added sip and dist calc for vasp results

diff --git a/vasp_tools/disp_calc b/vasp_tools/disp_calc
new file mode 100755 (executable)
index 0000000..253226f
--- /dev/null
+++ b/vasp_tools/disp_calc
@@ -0,0 +1,144 @@
+#!/bin/bash
+
+file=$1
+init=$2
+atom=$3
+
+if [ -n "$4" ]; then
+ref=$4
+else
+ref=$atom
+fi
+echo "atom number $ref is used as a reference ..."
+echo
+
+scale=`sed -n 2p $file`
+
+X1=`sed -n 3p $file | awk '{ print $1 }'`
+X2=`sed -n 3p $file | awk '{ print $2 }'`
+X3=`sed -n 3p $file | awk '{ print $3 }'`
+
+Y1=`sed -n 4p $file | awk '{ print $1 }'`
+Y2=`sed -n 4p $file | awk '{ print $2 }'`
+Y3=`sed -n 4p $file | awk '{ print $3 }'`
+
+Z1=`sed -n 5p $file | awk '{ print $1 }'`
+Z2=`sed -n 5p $file | awk '{ print $2 }'`
+Z3=`sed -n 5p $file | awk '{ print $3 }'`
+
+export X1 X2 X3
+export Y1 Y2 Y3
+export Z1 Z2 Z3
+
+((offset=8))
+
+echo "final:"
+echo "scale: $scale"
+echo "X: $X1 $X2 $X3"
+echo "Y: $Y1 $Y2 $Y3"
+echo "Z: $Z1 $Z2 $Z3"
+
+((line1=atom+offset))
+
+temp="`sed -n ${line1}p $1`"
+xa=`echo $temp | awk '{ print $1 }'`
+ya=`echo $temp | awk '{ print $2 }'`
+za=`echo $temp | awk '{ print $3 }'`
+echo "(x,y,z) = $xa $ya $za $scale"
+
+results=`echo "$xa $ya $za $scale" | \
+       awk ' \
+       BEGIN {
+               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)
+               x=$1*X
+               if(x>1.0)
+                       x-=1.0;
+               if(x<-1.0)
+                       x+=1.0;
+               y=$2*Y
+               if(y>1.0)
+                       y-=1.0;
+               if(y<-1.0)
+                       y+=1.0;
+               z=$3*Z
+               if(z>1.0)
+                       z-=1.0;
+               if(z<-1.0)
+                       z+=1.0;
+
+               print x*$4 " " y*$4 " " z*$4
+       }'`
+
+xf=`echo $results | awk '{ print $1 }'`
+yf=`echo $results | awk '{ print $2 }'`
+zf=`echo $results | awk '{ print $3 }'`
+echo "---> $xf $yf $zf"
+
+file=$init
+
+scale=`sed -n 2p $file`
+
+X1=`sed -n 3p $file | awk '{ print $1 }'`
+X2=`sed -n 3p $file | awk '{ print $2 }'`
+X3=`sed -n 3p $file | awk '{ print $3 }'`
+
+Y1=`sed -n 4p $file | awk '{ print $1 }'`
+Y2=`sed -n 4p $file | awk '{ print $2 }'`
+Y3=`sed -n 4p $file | awk '{ print $3 }'`
+
+Z1=`sed -n 5p $file | awk '{ print $1 }'`
+Z2=`sed -n 5p $file | awk '{ print $2 }'`
+Z3=`sed -n 5p $file | awk '{ print $3 }'`
+
+export X1 X2 X3
+export Y1 Y2 Y3
+export Z1 Z2 Z3
+
+((offset=8))
+
+echo
+echo "initial:"
+echo "scale: $scale"
+echo "X: $X1 $X2 $X3"
+echo "Y: $Y1 $Y2 $Y3"
+echo "Z: $Z1 $Z2 $Z3"
+
+((line1=ref+offset))
+
+temp="`sed -n ${line1}p $file`"
+xa=`echo $temp | awk '{ print $1 }'`
+ya=`echo $temp | awk '{ print $2 }'`
+za=`echo $temp | awk '{ print $3 }'`
+echo "(x,y,z) = $xa $ya $za $scale"
+
+results=`echo "$xa $ya $za $scale" | \
+       awk ' \
+       BEGIN {
+               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)*$4
+               Y=sqrt(Y1^2+Y2^2+Y3^2)*$4
+               Z=sqrt(Z1^2+Z2^2+Z3^2)*$4
+               print $1*X " " $2*Y " " $3*Z
+       }'`
+
+xi=`echo $results | awk '{ print $1 }'`
+yi=`echo $results | awk '{ print $2 }'`
+zi=`echo $results | awk '{ print $3 }'`
+echo "---> $xi $yi $zi"
+
+echo
+echo -en "displacement: "
+echo $xf $yf $zf $xi $yi $zi | awk '{ print $1-$4 " " $2-$5 " " $3-$6 }'
+echo
+

diff --git a/vasp_tools/dist_calc b/vasp_tools/dist_calc
new file mode 100755 (executable)
index 0000000..b397053
--- /dev/null
+++ b/vasp_tools/dist_calc
@@ -0,0 +1,88 @@
+#!/bin/bash
+
+file=$1
+atom=$2
+btom=$3
+
+scale=`sed -n 2p $1`
+
+X1=`sed -n 3p $file | awk '{ print $1 }'`
+X2=`sed -n 3p $file | awk '{ print $2 }'`
+X3=`sed -n 3p $file | awk '{ print $3 }'`
+
+Y1=`sed -n 4p $file | awk '{ print $1 }'`
+Y2=`sed -n 4p $file | awk '{ print $2 }'`
+Y3=`sed -n 4p $file | awk '{ print $3 }'`
+
+Z1=`sed -n 5p $file | awk '{ print $1 }'`
+Z2=`sed -n 5p $file | awk '{ print $2 }'`
+Z3=`sed -n 5p $file | awk '{ print $3 }'`
+
+export X1 X2 X3
+export Y1 Y2 Y3
+export Z1 Z2 Z3
+
+((offset=8))
+
+echo "scale: $scale"
+echo "X: $X1 $X2 $X3"
+echo "Y: $Y1 $Y2 $Y3"
+echo "Z: $Z1 $Z2 $Z3"
+echo
+
+((line1=atom+offset))
+((line2=btom+offset))
+
+temp="`sed -n ${line1}p $1`"
+xa=`echo $temp | awk '{ print $1 }'`
+ya=`echo $temp | awk '{ print $2 }'`
+za=`echo $temp | awk '{ print $3 }'`
+
+echo "atom 1:"
+echo $temp
+
+temp="`sed -n ${line2}p $1`"
+xb=`echo $temp | awk '{ print $1 }'`
+yb=`echo $temp | awk '{ print $2 }'`
+zb=`echo $temp | awk '{ print $3 }'`
+
+echo "atom 2:"
+echo $temp
+
+echo -en "distance: "
+echo "$xa $ya $za $xb $yb $zb $scale" | \
+       awk ' \
+       BEGIN {
+               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
+               if(dx>1/2)
+                       dx-=1
+               if(dx<-1/2)
+                       dx+=1
+               if(dy>1/2)
+                       dy-=1
+               if(dy<-1/2)
+                       dy+=1
+               if(dz>1/2)
+                       dz-=1
+               if(dz<-1/2)
+                       dz+=1
+               dxt=dx*X1+dy*Y1+dz*Z1
+               dyt=dx*X2+dy*Y2+dz*Z2
+               dzt=dx*X3+dy*Y3+dz*Z3
+               dist=sqrt(dxt^2+dyt^2+dzt^2)
+               dist*=$7
+               print dist
+       }'
+
+echo
+