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cif2cell
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cif2cell
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#!/usr/bin/env python
# Copyright 2010 Torbjorn Bjorkman
# This file is part of cif2cell
#
# cif2cell is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# cif2cell is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with cif2cell. If not, see <http://www.gnu.org/licenses/>.
#
#************************************************************************************
# Description: A command-line tool to generate the geometrical setup
# for various electronic structure codes from a CIF format file.
# This code was published in Comp. Phys. Comm. 182, 1183-1186 (2011).
# Author: Torbjorn Bjorkman, torbjorn.bjorkman(at)abo.fi
# Affiliation: Abo Akademi University
# Physics/Department of Natural Sciences
# Porthansgatan 3
# 20500 Turku, Finland
#************************************************************************************
from __future__ import division
import os
import sys
import string
import copy
from math import *
from datetime import datetime
from optparse import OptionParser, OptionGroup
import warnings
import CifFile
import subprocess
from utils import *
from uctools import *
from ESPInterfaces import *
from elementdata import *
# Name and version
programname = "cif2cell"
version = "1.2.10"
# Turn of warnings about deprecated stuff
warnings.simplefilter("ignore",DeprecationWarning)
# All supported output formats
outputprograms = set(['abinit','castep','cfg','coo','cpmd','cp2k','crystal09','dftb','elk','emto','exciting','fhi-aims',
## 'fleur','ncol','mcsqs','rspt','siesta','sprkkr','vasp', # mcsqs not ready
'fleur','hutsepot','mopac','ncol', 'pwscf', 'quantum-espresso', 'rspt','siesta','sprkkr','vasp',
'ase','bmdl','cellgen','cif','kgrn','kfcd','kstr','shape','spacegroup',
'spc','xband','xyz', 'lammps'])
# Programs that can deal with alloys
alloyprograms = set(["cfg","emto","kstr","bmdl","shape","kgrn","kfcd","cif","spc","sprkkr","xband"])
vcaprograms = set(["castep","vasp"])
#
setupallprogs = set(["vasp","pwscf","quantum-espresso","rspt","mopac"])
setupallstring = ""
for p in setupallprogs:
setupallstring += p+", "
setupallstring = setupallstring.rstrip(", ")
#
programlist = sorted(list(outputprograms))
outputprogramstring = ""
for p in programlist:
outputprogramstring += p+", "
outputprogramstring = outputprogramstring.rstrip(", ")
############################
# INPUT OPTIONS #
############################
description = "A program for generating input lattice structures to various electronic structure programs from a CIF (Crystallographic Information Framework) file. This code was published in Comput. Phys. Commun. 182, 1183 (2011). Please cite generously."
usage = "usage: %prog FILE [-p PROGRAM] [other options]"
parser = OptionParser(usage=usage, description=description)
parser.add_option("--version",dest="version",help="Print version number.",action="store_true")
parser.add_option("-v","--verbose",dest="verbose",help="Print a lot of extra information to screen",action="store_true")
parser.add_option("-q","--quiet",dest="quiet",help="Suppress most screen output, such as warnings and overrides --verbose flag, but will print all other requested output.",action="store_true")
# GENERAL OPTIONS
generalopts = OptionGroup(parser, "General options")
generalopts.add_option("-f","--file",dest="file",help="Input CIF file, unless given as first argument to the program.",metavar="FILE")
generalopts.add_option("-p","--program",dest="program",help="The electronic structure code you want to create input file(s) for. Currently supports: "+outputprogramstring+". This keyword is case insensitive.")
generalopts.add_option("-o","--outputfile",dest="outputfile",help="Name of output file (if other than default for you electronic structure code).",metavar="FILE")
generalopts.add_option("-a","--append",dest="append",help="Append the output to given output file rather than overwriting.",action="store_true")
generalopts.add_option("--grammar",dest="grammar",help="Set the CIF grammar to be used when parsing the input file (default is 1.1).")
generalopts.add_option("--which-filename",dest="filenamequery",help="If given together with the --program option, the name of the output file will be printed to screen.",action="store_true")
generalopts.add_option("-b","--block",dest="block",help="Block of data in input file (if there are more than one block in the CIF file).")
# CELL GENERATION OPTIONS
cellgenopts = OptionGroup(parser, "Cell generation options")
cellgenopts.add_option("--no-reduce",dest="noreduce",help="Do not reduce to the primitive cell.",action="store_true")
cellgenopts.add_option("--force",dest="force",help="Attempt to force generation of output file despite problems and/or ambiguities in the input file. There are no guarantees that what you get makes sense, but the program makes an honest attempt. Implies --force-alloy.",action="store_true")
cellgenopts.add_option("--force-alloy",dest="forcealloy",help="Force generation of output file for an alloy compound for an electronic structure code that does not implement any alloy theory (such as CPA).",action="store_true")
cellgenopts.add_option("--vca",dest="vca",help="Set up an alloy using the virtual crystal approximation (VCA). Currently only supported by the CASTEP interface.",action="store_true")
cellgenopts.add_option("--cartesian",dest="cartesian",help="Make the program generate any output in cartesian coordinates.",action="store_true")
cellgenopts.add_option("--coordinate-tolerance",dest="coordtol",help="Parameter for determining when two coordinates are the same (default=0.0002).")
cellgenopts.add_option("--setup-all",dest="setupall",help="Make a more complete setup, not just the geometrical part. This is currently only available for "+setupallstring+".",action="store_true")
cellgenopts.add_option("--k-resolution",dest="kresolution",help="The desired resolution in k-space (default=0.2). Used for generating k-space grid options if --setup-all is specified.")
cellgenopts.add_option("--transform-cell",dest="celltransformation",help="Transformation matrix applied to the lattice vectors and the symmetry operations if you, for example, want to realign the cell.",metavar="[[],[],[]]")
cellgenopts.add_option("--cubic-diagonal-z",dest="cubediagz",help="Set up cubic cell with [111] direction along the z-axis.",action="store_true")
cellgenopts.add_option("--rhombohedral-diagonal",dest="rhombdiag",help="Set up rhombohedral cell with threefold axis along pseudocubic [111] direction.",action="store_true")
cellgenopts.add_option("--random-displacements",dest="randomdisp",help="Randomly displace all atoms. Depending on the distribution, the displacement size is either the maximal displacement (for uniform distribution) or the standard deviation (for gaussian distribution) in Angstrom.",metavar="displacementsize")
cellgenopts.add_option("--random-displacements-distribution",dest="randomdistr",help="The distribution used for displacing the atoms.",metavar="uniform/gaussian")
cellgenopts.add_option("--export-cif-labels",dest="exportlabels",help="Export atom labels from the CIF file (currently only supported for castep and RSPt).",action="store_true")
# Supercell options
cellgenopts.add_option("--supercell",dest="supercellmap",help="Three integers separated with commas and enclosed in square brackets that specify the dimensions of a supercell OR three vectors of integers that gives the map to the supercell to be constructed from the primitive cell. If combined with the --no-reduce option the supercell will instead be generated based on the conventional cell.",metavar="[k,l,m]/[[],[],[]]")
cellgenopts.add_option("--supercell-dimensions",dest="supercelldims",help="Three numbers separated with commas and enclosed in square brackets that specify the desired ABSOLUTE dimensions of a supercell (in angstrom) OR three vectors of numbers that gives the desired lattice vectors. The program will automatically generate a supercell, attempting to get as close as possible to the desired dimensions.",metavar="[x,y,z]/[[],[],[]]")
cellgenopts.add_option("--supercell-vacuum",dest="supercellvacuum",help="Three numbers >=0 separated with commas and enclosed in square brackets that specify a number of unit cell units of vacuum to be added along the first, second or third of the generated lattice vectors.",metavar="[k,l,m]")
cellgenopts.add_option("--supercell-translation-vector","--supercell-prevacuum-translation",dest="supercellprevactransvec",help="Three numbers separated with commas and enclosed in square brackets that specify a shift of all atomic positions in the cell prior to vacuum generation (in units of the lattice vectors of the supercell).",metavar="[k,l,m]")
cellgenopts.add_option("--supercell-postvacuum-translation",dest="supercellpostvactransvec",help="Three numbers separated with commas and enclosed in square brackets that specify a final shift of all atomic positions in the final cell (in units of the lattice vectors of the new cell).",metavar="[k,l,m]")
cellgenopts.add_option("--supercell-sort",dest="supercellsort",help="Sort the atom positions by some scheme. Currently available are: 1) By cartesian coordinate - example: xzy will sort first on x then on z then on y. 2) by lattice vector - example: 132 will sort first by lattice vector 1 then by lattice vector 3 and last by lattice vector 2.")
# PRINTING OPTIONS
printopts = OptionGroup(parser, "Printing options")
printopts.add_option("--print-digits",dest="printdigits",help="Number of digits used when printing coordinates etc. to screen (default=8). Useful if you need to tweak the screen output for cutting and pasting into some unsupported program. There is no point in going over 16 because of the floating point accuracy.")
printopts.add_option("--print-atomic-units",dest="printau",help="Output lattice parameters in bohrradii rather than angstrom.",action="store_true")
printopts.add_option("--print-cartesian",dest="printcart",help="Atomic sites printed to screen in cartesian rather than lattice coordinates.",action="store_true")
printopts.add_option("--print-symmetry-operations",dest="printsymops",help="Print symmetry operations of the generated cell.",action="store_true")
printopts.add_option("--print-seitz-matrices",dest="printseitz",help="Print symmetry operations of the generated cell in Seitz matrix form.",action="store_true")
printopts.add_option("--print-charge-state","--print-oxidation-numbers",dest="printcharges",help="Print information about the oxidation state from the CIF file.",action="store_true")
printopts.add_option("--print-reference-bibtex",dest="bibtexref",help="Print citation in BibTeX format and exit.",action="store_true")
# PROGRAM SPECIFIC OPTIONS
progspec = OptionGroup(parser, "Program specific options")
# abinit
progspec.add_option("--abinit-braces",dest="abinitbraces",help="Put curly braces around input values for ABINIT.",action="store_true")
# cellgen
progspec.add_option("--cellgen-map",dest="cellgenmap",help="Nine integers separated with commas and enclosed three and three in square brackets (this is a matrix in Python) that specify the map to a supercell to be output for the RSPt supercell generator 'cellgen'. Overrides --cellgen-supercell-dims.",metavar="[[k,l,m],[n,o,p],[q,r,s]]")
progspec.add_option("--cellgen-supercell-dimensions",dest="cellgensupercelldims",help="Three integers separated with commas and enclosed in square brackets that specify the dimensions of a supercell to be output to the RSPt supercell generator 'cellgen' (the diagonal elements of the 'map').",metavar="[k,l,m]")
progspec.add_option("--cellgen-reference-vector",dest="cellgenrefvec",help="Three reals separated with commas and enclosed in square brackets that specify an optional shift of the origin used by the RSPt supercell generator 'cellgen'.",metavar="[x,y,z]")
# CASTEP
progspec.add_option("--castep-cartesian",dest="castepcartesian",help="Output atom positions in cartesian rather than lattice coordinates.",action="store_true")
progspec.add_option("--castep-atomic-units",dest="castepatomicunits",help="Output to CASTEP in atomic units (bohr radii) rather than angstrom.",action="store_true")
# CPMD
progspec.add_option("--cpmd-cutoff",dest="cpmdcutoff",help="Set the cutoff written to the &SYSTEM block (default=100.0 Ry).")
# emto
progspec.add_option("--emto-hard-sphere-radii",dest="hardsphereradii",help="Set hard spheres in KSTR to something other than the default (=0.67).")
# FHI-AIMS
progspec.add_option("--fhi-aims-cartesian", dest="aimscartesian", help="Store the coordinates for FHI-AIMS in cartesian format.", action="store_true")
# MOPAC
progspec.add_option("--mopac-first-line", dest="mopacfirstline", help="String to be used for the first line (the run commands) of the MOPAC input.",metavar='"string"')
progspec.add_option("--mopac-second-line", dest="mopacsecondline", help="String to be used for the second line (documentation) of the MOPAC input.",metavar='"string"')
progspec.add_option("--mopac-third-line", dest="mopacthirdline", help="String to be used for the third line (documentation) of the MOPAC input.",metavar='"string"')
progspec.add_option("--mopac-freeze-structure", dest="mopacfreeze", help="If set to 'T' then add a 0 after each coordinate (freezing the structure), if set to 'F' then add a 1 (allowing everything to relax).",metavar='T/F')
# PWSCF
progspec.add_option("--pwscf-pseudostring",dest="pwscfpseudostring",help='String to attach to the element name to identify the pseudopotential file (e.g. something like "_HSCV_PBE-1.0.UPF").',metavar="_PSEUDO")
progspec.add_option("--pwscf-atomic-units",dest="pwscfatomicunits",help="Write PWSCF .in file in atomic units (bohr) rather than angstrom.",action="store_true")
progspec.add_option("--pwscf-alat-units",dest="pwscfalatunits",help="Use 'alat' units for the positions in the PWSCF .in file.",action="store_true")
progspec.add_option("--pwscf-cartesian",dest="pwscfcart",help="Write lattice vectors and positions to PWSCF .in file in cartesian coordinates and set the lengths scale to 1.",action="store_true")
progspec.add_option("--pwscf-cartesian-latticevectors",dest="pwscfcartvects",help="Write lattice vectors to PWSCF .in file in cartesian coordinates and set the lengths scale to 1.",action="store_true")
progspec.add_option("--pwscf-cartesian-positions",dest="pwscfcartpos",help="Write lattice positions to PWSCF .in file in cartesian coordinates.",action="store_true")
# RSPt
progspec.add_option("--rspt-new", dest="newsymt", help="Generate a symt.inp file in the new format.", action="store_true")
progspec.add_option("--rspt-spinpol", dest="rsptspinpol", help="Generate new format symt.inp file with spin polarization.", action="store_true")
progspec.add_option("--rspt-relativistic", dest="rsptrelativistic", help="Generate new format symt.inp file with relativistic effects.", action="store_true")
progspec.add_option("--rspt-spinaxis", dest="rsptspinaxis", help="Spin axis for symt.inp (default is [0.0,0.0,0.0].", metavar="[x,y,z]")
progspec.add_option("--rspt-no-spin", dest="rsptnospin", help="Force a nonmagnetic setup in conjunction with --setup-all.", action="store_true")
progspec.add_option("--rspt-mtradii", dest="rsptmtradii", help="Integer that gives the method for setting muffin tin radii.", metavar="N")
progspec.add_option("--rspt-cartesian-latticevectors", dest="rsptcartlatvects", help="Put lattice vectors in atomic units and the lenght scale parameter to 1.", action="store_true")
progspec.add_option("--rspt-pass-wyckoff", dest="rsptpasswyckoff", help="Pass wyckoff labels from CIF file to the symt/rspt.inp file.", action="store_true")
# SPRKKR/xband
progspec.add_option("--sprkkr-minangmom",dest="sprkkrminangmom",help="Enforce minimum onsite angular momentum (=l+1, so that 3 will be d-states).")
# spacegroup
progspec.add_option("--spacegroup-supercell",dest="spacegroupsupercell",help="Three integers separated with commas and enclosed in square brackets that specify the dimensions of a supercell to be output to the elk input generator 'spacegroup'.",metavar="[k,l,m]")
# VASP
progspec.add_option("--vasp-format",dest="vaspformat",help="Format of the generated POSCAR file, either 4 or 5. Default is 4.")
progspec.add_option("--vasp-print-species",dest="vaspprintspcs",help="Print the atomic species to screen in the order they are put in the POSCAR file (useful for scripting).",action="store_true")
progspec.add_option("--vasp-cartesian",dest="vaspcart",help="Write lattice vectors and positions to POSCAR file in cartesian coordinates and set length to 1.",action="store_true")
progspec.add_option("--vasp-cartesian-lattice-vectors",dest="vaspcartvecs",help="Write lattice vectors to POSCAR file in cartesian coordinates and set the length scale to 1.",action="store_true")
progspec.add_option("--vasp-cartesian-positions",dest="vaspcartpos",help="Write atomic positions to POSCAR file in Cartesian rather than Direct coordinates.",action="store_true")
progspec.add_option("--vasp-selective-dynamics",dest="vaspselectivedyn",help="Output POSCAR in selective dynamics format (without any constrained atoms).",action="store_true")
progspec.add_option("--vasp-pseudo-libdr",dest="vasppseudolib",help="Path to the VASP pseudopotential library. Also settable by the VASP_PAWLIB environment variable.")
progspec.add_option("--vasp-pseudo-priority",dest="vasppppriority",help="Set the priority of different pseudopotentials by a list of suffixes. Also available via the VASP_PP_PRIORITY environment variable.", metavar='"_d,_pv,_sv,_h,_s"')
progspec.add_option("--vasp-encutfac",dest="vaspencutfac",help="Factor that multiplies the maximal ENCUT found in the POTCAR file.", metavar="1.5")
# xyz
progspec.add_option("--xyz-atomic-units",dest="xyzatomicunits",help="Output xyz file in atomic units (bohr radii) rather than angstrom.",action="store_true")
#
parser.add_option_group(generalopts)
parser.add_option_group(cellgenopts)
parser.add_option_group(printopts)
parser.add_option_group(progspec)
(options,args) = parser.parse_args()
# Print version number and exit
if options.version:
print programname+" version "+version
sys.exit(0)
#############################################################
# Check that options given are possible
if options.append and not options.outputfile:
sys.stderr.write("***Error: option --append requires an output file to be specified.\n")
sys.exit(1)
if options.append and (options.program == 'emto' or options.program == 'ncol'):
sys.stderr.write("***Error: option --append can not be used with "+options.program+".\n")
sys.exit(1)
if options.setupall and options.program not in setupallprogs:
sys.stderr.write("***Error: option --setup-all not supported for "+options.program+".\n")
sys.exit(1)
if options.filenamequery and not options.program:
sys.stderr.write("***Error: option --which-filename requires that --program is given.\n")
sys.exit(1)
if options.supercellmap and options.supercelldims:
sys.stderr.write("***Error: cannot use both --supercell and --supercell-dimensions.")
sys.exit(1)
#############################################################
# INITIAL PARSING OF VARIOUS INPUT DATA
# Electronic structure program
if options.program:
outputprogram = options.program.lower()
if not outputprogram in outputprograms:
print "Error: Unknown output format: "+outputprogram
sys.exit(1)
# Quantum Espresso is just an alias...
if outputprogram == 'quantum-espresso':
outputprogram = 'pwscf'
else:
outputprogram = None
# recast some input parameters
if options.noreduce:
reducetoprim = False
else:
reducetoprim = True
try:
printdigits = int(options.printdigits)
except:
printdigits = 8
# Set verbosity level
if options.verbose and not options.quiet:
verbose = True
else:
verbose = False
# Various parameters
# Cartesian?
if options.cartesian:
options.castepcartesian = True
options.printcart = True
options.vaspcart = True
options.aimscartesian = True
# Output reference in specific format?
if options.bibtexref:
bibtexref = True
else:
bibtexref = False
# Force generation despite problems?
if options.force:
force = True
else:
force = False
# force output for alloys
if options.forcealloy or force:
forcealloy = True
else:
forcealloy = False
# Make supercell?
if options.supercellmap or options.supercelldims or options.supercellvacuum or \
options.supercellprevactransvec or options.supercellpostvactransvec:
makesupercell = True
else:
makesupercell = False
# Initialize element data
ed = ElementData()
# Number of positions for printing decimal numbers to screen
if type(options.printdigits) == type(None):
decpos = 8 + 3
else:
decpos = int(options.printdigits) + 3
# format string for outputting decimal numbers to screen
decform = "%"+str(decpos)+"."+str(decpos-4)+"f"
threedecs = " "+decform+" "+decform+" "+decform
fourdecs = " "+decform+" "+decform+" "+decform+" "+decform
# For printing time
today = datetime.today()
datestring = str(today.year)+"-"+str(today.month).rjust(2,'0')+"-"+str(today.day).rjust(2,'0')+' '+str(today.hour)+":"+str(today.minute).rjust(2,'0')
# Printing of symmetry operations
if options.printsymops:
printsymops = True
else:
printsymops = False
if options.printseitz:
printseitz = True
else:
printseitz = False
if options.printcharges:
printcharges = True
else:
printcharges = False
# complete setup options
if options.setupall:
setupall = True
else:
setupall = False
# k-space resolution
if options.kresolution:
kresolution=float(options.kresolution)
else:
kresolution=0.2
# Cell transformations
if options.celltransformation or options.cubediagz or options.rhombdiag:
transformcell = True
else:
transformcell = False
#################################################################
# Open and read CIF file
cif_file = None
if len(args) > 0:
# input CIF file as argument
cif_file = args[0]
if options.file:
# input CIF file as option (overrides argument)
cif_file = options.file
if cif_file:
if not os.path.exists(cif_file):
sys.stderr.write("***Error: The file "+cif_file+" could not be found.\n")
sys.exit(2)
cif_file_name = cif_file.split("/")[-1]
# Set CIF grammar
if options.grammar:
cif_grammar = options.grammar
else:
cif_grammar = '1.1'
# Skip validation for now... it causes too much trouble.
## cdic = CifFile.CifDic("cif_core.dic",grammar='1.1')
## val_results = CifFile.validate(cif_file,dic=cdic)
## print validate_report(val_results)
## val_report = CifFile.ValidationResult(val_results)
try:
cf = CifFile.ReadCif(cif_file,grammar=cif_grammar)
except Exception, e:
# test if data_ statement in the beginning is missing
try:
f = open(cif_file,'r')
lines = f.readlines()
f.close()
tmpname = cif_file.replace('.cif','_tmp.cif')
f = open(tmpname,'w')
f.write("data_default\n")
for line in lines:
f.write(line)
f.close()
cf = CifFile.ReadCif(tmpname,grammar=cif_grammar)
wrongfile = cif_file.replace('.cif','_wrong.cif')
sys.stderr.write("***Warning: The cif file is missing a data statement.")
sys.stderr.write(" The file has been renamed '"+wrongfile+"' and replaced by a")
sys.stderr.write(" corrected file.\n")
os.rename(cif_file,wrongfile)
os.rename(tmpname,cif_file)
except:
try:
os.remove(tmpname)
except:
pass
sys.stderr.write("***Error: could not read "+cif_file+".\n")
sys.stderr.write("Something may be wrong with the CIF file, you can check it with ")
sys.stderr.write("the free IUCr CIF valitation tool at http://http://checkcif.iucr.org/\n")
sys.stderr.write(e.value+"\n")
sys.exit(2)
else:
sys.stderr.write("***Error: No input CIF file given\n")
sys.exit(2)
# Make supercell?
if makesupercell:
if options.supercellmap:
supercellmap = safe_matheval(options.supercellmap)
else:
supercellmap = [1,1,1]
if options.supercelldims:
t = safe_matheval(options.supercelldims)
try:
supercelldims = [[float(t[0]), 0.0, 0.0],
[0.0, float(t[1]), 0.0],
[0.0, 0.0, float(t[2])]]
except:
supercelldims = t
else:
supercelldims = None
if options.supercellvacuum:
supercellvacuum = safe_matheval(options.supercellvacuum)
else:
supercellvacuum = [0,0,0]
if options.supercellprevactransvec:
supercellprevactransvec = safe_matheval(options.supercellprevactransvec)
else:
supercellprevactransvec = [0,0,0]
if options.supercellpostvactransvec:
supercellpostvactransvec = safe_matheval(options.supercellpostvactransvec)
else:
supercellpostvactransvec = [0,0,0]
#
if options.supercellsort:
supercellsort = options.supercellsort.lower()
else:
supercellsort = ""
##############################################
# Get blocks
cfkeys = cf.keys()
if options.block:
cb = cf.get(options.block)
if type(cb) == type(None):
sys.stderr.write("***Error: No block "+options.block+" in "+cif_file+".\n")
sys.exit(2)
else:
cb = cf.get(cfkeys[0])
# Get reference data
ref = ReferenceData()
ref.getFromCIF(cb)
if bibtexref:
print ref.bibtexref()
sys.exit(0)
# Get cell data
cd = CellData()
# Suppress warnings if requested.
cd.quiet = options.quiet
# Force generation despite problems?
cd.force = force
if options.coordtol:
cd.coordepsilon = float(options.coordtol)
try:
cd.getFromCIF(cb)
except PositionError, e:
sys.stderr.write("***Error: cell setup: "+e.value+"\n")
sys.exit(2)
except CellError, e:
sys.stderr.write("***Error: cell setup: "+e.value+"\n")
sys.exit(2)
except SymmetryError, e:
sys.stderr.write("***Error: cell setup: "+e.value+"\n")
sys.exit(2)
##############################################
# Generate cell
try:
if reducetoprim:
cd.primitive()
else:
cd.conventional()
except SymmetryError, e:
sys.stderr.write("***Error: cell setup: "+e.value+"\n")
sys.exit(2)
except CellError, e:
sys.stderr.write("***Error: cell setup: "+e.value+"\n")
sys.exit(2)
# Test if generated cell agrees with given chemical formula.
# Too difficult for alloys.
if len(ref.ChemicalComposition) > 0 and not cd.alloy:
if ref.ChemicalComposition != cd.ChemicalComposition:
if force:
sys.stderr.write("***Warning: Chemical composition of the generated cell differs from that given\n"+\
" by _chemical_formula_sum.\n")
else:
sys.stderr.write("***Error: Chemical composition of the generated cell differs from that given\n"+\
" by _chemical_formula_sum. Use --force to generate a cell anyway.\n")
sys.exit(2)
inputcell = copy.copy(cd)
# Randomly displace atoms if requested. This erases all symmetry operations.
if options.randomdisp and not makesupercell:
if options.randomdistr:
distr = options.randomdistr
else:
distr = "uniform"
try:
cd.randomDisplacements(float(options.randomdisp),distribution=distr)
except SetupError, e:
sys.stderr.write("***Error: random displacements: "+e.value+"\n")
sys.exit(3)
# Reset space group operations
cd.HallSymbol = "P 1"
cd.spacegroupnr = 1
cd.HMSymbol = "P1"
cd.symops = set([SymmetryOperation(['x','y','z'])])
# Print cell
if verbose or not options.program and not options.quiet:
print string.upper(programname)+" "+version
print datestring
# Print compound
compoundstring = "Output for "
if ref.cpd == "" and ref.compound == "":
compoundstring += "unknown compound"
if ref.cpd != "":
compoundstring += ref.cpd
if ref.compound != "":
compoundstring += " ("+ref.compound+")"
print compoundstring
# Print database
print ref.databasestring
if cd.alloy and forcealloy and options.program:
print "\nEnforcing generation of file(s) for "+outputprogram+" for an alloy."
print "\n BIBLIOGRAPHIC INFORMATION"
refstrings = ref.referencestring().split()
tmpstring = ""
i = 0
while i < len(refstrings):
if len(tmpstring+refstrings[i]+" ") < 70:
tmpstring += refstrings[i]+" "
i += 1
else:
print tmpstring
tmpstring = ""
if tmpstring != "":
print tmpstring
print "\n INPUT CELL INFORMATION"
print "Symmetry information:"
if inputcell.HallSymbol != "":
print inputcell.crystal_system()[0].upper()+inputcell.crystal_system()[1:]+" crystal system."
print "Space group number : ".rjust(2)+str(inputcell.spacegroupnr)
print "Hall symbol : "+inputcell.HallSymbol
print "Hermann-Mauguin symbol : "+inputcell.HMSymbol
else:
print "No space group information found."
# only print these if verbose
if verbose:
print "Symmetry equivalent sites:"
symops = list(inputcell.symops)
symops.sort()
for i in range(len(symops)):
print "%4i %8s, %8s, %8s" % (i+1, symops[i].eqsite[0], symops[i].eqsite[1], symops[i].eqsite[2])
print "\nLattice parameters:"
tmpstring = ""
for i in ["a", "b", "c"]:
tmpstring += i.rjust(decpos)+" "
print tmpstring
formatstring = ""
if options.printau:
## aprint = inputcell.ainit*angtobohr
## bprint = inputcell.binit*angtobohr
## cprint = inputcell.cinit*angtobohr
aprint = inputcell.a*angtobohr
bprint = inputcell.b*angtobohr
cprint = inputcell.c*angtobohr
else:
## aprint = inputcell.ainit
## bprint = inputcell.binit
## cprint = inputcell.cinit
aprint = inputcell.a
bprint = inputcell.b
cprint = inputcell.c
for i in range(3):
formatstring = formatstring+decform+" "
print formatstring % (aprint, bprint, cprint)
tmpstring = ""
for i in ["alpha", "beta", "gamma"]:
tmpstring += i.rjust(decpos)+" "
print tmpstring
print formatstring % (inputcell.alpha, inputcell.beta, inputcell.gamma)
## print formatstring % (inputcell.alphainit, inputcell.betainit, inputcell.gammainit)
# Pretty printing in columns that need to have variable width
# w1 = width of the atomic species column
# w2 = width of a decimal column
# w3 = width of the occupancy column
# w4 = width of the charge state column
if inputcell.alloy:
w1 = 0
w3 = 0
w4 = 0
# Find atom and occupation column widths
for a in inputcell.atomdata:
for b in a:
tmpstring1 = ""
tmpstring2 = ""
tmpstring3 = ""
for k,v in b.species.iteritems():
tmpstring1 += k+"/"
tmpstring2 += str(v).rstrip("0.")+"/"
# charge output
for k2,v2 in inputcell.chargedict.iteritems():
if k2.strip(string.punctuation+string.digits) == k:
tmpstring3 += str(v2)+"/"
tmpstring1 = tmpstring1.rstrip("/")
tmpstring2 = tmpstring2.rstrip("/")
tmpstring3 = tmpstring3.rstrip("/")
w1 = max(w1,len(tmpstring1))
w3 = max(w3,len(tmpstring2))
w4 = max(w4,len(tmpstring3))
# small aesthetic adjustment
w1 = w1 + 1
w3 = w3 + 2
w4 = max(w4 + 2, 8)
else:
w1 = 5
w2 = decpos
w3 = 0
# width of charge column
if printcharges:
w4 = 7
else:
w4 = 0
# Now for the output...
tmpstring = "Representative sites :"
print tmpstring
siteheader = "Atom".ljust(w1)+" "
if options.printcart:
transmtx = []
for i in range(3):
transmtx.append([])
for j in range(3):
transmtx[i].append(inputcell.latticevectors[i][j]*inputcell.lengthscale)
i += 1
for i in ["x","y","z"]:
siteheader += i.rjust(decpos)+" "
else:
transmtx = [[1, 0, 0],
[0, 1, 0],
[0, 0, 1]]
for i in ["a1","a2","a3"]:
siteheader += i.rjust(decpos)+" "
if inputcell.alloy:
if w3 > 13:
siteheader += "occupancies".rjust(w3)
else:
siteheader += "occ.".rjust(w3)
if printcharges:
siteheader += " "+"charge".rjust(w4)
print siteheader
# Representative sites
for i in range(len(inputcell.ineqsites)):
tmpstring = ""
occstring = ""
chargestring = ""
for k,v in inputcell.occupations[i].iteritems():
tmpstring += k+"/"
occstring += str(v)+"/"
# charge output
for k2,v2 in inputcell.chargedict.iteritems():
if k2.strip(string.punctuation+string.digits) == k:
chargestring += str(v2)+"/"
tmpstring = tmpstring.rstrip("/")
occstring = occstring.rstrip("/")
chargestring = chargestring.rstrip("/")
v = [t for t in inputcell.ineqsites[i]]
tmpstring = tmpstring.ljust(w1) + threedecs % (v[0],v[1],v[2])
if inputcell.alloy:
tmpstring += " "+occstring.rjust(w3)
if printcharges:
tmpstring += " "+chargestring.rjust(w4)
print tmpstring
# Output cell
print "\n OUTPUT CELL INFORMATION"
print "Symmetry information:"
if cd.HallSymbol != "":
print cd.crystal_system()[0].upper()+cd.crystal_system()[1:]+" crystal system."
print "Space group number : ".rjust(2)+str(cd.spacegroupnr)
print "Hall symbol : "+cd.HallSymbol
print "Hermann-Mauguin symbol : "+cd.HMSymbol
else:
print "No space group information found."
# only print these if verbose
if verbose:
print "Symmetry equivalent sites:"
symops = list(cd.symops)
symops.sort()
for i in range(len(symops)):
print "%4i %8s, %8s, %8s" % (i+1, symops[i].eqsite[0], symops[i].eqsite[1], symops[i].eqsite[2])
print ""
cd.printCell(printcart=options.printcart, printdigits=printdigits, printcharges=options.printcharges)
# Print volume and density
if options.printau:
volume = cd.volume()*(cd.lengthscale*angtobohr)**3
volstring = "(a.u.)"
else:
volume = cd.volume()*cd.lengthscale**3
volstring = "A"
print "\nUnit cell volume : "+decform%volume+" "+volstring+"^3"
try:
weight = 0.0
for a in cd.atomdata:
for b in a:
for k,v in b.species.iteritems():
weight += ed.elementweight[k]*v
density = weight/volume
print "Unit cell density : "+decform%density+" u/"+volstring+"^3 = "+decform%(density*uperautogpercm)+" g/cm^3"
except:
if not options.quiet:
sys.stderr.write("***Warning: Error printing unit cell density.\n")
##############################################
# Rotate cell
if transformcell:
# pre-defined transformations
if options.cubediagz:
# Put [111] direction along z axis.
celltransformation = LatticeMatrix([[0.577350269189626,-1.000000000000000,0.816496580927725],
[0.577350269189626, 1.000000000000000,0.816496580927725],
[-1.154700538379250,0.000000000000000,0.816496580927725]])
if cd.crystal_system() != 'cubic':
sys.stderr.write("***Error: Only cubic structures are properly aligned to the z axis by --cubic-diagonal-z.\n")
if not force:
sys.stderr.write(" Use --force to go ahead anyway.\n")
sys.exit(1)
if options.rhombdiag:
# Put z direction along pseudocubic [111]. Kind of the opposite of the cubediagz.
t = 1/cd.latticevectors[0].length() # Normalization to 1
celltransformation = LatticeMatrix([[0.816496580927726*t,-0.408248290463863*t,-0.408248290463863*t],
[0.000000000000000, 0.707106781186547*t,-0.707106781186547*t],
[0.577350269189626*t, 0.577350269189626*t, 0.577350269189626*t]])
if not cd.rhombohedral:
sys.stderr.write("***Error: Only rhombohedral cells are properly aligned to the\n")
sys.stderr.write(" pseudocubic (111) axis by --rhombohedral-diagonal.\n")
if not force:
sys.stderr.write(" Use --force to go ahead anyway.\n")
sys.exit(1)
# explicitly giving the transformation overrides any other transformation
if options.celltransformation:
celltransformation = safe_matheval(options.celltransformation)
try:
cd.transformCell(celltransformation)
except CellError, e:
sys.stderr.write("***Error: Cell transformation: "+e.value+"\n")
sys.exit(2)
if verbose or not options.program and not options.quiet:
print "\n TRANSFORMED CELL"
cd.printCell(printcart=options.printcart, printdigits=printdigits, printcharges=options.printcharges)
##############################################
# Generate supercell
if makesupercell:
if supercelldims != None:
# Determine a suitable map to get the desired supercell dimensions.
t1 = []
for i in range(3):
t1.append([])
for j in range(3):
t1[i].append(cd.latticevectors[i][j]*cd.lengthscale)
t2 = minv3(t1)
t2 = mmmult3(supercelldims,t2)
supercellmap = []
for i in range(3):
supercellmap.append([])
for j in range(3):
supercellmap[i].append(int(round(t2[i][j])))
try:
cd.getSuperCell(supercellmap,supercellvacuum,supercellprevactransvec,postvactransvec=supercellpostvactransvec,sort=supercellsort)
except CellError, e:
sys.stderr.write("***Error: Supercell setup: "+e.value+"\n")
sys.exit(2)
# Randomly displace atoms if requested. This erases all symmetry operations.
if options.randomdisp:
if options.randomdistr:
distr = options.randomdistr
else:
distr = "uniform"
try:
cd.randomDisplacements(float(options.randomdisp),distribution=distr)
except SetupError,e:
sys.stderr.write("***Error: random displacements: "+e.value+"\n")
sys.exit(3)
cd.symops = set([SymmetryOperation(['x','y','z'])])
# Print supercell
if verbose or not options.program and not options.quiet:
print "\n SUPERCELL INFORMATION"
cd.printCell(printcart=options.printcart, printdigits=printdigits, printcharges=options.printcharges)
if printsymops or printseitz or verbose:
# Print symmetry operations. Need to make list of it to control order.
symoplist = sorted(list(cd.symops))
if printsymops or verbose:
print "\nSymmetry operations : "
print " 3x3 rotation matrix +"
print " 3x1 translation vector"
i = 1
for op in symoplist:
print "Operation "+str(i)
for v in op.rotation:
print threedecs%(v[0],v[1],v[2])
print threedecs%(op.translation[0],op.translation[1],op.translation[2])
i += 1
if printseitz:
print "\nSymmetry operations :"
print " In Seitz matrix form"
i = 1
for op in symoplist:
print "Operation "+str(i)
tmpstring = ""
for j in range(3):
tmpstring += fourdecs%(op.rotation[j][0],op.rotation[j][1],op.rotation[j][2],op.translation[j])+"\n"
tmpstring += fourdecs%(0,0,0,1)
print tmpstring
i += 1
# Remind that the result may be junk when using --force
if force:
sys.stderr.write("\n***Warning: You invoked the --force flag, presumably to bypass some error message.\n")
sys.stderr.write(" Carefully check the results, which may be rubbish, nonsense or both!\n")
##############################################
# Sort sites so that the ones occupied by the heaviest elements come first,
# if the Python version supports this form of the max function and there is
# nothing wrong with the site data.
if not (makesupercell and supercellsort):
try:
cd.atomdata.sort(key = lambda a: ed.elementnr[max(a[0].species, key = a[0].species.get)], reverse=True)
except:
pass
############################################################################################
# Output file mode (overwrite or append?)
if options.append:
outmode = "a"
else:
outmode = "w"
# Output file. ot parsed until this point, since the default file names for some of
# the codes contain the names of space group and compound.
if options.outputfile:
outputfile = options.outputfile
else:
# Default output filenames for different programs
if outputprogram == "vasp":
outputfile = "POSCAR"
elif outputprogram == "rspt":
if setupall:
outputfile = "rspt.inp"
else:
outputfile = "symt.inp"
elif outputprogram == "cellgen":
outputfile = "cellgen.inp"
elif outputprogram == "elk":
outputfile = "GEOMETRY.OUT"
elif outputprogram == "exciting":
outputfile = "input.xml"
elif outputprogram == "spacegroup":
outputfile = "spacegroup.in"
elif outputprogram == "cif":
outputfile = cif_file_name.replace(".cif","")+"_allatoms.cif"
elif outputprogram == "ase":
outputfile = "positions.py"
else:
# A bunch of programs get default output constructed as:
# 1. chemical abbreviation (i.e. something like "H2SO4" or CeRhIn5)
# 2. if this is too long, use the original cif filename
outputfile = ref.cpd.replace(" ", "").replace("(","").replace(")","")
# If the filename seems too long or strange, replace by the name of the cif file
if len(outputfile.strip(string.punctuation)) == 0:
outputfile = cif_file_name.replace(".cif","")
if len(outputfile) > 24:
if len(cif_file_name) < len(outputfile):
outputfile = cif_file_name.replace(".cif","")
else:
outputfile = outputfile[0:9]
# Append file endings etc.
if outputprogram == "abinit":
outputfile = outputfile+".in"
elif outputprogram == "castep":
outputfile = outputfile+".cell"
elif outputprogram == "cfg":
outputfile = outputfile+".cfg"
elif outputprogram == "coo":
outputfile = outputfile+".coo"
elif outputprogram == "cp2k":
outputfile = outputfile+".inp"
elif outputprogram == "cpmd":
outputfile = outputfile+".inp"
elif outputprogram == "crystal09":
# This is the naming convention from a large bunch of test cases, no idea why
outputfile = outputfile+".d12"
elif outputprogram == "dftb":
outputfile = outputfile+".gen"
elif outputprogram == "fhi-aims":
outputfile = "geometry.in"
elif outputprogram == "fleur":
outputfile = "inp_"+outputfile
elif outputprogram == "hutsepot":
outputfile = outputfile+".str"
elif outputprogram == "mopac":
outputfile = outputfile+".mop"
elif outputprogram == "pwscf":
outputfile = outputfile+".in"
elif outputprogram == "siesta":
outputfile = outputfile+".fdf"
elif outputprogram == "sprkkr" or outputprogram == "xband":
outputfile = outputfile+".sys"
elif outputprogram == "spc":
outputfile = outputfile+".dat"
elif outputprogram == "xyz":
outputfile = outputfile+".xyz"
elif outputprogram == "lammps":
outputfile = outputfile+".data"
else:
pass
# Print output filename to screen
if outputprogram !="":
if (verbose or options.filenamequery) and outputfile != "":
print "Data will be written to the file "+outputfile
################################################################################################
# stuff that should be printed irrespective of the verbose flag
if cd.alloy and forcealloy and options.program and not verbose:
tmpstring = "Enforcing file generation for alloy. "
if outputprogram == 'bstr' or outputprogram == 'vasp' or outputprogram == 'cpmd':
print tmpstring
else:
tmpstring += "Warning! The file(s) will be incomplete!"
print tmpstring
################################################################################################
# Stop here if no specific output was requested
if not options.program:
sys.exit(0)
# Don't generate output for alloys (for most programs)
if cd.alloy and not forcealloy and not (outputprogram in alloyprograms or outputprogram in vcaprograms):
print "Error: This system is an alloy, but "+codename[outputprogram]+" has no way of dealing with alloys.\n Run again with --force-alloy (or --force) if you want to generate an (incomplete) output file anyway."
sys.exit(17)
# Deal with VCA
if cd.alloy and outputprogram in vcaprograms:
if not options.vca and not forcealloy:
print "Error: This system is an alloy. "+codename[outputprogram]+" can deal with some alloys using the virtual crystal approximation (VCA).\n Run again with the flag --vca if you want to produce a VCA setup."
sys.exit(17)
vcawarning1 = False
vcawarning2 = False
if options.vca:
# Issue warning for precarious VCA setups
groups = []
for a in cd.atomdata:
if len(a[0].species) > 1:
t = [ed.elementgroup[sp] for sp,conc in a[0].species.iteritems()]
groups.append((min(t),max(t)))
if len(a[0].species) > 2:
vcawarning1 = True
for g in groups:
if g[1] - g[0] > 1:
vcawarning2 = True
if vcawarning1 and vcawarning2:
sys.stderr.write("Warning: You are setting up a VCA calculation for an alloy with more than two components\n and not all alloy sites are occupied by species from neighbouring groups in the periodic\n table. Make doubly sure that you know what you are doing!\n")
elif vcawarning1:
sys.stderr.write("Warning: You are setting up a VCA calculation for an alloy with more than two components.\n Make sure that you know what you are doing!\n")
elif vcawarning2:
sys.stderr.write("Warning: You are setting up a VCA calculation but not all alloy sites are occupied by species\n from neighbouring groups in the periodic table. Make sure that you know what you are doing!\n")
# Function for printing a standard docstring
def StandardDocstring():
cif2cellstring = ' T. Bjorkman, Comp. Phys. Commun. 182, 1183-1186 (2011). Please cite generously.'
stringlen = max(len(ref.referencestring()),len(ref.cpd+" ("+ref.compound+")"),len(cif2cellstring))
docstring = ""
tmpstring = ""
tmpstring = tmpstring.ljust(stringlen+4,'*')+'\n'
docstring += tmpstring
tmpstring2 = 'Generated by '+programname+' '+version+' '+datestring
tmpstring2 = '* '+tmpstring2.center(stringlen)+' *\n'
tmpstring3 = '* '+cif2cellstring.center(stringlen)+' *\n'
tmpstring4 = ''
tmpstring4 = '* '+tmpstring4.center(stringlen)+' *\n'
docstring += tmpstring2+tmpstring3+tmpstring4
if ref.database != "":
tmpstring2 = 'Data obtained from '+ref.databaseabbr[ref.database]
if ref.databasecode != "":
tmpstring2 += ". Reference number : "+ref.databasecode
tmpstring2 = '* '+tmpstring2.center(stringlen)+' *\n'
docstring += tmpstring2
tmpstring2 = ref.cpd+" ("+ref.compound+")"
tmpstring2 = '* '+tmpstring2.center(stringlen)+' *\n'
docstring += tmpstring2
docstring += '* '+ref.referencestring().center(stringlen)+' *\n'
docstring += tmpstring
return docstring
################################################################################################
# Output cell to new CIF file
if outputprogram == 'cif':
f = open(outputfile,'w')
cf = CifFile.CifFile()
cb = CifFile.CifBlock()
if makesupercell or (reducetoprim and cd.spacegroupsetting != 'P') or options.randomdisp:
a = Vector(cd.latticevectors[0].scalmult(cd.lengthscale))
b = Vector(cd.latticevectors[1].scalmult(cd.lengthscale))
c = Vector(cd.latticevectors[2].scalmult(cd.lengthscale))
cb['_cell_length_a'] = a.length()
cb['_cell_length_b'] = b.length()
cb['_cell_length_c'] = c.length()
cb['_cell_angle_alpha'] = acos(b.dot(c)/(b.length()*c.length()))*180/pi
cb['_cell_angle_beta'] = acos(a.dot(c)/(a.length()*c.length()))*180/pi
cb['_cell_angle_gamma'] = acos(b.dot(a)/(a.length()*b.length()))*180/pi
# Supercell may have broken symmetry, so just put P1
cb['_space_group_IT_number'] = 1
cb['_space_group_name_H-M_alt'] = "P1"
cb['_space_group_name_Hall'] = "P 1"
else:
# Else pass on original cell parameters and symmetry information
cb['_cell_length_a'] = cd.a