support bonds for more than one atom

diff --git a/vasp_tools/stdvis b/vasp_tools/stdvis
index c108a8d..b5685ec 100755 (executable)
--- a/vasp_tools/stdvis
+++ b/vasp_tools/stdvis
@@ -29,7 +29,7 @@ echo "type: 1 no rotation"
        -nll -0.20 -0.20 -0.50 -fur 1.20 1.20 1.20 \
        -b 0.0 0.0 0.0 1.0 1.0 1.0 \
        -c 0.8 -1.7 0.9 -L 0.5 -1.0 0.5 \
-       -r 0.6 -A 193 1.9
+       -r 0.6 -A 1 217 1.9
 fi
 
 # first unit cell in each direction without rotation displaying mirrored atoms
@@ -40,7 +40,7 @@ echo "type: 1 no rotation, mirrored"
        -b 0.0 0.0 0.0 1.0 1.0 1.0 \
        -c 0.8 -1.7 0.9 -L 0.5 -1.0 0.5 \
        -r 0.6 -m 3.0 0.0 0.0 0.0 3.0 0.0 0.0 0.0 3.0 \
-       -A 193 1.9
+       -A 2 217 218 1.9
 fi
 
 # three unit cells in each direction without rotation
@@ -77,11 +77,11 @@ fi
 if [ "$type" = "1rm" ]; then
 echo "type: 1 rotated, mirrored"
 ./visualize -w 640 -h 480 -d $i \
-       -nll -0.20 -0.20 -0.20 -fur 1.20 1.20 1.20 \
+       -nll -0.20 -0.20 -0.50 -fur 1.20 1.20 1.20 \
        -b 0.0 0.0 0.0 1.0 1.0 1.0 \
        -c 0.8 -1.7 0.9 -L 0.5 -1.0 0.5 \
        -r 0.6 -m 2.0 -2.0 0.0 2.0 2.0 0.0 0.0 0.0 3.0 \
-       -A 193 1.9
+       -A 1 193 1.9
 fi
 
 # three unit cells (rotated) in each direction displaying mirrored atoms

diff --git a/vasp_tools/visualize b/vasp_tools/visualize
index 793e72e..1ed430c 100755 (executable)
--- a/vasp_tools/visualize
+++ b/vasp_tools/visualize
@@ -71,8 +71,13 @@ 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;;
+               -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 "########"
@@ -351,7 +356,11 @@ EOF
        fi
 
        # auto bonds
-       if [ "$ab" = "1" ]; then
+       if [ "$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 }'`
@@ -409,6 +418,9 @@ EOF
                        }
 
                }' >> temp.pov
+
+                       ((cnt+=1))
+               done
        fi
 
        # add camera and light source