Source code for G2export_shelx

#!/usr/bin/env python
# -*- coding: utf-8 -*-
########### SVN repository information ###################
# $Date: 2017-10-23 16:39:16 +0000 (Mon, 23 Oct 2017) $
# $Author: vondreele $
# $Revision: 3136 $
# $URL: https://subversion.xray.aps.anl.gov/pyGSAS/trunk/exports/G2export_shelx.py $
# $Id: G2export_shelx.py 3136 2017-10-23 16:39:16Z vondreele $
########### SVN repository information ###################
'''
*Module G2export_shelx: Examples*
-------------------------------------------

Code to export coordinates in the SHELX .ins format
(as best as I can makes sense of it).

'''
from __future__ import division, print_function
import os.path
import GSASIIpath
GSASIIpath.SetVersionNumber("$Revision: 3136 $")
import GSASIIIO as G2IO
import GSASIIspc as G2spc

[docs]class ExportPhaseShelx(G2IO.ExportBaseclass): '''Used to create a SHELX .ins file for a phase :param wx.Frame G2frame: reference to main GSAS-II frame ''' def __init__(self,G2frame): super(self.__class__,self).__init__( # fancy way to say <parentclass>.__init__ G2frame=G2frame, formatName = 'SHELX .ins', extension='.ins', longFormatName = 'Export phase as SHELX .ins file' ) self.exporttype = ['phase'] self.multiple = True
[docs] def Exporter(self,event=None): '''Export as a SHELX .ins file ''' import re # the export process starts here self.InitExport(event) # load all of the tree into a set of dicts self.loadTree() # create a dict with refined values and their uncertainties self.loadParmDict() if self.ExportSelect(): return # set export parameters; filename = self.filename for phasenam in self.phasenam: phasedict = self.Phases[phasenam] # pointer to current phase info i = self.Phases[phasenam]['pId'] if len(self.phasenam) > 1: # if more than one filename is included, add a phase # self.filename = os.path.splitext(filename)[1] + "_" + str(i) + self.extension fp = self.OpenFile() # title line self.Write("TITL from "+str(self.G2frame.GSASprojectfile)+", phase "+str(phasenam)) # get & write cell parameters cell,sig = self.GetCell(phasenam) self.Write("CELL 0.5 {:.5f} {:.5f} {:.5f} {:.3f} {:.3f} {:.3f}".format(*cell[:6])) # Shelx lattice number lattnum = {'P':1,'I':2,'R':2,'F':3,'A':4,'B':5,'C':6}.get(phasedict['General']['SGData']['SGLatt'],0) if not phasedict['General']['SGData']['SGInv']: lattnum *= -1 self.Write("LATT "+str(lattnum)) # generate symmetry operations not including centering and center of symmetry for Opr in phasedict['General']['SGData']['SGOps']: sym = G2spc.MT2text(Opr).lower().replace(" ,",", ") self.Write('SYMM '+G2IO.trim(sym)) # scan through atom types, count the number of times that each element occurs AtomsList = self.GetAtoms(phasenam) maxmult = 0 elemtypes = {} for lbl,typ,mult,xyz,td in AtomsList: maxmult = max(maxmult,mult) typ = re.search('[A-Za-z]+',typ).group(0) typ = typ[0:2] typ = typ[0].upper()+typ[1:].lower() if elemtypes.get(typ) is None: elemtypes[typ] = 1 else: elemtypes[typ] += 1 # create scattering factor record s = "SFAC" elemlist = sorted(elemtypes) for elem in elemlist: s += " " + elem self.Write(s) # handle atom records count = {} for lbl,typ,mult,xyz,td in AtomsList: typ = re.search('[A-Za-z]+',typ).group(0) typ = typ[0:2] typ = typ[0].upper()+typ[1:].lower() if count.get(typ) is None: count[typ] = 0 else: count[typ] += 1 # make a unique <=4 character label, if possible if elemtypes[typ] <= 99: lbl = "{:s}{:d}".format(typ,count[typ]) else: # more than 99 atoms, use hexadecimal notation lbl = typ + "{:X}".format(count[typ])[-2:] sfnum = elemlist.index(typ)+1 # element number in scattering factor list l = lbl+" "+str(sfnum) l += " {:.5f} {:.5f} {:.5f}".format(*[x[0] for x in xyz[:3]]) if mult == maxmult: m = 1 else: m = 1.*mult/maxmult if xyz[3][0] == 1: # frac occ = 10 + m else: occ = m * xyz[3][0] l += " {:.3f}".format(occ) for val,sig in td: l += " {:.3f}".format(val) self.Write(l) self.Write('END') self.CloseFile() print('Phase '+phasenam+' written to file '+self.fullpath)