mirror of https://gitlab.com/QEF/q-e.git
Converter from CIF format to QE input data, and from CASTEP data.
Both are experimental and little-tested. Courtesy of Carlo Nervi git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@9590 c92efa57-630b-4861-b058-cf58834340f0
This commit is contained in:
giannozz
parent
0d55be2453
commit
090f3054e4
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!
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! Copyright (C) 2012 Carlo Nervi
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! This file is distributed under the terms of the
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! GNU General Public License. See the file `License'
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! in the root directory of the present distribution,
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! or http://www.gnu.org/copyleft/gpl.txt .
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!
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#!/bin/bash
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if [ $# != 1 ]; then
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printf "Usage: castep2qe.sh File (.cell extension not required!)\n Requires File.cell\n"
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exit
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fi
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if [ ! -f $1.cell ]; then
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echo "Error. Cannot find file $1.cell"
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exit
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fi
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#
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# 1 Bohr = 0.529177249 Angstrom
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#
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awk -v FILE="$1" '
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BEGIN {bohr = 0.52917720859;}
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/%BLOCK LATTICE_CART/ {
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for (i=0; i<3; i++) {
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getline;
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cell_px[i] = $1;
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cell_py[i] = $2;
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cell_pz[i] = $3;
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}
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}
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/%BLOCK POSITIONS_FRAC/ {
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natom=0;
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getline;
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do {
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frac[natom++] = $0;
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getline;
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} while ($0 !~ /%ENDBLOCK POSITIONS_FRAC/)
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}
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/%BLOCK KPOINTS_LIST/ {
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nks=0;
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getline;
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do {
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kpout[nks++] = sprintf (" %19.15f %19.15f %19.15f %19.15f", $1, $2, $3, $4);
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getline;
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} while ($0 !~ /%ENDBLOCK KPOINTS_LIST/)
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}
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/%BLOCK SPECIES_MASS/ {
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nspec=0;
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getline;
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do {
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species_symb[nspec] = $1;
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species_mass[nspec] = $2;
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nspec++;
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getline;
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} while ($0 !~ /%ENDBLOCK SPECIES_MASS/)
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}
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/%BLOCK SPECIES_POT/ {
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npot=0;
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getline;
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do {
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pot_symb[npot] = $1;
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pot_ps[npot] = $2;
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npot++;
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getline;
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} while ($0 !~ /%ENDBLOCK SPECIES_POT/)
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}
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END {
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print "&CONTROL"
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print " title = \x027" FILE "\x027"
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print " calculation = \x027" "relax\x027"
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print " restart_mode = \x027" "from_scratch\x027"
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print " outdir = \x27" "./1\x027"
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print " pseudo_dir = \x027" "../PP/atompaw\x027"
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print " prefix = \x027" FILE "\x027"
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print " disk_io = \x027" "none\x027"
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print " verbosity = \x027" "default\x027"
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print " etot_conv_thr = 0.00001"
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print " forc_conv_thr = 0.0001"
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print " nstep = 680"
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print " tstress = .true."
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print " tprnfor = .true."
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print " /"
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print " &SYSTEM"
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print " ibrav = 0"
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print " nat = " natom
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print " ntyp = " nspec
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print " ecutwfc = 60"
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print " ecutrho = 600"
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print "! london = .true."
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print " /"
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print " &ELECTRONS"
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print " electron_maxstep = 200"
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print " conv_thr = 1.0D-7"
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print " diago_thr_init = 1e-4"
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print " startingpot = \x027" "atomic\x027"
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print " startingwfc = \x027" "atomic\x027"
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print " mixing_mode = \x027" "plain\x027"
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print " mixing_beta = 0.5"
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print " mixing_ndim = 8"
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print " diagonalization = \x027" "david\x027"
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print " /"
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print "&IONS"
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print " ion_dynamics = \x027" "bfgs\x027"
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print " /"
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print "\n"
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print "ATOMIC_SPECIES"
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if (npot != nspec) {
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print "Error; npot [" npot "] != nspec [" nspec "]"
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exit;
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}
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for (i=0; i< npot; i++) printf " %3s %14.10f %s\n", species_symb[i], species_mass[i], pot_ps[i];
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print "\nATOMIC_POSITIONS crystal"
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for (i=0; i< natom; i++) print frac[i];
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print "\nK_POINTS crystal"
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print nks;
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for (i=0; i<nks; i++) print kpout[i];
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print "\nCELL_PARAMETERS"
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for (i=0; i<3; i++) printf " %19.15f %19.15f %19.15f\n", cell_px[i]/bohr, cell_py[i]/bohr, cell_pz[i]/bohr;
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print "\n\n\n"
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}
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' $1.cell
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@ -0,0 +1,192 @@
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!
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! Copyright (C) 2012 Carlo Nervi
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! This file is distributed under the terms of the
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! GNU General Public License. See the file `License'
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! in the root directory of the present distribution,
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! or http://www.gnu.org/copyleft/gpl.txt .
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!
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#!/bin/bash
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#
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# Convertitore da file cif a Quantum Espresso (C) Carlo Nervi 2012
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#
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#
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if [ $# != 1 ]; then
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printf "Usage: cif2qe.sh File (.cif extension not required!)\n Requires File.cif\n"
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exit
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fi
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if [ ! -f $1.cif ]; then
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echo "Error. Cannot find file $1.cif"
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exit
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fi
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awk -v FILE="$1" '
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BEGIN {
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bohr = 0.52917720859
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nfield=split("H He Li Be B C N O F Ne Na Mg Al Si P S Cl Ar K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe Cs Ba La Ce Pr Nd Pm Sm Eu Gd Tb Dy Ho Er Tm Yb Lu Hf Ta W Re Os Ir Pt Au Hg Tl Pb Bi Po At Rn Fr Ra Ac Th Pa U Np Pu Am Cm Bk Cf Es Fm Md No Lr Rf Db Sg Bh Hs Mt", AtomSymb, " ")
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split("1.0079 4.0026 6.941 9.0122 10.811 12.0107 14.0067 15.9994 18.9984 20.1797 22.9897 24.305 26.9815 28.0855 30.9738 32.065 35.453 39.948 39.0983 40.078 44.9559 47.867 50.9415 51.9961 54.938 55.845 58.9332 58.6934 63.546 65.39 69.723 72.64 74.9216 78.96 79.904 83.8 85.4678 87.62 88.9059 91.224 92.9064 95.94 98 101.07 102.906 106.42 107.868 112.411 114.818 118.71 121.76 127.6 126.904 131.293 132.905 137.327 138.905 140.116 140.908 144.24 145 150.36 151.964 157.25 158.925 162.5 164.93 167.259 168.934 173.04 174.967 178.49 180.948 183.84 186.207 190.23 192.217 195.078 196.966 200.59 204.383 207.2 208.98 209 210 222 223 226 227 232.038 231.036 238.029 237 244 243 247 247 251 252 257 258 259 262 261 262 266 264 277 268", AtomMass, " ")
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for (i=1; i<=nfield; i++) Atoms[AtomSymb[i]] = AtomMass[i]
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}
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function eval(cmd,expression) {
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expression = "awk \047BEGIN{printf \"%19.15f\", "cmd" }\047"
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expression|getline l
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return l
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}
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function norma(pat, repl, str) {
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gsub(pat, repl, str)
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gsub(/--/, "+", str)
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return eval(str)
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}
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# Salta il commento
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/^\#/ { next
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}
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/loop_/ { loop_switch=1; next }
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/^_/ {
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jvar=0
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if (loop_switch==1) {
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Var[ivar]=$1
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ivar++
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Num_Var=ivar
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# Debug:
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# print "D: " $1 "=" ivar
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if ($1 ~ /^_symmetry/) nsymm=0
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if ($1 ~ /^_atom/) natom=0
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# if ($1 == "_symmetry_equiv_pos_as_xyz") I_Symm=ivar
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} else {
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ivar=0
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loop_switch=0
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Var2[$1]=$2
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}
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}
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/^[^_]/ {
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ivar=0
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if (loop_switch==1 || loop_switch==2) {
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loop_switch=2
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for (i=0; i<Num_Var; i++) {
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Array[Var[i]][jvar]=$(i+1)
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# Debug:
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# printf "Array[" Var[i] "][" jvar "]= [" $(i+1) "] "
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}
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# Debug:
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# printf "\n"
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jvar++
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if (Var[0] ~ /^_atom/) natom++
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if (Var[0] ~ /^_symmetry/) nsymm++
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} else {
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jvar=0
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loop_switch=0
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}
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}
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END {
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a=strtonum(Var2["_cell_length_a"])
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b=strtonum(Var2["_cell_length_b"])
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c=strtonum(Var2["_cell_length_c"])
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alpha=strtonum(Var2["_cell_angle_alpha"])/180.0*3.14159265359
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beta=strtonum(Var2["_cell_angle_beta"])/180.0*3.14159265359
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gamma=strtonum(Var2["_cell_angle_gamma"])/180.0*3.14159265359
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ntyp=0
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for (i=0; i<natom; i++) {
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if (Type_Atom[Array["_atom_site_type_symbol"][i]] != 1) {
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Type_Atom[Array["_atom_site_type_symbol"][i]]=1
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AtomTyp[ntyp]=Array["_atom_site_type_symbol"][i]
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# Debug:
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# print "D: [" Array["_atom_site_type_symbol"][i] "] [" Atoms[Array["_atom_site_type_symbol"][i]] "] AtomTyp[" ntyp "]=[" AtomTyp[ntyp] "]"
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ntyp++
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}
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}
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print "&CONTROL"
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print " title = \x027" FILE "\x027"
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# print "! _symmetry_space_group_name_H-M = " Var2["_symmetry_space_group"]
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# print "! _symmetry_Int_Tables_number = " Var2["_symmetry_Int_Tables_number"]
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# print "! _symmetry_cell_setting = " Var2["_symmetry_cell_setting"]
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print " calculation = \x027" "relax\x027"
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print " restart_mode = \x027" "from_scratch\x027"
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print " outdir = \x027" "./1\x027"
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print " pseudo_dir = \x027" "../PP/atompaw\x027"
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print " prefix = \x027" FILE "\x027"
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print " disk_io = \x027" "none\x027"
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print " verbosity = \x027" "default\x027"
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print " etot_conv_thr = 0.00001"
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print " forc_conv_thr = 0.0001"
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print " nstep = 680"
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print " tstress = .true."
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print " tprnfor = .true."
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print " /"
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print " &SYSTEM"
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print " ibrav = 0"
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print " nat = " natom*nsymm
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print " ntyp = " ntyp
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print " ecutwfc = 60"
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print " ecutrho = 600"
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print "! london = .true."
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print " /"
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print " &ELECTRONS"
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print " electron_maxstep = 200"
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print " conv_thr = 1.0D-7"
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print " diago_thr_init = 1e-4"
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print " startingpot = \x027" "atomic\x027"
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print " startingwfc = \x027" "atomic\x027"
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print " mixing_mode = \x027" "plain\x027"
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print " mixing_beta = 0.5"
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print " mixing_ndim = 8"
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print " diagonalization = \x027" "david\x027"
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print " /"
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print "&IONS"
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print " ion_dynamics = \x027" "bfgs\x027"
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print " /"
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print "\n"
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print "ATOMIC_SPECIES"
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for (i=0; i<ntyp; i++) printf " %3s %14.10f %s.pbe-van_ak.UPF\n", AtomTyp[i], Atoms[AtomTyp[i]], AtomTyp[i];
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print "\nATOMIC_POSITIONS crystal"
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for (j=0; j<nsymm; j++) {
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for (i=0; i<natom; i++) {
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if (split(Array["_symmetry_equiv_pos_as_xyz"][j], Tmp, ",") != 3) {
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print "Error in _symmetry_equiv_pos_as_xyz. Number of fields != 3: [1]=" Tmp[1] " [2]=" Tmp[2] " [3]=" Tmp[3]
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print "D: " Array["_symmetry_equiv_pos_as_xyz"][j] " " Tmp[1] " " Tmp[2] " " Tmp[3]
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exit
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}
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p_X=norma("x", Array["_atom_site_fract_x"][i], Tmp[1])
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p_Y=norma("y", Array["_atom_site_fract_y"][i], Tmp[2])
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p_Z=norma("z", Array["_atom_site_fract_z"][i], Tmp[3])
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printf "%2s %19.15f %19.15f %19.15f\n", Array["_atom_site_type_symbol"][i], p_X, p_Y, p_Z
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}
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}
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print "\nK_POINTS crystal"
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print nks;
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for (i=0; i<nks; i++) print kpout[i];
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cell_px[0]=a
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cell_py[0]=0.0
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cell_pz[0]=0.0
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cell_px[1]=b*cos(gamma)
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cell_py[1]=b*sin(gamma)
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cell_pz[1]=0.0
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cell_px[2]=c*cos(beta)
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cell_py[2]=c*(cos(alpha)-cos(beta)*cos(gamma))/sin(gamma)
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cell_pz[2]=c*sqrt(1.0 - cos(alpha)^2 - cos(beta)^2 - cos(gamma)^2 + 2*cos(alpha)*cos(beta)*cos(gamma))/sin(gamma)
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print "\nCELL_PARAMETERS"
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# Debug:
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# print "a=" a " b=" b " c=" c " alfa=" alpha " beta=" beta " gamma=" gamma
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# for (i=0; i<3; i++) printf " %19.15f %19.15f %19.15f\n", cell_px[i], cell_py[i], cell_pz[i];
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for (i=0; i<3; i++) printf " %19.15f %19.15f %19.15f\n", cell_px[i]/bohr, cell_py[i]/bohr, cell_pz[i]/bohr;
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print "\n\n"
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} ' $1.cif
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