added fractional output (search bonds) + video{.*} feature (stdvis)

diff --git a/vasp_tools/search_bonds b/vasp_tools/search_bonds
index 88051ee..5fa2e93 100755 (executable)
--- a/vasp_tools/search_bonds
+++ b/vasp_tools/search_bonds
@@ -91,11 +91,15 @@ while [ "1" ]; do
                        BEGIN {
                        dxt=0; dyt=0; dzt=0
                        dx=0; dy=0; dz=0; dist=0
+                       X=0; Y=0; Z=0
                        X1=ENVIRON["X1"]; X2=ENVIRON["X2"]; X3=ENVIRON["X3"]
                        Y1=ENVIRON["Y1"]; Y2=ENVIRON["Y2"]; Y3=ENVIRON["Y3"]
                        Z1=ENVIRON["Z1"]; Z2=ENVIRON["Z2"]; Z3=ENVIRON["Z3"]
                        }       
                        {
+                       X=sqrt(X1^2+X2^2+X3^2)
+                       Y=sqrt(Y1^2+Y2^2+Y3^2)
+                       Z=sqrt(Z1^2+Z2^2+Z3^2)
                        dx=$1-$4
                        dy=$2-$5
                        dz=$3-$6
@@ -117,10 +121,10 @@ while [ "1" ]; do
                        dist=sqrt(dxt^2+dyt^2+dzt^2)
                        dist*=$7
                        if((dist>=($8-$9))&&(dist<=($8+$9))) {
-                               print "\n"
+                               print ""
                                print $1 " " $2 " " $3
                                print $4 " " $5 " " $6 " (" dist " - " $8 ")"
-                               print dx " " dy " " dz " " dxt " " dyt " " dzt
+                               print "displace: " dx*X " " dy*Y " " dz*Z
                        }
                        }'
                fi

diff --git a/vasp_tools/stdvis b/vasp_tools/stdvis
index b5685ec..0f30678 100755 (executable)
--- a/vasp_tools/stdvis
+++ b/vasp_tools/stdvis
@@ -11,9 +11,15 @@ else
        type=$2
 fi
 
+if [ -z "$3" ]; then
+       trg="video"
+else
+       type="video.*"
+fi
+
 if [ "$type" != "disp" ]; then
 
-for i in $1/video*; do
+for i in $1/$trg; do
 
        if [ -f $i/stdvis ]; then
                echo "$i already visualized ..."
@@ -36,11 +42,22 @@ fi
 if [ "$type" = "1m" ]; then
 echo "type: 1 no rotation, mirrored"
 ./visualize -w 640 -h 480 -d $i \
-       -nll -0.20 -0.20 -0.50 -fur 1.20 1.20 1.20 \
+       -nll -0.20 -0.20 -0.20 -fur 1.20 1.20 1.20 \
+       -b 0.0 0.0 0.0 1.0 1.0 1.0 \
+       -c 0.8 -1.7 0.9 -L 0.5 -1.0 0.5 \
+       -r 0.6 -m 3.0 0.0 0.0 0.0 3.0 0.0 0.0 0.0 3.0 \
+       -A 1 217 2.6
+fi
+
+# first unit cell in each direction without rotation displaying mirrored atoms
+if [ "$type" = "1m2" ]; then
+echo "type: 1 no rotation, mirrored, displaying bonds of the 2 C atoms"
+./visualize -w 640 -h 480 -d $i \
+       -nll -0.20 -0.20 -0.20 -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 3.0 0.0 0.0 0.0 3.0 0.0 0.0 0.0 3.0 \
-       -A 2 217 218 1.9
+       -A 2 217 218 2.6
 fi
 
 # three unit cells in each direction without rotation