X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=vasp_tools%2Fvisualize_contcar;h=611ed6dd74b7f6f3984be43405dc99df7f6d0865;hb=83fc5a2dccab15ccce5a579ca4b4975c4614e816;hp=d272d181ab23c450fc4978e6f2922d4696277c28;hpb=8d4b140464e036fe920497805d47cf53b28eeeb2;p=physik%2Fposic.git

diff --git a/vasp_tools/visualize_contcar b/vasp_tools/visualize_contcar
index d272d18..611ed6d 100755
--- a/vasp_tools/visualize_contcar
+++ b/vasp_tools/visualize_contcar
@@ -223,10 +223,23 @@ EOF
 
 	# 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 +254,7 @@ 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"];
@@ -271,6 +284,7 @@ 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 +297,7 @@ EOF
 
 		# see, whether there are bonds to draw
 		if [ "$ab" = "0" ]; then
+			echo -en "$count "
 			((count+=1))
 			continue
 		fi
@@ -297,9 +312,12 @@ 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
@@ -347,6 +365,9 @@ 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;
 				ixt=inx*X1+iny*Y1+inz*Z1;
 				iyt=inx*X2+iny*Y2+inz*Z2;
@@ -357,8 +378,8 @@ 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((xt>=x0)&&(yt>=y0)&&(zt>=z0)&&\
+				#   (xt<=x1)&&(yt<=y1)&&(zt<=z1)) {
 					if(dist<=$7) {
 						print "cylinder {";
 						print "<"xt","zt","yt">,";
@@ -366,6 +387,8 @@ EOF
 						print "pigment { color Blue }";
 						print "}";
 					}
+				#}
+
 				}
 	
 						}
@@ -381,6 +404,7 @@ EOF
 
 		done
 
+		echo -en "[$count] "
 		((count+=1))
 		[ $count -gt $ntot ] && break;
 
@@ -389,6 +413,7 @@ 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 +428,7 @@ 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