From 88c1733cf107670db154954879b59bc7bb8ce3f2 Mon Sep 17 00:00:00 2001 From: hackbard Date: Wed, 8 Jul 2009 15:46:35 +0200 Subject: [PATCH] added some helper tools for vasp usage --- vasp_tools/Makefile | 12 ++ vasp_tools/create_lattice.c | 111 +++++++++++++ vasp_tools/e_coh | 21 +++ vasp_tools/e_form | 13 ++ vasp_tools/outcar2moldyn | 50 ++++++ vasp_tools/ppm2avi | 13 ++ vasp_tools/stdvis | 14 ++ vasp_tools/visualize | 313 ++++++++++++++++++++++++++++++++++++ 8 files changed, 547 insertions(+) create mode 100644 vasp_tools/Makefile create mode 100644 vasp_tools/create_lattice.c create mode 100755 vasp_tools/e_coh create mode 100755 vasp_tools/e_form create mode 100755 vasp_tools/outcar2moldyn create mode 100755 vasp_tools/ppm2avi create mode 100755 vasp_tools/stdvis create mode 100755 vasp_tools/visualize diff --git a/vasp_tools/Makefile b/vasp_tools/Makefile new file mode 100644 index 0000000..177b5e9 --- /dev/null +++ b/vasp_tools/Makefile @@ -0,0 +1,12 @@ +CC = gcc-4.3 + +CFLAGS = -Wall -Winline +CFLAGS += -O3 -march=native -msse2 -mfpmath=sse +CFLAGS += -g + +LDFLAGS = -lm + +ALL = create_lattice + +all: $(ALL) + diff --git a/vasp_tools/create_lattice.c b/vasp_tools/create_lattice.c new file mode 100644 index 0000000..5f6cb8d --- /dev/null +++ b/vasp_tools/create_lattice.c @@ -0,0 +1,111 @@ +/* + * create lattice (for usage in vasp POSCAR file) + * + * author: Frank Zirkelbach + * + */ + +#include +#include +#include +#include +#include "../math/math.h" + +#define FCC 0x01 +#define DIAMOND 0x02 +#define ZINCBLENDE 0x03 + +int main(int argc,char **argv) { + + int i,j,k,l,cnt; + t_3dvec basis[3]; + t_3dvec offset; + t_3dvec r,n; + char type; + double zrot; + + if(argc<5) { + printf("usage: %s type lx ly lz\n",argv[0]); + return -1; + } + + type=argv[1][0]; + type=DIAMOND; + + zrot=0.0; + if(argc==6) + zrot=atof(argv[5]); + + offset.x=0.25; + offset.y=0.25; + offset.z=0.25; + + memset(basis,0,3*sizeof(t_3dvec)); + basis[0].x=0.5; + basis[0].y=0.5; + basis[1].x=0.5; + basis[1].z=0.5; + basis[2].y=0.5; + basis[2].z=0.5; + + cnt=0; + r.x=0.0; + for(i=0;i" > \ + video/atomic_conf_$time.xyz + + type="Si" + color="Yellow" + force=`echo "sqrt($fx*$fx+$fy*$fy+$fz*$fz)" | bc` + if [ $cnt -ge $sicnt ]; then + type="C" + color="Gray" + fi + echo "$type $x $y $z $color $force" >> \ + video/atomic_conf_$time.xyz + + ((cnt+=1)) + if [ $cnt -eq $total ]; then + cnt=0 + ((tcnt+=1)) + echo + fi +done + +echo + diff --git a/vasp_tools/ppm2avi b/vasp_tools/ppm2avi new file mode 100755 index 0000000..74c8370 --- /dev/null +++ b/vasp_tools/ppm2avi @@ -0,0 +1,13 @@ +#for i in $1/*.ppm; do +# convert $i $1/$(basename $i ppm)png +#done + +MFOPTS="-mf fps=13:type=png" +#MFOPTS="-mf fps=25:type=png" + +OUTFILE=md.avi +[ -n "$2" ] && OUTFILE=$2 + +#mencoder mf://$1/*.png -ovc copy -o $1/$OUTFILE >/dev/null 2>&1 +mencoder $MFOPTS mf://$1/*.png -ovc xvid -xvidencopts bitrate=1000 \ + -o $1/$OUTFILE >/dev/null 2>&1 diff --git a/vasp_tools/stdvis b/vasp_tools/stdvis new file mode 100755 index 0000000..12c7cd6 --- /dev/null +++ b/vasp_tools/stdvis @@ -0,0 +1,14 @@ +if [ -z "$1" ]; then + exit +fi + +./visualize -w 640 -h 480 -d $1/video \ + -nll -1.06 -1.06 -1.06 -fur 2.06 2.06 2.06 \ + -b 0.0 0.0 0.0 1.0 1.0 1.0 \ + -c 0.3 -2.5 1.1 -L 0.5 0.5 0.4 \ + -r 0.6 + +./ppm2avi $1/video + +mplayer $1/video/md.avi + diff --git a/vasp_tools/visualize b/vasp_tools/visualize new file mode 100755 index 0000000..7cc4496 --- /dev/null +++ b/vasp_tools/visualize @@ -0,0 +1,313 @@ +#!/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 Blue } +} +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=""; +clx="0"; cly="0"; clz="0"; +extra=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=$2; shift 2;; + -e) extra=1; shift 1;; + *) + echo "options:" + echo "########" + echo "directory to progress:" + echo " -d (mandatory)" + echo "png dim:" + echo " -w " + echo " -h " + echo "atom size:" + echo " -r " + echo " -B " + echo "unit cell:" + echo " -C " + echo "visualization volume:" + echo " -nll (near lower left)" + echo " -fur (far upper right)" + echo " -o (ortographic)" + echo "bounding box:" + echo " -b " + echo "povray:" + echo " -c (camera position)" + echo " -L (camera look)" + echo " -l (light source)" + exit 1;; + esac +done + +# calculation from lattic eunits to angstroms + +[ "$lc" = "sic" ] && lc=4.359 +[ "$lc" = "si" ] && lc=5.429 +[ "$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` + +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${height} -d" + +# convert options + +COPTS="-font /usr/share/fonts/truetype/ttf-dejavu/DejaVuSans.ttf" +COPTS="$COPTS -depth 8 -fill white -stroke blue -pointsize 24" + +# do it ... + +if [ -d $directory ]; then + filesource=$directory/atomic_conf_*.xyz +fi + +if [ -f $directory ]; then + filesource=$directory +fi + +for file in $filesource; do + + 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 + count=`grep '# \[P\]' $file | awk '{ print $3 }'` + time=`grep '# \[P\]' $file | awk '{ print $4 }'` + camloc=`grep '# \[P\]' $file | awk '{ print $5 }'` + [ -n "$cx" -a -n "$cy" -a -n "$cz" ] && camloc="<$cx,$cz,$cy>" + + # atoms +#echo "-----> $x0 $y0 $z0 $x1 $y1 $z1 <-----" + if [ -n "$x0" ]; then + export x0 y0 z0 x1 y1 z1 radius extra + cat $file | grep -v '#' | awk '\ + BEGIN { + x0=ENVIRON["x0"]; y0=ENVIRON["y0"]; z0=ENVIRON["z0"]; + x1=ENVIRON["x1"]; y1=ENVIRON["y1"]; z1=ENVIRON["z1"]; + radius=ENVIRON["radius"]; extra=ENVIRON["extra"]; + } + { +# print "----> " x0 " " y0 " " z0 " " $2 " " $3 " " $4 +# print "----> " x1 " " y1 " " z1 " " $2 " " $3 " " $4 +#if(($2>=x0)) print $2 " groesser " x0 +#if(($3>=y0)) print $3 " groesser " y0 +#if(($4>=z0)) print $4 " groesser " z0 +#if(($2<=x1)) print $2 " kleiner " x1 +#if(($3<=y1)) print $3 " kleiner " y1 +#if(($4<=z1)) print $4 " kleiner " z1 + if(($2>=x0)&&($3>=y0)&&($4>=z0)&&\ + ($2<=x1)&&($3<=y1)&&($4<=z1)) { +# if(($2<=x0)&&($3<=y0)&&($4<=z0)&&\ +# ($2>=x1)&&($3>=y1)&&($4>=z1)) { + print "sphere { <"$2","$4","$3">, "radius" "; + if(extra) + print "texture { pigment { color rgb<"$6/4.4",0,"1-$6/4.4"> } "; + else + print "texture { pigment { color "$5" } "; + print "finish { phong 1 metallic } } }"; + } + }' >> temp.pov + else + cat $file | grep -v '#' | while read name x y z color temp; do + cat >> temp.pov <<-EOF +sphere { +<$x, $z, $y>, $radius +texture { +pigment { color $color } +finish { +phong 1 +metallic +} +} +} +EOF + done + fi + + # boundaries + if [ -z "$bx0" ]; then + + #if [ -z "$x0" ]; then + + cat $file | grep '# \[D\]' | while read foo bar x1 y1 z1 x2 y2 z2 ; do + draw_cyl $x1 $y1 $z1 $x2 $y2 $z2 0.05 + done + + #else + + # manually drawing the 3x4 boundaries ... +# draw_cyl $x0 $y0 $z0 $x1 $y0 $z0 +# draw_cyl $x0 $y0 $z0 $x0 $y1 $z0 +# draw_cyl $x1 $y1 $z0 $x1 $y0 $z0 +# draw_cyl $x0 $y1 $z0 $x1 $y1 $z0 + +# draw_cyl $x0 $y0 $z1 $x1 $y0 $z1 +# draw_cyl $x0 $y0 $z1 $x0 $y1 $z1 +# draw_cyl $x1 $y1 $z1 $x1 $y0 $z1 +# draw_cyl $x0 $y1 $z1 $x1 $y1 $z1 + +# draw_cyl $x0 $y0 $z1 $x0 $y0 $z0 +# draw_cyl $x0 $y1 $z1 $x0 $y1 $z0 +# draw_cyl $x1 $y0 $z1 $x1 $y0 $z0 +# draw_cyl $x1 $y1 $z1 $x1 $y1 $z0 +# fi + + else + + # 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 $bz0 + + fi + + # bonds + if [ -n "$bcr" ]; then + + if [ -z "$x0" ]; then + + cat $file | grep '# \[B\]' | while read foo bar x1 y1 z1 x2 y2 z2 ; do + draw_bond $x1 $z1 $y1 $x2 $z2 $y2 $bcr + done + + else + + export x0 y0 z0 x1 y1 z1 bcr + cat $file | grep '# \[B\]' | awk '\ + BEGIN { + x0=ENVIRON["x0"]; y0=ENVIRON["y0"]; z0=ENVIRON["z0"]; + x1=ENVIRON["x1"]; y1=ENVIRON["y1"]; z1=ENVIRON["z1"]; + bcr=ENVIRON["bcr"]; + } + { + if(($3>=x0)&&($4>=y0)&&($5>=z0)&&\ + ($3<=x1)&&($4<=y1)&&($5<=z1)) { + print "cylinder {"; + print "<"$3","$5","$4">,"; + print "<"$6","$8","$7">, "bcr; + print "pigment { color Blue }"; + print "}"; + } + }' >> temp.pov + + fi + fi + + # add camera and light source + cat >> temp.pov <<-EOF +camera { +EOF + if [ -n "$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 + time=`basename $file | awk -F. '{ print $1 }' | awk -F_ '{ print $3 }'` + convert $COPTS -draw "text 5,20 't = $time fs'" temp.png temp.png + mv temp.png `echo $file | sed 's/\.xyz/\.png/'` + +done + +echo "done" -- 2.39.2