X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=vasp_tools%2Fvisualize;h=1ed430ca0786a2c479baaa8f8c32e37c08a7acff;hb=d13da35aeda0b12006d4568b271b26c8d9365c5a;hp=7cc4496f623cafffda8da79df2794fcc82ccfeb7;hpb=88c1733cf107670db154954879b59bc7bb8ce3f2;p=physik%2Fposic.git diff --git a/vasp_tools/visualize b/vasp_tools/visualize index 7cc4496..1ed430c 100755 --- a/vasp_tools/visualize +++ b/vasp_tools/visualize @@ -37,9 +37,15 @@ lx="0"; ly="-100"; lz="100"; ortographic="" bx0=""; by0=""; bz0=""; bx1=""; by1=""; bz1=""; -bcr=""; +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 @@ -60,6 +66,18 @@ while [ "$1" ]; do -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 "########" @@ -73,6 +91,7 @@ while [ "$1" ]; do echo " -B " echo "unit cell:" echo " -C " + echo " -m (mirror atoms)" echo "visualization volume:" echo " -nll (near lower left)" echo " -fur (far upper right)" @@ -83,6 +102,8 @@ while [ "$1" ]; do echo " -c (camera position)" echo " -L (camera look)" echo " -l (light source)" + echo "bonds:" + echo " -ab (auto bonds)" exit 1;; esac done @@ -90,7 +111,7 @@ done # calculation from lattic eunits to angstroms [ "$lc" = "sic" ] && lc=4.359 -[ "$lc" = "si" ] && lc=5.429 +[ "$lc" = "si" ] && lc=5.480 [ "$lc" = "c" ] && lc=3.566 #offset=`echo 0.125 \* $lc | bc` @@ -103,6 +124,16 @@ 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` @@ -163,25 +194,25 @@ EOF #echo "-----> $x0 $y0 $z0 $x1 $y1 $z1 <-----" if [ -n "$x0" ]; then export x0 y0 z0 x1 y1 z1 radius extra + export mx1 mx2 mx3 + export my1 my2 my3 + export mz1 mz2 mz3 + export mirror cat $file | grep -v '#' | awk '\ BEGIN { x0=ENVIRON["x0"]; y0=ENVIRON["y0"]; z0=ENVIRON["z0"]; x1=ENVIRON["x1"]; y1=ENVIRON["y1"]; z1=ENVIRON["z1"]; + mx1=ENVIRON["mx1"]; my1=ENVIRON["my1"]; + mz1=ENVIRON["mz1"]; mx2=ENVIRON["mx2"]; + my2=ENVIRON["my2"]; mz2=ENVIRON["mz2"]; + mx3=ENVIRON["mx3"]; my3=ENVIRON["my3"]; + mz3=ENVIRON["mz3"]; mirror=ENVIRON["mirror"]; radius=ENVIRON["radius"]; extra=ENVIRON["extra"]; + nx=0; ny=0; nz=0; } { -# 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"> } "; @@ -189,6 +220,43 @@ EOF print "texture { pigment { color "$5" } "; print "finish { phong 1 metallic } } }"; } + + if(mirror) { + + nx=$2-mx1; ny=$3-mx2; nz=$4-mx3; + if((nx>=x0)&&(ny>=y0)&&(nz>=z0)&&\ + (nx<=x1)&&(ny<=y1)&&(nz<=z1)) { +print "// translation: "$2/5.480" "$3/5.480" "$4/5.480" -> "nx/5.480" "ny/5.480" "nz/5.480" ..."; + print "sphere { <"nx","nz","ny">, "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 } } }"; + } + nx=$2-my1; ny=$3-my2; nz=$4-my3; + if((nx>=x0)&&(ny>=y0)&&(nz>=z0)&&\ + (nx<=x1)&&(ny<=y1)&&(nz<=z1)) { + print "sphere { <"nx","nz","ny">, "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 } } }"; + } + nx=$2-mz1; ny=$3-mz2; nz=$4-mz3; + if((nx>=x0)&&(ny>=y0)&&(nz>=z0)&&\ + (nx<=x1)&&(ny<=y1)&&(nz<=z1)) { + print "sphere { <"nx","nz","ny">, "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 $file | grep -v '#' | while read name x y z color temp; do @@ -285,7 +353,75 @@ EOF }' >> temp.pov fi - fi + fi + + # auto bonds + if [ "$ab" != "0" ]; then + ((cnt=1)) + while [ $cnt -le $ab ]; do + anr=${anr[$cnt]} + + ((tmp=anr+1)) + line="`sed -n ${tmp}p $file`" + aX=`echo $line | awk '{ print $2 }'` + aY=`echo $line | awk '{ print $3 }'` + aZ=`echo $line | awk '{ print $4 }'` + export aX aY aZ cutoff mirror + cat $file | grep -v '#' | awk '\ + BEGIN { + x=ENVIRON["aX"]; y=ENVIRON["aY"]; z=ENVIRON["aZ"]; + co=ENVIRON["cutoff"]; dist=0; bcr=ENVIRON["bcr"]; + mx1=ENVIRON["mx1"]; my1=ENVIRON["my1"]; + mz1=ENVIRON["mz1"]; mx2=ENVIRON["mx2"]; + my2=ENVIRON["my2"]; mz2=ENVIRON["mz2"]; + mx3=ENVIRON["mx3"]; my3=ENVIRON["my3"]; + mz3=ENVIRON["mz3"]; mirror=ENVIRON["mirror"]; + } + { + dist=sqrt((x-$2)^2+(y-$3)^2+(z-$4)^2); + if((dist<=co)&&(dist>0.01)) { + print "cylinder {"; + print "<"x","z","y">,"; + print "<"$2","$4","$3">, "bcr; + print "pigment { color Blue }"; + print "}"; + } + + if(mirror) { + nx=$2-mx1; ny=$3-mx2; nz=$4-mx3; + dist=sqrt((x-nx)^2+(y-ny)^2+(z-nz)^2) + if((dist<=co)&&(dist>0.01)) { + print "cylinder {"; + print "<"x","z","y">,"; + print "<"nx","nz","ny">, "bcr; + print "pigment { color Blue }"; + print "}"; + } + nx=$2-my1; ny=$3-my2; nz=$4-my3; + dist=sqrt((x-nx)^2+(y-ny)^2+(z-nz)^2) + if((dist<=co)&&(dist>0.01)) { + print "cylinder {"; + print "<"x","z","y">,"; + print "<"nx","nz","ny">, "bcr; + print "pigment { color Blue }"; + print "}"; + } + nx=$2-mz1; ny=$3-mz2; nz=$4-mz3; + dist=sqrt((x-nx)^2+(y-ny)^2+(z-nz)^2) + if((dist<=co)&&(dist>0.01)) { + print "cylinder {"; + print "<"x","z","y">,"; + print "<"nx","nz","ny">, "bcr; + print "pigment { color Blue }"; + print "}"; + } + } + + }' >> temp.pov + + ((cnt+=1)) + done + fi # add camera and light source cat >> temp.pov <<-EOF @@ -305,7 +441,11 @@ EOF # mv png $POVRAY temp.pov > /dev/null 2>&1 time=`basename $file | awk -F. '{ print $1 }' | awk -F_ '{ print $3 }'` + if [ ! -z $displace ]; then + convert $COPTS -draw "text 5,20 'd = $displace %'" temp.png temp.png + else convert $COPTS -draw "text 5,20 't = $time fs'" temp.png temp.png + fi mv temp.png `echo $file | sed 's/\.xyz/\.png/'` done