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[Pascal Boulet <pascal.boulet@univ-provence.fr>]

Hello Rob,

I am not sure this post will answer your question. Here is a piece of basic code I wrote to parse the ABINIT output file. Basically, it gets the coordinates out of the ouput file and dump them into a xyz "trajectory" suitable for VMD.
It should also work during the course of the calculation or if the job stopped for some reasons.

Only the coordinates are read (no energies, no gradients).

I would be glad to know if it works for you.

Hope this help,

Best Regards
Pascal



Rob wrote:

255164.18295.qm@web33308.mail.mud.yahoo.com" type="cite">

once you have the structure, you can probably run the same input with
a very lax tolerance, low ecut, 1 k-point, and nstep 1 (in a different
directory of course, and transferring the converged lattice and atomic
positions to the new input file) setting prtgeo 1: the electronic
states are not used to give geo information. Tell us if it works.

How do you use the GEO files for visualization?
    

I like VMD for visualization. I'm about to write a plugin for VMD,
so that ABINIT-generated files can be read directly by VMD.
I'm interested in structure configurations and charge densities.
The easiest files to parse for structure information are the _GEO files.

Rob.


  

On Mon, May 25, 2009 at 1:52 PM, Rob <spamrefuse@yahoo.com> wrote:
    

Hi,

I learned that a useful interface for visualization are the foobar_GEO
output files,
by specifying "prtgeo 1" in the input file.

Now, if I did not (or have fogotten to) add this variable in the input
file, is there a
way to generate these "_GEO" files afterwards, without running the whole
calculation
again....?

Thanks,
Rob.
      

-- 
Dr. Pascal Boulet, Computational Chemist
University Aix-Marseille I
Laboratoire Chimie Provence, UMR6264
Centre Saint-Jerome, Bat. MADIREL
F-13397 MARSEILLE Cedex 20, France
Tel. +33 (0) 491 63 71 17 Fax. +33 (0) 491 63 71 11
courriel: pascal.boulet@univ-provence.fr
http://www.lc-provence.fr
http://allos.up.univ-mrs.fr/boulet

program abinit2xmol

 implicit none

 real(kind=8),parameter :: r0=0.52917720859d0
 character(len=2),dimension(54),parameter :: sym=(/'H ','He',          &
 'Li','Be','B ','C ','N ','O ','F ','Ne',                              &
 'Na','Mg','Al','Si','P ','S ','Cl','Ar',                              &
 'K ','Ca','Sc','Ti','V ','Cr','Mn','Fe','Co','Ni','Cu','Zn',          &
 'Ga','Ge','As','Se','Br','Kr',                                        &
 'Rb','Sr','Y ','Zr','Nb','Mo','Tc','Ru','Rh','Pd','Ag','Cd',          &
 'In','Sn','Sb','Te','I ','Xe'/)
 real(kind=8),dimension(:,:),allocatable :: x
 character(len=2),dimension(:),allocatable :: elem
 real(kind=8),dimension(3) :: a 
 integer,dimension(:),allocatable :: typatom
 integer,dimension(:),allocatable :: znuc
 integer :: i,j,k,l,n,ierr
 integer(kind=8) :: natom
 integer(kind=8) :: ntypatom
 character(len=80) :: line
 character(len=25) :: abinitfn
 
 
  print*,'abinit output filename?'
  read*,abinitfn
  open(10,file=abinitfn,status='old')
  open(11,file='abinit.xmol',status='unknown')
 
  line=' '
  do while (index(line,'acell').eq.0)
    read(10,'(A80)') line
  enddo
 
  read(line(12:),*) (a(i),i=1,3)
  a=a*r0
 
  do while (index(line,'natom').eq.0)
    read(10,'(A80)') line
  enddo
 
  read(line(12:),*) natom
 
  allocate(x(natom,3))
  allocate(typatom(natom))
  allocate(elem(natom))
 
  do while (index(line,'ntypat').eq.0)
    read(10,'(A80)') line
  enddo
 
  read(line(12:),*) ntypatom
 
  allocate(znuc(ntypatom))
  
  line=' '
  do while (index(line,'typat').eq.0)
    read(10,'(A80)') line
  enddo
  
  i=int(natom/20)
  j=mod(natom,20)

  if (i.eq.0) then
    read(line(12:),*) (typatom(k),k=1,natom)
  else if (i.eq.1) then
    read(line(12:),*) (typatom(k),k=1,20)
    n=k
    read(10,'(A80)') line
    read(line(12:),*) (typatom(k),k=n,n+j-1)
  else if (i.gt.1) then
    read(line(12:),*) (typatom(k),k=1,20)
    n=k
    do l=1,i-1
      read(10,'(A80)') line
      read(line(12:),*) (typatom(k),k=n,n+19)
      n=k
    enddo
    read(10,'(A80)') line
    read(line(12:),*) (typatom(k),k=n,n+j-1)
  endif
  
  line=' '
  do while (index(line,'znucl').eq.0)
    read(10,'(A80)') line
  enddo
  
  read(line(12:),*) (znuc(i),i=1,ntypatom)
  
  l1:do
    do while (index(line,'Cartesian coordinates (bohr)').eq.0)
      read(10,'(A80)',iostat=ierr) line
      if (ierr.ne.0) exit l1
    enddo
    
    do i=1,natom
      read(10,'(A80)',iostat=ierr) line
      if (ierr.ne.0) exit l1

      read(line,*,iostat=ierr) (x(i,j),j=1,3)
      if (ierr.ne.0) exit l1
      elem(i)=sym(znuc(typatom(i)))
    enddo
    
    write(11,'(I5)') natom
    write(11,'(A)') ''
    x=x*r0
    do i=1,natom
      write(11,'(A2,X,3(F15.8))') elem(i),(x(i,j),j=1,3)
    enddo
      
  enddo l1
  
  close(10)
  close(11)

end program abinit2xmol