ABINIT Discussion Forums

Hi,

I've come across a bug in abi2xsf. The corrected script is attached below.

Scott
============

#!/bin/bash

# Shanavas K. V.
# Synchrotron Radiation Section
# Bhabha Atomic Research Center, Mumbai
# email: shanavas@barc.ernet.in, ph: 022-25591312
#
# script to convert abinit output file to
# Xcrysden Structure File format
# Written by Shanavas on Mon Apr 25 15:38:34 IST 2005


if [ $# -lt 1 ]; then
echo "
Usage: abi2xsf [option] abi-out

-c Convert from bohr to ang (default)
-i Initial structure
-f Final structure (default)
-a Animation file (initial & final)
-s Structural Optimization run

Defaults are assumed when no options are provided"
exit 1
fi

c=0.52918
st=2
case $1 in
-c|-c?|-?c)
echo $1
exit 0
c=0.52918;
shift
;;
-i|-?i|-i?)
st=1
shift
;;
-f|-?f|-f?)
st=2
shift
;;
-a|-?a|-a?)
st=0
shift
;;
-s|-?s|-s?)
st=-1
shift
;;*)
esac

if [ ! -r "$1" ]; then
echo "File $1 does not exist!"
exit 1
fi

oc=`grep -c 'Cartesian coordinates (bohr)' $1`
let rp=`grep -c 'rprim' $1`

if [ $st -eq -1 ]&&[ $rp -gt $oc ]; then
st=-2
fi
if [ $st -eq -1 ]&&[ $oc -lt 1 ]; then
echo "Not a structural optimization run!"
exit 1
fi
cat $1 | gawk -v co=$c -v fi=$st -v oc=$oc '
BEGIN {
st=0
cna=0
cnr=0
}

{ if ($1 ~ /^natom/) {nat=$2;}
if ($1 ~ /^ntypat/) {nty=$2;}
if ($1 ~ /^typat/) {cnt=1; nl=0; for (i=2; i<=nat+1; i++)
{if ($i == "" && nl != 1) {getline; nl=1;}
{if (nl) {typ[i]=$cnt; cnt++;}
else {typ[i]=$i;} cnt=1;}}}
if ($0 ~ /^- pspatm:/) {getline; getline; anu[cnt]= $1; cnt++;}
if (fi == -2) {
if ($1 ~ /^acell/) {cna++; acl[1,cna]=$2;acl[2,cna]=$3;acl[3,cna]=$4;}}
else {
if ($1 ~ /^acell/) {acl[1]=$2;acl[2]=$3;acl[3]=$4;}}
if (fi == -2) {
if ($1 ~ /^rprim/) {cnr++; rpr[1,cnr]=$2; rpr[2,cnr]=$3; rpr[3,cnr]=$4;
getline; rpr[4,cnr]=$1; rpr[5,cnr]=$2; rpr[6,cnr]=$3;
getline; rpr[7,cnr]=$1; rpr[8,cnr]=$2; rpr[9,cnr]=$3;
# BUG FIX by SPB 11/2011
# for (i=1; i<=9; i++) {rpr[i,cnr]=rpr[i,cnr]*acl[i-int((i-1)/3)*3,cnr]*co}}}
rpr[1,cnr]=rpr[1,cnr]*acl[1,cnr]*co
rpr[2,cnr]=rpr[2,cnr]*acl[1,cnr]*co
rpr[3,cnr]=rpr[3,cnr]*acl[1,cnr]*co
rpr[4,cnr]=rpr[4,cnr]*acl[2,cnr]*co
rpr[5,cnr]=rpr[5,cnr]*acl[2,cnr]*co
rpr[6,cnr]=rpr[6,cnr]*acl[2,cnr]*co
rpr[7,cnr]=rpr[7,cnr]*acl[3,cnr]*co
rpr[8,cnr]=rpr[8,cnr]*acl[3,cnr]*co
rpr[9,cnr]=rpr[9,cnr]*acl[3,cnr]*co}}
else {
if ($1 ~ /^rprim/) {rpr[1]=$2; rpr[2]=$3; rpr[3]=$4;
getline; rpr[4]=$1; rpr[5]=$2; rpr[6]=$3;
getline; rpr[7]=$1; rpr[8]=$2; rpr[9]=$3;
# BUG FIX by SPB 11/2011
# for (i=1; i<=9; i++) {rpr[i]=rpr[i]*acl[i-int((i-1)/3)*3]*co}
rpr[1]=rpr[1]*acl[1]*co
rpr[2]=rpr[2]*acl[1]*co
rpr[3]=rpr[3]*acl[1]*co
rpr[4]=rpr[4]*acl[2]*co
rpr[5]=rpr[5]*acl[2]*co
rpr[6]=rpr[6]*acl[2]*co
rpr[7]=rpr[7]*acl[3]*co
rpr[8]=rpr[8]*acl[3]*co
rpr[9]=rpr[9]*acl[3]*co}}


if (fi < 0)
{ if ($0 ~ /Cartesian \coordinates/)
{ st++;
for (i=1; i<=nat; i++) {getline; xca[i,1,st]=$1; xca[i,2,st]=$2; xca[i,3,st]=$3;}}}
else {
if ($1 ~ /^xcart/)
{ st++; xca[1,1,st]=$2; xca[1,2,st]=$3; xca[1,3,st]=$4;
for (i=2; i<=nat; i++) {getline; xca[i,1,st]=$1; xca[i,2,st]=$2; xca[i,3,st]=$3;}}}
}
END {
if (fi == 0) {
print "ANIMSTEPS 2";
print "CRYSTAL";print "PRIMVEC";
printf ("%10.5f %10.5f %10.5f\n", rpr[1],rpr[2],rpr[3]);
printf ("%10.5f %10.5f %10.5f\n",rpr[4],rpr[5],rpr[6]);
printf ("%10.5f %10.5f %10.5f\n",rpr[7],rpr[8],rpr[9]);
for (st=1;st<=2;st++) {
print "PRIMCOORD",st;
print nat,"1";
for (i=1; i<=nat; i++) {printf ("%d %10.5f %10.5f %10.5f\n",int(anu[typ[i+1]]),xca[i,1,st]*co,xca[i,2,st]*co,xca[i,3,st]*co);}}}
if (fi < 0) {
print "ANIMSTEPS",oc;print "CRYSTAL";
if (fi != -2) {
print " PRIMVEC";
printf (" %10.5f %10.5f %10.5f\n", rpr[1],rpr[2],rpr[3]);
printf (" %10.5f %10.5f %10.5f\n",rpr[4],rpr[5],rpr[6]);
printf (" %10.5f %10.5f %10.5f\n",rpr[7],rpr[8],rpr[9]);}

for (st=1;st<=oc;st++) {
if (fi == -2) {
print " PRIMVEC";
printf (" %10.5f %10.5f %10.5f\n", rpr[1,st+1],rpr[2,st+1],rpr[3,st+1]);
printf (" %10.5f %10.5f %10.5f\n",rpr[4,st+1],rpr[5,st+1],rpr[6,st+1]);
printf (" %10.5f %10.5f %10.5f\n",rpr[7,st+1],rpr[8,st+1],rpr[9,st+1]);}
print " PRIMCOORD",st;
print "",nat,"1";
for (i=1; i<=nat; i++) {printf (" %d %10.5f %10.5f %10.5f\n",int(anu[typ[i+1]]),xca[i,1,st]*co,xca[i,2,st]*co,xca[i,3,st]*co);}}}
if (fi > 0) {
print " CRYSTAL";print "PRIMVEC";
printf (" %10.5f %10.5f %10.5f\n", rpr[1],rpr[2],rpr[3]);
printf (" %10.5f %10.5f %10.5f\n",rpr[4],rpr[5],rpr[6]);
printf (" %10.5f %10.5f %10.5f\n",rpr[7],rpr[8],rpr[9]);
print " PRIMCOORD";
print "",nat,"1";
for (i=1; i<=nat; i++) {printf (" %d %10.5f %10.5f %10.5f\n",int(anu[typ[i+1]]),xca[i,1,fi]*co,xca[i,2,fi]*co,xca[i,3,fi]*co);}}
}'>$1.xsf

Hi Scott,

thanks a bundle, we will fix this in 6.11 - could you attach the file, or more simply send a diff of the changes? The forum has wiped any formatting, so it's hard for me to see what the diff is with your post alone

Matthieu