X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=vasp_tools%2Fvisualize_contcar;h=61ed14382264ab1c5b77bd9596023752d740e276;hb=HEAD;hp=d272d181ab23c450fc4978e6f2922d4696277c28;hpb=8d4b140464e036fe920497805d47cf53b28eeeb2;p=physik%2Fposic.git

diff --git a/vasp_tools/visualize_contcar b/vasp_tools/visualize_contcar
index d272d18..61ed143 100755
--- a/vasp_tools/visualize_contcar
+++ b/vasp_tools/visualize_contcar
@@ -49,6 +49,7 @@ mx1=0; mx2=0; mx3=0;
 my1=0; my2=0; my3=0;
 mz1=0; mz2=0; mz3=0;
 ab=0
+sym=0
 
 # parse argv
 
@@ -81,6 +82,7 @@ while [ "$1" ]; do
 					((cnt+=1))
 				done
 				cutoff=$1;		shift 1;;
+		-s)		sym=$2;			shift 2;;
 		*)
 				echo "options:"
 				echo "########"
@@ -107,6 +109,9 @@ while [ "$1" ]; do
 				echo "  -l <x> <y> <z> (light source)"
 				echo "bonds:"
 				echo "  -ab <atom number> <cutoff> (auto bonds)"
+				echo "symmetry:"
+				echo "  -s <sym nr>"
+				echo "     1: sym by <1 -1 0> at 1/4 <1 1 0>"
 				exit 1;;
 	esac
 done
@@ -221,12 +226,27 @@ EOF
 	
 	export x0 y0 z0 x1 y1 z1 radius
 
+	export sym
+
 	# atoms
 	((count=1))
-	((offset=8))
+	checktsd=`sed -n 7p $file | awk '{ print $1 }'`
+	if [ "$checktsd" = "Transformed" ]; then
+		((offset=9))
+		echo "tsd: yes, offset = $offset"
+		# but maybe not
+		checkmore=`sed -n 8p $file | awk '{ print $1 }'`
+		if [ "$checkmore" = "Direct" ]; then
+			((offset=8))
+			echo "tsd: yes, but anyways using offset $offset"
+		fi
+	else
+		((offset=8))
+		echo "tsd: no, offset = $offset"
+	fi
 	while [ "1" ]; do
 
-	echo -en "$count "
+		[ $count -gt $ntot ] && break
 
 		if [ $count -le $nsi ]; then
 			color="Yellow"
@@ -241,7 +261,7 @@ EOF
 		y=`echo $line | awk '{ print $2 }'`
 		z=`echo $line | awk '{ print $3 }'`
 
-		echo $x $y $z | awk '\
+		echo $x $y $z $count | awk '\
 		BEGIN {
 			x0=ENVIRON["x0"]; y0=ENVIRON["y0"]; z0=ENVIRON["z0"];
 			x1=ENVIRON["x1"]; y1=ENVIRON["y1"]; z1=ENVIRON["z1"];
@@ -250,6 +270,7 @@ EOF
 			Z1=ENVIRON["Z1"]; Z2=ENVIRON["Z2"]; Z3=ENVIRON["Z3"];
 			radius=ENVIRON["radius"]; scale=ENVIRON["scale"];
 			color=ENVIRON["color"]
+			sym=ENVIRON["sym"]
 			x=0; y=0; z=0;
 			xt=0; yt=0; zt=0;
 			i=0; j=0; k=0;
@@ -261,6 +282,15 @@ EOF
 
 			nx=$1+i; ny=$2+j; nz=$3+k;
 
+			if(sym==1) {
+				xt=nx-1.0/12.0;
+				yt=ny-1.0/12.0;
+				nx=-yt;
+				ny=-xt;
+				nx+=1.0/12.0;
+				ny+=1.0/12.0;
+			}
+
 			xt=nx*X1+ny*Y1+nz*Z1;
 			yt=nx*X2+ny*Y2+nz*Z2;
 			zt=nx*X3+ny*Y3+nz*Z3;
@@ -271,6 +301,7 @@ EOF
 
 			if((xt>=x0)&&(yt>=y0)&&(zt>=z0)&&\
 			   (xt<=x1)&&(yt<=y1)&&(zt<=z1)) {
+				print "// atom " $4;
 				print "sphere { <"xt","zt","yt">, "radius" ";
 				print "texture { pigment { color " color " } ";
 				print "finish { phong 1 metallic } } }";
@@ -283,6 +314,7 @@ EOF
 
 		# see, whether there are bonds to draw
 		if [ "$ab" = "0" ]; then
+			echo -en "$count "
 			((count+=1))
 			continue
 		fi
@@ -297,9 +329,12 @@ EOF
 			((cnt+=1))
 		done
 		if [ "$ab" = "-1" ]; then
-			dobond=yes
+			if [ -n "`grep \/\/\ atom\ $count temp.pov`" ]; then
+				dobond=yes
+			fi
 		fi
 		if [ "$dobond" = "no" ]; then
+			echo -en "$count "
 			((count+=1))
 			continue;
 		fi
@@ -329,6 +364,7 @@ EOF
 			Y1=ENVIRON["Y1"]; Y2=ENVIRON["Y2"]; Y3=ENVIRON["Y3"];
 			Z1=ENVIRON["Z1"]; Z2=ENVIRON["Z2"]; Z3=ENVIRON["Z3"];
 			bcr=ENVIRON["bcr"]; scale=ENVIRON["scale"];
+			sym=ENVIRON["sym"];
 			}
 			{
 				for(i=-1;i<=1;i++) {
@@ -340,6 +376,16 @@ EOF
 						for(ik=-1;ik<=1;ik++) {
 	
 				nx=$1+i; ny=$2+j; nz=$3+k;
+
+				if(sym==1) {
+					xt=nx-1.0/12.0;
+					yt=ny-1.0/12.0;
+					nx=-yt;
+					ny=-xt;
+					nx+=1.0/12.0;
+					ny+=1.0/12.0;
+				}
+
 				xt=nx*X1+ny*Y1+nz*Z1;
 				yt=nx*X2+ny*Y2+nz*Z2;
 				zt=nx*X3+ny*Y3+nz*Z3;
@@ -347,7 +393,20 @@ EOF
 				yt*=scale;
 				zt*=scale;
 
+				if((xt>=x0)&&(yt>=y0)&&(zt>=z0)&&\
+				   (xt<=x1)&&(yt<=y1)&&(zt<=z1)) {
+
 				inx=$4+ii; iny=$5+ij; inz=$6+ik;
+
+				if(sym==1) {
+					ixt=inx-1.0/12.0;
+					iyt=iny-1.0/12.0;
+					inx=-iyt;
+					iny=-ixt;
+					inx+=1.0/12.0;
+					iny+=1.0/12.0;
+				}
+
 				ixt=inx*X1+iny*Y1+inz*Z1;
 				iyt=inx*X2+iny*Y2+inz*Z2;
 				izt=inx*X3+iny*Y3+inz*Z3;
@@ -357,8 +416,11 @@ EOF
 
 				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((ixt>=x0)&&(iyt>=y0)&&(izt>=z0)&&\
+				   (ixt<=x1)&&(iyt<=y1)&&(izt<=z1)) {
+
+				#if((xt>=x0)&&(yt>=y0)&&(zt>=z0)&&\
+				#   (xt<=x1)&&(yt<=y1)&&(zt<=z1)) {
 					if(dist<=$7) {
 						print "cylinder {";
 						print "<"xt","zt","yt">,";
@@ -366,6 +428,10 @@ EOF
 						print "pigment { color Blue }";
 						print "}";
 					}
+				#}
+
+				}
+
 				}
 	
 						}
@@ -381,6 +447,7 @@ EOF
 
 		done
 
+		echo -en "[$count] "
 		((count+=1))
 		[ $count -gt $ntot ] && break;
 
@@ -389,6 +456,7 @@ EOF
 	echo
 
 	# manually drawing the 3x4 boundaries specified by argv ...
+	if [ -n "$bx0" ]; then
 	draw_cyl $bx0 $by0 $bz0 $bx1 $by0 $bz0
 	draw_cyl $bx0 $by0 $bz0 $bx0 $by1 $bz0
 	draw_cyl $bx1 $by1 $bz0 $bx1 $by0 $bz0
@@ -403,6 +471,7 @@ EOF
 	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
 
 	# add camera and light source
 	cat >> temp.pov <<-EOF