From 3a5c13f7bf7756f538292a79edee97ce518a5395 Mon Sep 17 00:00:00 2001
From: hackbard <hackbard@sage.physik.uni-augsburg.de>
Date: Wed, 23 Sep 2009 18:31:45 +0200
Subject: [PATCH] auto bond feature added

---
 vasp_tools/visualize | 71 ++++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 68 insertions(+), 3 deletions(-)

diff --git a/vasp_tools/visualize b/vasp_tools/visualize
index 8d1e98f..793e72e 100755
--- a/vasp_tools/visualize
+++ b/vasp_tools/visualize
@@ -37,7 +37,7 @@ 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=""
@@ -45,6 +45,7 @@ mirror=0
 mx1=0; mx2=0; mx3=0;
 my1=0; my2=0; my3=0;
 mz1=0; mz2=0; mz3=0;
+ab=0
 
 # parse argv
 
@@ -70,7 +71,8 @@ while [ "$1" ]; do
 				my1=$5; my2=$6; my3=$7;
 				mz1=$8; mz2=$9; mz3=${10};
 				mirror=1;		shift 10;;
-
+		-A)		ab=1;
+				anr=$2; cutoff=$3;	shift 3;;
 		*)
 				echo "options:"
 				echo "########"
@@ -95,6 +97,8 @@ while [ "$1" ]; do
 				echo "  -c <x> <y> <z> (camera position)"
 				echo "  -L <x> <y> <z> (camera look)"
 				echo "  -l <x> <y> <z> (light source)"
+				echo "bonds:"
+				echo "  -ab <atom number> <cutoff> (auto bonds)"
 				exit 1;;
 	esac
 done
@@ -344,7 +348,68 @@ EOF
 		}' >> temp.pov
 
 		fi
-	fi	
+	fi
+
+	# auto bonds
+	if [ "$ab" = "1" ]; then
+		((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
+	fi
 
 	# add camera and light source
 	cat >> temp.pov <<-EOF
-- 
2.20.1