format code

src/cenmass.f90

@@ -2,102 +2,102 @@
 !  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. 
+!            for fixed molecules, if required.
 !
 subroutine cenmass()
 
-  use sizes
-  use compute_data, only : ntype, coor, idfirst, natoms
-  use input, only : keyword, amass, nlines, linestrut
+   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
 
-  implicit none
-  integer :: k, iline
-  integer :: itype, iatom, idatom
-  double precision, allocatable :: cm(:,:), totm(:)
-  logical, allocatable :: domass(:)
+   allocate(cm(ntype,3),totm(ntype),domass(ntype))
 
-  ! Allocate local vectors
+   ! Setting the molecules for which the center of mass is computed
 
-  allocate(cm(ntype,3),totm(ntype),domass(ntype))
+   do itype = 1, ntype
+      domass(itype) = .true.
+   end do
 
-  ! Setting the molecules for which the center of mass is computed
+   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 itype = 1, ntype
-    domass(itype) = .true.
-  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
 
-  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
+   ! Computing the center of mass
+
+   do itype = 1, ntype
+      do k = 1, 3
+         cm(itype, k) = 0.d0
       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
+
+   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 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
+   end do
+
+   do itype = 1, ntype
       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
+         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 if
-  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)
+   deallocate(cm,totm,domass)
 
-  return
+   return
 end subroutine cenmass

src/checkpoint.f90

@@ -1,8 +1,8 @@
-!  
+!
 !  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
@@ -11,106 +11,106 @@
 
 subroutine checkpoint(n,x)
 
-  use sizes
-  use compute_data
-  use input
-  use usegencan
-  use ahestetic
+   use sizes
+   use compute_data
+   use input
+   use usegencan
+   use ahestetic
 
-  implicit none
-  integer :: i
-  integer :: n
-  double precision :: x(n)
-  double precision :: fx
-  logical :: movebadprint
-  character(len=strl) :: xyzout_forced
+   implicit none
+   integer :: i
+   integer :: n
+   double precision :: x(n)
+   double precision :: fx
+   logical :: movebadprint
+   character(len=strl) :: xyzout_forced
 
-  ! All molecules are important
+   ! All molecules are important
 
    do i = 1, ntfix
-     comptype(i) = .true.
+      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,xyzout)
-
-  write(*,*) ' The solution with the best function value was '
-  write(*,*) ' written to the output file: ', trim(adjustl(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_forced = trim(adjustl(xyzout))//'_FORCED'
-  call output(n,x,xyzout_forced)
-
-  write(*,*) ' The forced point was writen to the '
-  write(*,*) ' output file: ', trim(adjustl(xyzout_forced))
-  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(*,*) '   ', trim(adjustl(xyzout)) 
-  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
+   ! 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,xyzout)
+
+   write(*,*) ' The solution with the best function value was '
+   write(*,*) ' written to the output file: ', trim(adjustl(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_forced = trim(adjustl(xyzout))//'_FORCED'
+   call output(n,x,xyzout_forced)
+
+   write(*,*) ' The forced point was writen to the '
+   write(*,*) ' output file: ', trim(adjustl(xyzout_forced))
+   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(*,*) '   ', trim(adjustl(xyzout))
+   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