added trafo file (not working correctly by now) + mods to posca2moldyn script

diff --git a/vasp_tools/poscar2moldyn b/vasp_tools/poscar2moldyn
index 1c11741..29a527e 100755 (executable)
--- a/vasp_tools/poscar2moldyn
+++ b/vasp_tools/poscar2moldyn
@@ -2,24 +2,27 @@
 
 mkdir -p video
 
-echo "parsing POSCAR file ..."
+file=$1
+[ -z $1 ] && file=POSCAR
 
-sicnt=`sed -n 6p POSCAR | awk '{ print $1 }'`
-ccnt=`sed -n 6p POSCAR | awk '{ print $2 }'`
+echo "parsing $file file ..."
 
-lc=`sed -n 2p POSCAR | awk '{ print $1 }'`
+sicnt=`sed -n 6p $file | awk '{ print $1 }'`
+ccnt=`sed -n 6p $file | awk '{ print $2 }'`
 
-x1=`sed -n 3p POSCAR | awk '{ print $1 }'`
-x2=`sed -n 3p POSCAR | awk '{ print $2 }'`
-x3=`sed -n 3p POSCAR | awk '{ print $3 }'`
+lc=`sed -n 2p $file | awk '{ print $1 }'`
 
-y1=`sed -n 4p POSCAR | awk '{ print $1 }'`
-y2=`sed -n 4p POSCAR | awk '{ print $2 }'`
-y3=`sed -n 4p POSCAR | awk '{ print $3 }'`
+x1=`sed -n 3p $file | awk '{ print $1 }'`
+x2=`sed -n 3p $file | awk '{ print $2 }'`
+x3=`sed -n 3p $file | awk '{ print $3 }'`
 
-z1=`sed -n 5p POSCAR | awk '{ print $1 }'`
-z2=`sed -n 5p POSCAR | awk '{ print $2 }'`
-z3=`sed -n 5p POSCAR | 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 }'`
 
 ((total=sicnt+ccnt))
 
@@ -39,7 +42,7 @@ cz=0.8
 
 echo "# P $total init <$cx,$cy,$cz>" > video/atomic_conf_init.xyz
 
-tail -${total} POSCAR | \
+tail -${total} $file | \
        while read x y z fx fy fz; do
                type="Si"
                color="Yellow"

diff --git a/vasp_tools/trafoXposcar b/vasp_tools/trafoXposcar
new file mode 100755 (executable)
index 0000000..1aebc4f
--- /dev/null
+++ b/vasp_tools/trafoXposcar
@@ -0,0 +1,88 @@
+#!/bin/bash
+
+echo "parsing POSCAR file ..."
+
+trg=POSCAR.transformed
+
+theta=$1
+
+sicnt=`sed -n 6p POSCAR | awk '{ print $1 }'`
+ccnt=`sed -n 6p POSCAR | awk '{ print $2 }'`
+
+lc=`sed -n 2p POSCAR | awk '{ print $1 }'`
+
+x1=`sed -n 3p POSCAR | awk '{ print $1 }'`
+x2=`sed -n 3p POSCAR | awk '{ print $2 }'`
+x3=`sed -n 3p POSCAR | awk '{ print $3 }'`
+
+y1=`sed -n 4p POSCAR | awk '{ print $1 }'`
+y2=`sed -n 4p POSCAR | awk '{ print $2 }'`
+y3=`sed -n 4p POSCAR | awk '{ print $3 }'`
+
+z1=`sed -n 5p POSCAR | awk '{ print $1 }'`
+z2=`sed -n 5p POSCAR | awk '{ print $2 }'`
+z3=`sed -n 5p POSCAR | awk '{ print $3 }'`
+
+((total=sicnt+ccnt))
+
+echo "  Si: $sicnt, C: $ccnt, total: $total"
+echo "  Lattice constant: $lc A"
+echo "  Basis:"
+echo "      $x1      $y1      $z1"
+echo "  x = $x2  y = $y2  z = $z2"
+echo "      $x3      $y3      $z3"
+echo
+echo "  -----"
+echo "  Trafo: x axis, $theta degree"
+echo "  -----"
+
+costheta=`echo $theta | awk '{ print cos($1*3.1415927/180.0) }'`
+sintheta=`echo $theta | awk '{ print sin($1*3.1415927/180.0) }'`
+
+X1=$x1
+X2=`echo $x2 $x3 $costheta $sintheta | awk '{ print $3*$1-$4*$2 }'`
+X3=`echo $x2 $x3 $costheta $sintheta | awk '{ print $4*$1+$3*$2 }'`
+
+Y1=$y1
+Y2=`echo $y2 $y3 $costheta $sintheta | awk '{ print $3*$1-$4*$2 }'`
+Y3=`echo $y2 $y3 $costheta $sintheta | awk '{ print $4*$1+$3*$2 }'`
+
+Z1=$z1
+Z2=`echo $z2 $z3 $costheta $sintheta | awk '{ print $3*$1-$4*$2 }'`
+Z3=`echo $z2 $z3 $costheta $sintheta | awk '{ print $4*$1+$3*$2 }'`
+
+echo
+echo "  Transformed basis:"
+echo "      $X1      $Y1      $Z1"
+echo "  x = $X2  y = $Y2  z = $Z2"
+echo "      $X3      $Y3      $Z3"
+echo
+
+cnt=0
+tcnt=0
+
+cx=1.0
+cy=1.0
+cz=0.8
+
+# header
+sed -n 1p POSCAR > $trg
+echo " $lc" >> $trg
+echo " $X1 $X2 $X3" >> $trg
+echo " $Y1 $Y2 $Y3" >> $trg
+echo " $Z1 $Z2 $Z3" >> $trg
+echo " $sicnt $ccnt" >> $trg
+echo "selective dynamics" >> $trg
+echo "direct" >> $trg
+
+tail -${total} POSCAR | \
+       while read x y z fx fy fz; do
+               Y=`echo $y $z $costheta $sintheta | \
+                       awk '{ print $3*$1+$4*$2 }'`
+               Z=`echo $y $z $costheta $sintheta | \
+                       awk '{ print $3*$2-$4*$1 }'`
+               echo " $x $Y $Z $fx $fy $fz" >> $trg
+       done
+
+echo "done"
+