output arguments are related to information of the C solution and some few performance measurements. Basically, on C return, EASYGENCAN gives to the user the solution, the objective C functional value and its gradient at the solution, Euclidian and C sup-norm of the projected gradient at the solution, the number of C iterations, functional and gradient evaluations, and Conjugate C Gradient iterations used to reach the solution, and, finally, a C flag that indicates the stopping criterion that was satisfied. C C All the other arguments of GENCAN are setted with its default C values by EASYGENCAN. EASYGENCAN divides the arguments of GENCAN C in two sets. Those that are related to the behaviour of GENCAN are C declared as Fortran parameters (constants). The other arguments of C GENCAN, most of them related to alternative stopping criteria, and C that may depend of, for example, maxit, are declared as local C variables of EASYGENCAN. C C GENCAN arguments that are defined as Fortran parameters in this C subroutine are GENCAN arguments that should not be modified by a C common user. They are arguments that modify the behaviour of C GENCAN and whos values were selected because they are classical C values in some cases or because some numerical experiments seemed C to indicate that they are the best choices. C C GENCAN arguments that are declared as local variables in this C subroutine are GENCAN arguments that may be modified if, with C their suggested values, GENCAN does not give the desired result. C Most of them are related to Conjugate Gradients or to disabled C stopping criteria that may be useful in bad-scaled problems or C problems with not trustable derivatives. C C Finally, this subroutine declares as local variables some C arguments of GENCAN which in fact are output arguments. Most of C them are related to quantities that can be used for statistics C related to the GENCAN performance, like number Spectral Projected C Gradient iterations, Truncated Newton iterations, Conjugate C Gradient iterations, etc. As we assume that this values are not C useful for the common user, this subroutine throw all of them C away. C C We describe below the meaning of the arguments of the EASYGENCAN C subroutine. More detailed descriptions as well as the descriptions C of all the other GENCAN arguments that are not arguments of C EASYGENCAN are also described at the begining of the GENCAN C subroutine. C C On entry: C C n integer C number of variables C C x double precision x(n) C initial estimation of the solution C C l double precision l(n) C lower bounds on the variables C C u double precision u(n) C upper bounds on the variables C C m integer C lambda double precision lambda(m) C rho double precision rho(m) C These three parameters are not used nor modified by C GENCAN and they are passed as arguments to the user- C defined subroutines evalal and evalnal to compute the C objective function and its gradient, respectively. C Clearly, in an Augmented Lagrangian context, if GENCAN is C being used to solve the bound-constrainted subproblems, m C would be the number of constraints, lambda the Lagrange C multipliers approximation and rho the penalty parameters C C epsgpsn double precision C GENCAN stops declaring convergence if it finds a point C whos projected gradient sup-norm is smaller than or equal C to epsgpsn C C maxit integer C GENCAN stops declaring ''maximum number of iteration C achieved'' if the number of iterations exceeds maxit C C maxfc integer C the same as before but with the number of functional C evaluations C C iprint integer C indicates the degree of details of the output generated C by GENCAN. Setting iprint to a value smaller than 2 will C make GENCAN to generate no output at all. An iprint value C greater than or equal to 2 will generate information of C every GENCAN iteration. An iprint value greater than or C equal to 3 will also show information of the Conjugate C Gradient iterations (used to compute the Truncated Newton C direction) and also information related to the line C search procedures in the Spectral Projected Gradient C direction and the Truncated Newton direction. C C ncomp integer C Sometimes, vectors like the current point x, the gradient C of the objective function g, or the search directions C (Spectral Projected Gradient direction or Truncated C Newton direction), among other vector, are showed in the C screen. In such cases, if the problem dimension is large, C to show just a few elements of these vectors may be C preferable. Argument ncomp can be used to indicate how C many array elements must be displayed. C C wi integer wi(n) C integer working space C C wd double precision wd(8*n) C double precision working space C C On return: C C x double precision x(n) C estimation of the solution C C f double precision C objective function value at the solution C C g double precision g(n) C gradient of the objective function at the solution C C gpsupn double precision C sup-norm of the continuous projected gradient C C iter integer C number of iterations used to reach the solution C C fcnt integer C number of functional evaluations C C gcnt integer C number of gradient evaluations C C cgcnt integer C number of Conjugate Gradient iterations C C inform integer C termination criteria. inform equal to 1 means that C GENCAN converged with the sup-norm of the continuous C projected gradient stopping criterion (inform equal to 0 C means the same but with the Euclidian norm). Other C positive values means that GENCAN stopped by a may be not C successful stopping criteria. A negative value means that C there was an error in the user-defined subroutines that C computes the objective function (subroutine evalal), the C gradient (subroutine evalnal), or the Hessian-vector C product (subroutine evalhd). See the GENCAN description C for more details. C HERE STARTS THE DESCRIPTION OF SOME GENCAN ARGUMENTS THAT ARE C BEING SETTED INSIDE EASYGENCAN. THE FIRST SET OF ARGUMENTS ARE C THOSE ARGUMENTS THAT WE WILL CALL ''CONSTANTS'' AND THAT, AS THEIR C VALUES ALTER THE BEHAVIOUR OF GENCAN, SHOULD NOT BE MODIFIED BY A C COMMON USER. C CONSTANTS FOR GENERAL USES C Steps: h = max( steabs, sterel * abs( x ) ) should be a number C such that h is small ( relatively to x ) and x + h is different C from x. So, h is something that can be used a a step for a finite C differences approximation of a partial derivative relative to x. C Epsilons: something smaller than max( epsabs, epsrel * abs( x ) ) C should be considered as ``zero'' when compared with x. It is used, C for example, to detect that a step taken during a line search is C too small. C Infinitys: infrel is a big number that may appear in the C calculations. infabs is a number that should never be reached in C the calculations and is used the represent ``infinite''. Detailed C explanations of how are they used are rather cumbersome. double precision steabs,sterel,epsabs,epsrel,infabs,infrel parameter ( steabs = 1.0d-10 ) parameter ( sterel = 1.0d-07 ) parameter ( epsabs = 1.0d-20 ) parameter ( epsrel = 1.0d-10 ) parameter ( infabs = 1.0d+99 ) parameter ( infrel = 1.0d+20 ) C CONSTANTS FOR CLASSICAL LINE-SEARCH CONDITIONS C beta is the constant for the ''beta condition''. We use this C condition to test whether is promising to extrapolate or not. C gamma is the constant for the sufficient decrease ''Armijo C condition''. C theta is the constant for the ''angle condition''. C sigma1 and sigma2 are the constants for the safeguarding quadratic C interpolations. We use them in a rather unusual way. Instead of C discarding a new step anew if it does not belong to the interval C [ sigma1 * aprev, sigma2 * aprev ], we discard it if it does not C belong to the interval [ sigma1, sigma2 * aprev ]. In such a case C we take something similar to ''anew = aprev / 2''. double precision beta,gamma,theta,sigma1,sigma2 parameter ( beta = 0.5d0 ) parameter ( gamma = 1.0d-04 ) parameter ( theta = 1.0d-06 ) parameter ( sigma1 = 0.1d0 ) parameter ( sigma2 = 0.9d0 ) C CONSTANTS FOR SPECIFIC PROCEDURES (NOT SO CLASSICAL) C In line searches, when interpolating, the step may become so C small that we should declare a line search failure indicating that C direction may not be a descent direction. This decision is never C take before doing at least mininterp interpolations. C In line searches, the beta condition (see above) may recommend to C extrapolate. We never do more than maxextrap extrapolations. C In the line searches, when we need to interpolate and the result C of the quadratic interpolation is rejected, the new step is C computed as anew = aprev / nint. When the beta condition C recommends to extrapolate, we compute anew = aprev * next. C When computing the Newton direction by Conjugate Gradients we C never go further an artificial ''trust region''. This ''trust C radius'' is never smaller than delmin. C In active set strategies, constants eta is used to decide whether C the current face should be abandoned or not. In particular, the C current face is abandoned when the norm of the internal to face C component of the continuous projected gradient is smaller than C ( 1 - eta ) times the norm of the continuous projected gradient. C In this way, values of eta near 1 makes the method to work hard C inside the faces and values of eta near 0 makes the method to C abandon the faces very quickly. C We always use as a first step in a line search procedure along a C first order direction the spectral steplength. This steplength C must belong to the interval [lspgmi,lspgma]. integer maxextrap,mininterp parameter ( maxextrap = 100 ) parameter ( mininterp = 4 ) double precision nint,next,delmin,eta,lspgma,lspgmi parameter ( nint = 2.0d0 ) parameter ( next = 2.0d0 ) c parameter ( delmin = 1.d4 ) parameter ( eta = 0.9d0 ) parameter ( lspgma = 1.0d+10 ) parameter ( lspgmi = 1.0d-10 ) C DIMENSIONS FOR SOME WORKING SPACES C In non-monotone line searches, given p, the last p objective C functional values must be stored. For this reason we declare a C vector with pmax double precision elements. So p must be less than C or equal to pmax. C Sometimes, is the problem is bad scaled, to request a small C gradient norm at the solution may be inadequate. For this reason, C a test to verify if this norm is not decreasing during maxitngp C (MAXimum of ITerations with No Gradient Progress) consecutive C iterations then we stop the method with a warning. As it is not C expected a monotone decreasing of the gradient norm, again, the C norm of the last maxitngp iterations must be saved. For this C purpose, we declare a vector of tmax elements. So maxitngp must C be less than or equal to tmax. integer tmax parameter ( tmax = 10000 ) C HERE STARTS THE DESCRIPTION OF THE OTHER ARGUMENTS OF GENCAN BEING C SETTED BY EASYGENCAN. THESE ARGUMENTS MAY BE MODIFIED BY A COMMON C USER IF, WITH THEIR SUGGESTED VALUES, GENCAN DOES NOT GIVE THE C EXPECTED RESULT. C GENCAN INPUT ARGUMENTS THAT WILL BE SETTED BELOW logical nearlyq integer cgmaxit,cgscre,gtype,htvtype,maxitnfp,maxitngp,maxitnqmp, + trtype double precision cgepsf,cgepsi,cggpnf,delta0,epsgpen,epsnfp, + epsnqmp,fmin C GENCAN OUTPUT ARGUMENTS THAT WILL BE DISCARDED integer spgfcnt,spgiter,tnexbcnt,tnexgcnt,tnexbfe,tnexgfe,tnfcnt, + tnintcnt,tnintfe,tniter,tnstpcnt double precision gpeucn2 C GENCAN WORKING VECTORS (WHICH DIMENSION IS NOT RELATED TO THE C PROBLEM DIMENSION) double precision lastgpns(tmax) C ARGUMENTS RELATED TO DERIVATIVES CALCULATIONS C gtype indicates in which way the gradient of the objective C function will be computed. If the user have been implemented the C user-supplied evalnal subroutine to compute the gradient of the C objective function then gtype argument must be set to 0 (ZERO) and C the user-supplied evalnal subroutine will be called by GENCAN any C time the gradient would be required. C C The prototype of the evalnal subroutine must be: C C subroutine evalnal(n,x,m,lambda,rho,nal,flag) C C SCALAR ARGUMENTS C integer n,m,flag C C ARRAY ARGUMENTS C double precision x(n),lambda(m),rho(m),nal(n) C C ''Here must be written the subroutine body that calculates the C n-dimensional gradient vector of the objective function C evaluated at x and saves it in nal. It also must set flag to 0 C (ZERO) if the gradient was successfully computed and to any C other value if the gradient vector is not well defined at the C required point x. If GENCAN is been used stand-alone to solve C a unique bound-constrained problem then m, lambda and rho are C dummy arguments. On the other hand, if GENCAN is been used in C an Augmented Lagrangian framework then these arguments should C be used for the number of constraints, the Lagrange C multipliers approximation and the penalty parameters, C respectively.'' C C end C C If, on the other hand, the user is not able to provide evalnal C subroutine, gtype argument must be set to 1 (ONE). In this case, C every time GENCAN needs to compute the gradient of the objective C function, an internal subroutine that approximates it by finite- C differences will be used (be aware that it maybe very time C consuming). Moreover, note that the evalnal subroutine must still C be present (with an empty body). gtype = 0 C htvtype indicates in which way the product of the Hessian of the C objective function times an arbitrary vector will be computed. If C the user has not been implemented the user-supplied evalhd C subroutine to do this task then htvtype argument must be set to 1 C (ONE). In this case an internal subroutine that approximates this C product by incremental quotients will be used. Note that, even in C this case, evalhd subroutine must be present (with an empty body). C This is the default option and the empty-body subroutine follows: C C subroutine evalhd(nind,ind,n,x,m,lambda,rho,d,hd,flag) C C SCALAR ARGUMENTS C integer nind,n,m,flag C C ARRAY ARGUMENTS C integer ind(nind) C double precision d(n),hd(n),lambda(m),rho(m),x(n) C C flag = - 1 C C end C C If, on the other hand, the user prefers to implement his/her own C evalhd subroutine then htvtype argument must be set to 0 (ZERO). C In this case, the product of the Hessian times vector d (input C argument of evalhd subroutine) must be saved in vector hd (output C argument of evalhd subroutine). The other arguments description as C well as some hints on how to implement your own evalhd subroutine C can be found in the GENCAN arguments description. C When ALGENCAN uses GENCAN to solve the subproblems in the classical C Augmented Lagrangian framework, ALGENCAN uses its own evalhd C subroutine to overcome the lack of continuity of the second C derivatives. So, when GENCAN is being used toghether with ALGENCAN, C htvtype must be equal to 0 (ZERO). On the other hand, if GENCAN is C being used stand-alone, just set htvtype equal to 1 (ONE) and add C the empty-body subroutine described above. htvtype = 1 C ARGUMENTS RELATED TO STOPPING CRITERIA C Besides the stopping criterion related to the sup-norm of the C continuous projected gradient, there is another stopping criterion C related to its Euclidian norm. So, GENCAN stops the process if it C finds a point at which the Euclidian norm of the continuous C projected gradient is smaller than epsgpen. epsgpen = 0.0d0 C For an explanation of maxitngp see above the explanation of tmax C in ''DIMENSIONS FOR SOME WORKING SPACES''. Just note that the C value of maxitngp must be less than or equal to tmax. maxitngp = tmax C maxitnfp means MAXimum of allowed number of iterations with No C Progress in the objective functional value. ''Progress'' from one C iteration to the next one refers to ( fnew - fprev ). Since the C begining of the algorithm we save the ''best progress'' and C consider that there was no progress in an iteration if the C progress of this iterations was smaller than epsnfp times the best C progress. Finally, the algorithm stops if there was no progress C during maxitnfp consecutive iterations. maxitnfp = maxit epsnfp = 0.0d0 C There is a stopping criterion that stops the method if a point C with a functional value smaller than fmin is found. The idea C behind this stopping criterion is to stop the method if the C objective function is not bounded from below. fmin = 1.0d-05 C ARGUMENTS RELATED TO CONJUGATE GRADIENTS C When computing the Truncated Newton direction by Conjugate C Gradients there is something similar to a ''trust-region radius''. C This trust radius is updated from iteration to iteration depending C on the agreement of the objective function and its quadratic C model. But an initial value for the trust radius is required. If C the user has a good guess for this initial value then it should be C passed to GENCAN using the delta0 arguments. On the other hand, if C delta0 is set to -1, a default value depending on the norm of the C current point will be used. delta0 = - 1.0d0 delmin = 1.d-2 c delta0 = delmin C The ''trust-region'' can be like a ball (using Euclidian norm) or C like a box (using sup-norm). This choice can be made using trtype C (TRust region TYPE) argument. trtype equal to 0 means Euclidian C norm and trtype equal to 1 means sup-norm. trtype = 1 C When the method is far from the solution, it may be not useful to C do a very large effort in computing the Truncated Newton direction C precisely. To avoid it, a fixed maximum number of iterations for C Conjugate Gradients can be given to GENCAN. If the user would like C to choose this maximum number of iterations for Conjugate C Gradient then it should use the cgmaxit arguments. On the other C hand he/she prefers to leave this task to GENCAN then he/she C should set cgmaxit to -1. cgmaxit = -1 C If the task of deciding the accuracy for computing the Truncated C Newton direction is leaved to GENCAN then a default strategy based C on increasing accuracies will be used. The proximity to the C solution is estimated observing the norm of the projected gradient C at the current point and locating it between that norm at the C initial point and the expected value of that norm at the solution. C Then the accuracy for the Truncated Newton direction of the C current iteration will be computed taking a precision located in C the same relative position with respect to two given values for C the accuracies for the first and the last Truncated Newton C direction calculations. These two accuracies (cgepsi and cgepsf, C respectively) must be given by the user. Moreover, the expected C value of the projected gradient norm at the solution (cggpnf) must C also be given by the user who must indicate setting argument C cgscre to 1 or 2 if that norm is the Euclidian or the sup-norm. cggpnf = max( 1.0d-04, max( epsgpen, epsgpsn ) ) cgscre = 2 cgepsi = 1.0d-01 cgepsf = 1.0d-05 C The next two arguments are used for an alternative stopping C criterion for Conjugate Gradients. Conjugate Gradients method is C stopped if the quadratic model makes no progress during maxitnqmp C (MAXimum of ITerations with No Quadratic Model Progress) C consecutive iterations. In this context, ''no progress'' means C that the progress is smaller than epsnqmp (EPSilon to measure the C No Quadratic Model Progress) times the best progress obtained C during the previous iterations. epsnqmp = 1.0d-04 maxitnqmp = 5 C Depending on how much the objective function seems to be a C quadratic, function, Conjugate Gradients may take different C decision. So, if the objective function is a quadratic function or C is very similar to a quadratic function then the nearlyq argument C should be set to TRUE, else, it should be set to FALSE. However, C the option with nearlyq equal TRUE never showed good results. C Regarding this unexpected no good performance, rather recently it C was found a bug that affected the behaviour of GENCAN just in this C case (See the April 1st, 2003 modifications report at the end of C this file). So, new experiments setting nearlyq equal TRUE should C be made. nearlyq = .false. C FINALLY, CALL GENCAN call gencan(n,x,l,u,m,lambda,rho,epsgpen,epsgpsn,maxitnfp,epsnfp, +maxitngp,fmin,maxit,maxfc,delta0,cgmaxit,cgscre,cggpnf,cgepsi, +cgepsf,epsnqmp,maxitnqmp,nearlyq,nint,next,mininterp,maxextrap, +gtype,htvtype,trtype,iprint,ncomp,f,g,gpeucn2,gpsupn,iter,fcnt, +gcnt,cgcnt,spgiter,spgfcnt,tniter,tnfcnt,tnstpcnt,tnintcnt, +tnexgcnt,tnexbcnt,tnintfe,tnexgfe,tnexbfe,inform,wd(1),wd(n+1), +wd(2*n+1),wi,lastgpns,wd(3*n+1),eta,delmin,lspgma,lspgmi,theta, +gamma,beta,sigma1,sigma2,sterel,steabs,epsrel,epsabs,infrel, +infabs) end C ****************************************************************** C ****************************************************************** C Last update of GENCAN or any of its dependencies: C C February 18th, 2005. C C See report of modifications at the end of this file. subroutine gencan(n,x,l,u,m,lambda,rho,epsgpen,epsgpsn,maxitnfp, +epsnfp,maxitngp,fmin,maxit,maxfc,udelta0,ucgmaxit,cgscre,cggpnf, +cgepsi,cgepsf,epsnqmp,maxitnqmp,nearlyq,nint,next,mininterp, +maxextrap,gtype,htvtype,trtype,iprint,ncomp,f,g,gpeucn2,gpsupn, +iter,fcnt,gcnt,cgcnt,spgiter,spgfcnt,tniter,tnfcnt,tnstpcnt, +tnintcnt,tnexgcnt,tnexbcnt,tnintfe,tnexgfe,tnexbfe,inform,s,y,d, +ind,lastgpns,w,eta,delmin,lspgma,lspgmi,theta,gamma,beta,sigma1, +sigma2,sterel,steabs,epsrel,epsabs,infrel,infabs) implicit none C SCALAR ARGUMENTS logical nearlyq integer cgcnt,cgscre,fcnt,gcnt,gtype,htvtype,inform,iprint,iter,m, + maxextrap,maxfc,maxit,maxitnfp,maxitngp,maxitnqmp, + mininterp,n,ncomp,spgfcnt,spgiter,tnexbcnt,tnexbfe, + tnexgcnt,tnexgfe,tnfcnt,tnintcnt,tnintfe,tniter,tnstpcnt, + trtype,ucgmaxit double precision beta,cgepsf,cgepsi,cggpnf,delmin,epsabs,epsgpen, + epsgpsn,epsnfp,epsnqmp,epsrel,eta,f,fmin,gamma,gpeucn2, + gpsupn,infabs,infrel,lspgma,lspgmi,next,nint,sigma1, + sigma2,steabs,sterel,theta,udelta0 C ARRAY ARGUMENTS integer ind(n) double precision d(n),g(n),l(n),lambda(m),lastgpns(0:maxitngp-1), + rho(m),s(n),u(n),w(5*n),x(n),y(n) C Solves the box-constrained minimization problem C C Minimize f(x) C C subject to C C l <= x <= u C C using a method described in C C E. G. Birgin and J. M. Martinez, ''Large-scale active-set box- C constrained optimization method with spectral projected C gradients'', Computational Optimization and Applications 23, pp. C 101-125, 2002. C C Subroutine evalal must be supplied by the user to evaluate the C objective function. The prototype of evalal subroutine must be C C subroutine evalal(n,x,m,lambda,rho,f,flag) C C C On Entry: C C C C n integer C C number of variables C C C C x double precision x(n) C C current point C C C C m integer C C number of constraints (equalities plus inequalities) C C C C lambda double precision lambda(m) C C current estimation of the Lagrange multipliers C C C C rho double precision rho(m) C C penalty parameters C C C C NOTE: arguments m, lambda and rho are useful when GENCAN is C C being used for solving the box-constrained subproblems of an C C Augmented Lagrangian framework. When GENCAN is being used C C stand-alone for solving a bound-constrained problem, these C C arguments are dummy arguments and must be ignored. C C C C On Return C C C C f double precision C C objective function value at x C C C C flag integer C C 0 means ''no errors'' C C any other value means ''there was an error in the C C objective function calculation''. C C C C SCALAR ARGUMENTS C integer flag,m,n C double precision f C C C ARRAY ARGUMENTS C double precision lambda(m),rho(m),x(n) C C C ''Here it should be the body of evalal subroutine that saves C C in f the objective function value at x. Moreover, it sets C C flag equal to 0 if the calculation was successfully done and C C sets flag equal to any other value different from 0 if the C C objective function is not well defined at the current point C C x.'' C C end C C Subroutine evalnal to calculate the gradient of the objective C function may be supplied by the user or not, depending on the C value of gtype argument (gtype equal to 0 means that the evalnal C subroutine will be supplied by the user and gtype equal to 1 means C that an internal GENCAN subroutine will be used to estimate the C gradient vector by central finite differences). In any case, a C subroutine named evalnal with the following prototype must C present. C C subroutine evalnal(n,x,m,lambda,rho,g,flag) C C C On Entry: C C C n integer C C number of variables C C C C x double precision x(n) C C current point C C C C m integer C C number of constraints (equalities plus inequalities) C C C C lambda double precision lambda(m) C C current estimation of the Lagrange multipliers C C C C rho double precision rho(m) C C penalty parameters C C C C NOTE: arguments m, lambda and rho are useful when GENCAN is C C being used for solving the box-constrained subproblems of an C C Augmented Lagrangian framework. When GENCAN is being used C C stand-alone for solving a bound-constrained problem, these C C arguments are dummy arguments and must be ignored. C C C C On Return C C C C g double precision g(n) C C gradient of the objective function at x C C C C flag integer C C 0 means ''no errors'', C C any other value means ''there was an error in the C C gradient calculation''. C C C C SCALAR ARGUMENTS C integer flag,m,n C C C ARRAY ARGUMENTS C double precision g(n),lambda(m),rho(m),x(n) C C C ''Here it should be the body of evalnal subroutine that C C saves in g the gradient vector of the objective function at C C x. Moreover, it sets flag equal to 0 if the calculation was C C successfully done and sets flag equal to any other value C C different from 0 if the gradient vector is not well defined C C at the current point x. If GENCAN gtype argument was setted C C to 1, i.e., the finite difference approximation provided by C C GENCAN will be used, then this subroutine must even be C C present for compilation purpose but it will never be C C called.'' C C end C C Subroutine evalhd to calculate of the Hessian of the objective C function times a given vector may be supplied by the user or not, C depending on the value of htvtype argument (htvtype equal to 0 C means that the evalhd subroutine will be supplied by the user and C htvtype equal to 1 means tha an internal GENCAN subroutine will be C used to estimate the product by incremental quotients). In any C case, a subroutine named evalhd with the following prototype must C present. C C subroutine evalhd(nind,ind,n,x,m,lambda,rho,d,hd,flag) C C C On Entry: C C C C nind integer C C number of component of the Hessian-vector product that C C must be computed C C C C ind integer ind(nind) C C the component that must be computed are ind(1)-th ... C C ind(nind)-th C C C C n integer C C number of variables C C C C x double precision x(n) C C current point C C C C m integer C C number of constraints (equalities plus inequalities) C C C C lambda double precision lambda(m) C C current estimation of the Lagrange multipliers C C C C rho double precision rho(m) C C penalty parameters C C C C NOTE: arguments m, lambda and rho are useful when GENCAN is C C being used for solving the box-constrained subproblems of an C C Augmented Lagrangian framework. When GENCAN is being used C C stand-alone for solving a bound-constrained problem, these C C arguments are dummy arguments and must be ignored. C C C C d double precision d(n) C C vector of the Hessian-vector product C C C C On Return C C C C hd double precision g(n) C C Hessian-vector product C C C C flag integer C C 0 means ''no errors'', C C any other value means ''there was an error in the C C product calculation''. Just as an example, as it has C C no sense that an error occurs in a matrix-vector C C product, the error could happen in the Hessian C C calculation. But the possible errors will depend C C on the way this Hessian-vector product is computed C C or approximated. C C C SCALAR ARGUMENTS C integer flag,m,n,nind C C C ARRAY ARGUMENTS C integer ind(nind) C double precision d(n),hd(n),lambda(m),rho(m),x(n) C C C ''Here it should be the body of evalhd subroutine that saves C C in hd the product of the Hessian of the objective function C C times vector d. Moreover, it sets flag equal to 0 if the C C calculation was successfully done and sets flag equal to any C C other value different from 0 if the Hessian matrix is not C C well defined at the current point x. If GENCAN htvtype C C argument was setted to 1, i.e., the incremental quotients C C approximation provided by GENCAN will be used, then this C C subroutine must even be present for compilation purposes C C but it will never be called.'' C C end C C In evalhd subroutine, the information about the matrix H must be C passed by means of common declarations. This subroutine must be C coded by the user, taking into account that only nind components C of d are nonnull and that ind is the set of indices of those C components. In other words, the user must write evalhd in such a C way that hd is the vector whose i-th entry is C C hd(i) = \Sum_{j=1}^{nind} H_{i,ind(j)} d_ind(j) C C Moreover, the only components of hd that must be computed are C those which correspond to the indices ind(1),...,ind(nind). C However, observe that it must be assumed that, in d, the whole C dense vector is present, with its n components, even the null C ones. So, if the user decides to code evalhd without taking into C account the presence of ind and nind, it can be easily done. A C final observation: probably, if nind is close to n, it is not C worthwhile to use ind, due to the cost of accessing the correct C indices. C C Example: Assume that H is dense. The main steps of evalhd could C be: C C do i = 1,nind C indi = ind(i) C hd(indi) = 0.0d0 C do j = 1,nind C indj = ind(j) C hd(indi) = hd(indi) + H(indi,indj) * d(indj) C end do C end do C C C Description of the GENCAN arguments: C C On Entry C C n integer C number of variables C C x double precision x(n) C initial estimation of the solution C C l double precision l(n) C lower bounds on the variables C C u double precision u(n) C upper bounds on the variables C C m integer C lambda double precision lambda(m) C rho double precision rho(m) C These three parameters are not used nor modified by C GENCAN and they are passed as arguments to the user- C defined subroutines evalal and evalnal to compute the C objective function and its gradient, respectively. C Clearly, in an Augmented Lagrangian context, if GENCAN is C being used to solve the bound-constrainted subproblems, m C would be the number of constraints, lambda the Lagrange C multipliers approximation and rho the penalty parameters C C epsgpen double precision C epsgpen means EPSilon for the Projected Gradient Euclidian C Norm. It is a small positive number for declaring C convergence when the Euclidian norm of the continuous C projected gradient is less than or equal to epsgpen C C RECOMMENDED: epsgpen = 1.0d-05 C C CONSTRAINTS: epsgpen >= 0.0 C C epsgpsn double precision C epsgpsn means EPSilon for the Projected Gradient Sup Norm. C It is a small positive number for declaring convergence C when the sup norm of the continuous projected gradient is C less than or equal to epsgpsn C C RECOMMENDED: epsgpsn = 1.0d-05 C C CONSTRAINTS: epsgpsn >= 0.0 C C maxitnfp integer C maxitnfp means MAXimum of ITerations with No Function C Progress. See below for more details. C C epsnfp double precision C epsnfp means EPSilon for No Function Progress. It is a C small positive number for declaring ''lack of progress in C the objective function value'' if f(x_k) - f(x_{k+1}) <= C epsnfp * max{ f(x_j) - f(x_{j+1}, j < k } during maxitnfp C consecutive iterations. This stopping criterion may be C inhibited setting maxitnfp equal to maxit. C C RECOMMENDED: maxitnfp = 5 and epsnfp = 1.0d-02 C C CONSTRAINTS: maxitnfp >= 1 and epsnfp >= 0.0 C C maxitngp integer C maxitngp means MAXimum of ITerations with No Gradient C Progress. If the order of the Euclidian norm of the C continuous projected gradient did not change during C maxitngp consecutive iterations then the execution stops. C C RECOMMENDED: maxitngp = 10 C C CONSTRAINTS: maxitngp >= 1 C C fmin double precision C function value for the stopping criteria f <= fmin C C There is a stopping criterion that stops GENCAN if a C point with a functional value smaller than fmin is found. C The idea behind this stopping criterion is to stop the C method if the objective function is not bounded from C below. C C RECOMMENDED: fmin = - infabs C C CONSTRAINTS: there are no constraints for this argument C C maxit integer C maximum number of allowed iterations C C RECOMMENDED: maxit = 1000 C C CONSTRAINTS: maxit >= 0 C C maxfc integer C maximum allowed number of functional evaluations C C RECOMMENDED: maxfc = 5 * maxit C C CONSTRAINTS: maxfc >= 1 C C udelta0 double precision C initial ''trust-radius'' for Conjugate Gradients. The C default value max( delmin, 0.1 * max( 1, ||x|| ) ) is C used if the user sets udelta0 <= 0. C C RECOMMENDED: udelta0 = - 1.0 C C CONSTRAINTS: there are no constraints for this argument C C ucgmaxit integer C maximum allowed number of iterations for each run of the C Conjugate Gradient subalgorithm C C The default values for this argument is max( 1, 10 * C log( nind ) ), where nind is the number of free C variables, and it will be used if the user sets ucgmaxit C to any non-positive value. C C RECOMMENDED: ucgmaxit = - 1 C C CONSTRAINTS: there are no constraints for this argument C C cgscre integer C See below C C cggpnf double precision C cgscre means conjugate gradient stopping criterion C relation, and cggpnf means Conjugate Gradients projected C gradient final norm. Both are related to a stopping C criterion of Conjugate Gradients. This stopping criterion C depends on the norm of the residual of the linear system. C The norm of the residual should be less or equal than a C ''small'' quantity which decreases as we are C approximating the solution of the minimization problem C (near the solution, better the truncated-Newton direction C we aim). Then, the log of the required accuracy requested C to Conjugate Gradient has a linear dependence on the log C of the norm of the continuous projected gradient. This C linear relation uses the squared Euclidian norm of the C projected gradient if cgscre is equal to 1 and uses the C sup-norm if cgscre is equal to 2. In addition, the C precision required to CG is equal to cgepsi (conjugate C gradient initial epsilon) at x0 and cgepsf (conjugate C gradient final epsilon) when the Euclidian- or sup-norm C of the projected gradient is equal to cggpnf (conjugate C gradients projected gradient final norm) which is an C estimation of the value of the Euclidian- or sup-norm of C the projected gradient at the solution. C C RECOMMENDED: cgscre = 1, cggpnf = epsgpen; or C cgscre = 2, cggpnf = epsgpsn. C C CONSTRAINTS: allowed values for cgscre are just 1 or 2 C cggpnf >= 0.0 C C cgepsi double precision C See below C C cgepsf double precision C small positive numbers for declaring convergence of the C Conjugate Gradients subalgorithm when ||r||_2 < cgeps * C ||rhs||_2, where r is the residual and rhs is the right C hand side of the linear system, i.e., CG stops when the C relative error of the solution is smaller than cgeps. C C cgeps varies from cgepsi to cgepsf in a way that depends C on cgscre as follows: C C i) CASE cgscre = 1: log10(cgeps^2) depends linearly on C log10(||g_P(x)||_2^2) which varies from ||g_P(x_0)||_2^2 C to epsgpen^2 C C ii) CASE cgscre = 2: log10(cgeps) depends linearly on C log10(||g_P(x)||_inf) which varies from ||g_P(x_0)||_inf C to epsgpsn C C RECOMMENDED: cgepsi = 1.0d-01, cgepsf = 1.0d-05 C C CONSTRAINTS: cgepsi >= cgepsf >= 0.0 C C epsnqmp double precision C See below C C maxitnqmp integer C This and the previous argument are used for a stopping C criterion of the Conjugate Gradients subalgorithm. If the C progress in the quadratic model is smaller than fraction C of the best progress ( epsnqmp * bestprog ) during C maxitnqmp consecutive iterations then CG is stopped C declaring ''not enough progress of the quadratic model''. C C RECOMMENDED: epsnqmp = 1.0d-04, maxitnqmp = 5 C C CONSTRAINTS: epsnqmp >= 0.0, maxitnqmp >= 1. C C nearlyq logical C If the objective function is (nearly) quadratic, use the C option nearlyq = TRUE. Otherwise, keep the default C option. C C If, in an iteration of CG we find a direction d such that C d^T H d <= 0 then we take the following decision: C C (i) If nearlyq = TRUE then we take direction d and try to C go to the boundary choosing the best point among the two C points at the boundary and the current point. C C (ii) If nearlyq = FALSE then we stop at the current point. C C Moreover, if the objective function is quadratic more c effort is due in computing the Truncated Newton direction. C C RECOMMENDED: nearlyq = FALSE C C CONSTRAINTS: allowed values are just TRUE or FALSE. C C nint double precision C Constant for the interpolation. See the description of C sigma1 and sigma2 above. Sometimes, in a line search, we C take the new trial step as the previous one divided by C nint C C RECOMMENDED: nint = 2.0 C C CONSTRAINTS: nint > 1.0. C C next double precision C Constant for the extrapolation. When extrapolating we C try alpha_new = alpha * next C C RECOMMENDED: next = 2.0 C C CONSTRAINTS: next > 1.0 C C mininterp integer C Constant for testing if, after having made at least C mininterp interpolations, the steplength is too small. In C that case, failure of the line search is declared (may be C the direction is not a descent direction due to an error C in the gradient calculations). Use mininterp greater C than or equal to maxfc for inhibit this stopping C criterion C C RECOMMENDED: mininterp = 4 C C CONSTRAINTS: mininterp >= 1 C C maxextrap integer C Constant to limit the number of extrapolations in the C Truncated Newton direction. C C RECOMMENDED: maxextrap = 100 C C CONSTRAINTS: maxextrap >= 0 C C gtype integer C gtype indicates in which way the gradient of the C objective function will be computed. If the user have C been implemented the user-supplied evalnal subroutine to C compute the gradient of the objective function then C gtype argument must be set to 0 (ZERO) and the user- C supplied evalnal subroutine will be called by GENCAN any C time the gradient would be required. C C subroutine evalnal(n,x,m,lambda,rho,g,flag) C C C On Entry: C C C n integer, C C number of variables, C C C C x double precision x(n), C C current point, C C C C m integer, C C number of constraints (equalities plus C C inequalities), C C C C lambda double precision lambda(m), C C current estimation of the Lagrange C C multipliers, C C C C rho double precision rho(m) C C penalty parameters, C C C C NOTE: arguments m, lambda and rho are useful when C C GENCAN is being used for solving the box- C C constrained subproblems of an Augmented Lagrangian C C framework. When GENCAN is being used stand-alone C C for solving a bound-constrained problem, these C C arguments are dummy arguments. C C C C On Return C C C C g double precision g(n), C C gradient of the objective function at x, C C C C flag integer C C 0 means ''no errors'', C C 1 means ''some error occurs in the gradient C C evaluation''. C C C C SCALAR ARGUMENTS C integer flag,m,n C C C ARRAY ARGUMENTS C double precision g(n),lambda(m),rho(m),x(n) C C C ''Here it should be the body of evalnal subroutine C C that saves in g the gradient vector of the C C objective at x. Moreover, it sets flag equal to 0 C C if the calculation was successfully done and sets C C flag equal to any other value different from 0 if C C the gradient vector is not well defined at the C C current point x. If GENCAN gtype argument was C C setted to 1, i.e., the finite difference C C approximation provided by GENCAN will be used, then C C this subroutine must even be present for C C compilation purposes but it will never be called.'' C C end C C If, on the other hand, the user is not able to provide C evalnal subroutine, gtype argument must be set to 1 C (ONE). In this case, every time GENCAN needs to compute C the gradient of the objective function, an internal C subroutine that approximates it by finite-differences C will be used (be aware that it maybe very time C consuming). Moreover, note that the evalnal subroutine C must still be present (with an empty body). C C RECOMMENDED: gtype = 0 (provided you have the evalg C subroutine) C C CONSTRAINTS: allowed values are just 0 or 1. C C htvtype integer C htvtype indicates in which way the product of the Hessian C of the objective function times an arbitrary vector will be C computed. If the user has not been implemented the user- C supplied evalhd subroutine to do this task then htvtype C argument must be set to 1 (ONE). In this case an internal C subroutine that approximates this product by incremental C quotients will be used. Note that, even in this case, C evalhd subroutine must be present (with an empty body). C This is the default option and the empty-body subroutine C follows: C C subroutine evalhd(nind,ind,n,x,m,lambda,rho,d,hd,flag) C C C SCALAR ARGUMENTS C integer nind,n,m,flag C C C ARRAY ARGUMENTS C integer ind(nind) C double precision x(n),lambda(m),rho(m),d(n),hd(n) C C flag = - 1 C C end C C If, on the other hand, the user prefers to implement his/ C her own evalhd subroutine then htvtype argument must be C set to 0 (ZERO). In this case, the product of the Hessian C times vector d (input argument of evalhd subroutine) must C be saved in vector hd (output argument of evalhd C subroutine). The other arguments description as well as C some hints on how to implement your own evalhd subroutine C can be found in the GENCAN arguments description. C C RECOMMENDED: htvtype = 1 C C (you take some risk using this option but, unless you C have a good evalhd subroutine, incremental quotients is a C very cheap option) C C CONSTRAINTS: allowed values are just 0 or 1. C C trtype integer C Type of Conjugate Gradients ''trust-radius''. trtype C equal to 0 means Euclidian-norm trust-radius and trtype C equal to 1 means sup-norm trust radius C C RECOMMENDED: trtype = 0 C C CONSTRAINTS: allowed values are just 0 or 1. C C iprint integer C Commands printing. Nothing is printed if iprint is C smaller than 2. If iprint is greater than or equal to C 2, GENCAN iterations information is printed. If iprint C is greater than or equal to 3, line searches and C Conjugate Gradients information is printed. C C RECOMMENDED: iprint = 2 C C CONSTRAINTS: allowed values are just 2 or 3. C C ncomp integer C This constant is just for printing. In a detailed C printing option, ncomp component of some vectors will be C printed C C RECOMMENDED: ncomp = 5 C C CONSTRAINTS: ncomp >= 0 C C s double precision s(n) C y double precision y(n) C d double precision d(n) C ind integer ind(n) C lastgpns double precision lastgpns(maxitngp) C w double precision w(5*n) C working vectors C C eta double precision C Constant for deciding abandon the current face or not. We C abandon the current face if the norm of the internal C gradient (here, internal components of the continuous C projected gradient) is smaller than ( 1 - eta ) times the C norm of the continuous projected gradient. Using eta = C 0.9 is a rather conservative strategy in the sense that C internal iterations are preferred over SPG iterations. C C RECOMMENDED: eta = 0.9 C C CONSTRAINTS: 0.0 < eta < 1.0 C C delmin double precision C Smaller Conjugate Gradients ''trust radius'' to compute C the Truncated Newton direction C C RECOMMENDED: delmin = 0.1 C C CONSTRAINTS: delmin > 0.0 C C lspgmi double precision C See below C C lspgma double precision C The spectral steplength, called lamspg, is projected onto C the box [lspgmi,lspgma] C C RECOMMENDED: lspgmi = 1.0d-10 and lspgma = 1.0d+10 C C CONSTRAINTS: lspgma >= lspgmi > 0.0 C C theta double precision C Constant for the angle condition, i.e., at iteration k we C need a direction dk such that <= - theta C ||gk||_2 ||dk||_2, where gk is \nabla f(xk) C C RECOMMENDED: theta = 10^{-6} C C CONSTRAINTS: 0.0 < theta < 1.0 C C gamma double precision C Constant for the Armijo criterion C f(x + alpha d) <= f(x) + gamma * alpha * C C RECOMMENDED: gamma = 1.0d-04 C C CONSTRAINTS: 0.0 < gamma < 0.5. C C beta double precision C Constant for the beta condition < beta C * . If (xk + dk) satisfies the Armijo condition C but does not satisfy the beta condition then the point is C accepted, but if it satisfied the Armijo condition and C also satisfies the beta condition then we know that there C is the possibility for a successful extrapolation C C RECOMMENDED: beta = 0.5 C C CONSTRAINTS: 0.0 < beta < 1.0. C C sigma1 double precision C See below C C sigma2 double precision C Constant for the safeguarded interpolation. If alpha_new C is not inside the interval [sigma1, sigma * alpha] then C we take alpha_new = alpha / nint C C RECOMMENDED: sigma1 = 0.1 and sigma2 = 0.9 C C CONSTRAINTS: 0 < sigma1 < sigma2 < 1. C C sterel double precision C See below C C steabs double precision C This constants mean a ''relative small number'' and ''an C absolute small number'' for the increments in finite C difference approximations of derivatives C C RECOMMENDED: epsrel = 1.0d-07 and epsabs = 1.0d-10 C C CONSTRAINTS: sterel >= steabs > 0 C C epsrel double precision C See below C C epsabs double precision C See below C C infrel double precision C See below C C infabs double precision C This four constants mean a ''relative small number'', C ''an absolute small number'', ''a relative large number'' C and ''an absolute large number''. Basically, a quantity A C is considered negligible with respect to another quantity C B if |A| < max ( epsrel * |B|, epsabs ) C C RECOMMENDED: epsrel = 1.0d-10, epsabs = 1.0d-20, C infrel = 1.0d+20, infabs = 1.0d+99 C C CONSTRAINTS: epsrel >= epsabs >= 0.0 C infabs >= infrel >= 0.0 C C On Return C C x double precision x(n) C Final estimation to the solution C C f double precision C Function value at the final estimation C C g double precision g(n) C Gradient at the final estimation C C gpeucn2 double precision C Squared Euclidian norm of the continuous projected C gradient at the final estimation C C gpsupn double precision C the same as before but with sup-norm C C iter integer C number of iterations C C fcnt integer C number of function evaluations C C gcnt integer C number of gradient evaluations C C cgcnt integer C number of Conjugate Gradients iterations C C spgiter integer C number of Spectral Projected Gradient iterations C C spgfcnt integer C number of functional evaluations along Spectral Projected C Gradient directions C C tniter integer C number of Truncated-Newton iterations C C tnfcnt integer C number of functional evaluations along Truncated-Newton C directions C C tnintcnt integer C number of times a backtracking in a Truncated-Newton C direction was needed C C tnexgcnt integer C number of times an extrapolation in a Truncated-Newton C direction successfully decreased the objective funtional C value C C tnexbcnt integer C number of times an extrapolation was aborted in the first C extrapolated point by an increase in the objective C functional value C C tnstpcnt integer C number of times the Newton point was accepted (without C interpolations nor extrapolations) C C tnintfe integer C number of functional evaluations used in interpolations C along Truncated-Newton directions C C tnexgfe integer C number of functional evaluations used in successful C extrapolations along Truncated-Newton directions C C tnexbfe integer C number of functional evaluations used in unsuccessful C extrapolations along Truncated-Newton directions C C inform integer C This output parameter tells what happened in this C subroutine, according to the following conventions: C C 0 = convergence with small Euclidian norm of the C continuous projected gradient (smaller than epsgpen); C C 1 = convergence with small sup-norm of the continuous C projected gradient (smaller than epsgpsn); C C 2 = the algorithm stopped by ''lack of progress'', that C means that f(xk) - f(x_{k+1}) <= epsnfp * C max{ f(x_j) - f(x_{j+1}, j < k } during maxitnfp C consecutive iterations. If desired, set maxitnfp C equal to maxit to inhibit this stopping criterion. C C 3 = the algorithm stopped because the order of the C Euclidian norm of the continuous projected gradient C did not change during maxitngp consecutive C iterations. Probably, we are asking for an C exaggerated small norm of continuous projected C gradient for declaring convergence. If desired, set C maxitngp equal to maxit to inhibit this stopping C criterion. C C 4 = the algorithm stopped because the functional value c is very small (smaller than fmin). If desired, set C fmin equal to minus infabs to inhibit this stopping C criterion. C C 6 = too small step in a line search. After having made at C least mininterp interpolations, the steplength C becames small. ''small steplength'' means that we are C at point x with direction d and step alpha, and C C alpha * ||d||_infty < max( epsabs, epsrel * C ||x||_infty ). C C In that case failure of the line search is declared C (may be the direction is not a descent direction due C to an error in the gradient calculations). If C desired, set mininterp equal to maxfc to inhibit this C stopping criterion. C C 7 = it was achieved the maximum allowed number of C iterations (maxit); C C 8 = it was achieved the maximum allowed number of C function evaluations (maxfc); C C < 0 = error in evalal, evalnal or evalhd subroutines. C LOCAL SCALARS character * 3 ittype integer cgiter,cgmaxit,fcntprev,i,infotmp,itnfp,nind,nprint, + rbdind,rbdtype,tnexbprev,tnexgprev,tnintprev double precision acgeps,amax,amaxx,bestprog,bcgeps,cgeps,currprog, + delta,epsgpen2,fprev,gieucn2,gpeucn20,gpi,gpnmax,gpsupn0, + kappa,lamspg,ometa2,sts,sty,xnorm logical packmolprecision C ================================================================== C Initialization C ================================================================== C Set some initial values: C counters, iter = 0 fcnt = 0 gcnt = 0 cgcnt = 0 spgiter = 0 spgfcnt = 0 tniter = 0 tnfcnt = 0 tnstpcnt = 0 tnintcnt = 0 tnexgcnt = 0 tnexbcnt = 0 tnintfe = 0 tnexgfe = 0 tnexbfe = 0 C just for printing, nprint = min0( n, ncomp ) C for testing convergence, epsgpen2 = epsgpen ** 2 C for testing whether to abandon the current face or not, C (ometa2 means '(one minus eta) squared') ometa2 = ( 1.0d0 - eta ) ** 2 C for testing progress in f, and fprev = infabs bestprog = 0.0d0 itnfp = 0 C for testing progress in the projected gradient norm. do i = 0,maxitngp - 1 lastgpns(i) = infabs end do C Print problem information if( iprint .ge. 3 ) then write(*, 977) n write(*, 978) nprint,(l(i),i=1,nprint) write(*, 979) nprint,(u(i),i=1,nprint) write(*, 980) nprint,(x(i),i=1,nprint) write(10,977) n write(10,978) nprint,(l(i),i=1,nprint) write(10,979) nprint,(u(i),i=1,nprint) write(10,980) nprint,(x(i),i=1,nprint) end if C Project initial guess. If the initial guess is infeasible, C projection puts it into the box. do i = 1,n x(i) = max( l(i), min( x(i), u(i) ) ) end do C Compute x Euclidian norm xnorm = 0.0d0 do i = 1,n xnorm = xnorm + x(i) ** 2 end do xnorm = sqrt( xnorm ) C Compute function and gradient at the initial point call evalal(n,x,m,lambda,rho,f,inform) c LM: Added packmolprecision function test, for Packmol if ( packmolprecision(n,x) ) then if(iprint.gt.0) then write(*,780) 780 format(' Current point is a solution.') end if return end if fcnt = fcnt + 1 if ( inform .lt. 0 ) then if ( iprint .ge. 3 ) then write(*, 1000) inform write(10,1000) inform end if return end if if ( gtype .eq. 0 ) then call evalnal(n,x,m,lambda,rho,g,inform) else ! if ( gtype .eq. 1 ) then call evalnaldiff(n,x,m,lambda,rho,g,sterel,steabs,inform) end if gcnt = gcnt + 1 if ( inform .lt. 0 ) then if ( iprint .ge. 3 ) then write(*, 1000) inform write(10,1000) inform end if return end if C Compute continuous-project-gradient Euclidian and Sup norms, C internal gradient Euclidian norm, and store in nind the number of C free variables and in array ind their identifiers. nind = 0 gpsupn = 0.0d0 gpeucn2 = 0.0d0 gieucn2 = 0.0d0 do i = 1,n gpi = min( u(i), max( l(i), x(i) - g(i) ) ) - x(i) gpsupn = max( gpsupn, abs( gpi ) ) gpeucn2 = gpeucn2 + gpi ** 2 if ( x(i) .gt. l(i) .and. x(i) .lt. u(i) ) then gieucn2 = gieucn2 + gpi ** 2 nind = nind + 1 ind(nind) = i end if end do C Compute a linear relation between gpeucn2 and cgeps2, i.e., C scalars a and b such that c C a * log10(||g_P(x_0)||_2^2) + b = log10(cgeps_0^2) and c C a * log10(||g_P(x_f)||_2^2) + b = log10(cgeps_f^2), c C where cgeps_0 and cgeps_f are provided. Note that if C cgeps_0 is equal to cgeps_f then cgeps will be always C equal to cgeps_0 and cgeps_f. C We introduce now a linear relation between gpsupn and cgeps also. c LM: changed to avoid error with gpsupn=0 if ( gpsupn .ne. 0.0d0 ) then acgeps = log10( cgepsf / cgepsi ) / log10( cggpnf / gpsupn ) bcgeps = log10( cgepsi ) - acgeps * log10( gpsupn ) else acgeps = 0.0d0 bcgeps = cgepsf end if c if ( cgscre .eq. 1 ) then c acgeps = 2.0d0 * log10( cgepsf / cgepsi ) / c + log10( cggpnf ** 2 / gpeucn2 ) c bcgeps = 2.0d0 * log10( cgepsi ) - acgeps * log10( gpeucn2 ) c else ! if ( cgscre .eq. 2 ) then c acgeps = log10( cgepsf / cgepsi ) / log10( cggpnf / gpsupn ) c bcgeps = log10( cgepsi ) - acgeps * log10( gpsupn ) c end if C And it will be used for the linear relation of cgmaxit gpsupn0 = gpsupn gpeucn20 = gpeucn2 C Print initial information if( iprint .ge. 2 ) then c LM: output for packmol c write(*,1003) iter,f,gpsupn if((mod((iter-1),10).eq.0.or.iter.eq.0).and.iter.ne.1) then write(*,778) else if(mod(iter,10).eq.0) then write(*,779) else if(iter.ne.1) then write(*,777) end if end if 777 format('*******',$) 778 format(' |',$) 779 format('**********|') if( iprint .ge. 3 ) then write(*, 981) iter write(*, 985) nprint,(x(i),i=1,nprint) write(*, 986) nprint,(g(i),i=1,nprint) write(*, 987) nprint,(min(u(i),max(l(i),x(i)-g(i)))-x(i),i=1, + nprint) write(*, 988) min0(nprint,nind),nind,(ind(i),i=1,min0(nprint, + nind)) write(*, 1002) f,sqrt(gpeucn2),sqrt(gieucn2),gpsupn,nind,n, + spgiter,tniter,fcnt,gcnt,cgcnt write(10,981) iter write(10,985) nprint,(x(i),i=1,nprint) write(10,986) nprint,(g(i),i=1,nprint) write(10,987) nprint,(min(u(i),max(l(i),x(i)-g(i)))-x(i),i=1, + nprint) write(10,988) min0(nprint,nind),nind,(ind(i),i=1,min0(nprint, + nind)) write(10,1002) f,sqrt(gpeucn2),sqrt(gieucn2),gpsupn,nind,n, + spgiter,tniter,fcnt,gcnt,cgcnt end if C ================================================================== C Main loop C ================================================================== 100 continue C ================================================================== C Test stopping criteria C ================================================================== c LM: Added packmolprecision function test, for Packmol if ( packmolprecision(n,x) ) then goto 500 end if C Test whether the continuous-projected-gradient Euclidian norm C is small enough to declare convergence if ( gpeucn2 .le. epsgpen2 ) then inform = 0 if ( iprint .ge. 3 ) then write(*, 990) inform,epsgpen write(10,990) inform,epsgpen end if go to 500 end if C Test whether the continuous-projected-gradient Sup norm C is small enough to declare convergence if ( gpsupn .le. epsgpsn ) then inform = 1 if ( iprint .ge. 3 ) then write(*, 991) inform,epsgpsn write(10,991) inform,epsgpsn end if go to 500 end if C Test whether we performed many iterations without good progress C of the functional value currprog = fprev - f bestprog = max( currprog, bestprog ) if ( currprog .le. epsnfp * bestprog ) then itnfp = itnfp + 1 if ( itnfp .ge. maxitnfp ) then inform = 2 if ( iprint .ge. 3 ) then write(*, 992) inform,epsnfp,maxitnfp write(10,992) inform,epsnfp,maxitnfp end if go to 500 endif else itnfp = 0 endif C Test whether we have performed many iterations without good C reduction of the euclidian-norm of the projected gradient gpnmax = 0.0d0 do i = 0,maxitngp - 1 gpnmax = max( gpnmax, lastgpns(i) ) end do lastgpns(mod( iter, maxitngp )) = gpeucn2 if ( gpeucn2 .ge. gpnmax ) then inform = 3 if ( iprint .ge. 3 ) then write(*, 993) inform,maxitngp write(10,993) inform,maxitngp end if go to 500 endif C Test whether the functional value is very small if ( f .le. fmin ) then inform = 4 if ( iprint .ge. 3 ) then write(*, 994) inform,fmin write(10,994) inform,fmin end if go to 500 end if C Test whether the number of iterations is exhausted if ( iter .ge. maxit ) then inform = 7 if ( iprint .ge. 3 ) then write(*, 997) inform,maxit write(10,997) inform,maxit end if go to 500 end if C Test whether the number of functional evaluations is exhausted if ( fcnt .ge. maxfc ) then inform = 8 if ( iprint .ge. 3 ) then write(*, 998) inform,maxfc write(10,998) inform,maxfc end if go to 500 end if C ================================================================== C The stopping criteria were not satisfied, a new iteration will be C made C ================================================================== iter = iter + 1 C ================================================================== C Save current values, f, x and g C ================================================================== fprev = f do i = 1,n s(i) = x(i) y(i) = g(i) end do C ================================================================== C Compute new iterate C ================================================================== C We abandon the current face if the norm of the internal gradient C (here, internal components of the continuous projected gradient) C is smaller than (1-eta) times the norm of the continuous C projected gradient. Using eta=0.9 is a rather conservative C strategy in the sense that internal iterations are preferred over C SPG iterations. Replace eta = 0.9 by other tolerance in (0,1) if C you find it convenient. if ( gieucn2 .le. ometa2 * gpeucn2 ) then C ============================================================== C Some constraints should be abandoned. Compute the new iterate C using an SPG iteration C ============================================================== ittype = 'SPG' spgiter = spgiter + 1 C Compute spectral steplength if ( iter .eq. 1 .or. sty .le. 0.0d0 ) then lamspg = max( 1.0d0, xnorm ) / sqrt( gpeucn2 ) else lamspg = sts / sty end if lamspg = min( lspgma, max( lspgmi, lamspg ) ) C Perform a line search with safeguarded quadratic interpolation C along the direction of the spectral continuous projected C gradient fcntprev = fcnt call spgls(n,x,m,lambda,rho,f,g,l,u,lamspg,nint,mininterp, + fmin,maxfc,iprint,fcnt,inform,w(1),w(n+1),gamma,sigma1,sigma2, + sterel,steabs,epsrel,epsabs,infrel,infabs) spgfcnt = spgfcnt + ( fcnt - fcntprev ) if ( inform .lt. 0 ) then if ( iprint .ge. 3 ) then write(*, 1000) inform write(10,1000) inform end if return end if C Compute the gradient at the new iterate if ( gtype .eq. 0 ) then call evalnal(n,x,m,lambda,rho,g,inform) else ! if ( gtype .eq. 1 ) then call evalnaldiff(n,x,m,lambda,rho,g,sterel,steabs,inform) end if gcnt = gcnt + 1 if ( inform .lt. 0 ) then if ( iprint .ge. 3 ) then write(*, 1000) inform write(10,1000) inform end if return end if else C ============================================================== C The new iterate will belong to the closure of the current face C ============================================================== ittype = 'TN ' tniter = tniter + 1 C Compute trust-region radius if ( iter .eq. 1 ) then if( udelta0 .le. 0.0d0 ) then delta = max( delmin, 0.1d0 * max( 1.0d0, xnorm ) ) else delta = udelta0 end if else delta = max( delmin, 10.0d0 * sqrt( sts ) ) end if C Shrink the point, its gradient and the bounds call shrink(nind,ind,n,x) call shrink(nind,ind,n,g) call shrink(nind,ind,n,l) call shrink(nind,ind,n,u) C Compute the descent direction solving the newtonian system by C conjugate gradients C Set conjugate gradient stopping criteria. Default values are C taken if you set ucgeps < 0 and ucgmaxit < 0, respectively. C Otherwise, the parameters cgeps and cgmaxit will be the ones C set by the user. if( ucgmaxit .le. 0 ) then if ( nearlyq ) then cgmaxit = nind else if ( cgscre .eq. 1 ) then kappa = log10( gpeucn2 / gpeucn20 )/ + log10( epsgpen2 / gpeucn20 ) else ! if ( cgscre .eq. 2 ) then kappa= log10( gpsupn / gpsupn0 ) / + log10( epsgpsn / gpsupn0 ) end if kappa = max( 0.0d0, min( 1.0d0, kappa ) ) cgmaxit = int( + ( 1.0d0 - kappa ) * max( 1.0d0, 10.0d0 * + log10( dfloat( nind ) ) ) + kappa * dfloat( nind ) ) c L. Martinez added to accelerate the iterations near the solution cgmaxit = min(20,cgmaxit) end if c cgmaxit = 2 * nind else cgmaxit = ucgmaxit end if if ( cgscre .eq. 1 ) then cgeps = sqrt( 10.0d0 ** ( acgeps * log10( gpeucn2 ) + + bcgeps ) ) else ! if ( cgscre .eq. 2 ) then cgeps = 10.0d0 ** ( acgeps * log10( gpsupn ) + bcgeps ) end if cgeps = max( cgepsf, min( cgepsi, cgeps ) ) C Call conjugate gradients call cg(nind,ind,n,x,m,lambda,rho,g,delta,l,u,cgeps,epsnqmp, + maxitnqmp,cgmaxit,nearlyq,gtype,htvtype,trtype,iprint,ncomp,d, + cgiter,rbdtype,rbdind,inform,w(1),w(n+1),w(2*n+1),w(3*n+1), + w(4*n+1),theta,sterel,steabs,epsrel,epsabs,infrel,infabs) cgcnt = cgcnt + cgiter if ( inform .lt. 0 ) then if ( iprint .ge. 3 ) then write(*, 1000) inform write(10,1000) inform end if return end if C Compute maximum step if ( inform .eq. 2 ) then amax = 1.0d0 else amax = infabs do i = 1,nind if ( d(i) .gt. 0.0d0 ) then amaxx = ( u(i) - x(i) ) / d(i) if ( amaxx .lt. amax ) then amax = amaxx rbdind = i rbdtype = 2 end if else if ( d(i) .lt. 0.0d0 ) then amaxx = ( l(i) - x(i) ) / d(i) if ( amaxx .lt. amax ) then amax = amaxx rbdind = i rbdtype = 1 end if end if end do end if C Perform the line search tnintprev = tnintcnt tnexgprev = tnexgcnt tnexbprev = tnexbcnt fcntprev = fcnt call tnls(nind,ind,n,x,m,lambda,rho,l,u,f,g,d,amax,rbdtype, + rbdind,nint,next,mininterp,maxextrap,fmin,maxfc,gtype,iprint, + fcnt,gcnt,tnintcnt,tnexgcnt,tnexbcnt,inform,w(1),w(n+1), + w(2*n+1),gamma,beta,sigma1,sigma2,sterel,steabs,epsrel,epsabs, + infrel,infabs) if ( inform .lt. 0 ) then if ( iprint .ge. 3 ) then write(*, 1000) inform write(10,1000) inform end if return end if if ( tnintcnt .gt. tnintprev ) then tnintfe = tnintfe + ( fcnt - fcntprev ) else if ( tnexgcnt .gt. tnexgprev ) then tnexgfe = tnexgfe + ( fcnt - fcntprev ) else if ( tnexbcnt .gt. tnexbprev ) then tnexbfe = tnexbfe + ( fcnt - fcntprev ) else tnstpcnt = tnstpcnt + 1 end if tnfcnt = tnfcnt + ( fcnt - fcntprev ) C Expand the point, its gradient and the bounds call expand(nind,ind,n,x) call expand(nind,ind,n,g) call expand(nind,ind,n,l) call expand(nind,ind,n,u) C If the line search (interpolation) in the Truncated Newton C direction stopped due to a very small step (inform = 6), we C will discard this iteration and force a SPG iteration C Note that tnls subroutine was coded in such a way that in case C of inform = 6 termination the subroutine discards all what was C done and returns with the same point it started if ( inform .eq. 6 ) then if ( iprint .ge. 3 ) then write(*,*) write(*,*) + ' The previous TN iteration was discarded due to', + ' a termination for very small step in the line ', + ' search. A SPG iteration will be forced now. ' write(10,*) write(10,*) + ' The previous TN iteration was discarded due to', + ' a termination for very small step in the line ', + ' search. A SPG iteration will be forced now. ' end if ittype = 'SPG' spgiter = spgiter + 1 C Compute spectral steplength if ( iter .eq. 1 .or. sty .le. 0.0d0 ) then lamspg = max( 1.0d0, xnorm ) / sqrt( gpeucn2 ) else lamspg = sts / sty end if lamspg = min( lspgma, max( lspgmi, lamspg ) ) C Perform a line search with safeguarded quadratic C interpolation along the direction of the spectral C continuous projected gradient fcntprev = fcnt call spgls(n,x,m,lambda,rho,f,g,l,u,lamspg,nint,mininterp, + fmin,maxfc,iprint,fcnt,inform,w(1),w(n+1),gamma,sigma1, + sigma2,sterel,steabs,epsrel,epsabs,infrel,infabs) spgfcnt = spgfcnt + ( fcnt - fcntprev ) if ( inform .lt. 0 ) then if ( iprint .ge. 3 ) then write(*, 1000) inform write(10,1000) inform end if return end if C Compute the gradient at the new iterate infotmp = inform if ( gtype .eq. 0 ) then call evalnal(n,x,m,lambda,rho,g,inform) else ! if ( gtype .eq. 1 ) then call evalnaldiff(n,x,m,lambda,rho,g,sterel,steabs, + inform) end if gcnt = gcnt + 1 if ( inform .lt. 0 ) then if ( iprint .ge. 3 ) then write(*, 1000) inform write(10,1000) inform end if return end if inform = infotmp end if end if C ================================================================== C Prepare for the next iteration C ================================================================== C This adjustment/projection is ''por lo que las putas pudiera'' do i = 1,n if ( x(i) .le. l(i) + max( epsrel * abs( l(i) ), epsabs ) ) + then x(i) = l(i) else if (x(i). ge. u(i) - max( epsrel * abs( u(i) ), epsabs )) + then x(i) = u(i) end if end do C Compute x Euclidian norm xnorm = 0.0d0 do i = 1,n xnorm = xnorm + x(i) ** 2 end do xnorm = sqrt( xnorm ) C Compute s = x_{k+1} - x_k, y = g_{k+1} - g_k, and sts = 0.0d0 sty = 0.0d0 do i = 1,n s(i) = x(i) - s(i) y(i) = g(i) - y(i) sts = sts + s(i) ** 2 sty = sty + s(i) * y(i) end do C Compute continuous-project-gradient Euclidian and Sup norms, C internal gradient Euclidian norm, and store in nind the number of C free variables and in array ind their identifiers. nind = 0 gpsupn = 0.0d0 gpeucn2 = 0.0d0 gieucn2 = 0.0d0 do i = 1,n gpi = min( u(i), max( l(i), x(i) - g(i) ) ) - x(i) gpsupn = max( gpsupn, abs( gpi ) ) gpeucn2 = gpeucn2 + gpi ** 2 if ( x(i) .gt. l(i) .and. x(i) .lt. u(i) ) then gieucn2 = gieucn2 + gpi ** 2 nind = nind + 1 ind(nind) = i end if end do C Print information of this iteration if( iprint .ge. 2 ) then c Output for packmol c write(*, 1003) iter,f,gpsupn if((mod((iter-1),10).eq.0.or.iter.eq.0).and.iter.ne.1) then write(*,778) else if(mod(iter,10).eq.0) then write(*,779) else if(iter.ne.1) then write(*,777) end if end if if ( iprint .ge. 3 ) then write(*, 983) iter,ittype write(*, 985) nprint,(x(i),i=1,nprint) write(*, 986) nprint,(g(i),i=1,nprint) write(*, 987) nprint,(min(u(i),max(l(i),x(i)-g(i)))-x(i),i=1, + nprint) write(*, 988) min0(nprint,nind),nind,(ind(i),i=1,min0(nprint, + nind)) write(*, 1002) f,sqrt(gpeucn2),sqrt(gieucn2),gpsupn,nind,n, + spgiter,tniter,fcnt,gcnt,cgcnt write(10,983) iter,ittype write(10,985) nprint,(x(i),i=1,nprint) write(10,986) nprint,(g(i),i=1,nprint) write(10,987) nprint,(min(u(i),max(l(i),x(i)-g(i)))-x(i),i=1, + nprint) write(10,988) min0(nprint,nind),nind,(ind(i),i=1,min0(nprint, + nind)) write(10,1002) f,sqrt(gpeucn2),sqrt(gieucn2),gpsupn,nind,n, + spgiter,tniter,fcnt,gcnt,cgcnt end if C ================================================================== C Test some stopping criteria that may occur inside the line C searches C ================================================================== if ( inform .eq. 6 ) then if ( iprint .ge. 3 ) then write(*, 996) inform,mininterp,epsrel,epsabs write(10,996) inform,mininterp,epsrel,epsabs end if go to 500 end if C ================================================================== C Iterate C ================================================================== go to 100 C ================================================================== C End of main loop C ================================================================== C ================================================================== C Report output status and return C ================================================================== 500 continue C Print final information if ( iprint .ge. 3 ) then write(*, 982) iter write(*, 985) nprint,(x(i),i=1,nprint) write(*, 986) nprint,(g(i),i=1,nprint) write(*, 987) nprint,(min(u(i),max(l(i),x(i)-g(i)))-x(i),i=1, + nprint) write(*, 988) min0(nprint,nind),nind,(ind(i),i=1,min0(nprint, + nind)) write(*, 1002) f,sqrt(gpeucn2),sqrt(gieucn2),gpsupn,nind,n, + spgiter,tniter,fcnt,gcnt,cgcnt write(10,982) iter write(10,985) nprint,(x(i),i=1,nprint) write(10,986) nprint,(g(i),i=1,nprint) write(10,987) nprint,(min(u(i),max(l(i),x(i)-g(i)))-x(i),i=1, + nprint) write(10,988) min0(nprint,nind),nind,(ind(i),i=1,min0(nprint, + nind)) write(10,1002) f,sqrt(gpeucn2),sqrt(gieucn2),gpsupn,nind,n, + spgiter,tniter,fcnt,gcnt,cgcnt end if return C Non-executable statements 977 format(/1X, 'Entry to GENCAN. Number of variables: ',I7) 978 format(/1X,'Lower bounds (first ',I6, ' components): ', */,6(1X,1PD11.4)) 979 format(/1X,'Upper bounds (first ',I6, ' components): ', */,6(1X,1PD11.4)) 980 format(/1X,'Initial point (first ',I6, ' components): ', */,6(1X,1PD11.4)) 981 format(/1X,'GENCAN iteration: ',I6, ' (Initial point)') 982 format(/1X,'GENCAN iteration: ',I6, ' (Final point)') 983 format(/,1X,'GENCAN iteration: ',I6, *' (This point was obtained using a ',A3,' iteration)') 985 format(1X,'Current point (first ',I6, ' components): ', */,6(1X,1PD11.4)) 986 format(1X,'Current gradient (first ',I6, ' components): ', */,6(1X,1PD11.4)) 987 format(1X,'Current continuous projected gradient (first ',I6, *' components): ',/,6(1X,1PD11.4)) 988 format(1X,'Current free variables (first ',I6, *', total number ',I6,'): ',/,10(1X,I6)) 990 format(/1X,'Flag of GENCAN = ',I3, *' (convergence with Euclidian-norm of the projected gradient', */,1X,'smaller than ',1PD11.4,')') 991 format(/1X,'Flag of GENCAN = ',I3, *' (convergence with sup-norm of the projected gradient', */,1X,'smaller than ',1PD11.4,')') 992 format(/1X,'Flag of GENCAN= ',I3, *' (The algorithm stopped by lack of enough progress. This means', */,1X,'that f(x_k) - f(x_{k+1}) .le. ',1PD11.4, *' * max [ f(x_j)-f(x_{j+1}, j < k ]',/,1X,'during ',I7, *' consecutive iterations') 993 format(/1X,'Flag of GENCAN = ',I3, *' (The algorithm stopped because the order of the', */,1X,'Euclidian-norm of the continuous projected gradient did', *' not change during ',/,1X,I7,' consecutive iterations.', *' Probably, an exaggerated small norm of the',/,1X,'continuous', *' projected gradient is required for declaring convergence') 994 format(/1X,'Flag of GENCAN = ',I3, *' (The algorithm stopped because the functional value is', */,1X,'smaller than ',1PD11.4) 996 format(/1X,'Flag of GENCAN = ',I3, *' (Too small step in a line search. After having made at ', */,1X,'least ',I7,' interpolations, the steplength becames small.', *' Small means that',/,1X,'we were at point x with direction d', *' and took a step alpha such that',/,1X,'alpha * |d_i| .lt.', *' max [',1PD11.4,' * |x_i|,',1PD11.4,' ] for all i)') 997 format(/1X,'Flag of GENCAN = ',I3, *' (It was exceeded the maximum allowed number of iterations', */,1X,'(maxit=',I7,')') 998 format(/1X,'Flag of GENCAN = ',I3, *' (It was exceeded the maximum allowed number of functional', */,1X,'evaluations (maxfc=',I7,')') 1002 format(1X,'Functional value: ', 1PD11.4, */,1X,'Euclidian-norm of the continuous projected gradient: ', *1PD11.4, */,1X,'Euclidian-norm of the internal projection of gp: ',1PD11.4, */,1X,'Sup-norm of the continuous projected gradient: ',1PD11.4, */,1X,'Free variables at this point: ',I7, *' (over a total of ',I7,')', */,1X,'SPG iterations: ',I7, */,1X,'TN iterations: ',I7, */,1X,'Functional evaluations: ',I7, */,1X,'Gradient evaluations: ',I7, */,1X,'Conjugate gradient iterations: ',I7) 1003 format(6X,I6,T22,D17.6,T43,D17.6) C1003 format(6X,'Iter = ',I6,' f = ',1PD11.4,' gpsupn = ',1PD11.4) 1000 format(/1X,'Flag of GENCAN = ',I3,' Fatal Error') end C ****************************************************************** C ****************************************************************** subroutine spgls(n,x,m,lambda,rho,f,g,l,u,lamspg,nint,mininterp, +fmin,maxfc,iprint,fcnt,inform,xtrial,d,gamma,sigma1,sigma2,sterel, +steabs,epsrel,epsabs,infrel,infabs) implicit none C SCALAR ARGUMENTS integer fcnt,m,maxfc,mininterp,n,inform,iprint double precision epsabs,epsrel,f,fmin,gamma,infrel,infabs,lamspg, + nint,sigma1,sigma2,steabs,sterel C ARRAY ARGUMENTS double precision d(n),g(n),l(n),lambda(m),rho(m),u(n),x(n), + xtrial(n) C Safeguarded quadratic interpolation, used in the Spectral C Projected Gradient directions. C C On Entry C C n integer C the order of the x C C x double precision x(n) C current point C C m integer C lambda double precision lambda(m) C rho double precision rho(m) C These three parameters are not used nor modified by C GENCAN and they are passed as arguments to the user- C defined subroutines evalal and evalnal to compute the C objective function and its gradient, respectively. C Clearly, in an Augmented Lagrangian context, if GENCAN is C being used to solve the bound-constrainted subproblems, m C would be the number of constraints, lambda the Lagrange C multipliers approximation and rho the penalty parameters C C f double precision C function value at the current point C C g double precision g(n) C gradient vector at the current point C C l double precision l(n) C lower bounds C C u double precision u(n) C upper bounds C C lamspg double precision C spectral steplength C C nint double precision C constant for the interpolation. See the description of C sigma1 and sigma2 above. Sometimes we take as a new C trial step the previous one divided by nint C C RECOMMENDED: nint = 2.0 C C mininterp integer C constant for testing if, after having made at least C mininterp interpolations, the steplength is so small. In C that case failure of the line search is declared (may be C the direction is not a descent direction due to an error C in the gradient calculations) C C RECOMMENDED: mininterp = 4 C C fmin double precision C functional value for the stopping criterion f <= fmin C C maxfc integer C maximum number of functional evaluations C C iprint integer C Commands printing. Nothing is printed if iprint is C smaller than 2. If iprint is greater than or equal to C 2, GENCAN iterations information is printed. If iprint C is greater than or equal to 3, line searches and C Conjugate Gradients information is printed. C C RECOMMENDED: iprint = 2 C C CONSTRAINTS: allowed values are just 2 or 3. C C xtrial double precision xtrial(n) C d double precision d(n) C working vectors C C gamma double precision C constant for the Armijo criterion C f(x + alpha d) <= f(x) + gamma * alpha * <\nabla f(x),d> C C RECOMMENDED: gamma = 10^{-4} C C sigma1 double precision C sigma2 double precision C constant for the safeguarded interpolation C if alpha_new \notin [sigma1, sigma*alpha] then we take C alpha_new = alpha / nint C C RECOMMENDED: sigma1 = 0.1 and sigma2 = 0.9 C C sterel double precision C steabs double precision C this constants mean a ``relative small number'' and ``an C absolute small number'' for the increments in finite C difference approximations of derivatives C C RECOMMENDED: epsrel = 10^{-7}, epsabs = 10^{-10} C C epsrel double precision C epsabs double precision C infrel double precision C infabs double precision C this constants mean a ``relative small number'', ``an C absolute small number'', and ``infinite or a very big C number''. Basically, a quantity A is considered C negligible with respect to another quantity B if |A| < C max ( epsrel * |B|, epsabs ) C C RECOMMENDED: epsrel = 10^{-10}, epsabs = 10^{-20}, C infrel = 10^{+20}, infabs = 10^{+99} C C On Return C C x double precision C final estimation of the solution C C f double precision C functional value at the final estimation C C fcnt integer C number of functional evaluations used in the line search C C inform integer C This output parameter tells what happened in this C subroutine, according to the following conventions: C C 0 = convergence with an Armijo-like criterion C (f(xnew) <= f(x) + gamma * alpha * ); C C 4 = the algorithm stopped because the functional value C is smaller than fmin; C C 6 = too small step in the line search. After having made C at least mininterp interpolations, the steplength C becames small. ''small steplength'' means that we are C at point x with direction d and step alpha, and, for C all i, C C | alpha * d(i) | <= max ( epsrel * |x(i)|, epsabs ). C C In that case failure of the line search is declared C (maybe the direction is not a descent direction due C to an error in the gradient calculations). Use C mininterp > maxfc to inhibit this criterion; C C 8 = it was achieved the maximum allowed number of C function evaluations (maxfc); C C < 0 = error in evalf subroutine. C LOCAL SCALARS logical samep integer i,interp double precision alpha,atmp,ftrial,gtd C Print presentation information if ( iprint .ge. 4 ) then write(*, 980) lamspg write(10,980) lamspg end if C Initialization interp = 0 C Compute first trial point, spectral projected gradient direction, C and directional derivative . alpha = 1.0d0 gtd = 0.0d0 do i = 1,n xtrial(i) = min( u(i), max( l(i), x(i) - lamspg * g(i) ) ) d(i) = xtrial(i) - x(i) gtd = gtd + g(i) * d(i) end do call evalal(n,xtrial,m,lambda,rho,ftrial,inform) fcnt = fcnt + 1 if ( inform .lt. 0 ) then if ( iprint .ge. 4 ) then write(*, 1000) inform write(10,1000) inform end if return end if C Print information of the first trial if ( iprint .ge. 4 ) then write(*, 999) alpha,ftrial,fcnt write(10,999) alpha,ftrial,fcnt end if C Main loop 100 continue C Test Armijo stopping criterion if ( ftrial .le. f + gamma * alpha * gtd ) then f = ftrial do i = 1,n x(i) = xtrial(i) end do inform = 0 if ( iprint .ge. 4 ) then write(*, 990) inform write(10,990) inform end if go to 500 end if C Test whether f is very small if ( ftrial .le. fmin ) then f = ftrial do i = 1,n x(i) = xtrial(i) end do inform = 4 if ( iprint .ge. 4 ) then write(*, 994) inform write(10,994) inform end if go to 500 end if C Test whether the number of functional evaluations is exhausted if ( fcnt .ge. maxfc ) then if ( ftrial .lt. f ) then f = ftrial do i = 1,n x(i) = xtrial(i) end do end if inform = 8 if ( iprint .ge. 4 ) then write(*, 998) inform write(10,998) inform end if go to 500 end if C Compute new step (safeguarded quadratic interpolation) interp = interp + 1 if ( alpha .lt. sigma1 ) then alpha = alpha / nint else atmp = ( - gtd * alpha ** 2 ) / + ( 2.0d0 * ( ftrial - f - alpha * gtd ) ) if ( atmp .lt. sigma1 .or. atmp .gt. sigma2 * alpha ) then alpha = alpha / nint else alpha = atmp end if end if C Compute new trial point do i = 1,n xtrial(i) = x(i) + alpha * d(i) end do call evalal(n,xtrial,m,lambda,rho,ftrial,inform) fcnt = fcnt + 1 if ( inform .lt. 0 ) then if ( iprint .ge. 4 ) then write(*, 1000) inform write(10,1000) inform end if return end if C Print information of the current trial if ( iprint .ge. 4 ) then write(*, 999) alpha,ftrial,fcnt write(10,999) alpha,ftrial,fcnt end if C Test whether at least mininterp interpolations were made and two C consecutive iterates are close enough samep = .true. do i = 1,n if ( abs( alpha * d(i) ) .gt. + max( epsrel * abs( x(i) ), epsabs ) ) then samep = .false. end if end do if ( interp .ge. mininterp .and. samep ) then if ( ftrial .lt. f ) then f = ftrial do i = 1,n x(i) = xtrial(i) end do end if inform = 6 if ( iprint .ge. 4 ) then write(*, 996) inform write(10,996) inform end if go to 500 end if C Iterate go to 100 C Return 500 continue return C Non-executable statements 980 format(/,6x,'SPG (spectral steplength ',1PD11.4,')',/,/, * 6x,'SPG Line search') 999 format(6x,'Alpha= ',1PD11.4,' F= ',1PD11.4,' FE= ',I5) 990 format(6x,'Flag of SPG Line search = ',I3, * ' (Convergence with an Armijo-like criterion)') 994 format(6x,'Flag of SPG Line search = ',I3, * ' (Small functional value, smaller than ',/, * 6X,'parameter fmin)') 996 format(6x,'Flag of SPG Line search = ',I3, * ' (Too small step in the interpolation)') 998 format(6x,'Flag of SPG Line search = ',I3, * ' (Too many functional evaluations)') 1000 format(6x,'Flag of SPG Line search = ',I3,' Fatal Error') end C ****************************************************************** C ****************************************************************** subroutine cg(nind,ind,n,x,m,lambda,rho,g,delta,l,u,eps,epsnqmp, +maxitnqmp,maxit,nearlyq,gtype,htvtype,trtype,iprint,ncomp,s,iter, +rbdtype,rbdind,inform,w,y,r,d,sprev,theta,sterel,steabs,epsrel, +epsabs,infrel,infabs) implicit none C SCALAR ARGUMENTS logical nearlyq integer gtype,htvtype,inform,iprint,iter,m,maxit,maxitnqmp,n, + ncomp,nind,trtype,rbdind,rbdtype double precision delta,eps,epsnqmp,epsabs,epsrel,infrel,infabs, + steabs,sterel,theta C ARRAY ARGUMENTS integer ind(nind) double precision d(n),g(n),l(n),lambda(m),r(n),rho(m),s(n), + sprev(n),u(n),w(n),x(n),y(n) C This subroutine implements the Conjugate Gradients method for C minimizing the quadratic approximation q(s) of f(x) at x, where C C q(s) = 1/2 s^T H s + g^T s, C C H = \nabla^2 f(x), C C g = \nabla f(x), C C subject to || s || <= delta and l <= x + s <= u. C C In the constraint ''|| s || <= delta'', the norm will be the C Euclidian norm if the input parameter trtype is equal to 0, and C it will be the Sup norm if trtype is equal to 1. C C The method returns an approximation s to the solution such that C ||H s + g||_2 <= eps * ||g||_2; or converges to the boundary of C ||s||_2 <= delta and l <= x + s <= u; or finds a point s and a C direction d such that q(s + alpha d) = q(s) for any alpha, i.e., C d^T H d = g^T d = 0. C C On Entry C C nind integer C number of free variables (this is thee dimension in C which this subroutine will work) C C ind integer ind(n) C array which contains, in the first nind positions, the C identifiers of the free variables C C n integer C dimension of the full space C C x double precision x(n) C point at which f function is being approximated by the C quadratic model C C The first nind positions of x contains the free variables C x_ind(1), x_ind(2), ..., x_ind(nind). C C m integer C lambda double precision lambda(m) C rho double precision rho(m) C These three parameters are not used nor modified by C GENCAN and they are passed as arguments to the user- C defined subroutines evalal and evalnal to compute the C objective function and its gradient, respectively. C Clearly, in an Augmented Lagrangian context, if GENCAN is C being used to solve the bound-constrainted subproblems, m C would be the number of constraints, lambda the Lagrange C multipliers approximation and rho the penalty parameters C C g double precision g(n) C linear coefficient of the quadratic function C C This is \nabla f(x) and it also contains in the first C nind positions the components g_ind(1), g_ind(2), ..., C g_ind(nind). C C IMPORTANT: the linear algebra of this subroutine lies in C a space of dimension nind. The value of the full C dimension n, the non-free variables (which are at the end C of array x) and its gradient components (which are at the C and of array g) are, at this moment, being used to C approximate the Hessian times vector products by C incremental quotients. C C delta double precision C trust region radius (||s||_2 <= delta) C C l double precision l(n) C lower bounds on x + s. It components are ordered in the C same way as x and g. C C u double precision u(n) C upper bounds on x + s. It components are ordered in the C same way as x, g and l. C C eps double precision C tolerance for the stopping criterion ||H s + g||_2 < eps C * ||g||_2 C C epsnqmp double precision C See below C C maxitnqmp integer C This and the previous one parameter are used for a C stopping criterion of the conjugate gradient C subalgorithm. If the progress in the quadratic model is C less or equal than a fraction of the best progress C ( epsnqmp * bestprog ) during maxitnqmp consecutive C iterations then CG is stopped by not enough progress of C the quadratic model. C C RECOMMENDED: epsnqmp = 1.0d-4, maxitnqmp = 5 C C maxit integer C maximum number of iterations allowed C C nearlyq logical C if function f is (nearly) quadratic, use the option C nearlyq = TRUE. Otherwise, keep the default option. C C if, in an iteration of CG we find a direction d such that C d^T H d <= 0 then we take the following decision: C C (i) if nearlyq = TRUE then take direction d and try to go C to the boundary choosing the best point among the two C point at the boundary and the current point. C C (ii) if nearlyq = FALSE then we stop at the current C point. C C RECOMMENDED: nearlyq = FALSE C C gtype integer C type of gradient calculation C gtype = 0 means user suplied evalg subroutine, C gtype = 1 means central difference approximation. C C RECOMMENDED: gtype = 0 C C (provided you have the evalg subroutine) C C htvtype integer C type of Hessian times vector product calculation C htvtype = 0 means user supplied evalhd subroutine, C htvtype = 1 means incremental quotients approximation. C C RECOMMENDED: htvtype = 1 C C (you take some risk using this option but, unless you C have a good evalhd subroutine, incremental quotients is a C very cheap option) C C trtype integer C type of trust-region radius C trtype = 0 means 2-norm trust-region C trtype = 1 means infinite-norm trust-region C C RECOMMENDED: trtype = 0 C C iprint integer C Commands printing. Nothing is printed if iprint is C smaller than 2. If iprint is greater than or equal to C 2, GENCAN iterations information is printed. If iprint C is greater than or equal to 3, line searches and C Conjugate Gradients information is printed. C C RECOMMENDED: iprint = 2 C C CONSTRAINTS: allowed values are just 2 or 3. C C ncomp integer C This constant is just for printing. In a detailed C printing option, ncomp component of some vectors will be C printed C C RECOMMENDED: ncomp = 5 C C CONSTRAINTS: ncomp >= 0 C C w double precision w(n) C y double precision y(n) C r double precision r(n) C d double precision d(n) C sprev double precision sprev(n) C working vectors C C theta double precision C constant for the angle condition, i.e., at iteration k we C need a direction d_k such that <= - theta C ||gk||_2 ||dk||_2, where gk is \nabla f(xk) C C RECOMMENDED: theta = 10^{-6} C C sterel double precision C steabs double precision C this constants mean a ``relative small number'' and ``an C absolute small number'' for the increments in finite C difference approximations of derivatives C C RECOMMENDED: epsrel = 10^{-7}, epsabs = 10^{-10} C C epsrel double precision C epsabs double precision C infrel double precision C infabs double precision C this constants mean a ``relative small number'', ``an C absolute small number'', and ``infinite or a very big C number''. Basically, a quantity A is considered C negligible with respect to another quantity B if |A| < C max ( epsrel * |B|, epsabs ) C C RECOMMENDED: epsrel = 10^{-10}, epsabs = 10^{-20}, C infrel = 10^{+20}, infabs = 10^{+99} C C On Return C C s double precision s(n) C final estimation of the solution C C iter integer C number of Conjugate Gradient iterations performed C C inform integer C termination parameter: C C 0 = convergence with ||H s + g||_2 <= eps * ||g||_2; C C 1 = convergence to the boundary of ||s||_2 <= delta; C C 2 = convergence to the boundary of l - x <= s <= u - x; C C 3 = stopping with s = sk such that <= -t heta C ||gk||_2 ||sk||_2 and > - theta C ||gk||_2 ||s_{k+1}||_2; C C 4 = not enough progress of the quadratic model during C maxitnqmp iterations, i.e., during maxitnqmp C iterations | q - qprev | <= max ( epsrel * | q |, C epsabs ); C C 6 = very similar consecutive iterates, for two C consecutive iterates x and y, for all i | x(i) - C y(i) | <= max ( epsrel * | x(i) |, epsabs ); C C 7 = stopping with d such that d^T H d = 0 and g^T d = 0; C C 8 = too many iterations; C C < 0 = error in evalhd subroutine. C LOCAL SCALARS character * 5 rbdtypea logical samep integer i,itnqmp,rbdnegaind,rbdnegatype,rbdposaind,rbdposatype double precision aa,alpha,amax,amax1,amax1n,amaxn,amax2,amax2n, + amax2nx,amax2x,bb,bestprog,beta,cc,currprog,dd,dnorm2,dtr, + dts,dtw,gnorm2,gts,norm2s,q,qamax,qamaxn,qprev,rnorm2, + rnorm2prev,snorm2,snorm2prev C ================================================================== C Initialization C ================================================================== gnorm2 = norm2s(nind,g) iter = 0 itnqmp = 0 qprev = infabs bestprog = 0.0d0 do i = 1,nind s(i) = 0.0d0 r(i) = g(i) end do q = 0.0d0 gts = 0.0d0 snorm2 = 0.0d0 rnorm2 = gnorm2 C ================================================================== C Print initial information C ================================================================== if ( iprint .ge. 4 ) then write(*, 980) maxit,eps if ( trtype .eq. 0 ) then write(*, 981) delta else if ( trtype .eq. 1 ) then write(*, 982) delta else write(*, 983) end if write(*, 984) iter,rnorm2,sqrt(snorm2),q write(10,980) maxit,eps if ( trtype .eq. 0 ) then write(10,981) delta else if ( trtype .eq. 1 ) then write(10,982) delta else write(10,983) end if write(10,984) iter,rnorm2,sqrt(snorm2),q end if C ================================================================== C Main loop C ================================================================== 100 continue C ================================================================== C Test stopping criteria C ================================================================== C if ||r||_2 = ||H s + g||_2 <= eps * ||g||_2 then stop if ( rnorm2 .le. 1.0d-16 .or. + ( ( rnorm2 .le. eps ** 2 * gnorm2 .or. + ( rnorm2 .le. 1.0d-10 .and. iter .ne. 0 ) ) + .and. iter .ge. 4 ) ) then inform = 0 if ( iprint .ge. 4 ) then write(*, 990) inform write(10,990) inform end if go to 500 end if C if the maximum number of iterations was achieved then stop if ( iter .ge. max(4, maxit) ) then inform = 8 if ( iprint .ge. 4 ) then write(*, 998) inform write(10,998) inform end if go to 500 end if C ================================================================== C Compute direction C ================================================================== if ( iter .eq. 0 ) then do i = 1,nind d(i) = - r(i) end do dnorm2 = rnorm2 dtr = - rnorm2 else beta = rnorm2 / rnorm2prev do i = 1,nind d(i) = - r(i) + beta * d(i) end do dnorm2 = rnorm2 - 2.0d0 * beta * ( dtr + alpha * dtw ) + + beta ** 2 * dnorm2 dtr = - rnorm2 + beta * ( dtr + alpha * dtw ) end if C Force d to be a descent direction of q(s), i.e., C <\nabla q(s), d> = = \le 0. if ( dtr .gt. 0.0d0 ) then do i = 1,nind d(i) = - d(i) end do dtr = - dtr end if C ================================================================== C Compute d^T H d C ================================================================== C w = A d if ( htvtype .eq. 0 ) then call calchd(nind,ind,x,d,g,n,x,m,lambda,rho,w,y,sterel,steabs, + inform) else if ( htvtype .eq. 1 ) then call calchddiff(nind,ind,x,d,g,n,x,m,lambda,rho,gtype,w,y, + sterel,steabs,inform) end if if ( inform .lt. 0 ) then if ( iprint .ge. 4 ) then write(*, 1000) inform write(10,1000) inform end if return end if C Compute d^T w and ||w||^2 dtw = 0.0d0 do i = 1,nind dtw = dtw + d(i) * w(i) end do C ================================================================== C Compute maximum step C ================================================================== C amax1 > 0 and amax1n < 0 are the values of alpha such that C ||s + alpha * d||_2 or ||s + alpha * d||_\infty = delta dts = 0.0d0 do i = 1,nind dts = dts + d(i) * s(i) end do C Euclidian-norm trust radius if ( trtype .eq. 0 ) then aa = dnorm2 bb = 2.0d0 * dts cc = snorm2 - delta ** 2 dd = sqrt( bb ** 2 - 4.0d0 * aa * cc ) amax1 = ( - bb + dd ) / ( 2.0d0 * aa ) amax1n = ( - bb - dd ) / ( 2.0d0 * aa ) C Sup-norm trust radius else if ( trtype .eq. 1 ) then amax1 = infabs amax1n = -infabs do i = 1,nind if ( d(i) .gt. 0.0d0 ) then amax1 = min( amax1, ( delta - s(i) ) / d(i) ) amax1n = max( amax1n, ( - delta - s(i) ) / d(i) ) else if ( d(i) .lt. 0.0d0 ) then amax1 = min( amax1, ( - delta - s(i) ) / d(i) ) amax1n = max( amax1n, ( delta - s(i) ) / d(i) ) end if end do end if C amax2 > 0 and amax2n < 0 are the maximum and the minimum values of C alpha such that l - x <= s + alpha * d <= u - x, respectively amax2 = infabs amax2n = - infabs do i = 1,nind if ( d(i) .gt. 0.0d0 ) then C if (u(i).lt.infrel) then amax2x = ( u(i) - x(i) - s(i) ) / d(i) if ( amax2x .lt. amax2 ) then amax2 = amax2x rbdposaind = i rbdposatype = 2 end if C end if C if (l(i).gt.-infrel) then amax2nx = ( l(i) - x(i) - s(i) ) / d(i) if ( amax2nx .gt. amax2n ) then amax2n = amax2nx rbdnegaind = i rbdnegatype = 1 end if C end if else if ( d(i) .lt. 0.0d0 ) then C if (l(i).gt.-infrel) then amax2x = ( l(i) - x(i) - s(i) ) / d(i) if ( amax2x .lt. amax2 ) then amax2 = amax2x rbdposaind = i rbdposatype = 1 end if C end if C if (u(i).lt.infrel) then amax2nx = ( u(i) - x(i) - s(i) ) / d(i) if ( amax2nx .gt. amax2n ) then amax2n = amax2nx rbdnegaind = i rbdnegatype = 2 end if C end if end if end do C Compute amax as the minimum among amax1 and amax2, and amaxn as C the minimum among amax1n and amax2n. Moreover change amaxn by C - amaxn to have amax and amaxn as maximum steps along d direction C (and not -d in the case of amaxn) amax = min( amax1 , amax2 ) amaxn = max( amax1n, amax2n ) C ================================================================== C Compute the step (and the quadratic functional value at the new C point) C ================================================================== qprev = q C If d^T H d > 0 then take the conjugate gradients step if ( dtw .gt. 0.0d0 ) then alpha = min( amax, rnorm2 / dtw ) q = q + 0.5d0 * alpha ** 2 * dtw + alpha * dtr C If d^T H d <= 0 and function f is nearly quadratic then take the C point with the minimum functional value (q) among the current one C and the ones which are at the boundary, i.e., the best one between C q(s), q(s + amax*d) and q(s + amaxn*d). else qamax = q + 0.5d0 * amax ** 2 * dtw + amax * dtr C If we are at iteration zero then take the maximum positive C step in the minus gradient direction if ( iter .eq. 0 ) then alpha = amax q = qamax C If we are not in the first iteration then if function f is C nearly quadratic and q(s + amax * d) or q(s + amaxn * d) is C smaller than q(s), go to the best point in the boundary else qamaxn = q + 0.5d0 * amaxn ** 2 * dtw + amaxn * dtr if ( nearlyq .and. + ( qamax .lt. q .or. qamaxn .lt. q ) ) then if ( qamax .lt. qamaxn ) then alpha = amax q = qamax else alpha = amaxn q = qamaxn end if C Else, stop at the current point else inform = 7 if ( iprint .ge. 4 ) then write(*, 997) inform write(10,997) inform end if go to 500 end if end if end if C ================================================================== C Compute new s C ================================================================== do i = 1,nind sprev(i) = s(i) s(i) = s(i) + alpha * d(i) end do snorm2prev = snorm2 snorm2 = snorm2 + alpha ** 2 * dnorm2 + 2.0d0 * alpha * dts C ================================================================== C Compute the residual r = H s + g C ================================================================== rnorm2prev = rnorm2 do i = 1,nind r(i) = r(i) + alpha * w(i) end do rnorm2 = norm2s(nind,r) C ================================================================== C Increment number of iterations C ================================================================== iter = iter + 1 C ================================================================== C Print information of this iteration C ================================================================== if ( iprint .ge. 4 ) then write(*, 984) iter,sqrt(rnorm2),sqrt(snorm2),q write(10,984) iter,sqrt(rnorm2),sqrt(snorm2),q end if C ================================================================== C Test other stopping criteria C ================================================================== C Test angle condition gts = 0.0d0 do i = 1,nind gts = gts + g(i) * s(i) end do if ( gts .gt. 0.0d0 .or. + gts ** 2 .lt. theta ** 2 * gnorm2 * snorm2 ) then do i = 1,nind s(i) = sprev(i) end do snorm2 = snorm2prev q = qprev inform = 3 if ( iprint .ge. 4 ) then write(*, 993) inform write(10,993) inform end if go to 500 end if C If we are in the boundary of the box also stop if ( alpha .eq. amax2 .or. alpha .eq. amax2n ) then if ( alpha .eq. amax2 ) then rbdind = rbdposaind rbdtype = rbdposatype else ! if (alpha.eq.amax2n) then rbdind = rbdnegaind rbdtype = rbdnegatype end if if ( rbdtype .eq. 1 ) then rbdtypea = 'lower' else ! if (rbdtype.eq.2) then rbdtypea = 'upper' end if inform = 2 if ( iprint .ge. 4 ) then write(*, 992) inform,ind(rbdind),rbdtypea write(10,992) inform,ind(rbdind),rbdtypea end if go to 500 end if C If we are in the boundary of the trust region then stop if ( alpha .eq. amax1 .or. alpha .eq. amax1n ) then inform = 1 if ( iprint .ge. 4 ) then write(*, 991) inform write(10,991) inform end if go to 500 end if C If two consecutive iterates are much close then stop samep = .true. do i = 1,nind if ( abs( alpha * d(i) ) .gt. + max( epsrel * abs( s(i) ), epsabs ) ) then samep = .false. end if end do if ( samep ) then inform = 6 if ( iprint .ge. 4 ) then write(*, 996) inform write(10,996) inform end if go to 500 end if C Test whether we performed many iterations without good progress of C the quadratic model C if (abs( q - qprev ) .le. max( epsrel * abs( qprev ), epsabs ) ) C +then C itnqmp = itnqmp + 1 C if ( itnqmp .ge. maxitnqmp ) then C inform = 4 C if ( iprint .ge. 4 ) then C write(*,994) inform,itnqmp C write(10,994) inform,itnqmp C end if C go to 500 C endif C else C itnqmp= 0 C endif C Test whether we performed many iterations without good progress of C the quadratic model currprog = qprev - q bestprog = max( currprog, bestprog ) if ( currprog .le. epsnqmp * bestprog ) then itnqmp = itnqmp + 1 if ( itnqmp .ge. maxitnqmp ) then inform = 4 if ( iprint .ge. 4 ) then write(*, 994) inform,itnqmp,epsnqmp,bestprog write(10,994) inform,itnqmp,epsnqmp,bestprog end if go to 500 endif else itnqmp = 0 endif C ================================================================== C Iterate C ================================================================== go to 100 C ================================================================== C End of main loop C ================================================================== C ================================================================== C Return C ================================================================== 500 continue C Print final information if ( iprint .ge. 4 ) then write(*, 985) min0(nind,ncomp),(s(i),i=1,min0(nind,ncomp)) write(10,985) min0(nind,ncomp),(s(i),i=1,min0(nind,ncomp)) end if return C Non-executable statements 980 format(/,6x,'Conjugate gradients (maxit= ',I7,' acc= ',1PD11.4, *')') 981 format(6x,'Using Euclidian trust region (delta= ',1PD11.4, *')') 982 format(6x,'Using sup-norm trust region (delta= ',1PD11.4,')') 983 format(6x,'Unknown trust-region type') 984 format(6x,'CG iter= ',I5,' rnorm: ',1PD11.4,' snorm= ',1PD11.4, *' q= ',1PD11.4) 985 format(/,6x,'Truncated Newton direction (first ',I6, *' components): ',/,1(6x,6(1PD11.4,1x))) 990 format(6x,'Flag of CG = ',I3,' (Convergence with small residual)') 991 format(6x,'Flag of CG = ',I3, *' (Convergence to the trust region boundary)') 992 format(6x,'Flag of CG = ',I3, *' (Convergence to the boundary of the box constraints,',/,6x, *'taking step >= 1, variable ',I6,' will reaches its ',A5, *' bound)') 993 format(6x,'Flag of CG = ',I3, *' (The next CG iterate will not satisfy the angle condition)') 994 format(6x,'Flag of CG = ',I3, *' (Not enough progress in the quadratic model. This means',/,6x, *'that the progress of the last ',I7,' iterations was smaller ', *'than ',/,6x,1PD11.4,' times the best progress (',1PD11.4,')') 996 format(6x,'Flag of CG = ',I3, *' (Very near consecutive iterates)') 997 format(6x,'Flag of CG= ',I3, *' (d such that d^T H d = 0 and g^T d = 0 was found)') 998 format(6x,'Flag of CG = ',I3,' (Too many GC iterations)') 1000 format(6x,'Flag of CG = ',I3,' Fatal Error') end C ***************************************************************** C ***************************************************************** subroutine tnls(nind,ind,n,x,m,lambda,rho,l,u,f,g,d,amax,rbdtype, +rbdind,nint,next,mininterp,maxextrap,fmin,maxfc,gtype,iprint,fcnt, +gcnt,intcnt,exgcnt,exbcnt,inform,xplus,xtmp,xbext,gamma,beta, +sigma1,sigma2,sterel,steabs,epsrel,epsabs,infrel,infabs) implicit none C SCALAR ARGUMENTS integer exbcnt,exgcnt,fcnt,gcnt,gtype,inform,intcnt,iprint,m, + maxextrap,maxfc,mininterp,n,nind,rbdind,rbdtype double precision amax,beta,epsabs,epsrel,f,fmin,gamma,infabs, + infrel,next,nint,sigma1,sigma2,steabs,sterel C ARRAY ARGUMENTS integer ind(nind) double precision d(n),g(n),l(n),lambda(m),rho(m),u(n),x(n), + xbext(n),xplus(n),xtmp(n) C This subroutine implements the line search used in the Truncated C Newton direction. C C On Entry C C nind integer C number of free variables (this is thee dimension in C which this subroutine will work) C C ind integer ind(n) C array which contains, in the first nind positions, the C identifiers of the free variables C C n integer C dimension of the full space C C x double precision x(n) C current point C C The first nind positions of x contains the free variables C x_ind(1), x_ind(2), ..., x_ind(nind). C C m integer C lambda double precision lambda(m) C rho double precision rho(m) C These three parameters are not used nor modified by C GENCAN and they are passed as arguments to the user- C defined subroutines evalal and evalnal to compute the C objective function and its gradient, respectively. C Clearly, in an Augmented Lagrangian context, if GENCAN is C being used to solve the bound-constrainted subproblems, m C would be the number of constraints, lambda the Lagrange C multipliers approximation and rho the penalty parameters C C l double precision l(nind) C lower bounds on x. It components are ordered in the C same way as x and g. C C u double precision u(nind) C upper bounds on x. It components are ordered in the C same way as x, g and l. C C f double precision C functional value at x C C g double precision g(n) C gradient vector at x C C It also contains in the first nind positions the C components g_ind(1), g_ind(2), ..., g_ind(nind). C C IMPORTANT: the linear algebra of this subroutine lies in C a space of dimension nind. The value of the full C dimension n, the non-free variables (which are at the end C of array x) and its gradient components (which are at the C end of array g) are also used and updated any time the C gradient is being computed. C C d double precision d(nind) C descent direction C C amax double precision C C rbdtype integer C C rbdind integer C C nint double precision C constant for the interpolation. See the description of C sigma1 and sigma2 above. Sometimes we take as a new C trial step the previous one divided by nint C C RECOMMENDED: nint = 2.0 C C next double precision C constant for the extrapolation C when extrapolating we try alpha_new = alpha * next C C RECOMMENDED: next = 2.0 C C mininterp integer C constant for testing if, after having made at least C mininterp interpolations, the steplength is so small. C In that case failure of the line search is declared (may C be the direction is not a descent direction due to an C error in the gradient calculations) C C RECOMMENDED: mininterp = 4 C C maxextrap integer C constant to limit the number of extrapolations C C RECOMMENDED: maxextrap = 1000 (a big number) C C fmin double precision C functional value for the stopping criteria f <= fmin C C maxfc integer C maximum number of functional evaluations C C gtype integer C type of gradient calculation C gtype = 0 means user suplied evalg subroutine, C gtype = 1 means central difference approximation. C C RECOMMENDED: gtype = 0 C C (provided you have the evalg subroutine) C C iprint integer C Commands printing. Nothing is printed if iprint is C smaller than 2. If iprint is greater than or equal to C 2, GENCAN iterations information is printed. If iprint C is greater than or equal to 3, line searches and C Conjugate Gradients information is printed. C C RECOMMENDED: iprint = 2 C C CONSTRAINTS: allowed values are just 2 or 3. C C xplus double precision xplus(nind) C xtmp double precision xtmp(nind) C xbext double precision xbext(nind) C working vectors C C gamma double precision C constant for the Armijo criterion C f(x + alpha d) <= f(x) + gamma * alpha * <\nabla f(x),d> C C RECOMMENDED: gamma = 10^{-4} C C beta double precision C constant for the beta condition < beta C * . If (xk + dk) satisfies the Armijo condition C but does not satisfy the beta condition then the point is C accepted, but if it satisfied the Armijo condition and C also satisfies the beta condition then we know that there C is the possibility for a successful extrapolation C C RECOMMENDED: beta = 0.5 C C sigma1 double precision C sigma2 double precision C constant for the safeguarded interpolation C if alpha_new \notin [sigma1, sigma*alpha] then we take C alpha_new = alpha / nint C C RECOMMENDED: sigma1 = 0.1 and sigma2 = 0.9 C C sterel double precision C steabs double precision C this constants mean a ``relative small number'' and ``an C absolute small number'' for the increments in finite C difference approximations of derivatives C C RECOMMENDED: epsrel = 10^{-7}, epsabs = 10^{-10} C C epsrel double precision C epsabs double precision C infrel double precision C infabs double precision C this constants mean a ``relative small number'', ``an C absolute small number'', and ``infinite or a very big C number''. Basically, a quantity A is considered C negligible with respect to another quantity B if C |A| < max ( epsrel * |B|, epsabs ) C C RECOMMENDED: epsrel = 10^{-10}, epsabs = 10^{-20}, C infrel = 10^{+20}, infabs = 10^{+99} C C On Return C C x double precision x(n) C new current point C C f double precision C functional value at x C C g double precision g(n) C gradient vector at x C C fcnt integer C number of functional evaluations used in this line search C C gcnt integer C number of gradient evaluations used in this line search C C intcnt integer C number of interpolations C C exgcnt integer C number of good extrapolations C C exbcnt integer C number of bad extrapolations C C inform integer C This output parameter tells what happened in this C subroutine, according to the following conventions: C C 0 = convergence with an Armijo-like criterion C (f(xnew) <= f(x) + 1.0d-4 * alpha * ); C C 4 = the algorithm stopped because the functional value C is very small (f <= fmin); C C 6 = so small step in the line search. After having made C at least mininterp interpolations, the steplength C becames small. ``small steplength'' means that we are C at point x with direction d and step alpha, and, for C all i, C C |alpha * d(i)| .le. max ( epsrel * |x(i)|, epsabs ). C C In that case failure of the line search is declared C (may be the direction is not a descent direction C due to an error in the gradient calculations). Use C mininterp > maxfc for inhibit this criterion; C C 8 = it was achieved the maximum allowed number of C function evaluations (maxfc); C C < 0 = error in evalf or evalg subroutines. C LOCAL SCALARS logical samep integer extrap,i,interp double precision alpha,atmp,fbext,fplus,ftmp,gptd,gtd C ================================================================== C Initialization C ================================================================== C ================================================================== C Compute directional derivative C ================================================================== gtd = 0.0d0 do i = 1,nind gtd = gtd + g(i) * d(i) end do C ================================================================== C Compute first trial C ================================================================== alpha = min( 1.0d0, amax ) do i = 1,nind xplus(i) = x(i) + alpha * d(i) end do if ( alpha .eq. amax ) then if ( rbdtype .eq. 1 ) then xplus(rbdind) = l(rbdind) else ! if (rbdtype.eq.2) then xplus(rbdind) = u(rbdind) end if end if call calcf(nind,ind,xplus,n,x,m,lambda,rho,fplus,inform) fcnt = fcnt + 1 if ( inform .lt. 0 ) then if ( iprint .ge. 4 ) then write(*, 1000) inform write(10,1000) inform end if return end if C Print initial information if ( iprint .ge. 4 ) then write(*, 980) amax write(*, 999) alpha,fplus,fcnt write(10,980) amax write(10,999) alpha,fplus,fcnt end if C ================================================================== C Test Armijo and beta-condition and decide for accepting the trial C point, interpolate or extrapolate. C ================================================================== if ( amax .gt. 1.0d0 ) then C x + d belongs to the interior of the feasible set if ( iprint .ge. 4 ) then write(*, *) ' x+d belongs to int of the feasible set' write(10,*) ' x+d belongs to int of the feasible set' end if C Verify Armijo if ( fplus .le. f + gamma * alpha * gtd ) then C Armijo condition holds if ( iprint .ge. 4 ) then write(*, *) ' Armijo condition holds' write(10,*) ' Armijo condition holds' end if if ( gtype .eq. 0 ) then call calcg(nind,ind,xplus,n,x,m,lambda,rho,g,inform) else if ( gtype .eq. 1 ) then call calcgdiff(nind,ind,xplus,n,x,m,lambda,rho,g, + sterel,steabs,inform) end if gcnt = gcnt + 1 if ( inform .lt. 0 ) then if ( iprint .ge. 4 ) then write(*, 1000) inform write(10,1000) inform end if return end if gptd = 0.0d0 do i = 1,nind gptd = gptd + g(i) * d(i) end do C Verify directional derivative (beta condition) if ( gptd .lt. beta * gtd ) then C Extrapolate if ( iprint .ge. 4 ) then write(*, *)' The beta-condition does not hold' write(*, *)' We will extrapolate' write(10,*)' The beta-condition does not hold' write(10,*)' We will extrapolate' end if C f and x before extrapolation fbext = fplus do i = 1,nind xbext(i) = xplus(i) end do go to 100 else C Step = 1 was ok, finish the line search if ( iprint .ge. 4 ) then write(*, *) ' The beta condition is also true' write(*, *) ' Line search is over' write(10,*) ' The beta condition is also true' write(10,*) ' Line search is over' end if f = fplus do i = 1,nind x(i) = xplus(i) end do inform = 0 if ( iprint .ge. 4 ) then write(*, 990) inform write(10,990) inform end if go to 500 end if else C Interpolate if ( iprint .ge. 4 ) then write(*, *) ' Armijo does not hold' write(*, *) ' We will interpolate' write(10,*) ' Armijo does not hold' write(10,*) ' We will interpolate' end if go to 200 end if else C x + d does not belong to the feasible set (amax <= 1) if ( iprint .ge. 4 ) then write(*, *) ' x+d does not belong to box-interior' write(10,*) ' x+d does not belong to box-interior' end if if ( fplus .lt. f ) then C Extrapolate if ( iprint .ge. 4 ) then write(*, *) ' f(x+d) < f(x)' write(*, *) ' We will extrapolate' write(10,*) ' f(x+d) < f(x)' write(10,*) ' We will extrapolate' end if C f and x before extrapolation fbext = fplus do i = 1,nind xbext(i) = xplus(i) end do go to 100 else C Interpolate if ( iprint .ge. 4 ) then write(*, *) ' f(x+d) >= f(x)' write(*, *) ' We will interpolate' write(10,*) ' f(x+d) >= f(x)' write(10,*) ' We will interpolate' end if go to 200 end if end if C ================================================================== C Extrapolation C ================================================================== 100 continue extrap = 0 C Test f going to -inf 120 if ( fplus .le. fmin ) then C Finish the extrapolation with the current point f = fplus do i = 1,nind x(i) = xplus(i) end do if ( extrap .ne. 0 .or. amax .le. 1.0d0 ) then if ( gtype .eq. 0 ) then call calcg(nind,ind,x,n,x,m,lambda,rho,g,inform) else if ( gtype .eq. 1 ) then call calcgdiff(nind,ind,x,n,x,m,lambda,rho,g,sterel, + steabs,inform) end if gcnt = gcnt + 1 if ( inform .lt. 0 ) then if ( iprint .ge. 4 ) then write(*, 1000) inform write(10,1000) inform end if return end if if ( f .lt. fbext ) then exgcnt = exgcnt + 1 else exbcnt = exbcnt + 1 end if end if inform = 4 if ( iprint .ge.3 ) then write(*, 994) inform write(10,994) inform end if go to 500 end if C Test maximum number of functional evaluations if ( fcnt .ge. maxfc ) then C Finish the extrapolation with the current point f = fplus do i = 1,nind x(i) = xplus(i) end do C If extrap=0 and amax>1 the gradient was computed for testing C the beta condition and it is not necessary to compute it again if ( extrap .ne. 0 .or. amax .le. 1.0d0 ) then if ( gtype .eq. 0 ) then call calcg(nind,ind,x,n,x,m,lambda,rho,g,inform) else if ( gtype .eq. 1 ) then call calcgdiff(nind,ind,x,n,x,m,lambda,rho,g,sterel, + steabs,inform) end if gcnt = gcnt + 1 if ( inform .lt. 0 ) then if ( iprint .ge. 4 ) then write(*, 1000) inform write(10,1000) inform end if return end if if ( f .lt. fbext ) then exgcnt = exgcnt + 1 else exbcnt = exbcnt + 1 end if end if inform = 8 if ( iprint .ge. 4 ) then write(*, 998) inform write(10,998) inform end if go to 500 end if C Test if the maximum number of extrapolations was exceeded if ( extrap .ge. maxextrap ) then C Finish the extrapolation with the current point f = fplus do i = 1,nind x(i) = xplus(i) end do C If extrap=0 and amax>1 the gradient was computed for testing C the beta condition and it is not necessary to compute it again if ( extrap .ne. 0 .or. amax .le. 1.0d0 ) then if ( gtype .eq. 0 ) then call calcg(nind,ind,x,n,x,m,lambda,rho,g,inform) else if ( gtype .eq. 1 ) then call calcgdiff(nind,ind,x,n,x,m,lambda,rho,g,sterel, + steabs,inform) end if gcnt = gcnt + 1 if ( inform .lt. 0 ) then if ( iprint .ge. 4 ) then write(*, 1000) inform write(10,1000) inform end if return end if if ( f .lt. fbext ) then exgcnt = exgcnt + 1 else exbcnt = exbcnt + 1 end if end if inform = 7 if ( iprint .ge. 4 ) then write(*, 997) inform write(10,997) inform end if go to 500 end if C Chose new step if ( alpha .lt. amax .and. next * alpha .gt. amax ) then atmp = amax else atmp = next * alpha end if C Compute new trial point do i = 1,nind xtmp(i) = x(i) + atmp * d(i) end do if ( atmp .eq. amax ) then if ( rbdtype .eq. 1 ) then xtmp(rbdind) = l(rbdind) else ! if ( rbdtype .eq. 2 ) then xtmp(rbdind) = u(rbdind) end if end if C Project if ( atmp .gt. amax ) then do i = 1,nind xtmp(i) = max( l(i), min( xtmp(i), u(i) ) ) end do end if C Test if this is not the same point as the previous one. C This test is performed only when alpha > amax. if( alpha .gt. amax ) then samep = .true. do i = 1,nind if ( abs( xtmp(i) - xplus(i) ) .gt. + max( epsrel * abs( xplus(i) ), epsabs ) ) then samep = .false. end if end do if ( samep ) then C Finish the extrapolation with the current point f = fplus do i = 1,nind x(i) = xplus(i) end do C If extrap=0 and amax>1 the gradient was computed for C testing the beta condition and it is not necessary to C compute it again if ( extrap .ne. 0 .or. amax .le. 1.0d0 ) then if ( gtype .eq. 0 ) then call calcg(nind,ind,x,n,x,m,lambda,rho,g,inform) else if ( gtype .eq. 1 ) then call calcgdiff(nind,ind,x,n,x,m,lambda,rho,g, + sterel,steabs,inform) end if gcnt = gcnt + 1 if ( inform .lt. 0 ) then if ( iprint .ge. 4 ) then write(*, 1000) inform write(10,1000) inform end if return end if if ( f .lt. fbext ) then exgcnt = exgcnt + 1 else exbcnt = exbcnt + 1 end if end if inform = 0 if ( iprint .ge. 4 ) then write(*, 990) inform write(10,990) inform end if go to 500 end if end if C Evaluate function call calcf(nind,ind,xtmp,n,x,m,lambda,rho,ftmp,inform) fcnt = fcnt + 1 if ( inform .lt. 0 ) then C if ( iprint .ge. 4 ) then C write(*, 1000) inform C write(10,1000) inform C end if C return C If the objective function is not well defined in an C extrapolated point, we discard all the extrapolated points C and return to a safe region (where the point before C starting the extrapolations is) f = fbext do i = 1,nind x(i) = xbext(i) end do C If extrap=0 and amax>1 the gradient was computed for testing C the beta condition and it is not necessary to compute it again if ( extrap .ne. 0 .or. amax .le. 1.0d0 ) then if ( gtype .eq. 0 ) then call calcg(nind,ind,x,n,x,m,lambda,rho,g,inform) else if ( gtype .eq. 1 ) then call calcgdiff(nind,ind,x,n,x,m,lambda,rho,g,sterel, + steabs,inform) end if gcnt = gcnt + 1 if ( inform .lt. 0 ) then if ( iprint .ge. 4 ) then write(*, 1000) inform write(10,1000) inform end if return end if exbcnt = exbcnt + 1 end if inform = 0 if ( iprint .ge. 4 ) then write(*, 1010) inform write(10,1010) inform end if go to 500 end if C Print information of this iteration if ( iprint .ge. 4 ) then write(*, 999) atmp,ftmp,fcnt write(10,999) atmp,ftmp,fcnt end if C If the functional value decreases then set the current point and C continue the extrapolation if ( ftmp .lt. fplus ) then alpha = atmp fplus = ftmp do i = 1,nind xplus(i) = xtmp(i) end do extrap = extrap + 1 go to 120 C If the functional value does not decrease then discard the last C trial and finish the extrapolation with the previous point else f = fplus do i = 1,nind x(i) = xplus(i) end do C If extrap=0 and amax>1 the gradient was computed for testing C the beta condition and it is not necessary to compute it again if ( extrap .ne. 0 .or. amax .le. 1.0d0 ) then if ( gtype .eq. 0 ) then call calcg(nind,ind,x,n,x,m,lambda,rho,g,inform) else if ( gtype .eq. 1 ) then call calcgdiff(nind,ind,x,n,x,m,lambda,rho,g,sterel, + steabs,inform) end if gcnt = gcnt + 1 if ( inform .lt. 0 ) then if ( iprint .ge. 4 ) then write(*, 1000) inform write(10,1000) inform end if return end if if ( f .lt. fbext ) then exgcnt = exgcnt + 1 else exbcnt = exbcnt + 1 end if end if inform = 0 if ( iprint .ge.3 ) then write(*, 990) inform write(10,990) inform end if go to 500 end if C ================================================================== C End of extrapolation C ================================================================== C ================================================================== C Interpolation C ================================================================== 200 continue intcnt = intcnt + 1 interp = 0 210 continue C Test f going to -inf if ( fplus .le. fmin ) then C Finish the interpolation with the current point f = fplus do i = 1,nind x(i) = xplus(i) end do if ( gtype .eq. 0 ) then call calcg(nind,ind,x,n,x,m,lambda,rho,g,inform) else if ( gtype .eq. 1 ) then call calcgdiff(nind,ind,x,n,x,m,lambda,rho,g,sterel, + steabs,inform) end if gcnt = gcnt + 1 if ( inform .lt. 0 ) then if ( iprint .ge. 4 ) then write(*, 1000) inform write(10,1000) inform end if return end if inform = 4 if ( iprint .ge. 4 ) then write(*, 994) inform write(10,994) inform end if go to 500 end if C Test maximum number of functional evaluations if ( fcnt .ge. maxfc ) then C As this is an abrupt termination then the current point of the C interpolation may be worst than the initial one C If the current point is better than the initial one then C finish the interpolation with the current point else discard C all we did inside this line search and finish with the initial C point if ( fplus .lt. f ) then f = fplus do i = 1,nind x(i) = xplus(i) end do if ( gtype .eq. 0 ) then call calcg(nind,ind,x,n,x,m,lambda,rho,g,inform) else if ( gtype .eq. 1 ) then call calcgdiff(nind,ind,x,n,x,m,lambda,rho,g,sterel, + steabs,inform) end if gcnt = gcnt + 1 if ( inform .lt. 0 ) then if ( iprint .ge. 4 ) then write(*, 1000) inform write(10,1000) inform end if return end if end if inform = 8 if ( iprint .ge. 4 ) then write(*, 998) inform write(10,998) inform end if go to 500 end if C Test Armijo condition if ( fplus .le. f + gamma * alpha * gtd ) then C Finish the line search f = fplus do i = 1,nind x(i) = xplus(i) end do if ( gtype .eq. 0 ) then call calcg(nind,ind,x,n,x,m,lambda,rho,g,inform) else if ( gtype .eq. 1 ) then call calcgdiff(nind,ind,x,n,x,m,lambda,rho,g,sterel, + steabs,inform) end if gcnt = gcnt + 1 if ( inform .lt. 0 ) then if ( iprint .ge. 4 ) then write(*, 1000) inform write(10,1000) inform end if return end if inform = 0 if ( iprint .ge. 4 ) then write(*, 990) inform write(10,990) inform end if go to 500 end if C Compute new step interp = interp + 1 if ( alpha .lt. sigma1 ) then alpha = alpha / nint else atmp = ( - gtd * alpha **2 ) / + (2.0d0 * ( fplus - f - alpha * gtd ) ) if ( atmp .lt. sigma1 .or. atmp .gt. sigma2 * alpha ) then alpha = alpha / nint else alpha = atmp end if end if C Compute new trial point do i = 1,nind xplus(i) = x(i) + alpha * d(i) end do call calcf(nind,ind,xplus,n,x,m,lambda,rho,fplus,inform) fcnt = fcnt + 1 if ( inform .lt. 0 ) then if ( iprint .ge. 4 ) then write(*, 1000) inform write(10,1000) inform end if return end if C Print information of this iteration if ( iprint .ge. 4 ) then write(*, 999) alpha,fplus,fcnt write(10,999) alpha,fplus,fcnt end if C Test whether at least mininterp interpolations were made and two C consecutive iterates are much close samep = .true. do i = 1,nind if ( abs( alpha * d(i) ) .gt. + max( epsrel * abs( x(i) ), epsabs ) ) then samep = .false. end if end do if ( interp .ge. mininterp .and. samep ) then C As this is an abrupt termination then the current point of the C interpolation may be worst than the initial one C If the current point is better than the initial one then C finish the interpolation with the current point else discard C all we did inside this line search and finish with the initial C point C if ( fplus .lt. f ) then C f = fplus C do i = 1,nind C x(i) = xplus(i) C end do C if ( gtype .eq. 0 ) then C call calcg(nind,ind,x,n,x,m,lambda,rho,g,inform) C else if ( gtype .eq. 1 ) then C call calcgdiff(nind,ind,x,n,x,m,lambda,rho,g, c + sterel,steabs,inform) C end if C gcnt = gcnt + 1 C if ( inform .lt. 0 ) then C if ( iprint .ge. 4 ) then C write(*, 1000) inform C write(10,1000) inform C end if C return C end if C end if C The previous lines were commented because, as it is been used, C this subroutine must return with the initial point in case of C finding a very small interpolation step. From that initial C point, something different will be tried. inform = 6 if ( iprint .ge. 4 ) then write(*, 996) inform write(10,996) inform end if go to 500 end if C Else, iterate go to 210 C ================================================================== C End of interpolation C ================================================================== 500 continue C ================================================================== C Return C ================================================================== return C Non-executable statements 980 format(/,6X,'TN Line search (alphamax= ',1PD11.4,')') 999 format(6X,'Alpha= ',1PD11.4,' F= ',1PD11.4,' FE= ',I5) 990 format(6X,'Flag of TN Line search= ',I3, + ' (Convergence with an Armijo-like criterion)') 994 format(6X,'Flag of TN Line search= ',I3, + ' (Small functional value, smaller than ',/, + 6X,'parameter fmin)') 996 format(6X,'Flag of TN Line search= ',I3, + ' (Too small step in the interpolation)') 997 format(6X,'Flag of TN Line search= ',I3, + ' (Too many extrapolations)') 998 format(6X,'Flag of TN Line search= ',I3, + ' (Too many functional evaluations)') 1000 format(6X,'Flag of TN Line search = ',I3,' Fatal Error') 1010 format(6X,'Flag of TN Line search= ',I3, + ' (Fatal Error in an extrapolated point)') end C ****************************************************************** C ****************************************************************** subroutine calcf(nind,ind,x,n,xc,m,lambda,rho,f,inform) implicit none C SCALAR ARGUMENTS integer nind,n,m,inform double precision f C ARRAY ARGUMENTS integer ind(nind) double precision x(n),xc(n),lambda(m),rho(m) C This subroutines computes the objective function. C C It is called from the reduced space (dimension nind), expands the C point x where the function will be evaluated and call the C subroutine evalf to compute the objective function Finally, C shrinks vector x to the reduced space. C C About subroutines named calc[something]. The subroutines whos C names start with ``calc'' work in (are called from) the reduced C space. Their tasks are (i) expand the arguments to the full space, C (ii) call the corresponding ``eval'' subroutine (which works in C the full space), and (iii) shrink the parameters again and also C shrink a possible output of the ``eval'' subroutine. Subroutines C of this type are: calcf, calcg, calchd, calcgdiff and calchddiff. C The corresponding subroutines in the full space are the user C defined subroutines evalf, evalg and evalhd. C LOCAL SCALARS integer i C Complete x do i = nind + 1,n x(i) = xc(i) end do C Expand x to the full space call expand(nind,ind,n,x) C Compute f calling the user supplied subroutine evalf call evalal(n,x,m,lambda,rho,f,inform) C Shrink x to the reduced space call shrink(nind,ind,n,x) return end C ****************************************************************** C ****************************************************************** subroutine calcg(nind,ind,x,n,xc,m,lambda,rho,g,inform) implicit none C SCALAR ARGUMENTS integer nind,n,m,inform C ARRAY ARGUMENTS integer ind(nind) double precision x(n),xc(n),lambda(m),rho(m),g(n) C This subroutine computes the gradient vector g of the objective C function. C C It is called from the reduced space (dimension nind), expands the C point x where the gradient will be evaluated and calls the user C supplied subroutine evalg to compute the gradient vector. Finally, C shrinks vectors x and g to the reduced space. C C About subroutines named calc[something]. The subroutines whos C names start with ``calc'' work in (are called from) the reduced C space. Their tasks are (i) expand the arguments to the full space, C (ii) call the corresponding ``eval'' subroutine (which works in C the full space), and (iii) shrink the parameters again and also C shrink a possible output of the ``eval'' subroutine. Subroutines C of this type are: calcf, calcg, calchd, calcgdiff and calchddiff. C The corresponding subroutines in the full space are the user C defined subroutines evalf, evalg and evalhd. C LOCAL SCALARS integer i C Complete x do i = nind + 1,n x(i) = xc(i) end do C Expand x to the full space call expand(nind,ind,n,x) C Compute the gradient vector calling the user supplied subroutine C evalg call evalnal(n,x,m,lambda,rho,g,inform) C Shrink x and g to the reduced space call shrink(nind,ind,n,x) call shrink(nind,ind,n,g) return end C ****************************************************************** C ****************************************************************** subroutine calcgdiff(nind,ind,x,n,xc,m,lambda,rho,g,sterel,steabs, +inform) implicit none C SCALAR ARGUMENTS integer nind,n,m,inform double precision sterel,steabs C ARRAY ARGUMENTS integer ind(nind) double precision x(n),xc(n),lambda(m),rho(m),g(n) C This subroutine approximates the gradient vector g of the C objective function in the reduced space using central finite C differences. C C It is called from the reduced space (dimension nind), expands the C point x where the gradient will be estimated and calls evalf C subroutine (to evaluate the objective function) 2 * nind times. C Finally, shrinks vectors x and g to the reduced space. C C About subroutines named calc[something]. The subroutines whos C names start with ``calc'' work in (are called from) the reduced C space. Their tasks are (i) expand the arguments to the full space, C (ii) call the corresponding ``eval'' subroutine (which works in C the full space), and (iii) shrink the parameters again and also C shrink a possible output of the ``eval'' subroutine. Subroutines C of this type are: calcf, calcg, calchd, calcgdiff and calchddiff. C The corresponding subroutines in the full space are the user C defined subroutines evalf, evalg and evalhd. C LOCAL SCALARS integer i,indi double precision fminus,fplus,step,tmp C Complete x do i = nind + 1,n x(i) = xc(i) end do C Expand x to the full space call expand(nind,ind,n,x) C Approximate the gradient vector by central finite differences do i = 1,nind indi = ind(i) tmp = x(indi) step = max( steabs, sterel * abs( tmp ) ) x(indi) = tmp + step call evalal(n,x,m,lambda,rho,fplus,inform) if ( inform .lt. 0 ) then return end if x(indi) = tmp - step call evalal(n,x,m,lambda,rho,fminus,inform) if ( inform .lt. 0 ) then return end if g(indi) = ( fplus - fminus ) / ( 2.0d0 * step ) x(indi) = tmp end do C Shrink x and g to the reduced space call shrink(nind,ind,n,x) call shrink(nind,ind,n,g) return end C ****************************************************************** C ****************************************************************** subroutine calchd(nind,ind,x,d,g,n,xc,m,lambda,rho,hd,xtmp,sterel, +steabs,inform) implicit none C SCALAR ARGUMENTS integer inform,m,n,nind double precision steabs,sterel C ARRAY ARGUMENTS integer ind(nind) double precision d(n),g(n),hd(n),lambda(m),rho(m),x(n),xc(n), + xtmp(n) C This subroutine computes the product Hessian times vector d. As it C is called from the reduced space, it expands vectors x and d, C calls the user supplied subroutine evalhd to compute the Hessian C times vector d product, and shrinks vectors x, d and hd. C C About subroutines named calc[something]. The subroutines whos C names start with ``calc'' work in (are called from) the reduced C space. Their tasks are (i) expand the arguments to the full space, C (ii) call the corresponding ``eval'' subroutine (which works in C the full space), and (iii) shrink the parameters again and also C shrink a possible output of the ``eval'' subroutine. Subroutines C of this type are: calcf, calcg, calchd, calcgdiff and calchddiff. C The corresponding subroutines in the full space are the user C defined subroutines evalf, evalg and evalhd. C LOCAL SCALARS integer i C Complete d with zeroes do i = nind + 1,n d(i) = 0.0d0 end do C Complete x do i = nind + 1,n x(i) = xc(i) end do C Expand x and d to the full space call expand(nind,ind,n,x) call expand(nind,ind,n,d) call expand(nind,ind,n,g) C Compute the Hessian times vector d product calling the user C supplied subroutine evalhd call evalhd(n) C Shrink x, d and hd to the reduced space call shrink(nind,ind,n,x) call shrink(nind,ind,n,d) call shrink(nind,ind,n,g) call shrink(nind,ind,n,hd) end C ****************************************************************** C ****************************************************************** subroutine calchddiff(nind,ind,x,d,g,n,xc,m,lambda,rho,gtype,hd, +xtmp,sterel,steabs,inform) implicit none C SCALAR ARGUMENTS integer gtype,inform,m,n,nind double precision steabs,sterel C ARRAY ARGUMENTS integer ind(nind) double precision d(n),g(n),hd(n),lambda(m),rho(m),x(n),xc(n), + xtmp(n) C This subroutine computes the Hessian times vector d product by C means of a ``directional finite difference''. The idea is that, at C the current point x, the product H d is the limit of C C [ Gradient(x + t d) - Gradient(x) ] / t C C In this implementation we use C C t = max(steabs, sterel ||x||_\infty) / ||d||_\infty C C provided that d is not equal 0, of course. C C So, we evaluate the Gradient at the auxiliary point x + t d and C use the quotient above to approximate H d. To compute the gradient C vector at the auxiliary point it is used evalg or evalgdiff C depending on gtype parameter. C C About subroutines named calc[something]. The subroutines whos C names start with ``calc'' work in (are called from) the reduced C space. Their tasks are (i) expand the arguments to the full space, C (ii) call the corresponding ``eval'' subroutine (which works in C the full space), and (iii) shrink the parameters again and also C shrink a possible output of the ``eval'' subroutine. Subroutines C of this type are: calcf, calcg, calchd, calcgdiff and calchddiff. C The corresponding subroutines in the full space are the user C defined subroutines evalf, evalg and evalhd. C On Entry C C n integer C order of the x C C x double precision x(n) C point for which Hessian(x) times d will be approximated C C d double precision d(n) C vector for which the Hessian times vetor product will C be approximated C C g double precision g(n) C gradient at x C C xtmp double precision xtmp(n) C working vector C C sterel double precision C steabs double precision C these constants mean a ``relative small number'' and C ``an absolute small number'' C C On Return C C hd double precision hd(n) C approximation of H d C LOCAL SCALARS integer flag,i,indi double precision dsupn,step,tmp,xsupn inform = 0 C Compute incremental quotients step xsupn = 0.0d0 dsupn = 0.0d0 do i = 1,nind xsupn = max( xsupn, abs( x(i) ) ) dsupn = max( dsupn, abs( d(i) ) ) end do c Safeguard added by LM if(dsupn.lt.1.d-20) dsupn = 1.d-20 step = max( sterel * xsupn, steabs ) / dsupn C Set the point at which the gradient will be evaluated do i = 1,nind xtmp(i) = x(i) + step * d(i) end do C Evaluate the gradient at xtmp = x + step * d if ( gtype .eq. 0 ) then C Complete xtmp do i = nind + 1,n xtmp(i) = xc(i) end do C Expand xtmp to the full space do i = nind,1,-1 indi = ind(i) if ( i .ne. indi ) then tmp = xtmp(indi) xtmp(indi) = xtmp(i) xtmp(i) = tmp end if end do c Compute the gradient at xtmp = x + step * d call evalnal(n,xtmp,m,lambda,rho,hd,flag) C Shrink hd to the reduced space do i= 1, nind indi= ind(i) if (i.ne.indi) then tmp = hd(indi) hd(indi) = hd(i) hd(i) = tmp end if end do else if ( gtype .eq. 1 ) then call calcgdiff(nind,ind,xtmp,n,xc,m,lambda,rho,hd,sterel, + steabs,inform) end if C Compute incremental quotients do i = 1,nind hd(i) = ( hd(i) - g(i) ) / step end do return end C ****************************************************************** C ****************************************************************** subroutine shrink(nind,ind,n,v) implicit none C SCALAR ARGUMENTS integer n,nind C ARRAY ARGUMENTS integer ind(nind) double precision v(n) C This subroutine shrinks vector v from the full dimension space C (dimension n) to the reduced space (dimension nind). C C On entry: C C nind integer C dimension of the reduced space C C ind integer ind(nind) C components ind(1)-th, ..., ind(nind)-th are the C components that belong to the reduced space C C n integer C dimension of the full space C C v double precision v(n) C vector to be shrinked C C On Return C C v double precision v(n) C shrinked vector C LOCAL SCALARS integer i,indi double precision tmp do i = 1,nind indi = ind(i) if ( i .ne. indi ) then tmp = v(indi) v(indi) = v(i) v(i) = tmp end if end do return end C ****************************************************************** C ****************************************************************** subroutine expand(nind,ind,n,v) implicit none C SCALAR ARGUMENTS integer n, nind C ARRAY ARGUMENTS integer ind(nind) double precision v(n) C This subroutine expands vector v from the reduced space C (dimension nind) to the full space (dimension n). C C On entry: C C nind integer C dimension of the reduced space C C ind integer ind(nind) C components ind(1)-th, ..., ind(nind)-th are the C components that belong to the reduced space C C n integer C dimension of the full space C C v double precision v(n) C vector to be expanded C C On Return C C v double precision v(n) C expanded vector C LOCAL SCALARS integer i,indi double precision tmp do i = nind,1,- 1 indi = ind(i) if ( i .ne. indi ) then tmp = v(indi) v(indi) = v(i) v(i) = tmp end if end do return end C ****************************************************************** C ****************************************************************** subroutine evalnaldiff(n,x,m,lambda,rho,g,sterel,steabs,inform) implicit none C SCALAR ARGUMENTS integer n,m,inform double precision sterel,steabs C ARRAY ARGUMENTS double precision x(n),lambda(m),rho(m),g(n) C Approximates the gradient vector g(x) of the objective function by C central finite differences. This subroutine, which works in the C full space, is prepared to replace the subroutine evalnal (to C evaluate the gradient vector) in the case of the lastest have not C being provided by the user. C C On entry: C C n integer C number of variables C C x double precision x(n) C current point C C m integer C lambda double precision lambda(m) C rho double precision rho(m) C These three parameters are not used nor modified by C GENCAN and they are passed as arguments to the user- C defined subroutines evalal and evalnal to compute the C objective function and its gradient, respectively. C Clearly, in an Augmented Lagrangian context, if GENCAN is C being used to solve the bound-constrainted subproblems, m C would be the number of constraints, lambda the Lagrange C multipliers approximation and rho the penalty parameters C C sterel double precision C See below C C steabs double precision C This constants mean a ''relative small number'' and ''an C absolute small number'' for the increments in finite C difference approximations of derivatives C C RECOMMENDED: epsrel = 1.0d-07 and epsabs = 1.0d-10 C C CONSTRAINTS: sterel >= steabs > 0 C C On Return C C g double precision g(n) C approximation of the gradient vector at x C C inform integer C 0 = no errors, C < 0 = there was an error in the gradient calculation. C LOCAL SCALARS integer j double precision tmp,step,fplus,fminus inform = 0 do j = 1,n tmp = x(j) step = max( steabs, sterel * abs( tmp ) ) x(j) = tmp + step call evalal(n,x,m,lambda,rho,fplus,inform) if ( inform .lt. 0 ) then return end if x(j) = tmp - step call evalal(n,x,m,lambda,rho,fminus,inform) if ( inform .lt. 0 ) then return end if g(j) = ( fplus - fminus ) / ( 2.0d0 * step ) x(j) = tmp end do return end C ***************************************************************** C ***************************************************************** double precision function norm2s(n,x) implicit none C SCALAR ARGUMENTS integer n C ARRAY ARGUMENTS double precision x(n) C This subroutine computes the squared Euclidian norm of an C n-dimensional vector. C C On entry: C C n integer C dimension C C x double precision x(n) C vector C C On return: C C The function return the squared Euclidian norm of the C n-dimensional vector x. external hsldnrm2 double precision hsldnrm2 norm2s = hsldnrm2(n,x,1) ** 2 return end C ****************************************************************** C ****************************************************************** DOUBLE PRECISION FUNCTION HSLDNRM2(N,DX,INCX) DOUBLE PRECISION ZERO,ONE PARAMETER (ZERO=0.0D0,ONE=1.0D0) DOUBLE PRECISION CUTLO,CUTHI PARAMETER (CUTLO=8.232D-11,CUTHI=1.304D19) INTEGER INCX,N DOUBLE PRECISION DX(*) DOUBLE PRECISION HITEST,SUM,XMAX INTEGER I,J,NN INTRINSIC DABS,DSQRT,FLOAT IF (N.GT.0) GO TO 10 HSLDNRM2 = ZERO GO TO 300 10 CONTINUE SUM = ZERO NN = N*INCX I = 1 20 CONTINUE 30 IF (DABS(DX(I)).GT.CUTLO) GO TO 85 XMAX = ZERO 50 IF (DX(I).EQ.ZERO) GO TO 200 IF (DABS(DX(I)).GT.CUTLO) GO TO 85 GO TO 105 100 I = J SUM = (SUM/DX(I))/DX(I) 105 XMAX = DABS(DX(I)) GO TO 115 70 IF (DABS(DX(I)).GT.CUTLO) GO TO 75 110 IF (DABS(DX(I)).LE.XMAX) GO TO 115 SUM = ONE + SUM* (XMAX/DX(I))**2 XMAX = DABS(DX(I)) GO TO 200 115 SUM = SUM + (DX(I)/XMAX)**2 GO TO 200 75 SUM = (SUM*XMAX)*XMAX 85 HITEST = CUTHI/DFLOAT(N) DO 95 J = I,NN,INCX IF (DABS(DX(J)).GE.HITEST) GO TO 100 95 SUM = SUM + DX(J)**2 HSLDNRM2 = DSQRT(SUM) GO TO 300 200 CONTINUE I = I + INCX IF (I.LE.NN) GO TO 20 HSLDNRM2 = XMAX*DSQRT(SUM) 300 CONTINUE RETURN END C ****************************************************************** C ****************************************************************** C C Report of modifications. C C February 18th, 2005. C C 1) An unsed format statement, previously used to automaticaly C generates some tables, was deleted. C C 2) An unmateched parenthesis was corrected in the format C statement used to stop GENCAN due to a small step in a line search. C C February 16th, 2005. C C 1) The evalhd subroutine used by default in GENCAN is now the one C implemented in calchddiff, which approximates the Hessian-vector C product by incremental quotients. The implementation used to C overcome the non twice continuously differentiability of the C classical (PHR) Augmented Lagrangian function is now part of C ALGENCAN (and not GENCAN). So, to use GENCAN inside ALGENCAN, C htvtype argument must be set equal to 0 (ZERO). C C 2) The commented version of the empty function evalhd that must C be added when GENCAN is beinf used stand-alone was wrong. The C arguments declarations had been copied from evalnal. It was C corrected. C C November 10th, 2004. C C 1) After several test, all references to nonmontone line search C schemes were deleted. C C September 28th, 2004. C C 1) Subroutines were checked an some absent arguments explanations C were added C C 2) Some calling sequences were modified to group related arguments C C 3) Arguments and local variables declarations were reordered in C alphabetical order. C C 3) Shrink and expand subroutines were modified to deal with just C one vector at a time. In this way, they are now being called from C calc* subroutines. C C September 27th, 2004. C C 1) All comments were arranged to fit into the 72-columns format C C 2) Unused variable goth, which was prepared to indicate whether C the Hessian matrix have been evaluated at the current point, was C deleted from CG subroutine. C C 3) A spell check was used to correct the comments C C September 21th, 2004. C C 1) In the stopping criterion where the progress in the objective C function is verified, ''itnfp .ge. maxitnfp'' was changed for C ''itnfp .gt. maxitnfp'', to make the choice maxitnfp equal to 1 C sounds reasonable. C C 2) Moreover, the previous chance came from the addition in the C comments of GENCAN of the ''constraints'' information which makes C clear to the user the values each argument may assume. C C 3) In the calculations of the first ''trust-radius'' for Conjugate C Gradients, ''if( udelta0 .lt. 0.d0 ) then'' was changed by ''if C ( udelta0 .le. 0.0d0 ) then'' to also make the default GENCAN C choice of this initial trust-radius in the case of the user have C been setted udelta = 0 by mistake. C C 4) The same for ucgmaxit. C C 5) In the line search subroutines spgls and tnls, ''if ( interp C .gt. mininterp .and. samep ) then'' was changes by ''.ge.''. C C 6) Some comments of GENCAN arguments were re-written. C C September 16th, 2004. C C 1) With the reconfiguration of the calc* subroutines (see (1) C below) there were a number of redundant parameters in calchd and C evalhd subroutines. These parameters were eliminated. C C September 13th, 2004. C C 1) Subroutines named calc* that work in the reduced space always C call the corresponding eval* subroutine. As it was, calcg (that C computes the gradient in the reduced space) called evalg or C evalgdiff depending on gtype parameter. The same was for calchd. C Now, calcg calls evalg, calchd calls evalhd, and calchddiff (new) C approximates the Hessian times vector product by incremental C quotients calling calcg or calcgdiff depending on gtype parameter. C An improvement of this modification is that calcg does not call C evalg or evalgdiff (both work in the full space) any more but it C approximates the gradient vector in the reduced space (by central C finite differences) calling 2 * nind times evalf subroutine. C C 2) Some comments were added inside evalg and evalhd user supplied C subroutines alerting about the relation of these subroutines and C the parameters gtype and htvtype, respectively. C C 3) Description of tnls subroutine was slightly modified. C C 4) The description of htvtype parameter in gencan was again C slightly modified. C C 5) With the introduction of the parameter lambda (that in the C context of Augmented Lagrangians is used to store the C approximation of the Lagrange multipliers) the name of the C variable used for spectral steplength was changed from lambda to C lamspg. In addition, lammax was changed to lspgma and lammin to C lspgmi. C C 6) Modifications introduced in June 15th, 2004 and May 5th, 2004 C were, in fact, made in this version on September 13th, 2004. C C June 15th, 2004. C C 1) The fmin stopping criterion and the maximum number of C functional evaluation stopping criterion were erroneously being C tested before the main loop. It was just redundant and, for this C reason, deleted. C C May 5th, 2004. C C 1) Incorporated into an Augmented Lagrangian framework. C C a) evalf and evalg were renamed as evalal and evalnal, C respectively. C C b) m,lambda,rho were added as parameters of the subroutines evalal C and evalnal, and, as a consequence, as parameters of almost all C the other subroutines. C C 2) The comment of htvtype parameter of gencan was in portuguese C and it was translated into english. C C 3) A nonmonotone version of gencan is starting to be studied. C Parameters p and lastfv(0:p-1) were added to gencan, spgls, and C tnls to allow a nonmonotone line search. Array lastfv is now C been updated for saving the last p functional values and the C nonmonotone line searches are been done in a SPG or a C Truncated Newton direction. p = 1 means monotone line search C and is recommended until this study finish. C C April 13th, 2004. C C 1) The modifications introduced in the occasion of the IRLOC C development and re-development (October 21th, 2003 and February C 19th, 2003, respectively) were in fact made in this version on C April 13th, 2004. The motivation to do this was to unify two C parallel and different version of GENCAN (created, obviously, by C mistake). C C 2) The complete reference of the GENCAN paper was finally added. C C May 14th, 2003. c C 1) The way amax2 and amax2n were being computing may caused a C segmentation fault. Its initialization was changed from infty and C -infty to 1.0d+99 and -1.0d+99, respectively. Using infty, when C combined with a big trust region radius, the final value of amax2 C or amax2n may cause the impression that a bound is being attained, C when it is not. "Redundant" ifs inside the amax2 and anax2n C calculation were deleted. It should considered the possibility of C using two constants, namely, bignum = 1.0d+20 and infty = 1.0d+99, C instead of just infty. C C Modification introduced in October 21, 2003 in occasion of the C IRLOC re-development: C C 1) The stooping criteria related to functional value smaller than C fmin and exhaustion of maximum allowed number of functional C evaluations have been done after the line search. And the C questions were done as "if line search flag is equal to 4" or "if C line search flag is equal to 8". But it was wrong in the case, for C example, inside the line search, a functional value such that f <= C fmin and the Armijo criterion was satisfied. In such case, the C line search flag was being setted to 0 and not to 4. And gencan C did not stop by the fmin criterion. Now, both stooping criteria C are tested at the begining of the main gencan loop and just the C stooping criteria by small line search step is tested after the C line search. C C Modification introduced in February 19, 2003 in occasion of the C IRLOC development: C C 1) The description of epsnfp parameter of GENCAN was modified. It C was written that to inhibit the related stopping criterion (lack C of function progress) it was necessary just set epsnfp = 0 when C it is also necessary to set maxitnfp = maxit. it was added in the C explanation. C C 2) In the explanation at the beginning of GENCAN it was written C that cgscre parameter should be double precision. This comment was C wrong. The correct type for cgscre parameter is integer. C C Modifications introduced near April 1st 2003 in occasion of the C PHR and inequality-constraints Augmented Lagrangian methods C development: C C 1) The use of iprint was redefined and iprint2 was deleted. C C 2) The way to detect no progress in the log of the projected C gradient norm was changed. As it was, ''no progress'' means no C reduction in the projected gradient norm over M iterations. C But this criterion implicitly assumed that the projected C gradient norm must decrease monotonously. Is it is clearly not C true, the criterion was changed by a non-monotone decrease C criterion. Now, progress means that the projected gradient C norm is, at each iteration, smaller than the maximum over the C last M iterations. And "no progress" means the it does not C occurs during not smaller than the C C 3 ) The computation of qamaxn inside cg subroutine was in the C wrong place (it was being used before computed) and it may was C the reason for which the option nearlyq = .true. never worked C properly. With this correction this option should be tested again. C C On September 29th, 2004, we did a new test using the 41 bound C constrained problems with quadratic objective function from the C CUTE collection. The behaviour of GENCAN setting nearly equal C to true or false was indistinguishable. The test did not C include the different choices for the maximum number of CG C iterations being restricted to evaluate the different C alternatives for the case of finding a direction d such that C d^t H d <= 0. As a conclusion of this experiment we continue C recommending as a default choice to set nearlyq equal to false. C C Modifications introduced from March 1st to March 21th of 2002 C in occasion of the ISPG development: C C 1) Comments of some new parameters introduced in the previous C modification C C 2) As it was, in the first iteration of GENCAN (when kappa takes C value equal 1) and for one-dimensional faces, cgmaxit(the maximum C number of Conjugate Gradient iterations to compute the internal to C the face truncated-Newton direction) was being 0. As it is C obviously wrong, we add a max between what was being computed and C one to allow at least one CG iteration. C C 3) Parameter inform in subroutines evalf, evalg and evalhd C supplied by the user was added C C Modifications introduced from May 31th to November 2nd of 2001 C in occasion of the ALGENCAN development: C C Fixed bugs: C C 1) The first spectral steplength was not been projected in the C [lspgmi,lspgma] interval. C C 2) The conjugate gradients accuracy (cgeps) which is linearly C dependent of the Euclidian norm of the projected gradient, was C also not been projected in the interval [cgepsi,cgepsf]. C C 3) Conjugate gradients said that it was being used an Euclidian C norm trust region when it has really being used an infinite norm C trust region and viceversa. C C 4) Sometimes, the analytic gradient has been used although the C user choose the finite differences option. C C Modifications: C C 1) To avoid roundoff errors, an explicit detection of at least one C variable reaching its bound when a maximum step is being made was C added. C C 2) The way in which two points were considered very similar in, C for example, the interpolations and the extrapolations (which was C dependent of the infinity norm of the points) showed to be very C scale dependent. A new version which test the difference C coordinate to coordinate was done. In this was the calculus of the C current point x and the descent direction sup-norm is not done any C more. C C 3) The same constants epsrel and epsabs were used as small C relative and absolute values for, for example, detecting similar C points and for finite differences. Now, epsrel and epsabs are used C for detecting similar points (and the recommended values are C 10^{-10} and 10^{-20}, respectively) and new constants sterel and C steabs were introduced for finite differences (and the recommended C values are 10^{-7} and 10^{-10}, respectively). C C 4) Two new stopping criteria for CG were added: (i) we stop if C two consecutive iterates are too close; and (ii) we also C stop if there is no enough quadratic model progress during C maxitnqmp iterations. C C 5) The linear relation between the conjugate gradient accuracy C and the norm of the projected gradient can be computed using C the Euclidian- and the sup-norm of the projected gradient (only C Euclidian norm version was present in the previous version. The C linear relation is such that the CG accuracy is cgepsi when the C projected gradient norm value is equal to the value corresponding C to the initial guess and the CG accuracy is cgepsf when the C projected gradient norm value is cgrelf). C C 6) Inside Conjugate Gradients, the Euclidian-norm is been computed C using an algorithm developed by C.L.LAWSON, 1978 JAN 08. Numerical C experiments showed that the performance of GENCAN depends C basically on the conjugate gradients performance and stopping C criteria and that the conjugate gradients depends on the way the C Euclidian-norm is been computed. These things deserve further C research. C C 7) In the Augmented Lagrangian algorithm ALGENCAN, which uses C GENCAN to solve the bounded constrained subproblems, the maximum C number of Conjugate Gradients iterations (cgmaxit), which in this C version is linearly dependent of the projected gradient norm, was C set to 2 * (# of free variables). As CG is not using restarts we C do not know very well what this means. On the other hand, the C accuracy (given by cgeps) continues being more strict when we are C near to the solution and less strict when we ar far from the C solution. c C 8) Many things in the output were changed. packmol-20.010/getinp.f90000066400000000000000000001040161360620542100150310ustar00rootroot00000000000000! ! Written by Leandro Martínez, 2009-2011. ! Copyright (c) 2009-2018, Leandro Martínez, Jose Mario Martinez, ! Ernesto G. Birgin. ! ! Subroutine getinp: subroutine that reads the input file ! subroutine getinp() use sizes use compute_data, only : ntype, natoms, idfirst, nmols, ityperest, coor, restpars use input use usegencan implicit none integer :: i, k, ii, iarg, iline, idatom, iatom, in, lixo, irest, itype, itest,& imark, strlength, ioerr, nloop0 double precision :: clen character(len=200) :: record, blank logical :: inside_structure ! Clearing the blank character arrays do i = 1, 200 blank(i:i) = ' ' end do ! Getting random seed and optional optimization parameters if set seed = 1234567 randini = .false. check = .false. chkgrad = .false. iprint1 = 2 iprint2 = 2 discale = 1.1d0 writeout = 10 maxit = 20 nloop = 0 nloop0 = 0 movefrac = 0.05 movebadrandom = .false. precision = 1.d-2 writebad = .false. add_amber_ter = .false. add_box_sides = .false. add_sides_fix = 0.d0 sidemax = 1000.d0 ioerr = 0 avoidoverlap = .true. packall = .false. use_short_tol = .false. crd = .false. inside_structure = .false. do i = 1, nlines if ( keyword(i,1).eq.'structure') inside_structure = .true. if ( keyword(i,1).eq.'end' .and. & keyword(i,2).eq.'structure') inside_structure = .false. if(keyword(i,1).eq.'seed') then read(keyword(i,2),*,iostat=ioerr) seed if ( ioerr /= 0 ) exit if ( seed == -1 ) call seed_from_time(seed) else if(keyword(i,1).eq.'randominitialpoint') then randini = .true. else if(keyword(i,1).eq.'check') then check = .true. else if(keyword(i,1).eq.'writebad') then writebad = .true. else if(keyword(i,1).eq.'precision') then read(keyword(i,2),*,iostat=ioerr) precision if ( ioerr /= 0 ) exit write(*,*) ' Optional precision set: ', precision else if(keyword(i,1).eq.'movefrac') then read(keyword(i,2),*,iostat=ioerr) movefrac if ( ioerr /= 0 ) exit write(*,*) ' Optional movefrac set: ', movefrac else if(keyword(i,1).eq.'movebadrandom') then movebadrandom = .true. write(*,*) ' Will move randomly bad molecues (movebadrandom) ' else if(keyword(i,1).eq.'chkgrad') then chkgrad = .true. else if(keyword(i,1).eq.'writeout') then read(keyword(i,2),*,iostat=ioerr) writeout if ( ioerr /= 0 ) exit write(*,*) ' Output frequency: ', writeout else if(keyword(i,1).eq.'maxit') then read(keyword(i,2),*,iostat=ioerr) maxit if ( ioerr /= 0 ) exit write(*,*) ' User defined GENCAN number of iterations: ', maxit else if(keyword(i,1).eq.'nloop') then if( .not. inside_structure ) then read(keyword(i,2),*,iostat=ioerr) nloop if ( ioerr /= 0 ) exit end if else if(keyword(i,1).eq.'nloop0') then if( .not. inside_structure ) then read(keyword(i,2),*,iostat=ioerr) nloop0 if ( ioerr /= 0 ) exit end if else if(keyword(i,1).eq.'discale') then read(keyword(i,2),*,iostat=ioerr) discale if ( ioerr /= 0 ) exit write(*,*) ' Optional initial tolerance scale: ', discale else if(keyword(i,1).eq.'sidemax') then read(keyword(i,2),*,iostat=ioerr) sidemax if ( ioerr /= 0 ) exit write(*,*) ' User set maximum system dimensions: ', sidemax else if(keyword(i,1).eq.'fbins') then read(keyword(i,2),*,iostat=ioerr) fbins if ( ioerr /= 0 ) exit write(*,*) ' User set linked-cell bin parameter: ', fbins else if(keyword(i,1).eq.'add_amber_ter') then add_amber_ter = .true. write(*,*) ' Will add the TER flag between molecules. ' else if(keyword(i,1).eq.'avoid_overlap') then if ( keyword(i,2).eq.'yes') then avoidoverlap = .true. write(*,*) ' Will avoid overlap to fixed molecules at initial point. ' else avoidoverlap = .false. write(*,*) ' Will NOT avoid overlap to fixed molecules at initial point. ' end if else if(keyword(i,1).eq.'packall') then packall = .true. write(*,*) ' Will pack all molecule types from the beginning. ' else if(keyword(i,1).eq.'use_short_tol') then use_short_tol = .true. write(*,*) ' Will use a short distance penalty for all atoms. ' else if(keyword(i,1).eq.'writecrd') then crd = .true. write(*,*) ' Will write output also in CRD format ' read(keyword(i,2),*,iostat=ioerr) crdfile else if(keyword(i,1).eq.'add_box_sides') then add_box_sides = .true. write(*,*) ' Will print BOX SIDE informations. ' read(keyword(i,2),*,iostat=ioerr) add_sides_fix if ( ioerr /= 0 ) then ioerr = 0 cycle end if write(*,*) ' Will sum ', add_sides_fix,' to each side length on print' else if(keyword(i,1).eq.'iprint1') then read(keyword(i,2),*,iostat=ioerr) iprint1 if ( ioerr /= 0 ) exit write(*,*) ' Optional printvalue 1 set: ', iprint1 else if(keyword(i,1).eq.'iprint2') then read(keyword(i,2),*,iostat=ioerr) iprint2 if ( ioerr /= 0 ) exit write(*,*) ' Optional printvalue 2 set: ', iprint2 else if( keyword(i,1) /= 'tolerance' .and. & keyword(i,1) /= 'short_tol_dist' .and. & keyword(i,1) /= 'short_tol_scale' .and. & keyword(i,1) /= 'structure' .and. & keyword(i,1) /= 'end' .and. & keyword(i,1) /= 'atoms' .and. & keyword(i,1) /= 'output' .and. & keyword(i,1) /= 'filetype' .and. & keyword(i,1) /= 'number' .and. & keyword(i,1) /= 'inside' .and. & keyword(i,1) /= 'outside' .and. & keyword(i,1) /= 'fixed' .and. & keyword(i,1) /= 'center' .and. & keyword(i,1) /= 'centerofmass' .and. & keyword(i,1) /= 'over' .and. & keyword(i,1) /= 'below' .and. & keyword(i,1) /= 'constrain_rotation' .and. & keyword(i,1) /= 'radius' .and. & keyword(i,1) /= 'fscale' .and. & keyword(i,1) /= 'short_radius' .and. & keyword(i,1) /= 'short_radius_scale' .and. & keyword(i,1) /= 'resnumbers' .and. & keyword(i,1) /= 'changechains' .and. & keyword(i,1) /= 'chain' .and. & keyword(i,1) /= 'discale' .and. & keyword(i,1) /= 'maxit' .and. & keyword(i,1) /= 'movebadrandom' .and. & keyword(i,1) /= 'add_amber_ter' .and. & keyword(i,1) /= 'sidemax' .and. & keyword(i,1) /= 'seed' .and. & keyword(i,1) /= 'randominitialpoint' .and. & keyword(i,1) /= 'restart_from' .and. & keyword(i,1) /= 'restart_to' .and. & keyword(i,1) /= 'nloop' .and. & keyword(i,1) /= 'nloop0' .and. & keyword(i,1) /= 'writeout' .and. & keyword(i,1) /= 'writebad' .and. & keyword(i,1) /= 'check' .and. & keyword(i,1) /= 'iprint1' .and. & keyword(i,1) /= 'iprint2' .and. & keyword(i,1) /= 'writecrd' .and. & keyword(i,1) /= 'segid' .and. & keyword(i,1) /= 'chkgrad' ) then write(*,*) ' ERROR: Keyword not recognized: ', trim(keyword(i,1)) stop end if end do if ( ioerr /= 0 ) then write(*,*) ' ERROR: Some optional keyword was not used correctly: ', trim(keyword(i,1)) stop end if write(*,*) ' Seed for random number generator: ', seed call init_random_number(seed) ! Checking for the name of the output file to be created xyzout = '####' do iline = 1, nlines if(keyword(iline,1).eq.'output') then xyzout = keyword(iline,2) xyzout = xyzout(1:strlength(xyzout)) end if end do if(xyzout(1:4) == '####') then write(*,*)' ERROR: Output file not (correctly?) specified. ' stop end if write(*,*)' Output file: ', xyzout(1:strlength(xyzout)) ! Reading structure files itype = 0 do iline = 1, nlines if(keyword(iline,1).eq.'structure') then itype = itype + 1 record = keyword(iline,2) write(*,*) ' Reading coordinate file: ', record(1:strlength(record)) ! Reading pdb input files if(pdb) then name(itype) = record(1:strlength(record)) record = keyword(iline,2) pdbfile(itype) = record(1:80) idfirst(itype) = 1 do ii = itype - 1, 1, -1 idfirst(itype) = idfirst(itype) + natoms(ii) end do open(10,file=keyword(iline,2),status='old',iostat=ioerr) if ( ioerr /= 0 ) call failopen(keyword(iline,2)) record(1:6) = '######' do while(record(1:4).ne.'ATOM'.and.record(1:6).ne.'HETATM') read(10,"( a200 )") record end do idatom = idfirst(itype) - 1 do while(idatom.lt.natoms(itype)+idfirst(itype)-1) if(record(1:4).eq.'ATOM'.or.record(1:6).eq.'HETATM') then idatom = idatom + 1 amass(idatom) = 1.d0 read(record,"( t31,f8.3,t39,f8.3,t47,f8.3 )",iostat=ioerr) & (coor(idatom,k),k=1,3) if( ioerr /= 0 ) then record = keyword(iline,2) write(*,*) ' ERROR: Failed to read coordinates from', & ' file: ', record(1:strlength(record)) write(*,*) ' Probably the coordinates are not in', & ' standard PDB file format. ' write(*,*) ' Standard PDB format specifications', & ' can be found at: ' write(*,*) ' www.rcsb.org/pdb ' stop end if ! This only tests if residue numbers can be read, they are used ! only for output read(record(23:26),*,iostat=ioerr) itest if( ioerr /= 0 ) then record = pdbfile(itype) write(*,*) ' ERROR: Failed reading residue number',& ' from PDB file: ',record(1:strlength(record)) write(*,*) ' Residue numbers are integers that',& ' must be within columns 23 and 26. ' write(*,*) ' Other characters within these columns',& ' will cause input/output errors. ' write(*,*) ' Standard PDB format specifications',& ' can be found at: ' write(*,*) ' www.rcsb.org/pdb ' stop end if end if read(10,"( a200 )",iostat=ioerr) record if ( ioerr /= 0 ) exit end do close(10) end if ! Reading tinker input files if(tinker) then open(10,file=keyword(iline,2),status='old',iostat=ioerr) if ( ioerr /= 0 ) call failopen(keyword(iline,2)) idfirst(itype) = 1 do ii = itype - 1, 1, -1 idfirst(itype) = idfirst(itype) + natoms(ii) end do record = keyword(iline,2) call setcon(record(1:64),idfirst(itype)) open(10,file = keyword(iline,2), status = 'old') record = blank do while(record.le.blank) read(10,"( a200 )") record end do i = 1 do while(record(i:i).le.' ') i = i + 1 if ( i > 200 ) exit end do iarg = i if ( i < 200 ) then do while(record(i:i).gt.' ') i = i + 1 if ( i > 200 ) exit end do end if read(record(iarg:i-1),*) natoms(itype) if ( i < 200 ) then do while(record(i:i).le.' ') i = i + 1 if ( i > 200 ) exit end do end if iarg = i if ( i < 200 ) then do while(record(i:i).gt.' ') i = i + 1 if ( i > 200 ) exit end do end if read(record(iarg:i-1),"( a200 )") name(itype) record = name(itype) name(itype) = record(1:strlength(record)) if(name(itype).lt.' ') name(itype) = 'Without_title' idatom = idfirst(itype) - 1 do iatom = 1, natoms(itype) idatom = idatom + 1 record = blank do while(record.le.blank) read(10,"( a200 )") record end do i = 1 do while(record(i:i).le.' ') i = i + 1 if ( i > 200 ) exit end do iarg = i if ( i < 200 ) then do while(record(i:i).gt.' ') i = i + 1 if ( i > 200 ) exit end do end if read(record(iarg:i-1),*) in if ( i < 200 ) then do while(record(i:i).le.' ') i = i + 1 if ( i > 200 ) exit end do end if iarg = i if ( i < 200 ) then do while(record(i:i).gt.' ') i = i + 1 if ( i > 200 ) exit end do end if read(record(iarg:i-1),*) ele(idatom) read(record(i:200),*) (coor(idatom,k), k = 1, 3),& (nconnect(idatom, k), k = 1, maxcon(idatom)) amass(idatom) = 1.d0 end do close(10) end if ! Reading xyz input files if(xyz) then open(10,file=keyword(iline,2),status='old',iostat=ioerr) if ( ioerr /= 0 ) call failopen(keyword(iline,2)) read(10,*) natoms(itype) read(10,"( a200 )") name(itype) if(name(itype).lt.' ') name(itype) = 'Without_title' idfirst(itype) = 1 do ii = itype - 1, 1, -1 idfirst(itype) = idfirst(itype) + natoms(ii) end do idatom = idfirst(itype) - 1 do iatom = 1, natoms(itype) idatom = idatom + 1 record = blank read(10,"( a200 )") record read(record,*) ele(idatom), (coor(idatom,k),k=1,3) amass(idatom) = 1.d0 end do close(10) end if ! Reading moldy input files if(moldy) then open(10,file=keyword(iline,2), status ='old',iostat=ioerr) if ( ioerr /= 0 ) call failopen(keyword(iline,2)) read(10,*) name(itype), nmols(itype) natoms(itype) = 0 do while(.true.) read(10,"( a200 )",iostat=ioerr) record if ( ioerr /= 0 ) exit if(record.gt.' '.and.record(1:3).ne.'end') & natoms(itype) = natoms(itype) + 1 end do close(10) idfirst(itype) = 1 do ii = itype - 1, 1, -1 idfirst(itype) = idfirst(itype) + natoms(ii) end do open(10,file=keyword(iline,2),status='old') read(10,"( a200 )") record idatom = idfirst(itype) - 1 do iatom = 1, natoms(itype) idatom = idatom + 1 read(10,"( a200 )") record read(record,*) lixo, (coor(idatom,k), k = 1, 3),& amass(idatom), charge(idatom), ele(idatom) end do close(10) end if end if end do ntype = itype write(*,*) ' Number of independent structures: ', ntype write(*,*) ' The structures are: ' do itype = 1, ntype record = name(itype) write(*,*) ' Structure ', itype, ':',record(1:strlength(record)),& '(',natoms(itype),' atoms)' end do ! Setting the vectors for the number of GENCAN loops if(nloop.eq.0) then nloop_all = 200*ntype nloop = nloop_all else nloop_all = nloop end if write(*,*) ' Maximum number of GENCAN loops for all molecule packing: ', nloop_all do itype = 1, ntype if ( nloop_type(itype) == 0 ) then nloop_type(itype) = nloop_all else write(*,*) ' Maximum number of GENCAN loops for type: ', itype, ': ', nloop_type(itype) end if end do ! nloop0 are the number of loops for the initial phase packing if(nloop0.eq.0) then nloop0 = 20*ntype else write(*,*) ' Maximum number of GENCAN loops-0 for all molecule packing: ', nloop0 end if do itype = 1, ntype if ( nloop0_type(itype) == 0 ) then nloop0_type(itype) = nloop0 else write(*,*) ' Maximum number of GENCAN loops-0 for type: ', itype, ': ', nloop0_type(itype) end if end do ! Reading the restrictions that were set irest = 0 ioerr = 0 do iline = 1, nlines if(keyword(iline,1).eq.'fixed') then irest = irest + 1 irestline(irest) = iline ityperest(irest) = 1 read(keyword(iline,2),*,iostat=ioerr) restpars(irest,1) read(keyword(iline,3),*,iostat=ioerr) restpars(irest,2) read(keyword(iline,4),*,iostat=ioerr) restpars(irest,3) read(keyword(iline,5),*,iostat=ioerr) restpars(irest,4) read(keyword(iline,6),*,iostat=ioerr) restpars(irest,5) read(keyword(iline,7),*,iostat=ioerr) restpars(irest,6) end if if(keyword(iline,1).eq.'inside') then irest = irest + 1 irestline(irest) = iline if(keyword(iline,2).eq.'cube') then ityperest(irest) = 2 read(keyword(iline,3),*,iostat=ioerr) restpars(irest,1) read(keyword(iline,4),*,iostat=ioerr) restpars(irest,2) read(keyword(iline,5),*,iostat=ioerr) restpars(irest,3) read(keyword(iline,6),*,iostat=ioerr) restpars(irest,4) else if(keyword(iline,2).eq.'box') then ityperest(irest) = 3 read(keyword(iline,3),*,iostat=ioerr) restpars(irest,1) read(keyword(iline,4),*,iostat=ioerr) restpars(irest,2) read(keyword(iline,5),*,iostat=ioerr) restpars(irest,3) read(keyword(iline,6),*,iostat=ioerr) restpars(irest,4) read(keyword(iline,7),*,iostat=ioerr) restpars(irest,5) read(keyword(iline,8),*,iostat=ioerr) restpars(irest,6) else if(keyword(iline,2).eq.'sphere') then ityperest(irest) = 4 read(keyword(iline,3),*,iostat=ioerr) restpars(irest,1) read(keyword(iline,4),*,iostat=ioerr) restpars(irest,2) read(keyword(iline,5),*,iostat=ioerr) restpars(irest,3) read(keyword(iline,6),*,iostat=ioerr) restpars(irest,4) else if(keyword(iline,2).eq.'ellipsoid') then ityperest(irest) = 5 read(keyword(iline,3),*,iostat=ioerr) restpars(irest,1) read(keyword(iline,4),*,iostat=ioerr) restpars(irest,2) read(keyword(iline,5),*,iostat=ioerr) restpars(irest,3) read(keyword(iline,6),*,iostat=ioerr) restpars(irest,4) read(keyword(iline,7),*,iostat=ioerr) restpars(irest,5) read(keyword(iline,8),*,iostat=ioerr) restpars(irest,6) read(keyword(iline,9),*,iostat=ioerr) restpars(irest,7) else if(keyword(iline,2).eq.'cylinder') then ityperest(irest) = 12 read(keyword(iline,3),*,iostat=ioerr) restpars(irest,1) read(keyword(iline,4),*,iostat=ioerr) restpars(irest,2) read(keyword(iline,5),*,iostat=ioerr) restpars(irest,3) read(keyword(iline,6),*,iostat=ioerr) restpars(irest,4) read(keyword(iline,7),*,iostat=ioerr) restpars(irest,5) read(keyword(iline,8),*,iostat=ioerr) restpars(irest,6) read(keyword(iline,9),*,iostat=ioerr) restpars(irest,7) read(keyword(iline,10),*,iostat=ioerr) restpars(irest,9) restpars(irest,8) = restpars(irest,4)**2 + & restpars(irest,5)**2 + & restpars(irest,6)**2 if(restpars(irest,8).lt.1.d-10) then write(*,*) ' ERROR: The norm of the director vector', & ' of the cylinder constraint cannot be zero.' ioerr = 1 else clen = dsqrt(restpars(irest,8)) restpars(irest,4) = restpars(irest,4) / clen restpars(irest,5) = restpars(irest,5) / clen restpars(irest,6) = restpars(irest,6) / clen end if else ioerr = 1 end if end if if(keyword(iline,1).eq.'outside') then irest = irest + 1 irestline(irest) = iline if(keyword(iline,2).eq.'cube') then ityperest(irest) = 6 read(keyword(iline,3),*,iostat=ioerr) restpars(irest,1) read(keyword(iline,4),*,iostat=ioerr) restpars(irest,2) read(keyword(iline,5),*,iostat=ioerr) restpars(irest,3) read(keyword(iline,6),*,iostat=ioerr) restpars(irest,4) else if(keyword(iline,2).eq.'box') then ityperest(irest) = 7 read(keyword(iline,3),*,iostat=ioerr) restpars(irest,1) read(keyword(iline,4),*,iostat=ioerr) restpars(irest,2) read(keyword(iline,5),*,iostat=ioerr) restpars(irest,3) read(keyword(iline,6),*,iostat=ioerr) restpars(irest,4) read(keyword(iline,7),*,iostat=ioerr) restpars(irest,5) read(keyword(iline,8),*,iostat=ioerr) restpars(irest,6) else if(keyword(iline,2).eq.'sphere') then ityperest(irest) = 8 read(keyword(iline,3),*,iostat=ioerr) restpars(irest,1) read(keyword(iline,4),*,iostat=ioerr) restpars(irest,2) read(keyword(iline,5),*,iostat=ioerr) restpars(irest,3) read(keyword(iline,6),*,iostat=ioerr) restpars(irest,4) else if(keyword(iline,2).eq.'ellipsoid') then ityperest(irest) = 9 read(keyword(iline,3),*,iostat=ioerr) restpars(irest,1) read(keyword(iline,4),*,iostat=ioerr) restpars(irest,2) read(keyword(iline,5),*,iostat=ioerr) restpars(irest,3) read(keyword(iline,6),*,iostat=ioerr) restpars(irest,4) read(keyword(iline,7),*,iostat=ioerr) restpars(irest,5) read(keyword(iline,8),*,iostat=ioerr) restpars(irest,6) read(keyword(iline,9),*,iostat=ioerr) restpars(irest,7) else if(keyword(iline,2).eq.'cylinder') then ityperest(irest) = 13 read(keyword(iline,3),*,iostat=ioerr) restpars(irest,1) read(keyword(iline,4),*,iostat=ioerr) restpars(irest,2) read(keyword(iline,5),*,iostat=ioerr) restpars(irest,3) read(keyword(iline,6),*,iostat=ioerr) restpars(irest,4) read(keyword(iline,7),*,iostat=ioerr) restpars(irest,5) read(keyword(iline,8),*,iostat=ioerr) restpars(irest,6) read(keyword(iline,9),*,iostat=ioerr) restpars(irest,7) read(keyword(iline,10),*,iostat=ioerr) restpars(irest,9) restpars(irest,8) = restpars(irest,4)**2 + & restpars(irest,5)**2 + & restpars(irest,6)**2 if(restpars(irest,8).lt.1.d-10) then write(*,*) ' ERROR: The norm of the director vector',& ' of the cylinder constraint cannot be zero.' ioerr = 1 else clen = dsqrt(restpars(irest,8)) restpars(irest,4) = restpars(irest,4) / clen restpars(irest,5) = restpars(irest,5) / clen restpars(irest,6) = restpars(irest,6) / clen end if else ioerr = 1 end if end if if(keyword(iline,1).eq.'over') then irest = irest + 1 irestline(irest) = iline ityperest(irest) = 10 read(keyword(iline,3),*,iostat=ioerr) restpars(irest,1) read(keyword(iline,4),*,iostat=ioerr) restpars(irest,2) read(keyword(iline,5),*,iostat=ioerr) restpars(irest,3) read(keyword(iline,6),*,iostat=ioerr) restpars(irest,4) if(keyword(iline,2).ne.'plane') ioerr = 1 end if if(keyword(iline,1).eq.'below') then irest = irest + 1 irestline(irest) = iline ityperest(irest) = 11 read(keyword(iline,3),*,iostat=ioerr) restpars(irest,1) read(keyword(iline,4),*,iostat=ioerr) restpars(irest,2) read(keyword(iline,5),*,iostat=ioerr) restpars(irest,3) read(keyword(iline,6),*,iostat=ioerr) restpars(irest,4) if(keyword(iline,2).ne.'plane') ioerr = 1 end if if ( ioerr /= 0 ) then write(*,*) ' ERROR: Some restriction is not set correctly. ' stop end if end do nrest = irest write(*,*) ' Total number of restrictions: ', nrest ! Getting the tolerance ioerr = 1 dism = -1.d0 do iline = 1, nlines if(keyword(iline,1).eq.'tolerance') then read(keyword(iline,2),*,iostat=ioerr) dism if ( ioerr /= 0 ) then write(*,*) ' ERROR: Failed reading tolerance. ' stop end if exit end if end do if ( ioerr /= 0 ) then write(*,*) ' ERROR: Overall tolerance not set. Use, for example: tolerance 2.0 ' stop end if write(*,*) ' Distance tolerance: ', dism ! Reading, if defined, the short distance penalty parameters ioerr = 1 short_tol_dist = dism/2.d0 ! Reading short_tol_dist do iline = 1, nlines if(keyword(iline,1).eq.'short_tol_dist') then read(keyword(iline,2),*,iostat=ioerr) short_tol_dist if ( ioerr /= 0 ) then write(*,*) ' ERROR: Failed reading short_tol_dist. ' stop end if if ( short_tol_dist > dism ) then write(*,*) ' ERROR: The short_tol_dist parameter must be smaller than the tolerance. ' stop end if write(*,*) ' User defined short tolerance distance: ', short_tol_dist short_tol_dist = short_tol_dist**2 exit end if end do ! Reading short_tol_scale short_tol_scale = 3.d0 do iline = 1, nlines if(keyword(iline,1).eq.'short_tol_scale') then read(keyword(iline,2),*,iostat=ioerr) short_tol_scale if ( ioerr /= 0 ) then write(*,*) ' ERROR: Failed reading short_tol_scale. ' stop end if if ( short_tol_dist <= 0.d0 ) then write(*,*) ' ERROR: The short_tol_scale parameter must be positive. ' stop end if write(*,*) ' User defined short tolerance scale: ', short_tol_scale exit end if end do ! Assigning the input lines that correspond to each structure itype = 0 iline = 0 do while(iline < nlines) iline = iline + 1 if(keyword(iline,1).eq.'structure') then itype = itype + 1 linestrut(itype,1) = iline iline = iline + 1 do while(keyword(iline,1).ne.'end'.or.& keyword(iline,2).ne.'structure') if(keyword(iline,1) == 'structure'.or.& iline == nlines) then write(*,*) ' Input file ERROR: structure specification',& ' not ending with "end structure"' stop end if iline = iline + 1 end do linestrut(itype,2) = iline end if end do ! If pdb files, get the type of residue numbering output for each ! molecule if(pdb) then do itype = 1, ntype resnumbers(itype) = -1 changechains(itype) = .false. chain(itype) = "#" segid(itype) = "" do iline = 1, nlines if(iline.gt.linestrut(itype,1).and.& iline.lt.linestrut(itype,2)) then if(keyword(iline,1).eq.'changechains') then changechains(itype) = .true. end if if(keyword(iline,1).eq.'resnumbers') then read(keyword(iline,2),*) resnumbers(itype) end if if(keyword(iline,1).eq.'chain') then read(keyword(iline,2),*) chain(itype) end if if(keyword(iline,1).eq.'segid') then read(keyword(iline,2),*) segid(itype) end if end if end do if (crd) then if (itype.gt.1 .and. segid(itype)=="") then if (segid(itype-1) /= "") then write(*,*) ' Warning: Type of segid not defined for ', itype,'. Keeping it same as previous' endif segid(itype) = segid(itype-1) endif endif if ( resnumbers(itype) == -1 ) then write(*,*) ' Warning: Type of residue numbering not',& ' set for structure ',itype call setrnum(pdbfile(itype),imark) if(imark.eq.1) resnumbers(itype) = 0 if(imark.gt.1) resnumbers(itype) = 1 end if write(*,*) ' Residue numbering set for structure ',itype,':',& resnumbers(itype) write(*,*) ' Swap chains of molecules of structure ',& itype,':', changechains(itype) if ( chain(itype) /= "#" ) then write(*,*) ' Specific chain identifier set for structure ',itype,':',chain(itype) end if if ( chain(itype) /= "#" .and. changechains(itype) ) then write(*,*) " ERROR: 'changechains' and 'chain' input parameters are not compatible " write(*,*) " for a single structure. " stop end if end do end if ! Write the number of molecules of each type do itype = 1, ntype write(*,*) ' Number of molecules of type ', itype, ': ', nmols(itype) if(pdb.and.nmols(itype).gt.9999) then write(*,*) ' Warning: There will be more than 9999 molecules of type ',itype if (.not. crd) write(*,*) ' Residue numbering is reset after 9999. ' if (crd) write(*,*) ' Residue numbering is reset after 9999 in pdb but not in crd. ' if ( chain(itype) == "#" ) then write(*,*) ' Each set be will be assigned a different chain in the PDB output file. ' end if end if if(crd.and.nmols(itype).gt.99999999) then write(*,*) ' Warning: There will be more than 99999999 molecules of type ',itype write(*,*) ' Residue numbering is reset after 99999999 in crd. ' endif end do ! Checking if restart files will be used for each structure or for the whole system restart_from(0) = "none" restart_to(0) = "none" do itype = 1, ntype restart_from(itype) = "none" restart_to(itype) = "none" end do lines: do iline = 1, nlines if ( keyword(iline,1) == 'restart_from' ) then do itype = 1, ntype if(iline.gt.linestrut(itype,1).and.& iline.lt.linestrut(itype,2)) then restart_from(itype) = keyword(iline,2) cycle lines end if end do if( restart_from(0) == 'none' ) then restart_from(0) = keyword(iline,2) else write(*,*) ' ERROR: More than one definition of restart_from file for all system. ' stop end if end if if ( keyword(iline,1) == 'restart_to' ) then do itype = 1, ntype if(iline.gt.linestrut(itype,1).and.& iline.lt.linestrut(itype,2)) then restart_to(itype) = keyword(iline,2) cycle lines end if end do if( restart_to(0) == 'none' ) then restart_to(0) = keyword(iline,2) else write(*,*) ' ERROR: More than one definition of restart_to file for all system. ' stop end if end if end do lines return end subroutine getinp ! ! Subroutine that stops if failed to open file ! subroutine failopen(record) character(len=200) :: record write(*,*) write(*,*) ' ERROR: Could not open file. ' write(*,*) ' Could not find file: ',trim(record) write(*,*) ' Please check if all the input and structure ' write(*,*) ' files are in the current directory or if the' write(*,*) ' correct paths are provided.' write(*,*) stop end subroutine failopen ! ! Subroutine that checks if a pdb structure has one or more than ! one residue ! subroutine setrnum(file,nres) implicit none integer :: iread, ires, ireslast, nres, ioerr character(len=80) :: file character(len=200) :: record open(10,file=file,status='old') iread = 0 nres = 1 do while(nres.eq.1) read(10,"( a200 )",iostat=ioerr) record if ( ioerr /= 0 ) exit if(record(1:4).eq.'ATOM'.or.record(1:6).eq.'HETATM') then read(record(23:26),*,iostat=ioerr) ires if ( ioerr /= 0 ) cycle iread = iread + 1 if(iread.gt.1) then if(ires.ne.ireslast) then nres = 2 close(10) return end if end if ireslast = ires end if end do close(10) return end subroutine setrnum ! ! Subroutine that computes de number of connections of each atom ! for tinker xyz files ! subroutine setcon(xyzfile,idfirst) use sizes use input, only : maxcon implicit none integer :: idfirst integer :: natoms, idatom, iatom, ic, i character(len=64) :: xyzfile character(len=120) :: record open(10, file = xyzfile, status='old') read(10,*) natoms idatom = idfirst - 1 do iatom = 1, natoms idatom = idatom + 1 read(10,"( a120 )") record ic = 0 do i = 1, 119 if(record(i:i).gt.' '.and.record(i+1:i+1).le.' ') ic = ic + 1 end do maxcon(idatom) = ic - 5 end do close(10) return end subroutine setcon ! ! Subroutine getkeywords: gets keywords and values from the input ! file in a more robust way ! subroutine getkeywords() use sizes use input, only : keyword, nlines, inputfile implicit none character(len=200) :: record integer :: iline, i, j, ilast, ival, ioerr ! Clearing keyword array do i = 1, nlines do j = 1, maxkeywords keyword(i,j) = 'none' end do end do ! Filling keyword array do iline = 1, nlines read(inputfile(iline),"( a200 )",iostat=ioerr) record if ( ioerr /= 0 ) exit i = 0 ival = 0 do while(i < 200) i = i + 1 ilast = i do while(record(i:i) > ' '.and. i < 200) i = i + 1 end do if(i.gt.ilast) then ival = ival + 1 keyword(iline,ival) = record(ilast:i) end if end do end do return end subroutine getkeywords ! Subroutine that returns the chain character given an index subroutine chainc(i,chain) implicit none integer :: i character :: chain if(i.eq.0) chain = ' ' if(i.eq.1) chain = 'A' if(i.eq.2) chain = 'B' if(i.eq.3) chain = 'C' if(i.eq.4) chain = 'D' if(i.eq.5) chain = 'E' if(i.eq.6) chain = 'F' if(i.eq.7) chain = 'G' if(i.eq.8) chain = 'H' if(i.eq.9) chain = 'I' if(i.eq.10) chain = 'J' if(i.eq.11) chain = 'K' if(i.eq.12) chain = 'L' if(i.eq.13) chain = 'M' if(i.eq.14) chain = 'N' if(i.eq.15) chain = 'O' if(i.eq.16) chain = 'P' if(i.eq.17) chain = 'Q' if(i.eq.18) chain = 'R' if(i.eq.19) chain = 'S' if(i.eq.20) chain = 'T' if(i.eq.21) chain = 'U' if(i.eq.22) chain = 'V' if(i.eq.23) chain = 'W' if(i.eq.24) chain = 'X' if(i.eq.25) chain = 'Y' if(i.eq.26) chain = 'Z' if(i.eq.27) chain = '1' if(i.eq.28) chain = '2' if(i.eq.29) chain = '3' if(i.eq.30) chain = '4' if(i.eq.31) chain = '5' if(i.eq.32) chain = '6' if(i.eq.33) chain = '7' if(i.eq.34) chain = '8' if(i.eq.35) chain = '9' if(i.eq.36) chain = '0' if(i.gt.36) chain = '#' return end subroutine chainc ! Subroutine that clears a character variable subroutine clear(record) integer :: i character(len=80) :: record do i = 1, 80 record(i:i) = ' ' end do return end subroutine clear packmol-20.010/gparc.f90000066400000000000000000000055301360620542100146400ustar00rootroot00000000000000! ! Written by Leandro Martínez, 2009-2011. ! Copyright (c) 2009-2018, Leandro Martínez, Jose Mario Martinez, ! Ernesto G. Birgin. ! ! Compute gradient relative to atom-to-atom distances ! subroutine gparc(icart,firstjcart) use sizes use compute_data implicit none ! SCALAR ARGUMENTS integer :: icart,firstjcart ! LOCAL SCALARS integer :: jcart double precision :: datom, dtemp, xdiff, tol, & short_tol, short_tol_scale jcart = firstjcart do while ( jcart .ne. 0 ) ! ! Cycle if this type is not to be computed ! if ( .not. comptype(ibtype(jcart))) then jcart = latomnext(jcart) cycle end if ! ! Cycle if the atoms are from the same molecule ! if ( ibmol(icart) == ibmol(jcart) .and. & ibtype(icart) == ibtype(jcart) ) then jcart = latomnext(jcart) cycle end if ! ! Cycle if both atoms are from fixed molecules ! if ( fixedatom(icart) .and. fixedatom(jcart) ) then jcart = latomnext(jcart) cycle end if ! ! Otherwise, compute distance and evaluate function for this pair ! tol = (radius(icart)+radius(jcart))**2 datom = (xcart(icart, 1)-xcart(jcart, 1))**2 + & (xcart(icart, 2)-xcart(jcart, 2))**2 + & (xcart(icart, 3)-xcart(jcart, 3))**2 if( datom < tol ) then dtemp = fscale(icart)*fscale(jcart) * 4.d0 * (datom - tol) xdiff = dtemp*(xcart(icart,1) - xcart(jcart,1)) gxcar(icart,1)= gxcar(icart,1) + xdiff gxcar(jcart,1)= gxcar(jcart,1) - xdiff xdiff = dtemp*(xcart(icart,2) - xcart(jcart,2)) gxcar(icart,2)= gxcar(icart,2) + xdiff gxcar(jcart,2)= gxcar(jcart,2) - xdiff xdiff = dtemp*(xcart(icart,3) - xcart(jcart,3)) gxcar(icart,3)= gxcar(icart,3) + xdiff gxcar(jcart,3)= gxcar(jcart,3) - xdiff if ( use_short_radius(icart) .or. use_short_radius(jcart) ) then short_tol = ( short_radius(icart) + short_radius(jcart) )**2 if ( datom < short_tol ) then short_tol_scale = dsqrt(short_radius_scale(icart)*short_radius_scale(jcart)) short_tol_scale = short_tol_scale*( tol**2 / short_tol**2 ) dtemp = fscale(icart)*fscale(jcart) * 4.d0 * short_tol_scale*(datom - short_tol) xdiff = dtemp*(xcart(icart,1) - xcart(jcart,1)) gxcar(icart,1)= gxcar(icart,1) + xdiff gxcar(jcart,1)= gxcar(jcart,1) - xdiff xdiff = dtemp*(xcart(icart,2) - xcart(jcart,2)) gxcar(icart,2)= gxcar(icart,2) + xdiff gxcar(jcart,2)= gxcar(jcart,2) - xdiff xdiff = dtemp*(xcart(icart,3) - xcart(jcart,3)) gxcar(icart,3)= gxcar(icart,3) + xdiff gxcar(jcart,3)= gxcar(jcart,3) - xdiff end if end if end if jcart = latomnext(jcart) end do return end subroutine gparc packmol-20.010/gwalls.f90000066400000000000000000000244201360620542100150340ustar00rootroot00000000000000! ! Written by Leandro Martínez, 2009-2011. ! Copyright (c) 2009-2018, Leandro Martínez, Jose Mario Martinez, ! Ernesto G. Birgin. ! ! Gradient relative to restraints ! subroutine gwalls(icart,irest) use sizes use compute_data implicit none integer :: icart, irest double precision :: a1, a2, a3, a4, a5, a6, xmin, ymin, zmin, & xmax, ymax, zmax, & clength, b1, b2, b3, c1, c2, w, d, rg(3), & vnorm, vv1, vv2, vv3, frab, frac, frbc, & dfra(3), dfrb(3), dfrc(3) if(ityperest(irest).eq.2) then clength = restpars(irest,4) xmin = restpars(irest,1) ymin = restpars(irest,2) zmin = restpars(irest,3) xmax = restpars(irest,1) + clength ymax = restpars(irest,2) + clength zmax = restpars(irest,3) + clength a1 = xcart(icart,1) - xmin a2 = xcart(icart,2) - ymin a3 = xcart(icart,3) - zmin if(a1.lt.0.d0) gxcar(icart,1) = gxcar(icart,1) + scale * 2.d0 * a1 if(a2.lt.0.d0) gxcar(icart,2) = gxcar(icart,2) + scale * 2.d0 * a2 if(a3.lt.0.d0) gxcar(icart,3) = gxcar(icart,3) + scale * 2.d0 * a3 a1 = xcart(icart,1) - xmax a2 = xcart(icart,2) - ymax a3 = xcart(icart,3) - zmax if(a1.gt.0.d0) gxcar(icart,1) = gxcar(icart,1) + scale * 2.d0 * a1 if(a2.gt.0.d0) gxcar(icart,2) = gxcar(icart,2) + scale * 2.d0 * a2 if(a3.gt.0.d0) gxcar(icart,3) = gxcar(icart,3) + scale * 2.d0 * a3 else if(ityperest(irest).eq.3) then xmin = restpars(irest,1) ymin = restpars(irest,2) zmin = restpars(irest,3) xmax = restpars(irest,4) ymax = restpars(irest,5) zmax = restpars(irest,6) a1 = xcart(icart,1) - xmin a2 = xcart(icart,2) - ymin a3 = xcart(icart,3) - zmin if(a1.lt.0.d0) gxcar(icart,1) = gxcar(icart,1) + scale * 2.d0 * a1 if(a2.lt.0.d0) gxcar(icart,2) = gxcar(icart,2) + scale * 2.d0 * a2 if(a3.lt.0.d0) gxcar(icart,3) = gxcar(icart,3) + scale * 2.d0 * a3 a1 = xcart(icart,1) - xmax a2 = xcart(icart,2) - ymax a3 = xcart(icart,3) - zmax if(a1.gt.0.d0) gxcar(icart,1) = gxcar(icart,1) + scale * 2.d0 * a1 if(a2.gt.0.d0) gxcar(icart,2) = gxcar(icart,2) + scale * 2.d0 * a2 if(a3.gt.0.d0) gxcar(icart,3) = gxcar(icart,3) + scale * 2.d0 * a3 else if(ityperest(irest).eq.4) then d = (xcart(icart,1)-restpars(irest,1))**2 + & (xcart(icart,2)-restpars(irest,2))**2 + & (xcart(icart,3)-restpars(irest,3))**2 - & restpars(irest,4)**2 if(d.gt.0.d0) then gxcar(icart,1) = gxcar(icart,1) + 4.d0 * scale2 * & (xcart(icart,1)-restpars(irest,1))*d gxcar(icart,2) = gxcar(icart,2) + 4.d0 * scale2 * & (xcart(icart,2)-restpars(irest,2))*d gxcar(icart,3) = gxcar(icart,3) + 4.d0 * scale2 * & (xcart(icart,3)-restpars(irest,3))*d end if else if(ityperest(irest).eq.5) then a1 = xcart(icart,1)-restpars(irest,1) b1 = xcart(icart,2)-restpars(irest,2) c1 = xcart(icart,3)-restpars(irest,3) a2 = restpars(irest,4)**2 b2 = restpars(irest,5)**2 c2 = restpars(irest,6)**2 d = a1**2/a2+b1**2/b2+c1**2/c2-restpars(irest,7)**2 if(d.gt.0) then gxcar(icart,1) = gxcar(icart,1) + scale2*4.d0*d*a1/a2 gxcar(icart,2) = gxcar(icart,2) + scale2*4.d0*d*b1/b2 gxcar(icart,3) = gxcar(icart,3) + scale2*4.d0*d*c1/c2 end if else if(ityperest(irest).eq.6) then xmin = restpars(irest,1) ymin = restpars(irest,2) zmin = restpars(irest,3) xmax = restpars(irest,1) + restpars(irest,4) ymax = restpars(irest,2) + restpars(irest,4) zmax = restpars(irest,3) + restpars(irest,4) a1 = dmax1(xcart(icart,1) - xmin,0.d0) a2 = dmax1(xcart(icart,2) - ymin,0.d0) a3 = dmax1(xcart(icart,3) - zmin,0.d0) a4 = dmax1(xmax - xcart(icart,1),0.d0) a5 = dmax1(ymax - xcart(icart,2),0.d0) a6 = dmax1(zmax - xcart(icart,3),0.d0) w = a1*a2*a3*a4*a5*a6 if(w.gt.0.d0) then gxcar(icart,1) = gxcar(icart,1) + a2*a3*a5*a6*(a4-a1) gxcar(icart,2) = gxcar(icart,2) + a1*a3*a4*a6*(a5-a2) gxcar(icart,3) = gxcar(icart,3) + a1*a2*a4*a5*(a6-a3) end if else if(ityperest(irest).eq.7) then xmin = restpars(irest,1) ymin = restpars(irest,2) zmin = restpars(irest,3) xmax = restpars(irest,4) ymax = restpars(irest,5) zmax = restpars(irest,6) a1 = dmax1(xcart(icart,1) - xmin,0.d0) a2 = dmax1(xcart(icart,2) - ymin,0.d0) a3 = dmax1(xcart(icart,3) - zmin,0.d0) a4 = dmax1(xmax - xcart(icart,1),0.d0) a5 = dmax1(ymax - xcart(icart,2),0.d0) a6 = dmax1(zmax - xcart(icart,3),0.d0) w = a1*a2*a3*a4*a5*a6 if(w.gt.0.d0) then gxcar(icart,1) = gxcar(icart,1) + a2*a3*a5*a6*(a4-a1) gxcar(icart,2) = gxcar(icart,2) + a1*a3*a4*a6*(a5-a2) gxcar(icart,3) = gxcar(icart,3) + a1*a2*a4*a5*(a6-a3) end if else if(ityperest(irest).eq.8) then d = (xcart(icart,1)-restpars(irest,1))**2 + & (xcart(icart,2)-restpars(irest,2))**2 + & (xcart(icart,3)-restpars(irest,3))**2 - & restpars(irest,4)**2 if(d.lt.0.d0) then gxcar(icart,1) = gxcar(icart,1) + 4.d0 * scale2 * & (xcart(icart,1)-restpars(irest,1))*d gxcar(icart,2) = gxcar(icart,2) + 4.d0 * scale2 * & (xcart(icart,2)-restpars(irest,2))*d gxcar(icart,3) = gxcar(icart,3) + 4.d0 * scale2 * & (xcart(icart,3)-restpars(irest,3))*d end if else if(ityperest(irest).eq.9) then a1 = xcart(icart,1)-restpars(irest,1) b1 = xcart(icart,2)-restpars(irest,2) c1 = xcart(icart,3)-restpars(irest,3) a2 = restpars(irest,4)**2 b2 = restpars(irest,5)**2 c2 = restpars(irest,6)**2 d = a1**2/a2+b1**2/b2+c1**2/c2-restpars(irest,7)**2 if(d.lt.0) then d = scale2 * d gxcar(icart,1) = gxcar(icart,1) + 4.d0*d*a1/a2 gxcar(icart,2) = gxcar(icart,2) + 4.d0*d*b1/b2 gxcar(icart,3) = gxcar(icart,3) + 4.d0*d*c1/c2 end if else if(ityperest(irest).eq.10) then d = restpars(irest,1)*xcart(icart,1) + & restpars(irest,2)*xcart(icart,2) + & restpars(irest,3)*xcart(icart,3) - & restpars(irest,4) if(d.lt.0.d0) then d = scale * d gxcar(icart,1) = gxcar(icart,1) + 2.d0*restpars(irest,1)*d gxcar(icart,2) = gxcar(icart,2) + 2.d0*restpars(irest,2)*d gxcar(icart,3) = gxcar(icart,3) + 2.d0*restpars(irest,3)*d end if else if(ityperest(irest).eq.11) then d = restpars(irest,1)*xcart(icart,1) + & restpars(irest,2)*xcart(icart,2) + & restpars(irest,3)*xcart(icart,3) - & restpars(irest,4) if(d.gt.0.d0) then d = scale * d gxcar(icart,1) = gxcar(icart,1) + 2.d0*restpars(irest,1)*d gxcar(icart,2) = gxcar(icart,2) + 2.d0*restpars(irest,2)*d gxcar(icart,3) = gxcar(icart,3) + 2.d0*restpars(irest,3)*d end if else if(ityperest(irest).eq.12) then rg(1) = 0.0d0 rg(2) = 0.0d0 rg(3) = 0.0d0 a1 = xcart(icart,1) - restpars(irest,1) a2 = xcart(icart,2) - restpars(irest,2) a3 = xcart(icart,3) - restpars(irest,3) vnorm = sqrt(restpars(irest,4)**2 + restpars(irest,5)**2 & + restpars(irest,6)**2) vv1 = restpars(irest,4)/vnorm vv2 = restpars(irest,5)/vnorm vv3 = restpars(irest,6)/vnorm b1 = vv1 * a1 b2 = vv2 * a2 b3 = vv3 * a3 w = b1 + b2 + b3 d = (a1 - vv1*w)**2 + (a2 - vv2*w)**2 + (a3 - vv3*w)**2 rg(1) = scale2 * ( & -2*dmax1(-w , 0.d0) * vv1 + & 2*dmax1(w - restpars(irest,9), 0.d0) * vv1 + & 2*dmax1(d - restpars(irest,7)**2 , 0.d0) * & (2*(a1 - vv1*w)*(1 - vv1**2)+ & 2*(a2 - vv2*w)*(-vv2*vv1)+ & 2*(a3 - vv3*w)*(-vv3*vv1) )) rg(2) = scale2 * ( & -2*dmax1(-w , 0.d0) * vv2 + & 2*dmax1(w - restpars(irest,9), 0.d0) * vv2 + & 2*dmax1(d - restpars(irest,7)**2 , 0.d0) * & (2*(a1 - vv1*w)*(-vv1*vv2)+ & 2*(a2 - vv2*w)*(1 - vv2**2)+ & 2*(a3 - vv3*w)*(-vv3*vv2) )) rg(3) = scale2 * ( & -2*dmax1(-w , 0.d0) * vv3 + & 2*dmax1(w - restpars(irest,9), 0.d0) * vv3 + & 2*dmax1(d - restpars(irest,7)**2 , 0.d0) * & (2*(a1 - vv1*w)*(-vv1*vv3)+ & 2*(a2 - vv2*w)*(-vv2*vv3)+ & 2*(a3 - vv3*w)*(1 - vv3**2) )) gxcar(icart,1) = gxcar(icart,1) + rg(1) gxcar(icart,2) = gxcar(icart,2) + rg(2) gxcar(icart,3) = gxcar(icart,3) + rg(3) else if(ityperest(irest).eq.13) then rg(1) = 0.0d0 rg(2) = 0.0d0 rg(3) = 0.0d0 a1 = xcart(icart,1) - restpars(irest,1) a2 = xcart(icart,2) - restpars(irest,2) a3 = xcart(icart,3) - restpars(irest,3) vnorm = sqrt(restpars(irest,4)**2 + restpars(irest,5)**2 & + restpars(irest,6)**2) vv1 = restpars(irest,4)/vnorm vv2 = restpars(irest,5)/vnorm vv3 = restpars(irest,6)/vnorm b1 = vv1 * a1 b2 = vv2 * a2 b3 = vv3 * a3 w = b1 + b2 + b3 d = (a1 - vv1*w)**2 + (a2 - vv2*w)**2 + (a3 - vv3*w)**2 frab = dmin1(-w , 0.d0)**2 * dmin1(w - restpars(irest,9), 0.d0)**2 frac = dmin1(-w , 0.d0)**2 * dmin1(d - restpars(irest,7)**2 , 0.d0 )**2 frbc = dmin1(w - restpars(irest,9), 0.d0)**2 * & dmin1(d - restpars(irest,7)**2 , 0.d0 )**2 dfra(1) = -2*dmin1(-w , 0.d0) * vv1 dfrb(1) = 2*dmin1(w - restpars(irest,9), 0.d0) * vv1 dfrc(1) = 2*dmin1(d - restpars(irest,7)**2 , 0.d0) * & (2*(a1 - vv1*w)*(1 - vv1**2)+ & 2*(a2 - vv2*w)*(-vv2*vv1)+ & 2*(a3 - vv3*w)*(-vv3*vv1) ) dfra(2) = -2*dmin1(-w , 0.d0) * vv2 dfrb(2) = 2*dmin1(w - restpars(irest,9), 0.d0) * vv2 dfrc(2) = 2*dmin1(d - restpars(irest,7)**2 , 0.d0) * & (2*(a1 - vv1*w)*(-vv1*vv2)+ & 2*(a2 - vv2*w)*(1 - vv2**2)+ & 2*(a3 - vv3*w)*(-vv3*vv2) ) dfra(3) = -2*dmin1(-w , 0.d0) * vv3 dfrb(3) = 2*dmin1(w - restpars(irest,9), 0.d0) * vv3 dfrc(3) = 2*dmin1(d - restpars(irest,7)**2 , 0.d0) * & (2*(a1 - vv1*w)*(-vv1*vv3)+ & 2*(a2 - vv2*w)*(-vv2*vv3)+ & 2*(a3 - vv3*w)*(1 - vv3**2) ) rg(1) = scale2 * ( dfra(1)*frbc + dfrb(1)*frac + dfrc(1)*frab) rg(2) = scale2 * ( dfra(2)*frbc + dfrb(2)*frac + dfrc(2)*frab) rg(3) = scale2 * ( dfra(3)*frbc + dfrb(3)*frac + dfrc(3)*frab) gxcar(icart,1) = gxcar(icart,1) + rg(1) gxcar(icart,2) = gxcar(icart,2) + rg(2) gxcar(icart,3) = gxcar(icart,3) + rg(3) end if return end subroutine gwalls packmol-20.010/header000066400000000000000000000002161360620542100143730ustar00rootroot00000000000000! ! Written by Leandro Martínez, 2009-2011. ! Copyright (c) 2009-2011, Leandro Martínez, Jose Mario Martinez, ! Ernesto G. Birgin. ! packmol-20.010/heuristics.f90000066400000000000000000000107151360620542100157270ustar00rootroot00000000000000! ! Written by Leandro Martínez, 2009-2011. ! Copyright (c) 2009-2018, Leandro Martínez, Jose Mario Martinez, ! Ernesto G. Birgin. ! ! subroutine movebad: Move the worse molecules to new positions ! subroutine movebad(n,x,fx,movebadprint) use sizes use compute_data use input, only : movefrac, movebadrandom, precision use usegencan use flashsort use ahestetic implicit none ! Internal variables integer :: n, i, j, icart, itype, iatom, imol, ilubar, ilugan, & ilubar2, ilugan2, nbad, igood, ibad, nmove double precision :: x(n), fx, rnd, frac double precision :: fdist_mol, frest_mol logical :: movebadprint, hasbad if(movebadprint) write(*,*) ' Moving worst molecules ... ' icart = 0 do itype = 1, ntype if(.not.comptype(itype)) then icart = icart + nmols(itype)*natoms(itype) else do imol = 1, nmols(itype) do iatom = 1, natoms(itype) icart = icart + 1 fdist_atom(icart) = 0.d0 frest_atom(icart) = 0.d0 end do end do end if end do move = .true. if(movebadprint) write(*,*) ' Function value before moving molecules:',fx do i = 1, ntotat radiuswork(i) = radius(i) radius(i) = radius_ini(i) end do call computef(n,x,fx) move = .false. ! Moving the worst molecules hasbad = .false. icart = 0 do itype = 1, ntype if(.not.comptype(itype)) then icart = icart + nmols(itype)*natoms(itype) else ! Checking the function value for each molecule nbad = 0 do imol = 1, nmols(itype) fdist_mol = 0.d0 frest_mol = 0.d0 do iatom = 1, natoms(itype) icart = icart + 1 fdist_mol = dmax1(fdist_mol,fdist_atom(icart)) frest_mol = dmax1(frest_mol,frest_atom(icart)) end do if(fdist_mol > precision .or. & frest_mol > precision ) then hasbad = .true. nbad = nbad + 1 fmol(imol) = fdist_mol + frest_mol else fmol(imol) = 0.d0 end if end do frac = dfloat(nbad)/dfloat(nmols(itype)) if(movebadprint) write(*,"( a,i9,a,f8.2,a )") & ' Type ',itype,' molecules with non-zero contributions:', & 100.d0*frac,'%' if(nbad.gt.0) then frac = dmin1(movefrac,frac) ! Ordering molecules from best to worst mflash = 1 + nmols(itype)/10 call flash1(fmol,nmols(itype),lflash,mflash,indflash) ! Moving molecules nmove = max0(int(nmols(itype)*frac),1) if(movebadprint) then write(*,"( a,i9,a,i9 )") ' Moving ',nmove,' molecules of type ',itype if ( movebadrandom ) then write(*,*) ' New positions will be aleatory (movebadrandom is set) ' else write(*,*) ' New positions will be based on good molecules (movebadrandom is not set) ' end if end if imol = 0 do i = 1, itype - 1 if(comptype(i)) imol = imol + nmols(i) end do write(*,prog2_line) write(*,"( ' |',$)") j = 0 do i = 1, nmove ibad = nmols(itype) - i + 1 igood = int(rnd()*nmols(itype)*frac) + 1 ilubar = 3*(indflash(ibad)+imol-1) ilugan = 3*(indflash(ibad)+imol-1)+3*ntotmol ilubar2 = 3*(indflash(igood)+imol-1) ilugan2 = 3*(indflash(igood)+imol-1)+3*ntotmol if ( movebadrandom ) then x(ilubar+1) = sizemin(1) + rnd()*(sizemax(1)-sizemin(1)) x(ilubar+2) = sizemin(2) + rnd()*(sizemax(2)-sizemin(2)) x(ilubar+3) = sizemin(3) + rnd()*(sizemax(3)-sizemin(3)) else x(ilubar+1) = x(ilubar2+1) - 0.3*dmax(itype)+0.6*rnd()*dmax(itype) x(ilubar+2) = x(ilubar2+2) - 0.3*dmax(itype)+0.6*rnd()*dmax(itype) x(ilubar+3) = x(ilubar2+3) - 0.3*dmax(itype)+0.6*rnd()*dmax(itype) end if x(ilugan+1) = x(ilugan2+1) x(ilugan+2) = x(ilugan2+2) x(ilugan+3) = x(ilugan2+3) call restmol(itype,ilubar,n,x,fx,.true.) do while( j <= 65.d0*i/nmove ) write(*,"('*',$)") j = j + 1 end do end do write(*,"('|')") end if end if end do call computef(n,x,fx) if(movebadprint) write(*,*) ' Function value after moving molecules:', fx do i = 1, ntotat radius(i) = radiuswork(i) end do return end subroutine movebad packmol-20.010/initial.f90000066400000000000000000000462321360620542100152010ustar00rootroot00000000000000! ! Written by Leandro Martínez, 2009-2011. ! Copyright (c) 2009-2018, Leandro Martínez, Jose Mario Martinez, ! Ernesto G. Birgin. ! ! Subroutine initial: Subroutine that reset parameters and ! builds the initial point ! subroutine initial(n,x) use sizes use compute_data use input, only : randini, ntfix, fix, moldy, chkgrad, avoidoverlap,& discale, precision, sidemax, restart_from, input_itype,& nloop0_type use usegencan use ahestetic implicit none integer :: n, i, j, k, idatom, iatom, ilubar, ilugan, icart, itype, & imol, ntry, nb, iboxx, iboxy, iboxz, ifatom, & idfatom, iftype, jatom, ioerr double precision :: x(n), cmx, cmy, beta, gamma, theta, & cmz, fx, xlength, dbox, rnd, & radmax, v1(3), v2(3), v3(3), xbar, ybar, zbar double precision, parameter :: twopi = 8.d0*datan(1.d0) logical :: overlap, movebadprint, hasbad logical, allocatable :: hasfixed(:,:,:) character(len=200) :: record ! Allocate hasfixed array allocate(hasfixed(0:nbp+1,0:nbp+1,0:nbp+1)) ! We need to initialize the move logical variable move = .false. ! Default status of the function evaluation init1 = .false. ! Initialize the comptype logical array do i = 1, ntfix comptype(i) = .true. end do ! Penalty factors for the objective function relative to restrictions ! Default values: scale = 1.d2, scale2 = 1.d1 scale = 1.d0 scale2 = 1.d-2 ! Move molecules to their center of mass (not for moldy) if(.not.moldy) call tobar() ! Compute maximum internal distance within each type of molecule do itype = 1, ntype dmax(itype) = 0.d0 idatom = idfirst(itype) - 1 do iatom = 1, natoms(itype) - 1 do jatom = iatom + 1, natoms(itype) dmax(itype) = dmax1 ( dmax(itype),& (coor(idatom+iatom,1)-coor(idatom+jatom,1))**2+& (coor(idatom+iatom,2)-coor(idatom+jatom,2))**2+& (coor(idatom+iatom,3)-coor(idatom+jatom,3))**2 ) end do end do dmax(itype) = dsqrt(dmax(itype)) write(*,*) ' Maximum internal distance of type ',itype,': ',& dmax(itype) if(dmax(itype).eq.0.) dmax(itype) = 1.d0 end do ! Maximum size of the system: if you system is very large (about ! 80 nm wide), increase the sidemax parameter. ! Otherwise, the packing can be slow and unsucesful cmxmin(1) = -sidemax cmymin(1) = -sidemax cmzmin(1) = -sidemax cmxmax(1) = sidemax cmymax(1) = sidemax cmzmax(1) = sidemax do i = 1, 3 x(i) = 0.d0 x(i+ntotmol*3) = 0.d0 end do call restmol(1,0,n,x,fx,.true.) sizemin(1) = x(1) - sidemax sizemax(1) = x(1) + sidemax sizemin(2) = x(2) - sidemax sizemax(2) = x(2) + sidemax sizemin(3) = x(3) - sidemax sizemax(3) = x(3) + sidemax write(*,*) ' All atoms must be within these coordinates: ' write(*,*) ' x: [ ', sizemin(1),', ', sizemax(1), ' ] ' write(*,*) ' y: [ ', sizemin(2),', ', sizemax(2), ' ] ' write(*,*) ' z: [ ', sizemin(3),', ', sizemax(3), ' ] ' write(*,*) ' If the system is larger than this, increase the sidemax parameter. ' ! Create first aleatory guess i = 0 j = ntotmol*3 do itype = 1, ntype do imol = 1, nmols(itype) x(i+1) = sizemin(1) + rnd()*(sizemax(1)-sizemin(1)) x(i+2) = sizemin(2) + rnd()*(sizemax(2)-sizemin(2)) x(i+3) = sizemin(3) + rnd()*(sizemax(3)-sizemin(3)) if ( constrain_rot(itype,1) ) then x(j+1) = ( rot_bound(itype,1,1) - dabs(rot_bound(itype,1,2)) ) + & 2.d0*rnd()*dabs(rot_bound(itype,1,2)) else x(j+1) = twopi*rnd() end if if ( constrain_rot(itype,2) ) then x(j+2) = ( rot_bound(itype,2,1) - dabs(rot_bound(itype,2,2)) ) + & 2.d0*rnd()*dabs(rot_bound(itype,2,2)) else x(j+2) = twopi*rnd() end if if ( constrain_rot(itype,3) ) then x(j+3) = ( rot_bound(itype,3,1) - dabs(rot_bound(itype,3,2)) ) + & 2.d0*rnd()*dabs(rot_bound(itype,3,2)) else x(j+3) = twopi*rnd() end if i = i + 3 j = j + 3 end do end do ! Initialize cartesian coordinate array for the first time ilubar = 0 ilugan = ntotmol*3 icart = 0 do itype = 1, ntype do imol = 1, nmols(itype) xbar = x(ilubar+1) ybar = x(ilubar+2) zbar = x(ilubar+3) beta = x(ilugan+1) gamma = x(ilugan+2) theta = x(ilugan+3) call eulerrmat(beta,gamma,theta,v1,v2,v3) idatom = idfirst(itype) - 1 do iatom = 1, natoms(itype) icart = icart + 1 idatom = idatom + 1 call compcart(icart,xbar,ybar,zbar,& coor(idatom,1),coor(idatom,2),coor(idatom,3),& v1,v2,v3) fixedatom(icart) = .false. end do end do end do if(fix) then icart = ntotat - natfix do iftype = ntype + 1, ntfix idfatom = idfirst(iftype) - 1 do ifatom = 1, natoms(iftype) idfatom = idfatom + 1 icart = icart + 1 xcart(icart,1) = coor(idfatom,1) xcart(icart,2) = coor(idfatom,2) xcart(icart,3) = coor(idfatom,3) fixedatom(icart) = .true. end do end do end if ! Use the largest radius as the reference for binning the box radmax = 0.d0 do i = 1, ntotat radmax = dmax1(radmax,2.d0*radius(i)) end do ! Performing some steps of optimization for the restrictions only write(*,hash3_line) write(*,"(' Building initial approximation ... ' )") write(*,hash3_line) write(*,"(' Adjusting initial point to fit the constraints ')") write(*,dash2_line) init1 = .true. call swaptype(n,x,itype,0) ! Initialize swap arrays itype = 0 do while( itype <= ntype ) itype = itype + 1 if ( itype <= ntype ) then call swaptype(n,x,itype,1) ! Set arrays for this type else call swaptype(n,x,itype,3) ! Restore arrays if itype = ntype + 1 exit end if write(*,dash3_line) write(*,*) ' Molecules of type: ', input_itype(itype) write(*,*) i = 0 hasbad = .true. call computef(n,x,fx) do while( frest > precision .and. i.le. nloop0_type(itype)-1 .and. hasbad) i = i + 1 write(*,prog1_line) call pgencan(n,x,fx) call computef(n,x,fx) if(frest > precision) then write(*,"( a,i6,a,i6 )")' Fixing bad orientations ... ', i,' of ', nloop0_type(itype) movebadprint = .true. call movebad(n,x,fx,movebadprint) end if end do write(*,*) write(*,*) ' Restraint-only function value: ', fx write(*,*) ' Maximum violation of the restraints: ', frest call swaptype(n,x,itype,2) ! Save current type results if( hasbad .and. frest > precision ) then write(*,*) ' ERROR: Packmol was unable to put the molecules' write(*,*) ' in the desired regions even without' write(*,*) ' considering distance tolerances. ' write(*,*) ' Probably there is something wrong with' write(*,*) ' the constraints, since it seems that' write(*,*) ' the molecules cannot satisfy them at' write(*,*) ' at all. ' write(*,*) ' Please check the spatial constraints and' write(*,*) ' try again.' if ( i .ge. nloop0_type(itype)-1 ) then end if write(*,*) ' >The maximum number of cycles (',nloop0_type(itype),') was achieved.' write(*,*) ' You may try increasing it with the',' nloop0 keyword, as in: nloop0 1000 ' stop end if end do init1 = .false. ! Rescaling sizemin and sizemax in order to build the patch of boxes write(*,dash3_line) write(*,*) ' Rescaling maximum and minimum coordinates... ' do i = 1, 3 sizemin(i) = 1.d20 sizemax(i) = -1.d20 end do icart = 0 do itype = 1, ntfix do imol = 1, nmols(itype) do iatom = 1, natoms(itype) icart = icart + 1 sizemin(1) = dmin1(sizemin(1),xcart(icart,1)) sizemin(2) = dmin1(sizemin(2),xcart(icart,2)) sizemin(3) = dmin1(sizemin(3),xcart(icart,3)) sizemax(1) = dmax1(sizemax(1),xcart(icart,1)) sizemax(2) = dmax1(sizemax(2),xcart(icart,2)) sizemax(3) = dmax1(sizemax(3),xcart(icart,3)) end do end do end do ! Computing the size of the patches write(*,*) ' Computing size of patches... ' dbox = discale * radmax + 0.01d0 * radmax do i = 1, 3 xlength = sizemax(i) - sizemin(i) nb = int(xlength/dbox + 1.d0) if(nb.gt.nbp) nb = nbp boxl(i) = dmax1(xlength/dfloat(nb),dbox) nboxes(i) = nb nb2(i) = nboxes(i) + 2 end do ! Reseting latomfix array do i = 0, nbp + 1 do j = 0, nbp + 1 do k = 0, nbp + 1 latomfix(i,j,k) = 0 latomfirst(i,j,k) = 0 hasfixed(i,j,k) = .false. hasfree(i,j,k) = .false. end do end do end do ! If there are fixed molecules, add them permanently to the latomfix array write(*,*) ' Add fixed molecules to permanent arrays... ' if(fix) then icart = ntotat - natfix do iftype = ntype + 1, ntfix idfatom = idfirst(iftype) - 1 do ifatom = 1, natoms(iftype) idfatom = idfatom + 1 icart = icart + 1 call setibox(xcart(icart,1),xcart(icart,2),xcart(icart,3),& sizemin,boxl,nboxes,iboxx,iboxy,iboxz) latomnext(icart) = latomfix(iboxx,iboxy,iboxz) latomfix(iboxx,iboxy,iboxz) = icart latomfirst(iboxx,iboxy,iboxz) = icart ibtype(icart) = iftype ibmol(icart) = 1 hasfixed(iboxx,iboxy,iboxz) = .true. end do end do end if ! Reseting mass centers to be within the regions write(*,*) ' Reseting center of mass... ' do itype = 1, ntype cmxmin(itype) = 1.d20 cmymin(itype) = 1.d20 cmzmin(itype) = 1.d20 cmxmax(itype) = -1.d20 cmymax(itype) = -1.d20 cmzmax(itype) = -1.d20 end do icart = 0 do itype = 1, ntype do imol = 1, nmols(itype) cmx = 0.d0 cmy = 0.d0 cmz = 0.d0 do iatom = 1, natoms(itype) icart = icart + 1 cmx = cmx + xcart(icart,1) cmy = cmy + xcart(icart,2) cmz = cmz + xcart(icart,3) end do cmx = cmx / dfloat(natoms(itype)) cmy = cmy / dfloat(natoms(itype)) cmz = cmz / dfloat(natoms(itype)) cmxmin(itype) = dmin1(cmxmin(itype),cmx) cmymin(itype) = dmin1(cmymin(itype),cmy) cmzmin(itype) = dmin1(cmzmin(itype),cmz) cmxmax(itype) = dmax1(cmxmax(itype),cmx) cmymax(itype) = dmax1(cmymax(itype),cmy) cmzmax(itype) = dmax1(cmzmax(itype),cmz) end do end do ! If there is a restart file for all system, read it if ( restart_from(0) /= 'none' ) then record = restart_from(0) write(*,*) ' Restarting all system from file: ', trim(adjustl(record)) open(10,file=restart_from(0),status='old',action='read',iostat=ioerr) ilubar = 0 ilugan = ntotmol*3 do i = 1, ntotmol read(10,*,iostat=ioerr) x(ilubar+1), x(ilubar+2), x(ilubar+3), & x(ilugan+1), x(ilugan+2), x(ilugan+3) if ( ioerr /= 0 ) then write(*,*) ' ERROR: Could not read restart file: ', trim(adjustl(record)) stop end if ilubar = ilubar + 3 ilugan = ilugan + 3 end do close(10) return end if ! Building random initial point write(*,dash3_line) write(*,*) ' Setting initial trial coordinates ... ' write(*,dash2_line) if ( chkgrad ) then write(*,*) ' For checking gradient, will set avoidoverlap to false. ' avoidoverlap = .false. end if ! Setting random center of mass coordinates, within size limits ilubar = 0 do itype = 1, ntype if ( restart_from(itype) /= 'none' ) then ilubar = ilubar + nmols(itype)*3 cycle end if do imol = 1, nmols(itype) if ( .not. avoidoverlap ) then fx = 1.d0 ntry = 0 do while((fx.gt.precision).and.ntry.le.20) ntry = ntry + 1 x(ilubar+1) = cmxmin(itype) + rnd()*(cmxmax(itype)-cmxmin(itype)) x(ilubar+2) = cmymin(itype) + rnd()*(cmymax(itype)-cmymin(itype)) x(ilubar+3) = cmzmin(itype) + rnd()*(cmzmax(itype)-cmzmin(itype)) call restmol(itype,ilubar,n,x,fx,.false.) end do else fx = 1.d0 ntry = 0 overlap = .false. do while((overlap.or.fx.gt.precision).and.ntry.le.20) ntry = ntry + 1 x(ilubar+1) = cmxmin(itype) + rnd()*(cmxmax(itype)-cmxmin(itype)) x(ilubar+2) = cmymin(itype) + rnd()*(cmymax(itype)-cmymin(itype)) x(ilubar+3) = cmzmin(itype) + rnd()*(cmzmax(itype)-cmzmin(itype)) if(fix) then call setibox(x(ilubar+1),x(ilubar+2),x(ilubar+3),& sizemin,boxl,nboxes,iboxx,iboxy,iboxz) if(hasfixed(iboxx, iboxy, iboxz ).or.& hasfixed(iboxx+1,iboxy, iboxz ).or.& hasfixed(iboxx, iboxy+1,iboxz ).or.& hasfixed(iboxx, iboxy, iboxz+1).or.& hasfixed(iboxx-1,iboxy, iboxz ).or.& hasfixed(iboxx, iboxy-1,iboxz ).or.& hasfixed(iboxx, iboxy, iboxz-1).or.& hasfixed(iboxx+1,iboxy+1,iboxz ).or.& hasfixed(iboxx+1,iboxy, iboxz+1).or.& hasfixed(iboxx+1,iboxy-1,iboxz ).or.& hasfixed(iboxx+1,iboxy, iboxz-1).or.& hasfixed(iboxx, iboxy+1,iboxz+1).or.& hasfixed(iboxx, iboxy+1,iboxz-1).or.& hasfixed(iboxx, iboxy-1,iboxz+1).or.& hasfixed(iboxx, iboxy-1,iboxz-1).or.& hasfixed(iboxx-1,iboxy+1,iboxz ).or.& hasfixed(iboxx-1,iboxy, iboxz+1).or.& hasfixed(iboxx-1,iboxy-1,iboxz ).or.& hasfixed(iboxx-1,iboxy, iboxz-1).or.& hasfixed(iboxx+1,iboxy+1,iboxz+1).or.& hasfixed(iboxx+1,iboxy+1,iboxz-1).or.& hasfixed(iboxx+1,iboxy-1,iboxz+1).or.& hasfixed(iboxx+1,iboxy-1,iboxz-1).or.& hasfixed(iboxx-1,iboxy+1,iboxz+1).or.& hasfixed(iboxx-1,iboxy+1,iboxz-1).or.& hasfixed(iboxx-1,iboxy-1,iboxz+1).or.& hasfixed(iboxx-1,iboxy-1,iboxz-1)) then overlap = .true. else overlap = .false. end if end if if(.not.overlap) call restmol(itype,ilubar,n,x,fx,.false.) end do end if ilubar = ilubar + 3 end do end do ! Setting random angles, except if the rotations were constrained ilugan = ntotmol*3 do itype = 1, ntype if ( restart_from(itype) /= 'none' ) then ilugan = ilugan + nmols(itype)*3 cycle end if do imol = 1, nmols(itype) if ( constrain_rot(itype,1) ) then x(ilugan+1) = ( rot_bound(itype,1,1) - dabs(rot_bound(itype,1,2)) ) + & 2.d0*rnd()*dabs(rot_bound(itype,1,2)) else x(ilugan+1) = twopi*rnd() end if if ( constrain_rot(itype,2) ) then x(ilugan+2) = ( rot_bound(itype,2,1) - dabs(rot_bound(itype,2,2)) ) + & 2.d0*rnd()*dabs(rot_bound(itype,2,2)) else x(ilugan+2) = twopi*rnd() end if if ( constrain_rot(itype,3) ) then x(ilugan+3) = ( rot_bound(itype,3,1) - dabs(rot_bound(itype,3,2)) ) + & 2.d0*rnd()*dabs(rot_bound(itype,3,2)) else x(ilugan+3) = twopi*rnd() end if ilugan = ilugan + 3 end do end do ! Compare analytical and finite-difference gradients if(chkgrad) then dbox = discale * radmax + 0.01d0 * radmax do i = 1, 3 xlength = sizemax(i) - sizemin(i) nb = int(xlength/dbox + 1.d0) if(nb.gt.nbp) nb = nbp boxl(i) = dmax1(xlength/dfloat(nb),dbox) nboxes(i) = nb nb2(i) = nboxes(i) + 2 end do call comparegrad(n,x) stop end if ! ! Reading restart files of specific molecule types, if available ! ilubar = 0 ilugan = ntotmol*3 do itype = 1, ntype if ( restart_from(itype) /= 'none' ) then record = restart_from(itype) write(*,dash3_line) write(*,*) ' Molecules of type: ', input_itype(itype) write(*,*) ' Will restart coordinates from: ', trim(adjustl(record)) open(10,file=record,status='old',action='read',iostat=ioerr) if ( ioerr /= 0 ) then write(*,*) ' ERROR: Could not open restart file: ', trim(adjustl(record)) stop end if do i = 1, nmols(itype) read(10,*,iostat=ioerr) x(ilubar+1), x(ilubar+2), x(ilubar+3), & x(ilugan+1), x(ilugan+2), x(ilugan+3) if ( ioerr /= 0 ) then write(*,*) ' ERROR: Could not read restart file: ', trim(adjustl(record)) stop end if ilubar = ilubar + 3 ilugan = ilugan + 3 end do close(10) call swaptype(n,x,itype,0) ! Initialize swap arrays call swaptype(n,x,itype,1) ! Set arrays for this type call computef(n,x,fx) write(*,*) ' Maximum violation of the restraints: ', frest write(*,*) ' Maximum violation of minimum atom distances: ', fdist call swaptype(n,x,itype,3) ! Restore all-molecule arrays else ilubar = ilubar + nmols(itype)*3 ilugan = ilugan + nmols(itype)*3 end if end do ! Return with current random point (not default) if(randini) return ! Adjusting current point to fit the constraints init1 = .true. call swaptype(n,x,itype,0) ! Initialize swap arrays itype = 0 do while( itype <= ntype ) itype = itype + 1 if ( itype == ntype + 1 ) then call swaptype(n,x,itype,3) ! Restore arrays for all molecules exit end if if ( restart_from(itype) /= 'none' ) cycle call swaptype(n,x,itype,1) ! Set arrays for this type write(*,dash3_line) write(*,*) ' Molecules of type: ', input_itype(itype) write(*,*) ' Adjusting random positions to fit the constraints. ' i = 0 call computef(n,x,fx) hasbad = .true. do while( frest > precision .and. i <= nloop0_type(itype)-1 .and. hasbad) i = i + 1 write(*,prog1_line) call pgencan(n,x,fx) call computef(n,x,fx) if(frest > precision) then write(*,"( a,i6,a,i6 )")' Fixing bad orientations ... ', i,' of ', nloop0_type(itype) movebadprint = .true. call movebad(n,x,fx,movebadprint) end if end do write(*,*) ' Restraint-only function value: ', fx write(*,*) ' Maximum violation of the restraints: ', frest call swaptype(n,x,itype,2) ! Save results for this type end do init1 = .false. write(*,hash3_line) ! Deallocate hasfixed array deallocate(hasfixed) return end subroutine initial packmol-20.010/input.f90000066400000000000000000000043621360620542100147050ustar00rootroot00000000000000! ! Written by Leandro Martínez, 2009-2011. ! Copyright (c) 2009-2018, Leandro Martínez, Jose Mario Martinez, ! Ernesto G. Birgin. ! ! Module that carries the input parameters read from the input file ! module input use sizes implicit none integer :: nlines integer :: nrest integer :: seed integer :: nloop, nloop_all integer :: writeout integer :: ntfix integer :: ntcon(9) integer, allocatable :: nconnect(:,:) ! (ntotat,9) integer, allocatable :: irestline(:) ! (maxrest) integer, allocatable :: linestrut(:,:) ! (ntype,2) integer, allocatable :: resnumbers(:) ! (ntype) integer, allocatable :: maxcon(:) ! (ntotat) integer, allocatable :: input_itype(:) ! (ntype) integer, allocatable :: nloop_type(:) ! (ntype) integer, allocatable :: nloop0_type(:) ! (ntype) double precision :: dism double precision :: precison double precision :: sidemax double precision :: discale double precision :: movefrac double precision :: add_sides_fix double precision :: precision double precision :: fbins double precision :: short_tol_dist double precision :: short_tol_scale double precision, allocatable :: amass(:) ! (ntotat) double precision, allocatable :: charge(:) ! (ntotat) logical :: writebad logical :: tinker logical :: pdb logical :: crd logical :: xyz logical :: moldy logical :: check logical :: chkgrad logical :: randini logical :: movebadrandom logical :: add_amber_ter logical :: add_box_sides logical :: fix logical :: avoidoverlap logical :: packall logical :: use_short_tol logical, allocatable :: changechains(:) ! (ntype) logical, allocatable :: fixedoninput(:) ! (ntype) character(len=200) :: xyzout character(len=200) :: crdfile character(len=1), allocatable :: chain(:) ! (ntype) character(len=3), allocatable :: ele(:) ! (ntotat) character(len=8), allocatable :: segid(:) ! (segment identifier) character(len=80), allocatable :: pdbfile(:) ! (ntype) character(len=200), allocatable :: name(:) ! (ntype) character(len=200), allocatable :: keyword(:,:) ! (nlines,maxkeywords) character(len=200), allocatable :: inputfile(:) ! (nlines) character(len=200), allocatable :: restart_from(:), restart_to(:) ! (0:ntype) end module input packmol-20.010/jacobi.f90000066400000000000000000000060001360620542100147640ustar00rootroot00000000000000! ! JACOBI ! Jacobi diagonalizer with sorted output. Same calling sequence as ! EISPACK routine, but must specify nrot! ! SUBROUTINE jacobi (a, n, np, d, v, nrot) IMPLICIT CHARACTER (A-Z) ! INTEGER n, np, nrot DOUBLEPRECISION a (np, n) DOUBLEPRECISION d (n) DOUBLEPRECISION v (np, n) ! DOUBLEPRECISION onorm, dnorm DOUBLEPRECISION b, dma, q, t, c, s DOUBLEPRECISION atemp, vtemp, dtemp INTEGER i, j, k, l ! DO 10000 j = 1, n DO 10010 i = 1, n v (i, j) = 0.0D0 10010 CONTINUE v (j, j) = 1.0D0 d (j) = a (j, j) 10000 CONTINUE ! DO 20000 l = 1, nrot dnorm = 0.0D0 onorm = 0.0D0 DO 20100 j = 1, n dnorm = dnorm + ABS (d (j)) DO 20110 i = 1, j - 1 onorm = onorm + ABS (a (i, j)) 20110 CONTINUE 20100 CONTINUE IF (onorm / dnorm .LE. 0.0D0) GOTO 19999 DO 21000 j = 2, n DO 21010 i = 1, j - 1 b = a (i, j) IF (ABS (b) .GT. 0.0D0) THEN dma = d (j) - d (i) IF (ABS (dma) + ABS (b) .LE. ABS (dma)) THEN t = b / dma ELSE q = 0.5D0 * dma / b t = SIGN (1.0D0 / (ABS (q) + SQRT (1.0D0 + q * q)), q) ENDIF c = 1.0D0 / SQRT (t * t + 1.0D0) s = t * c a (i, j) = 0.0D0 DO 21110 k = 1, i - 1 atemp = c * a (k, i) - s * a (k, j) a (k, j) = s * a (k, i) + c * a (k, j) a (k, i) = atemp 21110 CONTINUE DO 21120 k = i + 1, j - 1 atemp = c * a (i, k) - s * a (k, j) a (k, j) = s * a (i, k) + c * a (k, j) a (i, k) = atemp 21120 CONTINUE DO 21130 k = j + 1, n atemp = c * a (i, k) - s * a (j, k) a (j, k) = s * a (i, k) + c * a (j, k) a (i, k) = atemp 21130 CONTINUE DO 21140 k = 1, n vtemp = c * v (k, i) - s * v (k, j) v (k, j) = s * v (k, i) + c * v (k, j) v (k, i) = vtemp 21140 CONTINUE dtemp = c * c * d (i) + s * s * d (j) -& 2.0D0 * c * s * b d (j) = s * s * d (i) + c * c * d (j) +& 2.0D0 * c * s * b d (i) = dtemp ENDIF 21010 CONTINUE 21000 CONTINUE 20000 CONTINUE 19999 CONTINUE nrot = l ! DO 30000 j = 1, n - 1 k = j dtemp = d (k) DO 30100 i = j + 1, n IF (d (i) .LT. dtemp) THEN k = i dtemp = d (k) ENDIF 30100 CONTINUE IF (k .GT. j) THEN d (k) = d (j) d (j) = dtemp DO 30200 i = 1, n dtemp = v (i, k) v (i, k) = v (i, j) v (i, j) = dtemp 30200 CONTINUE ENDIF 30000 CONTINUE ! RETURN END subroutine jacobi packmol-20.010/output.f90000066400000000000000000000613471360620542100151140ustar00rootroot00000000000000! ! Written by Leandro Martínez, 2009-2011. ! Copyright (c) 2009-2018, Leandro Martínez, Jose Mario Martinez, ! Ernesto G. Birgin. ! ! Subroutine output: Subroutine that writes the output file ! subroutine output(n,x) use sizes use compute_data use input implicit none integer :: n, k, i, ilugan, ilubar, itype, imol, idatom,& irest, iimol, ichain, iatom, irec, ilres, ifres,& iires, ciires, strlength, irescount,& icart, i_ref_atom, ioerr integer :: nr, nres, imark integer :: i_fixed, i_not_fixed double precision :: x(n) double precision :: tens(4,4), v(4,4), dv(4) double precision :: v1(3), v2(3), v3(3) double precision :: xbar, ybar, zbar, beta, gama, teta, xcm, ycm, zcm double precision :: xlength, ylength, zlength double precision :: xxyx, xxyy, xxyz, xyyz, xyyy, xzyx,& xzyy, xzyz, xyyx, xq, yq, zq, q0, q1, q2, q3 double precision :: xtemp, ytemp, ztemp double precision :: sxmin, symin, szmin, sxmax, symax, szmax character :: write_chain, even_chain, odd_chain character(len=64) :: title character(len=80) :: pdb_atom_line, pdb_hetatm_line, tinker_atom_line, format_line,& pdb_atom_line_hex, pdb_hetatm_line_hex, crd_format character(len=8) :: crdires,crdresn,crdsegi,atmname character(len=200) :: record ! Job title title = ' Built with Packmol ' ! ! Write restart files, if required ! ! Restart file for all system if ( restart_to(0) /= 'none' ) then record = restart_to(0) open(10,file=restart_to(0),iostat=ioerr) if ( ioerr /= 0 ) then write(*,*) ' ERROR: Could not open restart_to file: ', trim(adjustl(record)) stop end if ilubar = 0 ilugan = ntotmol*3 do i = 1, ntotmol write(10,"(6(tr1,es23.16))") x(ilubar+1), x(ilubar+2), x(ilubar+3), & x(ilugan+1), x(ilugan+2), x(ilugan+3) ilubar = ilubar + 3 ilugan = ilugan + 3 end do close(10) write(*,*) ' Wrote restart file for all system: ', trim(adjustl(record)) end if ! Restart files for specific molecule types ilubar = 0 ilugan = ntotmol*3 do itype = 1, ntype if ( restart_to(itype) /= 'none' ) then record = restart_to(itype) open(10,file=record,iostat=ioerr) if ( ioerr /= 0 ) then write(*,*) ' ERROR: Could not open restart_to file: ', trim(adjustl(record)) stop end if do i = 1, nmols(itype) write(10,"(6(tr1,es23.16))") x(ilubar+1), x(ilubar+2), x(ilubar+3), & x(ilugan+1), x(ilugan+2), x(ilugan+3) ilubar = ilubar + 3 ilugan = ilugan + 3 end do close(10) write(*,*) ' Wrote restart file: ', trim(adjustl(record)) else ilubar = ilubar + nmols(itype)*3 ilugan = ilugan + nmols(itype)*3 end if end do ! Write the output (xyz file) if(xyz) then open(30,file=xyzout,status='unknown') write(30,*) ntotat write(30,*) title ilubar = 0 ilugan = ntotmol*3 icart = 0 i_not_fixed = 0 i_fixed = ntype do itype = 1, ntfix if ( .not. fixedoninput(itype) ) then i_not_fixed = i_not_fixed + 1 do imol = 1, nmols(i_not_fixed) xbar = x(ilubar+1) ybar = x(ilubar+2) zbar = x(ilubar+3) beta = x(ilugan+1) gama = x(ilugan+2) teta = x(ilugan+3) call eulerrmat(beta,gama,teta,v1,v2,v3) idatom = idfirst(i_not_fixed) - 1 do iatom = 1, natoms(i_not_fixed) icart = icart + 1 idatom = idatom + 1 call compcart(icart,xbar,ybar,zbar,& coor(idatom,1),coor(idatom,2),& coor(idatom,3),& v1,v2,v3) write(30,"( tr2,a3,tr2,3(tr2,f14.6) )") ele(idatom), (xcart(icart, k), k = 1, 3) end do ilugan = ilugan + 3 ilubar = ilubar + 3 end do else i_fixed = i_fixed + 1 idatom = idfirst(i_fixed) - 1 do iatom = 1, natoms(i_fixed) idatom = idatom + 1 write(30,"( tr2,a3,tr2,3(tr2,f14.6) )") ele(idatom), (coor(idatom,k),k=1,3) end do end if end do close(30) end if ! write the output as a MOLDY file if(moldy) then open(30,file=xyzout,status='unknown') ! For square moldy boxes, this must be the side dimensions of the box sxmin = 1.d30 symin = 1.d30 szmin = 1.d30 sxmax = -1.d30 symax = -1.d30 szmax = -1.d30 do irest = 1, nrest if(ityperest(irest).eq.2) then sxmin = dmin1(restpars(irest,1),sxmin) symin = dmin1(restpars(irest,2),symin) szmin = dmin1(restpars(irest,3),szmin) sxmax = dmax1(restpars(irest,4)+restpars(irest,1),sxmax) symax = dmax1(restpars(irest,4)+restpars(irest,2),symax) szmax = dmax1(restpars(irest,4)+restpars(irest,3),szmax) else if(ityperest(irest).eq.3) then sxmin = dmin1(restpars(irest,1),sxmin) symin = dmin1(restpars(irest,2),symin) szmin = dmin1(restpars(irest,3),szmin) sxmax = dmax1(restpars(irest,4),sxmax) symax = dmax1(restpars(irest,5),symax) szmax = dmax1(restpars(irest,6),szmax) else write(*,*) ' WARNING: The first line of the moldy output' write(*,*) ' file contains the size of the sides of the' write(*,*) ' paralelogram that defines the system. ' write(*,*) ' The numbers printed may not be correct in ' write(*,*) ' this case because regions other than cubes ' write(*,*) ' or boxes were used. ' sxmin = dmin1(sxmin,sizemin(1)) symin = dmin1(symin,sizemin(2)) szmin = dmin1(szmin,sizemin(3)) sxmax = dmax1(sxmax,sizemax(1)) symax = dmax1(symax,sizemax(2)) szmax = dmax1(szmax,sizemax(3)) end if end do xlength = sxmax - sxmin ylength = symax - symin zlength = szmax - szmin write(30,"( 3(tr1,f12.6),' 90 90 90 1 1 1 ' )") xlength, ylength, zlength ilubar = 0 ilugan = ntotmol*3 i_not_fixed = 0 i_fixed = ntype do itype = 1, ntfix if ( .not. fixedoninput(itype) ) then i_not_fixed = i_not_fixed + 1 record = name(i_not_fixed) do imol = 1, nmols(i_not_fixed) xbar = (x(ilubar+1) - sxmin) / xlength ybar = (x(ilubar+2) - symin) / ylength zbar = (x(ilubar+3) - szmin) / zlength beta = x(ilugan+1) gama = x(ilugan+2) teta = x(ilugan+3) call eulerrmat(beta,gama,teta,v1,v2,v3) ! Computing cartesian coordinates and quaternions xxyx = 0.d0 xxyy = 0.d0 xxyz = 0.d0 xyyx = 0.d0 xyyy = 0.d0 xyyz = 0.d0 xzyx = 0.d0 xzyy = 0.d0 xzyz = 0.d0 idatom = idfirst(i_not_fixed) - 1 do iatom = 1, natoms(i_not_fixed) idatom = idatom + 1 xq = coor(idatom, 1)*v1(1) & + coor(idatom, 2)*v2(1) & + coor(idatom, 3)*v3(1) yq = coor(idatom, 1)*v1(2) & + coor(idatom, 2)*v2(2) & + coor(idatom, 3)*v3(2) zq = coor(idatom, 1)*v1(3) & + coor(idatom, 2)*v2(3) & + coor(idatom, 3)*v3(3) ! Recovering quaternions for molecule imol xxyx = xxyx + xq * coor(idatom,1) * amass(idatom) xxyy = xxyy + xq * coor(idatom,2) * amass(idatom) xxyz = xxyz + xq * coor(idatom,3) * amass(idatom) xyyx = xyyx + yq * coor(idatom,1) * amass(idatom) xyyy = xyyy + yq * coor(idatom,2) * amass(idatom) xyyz = xyyz + yq * coor(idatom,3) * amass(idatom) xzyx = xzyx + zq * coor(idatom,1) * amass(idatom) xzyy = xzyy + zq * coor(idatom,2) * amass(idatom) xzyz = xzyz + zq * coor(idatom,3) * amass(idatom) end do tens(1,1) = xxyx + xyyy + xzyz tens(1,2) = xzyy - xyyz tens(2,2) = xxyx - xyyy - xzyz tens(1,3) = xxyz - xzyx tens(2,3) = xxyy + xyyx tens(3,3) = xyyy - xzyz - xxyx tens(1,4) = xyyx - xxyy tens(2,4) = xzyx + xxyz tens(3,4) = xyyz + xzyy tens(4,4) = xzyz - xxyx - xyyy nr = 16 call jacobi (tens, 4, 4, dv, v, nr) q0 = v(1,4) q1 = v(2,4) q2 = v(3,4) q3 = v(4,4) record = name(i_not_fixed) xbar = dmin1(0.999999d0,xbar) ybar = dmin1(0.999999d0,ybar) zbar = dmin1(0.999999d0,zbar) write(30,"( a10,tr1,7(f12.6) )") record(1:strlength(record)), xbar, ybar, zbar, & q0, q1, q2, q3 ilugan = ilugan + 3 ilubar = ilubar + 3 end do else i_fixed = i_fixed + 1 idatom = idfirst(i_fixed) - 1 ! Getting the specified position of the molecule do irest = 1, nrest if(irestline(irest).gt.linestrut(i_fixed,1).and.& irestline(irest).lt.linestrut(i_fixed,2)) then xcm = restpars(irest,1) - sxmin ycm = restpars(irest,2) - symin zcm = restpars(irest,3) - szmin beta = -restpars(irest,4) gama = -restpars(irest,5) teta = -restpars(irest,6) end if end do call eulerrmat(beta,gama,teta,v1,v2,v3) ! Computing cartesian coordinates and quaternions xxyx = 0.d0 xxyy = 0.d0 xxyz = 0.d0 xyyx = 0.d0 xyyy = 0.d0 xyyz = 0.d0 xzyx = 0.d0 xzyy = 0.d0 xzyz = 0.d0 idatom = idfirst(i_fixed) - 1 do iatom = 1, natoms(i_fixed) idatom = idatom + 1 xtemp = coor(idatom,1) - xcm ytemp = coor(idatom,2) - ycm ztemp = coor(idatom,3) - zcm xq = xtemp*v1(1) + ytemp*v2(1) + ztemp*v3(1) yq = xtemp*v1(2) + ytemp*v2(2) + ztemp*v3(2) zq = xtemp*v1(3) + ytemp*v2(3) + ztemp*v3(3) xxyx = xxyx + xtemp * xq * amass(idatom) xxyy = xxyy + xtemp * yq * amass(idatom) xxyz = xxyz + xtemp * zq * amass(idatom) xyyx = xyyx + ytemp * xq * amass(idatom) xyyy = xyyy + ytemp * yq * amass(idatom) xyyz = xyyz + ytemp * zq * amass(idatom) xzyx = xzyx + ztemp * xq * amass(idatom) xzyy = xzyy + ztemp * yq * amass(idatom) xzyz = xzyz + ztemp * zq * amass(idatom) end do tens(1,1) = xxyx + xyyy + xzyz tens(1,2) = xzyy - xyyz tens(2,2) = xxyx - xyyy - xzyz tens(1,3) = xxyz - xzyx tens(2,3) = xxyy + xyyx tens(3,3) = xyyy - xzyz - xxyx tens(1,4) = xyyx - xxyy tens(2,4) = xzyx + xxyz tens(3,4) = xyyz + xzyy tens(4,4) = xzyz - xxyx - xyyy nr = 16 call jacobi (tens, 4, 4, dv, v, nr) q0 = v(1,4) q1 = v(2,4) q2 = v(3,4) q3 = v(4,4) xcm = xcm / xlength ycm = ycm / ylength zcm = zcm / zlength record = name(itype) xcm = dmin1(0.999999d0,xcm) ycm = dmin1(0.999999d0,ycm) zcm = dmin1(0.999999d0,zcm) write(30,"( a10,tr1,7(f12.6) )") record(1:strlength(record)),& xcm, ycm, zcm, q0, q1, q2, q3 end if end do close(30) end if ! write the output as pdb file if(pdb) then pdb_atom_line = "( t1,a5,t7,i5,t12,a10,t22,a1,t23,& &i4,t27,a1,t31,f8.3,t39,f8.3,t47,& &f8.3,t55,a26 )" pdb_atom_line_hex = "( t1,a5,t7,z5,t12,a10,t22,a1,t23,& &i4,t27,a1,t31,f8.3,t39,f8.3,t47,& &f8.3,t55,a26 )" pdb_hetatm_line = "( t1,a6,t7,i5,t12,a10,t22,a1,& &t23,i4,t27,a1,t31,f8.3,t39,& &f8.3,t47,f8.3,t55,a26 )" pdb_hetatm_line_hex = "( t1,a6,t7,z5,t12,a10,t22,a1,& &t23,i4,t27,a1,t31,f8.3,t39,& &f8.3,t47,f8.3,t55,a26 )" crd_format='(2I10,2X,A8,2X,A8,3F20.10,2X,A8,2X,A8,F20.10)' open(30,file=xyzout,status='unknown') if ( crd ) then open(40,file=crdfile,status='unknown') write(40,'("* TITLE ", a64,/& &"* Packmol generated CHARMM CRD File",/& &"* Home-Page:",/& &"* http://m3g.iqm.unicamp.br/packmol",/& &"* ")') title write(40,'(i10,2x,a)') ntotat,'EXT' end if write(30,"( & &'HEADER ',/& &'TITLE ', a64,/& &'REMARK Packmol generated pdb file ',/& &'REMARK Home-Page: ',& &'http://m3g.iqm.unicamp.br/packmol',/,& &'REMARK' )" ) title if(add_box_sides) then write(30,"( 'CRYST1',t7,f9.2,t16,f9.2,t25,f9.2,& &t34,f7.2,t41,f7.2,t48,f7.2,& &t56,'P 1 1' )") & sizemax(1)-sizemin(1) + add_sides_fix,& sizemax(2)-sizemin(2) + add_sides_fix,& sizemax(3)-sizemin(3) + add_sides_fix,& 90., 90., 90. end if ilubar = 0 ilugan = ntotmol*3 icart = 0 i_ref_atom = 0 iimol = 0 ichain = 0 i_not_fixed = 0 i_fixed = ntype irescount = 1 do itype = 1, ntfix if ( .not. fixedoninput(itype) ) then i_not_fixed = i_not_fixed + 1 ! Counting the number of residues of this molecule open(15,file=pdbfile(i_not_fixed),status='old') ifres = 0 do read(15,"( a80 )",iostat=ioerr) record if ( ioerr /= 0 ) exit if ( record(1:4).eq.'ATOM'.or.record(1:6).eq.'HETATM' ) then read(record(23:26),*,iostat=ioerr) imark if ( ioerr /= 0 ) then record = pdbfile(i_not_fixed) write(*,*) ' ERROR: Failed reading residue number ',& ' from PDB file: ', record(1:strlength(record)) write(*,*) ' Residue numbers are integers that must',& ' be between columns 23 and 26. ' write(*,*) ' Other characters within these columns',& ' will cause input/output errors. ' write(*,*) ' Standard PDB format specifications can',& ' be found at: ' write(*,*) ' www.rcsb.org/pdb ' stop end if if ( ifres .eq. 0 ) ifres = imark ilres = imark end if end do nres = ilres - ifres + 1 do irec = 1, 80 record(irec:irec) = ' ' end do mol: do imol = 1, nmols(i_not_fixed) iimol = iimol + 1 if( chain(i_not_fixed) == "#" ) then if(imol.eq.1.or.mod(imol,9999).eq.1) then ichain = ichain + 1 if( changechains(i_not_fixed) ) then call chainc(ichain,odd_chain) ichain = ichain + 1 call chainc(ichain,even_chain) else call chainc(ichain,even_chain) odd_chain = even_chain end if end if if ( mod(imol,2) == 0 ) write_chain = even_chain if ( mod(imol,2) /= 0 ) write_chain = odd_chain else write_chain = chain(i_not_fixed) end if xbar = x(ilubar+1) ybar = x(ilubar+2) zbar = x(ilubar+3) beta = x(ilugan+1) gama = x(ilugan+2) teta = x(ilugan+3) call eulerrmat(beta,gama,teta,v1,v2,v3) rewind(15) idatom = idfirst(i_not_fixed) - 1 iatom = 0 do while(iatom.lt.natoms(i_not_fixed)) read(15,"( a80 )",iostat=ioerr) record if ( ioerr /= 0 ) exit mol if(record(1:4).ne.'ATOM'.and.record(1:6).ne.'HETATM') then cycle end if iatom = iatom + 1 icart = icart + 1 idatom = idatom + 1 i_ref_atom = i_ref_atom + 1 call compcart(icart,xbar,ybar,zbar,& coor(idatom,1),coor(idatom,2),& coor(idatom,3),v1,v2,v3) ! Setting residue numbers for this molecule imark = 0 read(record(23:26),*,iostat=ioerr) imark if ( ioerr /= 0 ) imark = 1 if(resnumbers(i_not_fixed).eq.0) then iires = mod(imol,9999) ciires = mod(imol,99999999) else if(resnumbers(i_not_fixed).eq.1) then iires = imark ciires = imark else if(resnumbers(i_not_fixed).eq.2) then iires = mod(imark-ifres+irescount,9999) ciires = mod(imark-ifres+irescount,99999999) else if(resnumbers(i_not_fixed).eq.3) then iires = mod(iimol,9999) ciires = mod(iimol,99999999) end if if(iires.eq.0) iires = 9999 if(ciires.eq.0) ciires = 99999999 ! Writing output line if(record(1:4).eq.'ATOM') then format_line = pdb_atom_line if ( i_ref_atom > 99999 ) format_line = pdb_atom_line_hex write(30,format_line) record(1:5), i_ref_atom,& record(12:21), write_chain, iires,& record(27:27),& (xcart(icart,k), k = 1, 3),& record(55:80) end if if(record(1:6).eq.'HETATM') then format_line = pdb_hetatm_line if ( i_ref_atom > 99999 ) format_line = pdb_hetatm_line_hex write(30,format_line) record(1:6), i_ref_atom,& record(12:21), write_chain, iires,& record(27:27),& (xcart(icart,k), k = 1, 3),& record(55:80) end if if ( crd ) then write(crdires,'(I8)') ciires crdires = adjustl(crdires) crdresn = trim(adjustl(record(18:21))) crdsegi = crdresn if (len(trim(adjustl(segid(i_not_fixed))))/=0) crdsegi = trim(adjustl(segid(i_not_fixed))) atmname = adjustl(record(13:16)) write(40,crd_format) i_ref_atom, ciires,crdresn, atmname, & (xcart(icart,k), k = 1, 3), crdsegi,& crdires, 0. end if end do irescount = irescount + nres ilugan = ilugan + 3 ilubar = ilubar + 3 if(add_amber_ter) write(30,"('TER')") end do mol close(15) ! If fixed molecule on input: else i_fixed = i_fixed + 1 ! Counting the number of residues of this molecule open(15,file=pdbfile(i_fixed),status='old') ifres = 0 do read(15,"( a80 )",iostat=ioerr) record if ( ioerr /= 0 ) exit if ( record(1:4).eq.'ATOM'.or.record(1:6).eq.'HETATM' ) then read(record(23:26),*,iostat=ioerr) imark if ( ioerr /= 0 ) then record = pdbfile(i_not_fixed) write(*,*) ' ERROR: Failed reading residue number ',& ' from PDB file: ', record(1:strlength(record)) write(*,*) ' Residue numbers are integers that must',& ' be between columns 23 and 26. ' write(*,*) ' Other characters within these columns',& ' will cause input/output errors. ' write(*,*) ' Standard PDB format specifications can',& ' be found at: ' write(*,*) ' www.rcsb.org/pdb ' stop end if if ( ifres .eq. 0 ) ifres = imark ilres = imark end if end do nres = ilres - ifres + 1 iimol = iimol + 1 idatom = idfirst(i_fixed) - 1 rewind(15) iatom = 0 do while(iatom.lt.natoms(i_fixed)) read(15,"( a80 )",iostat=ioerr) record if ( ioerr /= 0 ) exit if(record(1:4).ne.'ATOM'.and.record(1:6).ne.'HETATM') then !write(30,"( a80 )") record(1:80) cycle end if iatom = iatom + 1 idatom = idatom + 1 i_ref_atom = i_ref_atom + 1 read(record(23:26),*) imark if(resnumbers(i_fixed).eq.0) then iires = 1 ciires = 1 else if(resnumbers(i_fixed).eq.1) then iires = imark ciires = imark else if(resnumbers(i_fixed).eq.2) then iires = mod(imark-ifres+irescount,9999) ciires = mod(imark-ifres+irescount,99999999) else if(resnumbers(i_fixed).eq.3) then iires = mod(iimol,9999) ciires = mod(iimol,99999999) end if if ( chain(i_fixed) == "#" ) then write_chain = record(22:22) else write_chain = chain(i_fixed) end if if(record(1:4).eq.'ATOM') then write(30,pdb_atom_line) record(1:5), i_ref_atom,& record(12:21), write_chain, iires,& record(27:27),& (coor(idatom,k), k = 1, 3),& record(55:80) end if if(record(1:6).eq.'HETATM') then write(30,pdb_hetatm_line) record(1:6), i_ref_atom,& record(12:21), write_chain, iires,& record(27:27),& (coor(idatom,k), k = 1, 3),& record(55:80) end if if ( crd ) then write(crdires,'(I8)') ciires crdires = adjustl(crdires) crdresn = trim(adjustl(record(18:21))) crdsegi = crdresn if (len(trim(adjustl(segid(i_fixed))))/=0) crdsegi = trim(adjustl(segid(i_fixed))) atmname = adjustl(record(13:16)) write(40,crd_format) i_ref_atom, iires,crdresn, atmname, & (xcart(icart,k), k = 1, 3), crdsegi,& crdires, 0. end if end do irescount = irescount + nres close(15) if(add_amber_ter) write(30,"('TER')") end if end do write(30,"('END')") close(30) if ( crd ) close(40) end if ! Write the output (tinker xyz file) if(tinker) then tinker_atom_line = "( i7,tr2,a3,3(tr2,f10.6),9(tr2,i7) )" open(30, file = xyzout,status='unknown') write(30,"( i6,tr2,a64 )") ntotat, title ilubar = 0 ilugan = ntotmol*3 icart = 0 i_ref_atom = 0 i_not_fixed = 0 i_fixed = ntype do itype = 1, ntfix if ( .not. fixedoninput(itype) ) then i_not_fixed = i_not_fixed + 1 do imol = 1, nmols(i_not_fixed) xbar = x(ilubar+1) ybar = x(ilubar+2) zbar = x(ilubar+3) beta = x(ilugan+1) gama = x(ilugan+2) teta = x(ilugan+3) call eulerrmat(beta,gama,teta,v1,v2,v3) idatom = idfirst(i_not_fixed) - 1 do iatom = 1, natoms(i_not_fixed) icart = icart + 1 idatom = idatom + 1 call compcart(icart,xbar,ybar,zbar,& coor(idatom,1),coor(idatom,2),& coor(idatom,3),& v1,v2,v3) ntcon(1) = nconnect(idatom,1) do k = 2, maxcon(idatom) ntcon(k) = nconnect(idatom,k) + i_ref_atom end do write(30,tinker_atom_line) i_ref_atom+iatom,& ele(idatom), (xcart(icart, k), k = 1, 3),& (ntcon(k), k = 1, maxcon(idatom)) end do i_ref_atom = i_ref_atom + natoms(i_not_fixed) ilugan = ilugan + 3 ilubar = ilubar + 3 end do else i_fixed = i_fixed + 1 idatom = idfirst(i_fixed) - 1 do iatom = 1, natoms(i_fixed) idatom = idatom + 1 ntcon(1) = nconnect(idatom,1) do k = 2, maxcon(idatom) ntcon(k) = nconnect(idatom,k) + i_ref_atom end do write(30,tinker_atom_line) i_ref_atom+iatom, ele(idatom),& (coor(idatom,k), k = 1, 3),& (ntcon(k), k = 1, maxcon(idatom)) end do i_ref_atom = i_ref_atom + natoms(i_fixed) end if end do close(30) end if return end subroutine output packmol-20.010/packmol.f90000066400000000000000000000723421360620542100151770ustar00rootroot00000000000000! ! Written by Leandro Martínez, 2009-2011. ! Copyright (c) 2009-2018, Leandro Martínez, Jose Mario Martinez, ! Ernesto G. Birgin. ! !----------------------------------------------------------------------------- ! ! http://m3g.iqm.unicamp.br/packmol ! ! Usage (see the page above for further information): ! ! ./packmol < inputfile.inp ! ! References: ! ! L. Martinez, R. Andrade, E. G. Birgin, J. M. Martinez, ! PACKMOL: A package for building initial configurations for ! molecular dynamics simulations, J. Comp. Chem. 30:2157-2164, 2009. ! ! J. M. Martinez and L. Martinez, ! Packing optimization for the automated generation of complex ! system's initial configurations for molcular dynamics and ! docking. J. Comp. Chem. 24:819-825, 2003. ! ! This version of Packmol uses the optimization method GENCAN which ! is a part of the TANGO (Trustable Algorithms for Nonlinear General ! Optimization) project. ! Reference: ! E. G. Birgin, J. M. Martinez, Comp. Opt. Appl. 23:101-125, 2002. ! http://www.ime.usp.br/~egbirgin/tango ! ! program packmol use sizes use compute_data use input use usegencan use flashsort use swaptypemod use ahestetic implicit none integer :: itype, irest, idatom, iatom integer :: idtemp, nmtemp, natemp, input_itypetemp integer :: linesttmp1, linesttmp2, jtype integer :: ntmol, n, iftype, icart, imol, iicart, iline_atoms integer :: i, iline, iiatom, iat, iirest, iratcount, ival integer :: loop integer :: resntemp, nloop_tmp integer :: strlength, ioerr double precision, allocatable :: x(:), xprint(:) ! (nn) double precision :: v1(3),v2(3),v3(3) double precision :: radscale, value double precision :: cmx, cmy, cmz, beta, gama, teta double precision :: xtemp, ytemp, ztemp double precision :: fx, bestf, flast, fprint, all_type_fx double precision :: fimp, fimprov double precision, parameter :: pi=4.d0*datan(1.d0) real :: etime, tarray(2), time0 character(len=200) :: record, restart_from_temp, restart_to_temp character(len=80) :: xyzfile character(len=1) :: chain_tmp logical :: fixtmp logical :: rests logical :: movebadprint logical :: changechains_tmp logical, allocatable :: fixed(:) ! ntype ! Printing title call title() ! Set dimensions of all arrays call setsizes() ! Allocate local array allocate(fixed(ntype),x(nn),xprint(nn),xfull(nn)) ! Start time computation time0 = etime(tarray) ! Reading input file call getinp() ! Put molecules in their center of mass call cenmass() ! Writting some input data write(*,*) ' Total number of atoms: ', ntotat ! Put fixed molecules in the specified position do itype = 1, ntype fixed(itype) = .false. end do do irest = 1, nrest if(ityperest(irest).eq.1) then do itype = 1, ntype if(irestline(irest).gt.linestrut(itype,1).and.& irestline(irest).lt.linestrut(itype,2)) then cmx = restpars(irest,1) cmy = restpars(irest,2) cmz = restpars(irest,3) beta = restpars(irest,4) gama = restpars(irest,5) teta = restpars(irest,6) ! Compute rotation matrix from euler angles call eulerfixed(beta,gama,teta,v1,v2,v3) idatom = idfirst(itype) - 1 do iatom = 1, natoms(itype) idatom = idatom + 1 xtemp = coor(idatom,1)*v1(1) & + coor(idatom,2)*v2(1) & + coor(idatom,3)*v3(1) ytemp = coor(idatom,1)*v1(2) & + coor(idatom,2)*v2(2) & + coor(idatom,3)*v3(2) ztemp = coor(idatom,1)*v1(3) & + coor(idatom,2)*v2(3) & + coor(idatom,3)*v3(3) coor(idatom, 1) = xtemp + cmx coor(idatom, 2) = ytemp + cmy coor(idatom, 3) = ztemp + cmz end do record = name(itype) write(*,*) ' Molecule ',record(1:strlength(record)),'(',itype,') will be fixed.' fixed(itype) = .true. if(nmols(itype).gt.1) then write(*,*)' ERROR: Cannot set number > 1',' for fixed molecules. ' write(*,*) ' Structure: ', itype,': ', trim(adjustl(record)) stop end if if ( restart_from(itype) /= 'none' .or. & restart_to(itype) /= 'none' ) then write(*,*) ' ERROR: Restart files cannot be used for fixed molecules. ' write(*,*) ' Structure: ', itype,': ', trim(adjustl(record)) stop end if end if end do end if end do ! Reseting parameters for removing the fixed molecules ! fix is the logical variable that informs that there are fixed molecules fix = .false. ntemp = 0 do itype = 1, ntype ! input_itype and fixedoninput vectors are used only to preserve the ! order of input in the output files input_itype(itype) = itype if(fixed(itype)) then fix = .true. fixedoninput(itype) = .true. else ntemp = ntemp + 1 fixedoninput(itype) = .false. end if end do ntfix = ntype ntype = ntemp do i = 1, ntfix - ntype do itype = 1, ntfix - 1 if(fixed(itype)) then record = name(itype) restart_to_temp = restart_to(itype) restart_from_temp = restart_from(itype) fixtmp = fixed(itype) idtemp = idfirst(itype) input_itypetemp = input_itype(itype) nmtemp = nmols(itype) natemp = natoms(itype) resntemp = resnumbers(itype) if(pdb) xyzfile = pdbfile(itype) linesttmp1 = linestrut(itype,1) linesttmp2 = linestrut(itype,2) changechains_tmp = changechains(itype) chain_tmp = chain(itype) nloop_tmp = nloop_type(itype) jtype = itype + 1 if(.not.fixed(jtype)) then name(itype) = name(jtype) name(jtype) = record(1:10) restart_to(itype) = restart_to(jtype) restart_to(jtype) = restart_to_temp restart_from(itype) = restart_from(jtype) restart_from(jtype) = restart_from_temp idfirst(itype) = idfirst(jtype) idfirst(jtype) = idtemp input_itype(itype) = input_itype(jtype) input_itype(jtype) = input_itypetemp fixed(itype) = fixed(jtype) fixed(jtype) = fixtmp nmols(itype) = nmols(jtype) nmols(jtype) = nmtemp natoms(itype) = natoms(jtype) natoms(jtype) = natemp resnumbers(itype) = resnumbers(jtype) resnumbers(jtype) = resntemp changechains(itype) = changechains(jtype) changechains(jtype) = changechains_tmp chain(itype) = chain(jtype) chain(jtype) = chain_tmp nloop_type(itype) = nloop_type(jtype) nloop_type(jtype) = nloop_tmp if(pdb) then pdbfile(itype) = pdbfile(jtype) pdbfile(jtype) = xyzfile end if linestrut(itype,1) = linestrut(jtype,1) linestrut(itype,2) = linestrut(jtype,2) linestrut(jtype,1) = linesttmp1 linestrut(jtype,2) = linesttmp2 end if end if end do end do ! Computing the number of variables ! ! ntype: 1...ntype (counter for the number of free structures) ! ! ntfix: 1...ntype...ntfix (counter for the total number of structures) ! ntmol = 0 do itype = 1, ntfix ntmol = ntmol + nmols(itype) end do ntotmol = 0 do itype = 1, ntype ntotmol = ntotmol + nmols(itype) end do n = ntotmol * 6 write(*,*) ' Total number of molecules: ', ntmol write(*,*) ' Number of fixed molecules: ', ntmol - ntotmol write(*,*) ' Number of free molecules: ', ntotmol write(*,*) ' Number of variables: ', n ! Computing the total number of fixed atoms natfix = 0 if(fix) then do iftype = ntype + 1, ntfix natfix = natfix + natoms(iftype) end do end if write(*,*) ' Total number of fixed atoms: ', natfix ! Setting the array that contains the restrictions per atom icart = 0 do itype = 1, ntype rests = .false. do imol = 1, nmols(itype) idatom = idfirst(itype) - 1 do iatom = 1, natoms(itype) icart = icart + 1 idatom = idatom + 1 nratom(icart) = 0 iratcount = 0 do i = 1, mrperatom iratom(icart,i) = 0 end do iline = linestrut(itype,1) do while(iline.lt.linestrut(itype,2)) iline = iline + 1 if(keyword(iline,1).eq.'atoms') then iiatom = -1 do iat = 2, maxkeywords read(keyword(iline,iat),*,iostat=ioerr) iiatom if ( ioerr /= 0 ) then if ( iiatom == -1 ) then write(*,*) ' ERROR: Could not read atom selection for type: ', itype stop else exit end if end if if ( iiatom > natoms(itype) ) then write(*,*) ' ERROR: atom selection with index greater than number of ' write(*,*) ' atoms in structure ', itype stop end if if(iatom.eq.iiatom) exit end do do while(keyword(iline,1).ne.'end'.and.& keyword(iline,2).ne.'atoms') iline = iline + 1 if(iatom.eq.iiatom) then if(keyword(iline,1).eq.'inside'.or.& keyword(iline,1).eq.'outside'.or.& keyword(iline,1).eq.'over'.or.& keyword(iline,1).eq.'below') then nratom(icart) = nratom(icart) + 1 iratcount = iratcount + 1 do irest = 1, nrest if(irestline(irest).eq.iline) iirest = irest end do iratom(icart,iratcount) = iirest end if end if end do iline = iline - 1 else if(keyword(iline,1).eq.'inside'.or.& keyword(iline,1).eq.'outside'.or.& keyword(iline,1).eq.'over'.or.& keyword(iline,1).eq.'below') then nratom(icart) = nratom(icart) + 1 iratcount = iratcount + 1 do irest = 1, nrest if(irestline(irest).eq.iline) iirest = irest end do iratom(icart,iratcount) = iirest end if end do if(nratom(icart).gt.0) rests = .true. end do if(.not.rests) then write(*,*) ' ERROR: Some molecule has no geometrical',& ' restriction defined: nothing to do.' stop end if end do end do ! Read the constraints to rotations about axis, if set do itype = 1, ntype constrain_rot(itype,1) = .false. constrain_rot(itype,2) = .false. constrain_rot(itype,3) = .false. iline = linestrut(itype,1) do while(iline.lt.linestrut(itype,2)) iline = iline + 1 if(keyword(iline,1).eq.'constrain_rotation') then if(iline.gt.linestrut(itype,1).and.& iline.lt.linestrut(itype,2)) then ! Note that for movable molecules, teta is a rotation on the x-axis, ! gama is a rotation on the z-axis, ! beta is a rotation on the y-axis ! (see eulerrmat routine) if(keyword(iline,2).eq.'x') then constrain_rot(itype,3) = .true. read(keyword(iline,3),*) rot_bound(itype,3,1) read(keyword(iline,4),*) rot_bound(itype,3,2) rot_bound(itype,3,1) = rot_bound(itype,3,1)*pi/180.d0 rot_bound(itype,3,2) = rot_bound(itype,3,2)*pi/180.d0 write(*,*) ' Rotations about x axis of molecules of ',& ' type ', itype, ' will be constrained. ' end if if(keyword(iline,2).eq.'y') then constrain_rot(itype,1) = .true. read(keyword(iline,3),*) rot_bound(itype,1,1) read(keyword(iline,4),*) rot_bound(itype,1,2) rot_bound(itype,1,1) = rot_bound(itype,1,1)*pi/180.d0 rot_bound(itype,1,2) = rot_bound(itype,1,2)*pi/180.d0 write(*,*) ' Rotations about y axis of molecules of ',& ' type ', itype, ' will be constrained. ' end if if(keyword(iline,2).eq.'z') then constrain_rot(itype,2) = .true. read(keyword(iline,3),*) rot_bound(itype,2,1) read(keyword(iline,4),*) rot_bound(itype,2,2) rot_bound(itype,2,1) = rot_bound(itype,2,1)*pi/180.d0 rot_bound(itype,2,2) = rot_bound(itype,2,2)*pi/180.d0 write(*,*) ' Rotations about z axis of molecules of ',& ' type ', itype, ' will be constrained. ' end if if ( keyword(iline,2) /= 'x' .and. & keyword(iline,2) /= 'y' .and. & keyword(iline,2) /= 'z' ) then write(*,*) ' ERROR: constrain_rotation option not properly defined (not x, y, or z) ' stop end if end if end if end do end do ! Setting the vector that contains the default tolerances do i = 1, ntotat radius(i) = dism/2.d0 fscale(i) = 1.d0 if ( use_short_tol ) then use_short_radius(i) = .true. else use_short_radius(i) = .false. end if short_radius(i) = short_tol_dist/2.d0 short_radius_scale(i) = short_tol_scale end do ! Setting the radius defined for atoms of each molecule, ! but not atom-specific, first icart = 0 do itype = 1, ntfix iline = linestrut(itype,1) iline_atoms = 0 do while( iline <= linestrut(itype,2) ) if ( keyword(iline,1) == "atoms" ) then iline_atoms = iline iline = iline + 1 cycle end if if ( keyword(iline,1) == "end" .and. & keyword(iline,2) == "atoms" ) then iline_atoms = 0 iline = iline + 1 cycle end if if ( iline_atoms == 0 ) then ! ! Read radius ! if ( keyword(iline,1) == "radius" ) then read(keyword(iline,2),*,iostat=ioerr) value if ( ioerr /= 0 ) then write(*,*) ' ERROR: Could not read radius from keyword. ' stop end if iicart = icart do imol = 1, nmols(itype) do iatom = 1, natoms(itype) iicart = iicart + 1 radius(iicart) = value end do end do end if ! ! Read minimum-distance function scale ! if ( keyword(iline,1) == "fscale" ) then read(keyword(iline,2),*,iostat=ioerr) value if ( ioerr /= 0 ) then write(*,*) ' ERROR: Could not read fscale value from keyword. ' stop end if iicart = icart do imol = 1, nmols(itype) do iatom = 1, natoms(itype) iicart = iicart + 1 fscale(iicart) = value end do end do end if ! ! Read short_radius ! if ( keyword(iline,1) == "short_radius" ) then read(keyword(iline,2),*,iostat=ioerr) value if ( ioerr /= 0 ) then write(*,*) ' ERROR: Could not read short_radius value from keyword. ' stop end if iicart = icart do imol = 1, nmols(itype) do iatom = 1, natoms(itype) iicart = iicart + 1 short_radius(iicart) = value use_short_radius(iicart) = .true. end do end do end if ! ! Read short_radius scale ! if ( keyword(iline,1) == "short_radius_scale" ) then read(keyword(iline,2),*,iostat=ioerr) value if ( ioerr /= 0 ) then write(*,*) ' ERROR: Could not read short_radius_scale value from keyword. ' stop end if iicart = icart do imol = 1, nmols(itype) do iatom = 1, natoms(itype) iicart = iicart + 1 short_radius_scale(iicart) = value use_short_radius(iicart) = .true. end do end do end if end if iline = iline + 1 end do icart = icart + nmols(itype)*natoms(itype) end do ! If some radius was defined using atom-specific definitions, overwrite ! the general radius defined for the molecule icart = 0 do itype = 1, ntfix iline = linestrut(itype,1) iline_atoms = 0 do while( iline <= linestrut(itype,2) ) if ( keyword(iline,1) == "atoms" ) then iline_atoms = iline iline = iline + 1 cycle end if if ( keyword(iline,1) == "end" .and. & keyword(iline,2) == "atoms" ) then iline_atoms = 0 iline = iline + 1 cycle end if if ( iline_atoms /= 0 ) then ! ! Read atom specific radius ! if ( keyword(iline,1) == "radius" ) then read(keyword(iline,2),*,iostat=ioerr) value if ( ioerr /= 0 ) then write(*,*) ' ERROR: Could not read radius from keyword. ' stop end if ival = 2 do read(keyword(iline_atoms,ival),*,iostat=ioerr) iat if ( ioerr /= 0 ) exit if ( iat > natoms(itype) ) then write(*,*) ' ERROR: atom selection with index greater than number of ' write(*,*) ' atoms in structure ', itype stop end if radius(icart+iat) = value ival = ival + 1 end do end if ! ! Read atom specific function scale ! if ( keyword(iline,1) == "fscale" ) then read(keyword(iline,2),*,iostat=ioerr) value if ( ioerr /= 0 ) then write(*,*) ' ERROR: Could not read fscale value from keyword. ' stop end if ival = 2 do read(keyword(iline_atoms,ival),*,iostat=ioerr) iat if ( ioerr /= 0 ) exit if ( iat > natoms(itype) ) then write(*,*) ' ERROR: atom selection with index greater than number of ' write(*,*) ' atoms in structure ', itype stop end if fscale(icart+iat) = value ival = ival + 1 end do end if ! ! Read atom specific short radius ! if ( keyword(iline,1) == "short_radius" ) then read(keyword(iline,2),*,iostat=ioerr) value if ( ioerr /= 0 ) then write(*,*) ' ERROR: Could not read short_radius value from keyword. ' stop end if ival = 2 do read(keyword(iline_atoms,ival),*,iostat=ioerr) iat if ( ioerr /= 0 ) exit if ( iat > natoms(itype) ) then write(*,*) ' ERROR: atom selection with index greater than number of ' write(*,*) ' atoms in structure ', itype stop end if short_radius(icart+iat) = value use_short_radius(icart+iat) = .true. ival = ival + 1 end do end if ! ! Read atom specific short radius function scale ! if ( keyword(iline,1) == "short_radius_scale" ) then read(keyword(iline,2),*,iostat=ioerr) value if ( ioerr /= 0 ) then write(*,*) ' ERROR: Could not read short_radius_scale value from keyword. ' stop end if ival = 2 do read(keyword(iline_atoms,ival),*,iostat=ioerr) iat if ( ioerr /= 0 ) exit if ( iat > natoms(itype) ) then write(*,*) ' ERROR: atom selection with index greater than number of ' write(*,*) ' atoms in structure ', itype stop end if short_radius_scale(icart+iat) = value use_short_radius(icart+iat) = .true. ival = ival + 1 end do end if end if iline = iline + 1 end do iicart = icart icart = icart + natoms(itype) do imol = 2, nmols(itype) do iatom = 1, natoms(itype) icart = icart + 1 radius(icart) = radius(iicart+iatom) fscale(icart) = fscale(iicart+iatom) short_radius(icart) = short_radius(iicart+iatom) short_radius_scale(icart) = short_radius_scale(iicart+iatom) use_short_radius(icart) = use_short_radius(iicart+iatom) end do end do end do ! Check if the short radii were set correctly, if the case ioerr = 0 do i = 1, ntotat if ( use_short_radius(i) ) then if ( short_radius(i) >= radius(i) ) then write(*,*) ' ERROR: The short radius must be smaller than the default radius. ' write(*,*) ' (the default radius is one half of the default tolerance).' stop end if end if end do ! If there are no variables (only fixed molecules, stop) if(n.eq.0) then call output(n,x) write(*,dash1_line) write(*,*) ' There are only fixed molecules, therefore there is nothing to do. ' write(*,*) ' The output file contains the fixed molecules in the desired positions. ' write(*,dash1_line) write(*,*) ' Wrote output file: ', trim(adjustl(xyzout)) if ( crd ) write(*,*) ' ... and to CRD file: ', trim(adjustl(crdfile)) write(*,dash1_line) stop end if ! ! (Re)setting parameters and building initial point ! call initial(n,x) ! Computing the energy at the initial point radscale = 1.d0 do i = 1, ntotat radius_ini(i) = radius(i) end do call computef(n,x,all_type_fx) write(*,*) ' Objective function at initial point: ', all_type_fx fprint = all_type_fx ! Stop if only checking the initial approximation if(check) then call output(n,x) write(*,*) ' Wrote initial point to output file: ', xyzout(1:strlength(xyzout)) if ( crd ) write(*,*) ' ... and to CRD file: ', trim(adjustl(crdfile)) stop end if ! ! Main loop: first pack types of molecules separately, then ! pack all molecules together ! call swaptype(n,x,itype,0) ! Save all-molecule vector data itype = 0 main : do while(itype <= ntype) itype = itype + 1 if ( packall ) itype = ntype + 1 ! Use larger tolerance than required to improve separation radscale = discale do i = 1, ntotat radius(i) = discale*radius_ini(i) end do ! Set vectors for specific or all-molecule packing if ( itype <= ntype ) then call swaptype(n,x,itype,1) ! Set vectors to pack only this type of molecule else call swaptype(n,x,itype,3) ! Restore all-molecule vectors end if ! Print titles write(*,hash3_line) if ( itype <= ntype ) then write(*,*) ' Packing molecules of type: ', input_itype(itype) else write(*,*) ' Packing all molecules together ' end if write(*,hash3_line) ! Checking if first approximation is a solution call computef(n,x,fx) if ( fdist < precision .and. frest < precision ) then write(*,*) write(*,*) ' Initial approximation is a solution. Nothing to do. ' write(*,*) call swaptype(n,x,itype,3) ! Restore all-molecule vectors call output(n,x) if( itype == ntype + 1 ) then write(*,*) ' Solution written to file: ', trim(adjustl(xyzout)) if ( crd ) write(*,*) ' ... and to CRD file: ', trim(adjustl(crdfile)) else write(*,*) ' Current point written to file: ', trim(adjustl(xyzout)) if ( crd ) write(*,*) ' ... and to CRD file: ', trim(adjustl(crdfile)) end if call writesuccess(itype,fdist,frest,fx) ! Otherwise, pack the molecules else loop = -1 gencanloop : do while(loop.lt.nloop) loop = loop + 1 ! Reseting the parameters relative to the improvement of the function if(loop.eq.0) then fimp = 1.d99 fimprov = fimp do i = 1, ntotat radiuswork(i) = radius(i) radius(i) = radius_ini(i) end do call computef(n,x,fx) do i = 1, ntotat radius(i) = radiuswork(i) end do bestf = fx flast = fx end if ! Moving bad molecules if(radscale == 1.d0 .and. fimp.le.10.d0) then movebadprint = .true. call movebad(n,x,fx,movebadprint) flast = fx end if write(*,dash3_line) write(*,*) ' Starting GENCAN loop: ', loop write(*,*) ' Scaling radii by: ', radscale write(*,*) ! CALL GENCAN write(*,prog1_line) call pgencan(n,x,fx) ! ! Compute the statistics of the last optimization loop ! ! Use the user-specified radii for statistics do i = 1, ntotat radiuswork(i) = radius(i) radius(i) = radius_ini(i) end do call computef(n,x,fx) if(bestf.gt.0.d0) fimprov = -100.d0 * (fx - bestf) / bestf if(bestf.eq.0.d0) fimprov = 100.d0 if(flast.gt.0.d0) fimp = -100.d0 * (fx - flast) / flast if(flast.eq.0.d0) fimp = 100.d0 fimp = dmin1(99.99d0,dmax1(-99.99d0,fimp)) fimprov = dmin1(99.99d0,dmax1(-99.99d0,fimprov)) write(*,"(/& &' Function value from last GENCAN loop: f = ', e10.5, /& &' Best function value before: f = ', e10.5, /& &' Improvement from best function value: ', f8.2, ' %',/& &' Improvement from last loop: ', f8.2, ' %', /& &' Maximum violation of target distance: ', f12.6, /& &' Maximum violation of the constraints: ', e10.5 & &)") fx, bestf, fimprov, fimp, fdist, frest flast = fx ! ! Analysis of final loop packing and output data ! if ( itype <= ntype ) then ! Save best function value for this packing if ( fx < bestf ) bestf = fx ! Check if this point is a solution call swaptype(n,x,itype,2) ! Save this type current point ! If the solution was found for this type if( fdist < precision .and. frest < precision ) then call swaptype(n,x,itype,3) ! Restore all molecule vectors call output(n,x) write(*,*) ' Current structure written to file: ', trim(adjustl(xyzout)) if ( crd ) write(*,*) ' ... and to CRD file: ', trim(adjustl(crdfile)) call writesuccess(itype,fdist,frest,fx) exit gencanloop end if ! Compute and report function value for all-type packing call swaptype(n,x,itype,3) ! Restore all molecule vectors call computef(n,x,all_type_fx) write(*,"(' All-type function value: ', e10.5 )") all_type_fx else call computef(n,x,fx) all_type_fx = fx if ( fx < bestf ) bestf = fx ! If solution was found for all system if ( fdist < precision .and. frest < precision ) then call output(n,x) call writesuccess(itype,fdist,frest,fx) write(*,*) ' Solution written to file: ', xyzout(1:strlength(xyzout)) if ( crd ) write(*,*) ' ... and to CRD file: ', trim(adjustl(crdfile)) write(*,dash3_line) exit main end if end if write(*,dash3_line) ! If this is the best structure so far if( mod(loop+1,writeout) == 0 .and. all_type_fx < fprint ) then call output(n,x) write(*,*) ' Current solution written to file: ', trim(adjustl(xyzout)) if ( crd ) write(*,*) ' ... and to CRD file: ', trim(adjustl(crdfile)) fprint = all_type_fx do i = 1, n xprint(i) = x(i) end do ! If the user required printing even bad structures else if ( mod(loop+1,writeout) == 0 .and. writebad ) then call output(n,x) write(*,*) ' Writing current (perhaps bad) structure to file: ', trim(adjustl(xyzout)) if ( crd ) write(*,*) ' ... and to CRD file: ', trim(adjustl(crdfile)) end if ! Restore vector for packing this type of molecule, if the case if ( itype <= ntype ) then call swaptype(n,x,itype,0) ! Reset type vectors call swaptype(n,x,itype,1) ! Set vector for molecules of this type call computef(n,x,fx) end if ! Restore the working radii do i = 1, ntotat radius(i) = radiuswork(i) end do if ( radscale > 1.d0 ) then if( ( fdist < precision .and. fimp < 10.d0 ) .or. & fimp < 2.d0 ) then radscale = dmax1(0.9*radscale,1.d0) do i = 1, ntotat radius(i) = dmax1(radius_ini(i),0.9d0*radius(i)) end do end if end if if(loop.eq.nloop) then if ( itype .eq. ntype+1 ) then write(*,*)' STOP: Maximum number of GENCAN loops achieved.' call checkpoint(n,xprint) exit main else write(*,*)' Maximum number of GENCAN loops achieved.' end if end if end do gencanloop end if end do main write(*,*) ' Running time: ', etime(tarray) - time0,' seconds. ' write(*,dash3_line) write(*,*) end program packmol packmol-20.010/pgencan.f90000066400000000000000000000050741360620542100151620ustar00rootroot00000000000000! ! Written by Ernesto G. Birgin, 2009-2011. ! Copyright (c) 2009-2018, Jose Mario Martinez, ! Ernesto G. Birgin. ! ! Subroutine pgencan: This is only a interface to set some ! parameters. What might be important here ! is the setup of the constraint_axis constraint. ! subroutine pgencan(n,x,fx) use sizes use compute_data use usegencan implicit none double precision :: lambda(1), rho(1) double precision :: epsgpsn,gpsupn,delmin double precision :: x(n), fx integer :: m,iprint,maxfc,ncomp,iter,fcnt,gcnt,cgcnt,inform integer :: n, i integer :: trtype1 integer :: itype, imol ! Setup upper and lower bounds for variables. Usually there are none, ! but one might want to restrict the rotation of the molecules in one ! or more axis do i = 1,n/2 l(i) = - 1.0d+20 u(i) = 1.0d+20 end do i = n/2 do itype = 1, ntype do imol = 1, nmols(itype) if ( constrain_rot(itype,1) ) then l(i+1) = rot_bound(itype,1,1) - dabs(rot_bound(itype,1,2)) u(i+1) = rot_bound(itype,1,1) + dabs(rot_bound(itype,1,2)) else l(i+1) = - 1.0d+20 u(i+1) = 1.0d+20 end if if ( constrain_rot(itype,2) ) then l(i+2) = rot_bound(itype,2,1) - dabs(rot_bound(itype,2,2)) u(i+2) = rot_bound(itype,2,1) + dabs(rot_bound(itype,2,2)) else l(i+2) = - 1.0d+20 u(i+2) = 1.0d+20 end if if ( constrain_rot(itype,3) ) then l(i+3) = rot_bound(itype,3,1) - dabs(rot_bound(itype,3,2)) u(i+3) = rot_bound(itype,3,1) + dabs(rot_bound(itype,3,2)) else l(i+3) = - 1.0d+20 u(i+3) = 1.0d+20 end if i = i + 3 end do end do m = 0 epsgpsn = 1.0d-06 maxfc = 10 * maxit if(init1) iprint = iprint1 if(.not.init1) iprint = iprint2 ncomp = 50 delmin = 2.d0 trtype1 = 1 call easygencan(n,x,l,u,m,lambda,rho,epsgpsn,maxit,maxfc,& trtype1,iprint,ncomp,fx,g,gpsupn,iter,fcnt,& gcnt,cgcnt,inform,wi,wd,delmin) if( inform.ne.7 .and.(iprint1.gt.0 .or. iprint2.gt.0) ) write(*,*) return end subroutine pgencan ! ! Function that test convergence according to Packmol precision ! function packmolprecision(n,x) use input, only : precision use compute_data, only : fdist, frest implicit none integer :: n double precision :: f, x(n) logical :: packmolprecision call computef(n,x,f) packmolprecision = .false. if ( fdist < precision .and. frest < precision ) then packmolprecision = .true. end if end function packmolprecision packmol-20.010/polartocart.f90000066400000000000000000000055371360620542100161050ustar00rootroot00000000000000! ! Written by Leandro Martínez, 2009-2011. ! Copyright (c) 2009-2018, Leandro Martínez, Jose Mario Martinez, ! Ernesto G. Birgin. ! ! Subroutine eulerrmat: Computes the rotation matrix from the ! Euler angles ! ! Note that: ! In this routine, beta is a rotation about the y-axis ! gama is a rotation about the z-axis ! teta is a rotation about the x-axis subroutine eulerrmat(beta,gama,teta,v1,v2,v3) implicit none double precision :: beta, gama, teta double precision :: cb, sb, cg, sg, ct, st double precision :: v1(3), v2(3), v3(3) cb = dcos(beta) sb = dsin(beta) cg = dcos(gama) sg = dsin(gama) ct = dcos(teta) st = dsin(teta) v1(1)=-sb * sg * ct + cb * cg v1(2)=-sb * cg * ct - cb * sg v1(3)= sb * st v2(1)= cb * sg * ct + sb * cg v2(2)= cb * cg * ct - sb * sg v2(3)=-cb * st v3(1)= sg * st v3(2)= cg * st v3(3)= ct return end subroutine eulerrmat ! ! Subroutine compcart: Compute cartesian coordinates using ! the center of mass, the canonical coordinates ! and the rotation matrix ! subroutine compcart(icart,xbar,ybar,zbar,& xcoor,ycoor,zcoor,v1,v2,v3) use compute_data, only : xcart implicit none integer :: icart double precision :: xbar, ybar, zbar double precision :: xcoor, ycoor, zcoor double precision :: v1(3), v2(3), v3(3) xcart(icart,1) = xbar + xcoor*v1(1) + ycoor*v2(1) + zcoor*v3(1) xcart(icart,2) = ybar + xcoor*v1(2) + ycoor*v2(2) + zcoor*v3(2) xcart(icart,3) = zbar + xcoor*v1(3) + ycoor*v2(3) + zcoor*v3(3) return end subroutine compcart ! ! Subroutine eulerfixed: This routine was added because it defines ! the rotation in the "human" way, an is thus used ! to set the position of the fixed molecules. ! That means: beta is a counterclockwise rotation around x axis. ! gama is a counterclockwise rotation around y axis. ! teta is a counterclockwise rotation around z axis. ! The other routine should better do this as well, but then we need to change ! all the derivative calculations, just for the sake of human interpretation ! of the rotation which, in that case, is not really important. Maybe some day. ! subroutine eulerfixed(beta,gama,teta,v1,v2,v3) implicit none double precision :: beta, gama, teta double precision :: c1, s1, c2, s2, c3, s3 double precision :: v1(3), v2(3), v3(3) c1 = dcos(beta) s1 = dsin(beta) c2 = dcos(gama) s2 = dsin(gama) c3 = dcos(teta) s3 = dsin(teta) v1(1) = c2*c3 v1(2) = c1*s3 + c3*s1*s2 v1(3) = s1*s3 - c1*c3*s2 v2(1) = -c2*s3 v2(2) = c1*c3 - s1*s2*s3 v2(3) = c1*s2*s3 + c3*s1 v3(1) = s2 v3(2) = -c2*s1 v3(3) = c1*c2 return end subroutine eulerfixed packmol-20.010/random.f90000066400000000000000000000021311360620542100150160ustar00rootroot00000000000000! ! Written by Leandro Martínez, 2009-2011. ! Copyright (c) 2009-2018, Leandro Martínez, Jose Mario Martinez, ! Ernesto G. Birgin. ! ! ! Function that returns a real random number between 0. and 1. ! double precision function rnd() call random_number(rnd) return end function rnd ! ! Subroutine that initializes the random number generator given a seed ! subroutine init_random_number(iseed) integer :: size integer :: i, iseed integer, allocatable :: seed(:) call random_seed(size=size) allocate(seed(size)) do i = 1, size seed(i) = i*iseed end do call random_seed(put=seed) deallocate(seed) return end subroutine init_random_number ! ! Subroutine that uses the date to create a random seed ! subroutine seed_from_time(seed) implicit none integer :: seed, value(8) character(len=10) :: b(3) call date_and_time( b(1), b(2), b(3), value ) seed = value(1)+value(2)+value(3)+value(4)+value(5)+value(6)+value(7)+value(8) seed = seed + value(1)+value(2)+value(3)+value(4)+value(5)/100+value(6)*100+value(7)/10+value(8)*10 end subroutine seed_from_time packmol-20.010/release.sh000077500000000000000000000050201360620542100151750ustar00rootroot00000000000000#!/bin/bash #################################################################################################### # Software name: package=packmol # HTML file containing download list: downloads=/home/leandro/public_html/packmol/versionhistory/index.html # GIT URL: giturl=https://github.com/leandromartinez98/packmol # Name of file containing version number versionfile=./title.f90 #################################################################################################### #git log --pretty=oneline 16.323...16.330 | awk '{$1=""; print "-"$0}' year=`date +%y` day=`date +%j` version="${year:0:1}${year:1:1}.$day" file="$package-$version.tar.gz" version_file=$version i=2 while grep -q $file $downloads ; do file=$package-$version.$i.tar.gz version_file=$version.$i i=`expr $i + 1` done version=$version_file file=$package-$version.tar.gz echo "Will create file: $file" cat $versionfile | sed -e "s/Version.*/Version\ $version \')\")/" > version_title_temp.f90 \mv -f version_title_temp.f90 $versionfile git add -A . git commit -m "Changed version file to $version" git tag -a $version -m "Release $version" git push origin master tag $version today=`date +"%b %d, %Y"` changelog="https://github.com/leandromartinez98/$package/releases/tag/$version" newline=" $file Released on $today - [change log at github] " htmlfile=$downloads echo "------------------------------" echo "CREATING RELEASE IN HOME-PAGE:" echo "------------------------------" mkdir TEMP cd TEMP wget https://github.com/leandromartinez98/packmol/archive/$version.tar.gz tar -xf $version.tar.gz mv packmol-$version packmol tar -cf packmol.tar ./packmol gzip packmol.tar #scp packmol.tar.gz martinez@ssh.ime.unicamp.br:./public_html/packmol/ \cp -f packmol.tar.gz ~/public_html/m3g/packmol/packmol.tar.gz ~/public_html/m3g/update.sh cd .. \rm -rf ./TEMP writeline=yes while IFS= read -r line ; do if [ "$writeline" = "yes" ] ; then echo $line >> ./htmlfile_new_temp fi if [ $writeline = "no" ] ; then writeline="yes" fi if [[ $line == *NEW_VERSION_HERE* ]] ; then echo $newline >> ./htmlfile_new_temp fi done < "$htmlfile" rm $htmlfile mv htmlfile_new_temp $htmlfile echo "----------------------" echo "CHANGE LOG:" echo "----------------------" range=`git tag | tail -n 2 | xargs | sed 's! !...!'` git log --pretty=oneline $range | awk '{$1=""; print "-"$0}' echo "----------------------" echo " Done. " packmol-20.010/resetboxes.f90000066400000000000000000000013571360620542100157320ustar00rootroot00000000000000! ! Written by Leandro Martínez, 2009-2011. ! Copyright (c) 2009-2018, Leandro Martínez, Jose Mario Martinez, ! Ernesto G. Birgin. ! ! Subroutine resetboxes: Subroutine that resets the occupancy of ! linked cell boxes ! subroutine resetboxes() use sizes use compute_data, only : latomfirst, latomfix, & lboxfirst, lboxnext, hasfree implicit none integer :: i, j, k, ibox ! Reset data for boxes that contain fixed atom ibox = lboxfirst do while( ibox > 0 ) call ibox_to_ijk(ibox,i,j,k) latomfirst(i,j,k) = latomfix(i,j,k) hasfree(i,j,k) = .false. ibox = lboxnext(ibox) end do lboxfirst = 0 end subroutine resetboxes packmol-20.010/restmol.f90000066400000000000000000000037301360620542100152310ustar00rootroot00000000000000! ! Written by Leandro Martínez, 2009-2011. ! Copyright (c) 2009-2018, Leandro Martínez, Jose Mario Martinez, ! Ernesto G. Birgin. ! ! subroutine restmol: either compute the restraint function ! value for a single molecule or solve ! the problem of puting this molecule ! in the restraint region ! subroutine restmol(itype,ilubar,n,x,fx,solve) use sizes use compute_data use usegencan implicit none integer :: n, nsafe, ntotsafe, itype, i, ilubar, nmoltype, ip1, ip2 double precision :: x(n), fx logical :: solve, initsafe ! Saving global problem variables nsafe = n ntotsafe = ntotmol nmoltype = nmols(itype) do i = 1, ntype compsafe(i) = comptype(i) end do initsafe = init1 ! Preparing system to solve for this molecule n = 6 ntotmol = 1 nmols(itype) = 1 xmol(1) = x(ilubar+1) xmol(2) = x(ilubar+2) xmol(3) = x(ilubar+3) xmol(4) = x(ilubar+ntotsafe*3+1) xmol(5) = x(ilubar+ntotsafe*3+2) xmol(6) = x(ilubar+ntotsafe*3+3) do i = 1, ntype if(i.eq.itype) then comptype(i) = .true. else comptype(i) = .false. end if end do init1 = .true. ! If not going to solve the problem, compute energy and return if(.not.solve) then call computef(n,xmol,fx) ! Otherwise, put this molecule in its constraints else ip1 = iprint1 ip2 = iprint2 iprint1 = 0 iprint2 = 0 call pgencan(n,xmol,fx) iprint1 = ip1 iprint2 = ip2 end if ! Restoring original problem data ntotmol = ntotsafe n = nsafe nmols(itype) = nmoltype x(ilubar+1) = xmol(1) x(ilubar+2) = xmol(2) x(ilubar+3) = xmol(3) x(ilubar+ntotmol*3+1) = xmol(4) x(ilubar+ntotmol*3+2) = xmol(5) x(ilubar+ntotmol*3+3) = xmol(6) do i = 1, ntype comptype(i) = compsafe(i) end do init1 = initsafe return end subroutine restmol packmol-20.010/setibox.f90000066400000000000000000000015241360620542100152200ustar00rootroot00000000000000! ! Written by Leandro Martínez, 2009-2011. ! Copyright (c) 2009-2018, Leandro Martínez, Jose Mario Martinez, ! Ernesto G. Birgin. ! ! Subroutine setibox: set box index for given coordinates ! subroutine setibox(x,y,z,sizemin,boxl,nboxes,iboxx,iboxy,iboxz) implicit none double precision :: x, y, z, sizemin(3), boxl(3), xtemp, ytemp, ztemp integer :: nboxes(3), iboxx, iboxy, iboxz xtemp = x - sizemin(1) ytemp = y - sizemin(2) ztemp = z - sizemin(3) iboxx = int(xtemp/boxl(1)) + 1 iboxy = int(ytemp/boxl(2)) + 1 iboxz = int(ztemp/boxl(3)) + 1 if(xtemp.le.0) iboxx = 1 if(ytemp.le.0) iboxy = 1 if(ztemp.le.0) iboxz = 1 if(iboxx.gt.nboxes(1)) iboxx = nboxes(1) if(iboxy.gt.nboxes(2)) iboxy = nboxes(2) if(iboxz.gt.nboxes(3)) iboxz = nboxes(3) return end subroutine setibox packmol-20.010/setijk.f90000066400000000000000000000017731360620542100150420ustar00rootroot00000000000000! ! Written by Leandro Martínez, 2009-2011. ! Copyright (c) 2009-2018, Leandro Martínez, Jose Mario Martinez, ! Ernesto G. Birgin. ! ! Subroutines that set the indexes of a three-dimensional array ! given the undimensional counter of the vector (for an array ! with dimensions (0:nboxes(1)+1,0:nboxes(2)+1,0:nboxes(3)+1), and ! vice-versa. ! subroutine ibox_to_ijk(ibox,i,j,k) use compute_data, only : nb2 implicit none integer :: ibox, i, j, k, iibox k = mod(ibox,nb2(3)) if ( k == 0 ) k = nb2(3) iibox = ibox - k iibox = iibox / nb2(3) + 1 j = mod(iibox,nb2(2)) if ( j == 0 ) j = nb2(2) iibox = iibox - j iibox = iibox / nb2(2) + 1 i = mod(iibox,nb2(1)) if ( i == 0 ) i = nb2(1) k = k - 1 j = j - 1 i = i - 1 end subroutine ibox_to_ijk subroutine ijk_to_ibox(i,j,k,ibox) use compute_data, only : nb2 implicit none integer :: i, j, k, ibox ibox = i*nb2(2)*nb2(3) + j*nb2(3) + k + 1 end subroutine ijk_to_ibox packmol-20.010/setsizes.f90000066400000000000000000000224641360620542100154220ustar00rootroot00000000000000! ! Written by Leandro Martínez, 2009-2011. ! Copyright (c) 2009-2018, Leandro Martínez, Jose Mario Martinez, ! Ernesto G. Birgin. ! ! Subroutine that sets the sizes of all allocatable arrays ! subroutine setsizes() use sizes use compute_data use input use usegencan use flashsort implicit none integer :: i, ival, ilast, iline, itype integer :: ioerr integer :: strlength character(len=200) :: record, word, blank, alltospace logical :: inside_structure ! Instructions on how to run packmol write(*,*) ' Packmol must be run with: packmol < inputfile.inp ' write(*,*) write(*,*) ' Userguide at: http://m3g.iqm.unicamp.br/packmol ' write(*,*) ! Getting input lines from the input file write(*,*) ' Reading input file... (Control-C aborts)' do i = 1, 200 blank(i:i) = ' ' end do nlines = 0 maxkeywords = 0 ntype = 0 do read(5,"(a200)",iostat=ioerr) record ! Replace any strange blank character by spaces record = alltospace(record) if ( ioerr /= 0 ) exit ! Remove comments i = 0 do while( i < 200 ) i = i + 1 if ( record(i:i) == '#' ) exit end do i = i - 1 if ( i > 0 ) then record = record(1:i)//blank(i+1:200) else cycle end if if ( strlength(record) < 1 ) cycle ! Number of lines of the input file nlines = nlines + 1 ! Check the number of keywords in this line i = 0 ival = 0 do while(i < 200) i = i + 1 ilast = i do while(record(i:i) > ' ' .and. i < 200) i = i + 1 end do if(i > ilast) then ival = ival + 1 maxkeywords = max(maxkeywords,ival) end if end do end do rewind(5) allocate(inputfile(nlines),keyword(nlines,maxkeywords)) ! Read input to inputfile array iline = 0 do read(5,"(a200)",iostat=ioerr) record if ( ioerr /= 0 ) exit ! Convert all strange blank characters to spaces record = alltospace(record) ! Remove comments i = 0 do while( i < 200 ) i = i + 1 if ( record(i:i) == '#' ) exit end do i = i - 1 if ( i > 0 ) then record = record(1:i)//blank(i+1:200) else cycle end if if ( strlength(record) < 1 ) cycle iline = iline + 1 inputfile(iline) = record end do ! Read all keywods into keyword array call getkeywords() ! Checking the filetype of coordinate files (default is pdb) tinker = .false. pdb = .false. xyz = .false. moldy = .false. fbins = dsqrt(3.d0) do i = 1, nlines if(keyword(i,1).eq.'filetype') then if(keyword(i,2).eq.'tinker') tinker = .true. if(keyword(i,2).eq.'pdb') pdb = .true. if(keyword(i,2).eq.'xyz') xyz = .true. if(keyword(i,2).eq.'moldy') moldy = .true. end if if(keyword(i,1).eq.'fbins') then record = keyword(i,2) read(record,*,iostat=ioerr) fbins if ( ioerr /= 0 ) then write(*,*) ' ERROR: Invalid value for fbins. ' stop end if end if end do if(.not.pdb.and..not.tinker.and..not.xyz.and..not.moldy) then pdb = .true. write(*,*) write(*,*)' WARNING: File type not (correctly?) specified, using PDB' end if ! Getting the number of different types of molecules ntype = 0 do iline = 1, nlines if ( keyword(iline,1) == "structure" ) then ntype = ntype + 1 if ( keyword(iline,2) == "none" ) then write(*,*) ' ERROR: structure without filename. ' write(*,*) ' The syntax must be, for example: structure water.pdb ' stop end if end if end do allocate(nmols(ntype),natoms(ntype),idfirst(ntype),constrain_rot(ntype,3),& rot_bound(ntype,3,2),dmax(ntype),& cmxmin(ntype),cmymin(ntype),cmzmin(ntype),& cmxmax(ntype),cmymax(ntype),cmzmax(ntype),& comptype(ntype),compsafe(ntype),& restart_from(0:ntype),restart_to(0:ntype),& nloop_type(ntype),nloop0_type(ntype)) ! Reading the number of molecules of each type, and the number of atoms ! of each molecule type itype = 0 inside_structure = .false. do iline = 1, nlines if ( keyword(iline,1) == "structure" ) then inside_structure = .true. itype = itype + 1 natoms(itype) = 0 nmols(itype) = 0 nloop_type(itype) = 0 nloop0_type(itype) = 0 ! Read the number of atoms of this type of molecule open(10,file=keyword(iline,2),status='old',iostat=ioerr) if( ioerr /= 0 ) call failopen(keyword(iline,2)) if ( pdb ) then do read(10,"(a200)",iostat=ioerr) record if ( ioerr /= 0 ) exit if ( record(1:4) == "ATOM" .or. record(1:6) == "HETATM" ) then natoms(itype) = natoms(itype) + 1 end if end do end if if ( tinker ) then do read(10,*,iostat=ioerr) i if ( ioerr /= 0 ) cycle natoms(itype) = i exit end do end if if ( xyz ) then read(10,*,iostat=ioerr) i if ( ioerr == 0 ) natoms(itype) = i end if if ( moldy ) then read(10,*,iostat=ioerr) word, i if ( ioerr == 0 ) natoms(itype) = i end if close(10) if ( natoms(itype) == 0 ) then write(*,*) ' ERROR: Could not read any atom from file: ', & trim(adjustl(keyword(iline,2))) end if end if if ( keyword(iline,1) == "end" .and. & keyword(iline,2) == "structure" ) inside_structure = .false. ! Read number of molecules for each type if ( keyword(iline,1) == "number" ) then read(keyword(iline,2),*,iostat=ioerr) nmols(itype) if ( ioerr /= 0 ) then write(*,*) ' ERROR: Error reading number of molecules of type ', itype stop end if if ( nmols(itype) < 1 ) then write(*,*) ' ERROR: Number of molecules of type ', itype, ' set to less than 1 ' stop end if end if ! Read the (optional) number of gencan loops for this molecule if ( keyword(iline,1) == "nloop" ) then if ( inside_structure ) then read(keyword(iline,2),*,iostat=ioerr) nloop_type(itype) if ( ioerr /= 0 ) then write(*,*) ' ERROR: Error reading number of loops of type ', itype stop end if if ( nloop_type(itype) < 1 ) then write(*,*) ' ERROR: Number of loops of type ', itype, ' set to less than 1 ' stop end if end if end if ! Read the (optional) number of gencan loops for initial setup for this molecule if ( keyword(iline,1) == "nloop0" ) then if ( inside_structure ) then read(keyword(iline,2),*,iostat=ioerr) nloop0_type(itype) if ( ioerr /= 0 ) then write(*,*) ' ERROR: Error reading number of loops-0 of type ', itype stop end if if ( nloop0_type(itype) < 1 ) then write(*,*) ' ERROR: Number of loops-0 of type ', itype, ' set to less than 1 ' stop end if end if end if end do do itype = 1, ntype if ( nmols(itype) == 0 ) then write(*,*) ' Warning: Number of molecules not set for type '& ,itype,': assuming 1 ' nmols(itype) = 1 end if end do ! Total number of atoms and molecules ntotat = 0 ntotmol = 0 do itype = 1, ntype ntotat = ntotat + nmols(itype)*natoms(itype) ntotmol = ntotmol + nmols(itype) end do ! The number of variables of the problem nn = ntotmol*6 ! The number of bins of the linked cell method in each direction nbp = int((fbins*dble(ntotat))**(1.d0/3.d0)) + 1 ! Allocate arrays depending on nbp parameter allocate(latomfirst(0:nbp+1,0:nbp+1,0:nbp+1),& latomfix(0:nbp+1,0:nbp+1,0:nbp+1),& hasfree(0:nbp+1,0:nbp+1,0:nbp+1),& lboxnext((nbp+2)**3)) ! Checking the total number of restrictions defined i = 0 do iline = 1, nlines if ( keyword(iline,1) == 'fixed' .or. & keyword(iline,1) == 'inside' .or. & keyword(iline,1) == 'outside' .or. & keyword(iline,1) == 'over' .or. & keyword(iline,1) == 'below' .or. & keyword(iline,1) == 'constrain_rotation' ) then i = i + 1 end if end do maxrest = i mrperatom = i ! Allocate arrays depending on ntotat, nn, maxrest, and mrperatom allocate(nratom(ntotat),iratom(ntotat,mrperatom),ibmol(ntotat),& ibtype(ntotat),xcart(ntotat,3),coor(ntotat,3),& radius(ntotat),radius_ini(ntotat),fscale(ntotat),& use_short_radius(ntotat), short_radius(ntotat), short_radius_scale(ntotat),& gxcar(ntotat,3),& latomnext(ntotat),& fdist_atom(ntotat), frest_atom(ntotat),& fmol(ntotat),radiuswork(ntotat),& fixedatom(ntotat)) allocate(ityperest(maxrest),restpars(maxrest,9)) allocate(xmol(nn)) ! Allocate other arrays used for input and output data allocate(nconnect(ntotat,9),maxcon(ntotat),& amass(ntotat),charge(ntotat),ele(ntotat)) allocate(irestline(maxrest),linestrut(ntype,2),resnumbers(ntype),& input_itype(ntype),changechains(ntype),chain(ntype),& fixedoninput(ntype),pdbfile(ntype),name(ntype),& segid(ntype)) ! Allocate vectors for flashsort allocate(indflash(ntotat),lflash(ntotat)) ! Allocate arrays for GENCAN allocate(l(nn),u(nn),wd(8*nn),wi(nn),g(nn)) end subroutine setsizes packmol-20.010/sizes.f90000066400000000000000000000014571360620542100147050ustar00rootroot00000000000000! ! Written by Leandro Martínez, 2009-2011. ! Copyright (c) 2009-2018, Leandro Martínez, Jose Mario Martinez, ! Ernesto G. Birgin. ! ! ! sizes.i: Define the maximum dimensions of the problems ! ! maxrest: Maximum number of restrictions ! mrperatom: Maximum number of restrictions per atom ! maxtry: Number of tries for building the initial point ! nbp: Maximum number of boxes for fast function evaluation (nbp**3) ! nn: Maximum number of variables ! (at least the number of molecules*6) ! maxkeywords: Maximum number of keywords in input file ! module sizes integer :: maxrest integer :: mrperatom integer :: maxtry integer :: nbp integer :: nn integer :: maxkeywords end module sizes packmol-20.010/solvate.tcl000077500000000000000000004010121360620542100154030ustar00rootroot00000000000000#!/usr/bin/tclsh # # This scripts writes a input file for packmol, and runs packmol, # that automatically setup # a solvation shell with 0.16 sodium and chloride concentrations such # that the whole system is neutral, considering neutral histidines and # charged # # Make it executable with: chmod +x solvate.tcl # Run with: ./solvate.tcl structure.pdb -shell 15. -charge +5 -density 1.0 -o solvated.pdb # # Where: # structure.pdb is the pdb file to be solvated (usually a protein) # # "15." is the size of the solvation shell. This # is an optional parameter. If not set, 15. will be used. # # +5 is the total charge of the system, to be neutralized. # This is also and optional parameter, if not used, the package # considers histidine residues as neutral, Arg and Lys as +1 # and Glu and Asp as -1, and sets up the Sodium and Chloride # concentrations automatically. # Alternatively, use the -noions to not add any ions, just water. # # 1.0 is the desired density. Optional. If not set, the density # will be set to 1.0 g/ml. # # solvated.pdb: is the (optional) name for the solvated system output # file. If this argument is not provided, it will be the default # "solvated.pdb" file. # # pack.inp: is the (optional) name for the packmol input file that # will be generated. If not provided, packmol_input.inp will be used. # # L. Martinez, Aug 2, 2011. (leandromartinez98@gmail.com) # set args [ split $argv " " ] set iarg 0 foreach arg $args { if { [ string trim $arg ] > " " } { incr iarg set input_argument($iarg) $arg } } if { $iarg == 0 } { puts " " puts " Solvate.tcl script for Packmol " puts " " puts " Run with: " puts " " puts " solvate.tcl structure.pdb -shell 15. -charge +5 -density 1.0 -i pack.inp -o solvated.pdb" puts " Where: structure.pdb is the pdb file to be solvated (usually a protein) \"15.\" is the size of the solvation shell. This is an optional parameter. If not set, 15. will be used. +5 is the total charge of the system, to be neutralized. This is also and optional parameter, if not used, the package considers histidine residues as neutral, Arg and Lys as +1 and Glu and Asp as -1. The Na+ and Cl- concentrations are set the closest possible to 0.16M, approximately the physiological concentration. Alternatively, use the -noions to not add any ions, just water. 1.0 is the desired density. Optional. If not set, the density will be set to 1.0 g/ml. solvated.pdb: is the (optional) name for the solvated system output file. If this argument is not provided, it will be the default solvated.pdb file. pack.inp: is the (optional) name for the packmol input file that will be generated. If not provided, packmol_input.inp will be used. " exit } set pdb_file $input_argument(1) set charge "none" set shell "none" set density "none" set output "solvated.pdb" set packmol_input "packmol_input.inp" set noions "false" for { set i 2 } { $i <= $iarg } { incr i } { if { $input_argument($i) == "-charge" } { set charge $input_argument([expr $i + 1]) } if { $input_argument($i) == "-shell" } { set shell $input_argument([expr $i + 1]) } if { $input_argument($i) == "-density" } { set density $input_argument([expr $i + 1]) } if { $input_argument($i) == "-o" } { set output $input_argument([expr $i + 1]) } if { $input_argument($i) == "-i" } { set packmol_input $input_argument([expr $i + 1]) } if { $input_argument($i) == "-noions" } { set noions "true" } } puts " ###########################################################################" puts " solvate.tcl script: Solvates a (protein) structure with water and ions," puts " using Packmol. " puts " ###########################################################################" puts " Input pdb file to be solvated: $pdb_file " puts -nonewline " User set structure charge: $charge " if { $charge == "none" } { puts " - will compute from structure. " } else { puts " " } puts -nonewline " User set shell size: $shell " if { $shell == "none" } { puts " - using default: 15.0 Angs. " } else { puts " " } puts -nonewline " User set density: $density " if { $density == "none" } { puts " - using default: 1.0 g/ml " } else { puts " " } # If the user didn't set the sell size, use default one if { $shell == "none" } { set shell 15. } # # Computing the size of the structure (maximum and minimum size on each direction) # set pdb_file_name $pdb_file set pdb_file [ open $pdb_file r ] set pdb_file [ read $pdb_file ] set pdb_file [ split $pdb_file "\n" ] set natoms 0 foreach line $pdb_file { if { [ string range $line 0 3 ] == "ATOM" | [ string range $line 0 5 ] == "HETATM" } { incr natoms set x [ string trim [ string range $line 30 37 ] ] set y [ string trim [ string range $line 38 45 ] ] set z [ string trim [ string range $line 46 54 ] ] if { [ info exists xmin ] == 1 } { if { $x < $xmin } { set xmin $x } if { $y < $ymin } { set ymin $y } if { $z < $zmin } { set zmin $z } if { $x > $xmax } { set xmax $x } if { $y > $ymax } { set ymax $y } if { $z > $zmax } { set zmax $z } } else { set xmin $x set ymin $y set zmin $z set xmax $x set ymax $y set zmax $z } } } set x_length [ expr $xmax - $xmin + 2.0*$shell ] set y_length [ expr $ymax - $ymin + 2.0*$shell ] set z_length [ expr $zmax - $zmin + 2.0*$shell ] puts " -------------------------------------------------------" puts " Minimum and maximum coordinates of structure atoms " puts " X_min = $xmin X_max = $xmax " puts " Y_min = $ymin Y_max = $ymax " puts " Z_min = $zmin Z_max = $zmax " puts " -------------------------------------------------------" puts " Box side length in each direction: " puts " x: $x_length " puts " y: $y_length " puts " z: $z_length " puts " -------------------------------------------------------" # # If the user didn't set the total charge of the system, compute the charge # if { $charge == "none" } { set charge 0 set number 0 set nhis 0; set narg 0; set nlys 0; set nglu 0; set nasp 0 foreach line $pdb_file { set amino [string range $line 17 19] if { [ string trim [ string range $line 12 15 ] ] == "N" } { if { $amino == "HIS" } { incr nhis } if { $amino == "HSD" } { incr nhis } if { $amino == "ARG" } { set charge [expr $charge + 1]; incr narg } if { $amino == "LYS" } { set charge [expr $charge + 1]; incr nlys } if { $amino == "GLU" } { set charge [expr $charge - 1]; incr nglu } if { $amino == "ASP" } { set charge [expr $charge - 1]; incr nasp } } } puts " -------------------------------------------------------" puts " HIS = $nhis (associated charge = 0) " puts " ARG = $narg (associated charge = +$narg) " puts " LYS = $nlys (associated charge = +$nlys) " puts " GLU = $nglu (associated charge = -$nglu) " puts " ASP = $nasp (associated charge = -$nasp) " puts " -------------------------------------------------------" puts " Total structure charge = $charge" puts " -------------------------------------------------------" } # # Compute the molar mass of the structure # foreach data { \ "H 1.00800 " \ "HC 1.00800 " \ "HA 1.00800 " \ "HT 1.00800 " \ "HP 1.00800 " \ "HB 1.00800 " \ "HR1 1.00800 " \ "HR2 1.00800 " \ "HR3 1.00800 " \ "HS 1.00800 " \ "HE1 1.00800 " \ "HE2 1.00800 " \ "HA1 1.00800 " \ "HA2 1.00800 " \ "HA3 1.00800 " \ "HF1 1.00800 " \ "HF2 1.00800 " \ "C 12.01100 " \ "CA 12.01100 " \ "CT1 12.01100 " \ "CT2 12.01100 " \ "CT3 12.01100 " \ "CPH1 12.01100 " \ "CPH2 12.01100 " \ "CPT 12.01100 " \ "CY 12.01100 " \ "CP1 12.01100 " \ "CP2 12.01100 " \ "CP3 12.01100 " \ "CC 12.01100 " \ "CD 12.01100 " \ "CPA 12.01100 " \ "CPB 12.01100 " \ "CPM 12.01100 " \ "CM 12.01100 " \ "CS 12.01100 " \ "CE1 12.01100 " \ "CE2 12.01100 " \ "CST 12.01100 " \ "CT 12.01100 " \ "CT1x 12.01100 " \ "CT2x 12.01100 " \ "CT3x 12.01100 " \ "CN 12.01100 " \ "CAP 12.01100 " \ "COA 12.01100 " \ "C3 12.01100 " \ "N 14.00700 " \ "NR1 14.00700 " \ "NR2 14.00700 " \ "NR3 14.00700 " \ "NH1 14.00700 " \ "NH2 14.00700 " \ "NH3 14.00700 " \ "NC2 14.00700 " \ "NY 14.00700 " \ "NP 14.00700 " \ "NPH 14.00700 " \ "NC 14.00700 " \ "O 15.99900 " \ "OB 15.99900 " \ "OC 15.99900 " \ "OH1 15.99900 " \ "OS 15.99940 " \ "OT 15.99940 " \ "OM 15.99900 " \ "OST 15.99900 " \ "OCA 15.99900 " \ "S 32.06000 " \ "SM 32.06000 " \ "SS 32.06000 " \ "HE 4.00260 " \ "NE 20.17970 " \ "CF1 12.01100 " \ "CF2 12.01100 " \ "CF3 12.01100 " \ "FE 55.84700 " \ "CLAL 35.45300 " \ "FA 18.99800 " \ "F1 18.99800 " \ "F2 18.99800 " \ "F3 18.99800 " \ "DUM 0.00000 " \ "SOD 22.989770 " \ "MG 24.305000 " \ "POT 39.102000 " \ "CES 132.900000 " \ "CAL 40.080000 " \ "CLA 35.450000 " \ "ZN 65.370000 " \ "H 1.00800 " \ "HC 1.00800 " \ "HA 1.00800 " \ "HT 1.00800 " \ "HP 1.00800 " \ "HB 1.00800 " \ "HR1 1.00800 " \ "HR2 1.00800 " \ "HR3 1.00800 " \ "HS 1.00800 " \ "HE1 1.00800 " \ "HE2 1.00800 " \ "HA1 1.00800 " \ "HA2 1.00800 " \ "HA3 1.00800 " \ "HF1 1.00800 " \ "HF2 1.00800 " \ "C 12.01100 " \ "CA 12.01100 " \ "CT1 12.01100 " \ "CT2 12.01100 " \ "CT3 12.01100 " \ "CPH1 12.01100 " \ "CPH2 12.01100 " \ "CPT 12.01100 " \ "CY 12.01100 " \ "CP1 12.01100 " \ "CP2 12.01100 " \ "CP3 12.01100 " \ "CC 12.01100 " \ "CD 12.01100 " \ "CPA 12.01100 " \ "CPB 12.01100 " \ "CPM 12.01100 " \ "CM 12.01100 " \ "CS 12.01100 " \ "CE1 12.01100 " \ "CE2 12.01100 " \ "CST 12.01100 " \ "CT 12.01100 " \ "CT1x 12.01100 " \ "CT2x 12.01100 " \ "CT3x 12.01100 " \ "CN 12.01100 " \ "CAP 12.01100 " \ "COA 12.01100 " \ "C3 12.01100 " \ "N 14.00700 " \ "NR1 14.00700 " \ "NR2 14.00700 " \ "NR3 14.00700 " \ "NH1 14.00700 " \ "NH2 14.00700 " \ "NH3 14.00700 " \ "NC2 14.00700 " \ "NY 14.00700 " \ "NP 14.00700 " \ "NPH 14.00700 " \ "NC 14.00700 " \ "O 15.99900 " \ "OB 15.99900 " \ "OC 15.99900 " \ "OH1 15.99900 " \ "OS 15.99940 " \ "OT 15.99940 " \ "OM 15.99900 " \ "OST 15.99900 " \ "OCA 15.99900 " \ "S 32.06000 " \ "SM 32.06000 " \ "SS 32.06000 " \ "HE 4.00260 " \ "NE 20.17970 " \ "CF1 12.01100 " \ "CF2 12.01100 " \ "CF3 12.01100 " \ "FE 55.84700 " \ "CLAL 35.45300 " \ "FA 18.99800 " \ "F1 18.99800 " \ "F2 18.99800 " \ "F3 18.99800 " \ "DUM 0.00000 " \ "SOD 22.989770 " \ "MG 24.305000 " \ "POT 39.102000 " \ "CES 132.900000 " \ "CAL 40.080000 " \ "CLA 35.450000 " \ "ZN 65.370000 " \ "HT 1.00800 " \ "OT 15.99940 " \ "HAS 1.00800 " \ "HOS 1.00800 " \ "CTS 12.01100 " \ "CBS 12.01100 " \ "OHS 15.99940 " \ "OES 15.99940 " \ "OXT 15.99940 " \ "HL 1.008000 " \ "HCL 1.008000 " \ "HT 1.008000 " \ "HOL 1.008000 " \ "HAL1 1.008000 " \ "HAL2 1.008000 " \ "HAL3 1.008000 " \ "HEL1 1.008000 " \ "HEL2 1.008000 " \ "CL 12.011000 " \ "CTL1 12.011000 " \ "CTL2 12.011000 " \ "CTL3 12.011000 " \ "CTL5 12.011000 " \ "CEL1 12.011000 " \ "CEL2 12.011000 " \ "NTL 14.007000 " \ "NH3L 14.007000 " \ "OBL 15.999400 " \ "OCL 15.999400 " \ "OT 15.999400 " \ "OSL 15.999400 " \ "O2L 15.999400 " \ "OHL 15.999400 " \ "PL 30.974000 " \ "SL 32.060000 " \ "SOD 22.989770 " \ "MG 24.305000 " \ "POT 39.102000 " \ "CES 132.900000 " \ "CAL 40.080000 " \ "CLA 35.450000 " \ "ZN 65.370000 " \ "DUM 0.000000 " \ "HT 1.008000 " \ "HN1 1.008000 " \ "HN2 1.008000 " \ "HN3 1.008000 " \ "HN3B 1.008000 " \ "HN3C 1.008000 " \ "HNP 1.008000 " \ "HN4 1.008000 " \ "HN5 1.008000 " \ "HN6 1.008000 " \ "HN7 1.008000 " \ "HN8 1.008000 " \ "HN9 1.008000 " \ "HNE1 1.008000 " \ "HNE2 1.008000 " \ "CN1 12.011000 " \ "CN1A 12.011000 " \ "CN1T 12.011000 " \ "CN2 12.011000 " \ "CN3 12.011000 " \ "CN3A 12.011000 " \ "CN3B 12.011000 " \ "CN3C 12.011000 " \ "CN3D 12.011000 " \ "CN3T 12.011000 " \ "CN4 12.011000 " \ "CN5 12.011000 " \ "CN5G 12.011000 " \ "CN7 12.011000 " \ "CN7B 12.011000 " \ "CN7C 12.011000 " \ "CN7D 12.011000 " \ "CN8 12.011000 " \ "CN8B 12.011000 " \ "CN9 12.011000 " \ "CNE1 12.011000 " \ "CNE2 12.011000 " \ "CNA 12.011000 " \ "CNA2 12.011000 " \ "CN6 12.011000 " \ "CN7E 12.011000 " \ "NN1 14.007000 " \ "NN1C 14.007000 " \ "NN2 14.007000 " \ "NN2B 14.007000 " \ "NN2C 14.007000 " \ "NN2U 14.007000 " \ "NN2G 14.007000 " \ "NN3 14.007000 " \ "NN3A 14.007000 " \ "NN3I 14.007000 " \ "NN3G 14.007000 " \ "NN4 14.007000 " \ "NN5 14.007000 " \ "NN6 14.007000 " \ "OT 15.999400 " \ "ON1 15.999400 " \ "ON1C 15.999400 " \ "ON2 15.999400 " \ "ON3 15.999400 " \ "ON4 15.999400 " \ "ON5 15.999400 " \ "ON6 15.999400 " \ "ON6B 15.999400 " \ "ON2B 15.999400 " \ "FN1 18.998400 " \ "FNA 18.998400 " \ "P 30.974000 " \ "P2 30.974000 " \ "P3 30.974000 " \ "SOD 22.989770 " \ "MG 24.305000 " \ "POT 39.102000 " \ "CES 132.900000 " \ "CAL 40.080000 " \ "CLA 35.450000 " \ "ZN 65.370000 " \ "DUM 0.001 " \ "CPH1 12.011000 " \ "CPH2 12.011000 " \ "HR3 1.008000 " \ "HR1 1.008000 " \ "NR1 14.007000 " \ "NR2 14.007000 " \ "HL 1.008000 " \ "HCL 1.008000 " \ "HT 1.008000 " \ "HOL 1.008000 " \ "HAL1 1.008000 " \ "HAL2 1.008000 " \ "HAL3 1.008000 " \ "HEL1 1.008000 " \ "HEL2 1.008000 " \ "CL 12.011000 " \ "CTL1 12.011000 " \ "CTL2 12.011000 " \ "CTL3 12.011000 " \ "CTL5 12.011000 " \ "CEL1 12.011000 " \ "CEL2 12.011000 " \ "NTL 14.007000 " \ "NH3L 14.007000 " \ "OBL 15.999400 " \ "OCL 15.999400 " \ "OT 15.999400 " \ "OSL 15.999400 " \ "O2L 15.999400 " \ "OHL 15.999400 " \ "PL 30.974000 " \ "SL 32.060000 " \ "CPH1 12.011000 " \ "CPH2 12.011000 " \ "HR3 1.008000 " \ "HR1 1.008000 " \ "NR1 14.007000 " \ "NR2 14.007000 " \ "HT 1.008000 " \ "HN1 1.008000 " \ "HN2 1.008000 " \ "HN3 1.008000 " \ "HN3B 1.008000 " \ "HN3C 1.008000 " \ "HNP 1.008000 " \ "HN4 1.008000 " \ "HN5 1.008000 " \ "HN6 1.008000 " \ "HN7 1.008000 " \ "HN8 1.008000 " \ "HN9 1.008000 " \ "HNE1 1.008000 " \ "HNE2 1.008000 " \ "CN1 12.011000 " \ "CN1A 12.011000 " \ "CN1T 12.011000 " \ "CN2 12.011000 " \ "CN3 12.011000 " \ "CN3A 12.011000 " \ "CN3B 12.011000 " \ "CN3C 12.011000 " \ "CN3D 12.011000 " \ "CN3T 12.011000 " \ "CN4 12.011000 " \ "CN5 12.011000 " \ "CN5G 12.011000 " \ "CN7 12.011000 " \ "CN7B 12.011000 " \ "CN7C 12.011000 " \ "CN7D 12.011000 " \ "CN8 12.011000 " \ "CN8B 12.011000 " \ "CN9 12.011000 " \ "CNE1 12.011000 " \ "CNE2 12.011000 " \ "CNA 12.011000 " \ "CNA2 12.011000 " \ "CN6 12.011000 " \ "CN7E 12.011000 " \ "NN1 14.007000 " \ "NN1C 14.007000 " \ "NN2 14.007000 " \ "NN2B 14.007000 " \ "NN2C 14.007000 " \ "NN2U 14.007000 " \ "NN2G 14.007000 " \ "NN3 14.007000 " \ "NN3A 14.007000 " \ "NN3I 14.007000 " \ "NN3G 14.007000 " \ "NN4 14.007000 " \ "NN5 14.007000 " \ "NN6 14.007000 " \ "OT 15.999400 " \ "ON1 15.999400 " \ "ON1C 15.999400 " \ "ON2 15.999400 " \ "ON3 15.999400 " \ "ON4 15.999400 " \ "ON5 15.999400 " \ "ON6 15.999400 " \ "ON6B 15.999400 " \ "ON2B 15.999400 " \ "FN1 18.998400 " \ "FNA 18.998400 " \ "P 30.974000 " \ "P2 30.974000 " \ "P3 30.974000 " \ "SOD 22.989770 " \ "MG 24.305000 " \ "POT 39.102000 " \ "CES 132.900000 " \ "CAL 40.080000 " \ "CLA 35.450000 " \ "ZN 65.370000 " \ "DUM 0.001 " \ "CPH1 12.011000 " \ "CPH2 12.011000 " \ "HR3 1.008000 " \ "HR1 1.008000 " \ "NR1 14.007000 " \ "NR2 14.007000 " \ "H 1.00800 " \ "HC 1.00800 " \ "HA 1.00800 " \ "HT 1.00800 " \ "HP 1.00800 " \ "HB 1.00800 " \ "HR1 1.00800 " \ "HR2 1.00800 " \ "HR3 1.00800 " \ "HS 1.00800 " \ "HE1 1.00800 " \ "HE2 1.00800 " \ "HA1 1.00800 " \ "HA2 1.00800 " \ "HA3 1.00800 " \ "HF1 1.00800 " \ "HF2 1.00800 " \ "C 12.01100 " \ "CA 12.01100 " \ "CT1 12.01100 " \ "CT2 12.01100 " \ "CT3 12.01100 " \ "CPH1 12.01100 " \ "CPH2 12.01100 " \ "CPT 12.01100 " \ "CY 12.01100 " \ "CP1 12.01100 " \ "CP2 12.01100 " \ "CP3 12.01100 " \ "CC 12.01100 " \ "CD 12.01100 " \ "CPA 12.01100 " \ "CPB 12.01100 " \ "CPM 12.01100 " \ "CM 12.01100 " \ "CS 12.01100 " \ "CE1 12.01100 " \ "CE2 12.01100 " \ "CST 12.01100 " \ "CT 12.01100 " \ "CT1x 12.01100 " \ "CT2x 12.01100 " \ "CT3x 12.01100 " \ "CN 12.01100 " \ "CAP 12.01100 " \ "COA 12.01100 " \ "C3 12.01100 " \ "N 14.00700 " \ "NR1 14.00700 " \ "NR2 14.00700 " \ "NR3 14.00700 " \ "NH1 14.00700 " \ "NH2 14.00700 " \ "NH3 14.00700 " \ "NC2 14.00700 " \ "NY 14.00700 " \ "NP 14.00700 " \ "NPH 14.00700 " \ "NC 14.00700 " \ "O 15.99900 " \ "OB 15.99900 " \ "OC 15.99900 " \ "OH1 15.99900 " \ "OS 15.99940 " \ "OT 15.99940 " \ "OM 15.99900 " \ "OST 15.99900 " \ "OCA 15.99900 " \ "S 32.06000 " \ "SM 32.06000 " \ "SS 32.06000 " \ "HE 4.00260 " \ "NE 20.17970 " \ "CF1 12.01100 " \ "CF2 12.01100 " \ "CF3 12.01100 " \ "FE 55.84700 " \ "CLAL 35.45300 " \ "FA 18.99800 " \ "F1 18.99800 " \ "F2 18.99800 " \ "F3 18.99800 " \ "DUM 0.00000 " \ "HL 1.008000 " \ "HCL 1.008000 " \ "HT 1.008000 " \ "HOL 1.008000 " \ "HAL1 1.008000 " \ "HAL2 1.008000 " \ "HAL3 1.008000 " \ "HEL1 1.008000 " \ "HEL2 1.008000 " \ "CL 12.011000 " \ "CTL1 12.011000 " \ "CTL2 12.011000 " \ "CTL3 12.011000 " \ "CTL5 12.011000 " \ "CEL1 12.011000 " \ "CEL2 12.011000 " \ "NTL 14.007000 " \ "NH3L 14.007000 " \ "OBL 15.999400 " \ "OCL 15.999400 " \ "OT 15.999400 " \ "OSL 15.999400 " \ "O2L 15.999400 " \ "OHL 15.999400 " \ "PL 30.974000 " \ "SL 32.060000 " \ "SOD 22.989770 " \ "MG 24.305000 " \ "POT 39.102000 " \ "CES 132.900000 " \ "CAL 40.080000 " \ "CLA 35.450000 " \ "ZN 65.370000 " \ "HN1 1.008000 " \ "HN2 1.008000 " \ "HN3 1.008000 " \ "HN3B 1.008000 " \ "HN3C 1.008000 " \ "HNP 1.008000 " \ "HN4 1.008000 " \ "HN5 1.008000 " \ "HN6 1.008000 " \ "HN7 1.008000 " \ "HN8 1.008000 " \ "HN9 1.008000 " \ "HNE1 1.008000 " \ "HNE2 1.008000 " \ "CN1 12.011000 " \ "CN1A 12.011000 " \ "CN1T 12.011000 " \ "CN2 12.011000 " \ "CN3 12.011000 " \ "CN3A 12.011000 " \ "CN3B 12.011000 " \ "CN3C 12.011000 " \ "CN3D 12.011000 " \ "CN3T 12.011000 " \ "CN4 12.011000 " \ "CN5 12.011000 " \ "CN5G 12.011000 " \ "CN7 12.011000 " \ "CN7B 12.011000 " \ "CN7C 12.011000 " \ "CN7D 12.011000 " \ "CN8 12.011000 " \ "CN8B 12.011000 " \ "CN9 12.011000 " \ "CNE1 12.011000 " \ "CNE2 12.011000 " \ "CNA 12.011000 " \ "CNA2 12.011000 " \ "CN6 12.011000 " \ "CN7E 12.011000 " \ "NN1 14.007000 " \ "NN1C 14.007000 " \ "NN2 14.007000 " \ "NN2B 14.007000 " \ "NN2C 14.007000 " \ "NN2U 14.007000 " \ "NN2G 14.007000 " \ "NN3 14.007000 " \ "NN3A 14.007000 " \ "NN3I 14.007000 " \ "NN3G 14.007000 " \ "NN4 14.007000 " \ "NN5 14.007000 " \ "NN6 14.007000 " \ "ON1 15.999400 " \ "ON1C 15.999400 " \ "ON2 15.999400 " \ "ON3 15.999400 " \ "ON4 15.999400 " \ "ON5 15.999400 " \ "ON6 15.999400 " \ "ON6B 15.999400 " \ "ON2B 15.999400 " \ "FN1 18.998400 " \ "FNA 18.998400 " \ "P 30.974000 " \ "P2 30.974000 " \ "P3 30.974000 " \ "SOD 22.989770 " \ "MG 24.305000 " \ "POT 39.102000 " \ "CES 132.900000 " \ "CAL 40.080000 " \ "CLA 35.450000 " \ "ZN 65.370000 " \ "DUM 0.001 " \ "H 1.00800 " \ "HC 1.00800 " \ "HA 1.00800 " \ "HT 1.00800 " \ "HP 1.00800 " \ "HR1 1.00800 " \ "HR2 1.00800 " \ "HR3 1.00800 " \ "HS 1.00800 " \ "HE1 1.00800 " \ "HE2 1.00800 " \ "HA1 1.00800 " \ "HA2 1.00800 " \ "HA3 1.00800 " \ "HB1 1.00800 " \ "HB2 1.00800 " \ "C 12.01100 " \ "CA 12.01100 " \ "CT1 12.01100 " \ "CT2 12.01100 " \ "CT3 12.01100 " \ "CPH1 12.01100 " \ "CPH2 12.01100 " \ "CPT 12.01100 " \ "CY 12.01100 " \ "CP1 12.01100 " \ "CP2 12.01100 " \ "CP3 12.01100 " \ "CC 12.01100 " \ "CD 12.01100 " \ "CPA 12.01100 " \ "CPB 12.01100 " \ "CPM 12.01100 " \ "CM 12.01100 " \ "CS 12.01100 " \ "CE1 12.01100 " \ "CE2 12.01100 " \ "N 14.00700 " \ "NR1 14.00700 " \ "NR2 14.00700 " \ "NR3 14.00700 " \ "NH1 14.00700 " \ "NH2 14.00700 " \ "NH3 14.00700 " \ "NC2 14.00700 " \ "NY 14.00700 " \ "NP 14.00700 " \ "NPH 14.00700 " \ "O 15.99900 " \ "OB 15.99900 " \ "OC 15.99900 " \ "OH1 15.99900 " \ "OS 15.99940 " \ "OT 15.99940 " \ "OM 15.99900 " \ "S 32.06000 " \ "SM 32.06000 " \ "SS 32.06000 " \ "HE 4.00260 " \ "NE 20.17970 " \ "LP 0.000000 " \ "CAL 40.08000 " \ "ZN 65.37000 " \ "FE 55.84700 " \ "DUM 0.00000 " \ "H 1.00800 " \ "HC 1.00800 " \ "HA 1.00800 " \ "HT 1.00800 " \ "LP 0.0 " \ "CT 12.01100 " \ "C 12.01100 " \ "CH1E 13.01900 " \ "CH2E 14.02700 " \ "CH3E 15.03500 " \ "CR1E 13.01900 " \ "CM 12.01100 " \ "N 14.00670 " \ "NR 14.00670 " \ "NP 14.00670 " \ "NH1E 15.01470 " \ "NH2E 16.02270 " \ "NH3E 17.03070 " \ "NC2E 16.02270 " \ "NH1 14.00670 " \ "NH2 14.00670 " \ "NH3 14.00670 " \ "NC2 14.00670 " \ "O 15.99940 " \ "OC 15.99940 " \ "OH1E 17.00740 " \ "OH2E 18.01540 " \ "OH1 15.99940 " \ "OH2 15.99940 " \ "OM 15.99940 " \ "OT 15.99940 " \ "OS 15.99940 " \ "S 32.06000 " \ "SH1E 33.06800 " \ "FE 55.84700 " \ "H 1.00800 " \ "H2 1.00800 " \ "HO 1.00800 " \ "HT 1.00800 " \ "LP 0.0 " \ "C 12.01100 " \ "CH 13.01900 " \ "C2 14.02700 " \ "CA 12.01100 " \ "CB 12.01100 " \ "CE 13.01900 " \ "CF 13.01900 " \ "C3 15.03500 " \ "CS 12.01100 " \ "N2 14.00670 " \ "NA 14.00670 " \ "NB 14.00670 " \ "NC 14.00670 " \ "NS 14.00670 " \ "NH2E 16.02270 " \ "NH3 14.00670 " \ "O 15.99940 " \ "O2 15.99940 " \ "OS 15.99940 " \ "OH 15.99940 " \ "OH2 15.99940 " \ "OT 15.99940 " \ "OSS 15.99940 " \ "OST 15.99940 " \ "SD 22.98980 " \ "P 30.97400 " \ "BR 79.90400 " \ "MG 24.30500 " } { set data [ split $data " " ] set i 0 foreach value $data { if { $value > " " } { incr i; set val($i) $value } if { $i == 2 } { set mass($val(1)) $val(2) } } } # # Charm atom classes # foreach data { \ "S S " \ "O1 OC " \ "O2 OC " \ "O3 OC " \ "O4 OC " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT3 " \ "HB1 HA " \ "HB2 HA " \ "HB3 HA " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "CG CT2 " \ "HG1 HA " \ "HG2 HA " \ "CD CT2 " \ "HD1 HA " \ "HD2 HA " \ "NE NC2 " \ "HE HC " \ "CZ C " \ "NH1 NC2 " \ "HH11 HC " \ "HH12 HC " \ "NH2 NC2 " \ "HH21 HC " \ "HH22 HC " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "CG CC " \ "OD1 O " \ "ND2 NH2 " \ "HD21 H " \ "HD22 H " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "CG CC " \ "OD1 OC " \ "OD2 OC " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "SG S " \ "HG1 HS " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "CG CT2 " \ "HG1 HA " \ "HG2 HA " \ "CD CC " \ "OE1 O " \ "NE2 NH2 " \ "HE21 H " \ "HE22 H " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "CG CT2 " \ "HG1 HA " \ "HG2 HA " \ "CD CC " \ "OE1 OC " \ "OE2 OC " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT2 " \ "HA1 HB " \ "HA2 HB " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "ND1 NR1 " \ "HD1 H " \ "CG CPH1 " \ "CE1 CPH2 " \ "HE1 HR1 " \ "NE2 NR2 " \ "CD2 CPH1 " \ "HD2 HR3 " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "ND1 NR2 " \ "CG CPH1 " \ "CE1 CPH2 " \ "HE1 HR1 " \ "NE2 NR1 " \ "HE2 H " \ "CD2 CPH1 " \ "HD2 HR3 " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "CD2 CPH1 " \ "HD2 HR1 " \ "CG CPH1 " \ "NE2 NR3 " \ "HE2 H " \ "ND1 NR3 " \ "HD1 H " \ "CE1 CPH2 " \ "HE1 HR2 " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT1 " \ "HB HA " \ "CG2 CT3 " \ "HG21 HA " \ "HG22 HA " \ "HG23 HA " \ "CG1 CT2 " \ "HG11 HA " \ "HG12 HA " \ "CD CT3 " \ "HD1 HA " \ "HD2 HA " \ "HD3 HA " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "CG CT1 " \ "HG HA " \ "CD1 CT3 " \ "HD11 HA " \ "HD12 HA " \ "HD13 HA " \ "CD2 CT3 " \ "HD21 HA " \ "HD22 HA " \ "HD23 HA " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "CG CT2 " \ "HG1 HA " \ "HG2 HA " \ "CD CT2 " \ "HD1 HA " \ "HD2 HA " \ "CE CT2 " \ "HE1 HA " \ "HE2 HA " \ "NZ NH3 " \ "HZ1 HC " \ "HZ2 HC " \ "HZ3 HC " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "CG CT2 " \ "HG1 HA " \ "HG2 HA " \ "SD S " \ "CE CT3 " \ "HE1 HA " \ "HE2 HA " \ "HE3 HA " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "CG CA " \ "CD1 CA " \ "HD1 HP " \ "CE1 CA " \ "HE1 HP " \ "CZ CA " \ "HZ HP " \ "CD2 CA " \ "HD2 HP " \ "CE2 CA " \ "HE2 HP " \ "C C " \ "O O " \ "N N " \ "CD CP3 " \ "HD1 HA " \ "HD2 HA " \ "CA CP1 " \ "HA HB " \ "CB CP2 " \ "HB1 HA " \ "HB2 HA " \ "CG CP2 " \ "HG1 HA " \ "HG2 HA " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "OG OH1 " \ "HG1 H " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT1 " \ "HB HA " \ "OG1 OH1 " \ "HG1 H " \ "CG2 CT3 " \ "HG21 HA " \ "HG22 HA " \ "HG23 HA " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "CG CY " \ "CD1 CA " \ "HD1 HP " \ "NE1 NY " \ "HE1 H " \ "CE2 CPT " \ "CD2 CPT " \ "CE3 CA " \ "HE3 HP " \ "CZ3 CA " \ "HZ3 HP " \ "CZ2 CA " \ "HZ2 HP " \ "CH2 CA " \ "HH2 HP " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "CG CA " \ "CD1 CA " \ "HD1 HP " \ "CE1 CA " \ "HE1 HP " \ "CZ CA " \ "OH OH1 " \ "HH H " \ "CD2 CA " \ "HD2 HP " \ "CE2 CA " \ "HE2 HP " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT1 " \ "HB HA " \ "CG1 CT3 " \ "HG11 HA " \ "HG12 HA " \ "HG13 HA " \ "CG2 CT3 " \ "HG21 HA " \ "HG22 HA " \ "HG23 HA " \ "C C " \ "O O " \ "CL CT3 " \ "HL1 HA " \ "HL2 HA " \ "HL3 HA " \ "CLP C " \ "OL O " \ "NL NH1 " \ "HL H " \ "CA CT1 " \ "HA HB " \ "CB CT3 " \ "HB1 HA " \ "HB2 HA " \ "HB3 HA " \ "CRP C " \ "OR O " \ "NR NH1 " \ "HR H " \ "CR CT3 " \ "HR1 HA " \ "HR2 HA " \ "HR3 HA " \ "OH2 OT " \ "H1 HT " \ "H2 HT " \ "OH2 OT " \ "H1 HT " \ "H2 HT " \ "SOD SOD " \ "MG MG " \ "POT POT " \ "CES CES " \ "CAL CAL " \ "CLA CLA " \ "ZN ZN " \ "N NH3 " \ "HT1 HC " \ "HT2 HC " \ "HT3 HC " \ "CA CT1 " \ "HA HB " \ "N NH3 " \ "HT1 HC " \ "HT2 HC " \ "HT3 HC " \ "CA CT2 " \ "HA1 HB " \ "HA2 HB " \ "N NP " \ "HN1 HC " \ "HN2 HC " \ "CD CP3 " \ "HD1 HA " \ "HD2 HA " \ "CA CP1 " \ "HA HB " \ "CAY CT3 " \ "HY1 HA " \ "HY2 HA " \ "HY3 HA " \ "CY C " \ "OY O " \ "CAY CT3 " \ "HY1 HA " \ "HY2 HA " \ "HY3 HA " \ "CY C " \ "OY O " \ "CAY CT3 " \ "HY1 HA " \ "HY2 HA " \ "HY3 HA " \ "CY C " \ "OY O " \ "CAY CT3 " \ "HY1 HA " \ "HY2 HA " \ "HY3 HA " \ "CY C " \ "OY O " \ "C CC " \ "OT1 OC " \ "OT2 OC " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "C CD " \ "OT1 OB " \ "OT2 OS " \ "CT CT3 " \ "HT1 HA " \ "HT2 HA " \ "HT3 HA " \ "C CC " \ "O O " \ "NT NH2 " \ "HT1 H " \ "HT2 H " \ "C C " \ "O O " \ "NT NH1 " \ "HNT H " \ "CAT CT3 " \ "HT1 HA " \ "HT2 HA " \ "HT3 HA " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "CG CD " \ "OD1 OB " \ "OD2 OH1 " \ "HD2 H " \ "CG CT2 " \ "HG1 HA " \ "HG2 HA " \ "CD CD " \ "OE1 OB " \ "OE2 OH1 " \ "HE2 H " \ "CE CT2 " \ "HE1 HA " \ "HE2 HA " \ "NZ NH2 " \ "HZ1 HC " \ "HZ2 HC " \ "1CB CT2 " \ "1SG SM " \ "2SG SM " \ "2CB CT2 " \ "CE1 CPH2 " \ "HE1 HR1 " \ "ND1 NR2 " \ "CG CPH1 " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "NE2 NR1 " \ "HE2 H " \ "CD2 CPH1 " \ "HD2 HR3 " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT3 " \ "HB1 HA " \ "HB2 HA " \ "HB3 HA " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "CG CT2 " \ "HG1 HA " \ "HG2 HA " \ "CD CT2 " \ "HD1 HA " \ "HD2 HA " \ "NE NC2 " \ "HE HC " \ "CZ C " \ "NH1 NC2 " \ "HH11 HC " \ "HH12 HC " \ "NH2 NC2 " \ "HH21 HC " \ "HH22 HC " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "CG CC " \ "OD1 O " \ "ND2 NH2 " \ "HD21 H " \ "HD22 H " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "CG CC " \ "OD1 OC " \ "OD2 OC " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "SG S " \ "HG1 HS " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "CG CT2 " \ "HG1 HA " \ "HG2 HA " \ "CD CC " \ "OE1 O " \ "NE2 NH2 " \ "HE21 H " \ "HE22 H " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "CG CT2 " \ "HG1 HA " \ "HG2 HA " \ "CD CC " \ "OE1 OC " \ "OE2 OC " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT2 " \ "HA1 HB " \ "HA2 HB " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "ND1 NR1 " \ "HD1 H " \ "CG CPH1 " \ "CE1 CPH2 " \ "HE1 HR1 " \ "NE2 NR2 " \ "CD2 CPH1 " \ "HD2 HR3 " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "ND1 NR2 " \ "CG CPH1 " \ "CE1 CPH2 " \ "HE1 HR1 " \ "NE2 NR1 " \ "HE2 H " \ "CD2 CPH1 " \ "HD2 HR3 " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "CD2 CPH1 " \ "HD2 HR1 " \ "CG CPH1 " \ "NE2 NR3 " \ "HE2 H " \ "ND1 NR3 " \ "HD1 H " \ "CE1 CPH2 " \ "HE1 HR2 " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT1 " \ "HB HA " \ "CG2 CT3 " \ "HG21 HA " \ "HG22 HA " \ "HG23 HA " \ "CG1 CT2 " \ "HG11 HA " \ "HG12 HA " \ "CD CT3 " \ "HD1 HA " \ "HD2 HA " \ "HD3 HA " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "CG CT1 " \ "HG HA " \ "CD1 CT3 " \ "HD11 HA " \ "HD12 HA " \ "HD13 HA " \ "CD2 CT3 " \ "HD21 HA " \ "HD22 HA " \ "HD23 HA " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "CG CT2 " \ "HG1 HA " \ "HG2 HA " \ "CD CT2 " \ "HD1 HA " \ "HD2 HA " \ "CE CT2 " \ "HE1 HA " \ "HE2 HA " \ "NZ NH3 " \ "HZ1 HC " \ "HZ2 HC " \ "HZ3 HC " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "CG CT2 " \ "HG1 HA " \ "HG2 HA " \ "SD S " \ "CE CT3 " \ "HE1 HA " \ "HE2 HA " \ "HE3 HA " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "CG CA " \ "CD1 CA " \ "HD1 HP " \ "CE1 CA " \ "HE1 HP " \ "CZ CA " \ "HZ HP " \ "CD2 CA " \ "HD2 HP " \ "CE2 CA " \ "HE2 HP " \ "C C " \ "O O " \ "N N " \ "CD CP3 " \ "HD1 HA " \ "HD2 HA " \ "CA CP1 " \ "HA HB " \ "CB CP2 " \ "HB1 HA " \ "HB2 HA " \ "CG CP2 " \ "HG1 HA " \ "HG2 HA " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "OG OH1 " \ "HG1 H " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT1 " \ "HB HA " \ "OG1 OH1 " \ "HG1 H " \ "CG2 CT3 " \ "HG21 HA " \ "HG22 HA " \ "HG23 HA " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "CG CY " \ "CD1 CA " \ "HD1 HP " \ "NE1 NY " \ "HE1 H " \ "CE2 CPT " \ "CD2 CPT " \ "CE3 CA " \ "HE3 HP " \ "CZ3 CA " \ "HZ3 HP " \ "CZ2 CA " \ "HZ2 HP " \ "CH2 CA " \ "HH2 HP " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "CG CA " \ "CD1 CA " \ "HD1 HP " \ "CE1 CA " \ "HE1 HP " \ "CZ CA " \ "OH OH1 " \ "HH H " \ "CD2 CA " \ "HD2 HP " \ "CE2 CA " \ "HE2 HP " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT1 " \ "HB HA " \ "CG1 CT3 " \ "HG11 HA " \ "HG12 HA " \ "HG13 HA " \ "CG2 CT3 " \ "HG21 HA " \ "HG22 HA " \ "HG23 HA " \ "C C " \ "O O " \ "CL CT3 " \ "HL1 HA " \ "HL2 HA " \ "HL3 HA " \ "CLP C " \ "OL O " \ "NL NH1 " \ "HL H " \ "CA CT1 " \ "HA HB " \ "CB CT3 " \ "HB1 HA " \ "HB2 HA " \ "HB3 HA " \ "CRP C " \ "OR O " \ "NR NH1 " \ "HR H " \ "CR CT3 " \ "HR1 HA " \ "HR2 HA " \ "HR3 HA " \ "OH2 OT " \ "H1 HT " \ "H2 HT " \ "OH2 OT " \ "H1 HT " \ "H2 HT " \ "SOD SOD " \ "MG MG " \ "POT POT " \ "CES CES " \ "CAL CAL " \ "CLA CLA " \ "ZN ZN " \ "N NH3 " \ "HT1 HC " \ "HT2 HC " \ "HT3 HC " \ "CA CT1 " \ "HA HB " \ "N NH3 " \ "HT1 HC " \ "HT2 HC " \ "HT3 HC " \ "CA CT2 " \ "HA1 HB " \ "HA2 HB " \ "N NP " \ "HN1 HC " \ "HN2 HC " \ "CD CP3 " \ "HD1 HA " \ "HD2 HA " \ "CA CP1 " \ "HA HB " \ "CAY CT3 " \ "HY1 HA " \ "HY2 HA " \ "HY3 HA " \ "CY C " \ "OY O " \ "CAY CT3 " \ "HY1 HA " \ "HY2 HA " \ "HY3 HA " \ "CY C " \ "OY O " \ "C CC " \ "OT1 OC " \ "OT2 OC " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "C CD " \ "OT1 OB " \ "OT2 OS " \ "CT CT3 " \ "HT1 HA " \ "HT2 HA " \ "HT3 HA " \ "C CC " \ "O O " \ "NT NH2 " \ "HT1 H " \ "HT2 H " \ "C C " \ "O O " \ "NT NH1 " \ "HNT H " \ "CAT CT3 " \ "HT1 HA " \ "HT2 HA " \ "HT3 HA " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "CG CD " \ "OD1 OB " \ "OD2 OH1 " \ "HD2 H " \ "CG CT2 " \ "HG1 HA " \ "HG2 HA " \ "CD CD " \ "OE1 OB " \ "OE2 OH1 " \ "HE2 H " \ "CE CT2 " \ "HE1 HA " \ "HE2 HA " \ "NZ NH2 " \ "HZ1 HC " \ "HZ2 HC " \ "1CB CT2 " \ "1SG SM " \ "2SG SM " \ "2CB CT2 " \ "CE1 CPH2 " \ "HE1 HR1 " \ "ND1 NR2 " \ "CG CPH1 " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "NE2 NR1 " \ "HE2 H " \ "CD2 CPH1 " \ "HD2 HR3 " \ "C1 CTS " \ "H1 HAS " \ "O1 OHS " \ "HO1 HOS " \ "C5 CTS " \ "H5 HAS " \ "O5 OES " \ "C2 CTS " \ "H2 HAS " \ "O2 OHS " \ "HO2 HOS " \ "C3 CTS " \ "H3 HAS " \ "O3 OHS " \ "HO3 HOS " \ "C4 CTS " \ "H4 HAS " \ "O4 OHS " \ "HO4 HOS " \ "C6 CTS " \ "H61 HAS " \ "H62 HAS " \ "O6 OHS " \ "HO6 HOS " \ "C1 CBS " \ "N NTL " \ "C13 CTL5 " \ "H13A HL " \ "H13B HL " \ "H13C HL " \ "C14 CTL5 " \ "H14A HL " \ "H14B HL " \ "H14C HL " \ "C15 CTL5 " \ "H15A HL " \ "H15B HL " \ "H15C HL " \ "C12 CTL2 " \ "H12A HL " \ "H12B HL " \ "C11 CTL2 " \ "H11A HAL2 " \ "H11B HAL2 " \ "P PL " \ "O13 O2L " \ "O14 O2L " \ "O11 OSL " \ "O12 OSL " \ "C1 CTL2 " \ "HA HAL2 " \ "HB HAL2 " \ "C2 CTL2 " \ "HS HAL2 " \ "HR HAL2 " \ "C3 CTL2 " \ "HX HAL2 " \ "HY HAL2 " \ "O31 OSL " \ "C31 CL " \ "O32 OBL " \ "C32 CTL2 " \ "H2X HAL2 " \ "H2Y HAL2 " \ "C33 CTL2 " \ "H3X HAL2 " \ "H3Y HAL2 " \ "C34 CTL2 " \ "H4X HAL2 " \ "H4Y HAL2 " \ "C35 CTL2 " \ "H5X HAL2 " \ "H5Y HAL2 " \ "C36 CTL2 " \ "H6X HAL2 " \ "H6Y HAL2 " \ "C37 CTL2 " \ "H7X HAL2 " \ "H7Y HAL2 " \ "C38 CTL2 " \ "H8X HAL2 " \ "H8Y HAL2 " \ "C39 CTL2 " \ "H9X HAL2 " \ "H9Y HAL2 " \ "C310 CTL2 " \ "H10X HAL2 " \ "H10Y HAL2 " \ "C311 CTL2 " \ "H11X HAL2 " \ "H11Y HAL2 " \ "C312 CTL3 " \ "H12X HAL3 " \ "H12Y HAL3 " \ "H12Z HAL3 " \ "N NH3 " \ "HN1 HCL " \ "HN2 HCL " \ "HN3 HCL " \ "C12 CTL " \ "H12A HAL " \ "H12B HAL " \ "C11 CTL2 " \ "H11A HAL2 " \ "H11B HAL2 " \ "P PL " \ "O13 O2L " \ "O14 O2L " \ "O11 OSL " \ "O12 OSL " \ "C1 CTL2 " \ "HA HAL2 " \ "HB HAL2 " \ "C2 CTL1 " \ "HS HAL1 " \ "OH2 OHL " \ "HO2 HOL " \ "C3 CTL2 " \ "HX HAL2 " \ "HY HAL2 " \ "OH3 OHL " \ "HO3 HOL " \ "N NH3 " \ "HN1 HCL " \ "HN2 HCL " \ "HN3 HCL " \ "C12 CTL " \ "H12A HAL " \ "H12B HAL " \ "C11 CTL2 " \ "H11A HAL2 " \ "H11B HAL2 " \ "P PL " \ "O13 O2L " \ "O14 O2L " \ "O11 OSL " \ "O12 OSL " \ "C1 CTL2 " \ "HA HAL2 " \ "HB HAL2 " \ "C2 CTL1 " \ "HS HAL1 " \ "O21 OSL " \ "C21 CL " \ "O22 OBL " \ "C22 CTL2 " \ "H2R HAL2 " \ "H2S HAL2 " \ "C3 CTL2 " \ "HX HAL2 " \ "HY HAL2 " \ "O31 OSL " \ "C31 CL " \ "O32 OBL " \ "C32 CTL2 " \ "H2X HAL2 " \ "H2Y HAL2 " \ "C23 CTL2 " \ "H3R HAL2 " \ "H3S HAL2 " \ "C24 CTL2 " \ "H4R HAL2 " \ "H4S HAL2 " \ "C25 CTL2 " \ "H5R HAL2 " \ "H5S HAL2 " \ "C26 CTL2 " \ "H6R HAL2 " \ "H6S HAL2 " \ "C27 CTL2 " \ "H7R HAL2 " \ "H7S HAL2 " \ "C28 CTL2 " \ "H8R HAL2 " \ "H8S HAL2 " \ "C29 CTL2 " \ "H9R HAL2 " \ "H9S HAL2 " \ "C210 CTL2 " \ "H10R HAL2 " \ "H10S HAL2 " \ "C211 CTL2 " \ "H11R HAL2 " \ "H11S HAL2 " \ "C212 CTL3 " \ "H12R HAL3 " \ "H12S HAL3 " \ "H12T HAL3 " \ "C33 CTL2 " \ "H3X HAL2 " \ "H3Y HAL2 " \ "C34 CTL2 " \ "H4X HAL2 " \ "H4Y HAL2 " \ "C35 CTL2 " \ "H5X HAL2 " \ "H5Y HAL2 " \ "C36 CTL2 " \ "H6X HAL2 " \ "H6Y HAL2 " \ "C37 CTL2 " \ "H7X HAL2 " \ "H7Y HAL2 " \ "C38 CTL2 " \ "H8X HAL2 " \ "H8Y HAL2 " \ "C39 CTL2 " \ "H9X HAL2 " \ "H9Y HAL2 " \ "C310 CTL2 " \ "H10X HAL2 " \ "H10Y HAL2 " \ "C311 CTL2 " \ "H11X HAL2 " \ "H11Y HAL2 " \ "C312 CTL3 " \ "H12X HAL3 " \ "H12Y HAL3 " \ "H12Z HAL3 " \ "N NTL " \ "C13 CTL5 " \ "H13A HL " \ "H13B HL " \ "H13C HL " \ "C14 CTL5 " \ "H14A HL " \ "H14B HL " \ "H14C HL " \ "C15 CTL5 " \ "H15A HL " \ "H15B HL " \ "H15C HL " \ "C12 CTL2 " \ "H12A HL " \ "H12B HL " \ "C11 CTL2 " \ "H11A HAL2 " \ "H11B HAL2 " \ "P PL " \ "O13 O2L " \ "O14 O2L " \ "O11 OSL " \ "O12 OSL " \ "C1 CTL2 " \ "HA HAL2 " \ "HB HAL2 " \ "C2 CTL1 " \ "HS HAL1 " \ "O21 OSL " \ "C21 CL " \ "O22 OBL " \ "C22 CTL2 " \ "H2R HAL2 " \ "H2S HAL2 " \ "C3 CTL2 " \ "HX HAL2 " \ "HY HAL2 " \ "O31 OSL " \ "C31 CL " \ "O32 OBL " \ "C32 CTL2 " \ "H2X HAL2 " \ "H2Y HAL2 " \ "C23 CTL2 " \ "H3R HAL2 " \ "H3S HAL2 " \ "C24 CTL2 " \ "H4R HAL2 " \ "H4S HAL2 " \ "C25 CTL2 " \ "H5R HAL2 " \ "H5S HAL2 " \ "C26 CTL2 " \ "H6R HAL2 " \ "H6S HAL2 " \ "C27 CTL2 " \ "H7R HAL2 " \ "H7S HAL2 " \ "C28 CTL2 " \ "H8R HAL2 " \ "H8S HAL2 " \ "C29 CTL2 " \ "H9R HAL2 " \ "H9S HAL2 " \ "C210 CTL2 " \ "H10R HAL2 " \ "H10S HAL2 " \ "C211 CTL2 " \ "H11R HAL2 " \ "H11S HAL2 " \ "C212 CTL2 " \ "H12R HAL2 " \ "H12S HAL2 " \ "C213 CTL2 " \ "H13R HAL2 " \ "H13S HAL2 " \ "C214 CTL3 " \ "H14R HAL3 " \ "H14S HAL3 " \ "H14T HAL3 " \ "C33 CTL2 " \ "H3X HAL2 " \ "H3Y HAL2 " \ "C34 CTL2 " \ "H4X HAL2 " \ "H4Y HAL2 " \ "C35 CTL2 " \ "H5X HAL2 " \ "H5Y HAL2 " \ "C36 CTL2 " \ "H6X HAL2 " \ "H6Y HAL2 " \ "C37 CTL2 " \ "H7X HAL2 " \ "H7Y HAL2 " \ "C38 CTL2 " \ "H8X HAL2 " \ "H8Y HAL2 " \ "C39 CTL2 " \ "H9X HAL2 " \ "H9Y HAL2 " \ "C310 CTL2 " \ "H10X HAL2 " \ "H10Y HAL2 " \ "C311 CTL2 " \ "H11X HAL2 " \ "H11Y HAL2 " \ "C312 CTL2 " \ "H12X HAL2 " \ "H12Y HAL2 " \ "C313 CTL2 " \ "H13X HAL2 " \ "H13Y HAL2 " \ "C314 CTL3 " \ "H14X HAL3 " \ "H14Y HAL3 " \ "H14Z HAL3 " \ "S SL " \ "OS1 OSL " \ "OS2 O2L " \ "OS3 O2L " \ "OS4 O2L " \ "C1 CTL2 " \ "H11 HAL2 " \ "H12 HAL2 " \ "C2 CTL2 " \ "H21 HAL2 " \ "H22 HAL2 " \ "C3 CTL2 " \ "H31 HAL2 " \ "H32 HAL2 " \ "C4 CTL2 " \ "H41 HAL2 " \ "H42 HAL2 " \ "C5 CTL2 " \ "H51 HAL2 " \ "H52 HAL2 " \ "C6 CTL2 " \ "H61 HAL2 " \ "H62 HAL2 " \ "C7 CTL2 " \ "H71 HAL2 " \ "H72 HAL2 " \ "C8 CTL2 " \ "H81 HAL2 " \ "H82 HAL2 " \ "C9 CTL2 " \ "H91 HAL2 " \ "H92 HAL2 " \ "C10 CTL2 " \ "H101 HAL2 " \ "H102 HAL2 " \ "C11 CTL2 " \ "H111 HAL2 " \ "H112 HAL2 " \ "C12 CTL3 " \ "H121 HAL3 " \ "H122 HAL3 " \ "H123 HAL3 " \ "N NTL " \ "C11 CTL2 " \ "C12 CTL5 " \ "C13 CTL5 " \ "C14 CTL5 " \ "H11 HL " \ "H12 HL " \ "H21 HL " \ "H22 HL " \ "H23 HL " \ "H31 HL " \ "H32 HL " \ "H33 HL " \ "H41 HL " \ "H42 HL " \ "H43 HL " \ "C15 CTL2 " \ "H51 HAL2 " \ "H52 HAL2 " \ "P1 PL " \ "O3 O2L " \ "O4 O2L " \ "O1 OSL " \ "O2 OSL " \ "C1 CTL2 " \ "HA HAL2 " \ "HB HAL2 " \ "C2 CTL1 " \ "HS HAL1 " \ "O21 OSL " \ "C21 CL " \ "O22 OBL " \ "C22 CTL2 " \ "H2R HAL2 " \ "H2S HAL2 " \ "C3 CTL2 " \ "HX HAL2 " \ "HY HAL2 " \ "O31 OSL " \ "C31 CL " \ "O32 OBL " \ "C32 CTL2 " \ "H2X HAL2 " \ "H2Y HAL2 " \ "C23 CTL2 " \ "H3R HAL2 " \ "H3S HAL2 " \ "C24 CTL2 " \ "H4R HAL2 " \ "H4S HAL2 " \ "C25 CTL2 " \ "H5R HAL2 " \ "H5S HAL2 " \ "C26 CTL2 " \ "H6R HAL2 " \ "H6S HAL2 " \ "C27 CTL2 " \ "H7R HAL2 " \ "H7S HAL2 " \ "C28 CTL2 " \ "H8R HAL2 " \ "H8S HAL2 " \ "C29 CEL1 " \ "H91 HEL1 " \ "C210 CEL1 " \ "H101 HEL1 " \ "C211 CTL2 " \ "H11R HAL2 " \ "H11S HAL2 " \ "C212 CTL2 " \ "H12R HAL2 " \ "H12S HAL2 " \ "C213 CTL2 " \ "H13R HAL2 " \ "H13S HAL2 " \ "C214 CTL2 " \ "H14R HAL2 " \ "H14S HAL2 " \ "C215 CTL2 " \ "H15R HAL2 " \ "H15S HAL2 " \ "C216 CTL2 " \ "H16R HAL2 " \ "H16S HAL2 " \ "C217 CTL2 " \ "H17R HAL2 " \ "H17S HAL2 " \ "C218 CTL3 " \ "H18R HAL3 " \ "H18S HAL3 " \ "H18T HAL3 " \ "C33 CTL2 " \ "H3X HAL2 " \ "H3Y HAL2 " \ "C34 CTL2 " \ "H4X HAL2 " \ "H4Y HAL2 " \ "C35 CTL2 " \ "H5X HAL2 " \ "H5Y HAL2 " \ "C36 CTL2 " \ "H6X HAL2 " \ "H6Y HAL2 " \ "C37 CTL2 " \ "H7X HAL2 " \ "H7Y HAL2 " \ "C38 CTL2 " \ "H8X HAL2 " \ "H8Y HAL2 " \ "C39 CTL2 " \ "H9X HAL2 " \ "H9Y HAL2 " \ "C310 CTL2 " \ "H10X HAL2 " \ "H10Y HAL2 " \ "C311 CTL2 " \ "H11X HAL2 " \ "H11Y HAL2 " \ "C312 CTL2 " \ "H12X HAL2 " \ "H12Y HAL2 " \ "C313 CTL2 " \ "H13X HAL2 " \ "H13Y HAL2 " \ "C314 CTL2 " \ "H14X HAL2 " \ "H14Y HAL2 " \ "C315 CTL2 " \ "H15X HAL2 " \ "H15Y HAL2 " \ "C316 CTL3 " \ "H16X HAL3 " \ "H16Y HAL3 " \ "H16Z HAL3 " \ "N NH3 " \ "HN1 HCL " \ "HN2 HCL " \ "HN3 HCL " \ "C12 CTL " \ "H12A HAL " \ "H12B HAL " \ "C11 CTL2 " \ "H11A HAL2 " \ "H11B HAL2 " \ "P PL " \ "O13 O2L " \ "O14 O2L " \ "O11 OSL " \ "O12 OSL " \ "C1 CTL2 " \ "HA HAL2 " \ "HB HAL2 " \ "C2 CTL1 " \ "HS HAL1 " \ "O21 OSL " \ "C21 CL " \ "O22 OBL " \ "C22 CTL2 " \ "H2R HAL2 " \ "H2S HAL2 " \ "C3 CTL2 " \ "HX HAL2 " \ "HY HAL2 " \ "O31 OSL " \ "C31 CL " \ "O32 OBL " \ "C32 CTL2 " \ "H2X HAL2 " \ "H2Y HAL2 " \ "C23 CTL2 " \ "H3R HAL2 " \ "H3S HAL2 " \ "C24 CTL2 " \ "H4R HAL2 " \ "H4S HAL2 " \ "C25 CTL2 " \ "H5R HAL2 " \ "H5S HAL2 " \ "C26 CTL2 " \ "H6R HAL2 " \ "H6S HAL2 " \ "C27 CTL2 " \ "H7R HAL2 " \ "H7S HAL2 " \ "C28 CTL2 " \ "H8R HAL2 " \ "H8S HAL2 " \ "C29 CEL1 " \ "H91 HEL1 " \ "C210 CEL1 " \ "H101 HEL1 " \ "C211 CTL2 " \ "H11R HAL2 " \ "H11S HAL2 " \ "C212 CTL2 " \ "H12R HAL2 " \ "H12S HAL2 " \ "C213 CTL2 " \ "H13R HAL2 " \ "H13S HAL2 " \ "C214 CTL2 " \ "H14R HAL2 " \ "H14S HAL2 " \ "C215 CTL2 " \ "H15R HAL2 " \ "H15S HAL2 " \ "C216 CTL2 " \ "H16R HAL2 " \ "H16S HAL2 " \ "C217 CTL2 " \ "H17R HAL2 " \ "H17S HAL2 " \ "C218 CTL3 " \ "H18R HAL3 " \ "H18S HAL3 " \ "H18T HAL3 " \ "C33 CTL2 " \ "H3X HAL2 " \ "H3Y HAL2 " \ "C34 CTL2 " \ "H4X HAL2 " \ "H4Y HAL2 " \ "C35 CTL2 " \ "H5X HAL2 " \ "H5Y HAL2 " \ "C36 CTL2 " \ "H6X HAL2 " \ "H6Y HAL2 " \ "C37 CTL2 " \ "H7X HAL2 " \ "H7Y HAL2 " \ "C38 CTL2 " \ "H8X HAL2 " \ "H8Y HAL2 " \ "C39 CTL2 " \ "H9X HAL2 " \ "H9Y HAL2 " \ "C310 CTL2 " \ "H10X HAL2 " \ "H10Y HAL2 " \ "C311 CTL2 " \ "H11X HAL2 " \ "H11Y HAL2 " \ "C312 CTL2 " \ "H12X HAL2 " \ "H12Y HAL2 " \ "C313 CTL2 " \ "H13X HAL2 " \ "H13Y HAL2 " \ "C314 CTL2 " \ "H14X HAL2 " \ "H14Y HAL2 " \ "C315 CTL2 " \ "H15X HAL2 " \ "H15Y HAL2 " \ "C316 CTL3 " \ "H16X HAL3 " \ "H16Y HAL3 " \ "H16Z HAL3 " \ "C1 CL " \ "O1 OCL " \ "O2 OCL " \ "C2 CTL2 " \ "H2A HAL2 " \ "H2B HAL2 " \ "C3 CTL2 " \ "H3A HAL2 " \ "H3B HAL2 " \ "C4 CTL2 " \ "H4A HAL2 " \ "H4B HAL2 " \ "C5 CTL2 " \ "H5A HAL2 " \ "H5B HAL2 " \ "C6 CTL2 " \ "H6A HAL2 " \ "H6B HAL2 " \ "C7 CTL2 " \ "H7A HAL2 " \ "H7B HAL2 " \ "C8 CTL2 " \ "H8A HAL2 " \ "H8B HAL2 " \ "C9 CTL2 " \ "H9A HAL2 " \ "H9B HAL2 " \ "C10 CTL2 " \ "H10A HAL2 " \ "H10B HAL2 " \ "C11 CTL2 " \ "H11A HAL2 " \ "H11B HAL2 " \ "C12 CTL2 " \ "H12A HAL2 " \ "H12B HAL2 " \ "C13 CTL2 " \ "H13A HAL2 " \ "H13B HAL2 " \ "C14 CTL2 " \ "H14A HAL2 " \ "H14B HAL2 " \ "C15 CTL2 " \ "H15A HAL2 " \ "H15B HAL2 " \ "C16 CTL3 " \ "H16A HAL3 " \ "H16B HAL3 " \ "H16C HAL3 " \ "C1 CL " \ "O1 OCL " \ "O2 OCL " \ "C2 CTL2 " \ "H2A HAL2 " \ "H2B HAL2 " \ "C3 CTL2 " \ "H3A HAL2 " \ "H3B HAL2 " \ "C4 CTL2 " \ "H4A HAL2 " \ "H4B HAL2 " \ "C5 CTL2 " \ "H5A HAL2 " \ "H5B HAL2 " \ "C6 CTL2 " \ "H6A HAL2 " \ "H6B HAL2 " \ "C7 CTL2 " \ "H7A HAL2 " \ "H7B HAL2 " \ "C8 CTL2 " \ "H8A HAL2 " \ "H8B HAL2 " \ "C9 CEL1 " \ "H9A HEL1 " \ "C10 CEL1 " \ "H10A HEL1 " \ "C11 CTL2 " \ "H11A HAL2 " \ "H11B HAL2 " \ "C12 CTL2 " \ "H12A HAL2 " \ "H12B HAL2 " \ "C13 CTL2 " \ "H13A HAL2 " \ "H13B HAL2 " \ "C14 CTL2 " \ "H14A HAL2 " \ "H14B HAL2 " \ "C15 CTL2 " \ "H15A HAL2 " \ "H15B HAL2 " \ "C16 CTL2 " \ "H16A HAL2 " \ "H16B HAL2 " \ "C17 CTL2 " \ "H17A HAL2 " \ "H17B HAL2 " \ "C18 CTL3 " \ "H18A HAL3 " \ "H18B HAL3 " \ "H18C HAL3 " \ "C1 CL " \ "O1 OCL " \ "O2 OCL " \ "C2 CTL2 " \ "H2A HAL2 " \ "H2B HAL2 " \ "C3 CTL2 " \ "H3A HAL2 " \ "H3B HAL2 " \ "C4 CEL1 " \ "H4 HEL1 " \ "C5 CEL1 " \ "H5 HEL1 " \ "C6 CTL2 " \ "H6A HAL2 " \ "H6B HAL2 " \ "C7 CEL1 " \ "H7 HEL1 " \ "C8 CEL1 " \ "H8 HEL1 " \ "C9 CTL2 " \ "H9A HAL2 " \ "H9B HAL2 " \ "C10 CEL1 " \ "H10 HEL1 " \ "C11 CEL1 " \ "H11 HEL1 " \ "C12 CTL2 " \ "H12A HAL2 " \ "H12B HAL2 " \ "C13 CEL1 " \ "H13 HEL1 " \ "C14 CEL1 " \ "H14 HEL1 " \ "C15 CTL2 " \ "H15A HAL2 " \ "H15B HAL2 " \ "C16 CEL1 " \ "H16 HEL1 " \ "C17 CEL1 " \ "H17 HEL1 " \ "C18 CTL2 " \ "H18A HAL2 " \ "H18B HAL2 " \ "C19 CEL1 " \ "H19 HEL1 " \ "C20 CEL1 " \ "H20 HEL1 " \ "C21 CTL2 " \ "H21A HAL2 " \ "H21B HAL2 " \ "C22 CTL3 " \ "H22A HAL3 " \ "H22B HAL3 " \ "H22C HAL3 " \ "C1 CL " \ "O1 OCL " \ "O2 OCL " \ "C2 CTL2 " \ "H2A HAL2 " \ "H2B HAL2 " \ "C3 CTL2 " \ "H3A HAL2 " \ "H3B HAL2 " \ "C4 CTL2 " \ "H4A HAL2 " \ "H4B HAL2 " \ "C5 CTL2 " \ "H5A HAL2 " \ "H5B HAL2 " \ "C6 CTL2 " \ "H6A HAL2 " \ "H6B HAL2 " \ "C7 CTL2 " \ "H7A HAL2 " \ "H7B HAL2 " \ "C8 CTL2 " \ "H8A HAL2 " \ "H8B HAL2 " \ "C9 CTL2 " \ "H9A HAL2 " \ "H9B HAL2 " \ "C10 CTL2 " \ "H10A HAL2 " \ "H10B HAL2 " \ "C11 CTL2 " \ "H11A HAL2 " \ "H11B HAL2 " \ "C12 CTL2 " \ "H12A HAL2 " \ "H12B HAL2 " \ "C13 CTL2 " \ "H13A HAL2 " \ "H13B HAL2 " \ "C14 CTL2 " \ "H14A HAL2 " \ "H14B HAL2 " \ "C15 CTL2 " \ "H15A HAL2 " \ "H15B HAL2 " \ "C16 CTL2 " \ "H16A HAL2 " \ "H16B HAL2 " \ "C17 CTL2 " \ "H17A HAL2 " \ "H17B HAL2 " \ "C18 CTL3 " \ "H18A HAL3 " \ "H18B HAL3 " \ "H18C HAL3 " \ "N NTL " \ "C5 CTL2 " \ "C6 CTL5 " \ "C7 CTL5 " \ "C8 CTL5 " \ "H5A HL " \ "H5B HL " \ "H6A HL " \ "H6B HL " \ "H6C HL " \ "H7A HL " \ "H7B HL " \ "H7C HL " \ "H8A HL " \ "H8B HL " \ "H8C HL " \ "C4 CTL2 " \ "H4A HAL2 " \ "H4B HAL2 " \ "P PL " \ "OP3 O2L " \ "OP4 O2L " \ "OP1 OSL " \ "OP2 OSL " \ "C3 CTL2 " \ "H3A HAL2 " \ "H3B HAL2 " \ "C2 CTL1 " \ "H2A HAL1 " \ "O2 OHL " \ "H2 HOL " \ "C1 CTL2 " \ "H1A HAL2 " \ "H1B HAL2 " \ "O1 OHL " \ "H1 HOL " \ "1C1 CTL2 " \ "1H1A HAL2 " \ "1H1B HAL2 " \ "1O1 OSL " \ "2C1 CL " \ "2O1 OBL " \ "2C2 CTL2 " \ "2H2A HAL2 " \ "2H2B HAL2 " \ "1C2 CTL1 " \ "1H2A HAL1 " \ "1O2 OSL " \ "2C1 CL " \ "2O1 OBL " \ "2C2 CTL2 " \ "2H2A HAL2 " \ "2H2B HAL2 " \ "OH2 OT " \ "H1 HT " \ "H2 HT " \ "OH2 OT " \ "H1 HT " \ "H2 HT " \ "SOD SOD " \ "MG MG " \ "POT POT " \ "CES CES " \ "CAL CAL " \ "CLA CLA " \ "ZN ZN " \ "P P " \ "O1P ON3 " \ "O2P ON3 " \ "O5' ON2 " \ "C5' CN8B " \ "H5' HN8 " \ "H5'' HN8 " \ "C4' CN7 " \ "H4' HN7 " \ "O4' ON6B " \ "C1' CN7B " \ "H1' HN7 " \ "N9 NN2B " \ "C4 CN5 " \ "N2 NN1 " \ "H21 HN1 " \ "H22 HN1 " \ "N3 NN3G " \ "C2 CN2 " \ "N1 NN2G " \ "H1 HN2 " \ "C6 CN1 " \ "O6 ON1 " \ "C5 CN5G " \ "N7 NN4 " \ "C8 CN4 " \ "H8 HN3 " \ "C2' CN7B " \ "H2'' HN7 " \ "O2' ON5 " \ "H2' HN5 " \ "C3' CN7 " \ "H3' HN7 " \ "O3' ON2 " \ "P P " \ "O1P ON3 " \ "O2P ON3 " \ "O5' ON2 " \ "C5' CN8B " \ "H5' HN8 " \ "H5'' HN8 " \ "C4' CN7 " \ "H4' HN7 " \ "O4' ON6B " \ "C1' CN7B " \ "H1' HN7 " \ "N9 NN2 " \ "C5 CN5 " \ "N7 NN4 " \ "C8 CN4 " \ "H8 HN3 " \ "N1 NN3A " \ "C2 CN4 " \ "H2 HN3 " \ "N3 NN3A " \ "C4 CN5 " \ "C6 CN2 " \ "N6 NN1 " \ "H61 HN1 " \ "H62 HN1 " \ "C2' CN7B " \ "H2'' HN7 " \ "O2' ON5 " \ "H2' HN5 " \ "C3' CN7 " \ "H3' HN7 " \ "O3' ON2 " \ "P P " \ "O1P ON3 " \ "O2P ON3 " \ "O5' ON2 " \ "C5' CN8B " \ "H5' HN8 " \ "H5'' HN8 " \ "C4' CN7 " \ "H4' HN7 " \ "O4' ON6B " \ "C1' CN7B " \ "H1' HN7 " \ "N1 NN2 " \ "C6 CN3 " \ "H6 HN3 " \ "C5 CN3 " \ "H5 HN3 " \ "C2 CN1 " \ "O2 ON1C " \ "N3 NN3 " \ "C4 CN2 " \ "N4 NN1 " \ "H41 HN1 " \ "H42 HN1 " \ "C2' CN7B " \ "H2'' HN7 " \ "O2' ON5 " \ "H2' HN5 " \ "C3' CN7 " \ "H3' HN7 " \ "O3' ON2 " \ "P P " \ "O1P ON3 " \ "O2P ON3 " \ "O5' ON2 " \ "C5' CN8B " \ "H5' HN8 " \ "H5'' HN8 " \ "C4' CN7 " \ "H4' HN7 " \ "O4' ON6B " \ "C1' CN7B " \ "H1' HN7 " \ "N1 NN2B " \ "C6 CN3 " \ "H6 HN3 " \ "C2 CN1T " \ "O2 ON1 " \ "N3 NN2U " \ "H3 HN2 " \ "C4 CN1 " \ "O4 ON1 " \ "C5 CN3T " \ "C5M CN9 " \ "H51 HN9 " \ "H52 HN9 " \ "H53 HN9 " \ "C2' CN7B " \ "H2'' HN7 " \ "O2' ON5 " \ "H2' HN5 " \ "C3' CN7 " \ "H3' HN7 " \ "O3' ON2 " \ "P P " \ "O1P ON3 " \ "O2P ON3 " \ "O5' ON2 " \ "C5' CN8B " \ "H5' HN8 " \ "H5'' HN8 " \ "C4' CN7 " \ "H4' HN7 " \ "O4' ON6B " \ "C1' CN7B " \ "H1' HN7 " \ "N1 NN2B " \ "C6 CN3 " \ "H6 HN3 " \ "C2 CN1T " \ "O2 ON1 " \ "N3 NN2U " \ "H3 HN2 " \ "C4 CN1 " \ "O4 ON1 " \ "C5 CN3 " \ "H5 HN3 " \ "C2' CN7B " \ "H2'' HN7 " \ "O2' ON5 " \ "H2' HN5 " \ "C3' CN7 " \ "H3' HN7 " \ "O3' ON2 " \ "C4' CN7 " \ "H4' HN7 " \ "O4' ON6 " \ "C1' CN7B " \ "H1' HN7 " \ "C2' CN8 " \ "H2' HN8 " \ "H2'' HN8 " \ "C4' CN7 " \ "H4' HN7 " \ "O4' ON6 " \ "C1' CN7B " \ "H1' HN7 " \ "C2' CN8 " \ "H2' HN8 " \ "H2'' HN8 " \ "H5T HN5 " \ "O5' ON5 " \ "C5' CN8B " \ "H5' HN8 " \ "H5'' HN8 " \ "C5' CN9 " \ "H5' HN9 " \ "H5'' HN9 " \ "H53' HN9 " \ "C5' CN8B " \ "H5' HN8 " \ "H5'' HN8 " \ "P P " \ "O1P ON3 " \ "O2P ON3 " \ "O5' ON2 " \ "O5T ON4 " \ "H5T HN4 " \ "C5' CN8B " \ "H5' HN8 " \ "H5'' HN8 " \ "P P " \ "O1P ON3 " \ "O2P ON3 " \ "O5' ON2 " \ "O5T ON2 " \ "C5T CN9 " \ "H5T1 HN9 " \ "H5T2 HN9 " \ "H5T3 HN9 " \ "C3' CN7 " \ "H3' HN7 " \ "O3' ON5 " \ "H3T HN5 " \ "C3' CN7 " \ "H3' HN7 " \ "P3 P " \ "O1P3 ON3 " \ "O2P3 ON3 " \ "O3' ON2 " \ "O3T ON4 " \ "H3T HN4 " \ "C3' CN7 " \ "H3' HN7 " \ "P3 P " \ "O1P3 ON3 " \ "O2P3 ON3 " \ "O3' ON2 " \ "O3T ON2 " \ "C3T CN9 " \ "H3T1 HN9 " \ "H3T2 HN9 " \ "H3T3 HN9 " \ "C3' CN7 " \ "H3' HN7 " \ "P3 P " \ "O3' ON2 " \ "O1P3 ON3 " \ "O2P3 ON3 " \ "O3P3 ON3 " \ "OH2 OT " \ "H1 HT " \ "H2 HT " \ "OH2 OT " \ "H1 HT " \ "H2 HT " \ "SOD SOD " \ "MG MG " \ "POT POT " \ "CES CES " \ "CAL CAL " \ "CLA CLA " \ "ZN ZN " \ "N NTL " \ "C13 CTL5 " \ "H13A HL " \ "H13B HL " \ "H13C HL " \ "C14 CTL5 " \ "H14A HL " \ "H14B HL " \ "H14C HL " \ "C15 CTL5 " \ "H15A HL " \ "H15B HL " \ "H15C HL " \ "C12 CTL2 " \ "H12A HL " \ "H12B HL " \ "C11 CTL2 " \ "H11A HAL2 " \ "H11B HAL2 " \ "P PL " \ "O13 O2L " \ "O14 O2L " \ "O11 OSL " \ "O12 OSL " \ "C1 CTL2 " \ "HA HAL2 " \ "HB HAL2 " \ "C2 CTL2 " \ "HS HAL2 " \ "HR HAL2 " \ "C3 CTL2 " \ "HX HAL2 " \ "HY HAL2 " \ "O31 OSL " \ "C31 CL " \ "O32 OBL " \ "C32 CTL2 " \ "H2X HAL2 " \ "H2Y HAL2 " \ "C33 CTL2 " \ "H3X HAL2 " \ "H3Y HAL2 " \ "C34 CTL2 " \ "H4X HAL2 " \ "H4Y HAL2 " \ "C35 CTL2 " \ "H5X HAL2 " \ "H5Y HAL2 " \ "C36 CTL2 " \ "H6X HAL2 " \ "H6Y HAL2 " \ "C37 CTL2 " \ "H7X HAL2 " \ "H7Y HAL2 " \ "C38 CTL2 " \ "H8X HAL2 " \ "H8Y HAL2 " \ "C39 CTL2 " \ "H9X HAL2 " \ "H9Y HAL2 " \ "C310 CTL2 " \ "H10X HAL2 " \ "H10Y HAL2 " \ "C311 CTL2 " \ "H11X HAL2 " \ "H11Y HAL2 " \ "C312 CTL3 " \ "H12X HAL3 " \ "H12Y HAL3 " \ "H12Z HAL3 " \ "N NH3 " \ "HN1 HCL " \ "HN2 HCL " \ "HN3 HCL " \ "C12 CTL " \ "H12A HAL " \ "H12B HAL " \ "C11 CTL2 " \ "H11A HAL2 " \ "H11B HAL2 " \ "P PL " \ "O13 O2L " \ "O14 O2L " \ "O11 OSL " \ "O12 OSL " \ "C1 CTL2 " \ "HA HAL2 " \ "HB HAL2 " \ "C2 CTL1 " \ "HS HAL1 " \ "OH2 OHL " \ "HO2 HOL " \ "C3 CTL2 " \ "HX HAL2 " \ "HY HAL2 " \ "OH3 OHL " \ "HO3 HOL " \ "N NH3 " \ "HN1 HCL " \ "HN2 HCL " \ "HN3 HCL " \ "C12 CTL " \ "H12A HAL " \ "H12B HAL " \ "C11 CTL2 " \ "H11A HAL2 " \ "H11B HAL2 " \ "P PL " \ "O13 O2L " \ "O14 O2L " \ "O11 OSL " \ "O12 OSL " \ "C1 CTL2 " \ "HA HAL2 " \ "HB HAL2 " \ "C2 CTL1 " \ "HS HAL1 " \ "O21 OSL " \ "C21 CL " \ "O22 OBL " \ "C22 CTL2 " \ "H2R HAL2 " \ "H2S HAL2 " \ "C3 CTL2 " \ "HX HAL2 " \ "HY HAL2 " \ "O31 OSL " \ "C31 CL " \ "O32 OBL " \ "C32 CTL2 " \ "H2X HAL2 " \ "H2Y HAL2 " \ "C23 CTL2 " \ "H3R HAL2 " \ "H3S HAL2 " \ "C24 CTL2 " \ "H4R HAL2 " \ "H4S HAL2 " \ "C25 CTL2 " \ "H5R HAL2 " \ "H5S HAL2 " \ "C26 CTL2 " \ "H6R HAL2 " \ "H6S HAL2 " \ "C27 CTL2 " \ "H7R HAL2 " \ "H7S HAL2 " \ "C28 CTL2 " \ "H8R HAL2 " \ "H8S HAL2 " \ "C29 CTL2 " \ "H9R HAL2 " \ "H9S HAL2 " \ "C210 CTL2 " \ "H10R HAL2 " \ "H10S HAL2 " \ "C211 CTL2 " \ "H11R HAL2 " \ "H11S HAL2 " \ "C212 CTL3 " \ "H12R HAL3 " \ "H12S HAL3 " \ "H12T HAL3 " \ "C33 CTL2 " \ "H3X HAL2 " \ "H3Y HAL2 " \ "C34 CTL2 " \ "H4X HAL2 " \ "H4Y HAL2 " \ "C35 CTL2 " \ "H5X HAL2 " \ "H5Y HAL2 " \ "C36 CTL2 " \ "H6X HAL2 " \ "H6Y HAL2 " \ "C37 CTL2 " \ "H7X HAL2 " \ "H7Y HAL2 " \ "C38 CTL2 " \ "H8X HAL2 " \ "H8Y HAL2 " \ "C39 CTL2 " \ "H9X HAL2 " \ "H9Y HAL2 " \ "C310 CTL2 " \ "H10X HAL2 " \ "H10Y HAL2 " \ "C311 CTL2 " \ "H11X HAL2 " \ "H11Y HAL2 " \ "C312 CTL3 " \ "H12X HAL3 " \ "H12Y HAL3 " \ "H12Z HAL3 " \ "N NTL " \ "C13 CTL5 " \ "H13A HL " \ "H13B HL " \ "H13C HL " \ "C14 CTL5 " \ "H14A HL " \ "H14B HL " \ "H14C HL " \ "C15 CTL5 " \ "H15A HL " \ "H15B HL " \ "H15C HL " \ "C12 CTL2 " \ "H12A HL " \ "H12B HL " \ "C11 CTL2 " \ "H11A HAL2 " \ "H11B HAL2 " \ "P PL " \ "O13 O2L " \ "O14 O2L " \ "O11 OSL " \ "O12 OSL " \ "C1 CTL2 " \ "HA HAL2 " \ "HB HAL2 " \ "C2 CTL1 " \ "HS HAL1 " \ "O21 OSL " \ "C21 CL " \ "O22 OBL " \ "C22 CTL2 " \ "H2R HAL2 " \ "H2S HAL2 " \ "C3 CTL2 " \ "HX HAL2 " \ "HY HAL2 " \ "O31 OSL " \ "C31 CL " \ "O32 OBL " \ "C32 CTL2 " \ "H2X HAL2 " \ "H2Y HAL2 " \ "C23 CTL2 " \ "H3R HAL2 " \ "H3S HAL2 " \ "C24 CTL2 " \ "H4R HAL2 " \ "H4S HAL2 " \ "C25 CTL2 " \ "H5R HAL2 " \ "H5S HAL2 " \ "C26 CTL2 " \ "H6R HAL2 " \ "H6S HAL2 " \ "C27 CTL2 " \ "H7R HAL2 " \ "H7S HAL2 " \ "C28 CTL2 " \ "H8R HAL2 " \ "H8S HAL2 " \ "C29 CTL2 " \ "H9R HAL2 " \ "H9S HAL2 " \ "C210 CTL2 " \ "H10R HAL2 " \ "H10S HAL2 " \ "C211 CTL2 " \ "H11R HAL2 " \ "H11S HAL2 " \ "C212 CTL2 " \ "H12R HAL2 " \ "H12S HAL2 " \ "C213 CTL2 " \ "H13R HAL2 " \ "H13S HAL2 " \ "C214 CTL3 " \ "H14R HAL3 " \ "H14S HAL3 " \ "H14T HAL3 " \ "C33 CTL2 " \ "H3X HAL2 " \ "H3Y HAL2 " \ "C34 CTL2 " \ "H4X HAL2 " \ "H4Y HAL2 " \ "C35 CTL2 " \ "H5X HAL2 " \ "H5Y HAL2 " \ "C36 CTL2 " \ "H6X HAL2 " \ "H6Y HAL2 " \ "C37 CTL2 " \ "H7X HAL2 " \ "H7Y HAL2 " \ "C38 CTL2 " \ "H8X HAL2 " \ "H8Y HAL2 " \ "C39 CTL2 " \ "H9X HAL2 " \ "H9Y HAL2 " \ "C310 CTL2 " \ "H10X HAL2 " \ "H10Y HAL2 " \ "C311 CTL2 " \ "H11X HAL2 " \ "H11Y HAL2 " \ "C312 CTL2 " \ "H12X HAL2 " \ "H12Y HAL2 " \ "C313 CTL2 " \ "H13X HAL2 " \ "H13Y HAL2 " \ "C314 CTL3 " \ "H14X HAL3 " \ "H14Y HAL3 " \ "H14Z HAL3 " \ "S SL " \ "OS1 OSL " \ "OS2 O2L " \ "OS3 O2L " \ "OS4 O2L " \ "C1 CTL2 " \ "H11 HAL2 " \ "H12 HAL2 " \ "C2 CTL2 " \ "H21 HAL2 " \ "H22 HAL2 " \ "C3 CTL2 " \ "H31 HAL2 " \ "H32 HAL2 " \ "C4 CTL2 " \ "H41 HAL2 " \ "H42 HAL2 " \ "C5 CTL2 " \ "H51 HAL2 " \ "H52 HAL2 " \ "C6 CTL2 " \ "H61 HAL2 " \ "H62 HAL2 " \ "C7 CTL2 " \ "H71 HAL2 " \ "H72 HAL2 " \ "C8 CTL2 " \ "H81 HAL2 " \ "H82 HAL2 " \ "C9 CTL2 " \ "H91 HAL2 " \ "H92 HAL2 " \ "C10 CTL2 " \ "H101 HAL2 " \ "H102 HAL2 " \ "C11 CTL2 " \ "H111 HAL2 " \ "H112 HAL2 " \ "C12 CTL3 " \ "H121 HAL3 " \ "H122 HAL3 " \ "H123 HAL3 " \ "N NTL " \ "C11 CTL2 " \ "C12 CTL5 " \ "C13 CTL5 " \ "C14 CTL5 " \ "H11 HL " \ "H12 HL " \ "H21 HL " \ "H22 HL " \ "H23 HL " \ "H31 HL " \ "H32 HL " \ "H33 HL " \ "H41 HL " \ "H42 HL " \ "H43 HL " \ "C15 CTL2 " \ "H51 HAL2 " \ "H52 HAL2 " \ "P1 PL " \ "O3 O2L " \ "O4 O2L " \ "O1 OSL " \ "O2 OSL " \ "C1 CTL2 " \ "HA HAL2 " \ "HB HAL2 " \ "C2 CTL1 " \ "HS HAL1 " \ "O21 OSL " \ "C21 CL " \ "O22 OBL " \ "C22 CTL2 " \ "H2R HAL2 " \ "H2S HAL2 " \ "C3 CTL2 " \ "HX HAL2 " \ "HY HAL2 " \ "O31 OSL " \ "C31 CL " \ "O32 OBL " \ "C32 CTL2 " \ "H2X HAL2 " \ "H2Y HAL2 " \ "C23 CTL2 " \ "H3R HAL2 " \ "H3S HAL2 " \ "C24 CTL2 " \ "H4R HAL2 " \ "H4S HAL2 " \ "C25 CTL2 " \ "H5R HAL2 " \ "H5S HAL2 " \ "C26 CTL2 " \ "H6R HAL2 " \ "H6S HAL2 " \ "C27 CTL2 " \ "H7R HAL2 " \ "H7S HAL2 " \ "C28 CTL2 " \ "H8R HAL2 " \ "H8S HAL2 " \ "C29 CEL1 " \ "H91 HEL1 " \ "C210 CEL1 " \ "H101 HEL1 " \ "C211 CTL2 " \ "H11R HAL2 " \ "H11S HAL2 " \ "C212 CTL2 " \ "H12R HAL2 " \ "H12S HAL2 " \ "C213 CTL2 " \ "H13R HAL2 " \ "H13S HAL2 " \ "C214 CTL2 " \ "H14R HAL2 " \ "H14S HAL2 " \ "C215 CTL2 " \ "H15R HAL2 " \ "H15S HAL2 " \ "C216 CTL2 " \ "H16R HAL2 " \ "H16S HAL2 " \ "C217 CTL2 " \ "H17R HAL2 " \ "H17S HAL2 " \ "C218 CTL3 " \ "H18R HAL3 " \ "H18S HAL3 " \ "H18T HAL3 " \ "C33 CTL2 " \ "H3X HAL2 " \ "H3Y HAL2 " \ "C34 CTL2 " \ "H4X HAL2 " \ "H4Y HAL2 " \ "C35 CTL2 " \ "H5X HAL2 " \ "H5Y HAL2 " \ "C36 CTL2 " \ "H6X HAL2 " \ "H6Y HAL2 " \ "C37 CTL2 " \ "H7X HAL2 " \ "H7Y HAL2 " \ "C38 CTL2 " \ "H8X HAL2 " \ "H8Y HAL2 " \ "C39 CTL2 " \ "H9X HAL2 " \ "H9Y HAL2 " \ "C310 CTL2 " \ "H10X HAL2 " \ "H10Y HAL2 " \ "C311 CTL2 " \ "H11X HAL2 " \ "H11Y HAL2 " \ "C312 CTL2 " \ "H12X HAL2 " \ "H12Y HAL2 " \ "C313 CTL2 " \ "H13X HAL2 " \ "H13Y HAL2 " \ "C314 CTL2 " \ "H14X HAL2 " \ "H14Y HAL2 " \ "C315 CTL2 " \ "H15X HAL2 " \ "H15Y HAL2 " \ "C316 CTL3 " \ "H16X HAL3 " \ "H16Y HAL3 " \ "H16Z HAL3 " \ "N NH3 " \ "HN1 HCL " \ "HN2 HCL " \ "HN3 HCL " \ "C12 CTL " \ "H12A HAL " \ "H12B HAL " \ "C11 CTL2 " \ "H11A HAL2 " \ "H11B HAL2 " \ "P PL " \ "O13 O2L " \ "O14 O2L " \ "O11 OSL " \ "O12 OSL " \ "C1 CTL2 " \ "HA HAL2 " \ "HB HAL2 " \ "C2 CTL1 " \ "HS HAL1 " \ "O21 OSL " \ "C21 CL " \ "O22 OBL " \ "C22 CTL2 " \ "H2R HAL2 " \ "H2S HAL2 " \ "C3 CTL2 " \ "HX HAL2 " \ "HY HAL2 " \ "O31 OSL " \ "C31 CL " \ "O32 OBL " \ "C32 CTL2 " \ "H2X HAL2 " \ "H2Y HAL2 " \ "C23 CTL2 " \ "H3R HAL2 " \ "H3S HAL2 " \ "C24 CTL2 " \ "H4R HAL2 " \ "H4S HAL2 " \ "C25 CTL2 " \ "H5R HAL2 " \ "H5S HAL2 " \ "C26 CTL2 " \ "H6R HAL2 " \ "H6S HAL2 " \ "C27 CTL2 " \ "H7R HAL2 " \ "H7S HAL2 " \ "C28 CTL2 " \ "H8R HAL2 " \ "H8S HAL2 " \ "C29 CEL1 " \ "H91 HEL1 " \ "C210 CEL1 " \ "H101 HEL1 " \ "C211 CTL2 " \ "H11R HAL2 " \ "H11S HAL2 " \ "C212 CTL2 " \ "H12R HAL2 " \ "H12S HAL2 " \ "C213 CTL2 " \ "H13R HAL2 " \ "H13S HAL2 " \ "C214 CTL2 " \ "H14R HAL2 " \ "H14S HAL2 " \ "C215 CTL2 " \ "H15R HAL2 " \ "H15S HAL2 " \ "C216 CTL2 " \ "H16R HAL2 " \ "H16S HAL2 " \ "C217 CTL2 " \ "H17R HAL2 " \ "H17S HAL2 " \ "C218 CTL3 " \ "H18R HAL3 " \ "H18S HAL3 " \ "H18T HAL3 " \ "C33 CTL2 " \ "H3X HAL2 " \ "H3Y HAL2 " \ "C34 CTL2 " \ "H4X HAL2 " \ "H4Y HAL2 " \ "C35 CTL2 " \ "H5X HAL2 " \ "H5Y HAL2 " \ "C36 CTL2 " \ "H6X HAL2 " \ "H6Y HAL2 " \ "C37 CTL2 " \ "H7X HAL2 " \ "H7Y HAL2 " \ "C38 CTL2 " \ "H8X HAL2 " \ "H8Y HAL2 " \ "C39 CTL2 " \ "H9X HAL2 " \ "H9Y HAL2 " \ "C310 CTL2 " \ "H10X HAL2 " \ "H10Y HAL2 " \ "C311 CTL2 " \ "H11X HAL2 " \ "H11Y HAL2 " \ "C312 CTL2 " \ "H12X HAL2 " \ "H12Y HAL2 " \ "C313 CTL2 " \ "H13X HAL2 " \ "H13Y HAL2 " \ "C314 CTL2 " \ "H14X HAL2 " \ "H14Y HAL2 " \ "C315 CTL2 " \ "H15X HAL2 " \ "H15Y HAL2 " \ "C316 CTL3 " \ "H16X HAL3 " \ "H16Y HAL3 " \ "H16Z HAL3 " \ "C1 CL " \ "O1 OCL " \ "O2 OCL " \ "C2 CTL2 " \ "H2A HAL2 " \ "H2B HAL2 " \ "C3 CTL2 " \ "H3A HAL2 " \ "H3B HAL2 " \ "C4 CTL2 " \ "H4A HAL2 " \ "H4B HAL2 " \ "C5 CTL2 " \ "H5A HAL2 " \ "H5B HAL2 " \ "C6 CTL2 " \ "H6A HAL2 " \ "H6B HAL2 " \ "C7 CTL2 " \ "H7A HAL2 " \ "H7B HAL2 " \ "C8 CTL2 " \ "H8A HAL2 " \ "H8B HAL2 " \ "C9 CTL2 " \ "H9A HAL2 " \ "H9B HAL2 " \ "C10 CTL2 " \ "H10A HAL2 " \ "H10B HAL2 " \ "C11 CTL2 " \ "H11A HAL2 " \ "H11B HAL2 " \ "C12 CTL2 " \ "H12A HAL2 " \ "H12B HAL2 " \ "C13 CTL2 " \ "H13A HAL2 " \ "H13B HAL2 " \ "C14 CTL2 " \ "H14A HAL2 " \ "H14B HAL2 " \ "C15 CTL2 " \ "H15A HAL2 " \ "H15B HAL2 " \ "C16 CTL3 " \ "H16A HAL3 " \ "H16B HAL3 " \ "H16C HAL3 " \ "C1 CL " \ "O1 OCL " \ "O2 OCL " \ "C2 CTL2 " \ "H2A HAL2 " \ "H2B HAL2 " \ "C3 CTL2 " \ "H3A HAL2 " \ "H3B HAL2 " \ "C4 CTL2 " \ "H4A HAL2 " \ "H4B HAL2 " \ "C5 CTL2 " \ "H5A HAL2 " \ "H5B HAL2 " \ "C6 CTL2 " \ "H6A HAL2 " \ "H6B HAL2 " \ "C7 CTL2 " \ "H7A HAL2 " \ "H7B HAL2 " \ "C8 CTL2 " \ "H8A HAL2 " \ "H8B HAL2 " \ "C9 CEL1 " \ "H9A HEL1 " \ "C10 CEL1 " \ "H10A HEL1 " \ "C11 CTL2 " \ "H11A HAL2 " \ "H11B HAL2 " \ "C12 CTL2 " \ "H12A HAL2 " \ "H12B HAL2 " \ "C13 CTL2 " \ "H13A HAL2 " \ "H13B HAL2 " \ "C14 CTL2 " \ "H14A HAL2 " \ "H14B HAL2 " \ "C15 CTL2 " \ "H15A HAL2 " \ "H15B HAL2 " \ "C16 CTL2 " \ "H16A HAL2 " \ "H16B HAL2 " \ "C17 CTL2 " \ "H17A HAL2 " \ "H17B HAL2 " \ "C18 CTL3 " \ "H18A HAL3 " \ "H18B HAL3 " \ "H18C HAL3 " \ "C1 CL " \ "O1 OCL " \ "O2 OCL " \ "C2 CTL2 " \ "H2A HAL2 " \ "H2B HAL2 " \ "C3 CTL2 " \ "H3A HAL2 " \ "H3B HAL2 " \ "C4 CEL1 " \ "H4 HEL1 " \ "C5 CEL1 " \ "H5 HEL1 " \ "C6 CTL2 " \ "H6A HAL2 " \ "H6B HAL2 " \ "C7 CEL1 " \ "H7 HEL1 " \ "C8 CEL1 " \ "H8 HEL1 " \ "C9 CTL2 " \ "H9A HAL2 " \ "H9B HAL2 " \ "C10 CEL1 " \ "H10 HEL1 " \ "C11 CEL1 " \ "H11 HEL1 " \ "C12 CTL2 " \ "H12A HAL2 " \ "H12B HAL2 " \ "C13 CEL1 " \ "H13 HEL1 " \ "C14 CEL1 " \ "H14 HEL1 " \ "C15 CTL2 " \ "H15A HAL2 " \ "H15B HAL2 " \ "C16 CEL1 " \ "H16 HEL1 " \ "C17 CEL1 " \ "H17 HEL1 " \ "C18 CTL2 " \ "H18A HAL2 " \ "H18B HAL2 " \ "C19 CEL1 " \ "H19 HEL1 " \ "C20 CEL1 " \ "H20 HEL1 " \ "C21 CTL2 " \ "H21A HAL2 " \ "H21B HAL2 " \ "C22 CTL3 " \ "H22A HAL3 " \ "H22B HAL3 " \ "H22C HAL3 " \ "C1 CL " \ "O1 OCL " \ "O2 OCL " \ "C2 CTL2 " \ "H2A HAL2 " \ "H2B HAL2 " \ "C3 CTL2 " \ "H3A HAL2 " \ "H3B HAL2 " \ "C4 CTL2 " \ "H4A HAL2 " \ "H4B HAL2 " \ "C5 CTL2 " \ "H5A HAL2 " \ "H5B HAL2 " \ "C6 CTL2 " \ "H6A HAL2 " \ "H6B HAL2 " \ "C7 CTL2 " \ "H7A HAL2 " \ "H7B HAL2 " \ "C8 CTL2 " \ "H8A HAL2 " \ "H8B HAL2 " \ "C9 CTL2 " \ "H9A HAL2 " \ "H9B HAL2 " \ "C10 CTL2 " \ "H10A HAL2 " \ "H10B HAL2 " \ "C11 CTL2 " \ "H11A HAL2 " \ "H11B HAL2 " \ "C12 CTL2 " \ "H12A HAL2 " \ "H12B HAL2 " \ "C13 CTL2 " \ "H13A HAL2 " \ "H13B HAL2 " \ "C14 CTL2 " \ "H14A HAL2 " \ "H14B HAL2 " \ "C15 CTL2 " \ "H15A HAL2 " \ "H15B HAL2 " \ "C16 CTL2 " \ "H16A HAL2 " \ "H16B HAL2 " \ "C17 CTL2 " \ "H17A HAL2 " \ "H17B HAL2 " \ "C18 CTL3 " \ "H18A HAL3 " \ "H18B HAL3 " \ "H18C HAL3 " \ "N NTL " \ "C5 CTL2 " \ "C6 CTL5 " \ "C7 CTL5 " \ "C8 CTL5 " \ "H5A HL " \ "H5B HL " \ "H6A HL " \ "H6B HL " \ "H6C HL " \ "H7A HL " \ "H7B HL " \ "H7C HL " \ "H8A HL " \ "H8B HL " \ "H8C HL " \ "C4 CTL2 " \ "H4A HAL2 " \ "H4B HAL2 " \ "P PL " \ "OP3 O2L " \ "OP4 O2L " \ "OP1 OSL " \ "OP2 OSL " \ "C3 CTL2 " \ "H3A HAL2 " \ "H3B HAL2 " \ "C2 CTL1 " \ "H2A HAL1 " \ "O2 OHL " \ "H2 HOL " \ "C1 CTL2 " \ "H1A HAL2 " \ "H1B HAL2 " \ "O1 OHL " \ "H1 HOL " \ "1C1 CTL2 " \ "1H1A HAL2 " \ "1H1B HAL2 " \ "1O1 OSL " \ "2C1 CL " \ "2O1 OBL " \ "2C2 CTL2 " \ "2H2A HAL2 " \ "2H2B HAL2 " \ "1C2 CTL1 " \ "1H2A HAL1 " \ "1O2 OSL " \ "2C1 CL " \ "2O1 OBL " \ "2C2 CTL2 " \ "2H2A HAL2 " \ "2H2B HAL2 " \ "P P " \ "O1P ON3 " \ "O2P ON3 " \ "O5' ON2 " \ "C5' CN8B " \ "H5' HN8 " \ "H5'' HN8 " \ "C4' CN7 " \ "H4' HN7 " \ "O4' ON6B " \ "C1' CN7B " \ "H1' HN7 " \ "N9 NN2B " \ "C4 CN5 " \ "N2 NN1 " \ "H21 HN1 " \ "H22 HN1 " \ "N3 NN3G " \ "C2 CN2 " \ "N1 NN2G " \ "H1 HN2 " \ "C6 CN1 " \ "O6 ON1 " \ "C5 CN5G " \ "N7 NN4 " \ "C8 CN4 " \ "H8 HN3 " \ "C2' CN7B " \ "H2'' HN7 " \ "O2' ON5 " \ "H2' HN5 " \ "C3' CN7 " \ "H3' HN7 " \ "O3' ON2 " \ "P P " \ "O1P ON3 " \ "O2P ON3 " \ "O5' ON2 " \ "C5' CN8B " \ "H5' HN8 " \ "H5'' HN8 " \ "C4' CN7 " \ "H4' HN7 " \ "O4' ON6B " \ "C1' CN7B " \ "H1' HN7 " \ "N9 NN2 " \ "C5 CN5 " \ "N7 NN4 " \ "C8 CN4 " \ "H8 HN3 " \ "N1 NN3A " \ "C2 CN4 " \ "H2 HN3 " \ "N3 NN3A " \ "C4 CN5 " \ "C6 CN2 " \ "N6 NN1 " \ "H61 HN1 " \ "H62 HN1 " \ "C2' CN7B " \ "H2'' HN7 " \ "O2' ON5 " \ "H2' HN5 " \ "C3' CN7 " \ "H3' HN7 " \ "O3' ON2 " \ "P P " \ "O1P ON3 " \ "O2P ON3 " \ "O5' ON2 " \ "C5' CN8B " \ "H5' HN8 " \ "H5'' HN8 " \ "C4' CN7 " \ "H4' HN7 " \ "O4' ON6B " \ "C1' CN7B " \ "H1' HN7 " \ "N1 NN2 " \ "C6 CN3 " \ "H6 HN3 " \ "C5 CN3 " \ "H5 HN3 " \ "C2 CN1 " \ "O2 ON1C " \ "N3 NN3 " \ "C4 CN2 " \ "N4 NN1 " \ "H41 HN1 " \ "H42 HN1 " \ "C2' CN7B " \ "H2'' HN7 " \ "O2' ON5 " \ "H2' HN5 " \ "C3' CN7 " \ "H3' HN7 " \ "O3' ON2 " \ "P P " \ "O1P ON3 " \ "O2P ON3 " \ "O5' ON2 " \ "C5' CN8B " \ "H5' HN8 " \ "H5'' HN8 " \ "C4' CN7 " \ "H4' HN7 " \ "O4' ON6B " \ "C1' CN7B " \ "H1' HN7 " \ "N1 NN2B " \ "C6 CN3 " \ "H6 HN3 " \ "C2 CN1T " \ "O2 ON1 " \ "N3 NN2U " \ "H3 HN2 " \ "C4 CN1 " \ "O4 ON1 " \ "C5 CN3T " \ "C5M CN9 " \ "H51 HN9 " \ "H52 HN9 " \ "H53 HN9 " \ "C2' CN7B " \ "H2'' HN7 " \ "O2' ON5 " \ "H2' HN5 " \ "C3' CN7 " \ "H3' HN7 " \ "O3' ON2 " \ "P P " \ "O1P ON3 " \ "O2P ON3 " \ "O5' ON2 " \ "C5' CN8B " \ "H5' HN8 " \ "H5'' HN8 " \ "C4' CN7 " \ "H4' HN7 " \ "O4' ON6B " \ "C1' CN7B " \ "H1' HN7 " \ "N1 NN2B " \ "C6 CN3 " \ "H6 HN3 " \ "C2 CN1T " \ "O2 ON1 " \ "N3 NN2U " \ "H3 HN2 " \ "C4 CN1 " \ "O4 ON1 " \ "C5 CN3 " \ "H5 HN3 " \ "C2' CN7B " \ "H2'' HN7 " \ "O2' ON5 " \ "H2' HN5 " \ "C3' CN7 " \ "H3' HN7 " \ "O3' ON2 " \ "C4' CN7 " \ "H4' HN7 " \ "O4' ON6 " \ "C1' CN7B " \ "H1' HN7 " \ "C2' CN8 " \ "H2' HN8 " \ "H2'' HN8 " \ "C4' CN7 " \ "H4' HN7 " \ "O4' ON6 " \ "C1' CN7B " \ "H1' HN7 " \ "C2' CN8 " \ "H2' HN8 " \ "H2'' HN8 " \ "H5T HN5 " \ "O5' ON5 " \ "C5' CN8B " \ "H5' HN8 " \ "H5'' HN8 " \ "C5' CN9 " \ "H5' HN9 " \ "H5'' HN9 " \ "H53' HN9 " \ "C5' CN8B " \ "H5' HN8 " \ "H5'' HN8 " \ "P P " \ "O1P ON3 " \ "O2P ON3 " \ "O5' ON2 " \ "O5T ON4 " \ "H5T HN4 " \ "C5' CN8B " \ "H5' HN8 " \ "H5'' HN8 " \ "P P " \ "O1P ON3 " \ "O2P ON3 " \ "O5' ON2 " \ "O5T ON2 " \ "C5T CN9 " \ "H5T1 HN9 " \ "H5T2 HN9 " \ "H5T3 HN9 " \ "C3' CN7 " \ "H3' HN7 " \ "O3' ON5 " \ "H3T HN5 " \ "C3' CN7 " \ "H3' HN7 " \ "P3 P " \ "O1P3 ON3 " \ "O2P3 ON3 " \ "O3' ON2 " \ "O3T ON4 " \ "H3T HN4 " \ "C3' CN7 " \ "H3' HN7 " \ "P3 P " \ "O1P3 ON3 " \ "O2P3 ON3 " \ "O3' ON2 " \ "O3T ON2 " \ "C3T CN9 " \ "H3T1 HN9 " \ "H3T2 HN9 " \ "H3T3 HN9 " \ "C3' CN7 " \ "H3' HN7 " \ "P3 P " \ "O3' ON2 " \ "O1P3 ON3 " \ "O2P3 ON3 " \ "O3P3 ON3 " \ "OH2 OT " \ "H1 HT " \ "H2 HT " \ "OH2 OT " \ "H1 HT " \ "H2 HT " \ "SOD SOD " \ "MG MG " \ "POT POT " \ "CES CES " \ "CAL CAL " \ "CLA CLA " \ "ZN ZN " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT3 " \ "HB1 HA " \ "HB2 HA " \ "HB3 HA " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "CG CT2 " \ "HG1 HA " \ "HG2 HA " \ "CD CT2 " \ "HD1 HA " \ "HD2 HA " \ "NE NC2 " \ "HE HC " \ "CZ C " \ "NH1 NC2 " \ "HH11 HC " \ "HH12 HC " \ "NH2 NC2 " \ "HH21 HC " \ "HH22 HC " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "CG CC " \ "OD1 O " \ "ND2 NH2 " \ "HD21 H " \ "HD22 H " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "CG CC " \ "OD1 OC " \ "OD2 OC " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "SG S " \ "HG1 HS " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "CG CT2 " \ "HG1 HA " \ "HG2 HA " \ "CD CC " \ "OE1 O " \ "NE2 NH2 " \ "HE21 H " \ "HE22 H " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "CG CT2 " \ "HG1 HA " \ "HG2 HA " \ "CD CC " \ "OE1 OC " \ "OE2 OC " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT2 " \ "HA1 HB " \ "HA2 HB " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "ND1 NR1 " \ "HD1 H " \ "CG CPH1 " \ "CE1 CPH2 " \ "HE1 HR1 " \ "NE2 NR2 " \ "CD2 CPH1 " \ "HD2 HR3 " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "ND1 NR2 " \ "CG CPH1 " \ "CE1 CPH2 " \ "HE1 HR1 " \ "NE2 NR1 " \ "HE2 H " \ "CD2 CPH1 " \ "HD2 HR3 " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "CD2 CPH1 " \ "HD2 HR1 " \ "CG CPH1 " \ "NE2 NR3 " \ "HE2 H " \ "ND1 NR3 " \ "HD1 H " \ "CE1 CPH2 " \ "HE1 HR2 " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT1 " \ "HB HA " \ "CG2 CT3 " \ "HG21 HA " \ "HG22 HA " \ "HG23 HA " \ "CG1 CT2 " \ "HG11 HA " \ "HG12 HA " \ "CD CT3 " \ "HD1 HA " \ "HD2 HA " \ "HD3 HA " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "CG CT1 " \ "HG HA " \ "CD1 CT3 " \ "HD11 HA " \ "HD12 HA " \ "HD13 HA " \ "CD2 CT3 " \ "HD21 HA " \ "HD22 HA " \ "HD23 HA " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "CG CT2 " \ "HG1 HA " \ "HG2 HA " \ "CD CT2 " \ "HD1 HA " \ "HD2 HA " \ "CE CT2 " \ "HE1 HA " \ "HE2 HA " \ "NZ NH3 " \ "HZ1 HC " \ "HZ2 HC " \ "HZ3 HC " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "CG CT2 " \ "HG1 HA " \ "HG2 HA " \ "SD S " \ "CE CT3 " \ "HE1 HA " \ "HE2 HA " \ "HE3 HA " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "CG CA " \ "CD1 CA " \ "HD1 HP " \ "CE1 CA " \ "HE1 HP " \ "CZ CA " \ "HZ HP " \ "CD2 CA " \ "HD2 HP " \ "CE2 CA " \ "HE2 HP " \ "C C " \ "O O " \ "N N " \ "CD CP3 " \ "HD1 HA " \ "HD2 HA " \ "CA CP1 " \ "HA HB " \ "CB CP2 " \ "HB1 HA " \ "HB2 HA " \ "CG CP2 " \ "HG1 HA " \ "HG2 HA " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "OG OH1 " \ "HG1 H " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT1 " \ "HB HA " \ "OG1 OH1 " \ "HG1 H " \ "CG2 CT3 " \ "HG21 HA " \ "HG22 HA " \ "HG23 HA " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "CG CY " \ "CD1 CA " \ "HD1 HP " \ "NE1 NY " \ "HE1 H " \ "CE2 CPT " \ "CD2 CPT " \ "CE3 CA " \ "HE3 HP " \ "CZ3 CA " \ "HZ3 HP " \ "CZ2 CA " \ "HZ2 HP " \ "CH2 CA " \ "HH2 HP " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "CG CA " \ "CD1 CA " \ "HD1 HP " \ "CE1 CA " \ "HE1 HP " \ "CZ CA " \ "OH OH1 " \ "HH H " \ "CD2 CA " \ "HD2 HP " \ "CE2 CA " \ "HE2 HP " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT1 " \ "HB HA " \ "CG1 CT3 " \ "HG11 HA " \ "HG12 HA " \ "HG13 HA " \ "CG2 CT3 " \ "HG21 HA " \ "HG22 HA " \ "HG23 HA " \ "C C " \ "O O " \ "CL CT3 " \ "HL1 HA " \ "HL2 HA " \ "HL3 HA " \ "CLP C " \ "OL O " \ "NL NH1 " \ "HL H " \ "CA CT1 " \ "HA HB " \ "CB CT3 " \ "HB1 HA " \ "HB2 HA " \ "HB3 HA " \ "CRP C " \ "OR O " \ "NR NH1 " \ "HR H " \ "CR CT3 " \ "HR1 HA " \ "HR2 HA " \ "HR3 HA " \ "OH2 OT " \ "H1 HT " \ "H2 HT " \ "OH2 OT " \ "H1 HT " \ "H2 HT " \ "N NH3 " \ "HT1 HC " \ "HT2 HC " \ "HT3 HC " \ "CA CT1 " \ "HA HB " \ "N NH3 " \ "HT1 HC " \ "HT2 HC " \ "HT3 HC " \ "CA CT2 " \ "HA1 HB " \ "HA2 HB " \ "N NP " \ "HN1 HC " \ "HN2 HC " \ "CD CP3 " \ "HD1 HA " \ "HD2 HA " \ "CA CP1 " \ "HA HB " \ "CAY CT3 " \ "HY1 HA " \ "HY2 HA " \ "HY3 HA " \ "CY C " \ "OY O " \ "CAY CT3 " \ "HY1 HA " \ "HY2 HA " \ "HY3 HA " \ "CY C " \ "OY O " \ "C CC " \ "OT1 OC " \ "OT2 OC " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "C CD " \ "OT1 OB " \ "OT2 OS " \ "CT CT3 " \ "HT1 HA " \ "HT2 HA " \ "HT3 HA " \ "C CC " \ "O O " \ "NT NH2 " \ "HT1 H " \ "HT2 H " \ "C C " \ "O O " \ "NT NH1 " \ "HNT H " \ "CAT CT3 " \ "HT1 HA " \ "HT2 HA " \ "HT3 HA " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "CG CD " \ "OD1 OB " \ "OD2 OH1 " \ "HD2 H " \ "CG CT2 " \ "HG1 HA " \ "HG2 HA " \ "CD CD " \ "OE1 OB " \ "OE2 OH1 " \ "HE2 H " \ "CE CT2 " \ "HE1 HA " \ "HE2 HA " \ "NZ NH2 " \ "HZ1 HC " \ "HZ2 HC " \ "1CB CT2 " \ "1SG SM " \ "2SG SM " \ "2CB CT2 " \ "CE1 CPH2 " \ "HE1 HR1 " \ "ND1 NR2 " \ "CG CPH1 " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "NE2 NR1 " \ "HE2 H " \ "CD2 CPH1 " \ "HD2 HR3 " \ "N NTL " \ "C13 CTL5 " \ "H13A HL " \ "H13B HL " \ "H13C HL " \ "C14 CTL5 " \ "H14A HL " \ "H14B HL " \ "H14C HL " \ "C15 CTL5 " \ "H15A HL " \ "H15B HL " \ "H15C HL " \ "C12 CTL2 " \ "H12A HL " \ "H12B HL " \ "C11 CTL2 " \ "H11A HAL2 " \ "H11B HAL2 " \ "P PL " \ "O13 O2L " \ "O14 O2L " \ "O11 OSL " \ "O12 OSL " \ "C1 CTL2 " \ "HA HAL2 " \ "HB HAL2 " \ "C2 CTL2 " \ "HS HAL2 " \ "HR HAL2 " \ "C3 CTL2 " \ "HX HAL2 " \ "HY HAL2 " \ "O31 OSL " \ "C31 CL " \ "O32 OBL " \ "C32 CTL2 " \ "H2X HAL2 " \ "H2Y HAL2 " \ "C33 CTL2 " \ "H3X HAL2 " \ "H3Y HAL2 " \ "C34 CTL2 " \ "H4X HAL2 " \ "H4Y HAL2 " \ "C35 CTL2 " \ "H5X HAL2 " \ "H5Y HAL2 " \ "C36 CTL2 " \ "H6X HAL2 " \ "H6Y HAL2 " \ "C37 CTL2 " \ "H7X HAL2 " \ "H7Y HAL2 " \ "C38 CTL2 " \ "H8X HAL2 " \ "H8Y HAL2 " \ "C39 CTL2 " \ "H9X HAL2 " \ "H9Y HAL2 " \ "C310 CTL2 " \ "H10X HAL2 " \ "H10Y HAL2 " \ "C311 CTL2 " \ "H11X HAL2 " \ "H11Y HAL2 " \ "C312 CTL3 " \ "H12X HAL3 " \ "H12Y HAL3 " \ "H12Z HAL3 " \ "N NH3 " \ "HN1 HCL " \ "HN2 HCL " \ "HN3 HCL " \ "C12 CTL " \ "H12A HAL " \ "H12B HAL " \ "C11 CTL2 " \ "H11A HAL2 " \ "H11B HAL2 " \ "P PL " \ "O13 O2L " \ "O14 O2L " \ "O11 OSL " \ "O12 OSL " \ "C1 CTL2 " \ "HA HAL2 " \ "HB HAL2 " \ "C2 CTL1 " \ "HS HAL1 " \ "OH2 OHL " \ "HO2 HOL " \ "C3 CTL2 " \ "HX HAL2 " \ "HY HAL2 " \ "OH3 OHL " \ "HO3 HOL " \ "N NH3 " \ "HN1 HCL " \ "HN2 HCL " \ "HN3 HCL " \ "C12 CTL " \ "H12A HAL " \ "H12B HAL " \ "C11 CTL2 " \ "H11A HAL2 " \ "H11B HAL2 " \ "P PL " \ "O13 O2L " \ "O14 O2L " \ "O11 OSL " \ "O12 OSL " \ "C1 CTL2 " \ "HA HAL2 " \ "HB HAL2 " \ "C2 CTL1 " \ "HS HAL1 " \ "O21 OSL " \ "C21 CL " \ "O22 OBL " \ "C22 CTL2 " \ "H2R HAL2 " \ "H2S HAL2 " \ "C3 CTL2 " \ "HX HAL2 " \ "HY HAL2 " \ "O31 OSL " \ "C31 CL " \ "O32 OBL " \ "C32 CTL2 " \ "H2X HAL2 " \ "H2Y HAL2 " \ "C23 CTL2 " \ "H3R HAL2 " \ "H3S HAL2 " \ "C24 CTL2 " \ "H4R HAL2 " \ "H4S HAL2 " \ "C25 CTL2 " \ "H5R HAL2 " \ "H5S HAL2 " \ "C26 CTL2 " \ "H6R HAL2 " \ "H6S HAL2 " \ "C27 CTL2 " \ "H7R HAL2 " \ "H7S HAL2 " \ "C28 CTL2 " \ "H8R HAL2 " \ "H8S HAL2 " \ "C29 CTL2 " \ "H9R HAL2 " \ "H9S HAL2 " \ "C210 CTL2 " \ "H10R HAL2 " \ "H10S HAL2 " \ "C211 CTL2 " \ "H11R HAL2 " \ "H11S HAL2 " \ "C212 CTL3 " \ "H12R HAL3 " \ "H12S HAL3 " \ "H12T HAL3 " \ "C33 CTL2 " \ "H3X HAL2 " \ "H3Y HAL2 " \ "C34 CTL2 " \ "H4X HAL2 " \ "H4Y HAL2 " \ "C35 CTL2 " \ "H5X HAL2 " \ "H5Y HAL2 " \ "C36 CTL2 " \ "H6X HAL2 " \ "H6Y HAL2 " \ "C37 CTL2 " \ "H7X HAL2 " \ "H7Y HAL2 " \ "C38 CTL2 " \ "H8X HAL2 " \ "H8Y HAL2 " \ "C39 CTL2 " \ "H9X HAL2 " \ "H9Y HAL2 " \ "C310 CTL2 " \ "H10X HAL2 " \ "H10Y HAL2 " \ "C311 CTL2 " \ "H11X HAL2 " \ "H11Y HAL2 " \ "C312 CTL3 " \ "H12X HAL3 " \ "H12Y HAL3 " \ "H12Z HAL3 " \ "N NTL " \ "C13 CTL5 " \ "H13A HL " \ "H13B HL " \ "H13C HL " \ "C14 CTL5 " \ "H14A HL " \ "H14B HL " \ "H14C HL " \ "C15 CTL5 " \ "H15A HL " \ "H15B HL " \ "H15C HL " \ "C12 CTL2 " \ "H12A HL " \ "H12B HL " \ "C11 CTL2 " \ "H11A HAL2 " \ "H11B HAL2 " \ "P PL " \ "O13 O2L " \ "O14 O2L " \ "O11 OSL " \ "O12 OSL " \ "C1 CTL2 " \ "HA HAL2 " \ "HB HAL2 " \ "C2 CTL1 " \ "HS HAL1 " \ "O21 OSL " \ "C21 CL " \ "O22 OBL " \ "C22 CTL2 " \ "H2R HAL2 " \ "H2S HAL2 " \ "C3 CTL2 " \ "HX HAL2 " \ "HY HAL2 " \ "O31 OSL " \ "C31 CL " \ "O32 OBL " \ "C32 CTL2 " \ "H2X HAL2 " \ "H2Y HAL2 " \ "C23 CTL2 " \ "H3R HAL2 " \ "H3S HAL2 " \ "C24 CTL2 " \ "H4R HAL2 " \ "H4S HAL2 " \ "C25 CTL2 " \ "H5R HAL2 " \ "H5S HAL2 " \ "C26 CTL2 " \ "H6R HAL2 " \ "H6S HAL2 " \ "C27 CTL2 " \ "H7R HAL2 " \ "H7S HAL2 " \ "C28 CTL2 " \ "H8R HAL2 " \ "H8S HAL2 " \ "C29 CTL2 " \ "H9R HAL2 " \ "H9S HAL2 " \ "C210 CTL2 " \ "H10R HAL2 " \ "H10S HAL2 " \ "C211 CTL2 " \ "H11R HAL2 " \ "H11S HAL2 " \ "C212 CTL2 " \ "H12R HAL2 " \ "H12S HAL2 " \ "C213 CTL2 " \ "H13R HAL2 " \ "H13S HAL2 " \ "C214 CTL3 " \ "H14R HAL3 " \ "H14S HAL3 " \ "H14T HAL3 " \ "C33 CTL2 " \ "H3X HAL2 " \ "H3Y HAL2 " \ "C34 CTL2 " \ "H4X HAL2 " \ "H4Y HAL2 " \ "C35 CTL2 " \ "H5X HAL2 " \ "H5Y HAL2 " \ "C36 CTL2 " \ "H6X HAL2 " \ "H6Y HAL2 " \ "C37 CTL2 " \ "H7X HAL2 " \ "H7Y HAL2 " \ "C38 CTL2 " \ "H8X HAL2 " \ "H8Y HAL2 " \ "C39 CTL2 " \ "H9X HAL2 " \ "H9Y HAL2 " \ "C310 CTL2 " \ "H10X HAL2 " \ "H10Y HAL2 " \ "C311 CTL2 " \ "H11X HAL2 " \ "H11Y HAL2 " \ "C312 CTL2 " \ "H12X HAL2 " \ "H12Y HAL2 " \ "C313 CTL2 " \ "H13X HAL2 " \ "H13Y HAL2 " \ "C314 CTL3 " \ "H14X HAL3 " \ "H14Y HAL3 " \ "H14Z HAL3 " \ "S SL " \ "OS1 OSL " \ "OS2 O2L " \ "OS3 O2L " \ "OS4 O2L " \ "C1 CTL2 " \ "H11 HAL2 " \ "H12 HAL2 " \ "C2 CTL2 " \ "H21 HAL2 " \ "H22 HAL2 " \ "C3 CTL2 " \ "H31 HAL2 " \ "H32 HAL2 " \ "C4 CTL2 " \ "H41 HAL2 " \ "H42 HAL2 " \ "C5 CTL2 " \ "H51 HAL2 " \ "H52 HAL2 " \ "C6 CTL2 " \ "H61 HAL2 " \ "H62 HAL2 " \ "C7 CTL2 " \ "H71 HAL2 " \ "H72 HAL2 " \ "C8 CTL2 " \ "H81 HAL2 " \ "H82 HAL2 " \ "C9 CTL2 " \ "H91 HAL2 " \ "H92 HAL2 " \ "C10 CTL2 " \ "H101 HAL2 " \ "H102 HAL2 " \ "C11 CTL2 " \ "H111 HAL2 " \ "H112 HAL2 " \ "C12 CTL3 " \ "H121 HAL3 " \ "H122 HAL3 " \ "H123 HAL3 " \ "N NTL " \ "C11 CTL2 " \ "C12 CTL5 " \ "C13 CTL5 " \ "C14 CTL5 " \ "H11 HL " \ "H12 HL " \ "H21 HL " \ "H22 HL " \ "H23 HL " \ "H31 HL " \ "H32 HL " \ "H33 HL " \ "H41 HL " \ "H42 HL " \ "H43 HL " \ "C15 CTL2 " \ "H51 HAL2 " \ "H52 HAL2 " \ "P1 PL " \ "O3 O2L " \ "O4 O2L " \ "O1 OSL " \ "O2 OSL " \ "C1 CTL2 " \ "HA HAL2 " \ "HB HAL2 " \ "C2 CTL1 " \ "HS HAL1 " \ "O21 OSL " \ "C21 CL " \ "O22 OBL " \ "C22 CTL2 " \ "H2R HAL2 " \ "H2S HAL2 " \ "C3 CTL2 " \ "HX HAL2 " \ "HY HAL2 " \ "O31 OSL " \ "C31 CL " \ "O32 OBL " \ "C32 CTL2 " \ "H2X HAL2 " \ "H2Y HAL2 " \ "C23 CTL2 " \ "H3R HAL2 " \ "H3S HAL2 " \ "C24 CTL2 " \ "H4R HAL2 " \ "H4S HAL2 " \ "C25 CTL2 " \ "H5R HAL2 " \ "H5S HAL2 " \ "C26 CTL2 " \ "H6R HAL2 " \ "H6S HAL2 " \ "C27 CTL2 " \ "H7R HAL2 " \ "H7S HAL2 " \ "C28 CTL2 " \ "H8R HAL2 " \ "H8S HAL2 " \ "C29 CEL1 " \ "H91 HEL1 " \ "C210 CEL1 " \ "H101 HEL1 " \ "C211 CTL2 " \ "H11R HAL2 " \ "H11S HAL2 " \ "C212 CTL2 " \ "H12R HAL2 " \ "H12S HAL2 " \ "C213 CTL2 " \ "H13R HAL2 " \ "H13S HAL2 " \ "C214 CTL2 " \ "H14R HAL2 " \ "H14S HAL2 " \ "C215 CTL2 " \ "H15R HAL2 " \ "H15S HAL2 " \ "C216 CTL2 " \ "H16R HAL2 " \ "H16S HAL2 " \ "C217 CTL2 " \ "H17R HAL2 " \ "H17S HAL2 " \ "C218 CTL3 " \ "H18R HAL3 " \ "H18S HAL3 " \ "H18T HAL3 " \ "C33 CTL2 " \ "H3X HAL2 " \ "H3Y HAL2 " \ "C34 CTL2 " \ "H4X HAL2 " \ "H4Y HAL2 " \ "C35 CTL2 " \ "H5X HAL2 " \ "H5Y HAL2 " \ "C36 CTL2 " \ "H6X HAL2 " \ "H6Y HAL2 " \ "C37 CTL2 " \ "H7X HAL2 " \ "H7Y HAL2 " \ "C38 CTL2 " \ "H8X HAL2 " \ "H8Y HAL2 " \ "C39 CTL2 " \ "H9X HAL2 " \ "H9Y HAL2 " \ "C310 CTL2 " \ "H10X HAL2 " \ "H10Y HAL2 " \ "C311 CTL2 " \ "H11X HAL2 " \ "H11Y HAL2 " \ "C312 CTL2 " \ "H12X HAL2 " \ "H12Y HAL2 " \ "C313 CTL2 " \ "H13X HAL2 " \ "H13Y HAL2 " \ "C314 CTL2 " \ "H14X HAL2 " \ "H14Y HAL2 " \ "C315 CTL2 " \ "H15X HAL2 " \ "H15Y HAL2 " \ "C316 CTL3 " \ "H16X HAL3 " \ "H16Y HAL3 " \ "H16Z HAL3 " \ "N NH3 " \ "HN1 HCL " \ "HN2 HCL " \ "HN3 HCL " \ "C12 CTL " \ "H12A HAL " \ "H12B HAL " \ "C11 CTL2 " \ "H11A HAL2 " \ "H11B HAL2 " \ "P PL " \ "O13 O2L " \ "O14 O2L " \ "O11 OSL " \ "O12 OSL " \ "C1 CTL2 " \ "HA HAL2 " \ "HB HAL2 " \ "C2 CTL1 " \ "HS HAL1 " \ "O21 OSL " \ "C21 CL " \ "O22 OBL " \ "C22 CTL2 " \ "H2R HAL2 " \ "H2S HAL2 " \ "C3 CTL2 " \ "HX HAL2 " \ "HY HAL2 " \ "O31 OSL " \ "C31 CL " \ "O32 OBL " \ "C32 CTL2 " \ "H2X HAL2 " \ "H2Y HAL2 " \ "C23 CTL2 " \ "H3R HAL2 " \ "H3S HAL2 " \ "C24 CTL2 " \ "H4R HAL2 " \ "H4S HAL2 " \ "C25 CTL2 " \ "H5R HAL2 " \ "H5S HAL2 " \ "C26 CTL2 " \ "H6R HAL2 " \ "H6S HAL2 " \ "C27 CTL2 " \ "H7R HAL2 " \ "H7S HAL2 " \ "C28 CTL2 " \ "H8R HAL2 " \ "H8S HAL2 " \ "C29 CEL1 " \ "H91 HEL1 " \ "C210 CEL1 " \ "H101 HEL1 " \ "C211 CTL2 " \ "H11R HAL2 " \ "H11S HAL2 " \ "C212 CTL2 " \ "H12R HAL2 " \ "H12S HAL2 " \ "C213 CTL2 " \ "H13R HAL2 " \ "H13S HAL2 " \ "C214 CTL2 " \ "H14R HAL2 " \ "H14S HAL2 " \ "C215 CTL2 " \ "H15R HAL2 " \ "H15S HAL2 " \ "C216 CTL2 " \ "H16R HAL2 " \ "H16S HAL2 " \ "C217 CTL2 " \ "H17R HAL2 " \ "H17S HAL2 " \ "C218 CTL3 " \ "H18R HAL3 " \ "H18S HAL3 " \ "H18T HAL3 " \ "C33 CTL2 " \ "H3X HAL2 " \ "H3Y HAL2 " \ "C34 CTL2 " \ "H4X HAL2 " \ "H4Y HAL2 " \ "C35 CTL2 " \ "H5X HAL2 " \ "H5Y HAL2 " \ "C36 CTL2 " \ "H6X HAL2 " \ "H6Y HAL2 " \ "C37 CTL2 " \ "H7X HAL2 " \ "H7Y HAL2 " \ "C38 CTL2 " \ "H8X HAL2 " \ "H8Y HAL2 " \ "C39 CTL2 " \ "H9X HAL2 " \ "H9Y HAL2 " \ "C310 CTL2 " \ "H10X HAL2 " \ "H10Y HAL2 " \ "C311 CTL2 " \ "H11X HAL2 " \ "H11Y HAL2 " \ "C312 CTL2 " \ "H12X HAL2 " \ "H12Y HAL2 " \ "C313 CTL2 " \ "H13X HAL2 " \ "H13Y HAL2 " \ "C314 CTL2 " \ "H14X HAL2 " \ "H14Y HAL2 " \ "C315 CTL2 " \ "H15X HAL2 " \ "H15Y HAL2 " \ "C316 CTL3 " \ "H16X HAL3 " \ "H16Y HAL3 " \ "H16Z HAL3 " \ "C1 CL " \ "O1 OCL " \ "O2 OCL " \ "C2 CTL2 " \ "H2A HAL2 " \ "H2B HAL2 " \ "C3 CTL2 " \ "H3A HAL2 " \ "H3B HAL2 " \ "C4 CTL2 " \ "H4A HAL2 " \ "H4B HAL2 " \ "C5 CTL2 " \ "H5A HAL2 " \ "H5B HAL2 " \ "C6 CTL2 " \ "H6A HAL2 " \ "H6B HAL2 " \ "C7 CTL2 " \ "H7A HAL2 " \ "H7B HAL2 " \ "C8 CTL2 " \ "H8A HAL2 " \ "H8B HAL2 " \ "C9 CTL2 " \ "H9A HAL2 " \ "H9B HAL2 " \ "C10 CTL2 " \ "H10A HAL2 " \ "H10B HAL2 " \ "C11 CTL2 " \ "H11A HAL2 " \ "H11B HAL2 " \ "C12 CTL2 " \ "H12A HAL2 " \ "H12B HAL2 " \ "C13 CTL2 " \ "H13A HAL2 " \ "H13B HAL2 " \ "C14 CTL2 " \ "H14A HAL2 " \ "H14B HAL2 " \ "C15 CTL2 " \ "H15A HAL2 " \ "H15B HAL2 " \ "C16 CTL3 " \ "H16A HAL3 " \ "H16B HAL3 " \ "H16C HAL3 " \ "C1 CL " \ "O1 OCL " \ "O2 OCL " \ "C2 CTL2 " \ "H2A HAL2 " \ "H2B HAL2 " \ "C3 CTL2 " \ "H3A HAL2 " \ "H3B HAL2 " \ "C4 CTL2 " \ "H4A HAL2 " \ "H4B HAL2 " \ "C5 CTL2 " \ "H5A HAL2 " \ "H5B HAL2 " \ "C6 CTL2 " \ "H6A HAL2 " \ "H6B HAL2 " \ "C7 CTL2 " \ "H7A HAL2 " \ "H7B HAL2 " \ "C8 CTL2 " \ "H8A HAL2 " \ "H8B HAL2 " \ "C9 CEL1 " \ "H9A HEL1 " \ "C10 CEL1 " \ "H10A HEL1 " \ "C11 CTL2 " \ "H11A HAL2 " \ "H11B HAL2 " \ "C12 CTL2 " \ "H12A HAL2 " \ "H12B HAL2 " \ "C13 CTL2 " \ "H13A HAL2 " \ "H13B HAL2 " \ "C14 CTL2 " \ "H14A HAL2 " \ "H14B HAL2 " \ "C15 CTL2 " \ "H15A HAL2 " \ "H15B HAL2 " \ "C16 CTL2 " \ "H16A HAL2 " \ "H16B HAL2 " \ "C17 CTL2 " \ "H17A HAL2 " \ "H17B HAL2 " \ "C18 CTL3 " \ "H18A HAL3 " \ "H18B HAL3 " \ "H18C HAL3 " \ "C1 CL " \ "O1 OCL " \ "O2 OCL " \ "C2 CTL2 " \ "H2A HAL2 " \ "H2B HAL2 " \ "C3 CTL2 " \ "H3A HAL2 " \ "H3B HAL2 " \ "C4 CEL1 " \ "H4 HEL1 " \ "C5 CEL1 " \ "H5 HEL1 " \ "C6 CTL2 " \ "H6A HAL2 " \ "H6B HAL2 " \ "C7 CEL1 " \ "H7 HEL1 " \ "C8 CEL1 " \ "H8 HEL1 " \ "C9 CTL2 " \ "H9A HAL2 " \ "H9B HAL2 " \ "C10 CEL1 " \ "H10 HEL1 " \ "C11 CEL1 " \ "H11 HEL1 " \ "C12 CTL2 " \ "H12A HAL2 " \ "H12B HAL2 " \ "C13 CEL1 " \ "H13 HEL1 " \ "C14 CEL1 " \ "H14 HEL1 " \ "C15 CTL2 " \ "H15A HAL2 " \ "H15B HAL2 " \ "C16 CEL1 " \ "H16 HEL1 " \ "C17 CEL1 " \ "H17 HEL1 " \ "C18 CTL2 " \ "H18A HAL2 " \ "H18B HAL2 " \ "C19 CEL1 " \ "H19 HEL1 " \ "C20 CEL1 " \ "H20 HEL1 " \ "C21 CTL2 " \ "H21A HAL2 " \ "H21B HAL2 " \ "C22 CTL3 " \ "H22A HAL3 " \ "H22B HAL3 " \ "H22C HAL3 " \ "C1 CL " \ "O1 OCL " \ "O2 OCL " \ "C2 CTL2 " \ "H2A HAL2 " \ "H2B HAL2 " \ "C3 CTL2 " \ "H3A HAL2 " \ "H3B HAL2 " \ "C4 CTL2 " \ "H4A HAL2 " \ "H4B HAL2 " \ "C5 CTL2 " \ "H5A HAL2 " \ "H5B HAL2 " \ "C6 CTL2 " \ "H6A HAL2 " \ "H6B HAL2 " \ "C7 CTL2 " \ "H7A HAL2 " \ "H7B HAL2 " \ "C8 CTL2 " \ "H8A HAL2 " \ "H8B HAL2 " \ "C9 CTL2 " \ "H9A HAL2 " \ "H9B HAL2 " \ "C10 CTL2 " \ "H10A HAL2 " \ "H10B HAL2 " \ "C11 CTL2 " \ "H11A HAL2 " \ "H11B HAL2 " \ "C12 CTL2 " \ "H12A HAL2 " \ "H12B HAL2 " \ "C13 CTL2 " \ "H13A HAL2 " \ "H13B HAL2 " \ "C14 CTL2 " \ "H14A HAL2 " \ "H14B HAL2 " \ "C15 CTL2 " \ "H15A HAL2 " \ "H15B HAL2 " \ "C16 CTL2 " \ "H16A HAL2 " \ "H16B HAL2 " \ "C17 CTL2 " \ "H17A HAL2 " \ "H17B HAL2 " \ "C18 CTL3 " \ "H18A HAL3 " \ "H18B HAL3 " \ "H18C HAL3 " \ "N NTL " \ "C5 CTL2 " \ "C6 CTL5 " \ "C7 CTL5 " \ "C8 CTL5 " \ "H5A HL " \ "H5B HL " \ "H6A HL " \ "H6B HL " \ "H6C HL " \ "H7A HL " \ "H7B HL " \ "H7C HL " \ "H8A HL " \ "H8B HL " \ "H8C HL " \ "C4 CTL2 " \ "H4A HAL2 " \ "H4B HAL2 " \ "P PL " \ "OP3 O2L " \ "OP4 O2L " \ "OP1 OSL " \ "OP2 OSL " \ "C3 CTL2 " \ "H3A HAL2 " \ "H3B HAL2 " \ "C2 CTL1 " \ "H2A HAL1 " \ "O2 OHL " \ "H2 HOL " \ "C1 CTL2 " \ "H1A HAL2 " \ "H1B HAL2 " \ "O1 OHL " \ "H1 HOL " \ "1C1 CTL2 " \ "1H1A HAL2 " \ "1H1B HAL2 " \ "1O1 OSL " \ "2C1 CL " \ "2O1 OBL " \ "2C2 CTL2 " \ "2H2A HAL2 " \ "2H2B HAL2 " \ "1C2 CTL1 " \ "1H2A HAL1 " \ "1O2 OSL " \ "2C1 CL " \ "2O1 OBL " \ "2C2 CTL2 " \ "2H2A HAL2 " \ "2H2B HAL2 " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT3 " \ "HB1 HA " \ "HB2 HA " \ "HB3 HA " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "CG CT2 " \ "HG1 HA " \ "HG2 HA " \ "CD CT2 " \ "HD1 HA " \ "HD2 HA " \ "NE NC2 " \ "HE HC " \ "CZ C " \ "NH1 NC2 " \ "HH11 HC " \ "HH12 HC " \ "NH2 NC2 " \ "HH21 HC " \ "HH22 HC " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "CG CC " \ "OD1 O " \ "ND2 NH2 " \ "HD21 H " \ "HD22 H " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "CG CC " \ "OD1 OC " \ "OD2 OC " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "SG S " \ "HG1 HS " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "CG CT2 " \ "HG1 HA " \ "HG2 HA " \ "CD CC " \ "OE1 O " \ "NE2 NH2 " \ "HE21 H " \ "HE22 H " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "CG CT2 " \ "HG1 HA " \ "HG2 HA " \ "CD CC " \ "OE1 OC " \ "OE2 OC " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT2 " \ "HA1 HB " \ "HA2 HB " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "ND1 NR1 " \ "HD1 H " \ "CG CPH1 " \ "CE1 CPH2 " \ "HE1 HR1 " \ "NE2 NR2 " \ "CD2 CPH1 " \ "HD2 HR3 " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "ND1 NR2 " \ "CG CPH1 " \ "CE1 CPH2 " \ "HE1 HR1 " \ "NE2 NR1 " \ "HE2 H " \ "CD2 CPH1 " \ "HD2 HR3 " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "CD2 CPH1 " \ "HD2 HR1 " \ "CG CPH1 " \ "NE2 NR3 " \ "HE2 H " \ "ND1 NR3 " \ "HD1 H " \ "CE1 CPH2 " \ "HE1 HR2 " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT1 " \ "HB HA " \ "CG2 CT3 " \ "HG21 HA " \ "HG22 HA " \ "HG23 HA " \ "CG1 CT2 " \ "HG11 HA " \ "HG12 HA " \ "CD CT3 " \ "HD1 HA " \ "HD2 HA " \ "HD3 HA " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "CG CT1 " \ "HG HA " \ "CD1 CT3 " \ "HD11 HA " \ "HD12 HA " \ "HD13 HA " \ "CD2 CT3 " \ "HD21 HA " \ "HD22 HA " \ "HD23 HA " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "CG CT2 " \ "HG1 HA " \ "HG2 HA " \ "CD CT2 " \ "HD1 HA " \ "HD2 HA " \ "CE CT2 " \ "HE1 HA " \ "HE2 HA " \ "NZ NH3 " \ "HZ1 HC " \ "HZ2 HC " \ "HZ3 HC " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "CG CT2 " \ "HG1 HA " \ "HG2 HA " \ "SD S " \ "CE CT3 " \ "HE1 HA " \ "HE2 HA " \ "HE3 HA " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "CG CA " \ "CD1 CA " \ "HD1 HP " \ "CE1 CA " \ "HE1 HP " \ "CZ CA " \ "HZ HP " \ "CD2 CA " \ "HD2 HP " \ "CE2 CA " \ "HE2 HP " \ "C C " \ "O O " \ "N N " \ "CD CP3 " \ "HD1 HA " \ "HD2 HA " \ "CA CP1 " \ "HA HB " \ "CB CP2 " \ "HB1 HA " \ "HB2 HA " \ "CG CP2 " \ "HG1 HA " \ "HG2 HA " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "OG OH1 " \ "HG1 H " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT1 " \ "HB HA " \ "OG1 OH1 " \ "HG1 H " \ "CG2 CT3 " \ "HG21 HA " \ "HG22 HA " \ "HG23 HA " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "CG CY " \ "CD1 CA " \ "HD1 HP " \ "NE1 NY " \ "HE1 H " \ "CE2 CPT " \ "CD2 CPT " \ "CE3 CA " \ "HE3 HP " \ "CZ3 CA " \ "HZ3 HP " \ "CZ2 CA " \ "HZ2 HP " \ "CH2 CA " \ "HH2 HP " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "CG CA " \ "CD1 CA " \ "HD1 HP " \ "CE1 CA " \ "HE1 HP " \ "CZ CA " \ "OH OH1 " \ "HH H " \ "CD2 CA " \ "HD2 HP " \ "CE2 CA " \ "HE2 HP " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "CB CT1 " \ "HB HA " \ "CG1 CT3 " \ "HG11 HA " \ "HG12 HA " \ "HG13 HA " \ "CG2 CT3 " \ "HG21 HA " \ "HG22 HA " \ "HG23 HA " \ "C C " \ "O O " \ "CL CT3 " \ "HL1 HA " \ "HL2 HA " \ "HL3 HA " \ "CLP C " \ "OL O " \ "NL NH1 " \ "HL H " \ "CA CT1 " \ "HA HB " \ "CB CT3 " \ "HB1 HA " \ "HB2 HA " \ "HB3 HA " \ "CRP C " \ "OR O " \ "NR NH1 " \ "HR H " \ "CR CT3 " \ "HR1 HA " \ "HR2 HA " \ "HR3 HA " \ "OH2 OT " \ "H1 HT " \ "H2 HT " \ "OH2 OT " \ "H1 HT " \ "H2 HT " \ "N NH3 " \ "HT1 HC " \ "HT2 HC " \ "HT3 HC " \ "CA CT1 " \ "HA HB " \ "N NH3 " \ "HT1 HC " \ "HT2 HC " \ "HT3 HC " \ "CA CT2 " \ "HA1 HB " \ "HA2 HB " \ "N NP " \ "HN1 HC " \ "HN2 HC " \ "CD CP3 " \ "HD1 HA " \ "HD2 HA " \ "CA CP1 " \ "HA HB " \ "CAY CT3 " \ "HY1 HA " \ "HY2 HA " \ "HY3 HA " \ "CY C " \ "OY O " \ "CAY CT3 " \ "HY1 HA " \ "HY2 HA " \ "HY3 HA " \ "CY C " \ "OY O " \ "C CC " \ "OT1 OC " \ "OT2 OC " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB " \ "C CD " \ "OT1 OB " \ "OT2 OS " \ "CT CT3 " \ "HT1 HA " \ "HT2 HA " \ "HT3 HA " \ "C CC " \ "O O " \ "NT NH2 " \ "HT1 H " \ "HT2 H " \ "C C " \ "O O " \ "NT NH1 " \ "HNT H " \ "CAT CT3 " \ "HT1 HA " \ "HT2 HA " \ "HT3 HA " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "CG CD " \ "OD1 OB " \ "OD2 OH1 " \ "HD2 H " \ "CG CT2 " \ "HG1 HA " \ "HG2 HA " \ "CD CD " \ "OE1 OB " \ "OE2 OH1 " \ "HE2 H " \ "CE CT2 " \ "HE1 HA " \ "HE2 HA " \ "NZ NH2 " \ "HZ1 HC " \ "HZ2 HC " \ "1CB CT2 " \ "1SG SM " \ "2SG SM " \ "2CB CT2 " \ "CE1 CPH2 " \ "HE1 HR1 " \ "ND1 NR2 " \ "CG CPH1 " \ "CB CT2 " \ "HB1 HA " \ "HB2 HA " \ "NE2 NR1 " \ "HE2 H " \ "CD2 CPH1 " \ "HD2 HR3 " \ "P P " \ "O1P ON3 " \ "O2P ON3 " \ "O5' ON2 " \ "C5' CN8B " \ "H5' HN8 " \ "H5'' HN8 " \ "C4' CN7 " \ "H4' HN7 " \ "O4' ON6B " \ "C1' CN7B " \ "H1' HN7 " \ "N9 NN2B " \ "C4 CN5 " \ "N2 NN1 " \ "H21 HN1 " \ "H22 HN1 " \ "N3 NN3G " \ "C2 CN2 " \ "N1 NN2G " \ "H1 HN2 " \ "C6 CN1 " \ "O6 ON1 " \ "C5 CN5G " \ "N7 NN4 " \ "C8 CN4 " \ "H8 HN3 " \ "C2' CN7B " \ "H2'' HN7 " \ "O2' ON5 " \ "H2' HN5 " \ "C3' CN7 " \ "H3' HN7 " \ "O3' ON2 " \ "P P " \ "O1P ON3 " \ "O2P ON3 " \ "O5' ON2 " \ "C5' CN8B " \ "H5' HN8 " \ "H5'' HN8 " \ "C4' CN7 " \ "H4' HN7 " \ "O4' ON6B " \ "C1' CN7B " \ "H1' HN7 " \ "N9 NN2 " \ "C5 CN5 " \ "N7 NN4 " \ "C8 CN4 " \ "H8 HN3 " \ "N1 NN3A " \ "C2 CN4 " \ "H2 HN3 " \ "N3 NN3A " \ "C4 CN5 " \ "C6 CN2 " \ "N6 NN1 " \ "H61 HN1 " \ "H62 HN1 " \ "C2' CN7B " \ "H2'' HN7 " \ "O2' ON5 " \ "H2' HN5 " \ "C3' CN7 " \ "H3' HN7 " \ "O3' ON2 " \ "P P " \ "O1P ON3 " \ "O2P ON3 " \ "O5' ON2 " \ "C5' CN8B " \ "H5' HN8 " \ "H5'' HN8 " \ "C4' CN7 " \ "H4' HN7 " \ "O4' ON6B " \ "C1' CN7B " \ "H1' HN7 " \ "N1 NN2 " \ "C6 CN3 " \ "H6 HN3 " \ "C5 CN3 " \ "H5 HN3 " \ "C2 CN1 " \ "O2 ON1C " \ "N3 NN3 " \ "C4 CN2 " \ "N4 NN1 " \ "H41 HN1 " \ "H42 HN1 " \ "C2' CN7B " \ "H2'' HN7 " \ "O2' ON5 " \ "H2' HN5 " \ "C3' CN7 " \ "H3' HN7 " \ "O3' ON2 " \ "P P " \ "O1P ON3 " \ "O2P ON3 " \ "O5' ON2 " \ "C5' CN8B " \ "H5' HN8 " \ "H5'' HN8 " \ "C4' CN7 " \ "H4' HN7 " \ "O4' ON6B " \ "C1' CN7B " \ "H1' HN7 " \ "N1 NN2B " \ "C6 CN3 " \ "H6 HN3 " \ "C2 CN1T " \ "O2 ON1 " \ "N3 NN2U " \ "H3 HN2 " \ "C4 CN1 " \ "O4 ON1 " \ "C5 CN3T " \ "C5M CN9 " \ "H51 HN9 " \ "H52 HN9 " \ "H53 HN9 " \ "C2' CN7B " \ "H2'' HN7 " \ "O2' ON5 " \ "H2' HN5 " \ "C3' CN7 " \ "H3' HN7 " \ "O3' ON2 " \ "P P " \ "O1P ON3 " \ "O2P ON3 " \ "O5' ON2 " \ "C5' CN8B " \ "H5' HN8 " \ "H5'' HN8 " \ "C4' CN7 " \ "H4' HN7 " \ "O4' ON6B " \ "C1' CN7B " \ "H1' HN7 " \ "N1 NN2B " \ "C6 CN3 " \ "H6 HN3 " \ "C2 CN1T " \ "O2 ON1 " \ "N3 NN2U " \ "H3 HN2 " \ "C4 CN1 " \ "O4 ON1 " \ "C5 CN3 " \ "H5 HN3 " \ "C2' CN7B " \ "H2'' HN7 " \ "O2' ON5 " \ "H2' HN5 " \ "C3' CN7 " \ "H3' HN7 " \ "O3' ON2 " \ "C4' CN7 " \ "H4' HN7 " \ "O4' ON6 " \ "C1' CN7B " \ "H1' HN7 " \ "C2' CN8 " \ "H2' HN8 " \ "H2'' HN8 " \ "C4' CN7 " \ "H4' HN7 " \ "O4' ON6 " \ "C1' CN7B " \ "H1' HN7 " \ "C2' CN8 " \ "H2' HN8 " \ "H2'' HN8 " \ "H5T HN5 " \ "O5' ON5 " \ "C5' CN8B " \ "H5' HN8 " \ "H5'' HN8 " \ "C5' CN9 " \ "H5' HN9 " \ "H5'' HN9 " \ "H53' HN9 " \ "C5' CN8B " \ "H5' HN8 " \ "H5'' HN8 " \ "P P " \ "O1P ON3 " \ "O2P ON3 " \ "O5' ON2 " \ "O5T ON4 " \ "H5T HN4 " \ "C5' CN8B " \ "H5' HN8 " \ "H5'' HN8 " \ "P P " \ "O1P ON3 " \ "O2P ON3 " \ "O5' ON2 " \ "O5T ON2 " \ "C5T CN9 " \ "H5T1 HN9 " \ "H5T2 HN9 " \ "H5T3 HN9 " \ "C3' CN7 " \ "H3' HN7 " \ "O3' ON5 " \ "H3T HN5 " \ "C3' CN7 " \ "H3' HN7 " \ "P3 P " \ "O1P3 ON3 " \ "O2P3 ON3 " \ "O3' ON2 " \ "O3T ON4 " \ "H3T HN4 " \ "C3' CN7 " \ "H3' HN7 " \ "P3 P " \ "O1P3 ON3 " \ "O2P3 ON3 " \ "O3' ON2 " \ "O3T ON2 " \ "C3T CN9 " \ "H3T1 HN9 " \ "H3T2 HN9 " \ "H3T3 HN9 " \ "C3' CN7 " \ "H3' HN7 " \ "P3 P " \ "O3' ON2 " \ "O1P3 ON3 " \ "O2P3 ON3 " \ "O3P3 ON3 " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB1 " \ "CB CT1 " \ "HB HA1 " \ "CG2 CT3 " \ "HG21 HA3 " \ "HG22 HA3 " \ "HG23 HA3 " \ "CG1 CT2 " \ "HG11 HA2 " \ "HG12 HA2 " \ "CD CT3 " \ "HD1 HA3 " \ "HD2 HA3 " \ "HD3 HA3 " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB1 " \ "CB CT3 " \ "HB1 HA3 " \ "HB2 HA3 " \ "HB3 HA3 " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB1 " \ "CB CT2 " \ "HB1 HA2 " \ "HB2 HA2 " \ "CG CT1 " \ "HG HA1 " \ "CD1 CT3 " \ "HD11 HA3 " \ "HD12 HA3 " \ "HD13 HA3 " \ "CD2 CT3 " \ "HD21 HA3 " \ "HD22 HA3 " \ "HD23 HA3 " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB1 " \ "CB CT2 " \ "HB1 HA2 " \ "HB2 HA2 " \ "OG OH1 " \ "HG1 H " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB1 " \ "CB CT2 " \ "HB1 HA2 " \ "HB2 HA2 " \ "CG CT2 " \ "HG1 HA2 " \ "HG2 HA2 " \ "CD CT2 " \ "HD1 HA2 " \ "HD2 HA2 " \ "CE CT2 " \ "HE1 HA2 " \ "HE2 HA2 " \ "NZ NH3 " \ "HZ1 HC " \ "HZ2 HC " \ "HZ3 HC " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB1 " \ "CB CT2 " \ "HB1 HA2 " \ "HB2 HA2 " \ "SG S " \ "HG1 HS " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB1 " \ "CB CT2 " \ "HB1 HA2 " \ "HB2 HA2 " \ "CG CT2 " \ "HG1 HA2 " \ "HG2 HA2 " \ "CD CC " \ "OE1 O " \ "NE2 NH2 " \ "HE21 H " \ "HE22 H " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB1 " \ "CB CT2 " \ "HB1 HA2 " \ "HB2 HA2 " \ "CG CC " \ "OD1 O " \ "ND2 NH2 " \ "HD21 H " \ "HD22 H " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB1 " \ "CB CT2 " \ "HB1 HA2 " \ "HB2 HA2 " \ "CG CT2 " \ "HG1 HA2 " \ "HG2 HA2 " \ "CD CC " \ "OE1 OC " \ "OE2 OC " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB1 " \ "CB CT2 " \ "HB1 HA2 " \ "HB2 HA2 " \ "CG CC " \ "OD1 OC " \ "OD2 OC " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB1 " \ "CB CT1 " \ "HB HA1 " \ "OG1 OH1 " \ "HG1 H " \ "CG2 CT3 " \ "HG21 HA3 " \ "HG22 HA3 " \ "HG23 HA3 " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB1 " \ "CB CT2 " \ "HB1 HA2 " \ "HB2 HA2 " \ "CG CY " \ "CD1 CA " \ "HD1 HP " \ "NE1 NY " \ "HE1 H " \ "CE2 CPT " \ "CD2 CPT " \ "CE3 CA " \ "HE3 HP " \ "CZ3 CA " \ "HZ3 HP " \ "CZ2 CA " \ "HZ2 HP " \ "CH2 CA " \ "HH2 HP " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB1 " \ "CB CT2 " \ "HB1 HA2 " \ "HB2 HA2 " \ "CG CT2 " \ "HG1 HA2 " \ "HG2 HA2 " \ "SD S " \ "CE CT3 " \ "HE1 HA3 " \ "HE2 HA3 " \ "HE3 HA3 " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB1 " \ "CB CT2 " \ "HB1 HA2 " \ "HB2 HA2 " \ "CG CA " \ "CD1 CA " \ "HD1 HP " \ "CE1 CA " \ "HE1 HP " \ "CZ CA " \ "HZ HP " \ "CD2 CA " \ "HD2 HP " \ "CE2 CA " \ "HE2 HP " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB1 " \ "CB CT2 " \ "HB1 HA2 " \ "HB2 HA2 " \ "CG CA " \ "CD1 CA " \ "HD1 HP " \ "CE1 CA " \ "HE1 HP " \ "CZ CA " \ "OH OH1 " \ "HH H " \ "CD2 CA " \ "HD2 HP " \ "CE2 CA " \ "HE2 HP " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB1 " \ "CB CT2 " \ "HB1 HA2 " \ "HB2 HA2 " \ "ND1 NR1 " \ "HD1 H " \ "CG CPH1 " \ "CE1 CPH2 " \ "HE1 HR1 " \ "NE2 NR2 " \ "CD2 CPH1 " \ "HD2 HR3 " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB1 " \ "CB CT1 " \ "HB HA1 " \ "CG1 CT3 " \ "HG11 HA3 " \ "HG12 HA3 " \ "HG13 HA3 " \ "CG2 CT3 " \ "HG21 HA3 " \ "HG22 HA3 " \ "HG23 HA3 " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB1 " \ "CB CT2 " \ "HB1 HA2 " \ "HB2 HA2 " \ "CD2 CPH1 " \ "HD2 HR1 " \ "CG CPH1 " \ "NE2 NR3 " \ "HE2 H " \ "ND1 NR3 " \ "HD1 H " \ "CE1 CPH2 " \ "HE1 HR2 " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB1 " \ "CB CT2 " \ "HB1 HA2 " \ "HB2 HA2 " \ "ND1 NR2 " \ "CG CPH1 " \ "CE1 CPH2 " \ "HE1 HR1 " \ "NE2 NR1 " \ "HE2 H " \ "CD2 CPH1 " \ "HD2 HR3 " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA1 HB2 " \ "HA2 HB2 " \ "C C " \ "O O " \ "N NH1 " \ "HN H " \ "CA CT1 " \ "HA HB1 " \ "CB CT2 " \ "HB1 HA2 " \ "HB2 HA2 " \ "CG CT2 " \ "HG1 HA2 " \ "HG2 HA2 " \ "CD CT2 " \ "HD1 HA2 " \ "HD2 HA2 " \ "NE NC2 " \ "HE HC " \ "CZ C " \ "NH1 NC2 " \ "HH11 HC " \ "HH12 HC " \ "NH2 NC2 " \ "HH21 HC " \ "HH22 HC " \ "C C " \ "O O " \ "N N " \ "CD CP3 " \ "HD1 HA2 " \ "HD2 HA2 " \ "CA CP1 " \ "HA HB1 " \ "CB CP2 " \ "HB1 HA2 " \ "HB2 HA2 " \ "CG CP2 " \ "HG1 HA2 " \ "HG2 HA2 " \ "C C " \ "O O " \ "N NH3 " \ "HT1 HC " \ "HT2 HC " \ "HT3 HC " \ "CA CT1 " \ "HA HB1 " \ "C CC " \ "OT1 OC " \ "OT2 OC " \ "CAY CT3 " \ "HY1 HA3 " \ "HY2 HA3 " \ "HY3 HA3 " \ "CY C " \ "OY O " \ "C C " \ "O O " \ "NT NH1 " \ "HNT H " \ "CAT CT3 " \ "HT1 HA3 " \ "HT2 HA3 " \ "HT3 HA3 " \ "1CB CT2 " \ "1SG SM " \ "2SG SM " \ "2CB CT2 " \ "OH2 OT " \ "OM LP " \ "H1 HT " \ "H2 HT " \ "OH2 OT " \ "H1 HT " \ "H2 HT " \ "h11 ha3 " \ "h12 ha3 " \ "h13 ha3 " \ "c1 ct3 " \ "h21 ha3 " \ "h22 ha3 " \ "h23 ha3 " \ "c2 ct3 " \ "h11 ha3 " \ "h12 ha3 " \ "h13 ha3 " \ "c1 ct3 " \ "c2 ct2 " \ "h21 ha2 " \ "H22 ha2 " \ "h31 ha3 " \ "h32 ha3 " \ "h33 ha3 " \ "c3 ct3 " \ "h11 ha3 " \ "h12 ha3 " \ "h13 ha3 " \ "c1 ct3 " \ "h21 ha2 " \ "h22 ha2 " \ "c2 ct2 " \ "h31 ha2 " \ "h32 ha2 " \ "c3 ct2 " \ "h41 ha3 " \ "h42 ha3 " \ "h43 ha3 " \ "c4 ct3 " \ "CB CT3 " \ "OG OH1 " \ "HG1 H " \ "HB1 HA3 " \ "HB2 HA3 " \ "HB3 HA3 " \ "CL CT3 " \ "HL1 HA3 " \ "HL2 HA3 " \ "HL3 HA3 " \ "C C " \ "O O " \ "N NH1 " \ "H H " \ "CR CT3 " \ "HR1 HA3 " \ "HR2 HA3 " \ "HR3 HA3 " \ "C1 CT3 " \ "C CD " \ "OM OS " \ "C2 CT3 " \ "O OB " \ "H11 HA3 " \ "H12 HA3 " \ "H13 HA3 " \ "H21 HA3 " \ "H22 HA3 " \ "H23 HA3 " \ "HA HA1 " \ "C CC " \ "N NH2 " \ "Hc H " \ "Ht H " \ "O O " \ "C2 CT3 " \ "C1 CD " \ "H21 HA3 " \ "H22 HA3 " \ "H23 HA3 " \ "O2 OB " \ "O1 OH1 " \ "HO1 H " \ "HL HA1 " \ "C C " \ "O O " \ "N NH1 " \ "H H " \ "CR CT3 " \ "HR1 HA3 " \ "HR2 HA3 " \ "HR3 HA3 " \ "N NH1 " \ "H H " \ "CA CH1E " \ "CB CH3E " \ "C C " \ "O O " \ "N NH1 " \ "H H " \ "CA CH1E " \ "CB CH2E " \ "CG CH2E " \ "CD CH2E " \ "NE NH1 " \ "HE H " \ "CZ C " \ "NH1 NC2 " \ "HH11 HC " \ "HH12 HC " \ "NH2 NC2 " \ "HH21 HC " \ "HH22 HC " \ "C C " \ "O O " \ "N NH1 " \ "H H " \ "CA CH1E " \ "CB CH2E " \ "CG C " \ "OD1 O " \ "ND2 NH2 " \ "HD21 H " \ "HD22 H " \ "C C " \ "O O " \ "N NH1 " \ "H H " \ "CA CH1E " \ "CB CH2E " \ "CG C " \ "OD1 OC " \ "OD2 OC " \ "C C " \ "O O " \ "N NH1 " \ "H H " \ "CA CH1E " \ "CB CH2E " \ "SG SH1E " \ "C C " \ "O O " \ "N NH1 " \ "H H " \ "CA CH1E " \ "CB CH2E " \ "CG CH2E " \ "CD C " \ "OE1 O " \ "NE2 NH2 " \ "HE21 H " \ "HE22 H " \ "C C " \ "O O " \ "N NH1 " \ "H H " \ "CA CH1E " \ "CB CH2E " \ "CG CH2E " \ "CD C " \ "OE1 OC " \ "OE2 OC " \ "C C " \ "O O " \ "N NH1 " \ "H H " \ "CA CH2E " \ "C C " \ "O O " \ "N NH1 " \ "H H " \ "CA CH1E " \ "CB CH2E " \ "CG C " \ "ND1 NH1 " \ "HD1 H " \ "CD2 CR1E " \ "NE2 NR " \ "CE1 CR1E " \ "C C " \ "O O " \ "N NH1 " \ "H H " \ "CA CH1E " \ "CB CH2E " \ "CG C " \ "ND1 NR " \ "CE1 CR1E " \ "CD2 CR1E " \ "NE2 NH1 " \ "HE2 H " \ "C C " \ "O O " \ "N NH1 " \ "H H " \ "CA CH1E " \ "CB CH2E " \ "CG C " \ "CD2 CR1E " \ "ND1 NH1 " \ "HD1 H " \ "CE1 CR1E " \ "NE2 NH1 " \ "HE2 H " \ "C C " \ "O O " \ "N NH1 " \ "H H " \ "CA CH1E " \ "CB CH1E " \ "CG2 CH3E " \ "CG1 CH2E " \ "CD CH3E " \ "C C " \ "O O " \ "N NH1 " \ "H H " \ "CA CH1E " \ "CB CH2E " \ "CG CH1E " \ "CD1 CH3E " \ "CD2 CH3E " \ "C C " \ "O O " \ "N NH1 " \ "H H " \ "CA CH1E " \ "CB CH2E " \ "CG CH2E " \ "CD CH2E " \ "CE CH2E " \ "NZ NH3 " \ "HZ1 HC " \ "HZ2 HC " \ "HZ3 HC " \ "C C " \ "O O " \ "N NH1 " \ "H H " \ "CA CH1E " \ "CB CH2E " \ "CG CH2E " \ "SD S " \ "CE CH3E " \ "C C " \ "O O " \ "N NH1 " \ "H H " \ "CA CH1E " \ "CB CT " \ "CG1 CH3E " \ "CG2 CH3E " \ "SG SH1E " \ "C C " \ "O O " \ "N NH1 " \ "H H " \ "CA CH1E " \ "CB CH2E " \ "CG C " \ "CD1 CR1E " \ "CD2 CR1E " \ "CE1 CR1E " \ "CE2 CR1E " \ "CZ CR1E " \ "C C " \ "O O " \ "N N " \ "CD CH2E " \ "CA CH1E " \ "CB CH2E " \ "CG CH2E " \ "C C " \ "O O " \ "N NH1 " \ "H H " \ "CA CH1E " \ "CB CH2E " \ "OG OH1 " \ "HG H " \ "C C " \ "O O " \ "N NH1 " \ "H H " \ "CA CH1E " \ "CB CH1E " \ "OG1 OH1 " \ "HG1 H " \ "CG2 CH3E " \ "C C " \ "O O " \ "N NH1 " \ "H H " \ "CA CH1E " \ "CB CH2E " \ "CG C " \ "CD2 C " \ "CE2 C " \ "CE3 CR1E " \ "CD1 CR1E " \ "NE1 NH1 " \ "HE1 H " \ "CZ2 CR1E " \ "CZ3 CR1E " \ "CH2 CR1E " \ "C C " \ "O O " \ "N NH1 " \ "H H " \ "CA CH1E " \ "CB CH2E " \ "CG C " \ "CD1 CR1E " \ "CE1 CR1E " \ "CD2 CR1E " \ "CE2 CR1E " \ "CZ C " \ "OH OH1 " \ "HH H " \ "C C " \ "O O " \ "N NH1 " \ "H H " \ "CA CH1E " \ "CB CH1E " \ "CG1 CH3E " \ "CG2 CH3E " \ "C C " \ "O O " \ "FE FE " \ "NA NP " \ "NB NP " \ "NC NP " \ "ND NP " \ "C1A C " \ "CHA CR1E " \ "C4D C " \ "C1B C " \ "CHB CR1E " \ "C4A C " \ "C1C C " \ "CHC CR1E " \ "C4B C " \ "C1D C " \ "CHD CR1E " \ "C4C C " \ "C2A C " \ "CAA CH2E " \ "C3A C " \ "CMA CH3E " \ "CBA CH2E " \ "CGA C " \ "O1A OC " \ "O2A OC " \ "C2B C " \ "CMB CH3E " \ "C3B C " \ "CAB CR1E " \ "CBB CH2E " \ "C2C C " \ "CMC CH3E " \ "C3C C " \ "CAC CR1E " \ "CBC CH2E " \ "C2D C " \ "CMD CH3E " \ "C3D C " \ "CAD CH2E " \ "CBD CH2E " \ "CGD C " \ "O1D OC " \ "O2D OC " \ "CH3 CH3E " \ "C C " \ "O O " \ "HA HA " \ "C C " \ "O O " \ "N NH2 " \ "H1 H " \ "H2 H " \ "CL CH3E " \ "C C " \ "O O " \ "N NH1 " \ "H H " \ "CA CH3E " \ "HT1 HC " \ "HT2 HC " \ "N NH3 " \ "HT3 HC " \ "CA CH1E " \ "HT1 HC " \ "HT2 HC " \ "N NH3 " \ "HT3 HC " \ "CA CH2E " \ "HT1 HC " \ "HT2 HC " \ "N NH3 " \ "CD CH2E " \ "CA CH1E " \ "C C " \ "OT1 OC " \ "OT2 OC " \ "O1 OM " \ "O2 OM " \ "C CM " \ "O OM " \ "C CM " \ "O OM " \ "C2 CH3E " \ "C1 CH2E " \ "O OH1 " \ "H H " \ "OX2 OH2 " \ "HX1 H " \ "HX2 H " \ "LX1 LP " \ "LX2 LP " \ "OH2 OT " \ "H1 HT " \ "H2 HT " \ "OH2 OT " \ "H1 HT " \ "H2 HT " \ "S S " \ "O1 OC " \ "O2 OC " \ "O3 OC " \ "O4 OC " \ "C CH3E " \ "O OH1 " \ "H H " \ "1CB CH2E " \ "1SG S " \ "2SG S " \ "2CB CH2E " \ "CG C " \ "ND1 NR " \ "CE1 CR1E " \ "CD2 CR1E " \ "NE2 NH1 " \ "HE2 H " \ "P P " \ "O1P O2 " \ "O2P O2 " \ "O5' OS " \ "C5' C2 " \ "C4' CH " \ "O4' OSS " \ "C1' CH " \ "N9 NS " \ "C4 CB " \ "N3 NC " \ "C2 CA " \ "N2 N2 " \ "H21 H2 " \ "H22 H2 " \ "N1 NA " \ "H1 H " \ "C6 C " \ "O6 O " \ "C5 CB " \ "N7 NB " \ "C8 CE " \ "C2' CH " \ "O2' OH " \ "H2' HO " \ "C3' CH " \ "O3' OS " \ "P P " \ "O1P O2 " \ "O2P O2 " \ "O5' OS " \ "C5' C2 " \ "C4' CH " \ "O4' OSS " \ "C1' CH " \ "N9 NS " \ "C4 CB " \ "N3 NC " \ "C2 CE " \ "N1 NC " \ "C6 CA " \ "N6 N2 " \ "H61 H2 " \ "H62 H2 " \ "C5 CB " \ "N7 NB " \ "C8 CE " \ "C2' CH " \ "O2' OH " \ "H2' HO " \ "C3' CH " \ "O3' OS " \ "P P " \ "O1P O2 " \ "O2P O2 " \ "O5' OS " \ "C5' C2 " \ "C4' CH " \ "O4' OSS " \ "C1' CH " \ "N1 NS " \ "C6 CF " \ "C2 C " \ "O2 O " \ "N3 NC " \ "C4 CA " \ "N4 N2 " \ "H41 H2 " \ "H42 H2 " \ "C5 CF " \ "C2' CH " \ "O2' OH " \ "H2' HO " \ "C3' CH " \ "O3' OS " \ "P P " \ "O1P O2 " \ "O2P O2 " \ "O5' OS " \ "C5' C2 " \ "C4' CH " \ "O4' OSS " \ "C1' CH " \ "N1 NS " \ "C6 CF " \ "C2 C " \ "O2 O " \ "N3 NA " \ "H3 H " \ "C4 C " \ "O4 O " \ "C5 CS " \ "C5A C3 " \ "C2' CH " \ "O2' OH " \ "H2' HO " \ "C3' CH " \ "O3' OS " \ "P P " \ "O1P O2 " \ "O2P O2 " \ "O5' OS " \ "C5' C2 " \ "C4' CH " \ "O4' OSS " \ "C1' CH " \ "N1 NS " \ "C6 CF " \ "C2 C " \ "O2 O " \ "N3 NA " \ "H3 H " \ "C4 C " \ "O4 O " \ "C5 CF " \ "C2' CH " \ "O2' OH " \ "H2' HO " \ "C3' CH " \ "O3' OS " \ "O4' OST " \ "C2' C2 " \ "C1 C3 " \ "O1 OS " \ "P P " \ "O1P O2 " \ "O2P O2 " \ "O2 OS " \ "C2 C3 " \ "C1 C3 " \ "C2 C2 " \ "O1 OS " \ "P P " \ "O1P O2 " \ "O2P O2 " \ "O2 OS " \ "C3 C2 " \ "C4 C3 " \ "C5' C3 " \ "C4' CH " \ "O4' OSS " \ "C1' CH " \ "N1 NH2E " \ "C2' CH " \ "O2' OH " \ "C3' CH " \ "O3' OS " \ "C5' C3 " \ "C4' CH " \ "O4' OST " \ "C1' CH " \ "N1 NH2E " \ "C2' C2 " \ "C3' CH " \ "O3' OS " \ "C1 C3 " \ "C2 C2 " \ "C3 C2 " \ "C4 C2 " \ "C5 C2 " \ "C6 C2 " \ "C7 C2 " \ "C8 C3 " \ "N1 NA " \ "C6 CF " \ "H1 H " \ "N9 NA " \ "C4 CB " \ "H9 H " \ "H5T HO " \ "O5' OH " \ "C5' C2 " \ "H5T HO " \ "O5T OH " \ "C3' CH " \ "O3' OH " \ "H3T HO " \ "1O3' OS " \ "2P P " \ "2O1P O2 " \ "2O2P O2 " \ "2O5' OS " \ "OH2 OH2 " \ "H1 H " \ "H2 H " \ "NA SD " \ "NA SD " \ "N1 NH3 " \ "C2 C2 " \ "C3 C2 " \ "C4 C2 " \ "N5 NH3 " \ "C6 C2 " \ "C7 C2 " \ "C8 C2 " \ "C9 C2 " \ "NA NH3 " \ "CB C2 " \ "CC C2 " \ "CD C2 " \ "NE NH3 " \ "H11 H " \ "H12 H " \ "H13 H " \ "H51 H " \ "H52 H " \ "HA1 H " \ "HA2 H " \ "HE1 H " \ "HE2 H " \ "HE3 H " \ "MG MG 2. " \ "ST2 . " \ "OX2 OH2 " \ "HX1 H " \ "HX2 H " \ "LX1 LP " \ "LX2 LP " \ "OH2 OT " \ "H1 HT " \ "H2 HT " \ "C5 C2 " \ "C6 C2 " \ "C5 CB " \ "C7 C3 " \ "N7 NB " \ "C8 CE " \ "N2 N2 " \ "C2B C3 " \ "C2A C3 " \ "N2 N2 " \ "H21 H2 " \ "C2A C3 " \ "C2' CH " \ "O2' OH " \ "C2A C3 " \ "C5 CS " \ "C6 CF " \ "N1 NA " \ "H11 H " \ "C5 CS " \ "C5A C3 " \ "N1 NA " \ "C1 C3 " \ "C6 CH " \ "C3 C3 " \ "N3 NA " \ "C2 CB " \ "N2 NB " \ "C11 CA " \ "C10 C3 " \ "C12 CA " \ "N1 NA " \ "C13 C2 " \ "C14 C2 " \ "C15 CH " \ "C16 C " \ "O18 OS " \ "C19 C3 " \ "O17 O " \ "N20 NA " \ "H20 H " \ "C21 C " \ "O23 O " \ "O22 OS " \ "C24 C3 " \ "C2 CA " \ "C6 CE " \ "N2 N2 " \ "H21 H2 " \ "H22 H2 " } { set data [ split $data " " ] set i 0 foreach value $data { if { $value > " " } { incr i; set val($i) $value } if { $i == 2 } { set class $val(2) if { [ info exists mass($class) ] } { set mass($val(1)) $mass($class) } } } } set natoms 0 set molmass 0. foreach line $pdb_file { if { [ string range $line 0 3 ] == "ATOM" | [ string range $line 0 5 ] == "HETATM" } { incr natoms set at [ string trim [ string range $line 12 15 ] ] if { [ info exists mass($at) ] == 0 } { if { [ info exists mass([ string range $at 0 0 ]) ] } { set mass($at) $mass([ string range $at 0 0 ]) puts -nonewline " Unsure about mass of element $at: $mass($at)." puts -nonewline " Is this correct? (y/n)" flush stdout; gets stdin correct if { $correct != "y" & $correct != "yes" & $correct != "Y" & $correct != "YES" } { puts -nonewline "Type the mass of this atom:" flush stdout; gets stdin mass($at) } } else { puts "Could not find mass for atom type: $at" puts -nonewline "Type the mass of this atom:" flush stdout; gets stdin mass($at) } } set atommass $mass($at) set molmass [ expr $molmass + $atommass ] } } puts " -------------------------------------------------------" puts " Molar mass of structure: $molmass" puts " -------------------------------------------------------" # Total volume of the box if { $density == "none" } { set density 1. } set volume [ expr $x_length * $y_length * $z_length ] # We use the approximation that the volume occupied by each type of molecule # in the system is proportional to its molar mass, therefore: set water_molar_mass 18. set n_water [ format %7.0f "[ expr ( $volume*($density*0.602) - $molmass ) / $water_molar_mass ]" ] puts " Number of water molecules to be put: $n_water " # Fraction of the volume occupied by water set water_vol [ expr $n_water*$water_molar_mass/($n_water*$water_molar_mass + $molmass) ] set water_vol [ expr $water_vol * $volume ] # Computing the required number of ions for an approximate concentration # of 0.16 mol/L (approximate physiological concentration on water) puts " Total volume: [ format %8.2f $volume ] A^3" puts " Volume occupied by water: [ format %8.2f "$water_vol" ] A^3 " # Set the number of ions of each type if { $noions == "true" } { set n_chloride 0 set n_sodium 0 } else { if { $charge <= 0 } { set n_sodium [ format %8.0f [ expr 0.16 * 0.000602 * $water_vol ] ] if { $n_sodium > [ expr -1.*$charge ] } { set n_chloride [ expr $n_sodium + $charge ] } else { set n_sodium [ expr -1.*$charge ] set n_chloride 0 } } if { $charge > 0 } { set n_chloride [ format %8.0f [ expr 0.16 * 0.000602 * $water_vol ] ] if { $n_chloride > $charge } { set n_sodium [ expr $n_chloride - $charge ] } else { set n_chloride $charge set n_sodium 0 } } } puts " Number of Sodium ions to be put: [ string trim $n_sodium ]" puts " Number of Chloride ions to be put: [ string trim $n_chloride ]" # Minimum and maximum coordinates of the box set xmin [ expr -1.*$x_length / 2. ] set xmax [ expr $x_length / 2. ] set ymin [ expr -1.*$y_length / 2. ] set ymax [ expr $y_length / 2. ] set zmin [ expr -1.*$z_length / 2. ] set zmax [ expr $z_length / 2. ] # # Write packmol input file # set packmol_input_file [ open ./$packmol_input w ] puts $packmol_input_file " tolerance 2.0 filetype pdb output $output structure $pdb_file_name number 1 center fixed 0. 0. 0. 0. 0. 0. end structure structure WATER.pdb number $n_water inside box $xmin $ymin $zmin $xmax $ymax $zmax end structure " if { $n_sodium > 0 } { puts $packmol_input_file " structure SODIUM.pdb number $n_sodium inside box $xmin $ymin $zmin $xmax $ymax $zmax end structure " } if { $n_chloride > 0 } { puts $packmol_input_file " structure CHLORIDE.pdb number $n_chloride inside box $xmin $ymin $zmin $xmax $ymax $zmax end structure " } close $packmol_input_file puts " Wrote packmol input. " # # This are the temporary pdb file that will be temporaritly created # set water_file [ open ./WATER.pdb w ] puts $water_file \ "HETATM 1 H1 TIP3 1 9.626 6.787 12.673 H" puts $water_file \ "HETATM 2 H2 TIP3 1 9.626 8.420 12.673 H" puts $water_file \ "HETATM 3 OH2 TIP3 1 10.203 7.604 12.673 O" close $water_file set sod_file [ open ./SODIUM.pdb w ] puts $sod_file \ "HETATM 1 SOD SOD 2 0.000 0.000 0.000 Na" close $sod_file set cl_file [ open ./CHLORIDE.pdb w ] puts $cl_file \ "HETATM 1 CLA CLA 2 0.000 0.000 0.000 Cl" close $cl_file # Run packmol puts " -------------------------------------------------------" puts " Use these lengths for periodic boundary conditions: " puts " x: [ expr $x_length + 1. ]" puts " y: [ expr $y_length + 1. ]" puts " z: [ expr $z_length + 1. ]" puts " -------------------------------------------------------" puts " -------------------------------------------------------" puts " Now, run packmol with: packmol < $packmol_input " puts " -------------------------------------------------------" puts " The solvated file will be: $output " puts " -------------------------------------------------------" packmol-20.010/strlength.f90000066400000000000000000000024241360620542100155550ustar00rootroot00000000000000! ! Written by Leandro Martínez, 2009-2011. ! Copyright (c) 2009-2018, Leandro Martínez, Jose Mario Martinez, ! Ernesto G. Birgin. ! ! Function that determines the length of a string (better than ! intrinsic "len" because considers tabs as empty characters) ! function strlength(string) implicit none integer :: strlength character(len=200) :: string logical empty_char strlength = 200 do while(empty_char(string(strlength:strlength))) strlength = strlength - 1 if ( strlength == 0 ) exit end do end function strlength ! ! Function that determines if a character is empty (empty, space, or tab) ! (nice suggestion from Ian Harvey -IanH0073- at github) ! function empty_char(ch) character :: ch logical empty_char empty_char = .false. if ( ch == '' .or. & ch == achar(9) .or. & ch == achar(32) ) then empty_char = .true. end if end function empty_char ! ! Function that replaces all non-space empty characters by spaces ! function alltospace(record) implicit none integer :: i logical :: empty_char character(len=200) :: alltospace, record do i = 1, 200 if ( empty_char(record(i:i)) ) then alltospace(i:i) = " " else alltospace(i:i) = record(i:i) end if end do end function alltospace packmol-20.010/swaptype.f90000066400000000000000000000034671360620542100154270ustar00rootroot00000000000000! ! Written by Leandro Martínez, 2009-2011. ! Copyright (c) 2009-2018, Leandro Martínez, Jose Mario Martinez, ! Ernesto G. Birgin. ! ! Subroutine that swaps indexes for packing molecules one at a time ! subroutine swaptype(n,x,itype,action) use sizes, only : nn use compute_data, only : ntype, comptype, nmols, ntotmol use input, only : nloop, nloop_all, nloop_type use swaptypemod use ahestetic implicit none integer ::n, itype, ilubar, ilugan, i, action double precision :: x(nn) ! Save original data if ( action == 0 ) then do i = 1, nn xfull(i) = x(i) end do ntemp = n ntottemp = ntotmol end if ! Swapping data for packing this itype if ( action == 1 ) then do i = 1, ntype if(i == itype) then comptype(i) = .true. else comptype(i) = .false. end if end do n = nmols(itype) * 6 ntotmol = nmols(itype) nloop = nloop_type(itype) ilubar = 0 do i = 1, itype - 1 ilubar = ilubar + nmols(i) * 3 end do ilubar = ilubar + 1 ilugan = ntemp/2 + ilubar do i = 1, n / 2 x(i) = xfull(ilubar) x(i+n/2) = xfull(ilugan) ilubar = ilubar + 1 ilugan = ilugan + 1 end do end if ! Save results for this type if ( action == 2 ) then ilubar = 0 do i = 1, itype - 1 ilubar = ilubar + nmols(i)*3 end do ilubar = ilubar + 1 ilugan = ntemp/2 + ilubar do i = 1, n/2 xfull(ilubar) = x(i) xfull(ilugan) = x(i+n/2) ilubar = ilubar + 1 ilugan = ilugan + 1 end do end if ! Restore all-molecule vectors if ( action == 3 ) then n = ntemp ntotmol = ntottemp nloop = nloop_all do i = 1, n x(i) = xfull(i) end do do i = 1, ntype comptype(i) = .true. end do end if end subroutine swaptype packmol-20.010/swaptypemod.f90000066400000000000000000000005441360620542100161200ustar00rootroot00000000000000! ! Written by Leandro Martínez, 2009-2011. ! Copyright (c) 2009-2018, Leandro Martínez, Jose Mario Martinez, ! Ernesto G. Birgin. ! ! Module that contains the temporary data for swap molecules ! for individual packing ! module swaptypemod integer :: ntemp, ntottemp double precision, allocatable :: xfull(:) ! (nn) end module swaptypemod packmol-20.010/title.f90000066400000000000000000000007561360620542100146720ustar00rootroot00000000000000! ! Written by Leandro Martínez, 2009-2011. ! Copyright (c) 2009-2018, Leandro Martínez, Jose Mario Martinez, ! Ernesto G. Birgin. ! ! Routine to print the title subroutine title() use ahestetic write(*,hash3_line) write(*,"(' PACKMOL - Packing optimization for the automated generation of', /& &' starting configurations for molecular dynamics simulations.', /& &' ',/& &t62,' Version 20.010 ')") write(*,hash3_line) end subroutine title packmol-20.010/tobar.f90000066400000000000000000000021211360620542100146440ustar00rootroot00000000000000! ! Written by Leandro Martínez, 2009-2011. ! Copyright (c) 2009-2018, Leandro Martínez, Jose Mario Martinez, ! Ernesto G. Birgin. ! ! subroutine tobar: moves molecules to their baricentres ! subroutine tobar() use sizes use compute_data, only : coor, ntype, natoms, idfirst implicit none integer :: idatom, itype, iatom double precision :: xcm, ycm, zcm do itype = 1, ntype idatom = idfirst(itype) - 1 xcm = 0.d0 ycm = 0.d0 zcm = 0.d0 do iatom = 1, natoms(itype) idatom = idatom + 1 xcm = xcm + coor(idatom,1) ycm = ycm + coor(idatom,2) zcm = zcm + coor(idatom,3) end do xcm = xcm / natoms(itype) ycm = ycm / natoms(itype) zcm = zcm / natoms(itype) idatom = idfirst(itype) - 1 do iatom = 1, natoms(itype) idatom = idatom + 1 coor(idatom,1) = coor(idatom,1) - xcm coor(idatom,2) = coor(idatom,2) - ycm coor(idatom,3) = coor(idatom,3) - zcm end do end do return end subroutine tobar packmol-20.010/usegencan.f90000066400000000000000000000007021360620542100155100ustar00rootroot00000000000000! ! Written by Leandro Martínez, 2009-2011. ! Copyright (c) 2009-2018, Leandro Martínez, Jose Mario Martinez, ! Ernesto G. Birgin. ! ! Optimization variables passed as common go pgencan module usegencan use sizes implicit none integer :: maxit, iprint1, iprint2 integer, allocatable :: wi(:) ! (nn) double precision, allocatable :: l(:), u(:), g(:) ! (nn) double precision, allocatable :: wd(:) ! (8*nn) end module usegencan packmol-20.010/writesuccess.f90000066400000000000000000000030561360620542100162700ustar00rootroot00000000000000! ! Written by Leandro Martínez, 2009-2011. ! Copyright (c) 2009-2018, Leandro Martínez, Jose Mario Martinez, ! Ernesto G. Birgin. ! ! Subroutine writesuccess ! ! Writes the success messages for good packings ! subroutine writesuccess(itype,fdist,frest,f) use input, only : input_itype use compute_data, only : ntype use ahestetic implicit none integer :: itype double precision :: fdist, frest, f if(itype.le.ntype) then write(*,dash1_line) write(*,*)' Packing solved for molecules of type', input_itype(itype) write(*,*)' Objective function value: ', f write(*,*)' Maximum violation of target distance: ',fdist write(*,*)' Max. constraint violation: ', frest write(*,dash1_line) else write(*,hash3_line) write(*,"(& &t33, ' Success! ', /,& &t14, ' Final objective function value: ', e10.5, /,& &t14, ' Maximum violation of target distance: ', f10.6, /,& &t14, ' Maximum violation of the constraints: ', e10.5 & &)") f, fdist, frest write(*,dash3_line) write(*,"(& &t14,' Please cite this work if Packmol was useful: ',/,/,& &t11,' L. Martinez, R. Andrade, E. G. Birgin, J. M. Martinez, ',/,& &t9,' PACKMOL: A package for building initial configurations for',/,& &t19,' molecular dynamics simulations. ',/,& &t10,' Journal of Computational Chemistry, 30:2157-2164,2009.' )") write(*,hash3_line) end if end subroutine writesuccess