little_helpers/tikz/contcar2dmol.sh

   1 #!/bin/bash -eu
   2 #------------------------------------------------
   3 #    contcar2dmol.sh
   4 #    Hackish script to convert VASP structure file with periodic
   5 #    boundary conditions and orthogonal lattice into dmol file
   6 #    Copyright (C) Max J. Hoffmann 2009 mjhoffmann@gmail.com
   7 #
   8 #    This program is free software: you can redistribute it and/or modify
   9 #    it under the terms of the GNU General Public License as published by
  10 #    the Free Software Foundation, either version 3 of the License, or
  11 #    (at your option) any later version.
  12 #
  13 #    This program is distributed in the hope that it will be useful,
  14 #    but WITHOUT ANY WARRANTY; without even the implied warranty of
  15 #    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  16 #    GNU General Public License for more details.
  17 #
  18 #    You should have received a copy of the GNU General Public License
  19 #    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  20 #
  21 #  Based on documentation found at
  22 #  http://cms.mpi.univie.ac.at/vasp/vasp.pdf.gz , subsection 5.7 POSCAR file
  23 #------------------------------------------------
  24
  25 #Initialize variables
  26 contcar=""
  27
  28 for i in $(seq 7)
  29 do
  30   species_name[${i}]=""
  31 done
  32
  33 #Parse options
  34 while getopts "hi:a:b:c:d:e:f:g:" optionName
  35 #Sorry, about the clumsy option names, but getopts does
  36 #not handle long options
  37 do
  38   case "${optionName}" in
  39     a) species_name[1]=${OPTARG} ;;
  40     b) species_name[2]=${OPTARG} ;;
  41     c) species_name[3]=${OPTARG} ;;
  42     d) species_name[4]=${OPTARG} ;;
  43     e) species_name[5]=${OPTARG} ;;
  44     f) species_name[6]=${OPTARG} ;;
  45     g) species_name[7]=${OPTARG} ;;
  46     h) echo "Usage: ${0} -i CONTCAR_FILE [-a Species1 -b Species2 ...] > DMOL_FILE " ;
  47        echo "Only 7 species can be specified due to limitations of getopts"
  48        exit ;;
  49     i) contcar=${OPTARG} ;;
  50   esac
  51 done
  52
  53
  54 #Exit with usage message if no input file is provided
  55 if [ "${contcar}" = "" ]
  56 then
  57    ${0} -h
  58    exit
  59 fi
  60
  61 #INPUT
  62 #fetch maximum number of species
  63 max_spec=$(awk '{if(NR==6) print $0}' ${contcar} | wc -w)
  64
  65
  66 #global scaling factor
  67 a=$(awk '{if(NR==2) print $1}' ${contcar})
  68 #first lattice vector
  69 x1=$(awk '{if(NR==3) print $1}' ${contcar})
  70 x2=$(awk '{if(NR==3) print $2}' ${contcar})
  71 x3=$(awk '{if(NR==3) print $3}' ${contcar})
  72
  73 #second lattice vector
  74 y1=$(awk '{if(NR==4) print $1}' ${contcar})
  75 y2=$(awk '{if(NR==4) print $2}' ${contcar})
  76 y3=$(awk '{if(NR==4) print $3}' ${contcar})
  77
  78 #third lattice vector
  79 y1=$(awk '{if(NR==4) print $1}' ${contcar})
  80 z1=$(awk '{if(NR==5) print $1}' ${contcar})
  81 z2=$(awk '{if(NR==5) print $2}' ${contcar})
  82 z3=$(awk '{if(NR==5) print $3}' ${contcar})
  83
  84 #fetch numbers of species
  85 for i in $(seq ${max_spec})
  86 do
  87   sp[${i}]=$(awk "{if(NR==6) print \$${i}}" ${contcar})
  88 done
  89
  90
  91 #OUTPUT
  92 #lattice constants
  93 echo "\$cell vectors"
  94 head -n 5 ${contcar} | tail -n 3
  95 echo "\$coordinates"
  96
  97 #atomic coordinates
  98 accum=0
  99 species_nr=1
 100 for atoms in ${sp[@]}
 101 do
 102
 103   #The seventh line may contain [sS]elective Dynamics and is optional, so check ...
 104   #I did not understand the meaning of this line. So the results might be wrong if there is
 105   #no 'selective dynamics' printed.
 106   if [  -n "$(sed -n 7p ${contcar} | grep -i "^\s*s")" ]; then offset=8; else offset=7; fi
 107   for i in $(seq ${atoms})
 108   do
 109     line=$(expr "${offset}+${accum}+${i}" | bc -l)
 110
 111     #Switch between direct (fractional) coordinates and cartesian(absolute) coordinates
 112     if [ $(sed -n ${offset}p ${contcar} | grep -oi "^\s*d" )  ]
 113     then
 114       abs_x=$(expr "${a}*($(awk "{if(NR==${line}) print \$1 }" ${contcar})*${x1}+\
 115       $(awk "{if(NR==${line}) print \$2 }" ${contcar})*${y1}+\
 116       $(awk "{if(NR==${line}) print \$3 }" ${contcar})*${z1})" | bc -l )
 117       abs_y=$(expr "${a}*($(awk "{if(NR==${line}) print \$1 }" ${contcar})*${x2}+\
 118       $(awk "{if(NR==${line}) print \$2 }" ${contcar})*${y2}+\
 119       $(awk "{if(NR==${line}) print \$3 }" ${contcar})*${z2})" | bc -l )
 120       abs_z=$(expr "${a}*($(awk "{if(NR==${line}) print \$1 }" ${contcar})*${x3}+\
 121       $(awk "{if(NR==${line}) print \$2 }" ${contcar})*${y3}+\
 122       $(awk "{if(NR==${line}) print \$3 }" ${contcar})*${z3})" | bc -l )
 123     else
 124       abs_x=$(awk "{if(NR==${line}) print \$1 }" ${contcar})
 125       abs_y=$(awk "{if(NR==${line}) print \$2 }" ${contcar})
 126       abs_z=$(awk "{if(NR==${line}) print \$3 }" ${contcar})
 127     fi
 128     if [ "${species_name[${species_nr}]}" = "" ]
 129     then
 130       echo "Species${species_nr} ${abs_x} ${abs_y} ${abs_z}"
 131     else
 132       echo "${species_name[${species_nr}]} ${abs_x} ${abs_y} ${abs_z}"
 133     fi
 134
 135   done
 136   accum=$(expr "${accum}+${atoms}" | bc -l)
 137   species_nr=$(expr "${species_nr} + 1" | bc -l)
 138
 139 done
 140
 141 #And we are done!
 142 echo "\$end"