source: trunk/exports/G2export_shelx.py @ 1115

#!/usr/bin/env python
# -*- coding: utf-8 -*-
########### SVN repository information ###################
# $Date: 2013-10-18 21:00:32 +0000 (Fri, 18 Oct 2013) $
# $Author: toby $
# $Revision: 1115 $
# $URL: trunk/exports/G2export_shelx.py $
# $Id: G2export_shelx.py 1115 2013-10-18 21:00:32Z toby $
########### SVN repository information ###################
'''Code to export coordinates in SHELX format, as best as I can makes sense of it
'''
import os.path
import GSASIIpath
GSASIIpath.SetVersionNumber("$Revision: 1115 $")
import GSASIIIO as G2IO
import GSASIIstrIO as G2stIO
import GSASIIlattice as G2lat
import GSASIIspc as G2spc

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

    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(  # set export parameters
            AskFile=True): return 
        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 #
                nam,ext = os.path.splitext(self.filename)
                fil = nam+"_"+str(i)+ext
            else:
                fil = self.filename
            fp = self.OpenFile(fil)
            # 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 M,T in phasedict['General']['SGData']['SGOps']:
                sym = G2spc.MT2text(M,T).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.CloseFile()
            print('Phase '+str(phasenam)+' written to file '+str(fil))