From 83fc5a2dccab15ccce5a579ca4b4975c4614e816 Mon Sep 17 00:00:00 2001
From: hackbard <hackbard@sage.physik.uni-augsburg.de>
Date: Thu, 4 Mar 2010 13:03:35 +0100
Subject: [PATCH] small fx and new features

---
 vasp_tools/visualize_contcar | 29 ++++++++++++++++++++++++-----
 1 file changed, 24 insertions(+), 5 deletions(-)

diff --git a/vasp_tools/visualize_contcar b/vasp_tools/visualize_contcar
index f25d155..611ed6d 100755
--- a/vasp_tools/visualize_contcar
+++ b/vasp_tools/visualize_contcar
@@ -227,13 +227,19 @@ EOF
 	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"
@@ -248,7 +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"];
@@ -278,6 +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 } } }";
@@ -290,6 +297,7 @@ EOF
 
 		# see, whether there are bonds to draw
 		if [ "$ab" = "0" ]; then
+			echo -en "$count "
 			((count+=1))
 			continue
 		fi
@@ -304,9 +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
@@ -354,6 +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;
@@ -364,8 +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">,";
@@ -373,6 +387,8 @@ EOF
 						print "pigment { color Blue }";
 						print "}";
 					}
+				#}
+
 				}
 	
 						}
@@ -388,6 +404,7 @@ EOF
 
 		done
 
+		echo -en "[$count] "
 		((count+=1))
 		[ $count -gt $ntot ] && break;
 
@@ -396,6 +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
@@ -410,6 +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
-- 
2.39.2