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replace.f
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module replace
! contains routines that replace, remove, or add atoms
implicit none
contains
c---------------------------------------------------------------------
subroutine rmatoms(infile,informat,thespecies,nrm,
& outputfile)
use defs
use readcoords
use misc
use writecoords
implicit none
character(len=*) infile,informat,thespecies,outputfile
integer nrm
! local
type(atom),allocatable :: atoms(:),newatoms(:)
type(element),allocatable :: species(:),newspecies(:)
integer natoms,nspecies,nnewspecies,iatom,ispecies,nthere
integer inewatom,ithespecies,n,n1
integer, allocatable :: vacs(:)
double precision vecs(1:3,1:3)
logical isopen12,isdrawn
!character FMT1*1024,FMT2*1024
talk=.true.
! write hello
inquire(unit=12,opened=isopen12)
if(talk) then
if(isopen12) then
write(12,fsubstart)'rmatoms'
else
print fsubstart, 'rmatoms'
end if
end if
thespecies=adjustl(thespecies)
! read the coordinate file
call read_coords(infile,informat,atoms,natoms,species,
& nspecies,vecs)
! get the total number of atoms of
! the species of which you want to remove atoms
do ispecies=1,nspecies
if(species(ispecies)%name(1:2).eq.thespecies(1:2))
& nthere=species(ispecies)%howmany
end do
if(talk) then
if(isopen12) then
! write(12,'(8x,"There are ",I,1x,A2," atoms altogether.")')
! & nthere,thespecies(1:2)
WRITE(FMT2,*) nthere
WRITE(FMT1,*) '(8x,"There are ",I',
& len(trim(FMT2)),',1x,A2," atoms altogether.")'
write(12,FMT1) nthere,thespecies(1:2)
! write(12,'(8x,I," of them will be removed.")')nrm
WRITE(FMT2,*) nrm
WRITE(FMT1,*) '(8x,I',len(trim(FMT2)),'" of them will be rem
&oved.")'
write(12,FMT1) nrm
else
! print '(8x,"There are ",I,1x,A2," atoms altogether.")',
! & nthere,thespecies(1:2)
WRITE(FMT2,*) nthere
WRITE(FMT1,*) '(8x,"There are ",I',
& len(trim(FMT2)),',1x,A2," atoms altogether.")'
print FMT1, nthere,thespecies(1:2)
! print '(8x,I," of them will be removed.")',nrm
WRITE(FMT2,*) nrm
WRITE(FMT1,*) '(8x,I',len(trim(FMT2)),'" of them will be rem
&oved.")'
print FMT1, nrm
end if
end if
!
! if positive number to be removed
!
if (nrm.ge.0) then
!
! call subroutine that draws balls from an urn
call drawballs(nthere,nrm,vacs)
! get new structure
allocate(newatoms(natoms-nrm))
inewatom=0
ithespecies=0
do iatom=1,natoms
if (atoms(iatom)%name(1:2).ne.thespecies(1:2)) then
inewatom=inewatom+1
newatoms(inewatom)=atoms(iatom)
end if
if (atoms(iatom)%name(1:2).eq.thespecies(1:2)) then
ithespecies=ithespecies+1
if(.not.any(vacs.eq.ithespecies)) then
inewatom=inewatom+1
newatoms(inewatom)=atoms(iatom)
end if
!if (atoms(iatom)%name(1:2).eq.thespecies(1:2)) then
! ithespecies=ithespecies+1
! if(.not.any(vacs.eq.ithespecies)) then
! inewatom=inewatom+1
! newatoms(inewatom)=atoms(iatom)
! end if
!end if
end if
end do
!
! end if positive number to be removed
!
end if
!
! if negative number to be removed
!
if (nrm.lt.0) then
allocate(vacs(1))
allocate(newatoms(natoms-1))
inewatom=0
ithespecies=0
do iatom=1,natoms
if (atoms(iatom)%name(1:2).ne.thespecies(1:2)) then
inewatom=inewatom+1
newatoms(inewatom)=atoms(iatom)
end if
if (atoms(iatom)%name(1:2).eq.thespecies(1:2)) then
ithespecies=ithespecies+1
if(-nrm.ne.ithespecies) then
inewatom=inewatom+1
newatoms(inewatom)=atoms(iatom)
else
vacs(1)=iatom
end if
end if
end do
end if
!
! end if negative number to be removed
!
! get new numbers of species
call getspecies(newatoms,newspecies)
nnewspecies=size(newspecies)
call write_coords(outputfile,informat,newatoms,size(newatoms), &
& newspecies,nnewspecies,vecs)
! write a file with the atoms that were removed
open(51,file="VACS.DAT",status="replace")
write(51,'("# The ",A," atoms that were removed are:")')
& trim(thespecies)
do n1=1,max(nrm,1)
write(51,*) vacs(n1)
end do
close(51)
! write goodbye
if(talk) then
if(isopen12) then
write(12,fsubendext)'rmatoms'
else
print fsubendext, 'rmatoms'
end if
end if
end subroutine
c---------------------------------------------------------------------
subroutine rpatoms(infile,informat,thespecies,nrp,
& theotherspecies,outputfile)
use defs
use readcoords
use misc
use writecoords
implicit none
character(len=*) infile,informat,thespecies,theotherspecies,
& outputfile
integer nrp
! local
type(atom),allocatable :: atoms(:)!,newatoms(:)
type(element),allocatable :: species(:),newspecies(:)
integer natoms,nspecies,nnewspecies,iatom,ispecies,nthere
integer ithespecies,n,n1 !,inewatom
integer, allocatable :: replaced(:)
double precision vecs(1:3,1:3)
logical isopen12,isdrawn
!character FMT1*1024,FMT2*1024
talk=.true.
! write hello
inquire(unit=12,opened=isopen12)
if(talk) then
if(isopen12) then
write(12,fsubstart)'rpatoms'
else
print fsubstart, 'rpatoms'
end if
end if
thespecies=adjustl(thespecies)
! read the coordinate file
call read_coords(infile,informat,atoms,natoms,species,
& nspecies,vecs)
! get the total number of atoms of
! the species of which you want to remove atoms
do ispecies=1,nspecies
if(species(ispecies)%name(1:2).eq.thespecies(1:2))
& nthere=species(ispecies)%howmany
end do
if(talk) then
if(isopen12) then
! write(12,'(8x,"There are ",I,1x,A2," atoms altogether.")')
! & nthere,thespecies(1:2)
WRITE(FMT2,*) nthere
WRITE(FMT1,*) '(8x,"There are ",I',len(trim(FMT2)),',A2," at
&oms altogether.")'
write(12,FMT1) nthere,thespecies(1:2)
! write(12,'(8x,I," of them will be replaced by ",A2,".")')
! & nrp,trim(adjustl(theotherspecies))
if(nrp.ge.0) then
WRITE(FMT2,*) nrp
WRITE(FMT1,*) '(8x,I',len(trim(FMT2)),',"of them will be r
&eplaced by ",A2,".")'
write(12,FMT1) nrp,trim(adjustl(theotherspecies))
end if
if(nrp.lt.0) then
WRITE(FMT2,*) -nrp
WRITE(FMT1,*) '(8x,A2, " number ",I',len(trim(FMT2)),
& '," will be replaced by ",A2,".")'
write(12,FMT1) thespecies(1:2),-nrp,
& trim(adjustl(theotherspecies))
end if
else
! print '(8x,"There are ",I,1x,A2," atoms altogether.")',
! & nthere,thespecies(1:2)
WRITE(FMT2,*) nthere
WRITE(FMT1,*) '(8x,"There are ",I',len(trim(FMT2)),',A2," at
&oms altogether.")'
print FMT1, nthere,thespecies(1:2)
! print '(8x,I," of them will be replaced by",A2,".")',nrp,
! & trim(adjustl(theotherspecies))
!WRITE(FMT2,*) nrp
!WRITE(FMT1,*) '(8x,I',len(trim(FMT2)),',"of them will be rep
! &laced by ",A2,".")'
!print FMT1, nrp,trim(adjustl(theotherspecies))
if(nrp.ge.0) then
WRITE(FMT2,*) nrp
WRITE(FMT1,*) '(8x,I',len(trim(FMT2)),',"of them will be r
&eplaced by ",A2,".")'
print FMT1, nrp,trim(adjustl(theotherspecies))
end if
if(nrp.lt.0) then
WRITE(FMT2,*) -nrp
WRITE(FMT1,*) '(8x,A2, " number ",I',len(trim(FMT2)),
& '," will be replaced by ",A2,".")'
print FMT1, thespecies(1:2),-nrp,
& trim(adjustl(theotherspecies))
end if
end if
end if
! ! if the species is new, increase the number of elements you have
! ! in your system
! nnewspecies=nspecies
! if(.not.any(species%name(1:8).eq.theotherspecies(1:8))) then
! nnewspecies=nspecies+1
! end if
! allocate(newspecies(nnewspecies))
! do ispecies=1,nspecies
! newspecies(ispecies)=species(ispecies)
! end do
! if (nnewspecies.gt.nspecies) then
! newspecies(nnewspecies)%name=theotherspecies
! newspecies(nnewspecies)%howmany=nrp
! newspecies(nnewspecies)%mass=0.0D0
! newspecies(nnewspecies)%charge=0.0D0
! end if
! if random replacement:
if(nrp.ge.0) then
! call subroutine that draws balls from an urn
call drawballs(nthere,nrp,replaced)
! get new structure
!allocate(newatoms(natoms-nrp))
!inewatom=0
ithespecies=0
do iatom=1,natoms
!if (atoms(iatom)%name(1:2).ne.thespecies(1:2)) then
! inewatom=inewatom+1
! newatoms(inewatom)=atoms(iatom)
!end if
if (atoms(iatom)%name(1:2).eq.thespecies(1:2)) then
ithespecies=ithespecies+1
!if(.not.any(replaced.eq.ithespecies)) then
if(any(replaced.eq.ithespecies)) then
!inewatom=inewatom+1
!newatoms(inewatom)=atoms(iatom)
atoms(iatom)%name(1:8)
& =trim(adjustl(theotherspecies(1:8)))
end if
end if
end do
end if
! if a special atom i sto be replaced:
if(nrp.lt.0) then
ithespecies=0
do iatom=1,natoms
if (atoms(iatom)%name(1:2).eq.thespecies(1:2)) then
ithespecies=ithespecies+1
!if(any(replaced.eq.ithespecies)) then
if (ithespecies.eq.-nrp) then
atoms(iatom)%name(1:2)
& =trim(adjustl(theotherspecies(1:2)))
end if
end if
end do
end if
! get new numbers of species
call getspecies(atoms,newspecies)
nnewspecies=size(newspecies)
call write_coords(outputfile,informat,atoms,natoms,newspecies,
& nnewspecies,vecs)
! write a file with the atoms that were replaced
open(51,file="REPLACED.DAT",status="replace")
write(51,'("# The ",A," atoms that were replaced are:")')
& trim(thespecies)
do n1=1,nrp
write(51,*) replaced(n1)
end do
close(51)
! write goodbye
if(talk) then
if(isopen12) then
write(12,fsubendext)'rpatoms'
else
print fsubendext, 'rpatoms'
end if
end if
end subroutine
c---------------------------------------------------------------------
subroutine rpatoms2(atoms,thespecies,nrp,
& theotherspecies)
! replaces nrp atoms of species "thespecies" by "theotherspecies"
! in array "atoms". result: atoms
use defs
use misc
implicit none
character(len=*) thespecies,theotherspecies
integer nrp
! local
type(atom),allocatable :: atoms(:)!,newatoms(:)
type(element),allocatable :: species(:),newspecies(:)
integer natoms,nspecies,nnewspecies,iatom,ispecies,nthere
integer ithespecies,n,n1 !,inewatom
integer, allocatable :: replaced(:)
double precision vecs(1:3,1:3)
logical isopen12,isdrawn
!character FMT1*1024,FMT2*1024
talk=.true.
! write hello
inquire(unit=12,opened=isopen12)
if(talk) then
if(isopen12) then
write(12,fsubstart)'rpatoms2'
else
print fsubstart, 'rpatoms2'
end if
end if
thespecies=adjustl(thespecies)
natoms=size(atoms)
call getspecies(atoms,species)
nspecies=size(species)
! get the total number of atoms of
! the species of which you want to remove atoms
do ispecies=1,nspecies
if(species(ispecies)%name(1:2).eq.thespecies(1:2))
& nthere=species(ispecies)%howmany
end do
if(talk) then
if(isopen12) then
WRITE(FMT2,*) nthere
WRITE(FMT1,*) '(8x,"There are ",I',len(trim(FMT2)),',1x,A2,
& " atoms altogether.")'
write(12,FMT1) nthere,thespecies(1:2)
if(nrp.ge.0) then
WRITE(FMT2,*) nrp
WRITE(FMT1,*) '(8x,I',len(trim(FMT2)),',"of them will be r
&eplaced by ",A2,".")'
write(12,FMT1) nrp,trim(adjustl(theotherspecies))
end if
if(nrp.lt.0) then
WRITE(FMT2,*) -nrp
WRITE(FMT1,*) '(8x,A2, " number ",I',len(trim(FMT2)),
& '," will be replaced by ",A2,".")'
write(12,FMT1) thespecies(1:2),-nrp,
& trim(adjustl(theotherspecies))
end if
else
WRITE(FMT2,*) nthere
WRITE(FMT1,*) '(8x,"There are ",I',len(trim(FMT2)),',1x,A2,
&" atoms altogether.")'
print FMT1, nthere,thespecies(1:2)
if(nrp.ge.0) then
WRITE(FMT2,*) nrp
WRITE(FMT1,*) '(8x,I',len(trim(FMT2)),'," of them will be
&replaced by ",A2,".")'
print FMT1, nrp,trim(adjustl(theotherspecies))
end if
if(nrp.lt.0) then
WRITE(FMT2,*) -nrp
WRITE(FMT1,*) '(8x,A2, " number ",I',len(trim(FMT2)),
& '," will be replaced by ",A2,".")'
print FMT1, thespecies(1:2),-nrp,
& trim(adjustl(theotherspecies))
end if
end if
end if
! if random replacement:
if(nrp.ge.0) then
! call subroutine that draws balls from an urn
call drawballs(nthere,nrp,replaced)
! get new structure
!allocate(newatoms(natoms-nrp))
!inewatom=0
ithespecies=0
do iatom=1,natoms
!if (atoms(iatom)%name(1:2).ne.thespecies(1:2)) then
! inewatom=inewatom+1
! newatoms(inewatom)=atoms(iatom)
!end if
if (atoms(iatom)%name(1:2).eq.thespecies(1:2)) then
ithespecies=ithespecies+1
!if(.not.any(replaced.eq.ithespecies)) then
if(any(replaced.eq.ithespecies)) then
!inewatom=inewatom+1
!newatoms(inewatom)=atoms(iatom)
atoms(iatom)%name(1:2)
& =theotherspecies(1:2)
end if
end if
end do
end if
! if a special atom i sto be replaced:
if(nrp.lt.0) then
ithespecies=0
do iatom=1,natoms
if (atoms(iatom)%name(1:2).eq.thespecies(1:2)) then
ithespecies=ithespecies+1
!if(any(replaced.eq.ithespecies)) then
if (ithespecies.eq.-nrp) then
atoms(iatom)%name(1:2)
& =trim(adjustl(theotherspecies(1:2)))
end if
end if
end do
end if
! write goodbye
if(talk) then
if(isopen12) then
write(12,fsubendext)'rpatoms2'
else
print fsubendext, 'rpatoms2'
end if
end if
end subroutine
c---------------------------------------------------------------------
subroutine get_molecule(infile,informat,theatom,nndist,molatoms, &
&vecs,maxiter)
use defs
use readcoords
use misc
use writecoords
implicit none
character(len=*) infile,informat
integer theatom, maxiter
double precision nndist
! local
type(atom),allocatable :: atoms(:),molatoms(:),molatoms_temp(:)
type(element),allocatable :: species(:)
integer natoms,nspecies,iatom,ispecies,coordmin,coordmax
integer nmolatoms,iter,inewatom,iatom2,nnew_neighbors
integer, allocatable :: imolatoms(:),old_neighbors(:)
integer, allocatable :: new_neighbors(:),new_neighbors_temp(:)
integer, allocatable :: imolatoms_temp(:)
double precision coordmean
double precision vecs(1:3,1:3)
!double precision tol
logical isopen12,l_continue,l_found_new,is_new
!character FMT1*1024,FMT2*1024
talk=.true.
! write hello
inquire(unit=12,opened=isopen12)
if(talk) then
if(isopen12) then
write(12,fsubstart)'get_molecule'
else
print fsubstart, 'get_molecule'
end if
end if
! read the coordinate file
call read_coords(infile,informat,atoms,natoms,species,
& nspecies,vecs)
natoms=size(atoms)
call getspecies(atoms,species)
nspecies=size(species)
if(talk) then
if(isopen12) then
write(12,'(8x,"Searching molecule starting from atom # ", &
&I0)') theatom
write(12,'(8x,"Using as cutoff ",F9.6," Angs")')nndist
write(12,'(8x,"Using up to ",I12," iterations")') maxiter
else
print '(8x,"Searching molecule starting from atom # ",I0)', &
& theatom
print '(8x,"Using as cutoff ",F9.6," Angs")',nndist
print '(8x,"Using up to ",I12," iterations")',maxiter
end if
end if
! First(zeroth) iteration. Find neighbors of teh starting atom and add them to the
! "molecule".
iter=0
call coord(atoms,vecs,nndist,coordmin,coordmax,coordmean)
allocate(molatoms(1))
allocate(imolatoms(1))
imolatoms(1)=theatom
molatoms(1)=atoms(theatom)
l_continue=.false.
if (molatoms(1)%coord.gt.0) then
l_continue=.true.
allocate (old_neighbors(molatoms(1)%coord))
old_neighbors(:)=molatoms(1)%ineighbors(:)
if (allocated(molatoms_temp)) deallocate(molatoms_temp)
if (allocated(imolatoms_temp)) deallocate(imolatoms_temp)
nmolatoms=size(molatoms)+size(old_neighbors)
allocate(molatoms_temp(nmolatoms),imolatoms_temp(nmolatoms))
imolatoms_temp(1:size(molatoms))=imolatoms
imolatoms_temp(size(molatoms)+1:)=old_neighbors(:)
deallocate(imolatoms)
allocate(imolatoms(nmolatoms))
imolatoms=imolatoms_temp
molatoms_temp(1:size(molatoms))=molatoms
molatoms_temp(size(molatoms)+1:)=atoms(old_neighbors(:))
deallocate(molatoms)
allocate(molatoms(nmolatoms))
molatoms=molatoms_temp
end if
!
! iteratively add more neighbor atoms until maxiter is reached or
! no more new neighbors can be found
!
do while (l_continue.and.iter.lt.maxiter)
iter=iter+1
!print*, "" !DEBUG
!print*, "#######################" !DEBUG
!print*, "iter:",iter ! DEBUG
!print*, "#######################" !DEBUG
l_found_new=.false.
nnew_neighbors=0
if(allocated(new_neighbors)) deallocate(new_neighbors)
if (allocated(new_neighbors_temp))deallocate(new_neighbors_temp)
!print*,"old neighbors:",old_neighbors ! DEBUG
do iatom=1,size(old_neighbors)
!print*, "" !DEBUG
!print*, "iatom:", iatom ! DEBUG
!print*,"atom: ", old_neighbors(iatom) ! DEBUG
!print*,"neighbors: ", atoms(old_neighbors(iatom))%ineighbors ! DEBUG
do iatom2=1,atoms(old_neighbors(iatom))%coord
inewatom=atoms(old_neighbors(iatom))%ineighbors(iatom2)
if (.not.(any(imolatoms==inewatom))) then
! new neighbor found. Add it to molecule and to list of
! new neighbors
l_found_new=.true.
nnew_neighbors=0
!print*, "new atom:",inewatom ! DEBUG
if (allocated(new_neighbors)) &
& nnew_neighbors=size(new_neighbors)
!
! add new atom to list of new neighbors
!
if (allocated(new_neighbors_temp)) &
& deallocate(new_neighbors_temp)
if (nnew_neighbors.gt.0) then
allocate(new_neighbors_temp(nnew_neighbors))
new_neighbors_temp=new_neighbors
end if
!print*, "nnew neighbors:",nnew_neighbors ! DEBUG
if (allocated(new_neighbors)) deallocate(new_neighbors)
allocate(new_neighbors(nnew_neighbors+1))
if (nnew_neighbors.gt.0) then
new_neighbors(1:nnew_neighbors)=new_neighbors_temp
end if
new_neighbors(nnew_neighbors+1)=inewatom
!print*, "new neighbors:",new_neighbors ! DEBUG
nnew_neighbors=nnew_neighbors+1
!
! add new atom to molecule
!
if (allocated(molatoms_temp)) deallocate(molatoms_temp)
if (allocated(imolatoms_temp)) deallocate(imolatoms_temp)
nmolatoms=size(molatoms)+1
allocate(molatoms_temp(nmolatoms), &
& imolatoms_temp(nmolatoms))
imolatoms_temp(1:size(molatoms))=imolatoms
imolatoms_temp(size(molatoms)+1)=inewatom
deallocate(imolatoms)
allocate(imolatoms(nmolatoms))
imolatoms=imolatoms_temp
molatoms_temp(1:size(molatoms))=molatoms
molatoms_temp(size(molatoms)+1)=atoms(inewatom)
deallocate(molatoms)
allocate(molatoms(nmolatoms))
molatoms=molatoms_temp
!print*,"molecule atoms: ", imolatoms! DEBUG
end if ! new neighbor atom found
!print*, "new atom found:", l_found_new !DEBUG
end do ! iatom2
end do ! iatom
l_continue=l_found_new
deallocate(old_neighbors)
!print*,"nnew_neighbors:",nnew_neighbors !DEBUG
if (nnew_neighbors.gt.0) then
allocate(old_neighbors(nnew_neighbors))
old_neighbors=new_neighbors
end if
!print*, "continue:",l_continue ! DEBUG
end do ! while loop
!
if(l_continue) &
& call warning('molecule may be incomplete. Increase maxiter')
!
! write molecule info to file
!
open(51,file="MOLECULE_LIST")
do iatom=1,size(molatoms)
write(51,*) imolatoms(iatom), molatoms(iatom)%name
end do
close(51)
! write goodbye
if(talk) then
if(isopen12) then
write(12,fsubendext)'get_molecule'
else
print fsubendext, 'get_molecule'
end if
end if
end subroutine get_molecule
c---------------------------------------------------------------------
subroutine rmeqv(infile,informat,symmformat,outfile,tol)
use defs
use readcoords
use misc
use writecoords
implicit none
character(len=*) infile,informat,symmformat,outfile
! local
type(atom),allocatable :: atoms(:),irredatoms(:),redatoms(:)
type(element),allocatable :: species(:),irredspecies(:),
& redspecies(:)
type(symop), allocatable :: symops(:)
integer natoms,nspecies,iatom,ispecies
integer nsym,nred,nirred,ired,iirred
integer n,k,i,idum
double precision vecs(1:3,1:3),xtrans(1:3),distvec(1:3),tol
character redoutfile*40,line*256
logical isopen12
talk=.true.
! write hello
inquire(unit=12,opened=isopen12)
if(talk) then
if(isopen12) then
write(12,fsubstart)'rmeqv'
write(12,'(8x,"using as tolerance ",F10.6)'),tol
else
print fsubstart, 'rmeqv'
print '(8x,"using as tolerance ",F10.6)',tol
end if
end if
! read the coordinate file
call read_coords(infile,informat,atoms,natoms,species,
& nspecies,vecs)
c read number of symmetry operations to be read in,
c and symmetry operations
open(51,file='SYMM.DAT',status='old')
read(51,*) nsym
allocate(symops(nsym))
select case(symmformat)
case('gulp','GULP')
c (in gulp format, with 'symmetry_operator'
c before each operation)
do n=1,nsym
read(51,'(A40)')line
read(51,*) symops(n)%mat(1,1:3),symops(n)%trala(1)
read(51,*) symops(n)%mat(2,1:3),symops(n)%trala(2)
read(51,*) symops(n)%mat(3,1:3),symops(n)%trala(3)
end do
case('mbpp','MBPP')
c (in MBPP format)
do n=1,nsym
read(51,*) idum,symops(n)%mat(1,1:3),
& symops(n)%mat(2,1:3),symops(n)%mat(3,1:3),
& symops(n)%trala(1:3)
end do
case default
if(isopen12) then
write(12,ferrmssg) "unknown format of symmetry operati
&ons"
else
print ferrmssg, "unknown format of symmetry operations
&"
end if
close(51)
nerr=nerr+1
return
end select
close(51)
! find irreducible atoms
! at the beginning assume that every atom is irreducible:
nred=0
nirred=natoms
atoms%reducible=.false.
c for each atom check if it is reducible
!xall(n,1:3)=x(1:3)
!reducible(n)=.False.
!nstart=1
c if(n.gt.n_atom/2) nstart=n_atom/2+1
do iatom=1,natoms ! for all atoms
do k=1,nsym ! for all symmetry operations apply the symmetry operation to
! the atom coordinates
xtrans=matmul(symops(k)%mat,atoms(iatom)%where)
& +symops(k)%trala
! do i=1,3
! xtrans(i)=xall(iatom,1)*matrix(k,i,1)!+trala(k,i)
! & +xall(iatom,2)*matrix(k,i,2)!+trala(k,i)
! & +xall(iatom,3)*matrix(k,i,3)+trala(k,i)
!do while (xtrans(i).gt.0.5)
! xtrans(i)=xtrans(i)-1.0
!end do
!do while (xtrans(i).le.-0.5)
! xtrans(i)=xtrans(i)+1.0
!end do
! end do
! look if another atom is equivalent by symmetry
do n=1,iatom-1
! if (abs(xall(m,1)-xtrans(1)).lt.tol.and.
! & abs(xall(m,2)-xtrans(2)).lt.tol.and.
! & abs(xall(m,3)-xtrans(3)).lt.tol.and.
! & nameat(n)==nameat(m).and.cs(n)==cs(m))
! & reducible(n)=.True.
! If the atoms belong to the same species,
! get the distance between the transposed original atom and
! the other atom
if (atoms(iatom)%name.eq.atoms(n)%name.and.
& atoms(iatom)%core.eq.atoms(n)%core) then
distvec=xtrans-atoms(n)%where
! use the distance modulo the lattice constants
do i=1,3
do while (distvec(i).gt.0.5D0)
distvec(i)=distvec(i)-1.0D0
end do
do while (distvec(i).le.-0.5D0)
distvec(i)=distvec(i)+1.0D0
end do
end do
! if the distance is below a threshold, the atom
! coordinates are equal
if (absvec(distvec).lt.tol) then
atoms(iatom)%reducible=.true.
!nred=nred+1
end if
end if
end do
end do
if (atoms(iatom)%reducible) nred=nred+1
end do
if(talk) print '(8x,"number of red. atoms:",I5)',nred
! get reducible and irreducible atoms
nirred=natoms-nred
!print '(8x,"number of red./irred. atoms:",I,I)', nred,nirred
!do i=1,natoms
! print*,atoms(i)%name,atoms(i)%reducible
!end do
allocate(redatoms(nred),irredatoms(nirred))
ired=0
iirred=0
do iatom=1,natoms
if (atoms(iatom)%reducible.eqv..true.) then
ired=ired+1
redatoms(ired)=atoms(iatom)
else
iirred=iirred+1
irredatoms(iirred)=atoms(iatom)
end if
end do
!do i=1,nred
! print*,redatoms(i)%name,redatoms(i)%reducible
!end do
!do i=1,nirred
! print*,irredatoms(i)%name,irredatoms(i)%reducible
!end do
! get number of reducible and irreducible atoms of each species
! ispecies=1
! do iatom=1,nred
! newspecies=.true.
! do i=1,iatom-1
! if (redatoms(i)%name(1:2).eq.redatoms(iatom)%name(1:2))
! & newspecies=.false.
! end do
! if(newspecies) then
! species(ispecies)%name=redatoms(iatom)%name
! ispecies=ispecies+1
! end if
! end do
! get numbers of reducible atoms of each species
allocate(redspecies(nspecies),irredspecies(nspecies))
redspecies=species
irredspecies=species
do ispecies=1,nspecies
redspecies(ispecies)%howmany=0
do i=1,nred
if(redatoms(i)%name(1:2).eq.redspecies(ispecies)%name(1:2))
& redspecies(ispecies)%howmany=
& redspecies(ispecies)%howmany+1
end do
end do
! get numbers of irreducible atoms of each species
do ispecies=1,nspecies
irredspecies(ispecies)%howmany=0
do i=1,nirred
if(irredatoms(i)%name(1:2).eq.
& irredspecies(ispecies)%name(1:2))
& irredspecies(ispecies)%howmany=
& irredspecies(ispecies)%howmany+1
end do
end do
! ! get new structure
! allocate(newatoms(natoms-nrm))
! inewatom=0
! ithespecies=0
! do iatom=1,natoms
! if (atoms(iatom)%name(1:2).ne.thespecies(1:2)) then
! inewatom=inewatom+1
! newatoms(inewatom)=atoms(iatom)
! end if
! if (atoms(iatom)%name(1:2).eq.thespecies(1:2)) then
! ithespecies=ithespecies+1
! if(.not.any(vacs.eq.ithespecies)) then
! inewatom=inewatom+1
! newatoms(inewatom)=atoms(iatom)
! end if
! end if
! end do
! write a file with the irreducible atoms
call write_coords(outfile,informat,irredatoms,nirred,
& irredspecies,nspecies,vecs)
! write a file with the reducible atoms
write(redoutfile,*)"REDUCIBLE.",trim(adjustl(informat))
redoutfile=adjustl(redoutfile)
call write_coords(redoutfile,informat,redatoms,
& nred,redspecies,nspecies,vecs)
! write a file with the symmetry operations in other formats
open(51,file="SYMM.OUT",status="replace")
do k=1,nsym
write(51,'("symmetry_operator")')
do i=1,3
write(51,'(4(F10.6))')
& symops(k)%mat(i,1:3),symops(k)%trala(i)
end do
end do
close(51)
! write goodbye
if(talk) then
if(isopen12) then
write(12,fsubendext)'rmeqv'
else
print fsubendext, 'rmeqv'
end if
end if
end subroutine rmeqv
c---------------------------------------------------------------------
subroutine addeqv(infile,informat,symmformat,outfile,tol)
use defs
use readcoords
use misc
use writecoords
implicit none
character(len=*) infile,informat,symmformat,outfile
! local
type(atom),allocatable :: atoms(:),irredatoms(:),redatoms(:)
type(atom),allocatable :: addedatoms(:),dummyatoms(:),allatoms(:)
type(element),allocatable :: species(:),irredspecies(:),
& redspecies(:),addedspecies(:),allspecies(:)
type(symop), allocatable :: symops(:)
integer natoms,nspecies,iatom,ispecies,naddedspecies,nirredspecies
integer nredspecies,nallspecies
integer nsym,nred,nirred,ired,iirred,iadded,nadded,nall
integer n,k,i,idum
double precision vecs(1:3,1:3),xtrans(1:3),distvec(1:3),tol
character redoutfile*256,line*256
logical isopen12,add
talk=.true.
! write hello
inquire(unit=12,opened=isopen12)
if(talk) then
if(isopen12) then
write(12,fsubstart)'addeqv'
write(12,'(8x,"using as tolerance ",F10.6)'),tol
else
print fsubstart, 'addeqv'
print '(8x,"using as tolerance ",F10.6)',tol
end if
end if
! read the coordinate file
call read_coords(infile,informat,atoms,natoms,species,
& nspecies,vecs)
c read number of symmetry operations to be read in,
c and symmetry operations
open(51,file='SYMM.DAT',status='old')
read(51,*) nsym
allocate(symops(nsym))
select case(symmformat)
case('gulp','GULP')
c (in gulp format, with 'symmetry_operator'
c before each operation)
do n=1,nsym
read(51,'(A40)')line
read(51,*) symops(n)%mat(1,1:3),symops(n)%trala(1)
read(51,*) symops(n)%mat(2,1:3),symops(n)%trala(2)
read(51,*) symops(n)%mat(3,1:3),symops(n)%trala(3)
end do
case('mbpp','MBPP')
c (in MBPP format)
do n=1,nsym
read(51,*) idum,symops(n)%mat(1,1:3),
& symops(n)%mat(2,1:3),symops(n)%mat(3,1:3),
& symops(n)%trala(1:3)
end do
case default
if(isopen12) then
write(12,ferrmssg) "unknown format of symmetry operati
&ons"
else
print ferrmssg, "unknown format of symmetry operations
&"
end if
close(51)
nerr=nerr+1
return
end select