adisttrj

#!/bin/bash
#
# adist  for TRAJECTORY.xyz or CREST.xyz etc files
# use  adist Atom1 Atom2 Filename
###

atom_A=$1
atom_B=$2
FILE=$3

#for F in $@
#for F in $*
#do
#FILE=$3
#if ["$1" != "$F"]; then
#fi
# echo "$F"

# 1) PLOT ASCII dump or PLOT png

awk -v ATOM_A="$atom_A" -v ATOM_B="$atom_B"  '
$1 ~ /^[0-9]/  {NAtoms = $1; Nline = NR};
NR==(Nline + 1 + ATOM_A) { split($0 , A) }
NR==(Nline + 1 + ATOM_B) { split($0 , B) ;

printf(" %.3f\n ",  sqrt( (A[2]-B[2])**2 + (A[3]-B[3])**2 + (A[4]-B[4])**2) ) ;

#print A[2] ;
#for (x in A) print A[x] ;

};
#    prime    $3  | gnuplot -p -e "set term dumb ; plot '-' w l"
            ' $3  | gnuplot -p -e "set term png ; set output '$3"_"$1"_"$2.png' ; plot '-' w l"

# 2) ANALYSIS
awk -v ATOM_A="$atom_A" -v ATOM_B="$atom_B"  '
$1 ~ /^[0-9]/  {NAtoms = $1; Nline = NR};
NR==(Nline + 1) { ENERGY = $1 }            ;
NR==(Nline + 1 + ATOM_A) { split($0 , A) } ;
NR==(Nline + 1 + ATOM_B) { split($0 , B) ;
printf(" %.8f  "  "%.3f\n" , ENERGY , (sqrt( (A[2]-B[2])**2 + (A[3]-B[3])**2 + (A[4]-B[4])**2) ) ) ;
                          };
#    prime    $3  | gnuplot -p -e "set term dumb ; plot '-' w l"
#    prime    $3  | gnuplot -p -e "set term png ; set output '$3"_"$1"_"$2.png' ; plot '-' w l"
   ' $3

# 3) THRESHOLD
awk -v ATOM_A="$atom_A" -v ATOM_B="$atom_B"  '
$1 ~ /^[0-9]/  {NAtoms = $1; Nline = NR};
NR==(Nline + 1) { ENERGY = $1 }            ;
NR==(Nline + 1 + ATOM_A) { split($0 , A) } ;
NR==(Nline + 1 + ATOM_B) { split($0 , B) ;
     DIST= (sqrt( (A[2]-B[2])**2 + (A[3]-B[3])**2 + (A[4]-B[4])**2) ) ;
     if (DIST < 3.0) {
                       print "    " ENERGY " " DIST " <_THRESHOLD" ;
                       ThreshCount++ }
                          };
  END {print "ThresholdCount = " ThreshCount}
   ' $3

####