From: hackbard Date: Thu, 8 Oct 2009 07:46:02 +0000 (+0200) Subject: added script to visualize contcar results X-Git-Url: https://hackdaworld.org/gitweb/?a=commitdiff_plain;h=8d4b140464e036fe920497805d47cf53b28eeeb2;p=physik%2Fposic.git added script to visualize contcar results --- diff --git a/vasp_tools/visualize_contcar b/vasp_tools/visualize_contcar new file mode 100755 index 0000000..d272d18 --- /dev/null +++ b/vasp_tools/visualize_contcar @@ -0,0 +1,428 @@ +#!/bin/sh + +# +# visualization script +# author: frank.zirkelbach@physik.uni-augsburg.de +# + +# help function +draw_cyl() { + cat >> temp.pov <<-EOF +cylinder { +<$1, $3, $2>, <$4, $6, $5>, 0.05 +pigment { color White } +} +EOF +} +draw_bond() { + cat >> temp.pov <<-EOF +cylinder { +<$1, $3, $2>, <$4, $6, $5>, $7 +pigment { + color rgbf <0, 0, 1.0, 0.8> + finish { phong 1 metallic } +} +} +EOF +} + +# defaults + +lc=5.429 +directory="doesnt_exist____for_sure" +width="640" +height="480" +radius="0.6" +x0="-0.6"; y0="-0.6"; z0="-0.6"; +x1="0.6"; y1="0.6"; z1="0.6"; +cx=""; cy=""; cz=""; +lx="0"; ly="-100"; lz="100"; +ortographic="" +bx0=""; by0=""; bz0=""; +bx1=""; by1=""; bz1=""; +bcr="0.1"; +clx="0"; cly="0"; clz="0"; +extra=0 +displace="" +mirror=0 +mx1=0; mx2=0; mx3=0; +my1=0; my2=0; my3=0; +mz1=0; mz2=0; mz3=0; +ab=0 + +# parse argv + +while [ "$1" ]; do + case "$1" in + -d) directory=$2; shift 2;; + -w) width=$2; shift 2;; + -h) height=$2; shift 2;; + -r) radius=$2; shift 2;; + -nll) x0=$2; y0=$3; z0=$4; shift 4;; + -fur) x1=$2; y1=$3; z1=$4; shift 4;; + -c) cx=$2; cy=$3; cz=$4; shift 4;; + -L) clx=$2; cly=$3; clz=$4; shift 4;; + -l) lx=$2; ly=$3; lz=$4; shift 4;; + -o) ortographic=1; shift 1;; + -b) bx0=$2; by0=$3; bz0=$4; + bx1=$5; by1=$6; bz1=$7; shift 7;; + -B) bcr=$2; shift 2;; + -C) lc=$2; shift 2;; + -e) extra=1; shift 1;; + -D) displace=$2; shift 2;; + -m) mx1=$2; mx2=$3; mx3=$4; + my1=$5; my2=$6; my3=$7; + mz1=$8; mz2=$9; mz3=${10}; + mirror=1; shift 10;; + -A) ab=$2; shift 2; + ((cnt=1)) + while [ $cnt -le $ab ]; do + anr[$cnt]=$1; shift 1; + ((cnt+=1)) + done + cutoff=$1; shift 1;; + *) + echo "options:" + echo "########" + echo "directory to progress:" + echo " -d (mandatory)" + echo "png dim:" + echo " -w " + echo " -h " + echo "atom size:" + echo " -r " + echo " -B " + echo "unit cell:" + echo " -C " + echo " -m (mirror atoms)" + echo "visualization volume:" + echo " -nll (near lower left)" + echo " -fur (far upper right)" + echo " -o (ortographic)" + echo "bounding box:" + echo " -b " + echo "povray:" + echo " -c (camera position)" + echo " -L (camera look)" + echo " -l (light source)" + echo "bonds:" + echo " -ab (auto bonds)" + exit 1;; + esac +done + +# calculation from lattic eunits to angstroms + +[ "$lc" = "sic" ] && lc=4.359 +[ "$lc" = "si" ] && lc=5.480 +[ "$lc" = "c" ] && lc=3.566 + +#offset=`echo 0.125 \* $lc | bc` +offset=0.0 + +x0=`echo $x0 \* $lc + $offset | bc` +y0=`echo $y0 \* $lc + $offset | bc` +z0=`echo $z0 \* $lc + $offset | bc` +x1=`echo $x1 \* $lc + $offset | bc` +y1=`echo $y1 \* $lc + $offset | bc` +z1=`echo $z1 \* $lc + $offset | bc` + +mx1=`echo $mx1 \* $lc + $offset | bc` +my1=`echo $my1 \* $lc + $offset | bc` +mz1=`echo $mz1 \* $lc + $offset | bc` +mx2=`echo $mx2 \* $lc + $offset | bc` +my2=`echo $my2 \* $lc + $offset | bc` +mz2=`echo $mz2 \* $lc + $offset | bc` +mx3=`echo $mx3 \* $lc + $offset | bc` +my3=`echo $my3 \* $lc + $offset | bc` +mz3=`echo $mz3 \* $lc + $offset | bc` + +clx=`echo $clx \* $lc + $offset | bc` +cly=`echo $cly \* $lc + $offset | bc` +clz=`echo $clz \* $lc + $offset | bc` + +if [ -n "$cx" -a -n "$cy" -a -n "$cz" ]; then + cx=`echo $cx \* $lc + $offset | bc` + cy=`echo $cy \* $lc + $offset | bc` + cz=`echo $cz \* $lc + $offset | bc` +fi + +if [ -n "$bx0" ]; then + bx0=`echo $bx0 \* $lc + $offset | bc` + by0=`echo $by0 \* $lc + $offset | bc` + bz0=`echo $bz0 \* $lc + $offset | bc` + bx1=`echo $bx1 \* $lc + $offset | bc` + by1=`echo $by1 \* $lc + $offset | bc` + bz1=`echo $bz1 \* $lc + $offset | bc` +fi + +# povray command +POVRAY="povray -W${width} -H${height} -d" + +# camera location +[ -n "$cx" -a -n "$cy" -a -n "$cz" ] && camloc="<$cx,$cz,$cy>" + +# convert options +COPTS="-font /usr/share/fonts/truetype/ttf-dejavu/DejaVuSans.ttf" +COPTS="$COPTS -depth 8 -fill white -stroke blue -pointsize 24" + +# do it ... + +if [ -d $directory ]; then + filesource=$directory/CONTCAR* +fi + +if [ -f $directory ]; then + filesource=$directory +fi + +for file in $filesource; do + + echo "working on $file ..." + + cat > temp.pov <<-EOF +#include "colors.inc" +#include "textures.inc" +#include "shapes.inc" +#include "glass.inc" +#include "metals.inc" +#include "woods.inc" +#include "stones.inc" +EOF + + # meta info + scale=`sed -n 2p $file | awk '{ print $1 }'` + line="`sed -n 3p $file`" + X1=`echo $line | awk '{ print $1 }'` + X2=`echo $line | awk '{ print $2 }'` + X3=`echo $line | awk '{ print $3 }'` + line="`sed -n 4p $file`" + Y1=`echo $line | awk '{ print $1 }'` + Y2=`echo $line | awk '{ print $2 }'` + Y3=`echo $line | awk '{ print $3 }'` + line="`sed -n 5p $file`" + Z1=`echo $line | awk '{ print $1 }'` + Z2=`echo $line | awk '{ print $2 }'` + Z3=`echo $line | awk '{ print $3 }'` + line="`sed -n 6p $file`" + nsi=`echo $line | awk '{ print $1 }'` + nc=`echo $line | awk '{ print $2 }'` + ((ntot=nsi+nc)) + + echo "Si : $nsi" + echo "C : $nc" + echo "tot: $ntot" + echo "cutoff: $cutoff" + + export scale + export X1 X2 X3 + export Y1 Y2 Y3 + export Z1 Z2 Z3 + + export x0 y0 z0 x1 y1 z1 radius + + # atoms + ((count=1)) + ((offset=8)) + while [ "1" ]; do + + echo -en "$count " + + if [ $count -le $nsi ]; then + color="Yellow" + else + color="Gray" + fi + export color + + ((gl=offset+count)) + line="`sed -n ${gl}p $file`" + x=`echo $line | awk '{ print $1 }'` + y=`echo $line | awk '{ print $2 }'` + z=`echo $line | awk '{ print $3 }'` + + echo $x $y $z | awk '\ + BEGIN { + x0=ENVIRON["x0"]; y0=ENVIRON["y0"]; z0=ENVIRON["z0"]; + x1=ENVIRON["x1"]; y1=ENVIRON["y1"]; z1=ENVIRON["z1"]; + X1=ENVIRON["X1"]; X2=ENVIRON["X2"]; X3=ENVIRON["X3"]; + Y1=ENVIRON["Y1"]; Y2=ENVIRON["Y2"]; Y3=ENVIRON["Y3"]; + Z1=ENVIRON["Z1"]; Z2=ENVIRON["Z2"]; Z3=ENVIRON["Z3"]; + radius=ENVIRON["radius"]; scale=ENVIRON["scale"]; + color=ENVIRON["color"] + x=0; y=0; z=0; + xt=0; yt=0; zt=0; + i=0; j=0; k=0; + } + { + for(i=-1;i<=1;i++) { + for(j=-1;j<=1;j++) { + for(k=-1;k<=1;k++) { + + nx=$1+i; ny=$2+j; nz=$3+k; + + xt=nx*X1+ny*Y1+nz*Z1; + yt=nx*X2+ny*Y2+nz*Z2; + zt=nx*X3+ny*Y3+nz*Z3; + + xt*=scale; + yt*=scale; + zt*=scale; + + if((xt>=x0)&&(yt>=y0)&&(zt>=z0)&&\ + (xt<=x1)&&(yt<=y1)&&(zt<=z1)) { + print "sphere { <"xt","zt","yt">, "radius" "; + print "texture { pigment { color " color " } "; + print "finish { phong 1 metallic } } }"; + } + + } + } + } + }' >> temp.pov + + # see, whether there are bonds to draw + if [ "$ab" = "0" ]; then + ((count+=1)) + continue + fi + ((cnt=1)) + dobond=no + while [ $cnt -le $ab ]; do + anr=${anr[$cnt]} + if [ $anr -eq $count ]; then + dobond=yes + break + fi + ((cnt+=1)) + done + if [ "$ab" = "-1" ]; then + dobond=yes + fi + if [ "$dobond" = "no" ]; then + ((count+=1)) + continue; + fi + + # draw bonds + ((ic=1)) + while [ "1" ]; do + + [ $ic -gt $count ] && break + + if [ $ic -eq $count ]; then + ((ic+=1)) + continue + fi + + ((il=ic+offset)) + line="`sed -n ${il}p $file`" + xb=`echo $line | awk '{ print $1 }'` + yb=`echo $line | awk '{ print $2 }'` + zb=`echo $line | awk '{ print $3 }'` + + echo $x $y $z $xb $yb $zb $cutoff | awk '\ + BEGIN { + x0=ENVIRON["x0"]; y0=ENVIRON["y0"]; z0=ENVIRON["z0"]; + x1=ENVIRON["x1"]; y1=ENVIRON["y1"]; z1=ENVIRON["z1"]; + X1=ENVIRON["X1"]; X2=ENVIRON["X2"]; X3=ENVIRON["X3"]; + Y1=ENVIRON["Y1"]; Y2=ENVIRON["Y2"]; Y3=ENVIRON["Y3"]; + Z1=ENVIRON["Z1"]; Z2=ENVIRON["Z2"]; Z3=ENVIRON["Z3"]; + bcr=ENVIRON["bcr"]; scale=ENVIRON["scale"]; + } + { + for(i=-1;i<=1;i++) { + for(j=-1;j<=1;j++) { + for(k=-1;k<=1;k++) { + + for(ii=-1;ii<=1;ii++) { + for(ij=-1;ij<=1;ij++) { + for(ik=-1;ik<=1;ik++) { + + nx=$1+i; ny=$2+j; nz=$3+k; + xt=nx*X1+ny*Y1+nz*Z1; + yt=nx*X2+ny*Y2+nz*Z2; + zt=nx*X3+ny*Y3+nz*Z3; + xt*=scale; + yt*=scale; + zt*=scale; + + inx=$4+ii; iny=$5+ij; inz=$6+ik; + ixt=inx*X1+iny*Y1+inz*Z1; + iyt=inx*X2+iny*Y2+inz*Z2; + izt=inx*X3+iny*Y3+inz*Z3; + ixt*=scale; + iyt*=scale; + izt*=scale; + + dist=sqrt((xt-ixt)^2+(yt-iyt)^2+(zt-izt)^2); + + if((xt>=x0)&&(yt>=y0)&&(zt>=z0)&&\ + (xt<=x1)&&(yt<=y1)&&(zt<=z1)) { + if(dist<=$7) { + print "cylinder {"; + print "<"xt","zt","yt">,"; + print "<"ixt","izt","iyt">,0.1"; + print "pigment { color Blue }"; + print "}"; + } + } + + } + } + } + } + } + } + }' >> temp.pov + + ((ic+=1)) + [ $ic -gt $ntot ] && break; + + done + + ((count+=1)) + [ $count -gt $ntot ] && break; + + done + + echo + + # manually drawing the 3x4 boundaries specified by argv ... + draw_cyl $bx0 $by0 $bz0 $bx1 $by0 $bz0 + draw_cyl $bx0 $by0 $bz0 $bx0 $by1 $bz0 + draw_cyl $bx1 $by1 $bz0 $bx1 $by0 $bz0 + draw_cyl $bx0 $by1 $bz0 $bx1 $by1 $bz0 + + draw_cyl $bx0 $by0 $bz1 $bx1 $by0 $bz1 + draw_cyl $bx0 $by0 $bz1 $bx0 $by1 $bz1 + draw_cyl $bx1 $by1 $bz1 $bx1 $by0 $bz1 + draw_cyl $bx0 $by1 $bz1 $bx1 $by1 $bz1 + + draw_cyl $bx0 $by0 $bz1 $bx0 $by0 $bz0 + draw_cyl $bx0 $by1 $bz1 $bx0 $by1 $bz0 + draw_cyl $bx1 $by0 $bz1 $bx1 $by0 $bz0 + draw_cyl $bx1 $by1 $bz1 $bx1 $by1 $bz0 + + # add camera and light source + cat >> temp.pov <<-EOF +camera { +EOF + if [ -n "$ortographic" ]; then cat >> temp.pov <<-EOF +orthographic +EOF + fi + cat >> temp.pov <<-EOF +location $camloc +look_at <$clx,$clz,$clz> +} +light_source { <0,100,-100> color White shadowless } +EOF + + # mv png + $POVRAY temp.pov > /dev/null 2>&1 + mv temp.png `dirname $file`/ + +done + +echo "done"