| 1 | #!/usr/bin/env python |
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| 2 | # -*- coding: utf-8 -*- |
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| 3 | #G2cif |
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| 4 | ########### SVN repository information ################### |
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| 5 | # $Date: 2013-07-22 20:57:37 -0500 (Mon, 22 Jul 2013) $ |
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| 6 | # $Author: toby $ |
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| 7 | # $Revision: 1006 $ |
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| 8 | # $URL: https://subversion.xray.aps.anl.gov/pyGSAS/trunk/exports/G2cif.py $ |
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| 9 | # $Id: G2cif.py 1006 2013-07-23 01:57:37Z toby $ |
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| 10 | ########### SVN repository information ################### |
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| 11 | '''Development code to export a GSAS-II project as a CIF |
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| 12 | The heavy lifting is done in method export |
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| 13 | ''' |
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| 14 | |
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| 15 | # TODO: need a mechanism for editing of instrument names, bond pub flags, templates,... |
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| 16 | |
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| 17 | import datetime as dt |
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| 18 | import os.path |
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| 19 | import numpy as np |
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| 20 | import GSASIIpath |
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| 21 | GSASIIpath.SetVersionNumber("$Revision: 1006 $") |
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| 22 | import GSASIIIO as G2IO |
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| 23 | #reload(G2IO) |
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| 24 | import GSASIIgrid as G2gd |
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| 25 | import GSASIIstrIO as G2stIO |
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| 26 | #reload(G2stIO) |
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| 27 | #import GSASIImapvars as G2mv |
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| 28 | import GSASIImath as G2mth |
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| 29 | reload(G2mth) |
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| 30 | import GSASIIlattice as G2lat |
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| 31 | import GSASIIspc as G2spg |
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| 32 | #reload(G2spg) |
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| 33 | |
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| 34 | DEBUG = True #True to skip printing of reflection/powder profile lists |
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| 35 | |
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| 36 | def getCallerDocString(): # for development |
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| 37 | "Return the calling function's doc string" |
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| 38 | import inspect as ins |
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| 39 | for item in ins.stack()[1][0].f_code.co_consts: |
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| 40 | if type(item) is str: |
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| 41 | return item |
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| 42 | else: |
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| 43 | return '?' |
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| 44 | |
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| 45 | class ExportCIF(G2IO.ExportBaseclass): |
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| 46 | def __init__(self,G2frame): |
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| 47 | super(self.__class__,self).__init__( # fancy way to say <parentclass>.__init__ |
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| 48 | G2frame=G2frame, |
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| 49 | formatName = 'full CIF', |
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| 50 | longFormatName = 'Export project as complete CIF' |
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| 51 | ) |
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| 52 | self.author = '' |
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| 53 | |
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| 54 | def export(self,mode='full'): |
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| 55 | '''Export a CIF |
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| 56 | |
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| 57 | :param str mode: "full" (default) to create a complete CIF of project, |
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| 58 | "simple" for a simple CIF with only coordinates |
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| 59 | ''' |
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| 60 | |
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| 61 | def WriteCIFitem(name,value=''): |
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| 62 | if value: |
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| 63 | if "\n" in value or len(value)> 70: |
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| 64 | if name.strip(): print name |
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| 65 | print '; '+value |
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| 66 | print '; ' |
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| 67 | elif " " in value: |
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| 68 | if len(name)+len(value) > 65: |
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| 69 | print name,'\n ','"' + str(value) + '"' |
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| 70 | else: |
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| 71 | print name,' ','"' + str(value) + '"' |
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| 72 | else: |
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| 73 | if len(name)+len(value) > 65: |
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| 74 | print name,'\n ',value |
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| 75 | else: |
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| 76 | print name,' ',value |
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| 77 | else: |
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| 78 | print name |
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| 79 | |
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| 80 | def WriteAudit(): |
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| 81 | WriteCIFitem('_audit_creation_method', |
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| 82 | 'created in GSAS-II') |
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| 83 | WriteCIFitem('_audit_creation_date',self.CIFdate) |
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| 84 | if self.author: |
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| 85 | WriteCIFitem('_audit_author_name',self.author) |
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| 86 | WriteCIFitem('_audit_update_record', |
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| 87 | self.CIFdate+' Initial software-generated CIF') |
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| 88 | |
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| 89 | def WriteOverall(): |
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| 90 | '''Write out overall refinement information. |
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| 91 | |
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| 92 | More could be done here, but this is a good start. |
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| 93 | ''' |
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| 94 | WriteCIFitem('_pd_proc_info_datetime', self.CIFdate) |
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| 95 | WriteCIFitem('_pd_calc_method', 'Rietveld Refinement') |
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| 96 | #WriteCIFitem('_refine_ls_shift/su_max',DAT1) |
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| 97 | #WriteCIFitem('_refine_ls_shift/su_mean',DAT2) |
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| 98 | WriteCIFitem('_computing_structure_refinement','GSAS-II') |
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| 99 | try: |
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| 100 | vars = str(len(self.OverallParms['Covariance']['varyList'])) |
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| 101 | except: |
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| 102 | vars = '?' |
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| 103 | WriteCIFitem('_refine_ls_number_parameters',vars) |
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| 104 | try: |
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| 105 | GOF = G2mth.ValEsd(self.OverallParms['Covariance']['Rvals']['GOF'],-0.009) |
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| 106 | except: |
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| 107 | GOF = '?' |
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| 108 | WriteCIFitem('_refine_ls_goodness_of_fit_all',GOF) |
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| 109 | |
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| 110 | # get restraint info |
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| 111 | # restraintDict = self.OverallParms.get('Restraints',{}) |
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| 112 | # for i in self.OverallParms['Constraints']: |
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| 113 | # print i |
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| 114 | # for j in self.OverallParms['Constraints'][i]: |
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| 115 | # print j |
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| 116 | #WriteCIFitem('_refine_ls_number_restraints',TEXT) |
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| 117 | |
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| 118 | # other things to consider reporting |
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| 119 | # _refine_ls_number_reflns |
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| 120 | # _refine_ls_goodness_of_fit_obs |
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| 121 | # _refine_ls_R_factor_all |
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| 122 | # _refine_ls_R_factor_obs |
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| 123 | # _refine_ls_wR_factor_all |
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| 124 | # _refine_ls_wR_factor_obs |
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| 125 | # _refine_ls_restrained_S_all |
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| 126 | # _refine_ls_restrained_S_obs |
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| 127 | |
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| 128 | # include an overall profile r-factor, if there is more than one powder histogram |
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| 129 | if len(self.powderDict) > 1: |
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| 130 | WriteCIFitem('\n# OVERALL POWDER R-FACTOR') |
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| 131 | try: |
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| 132 | R = str(self.OverallParms['Covariance']['Rvals']['Rwp']) |
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| 133 | except: |
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| 134 | R = '?' |
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| 135 | WriteCIFitem('_pd_proc_ls_prof_wR_factor',R) |
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| 136 | #WriteCIFitem('_pd_proc_ls_prof_R_factor',TEXT(11:20)) # who cares! |
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| 137 | WriteCIFitem('_refine_ls_matrix_type','full') |
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| 138 | #WriteCIFitem('_refine_ls_matrix_type','userblocks') |
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| 139 | |
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| 140 | def WritePubTemplate(): |
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| 141 | '''TODO: insert the publication template ``template_publ.cif`` or some modified |
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| 142 | version for this project. Store this in the GPX file? |
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| 143 | ''' |
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| 144 | print getCallerDocString() |
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| 145 | |
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| 146 | def WritePhaseTemplate(): |
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| 147 | '''TODO: insert the phase template ``template_phase.cif`` or some modified |
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| 148 | version for this project |
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| 149 | ''' |
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| 150 | print getCallerDocString() |
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| 151 | |
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| 152 | def WritePowderTemplate(): |
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| 153 | '''TODO: insert the phase template ``template_instrument.cif`` or some modified |
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| 154 | version for this project |
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| 155 | ''' |
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| 156 | print getCallerDocString() |
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| 157 | |
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| 158 | def WriteSnglXtalTemplate(): |
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| 159 | '''TODO: insert the single-crystal histogram template |
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| 160 | for this project |
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| 161 | ''' |
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| 162 | print getCallerDocString() |
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| 163 | |
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| 164 | def FormatSH(phasenam): |
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| 165 | 'Format a full spherical harmonics texture description as a string' |
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| 166 | phasedict = self.Phases[phasenam] # pointer to current phase info |
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| 167 | pfx = str(phasedict['pId'])+'::' |
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| 168 | s = "" |
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| 169 | textureData = phasedict['General']['SH Texture'] |
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| 170 | if textureData.get('Order'): |
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| 171 | s += "Spherical Harmonics correction. Order = "+str(textureData['Order']) |
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| 172 | s += " Model: " + str(textureData['Model']) + "\n Orientation angles: " |
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| 173 | for name in ['omega','chi','phi']: |
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| 174 | aname = pfx+'SH '+name |
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| 175 | s += name + " = " |
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| 176 | sig = self.sigDict.get(aname,-0.09) |
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| 177 | s += G2mth.ValEsd(self.parmDict[aname],sig) |
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| 178 | s += "; " |
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| 179 | s += "\n" |
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| 180 | s1 = " Coefficients: " |
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| 181 | for name in textureData['SH Coeff'][1]: |
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| 182 | aname = pfx+name |
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| 183 | if len(s1) > 60: |
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| 184 | s += s1 + "\n" |
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| 185 | s1 = " " |
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| 186 | s1 += aname + ' = ' |
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| 187 | sig = self.sigDict.get(aname,-0.0009) |
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| 188 | s1 += G2mth.ValEsd(self.parmDict[aname],sig) |
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| 189 | s1 += "; " |
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| 190 | s += s1 |
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| 191 | return s |
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| 192 | |
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| 193 | def FormatHAPpo(phasenam): |
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| 194 | '''return the March-Dollase/SH correction for every |
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| 195 | histogram in the current phase formatted into a |
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| 196 | character string |
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| 197 | ''' |
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| 198 | phasedict = self.Phases[phasenam] # pointer to current phase info |
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| 199 | s = '' |
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| 200 | for histogram in sorted(phasedict['Histograms']): |
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| 201 | if histogram.startswith("HKLF"): continue # powder only |
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| 202 | Histogram = self.Histograms.get(histogram) |
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| 203 | if not Histogram: continue |
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| 204 | hapData = phasedict['Histograms'][histogram] |
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| 205 | if hapData['Pref.Ori.'][0] == 'MD': |
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| 206 | aname = str(phasedict['pId'])+':'+str(Histogram['hId'])+':MD' |
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| 207 | if self.parmDict.get(aname,1.0) != 1.0: continue |
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| 208 | sig = self.sigDict.get(aname,-0.009) |
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| 209 | if s != "": s += '\n' |
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| 210 | s += 'March-Dollase correction' |
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| 211 | if len(self.powderDict) > 1: |
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| 212 | s += ', histogram '+str(Histogram['hId']+1) |
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| 213 | s += ' coef. = ' + G2mth.ValEsd(self.parmDict[aname],sig) |
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| 214 | s += ' axis = ' + str(hapData['Pref.Ori.'][3]) |
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| 215 | else: # must be SH |
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| 216 | if s != "": s += '\n' |
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| 217 | s += 'Simple spherical harmonic correction' |
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| 218 | if len(self.powderDict) > 1: |
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| 219 | s += ', histogram '+str(Histogram['hId']+1) |
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| 220 | s += ' Order = '+str(hapData['Pref.Ori.'][4])+'\n' |
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| 221 | s1 = " Coefficients: " |
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| 222 | for item in hapData['Pref.Ori.'][5]: |
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| 223 | print item |
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| 224 | aname = str(phasedict['pId'])+':'+str(Histogram['hId'])+':'+item |
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| 225 | print aname |
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| 226 | if len(s1) > 60: |
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| 227 | s += s1 + "\n" |
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| 228 | s1 = " " |
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| 229 | s1 += aname + ' = ' |
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| 230 | sig = self.sigDict.get(aname,-0.0009) |
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| 231 | s1 += G2mth.ValEsd(self.parmDict[aname],sig) |
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| 232 | s1 += "; " |
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| 233 | s += s1 |
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| 234 | return s |
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| 235 | def FormatBackground(bkg): |
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| 236 | '''Display the Background information as a descriptive text string. |
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| 237 | |
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| 238 | TODO: this needs to be expanded to show the diffuse peak and |
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| 239 | Debye term information as well. |
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| 240 | |
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| 241 | :returns: the text description (str) |
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| 242 | ''' |
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| 243 | fxn, bkgdict = bkg |
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| 244 | terms = fxn[2] |
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| 245 | txt = 'Background function: "'+fxn[0]+'" function with '+str(terms)+' terms:\n' |
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| 246 | l = " " |
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| 247 | for v in fxn[3:]: |
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| 248 | if len(l) > 60: |
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| 249 | txt += l + '\n' |
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| 250 | l = ' ' |
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| 251 | l += G2mth.ValEsd(v,-.009)+', ' |
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| 252 | txt += l |
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| 253 | return txt |
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| 254 | |
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| 255 | def FormatInstProfile(instparmdict): |
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| 256 | '''Format the instrumental profile parameters with a |
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| 257 | string description. Will only be called on PWDR histograms |
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| 258 | ''' |
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| 259 | s = '' |
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| 260 | inst = instparmdict[0] |
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| 261 | if 'C' in inst['Type'][0]: |
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| 262 | s = 'Finger-Cox-Jephcoat function parameters U, V, W, X, Y, SH/L:\n ' |
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| 263 | for item in ['U','V','W','X','Y','SH/L']: |
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| 264 | s += G2mth.ValEsd(inst[item][1],-.009)+', ' |
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| 265 | elif 'T' in inst['Type'][0]: #to be tested after TOF Rietveld done |
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| 266 | s = 'Von Dreele-Jorgenson-Windsor function parameters\n'+ \ |
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| 267 | ' alpha, beta-0, beta-1, beta-q, sig-0, sig-1, sig-q, X, Y:\n ' |
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| 268 | for item in ['alpha','bet-0','bet-1','bet-q','sig-0','sig-1','sig-q','X','Y']: |
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| 269 | s += G2mth.ValEsd(inst[item][1],-.009)+', ' |
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| 270 | return s |
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| 271 | |
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| 272 | def FormatPhaseProfile(phasenam): |
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| 273 | '''Format the phase-related profile parameters (size/strain) |
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| 274 | with a string description. |
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| 275 | return an empty string or None there are no |
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| 276 | powder histograms for this phase. |
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| 277 | ''' |
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| 278 | s = '' |
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| 279 | phasedict = self.Phases[phasenam] # pointer to current phase info |
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| 280 | for histogram in sorted(phasedict['Histograms']): |
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| 281 | if histogram.startswith("HKLF"): continue # powder only |
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| 282 | Histogram = self.Histograms.get(histogram) |
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| 283 | if not Histogram: continue |
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| 284 | hapData = phasedict['Histograms'][histogram] |
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| 285 | return 'TODO: Phase profile goes here' |
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| 286 | |
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| 287 | def FmtAtomType(sym): |
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| 288 | 'Reformat a GSAS-II atom type symbol to match CIF rules' |
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| 289 | sym = sym.replace('_','') # underscores are not allowed: no isotope designation? |
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| 290 | # in CIF, oxidation state sign symbols come after, not before |
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| 291 | if '+' in sym: |
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| 292 | sym = sym.replace('+','') + '+' |
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| 293 | elif '-' in sym: |
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| 294 | sym = sym.replace('-','') + '-' |
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| 295 | return sym |
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| 296 | |
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| 297 | def PutInCol(val,wid): |
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| 298 | '''Pad a value to >=wid+1 columns by adding spaces at the end. Always |
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| 299 | adds at least one space |
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| 300 | ''' |
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| 301 | val = str(val).replace(' ','') |
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| 302 | if not val: val = '?' |
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| 303 | fmt = '{:' + str(wid) + '} ' |
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| 304 | return fmt.format(val) |
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| 305 | |
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| 306 | def MakeUniqueLabel(lbl,labellist): |
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| 307 | 'Make sure that every atom label is unique' |
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| 308 | lbl = lbl.strip() |
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| 309 | if not lbl: # deal with a blank label |
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| 310 | lbl = 'A_1' |
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| 311 | if lbl not in labellist: |
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| 312 | labellist.append(lbl) |
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| 313 | return lbl |
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| 314 | i = 1 |
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| 315 | prefix = lbl |
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| 316 | if '_' in lbl: |
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| 317 | prefix = lbl[:lbl.rfind('_')] |
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| 318 | suffix = lbl[lbl.rfind('_')+1:] |
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| 319 | try: |
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| 320 | i = int(suffix)+1 |
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| 321 | except: |
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| 322 | pass |
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| 323 | while prefix+'_'+str(i) in labellist: |
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| 324 | i += 1 |
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| 325 | else: |
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| 326 | lbl = prefix+'_'+str(i) |
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| 327 | labellist.append(lbl) |
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| 328 | |
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| 329 | def WriteAtomsNuclear(phasenam): |
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| 330 | 'Write atom positions to CIF' |
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| 331 | phasedict = self.Phases[phasenam] # pointer to current phase info |
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| 332 | General = phasedict['General'] |
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| 333 | cx,ct,cs,cia = General['AtomPtrs'] |
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| 334 | Atoms = phasedict['Atoms'] |
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| 335 | cfrac = cx+3 |
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| 336 | fpfx = str(phasedict['pId'])+'::Afrac:' |
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| 337 | for i,at in enumerate(Atoms): |
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| 338 | fval = self.parmDict.get(fpfx+str(i),at[cfrac]) |
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| 339 | if fval != 0.0: |
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| 340 | break |
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| 341 | else: |
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| 342 | WriteCIFitem('\n# PHASE HAS NO ATOMS!') |
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| 343 | return |
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| 344 | |
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| 345 | WriteCIFitem('\n# ATOMIC COORDINATES AND DISPLACEMENT PARAMETERS') |
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| 346 | WriteCIFitem('loop_ '+ |
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| 347 | '\n\t_atom_site_label'+ |
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| 348 | '\n\t_atom_site_type_symbol'+ |
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| 349 | '\n\t_atom_site_fract_x'+ |
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| 350 | '\n\t_atom_site_fract_y'+ |
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| 351 | '\n\t_atom_site_fract_z'+ |
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| 352 | '\n\t_atom_site_occupancy'+ |
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| 353 | '\n\t_atom_site_adp_type'+ |
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| 354 | '\n\t_atom_site_U_iso_or_equiv'+ |
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| 355 | '\n\t_atom_site_symmetry_multiplicity') |
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| 356 | |
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| 357 | varnames = {cx:'Ax',cx+1:'Ay',cx+2:'Az',cx+3:'Afrac', |
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| 358 | cia+1:'AUiso',cia+2:'AU11',cia+3:'AU22',cia+4:'AU33', |
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| 359 | cia+5:'AU12',cia+6:'AU13',cia+7:'AU23'} |
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| 360 | self.labellist = [] |
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| 361 | |
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| 362 | pfx = str(phasedict['pId'])+'::' |
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| 363 | # loop over all atoms |
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| 364 | naniso = 0 |
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| 365 | for i,at in enumerate(Atoms): |
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| 366 | s = PutInCol(MakeUniqueLabel(at[ct-1],self.labellist),6) # label |
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| 367 | fval = self.parmDict.get(fpfx+str(i),at[cfrac]) |
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| 368 | if fval == 0.0: continue # ignore any atoms that have a occupancy set to 0 (exact) |
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| 369 | s += PutInCol(FmtAtomType(at[ct]),4) # type |
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| 370 | if at[cia] == 'I': |
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| 371 | adp = 'Uiso ' |
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| 372 | else: |
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| 373 | adp = 'Uani ' |
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| 374 | naniso += 1 |
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| 375 | # compute Uequiv crudely |
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| 376 | # correct: Defined as "1/3 trace of diagonalized U matrix". |
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| 377 | # SEE cell2GS & Uij2Ueqv to GSASIIlattice. Former is needed to make the GS matrix used by the latter. |
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| 378 | t = 0.0 |
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| 379 | for j in (2,3,4): |
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| 380 | var = pfx+varnames[cia+j]+":"+str(i) |
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| 381 | t += self.parmDict.get(var,at[cia+j]) |
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| 382 | for j in (cx,cx+1,cx+2,cx+3,cia+1): |
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| 383 | if j in (cx,cx+1,cx+2): |
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| 384 | dig = 11 |
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| 385 | sigdig = -0.00009 |
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| 386 | else: |
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| 387 | dig = 10 |
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| 388 | sigdig = -0.009 |
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| 389 | var = pfx+varnames[j]+":"+str(i) |
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| 390 | dvar = pfx+"d"+varnames[j]+":"+str(i) |
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| 391 | if dvar not in self.sigDict: |
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| 392 | dvar = var |
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| 393 | if j == cia+1 and adp == 'Uani ': |
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| 394 | val = t/3. |
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| 395 | sig = sigdig |
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| 396 | else: |
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| 397 | #print var,(var in self.parmDict),(var in self.sigDict) |
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| 398 | val = self.parmDict.get(var,at[j]) |
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| 399 | sig = self.sigDict.get(dvar,sigdig) |
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| 400 | s += PutInCol(G2mth.ValEsd(val,sig),dig) |
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| 401 | s += adp |
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| 402 | s += PutInCol(at[cs+1],3) |
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| 403 | WriteCIFitem(s) |
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| 404 | if naniso == 0: return |
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| 405 | # now loop over aniso atoms |
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| 406 | WriteCIFitem('\nloop_' + '\n\t_atom_site_aniso_label' + |
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| 407 | '\n\t_atom_site_aniso_U_11' + '\n\t_atom_site_aniso_U_12' + |
|---|
| 408 | '\n\t_atom_site_aniso_U_13' + '\n\t_atom_site_aniso_U_22' + |
|---|
| 409 | '\n\t_atom_site_aniso_U_23' + '\n\t_atom_site_aniso_U_33') |
|---|
| 410 | for i,at in enumerate(Atoms): |
|---|
| 411 | fval = self.parmDict.get(fpfx+str(i),at[cfrac]) |
|---|
| 412 | if fval == 0.0: continue # ignore any atoms that have a occupancy set to 0 (exact) |
|---|
| 413 | if at[cia] == 'I': continue |
|---|
| 414 | s = PutInCol(self.labellist[i],6) # label |
|---|
| 415 | for j in (2,3,4,5,6,7): |
|---|
| 416 | sigdig = -0.0009 |
|---|
| 417 | var = pfx+varnames[cia+j]+":"+str(i) |
|---|
| 418 | val = self.parmDict.get(var,at[cia+j]) |
|---|
| 419 | sig = self.sigDict.get(var,sigdig) |
|---|
| 420 | s += PutInCol(G2mth.ValEsd(val,sig),11) |
|---|
| 421 | WriteCIFitem(s) |
|---|
| 422 | |
|---|
| 423 | def HillSortElements(elmlist): |
|---|
| 424 | '''Sort elements in "Hill" order: C, H, others, (where others |
|---|
| 425 | are alphabetical). |
|---|
| 426 | |
|---|
| 427 | :params list elmlist: a list of element strings |
|---|
| 428 | |
|---|
| 429 | :returns: a sorted list of element strings |
|---|
| 430 | ''' |
|---|
| 431 | newlist = [] |
|---|
| 432 | oldlist = elmlist[:] |
|---|
| 433 | for elm in ('C','H'): |
|---|
| 434 | if elm in elmlist: |
|---|
| 435 | newlist.append(elm) |
|---|
| 436 | oldlist.pop(oldlist.index(elm)) |
|---|
| 437 | return newlist+sorted(oldlist) |
|---|
| 438 | |
|---|
| 439 | def WriteComposition(phasenam): |
|---|
| 440 | '''determine the composition for the unit cell, crudely determine Z and |
|---|
| 441 | then compute the composition in formula units |
|---|
| 442 | ''' |
|---|
| 443 | phasedict = self.Phases[phasenam] # pointer to current phase info |
|---|
| 444 | General = phasedict['General'] |
|---|
| 445 | Z = General.get('cellZ',0.0) |
|---|
| 446 | cx,ct,cs,cia = General['AtomPtrs'] |
|---|
| 447 | Atoms = phasedict['Atoms'] |
|---|
| 448 | fpfx = str(phasedict['pId'])+'::Afrac:' |
|---|
| 449 | cfrac = cx+3 |
|---|
| 450 | cmult = cs+1 |
|---|
| 451 | compDict = {} # combines H,D & T |
|---|
| 452 | sitemultlist = [] |
|---|
| 453 | massDict = dict(zip(General['AtomTypes'],General['AtomMass'])) |
|---|
| 454 | cellmass = 0 |
|---|
| 455 | for i,at in enumerate(Atoms): |
|---|
| 456 | atype = at[ct].strip() |
|---|
| 457 | if atype.find('-') != -1: atype = atype.split('-')[0] |
|---|
| 458 | if atype.find('+') != -1: atype = atype.split('+')[0] |
|---|
| 459 | atype = atype[0].upper()+atype[1:2].lower() # force case conversion |
|---|
| 460 | if atype == "D" or atype == "D": atype = "H" |
|---|
| 461 | fvar = fpfx+str(i) |
|---|
| 462 | fval = self.parmDict.get(fvar,at[cfrac]) |
|---|
| 463 | mult = at[cmult] |
|---|
| 464 | if not massDict.get(at[ct]): |
|---|
| 465 | print 'No mass found for atom type '+at[ct] |
|---|
| 466 | print 'Will not compute cell contents for phase '+phasenam |
|---|
| 467 | return |
|---|
| 468 | cellmass += massDict[at[ct]]*mult*fval |
|---|
| 469 | compDict[atype] = compDict.get(atype,0.0) + mult*fval |
|---|
| 470 | if fval == 1: sitemultlist.append(mult) |
|---|
| 471 | if len(compDict.keys()) == 0: return # no elements! |
|---|
| 472 | if Z < 1: # Z has not been computed or set by user |
|---|
| 473 | Z = 1 |
|---|
| 474 | for i in range(2,min(sitemultlist)+1): |
|---|
| 475 | for m in sitemultlist: |
|---|
| 476 | if m % i != 0: |
|---|
| 477 | break |
|---|
| 478 | else: |
|---|
| 479 | Z = i |
|---|
| 480 | General['cellZ'] = Z # save it |
|---|
| 481 | |
|---|
| 482 | # when scattering factors are included in the CIF, this needs to be |
|---|
| 483 | # added to the loop here but only in the one-block case. |
|---|
| 484 | # For multiblock CIFs, scattering factors go in the histogram |
|---|
| 485 | # blocks (for all atoms in all appropriate phases) |
|---|
| 486 | |
|---|
| 487 | #if oneblock: # add scattering factors for current phase here |
|---|
| 488 | WriteCIFitem('\nloop_ _atom_type_symbol _atom_type_number_in_cell') |
|---|
| 489 | formula = '' |
|---|
| 490 | reload(G2mth) |
|---|
| 491 | for elem in HillSortElements(compDict.keys()): |
|---|
| 492 | WriteCIFitem(' ' + PutInCol(elem,4) + |
|---|
| 493 | G2mth.ValEsd(compDict[elem],-0.009,True)) |
|---|
| 494 | if formula: formula += " " |
|---|
| 495 | formula += elem |
|---|
| 496 | if compDict[elem] == Z: continue |
|---|
| 497 | formula += G2mth.ValEsd(compDict[elem]/Z,-0.009,True) |
|---|
| 498 | WriteCIFitem( '\n# Note that Z affects _cell_formula_sum and _weight') |
|---|
| 499 | WriteCIFitem( '_cell_formula_units_Z',str(Z)) |
|---|
| 500 | WriteCIFitem( '_chemical_formula_sum',formula) |
|---|
| 501 | WriteCIFitem( '_chemical_formula_weight', |
|---|
| 502 | G2mth.ValEsd(cellmass/Z,-0.09,True)) |
|---|
| 503 | |
|---|
| 504 | def WriteDistances(phasenam,SymOpList,offsetList,symOpList,G2oprList): |
|---|
| 505 | '''Report bond distances and angles for the CIF |
|---|
| 506 | |
|---|
| 507 | Note that _geom_*_symmetry_* fields are values of form |
|---|
| 508 | n_klm where n is the symmetry operation in SymOpList (counted |
|---|
| 509 | starting with 1) and (k-5, l-5, m-5) are translations to add |
|---|
| 510 | to (x,y,z). See |
|---|
| 511 | http://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Igeom_angle_site_symmetry_.html |
|---|
| 512 | |
|---|
| 513 | TODO: need a method to select publication flags for distances/angles |
|---|
| 514 | ''' |
|---|
| 515 | phasedict = self.Phases[phasenam] # pointer to current phase info |
|---|
| 516 | Atoms = phasedict['Atoms'] |
|---|
| 517 | cx,ct,cs,cia = phasedict['General']['AtomPtrs'] |
|---|
| 518 | fpfx = str(phasedict['pId'])+'::Afrac:' |
|---|
| 519 | cfrac = cx+3 |
|---|
| 520 | # loop over interatomic distances for this phase |
|---|
| 521 | WriteCIFitem('\n# MOLECULAR GEOMETRY') |
|---|
| 522 | WriteCIFitem('loop_' + |
|---|
| 523 | '\n\t_geom_bond_atom_site_label_1' + |
|---|
| 524 | '\n\t_geom_bond_atom_site_label_2' + |
|---|
| 525 | '\n\t_geom_bond_distance' + |
|---|
| 526 | '\n\t_geom_bond_site_symmetry_1' + |
|---|
| 527 | '\n\t_geom_bond_site_symmetry_2' + |
|---|
| 528 | '\n\t_geom_bond_publ_flag') |
|---|
| 529 | |
|---|
| 530 | # Note that labels should be read from self.labellist to correspond |
|---|
| 531 | # to the values reported in the atoms table and zero occupancy atoms |
|---|
| 532 | # should not be included |
|---|
| 533 | fpfx = str(phasedict['pId'])+'::Afrac:' |
|---|
| 534 | for i,at in enumerate(Atoms): |
|---|
| 535 | if self.parmDict.get(fpfx+str(i),at[cfrac]) == 0.0: continue |
|---|
| 536 | lbl = self.labellist[i] |
|---|
| 537 | |
|---|
| 538 | |
|---|
| 539 | # loop over interatomic angles for this phase |
|---|
| 540 | WriteCIFitem('loop_' + |
|---|
| 541 | '\n\t_geom_angle_atom_site_label_1' + |
|---|
| 542 | '\n\t_geom_angle_atom_site_label_2' + |
|---|
| 543 | '\n\t_geom_angle_atom_site_label_3' + |
|---|
| 544 | '\n\t_geom_angle' + |
|---|
| 545 | '\n\t_geom_angle_site_symmetry_1' + |
|---|
| 546 | '\n\t_geom_angle_site_symmetry_2' + |
|---|
| 547 | '\n\t_geom_angle_site_symmetry_3' + |
|---|
| 548 | '\n\t_geom_angle_publ_flag') |
|---|
| 549 | |
|---|
| 550 | |
|---|
| 551 | def WritePhaseInfo(phasenam): |
|---|
| 552 | WriteCIFitem('\n# phase info for '+str(phasenam) + ' follows') |
|---|
| 553 | phasedict = self.Phases[phasenam] # pointer to current phase info |
|---|
| 554 | WriteCIFitem('_pd_phase_name', phasenam) |
|---|
| 555 | pfx = str(phasedict['pId'])+'::' |
|---|
| 556 | A,sigA = G2stIO.cellFill(pfx,phasedict['General']['SGData'],self.parmDict,self.sigDict) |
|---|
| 557 | cellSig = G2stIO.getCellEsd(pfx, |
|---|
| 558 | phasedict['General']['SGData'],A, |
|---|
| 559 | self.OverallParms['Covariance']) # returns 7 vals, includes sigVol |
|---|
| 560 | cellList = G2lat.A2cell(A) + (G2lat.calc_V(A),) |
|---|
| 561 | defsigL = 3*[-0.00001] + 3*[-0.001] + [-0.01] # significance to use when no sigma |
|---|
| 562 | names = ['length_a','length_b','length_c', |
|---|
| 563 | 'angle_alpha','angle_beta ','angle_gamma', |
|---|
| 564 | 'volume'] |
|---|
| 565 | prevsig = 0 |
|---|
| 566 | for lbl,defsig,val,sig in zip(names,defsigL,cellList,cellSig): |
|---|
| 567 | if sig: |
|---|
| 568 | txt = G2mth.ValEsd(val,sig) |
|---|
| 569 | prevsig = -sig # use this as the significance for next value |
|---|
| 570 | else: |
|---|
| 571 | txt = G2mth.ValEsd(val,min(defsig,prevsig),True) |
|---|
| 572 | WriteCIFitem('_cell_'+lbl,txt) |
|---|
| 573 | |
|---|
| 574 | WriteCIFitem('_symmetry_cell_setting', |
|---|
| 575 | phasedict['General']['SGData']['SGSys']) |
|---|
| 576 | |
|---|
| 577 | spacegroup = phasedict['General']['SGData']['SpGrp'].strip() |
|---|
| 578 | # regularize capitalization and remove trailing H/R |
|---|
| 579 | spacegroup = spacegroup[0].upper() + spacegroup[1:].lower().rstrip('rh ') |
|---|
| 580 | WriteCIFitem('_symmetry_space_group_name_H-M',spacegroup) |
|---|
| 581 | |
|---|
| 582 | # generate symmetry operations including centering and center of symmetry |
|---|
| 583 | SymOpList,offsetList,symOpList,G2oprList = G2spg.AllOps( |
|---|
| 584 | phasedict['General']['SGData']) |
|---|
| 585 | WriteCIFitem('loop_ _space_group_symop_id _space_group_symop_operation_xyz') |
|---|
| 586 | for i,op in enumerate(SymOpList,start=1): |
|---|
| 587 | WriteCIFitem(' {:3d} {:}'.format(i,op.lower())) |
|---|
| 588 | |
|---|
| 589 | # loop over histogram(s) used in this phase |
|---|
| 590 | if not oneblock and not self.quickmode: |
|---|
| 591 | # report pointers to the histograms used in this phase |
|---|
| 592 | histlist = [] |
|---|
| 593 | for hist in self.Phases[phasenam]['Histograms']: |
|---|
| 594 | if self.Phases[phasenam]['Histograms'][hist]['Use']: |
|---|
| 595 | if phasebyhistDict.get(hist): |
|---|
| 596 | phasebyhistDict[hist].append(phasenam) |
|---|
| 597 | else: |
|---|
| 598 | phasebyhistDict[hist] = [phasenam,] |
|---|
| 599 | blockid = datablockidDict.get(hist) |
|---|
| 600 | if not blockid: |
|---|
| 601 | print "Internal error: no block for data. Phase "+str( |
|---|
| 602 | phasenam)+" histogram "+str(hist) |
|---|
| 603 | histlist = [] |
|---|
| 604 | break |
|---|
| 605 | histlist.append(blockid) |
|---|
| 606 | |
|---|
| 607 | if len(histlist) == 0: |
|---|
| 608 | WriteCIFitem('# Note: phase has no associated data') |
|---|
| 609 | else: |
|---|
| 610 | WriteCIFitem('loop_ _pd_block_diffractogram_id') |
|---|
| 611 | |
|---|
| 612 | # report atom params |
|---|
| 613 | if phasedict['General']['Type'] == 'nuclear': #this needs macromolecular variant, etc! |
|---|
| 614 | WriteAtomsNuclear(phasenam) |
|---|
| 615 | else: |
|---|
| 616 | raise Exception,"no export for mm coordinates implemented" |
|---|
| 617 | # report cell contents |
|---|
| 618 | WriteComposition(phasenam) |
|---|
| 619 | if not self.quickmode: # report distances and angles |
|---|
| 620 | WriteDistances(phasenam,SymOpList,offsetList,symOpList,G2oprList) |
|---|
| 621 | |
|---|
| 622 | def WritePowderData(histlbl): |
|---|
| 623 | text = '?' |
|---|
| 624 | histblk = self.Histograms[histlbl] |
|---|
| 625 | inst = histblk['Instrument Parameters'][0] |
|---|
| 626 | hId = histblk['hId'] |
|---|
| 627 | pfx = ':' + str(hId) + ':' |
|---|
| 628 | print 'TODO: powder here data for',histblk["Sample Parameters"]['InstrName'] |
|---|
| 629 | # see wrpowdhist.for & wrreflist.for |
|---|
| 630 | |
|---|
| 631 | if 'Lam1' in inst: |
|---|
| 632 | ratio = self.parmDict.get('I(L2)/I(L1)',inst['I(L2)/I(L1)'][1]) |
|---|
| 633 | sratio = self.sigDict.get('I(L2)/I(L1)',-0.0009) |
|---|
| 634 | lam1 = self.parmDict.get('Lam1',inst['Lam1'][1]) |
|---|
| 635 | slam1 = self.sigDict.get('Lam1',-0.00009) |
|---|
| 636 | lam2 = self.parmDict.get('Lam2',inst['Lam2'][1]) |
|---|
| 637 | slam2 = self.sigDict.get('Lam2',-0.00009) |
|---|
| 638 | # always assume Ka1 & Ka2 if two wavelengths are present |
|---|
| 639 | WriteCIFitem('loop_' + |
|---|
| 640 | '\n\t_diffrn_radiation_wavelength' + |
|---|
| 641 | '\n\t_diffrn_radiation_wavelength_wt' + |
|---|
| 642 | '\n\t_diffrn_radiation_type' + |
|---|
| 643 | '\n\t_diffrn_radiation_wavelength_id') |
|---|
| 644 | WriteCIFitem(' ' + PutInCol(G2mth.ValEsd(lam1,slam1),15)+ |
|---|
| 645 | PutInCol('1.0',15) + |
|---|
| 646 | PutInCol('K\\a~1~',10) + |
|---|
| 647 | PutInCol('1',5)) |
|---|
| 648 | WriteCIFitem(' ' + PutInCol(G2mth.ValEsd(lam2,slam2),15)+ |
|---|
| 649 | PutInCol(G2mth.ValEsd(ratio,sratio),15)+ |
|---|
| 650 | PutInCol('K\\a~2~',10) + |
|---|
| 651 | PutInCol('2',5)) |
|---|
| 652 | else: |
|---|
| 653 | lam1 = self.parmDict.get('Lam',inst['Lam'][1]) |
|---|
| 654 | slam1 = self.sigDict.get('Lam',-0.00009) |
|---|
| 655 | WriteCIFitem('_diffrn_radiation_wavelength',G2mth.ValEsd(lam1,slam1)) |
|---|
| 656 | |
|---|
| 657 | |
|---|
| 658 | if not oneblock: |
|---|
| 659 | if not phasebyhistDict.get(histlbl): |
|---|
| 660 | WriteCIFitem('\n# No phases associated with this data set') |
|---|
| 661 | else: |
|---|
| 662 | WriteCIFitem('\n# PHASE TABLE') |
|---|
| 663 | WriteCIFitem('loop_' + |
|---|
| 664 | '\n\t_pd_phase_id' + |
|---|
| 665 | '\n\t_pd_phase_block_id' + |
|---|
| 666 | '\n\t_pd_phase_mass_%') |
|---|
| 667 | wtFrSum = 0. |
|---|
| 668 | for phasenam in phasebyhistDict.get(histlbl): |
|---|
| 669 | hapData = self.Phases[phasenam]['Histograms'][histlbl] |
|---|
| 670 | General = self.Phases[phasenam]['General'] |
|---|
| 671 | wtFrSum += hapData['Scale'][0]*General['Mass'] |
|---|
| 672 | |
|---|
| 673 | for phasenam in phasebyhistDict.get(histlbl): |
|---|
| 674 | hapData = self.Phases[phasenam]['Histograms'][histlbl] |
|---|
| 675 | General = self.Phases[phasenam]['General'] |
|---|
| 676 | wtFr = hapData['Scale'][0]*General['Mass']/wtFrSum |
|---|
| 677 | pfx = str(self.Phases[phasenam]['pId'])+':'+str(hId)+':' |
|---|
| 678 | if pfx+'Scale' in self.sigDict: |
|---|
| 679 | sig = self.sigDict[pfx+'Scale']*wtFr/hapData['Scale'][0] |
|---|
| 680 | else: |
|---|
| 681 | sig = -0.0001 |
|---|
| 682 | WriteCIFitem( |
|---|
| 683 | ' '+ |
|---|
| 684 | str(self.Phases[phasenam]['pId']) + |
|---|
| 685 | ' '+datablockidDict[phasenam]+ |
|---|
| 686 | ' '+G2mth.ValEsd(wtFr,sig) |
|---|
| 687 | ) |
|---|
| 688 | |
|---|
| 689 | # TODO: this will need help from Bob |
|---|
| 690 | # WriteCIFitem('_pd_proc_ls_prof_R_factor','?') |
|---|
| 691 | # WriteCIFitem('_pd_proc_ls_prof_wR_factor','?') |
|---|
| 692 | # WriteCIFitem('_pd_proc_ls_prof_wR_expected','?') |
|---|
| 693 | # WriteCIFitem('_refine_ls_R_Fsqd_factor','?') |
|---|
| 694 | |
|---|
| 695 | if histblk['Instrument Parameters'][0]['Type'][1][1] == 'X': |
|---|
| 696 | WriteCIFitem('_diffrn_radiation_probe','x-ray') |
|---|
| 697 | pola = histblk['Instrument Parameters'][0].get('Polariz.') |
|---|
| 698 | if pola: |
|---|
| 699 | pfx = ':' + str(hId) + ':' |
|---|
| 700 | sig = self.sigDict.get(pfx+'Polariz.',-0.0009) |
|---|
| 701 | txt = G2mth.ValEsd(pola[1],sig) |
|---|
| 702 | WriteCIFitem('_diffrn_radiation_polarisn_ratio',txt) |
|---|
| 703 | elif histblk['Instrument Parameters'][0]['Type'][1][1] == 'N': |
|---|
| 704 | WriteCIFitem('_diffrn_radiation_probe','neutron') |
|---|
| 705 | # TOF (note that this may not be defined) |
|---|
| 706 | #if histblk['Instrument Parameters'][0]['Type'][1][2] == 'T': |
|---|
| 707 | # WriteCIFitem('_pd_meas_2theta_fixed',text) |
|---|
| 708 | |
|---|
| 709 | |
|---|
| 710 | # TODO: this will need help from Bob |
|---|
| 711 | #if not oneblock: |
|---|
| 712 | #WriteCIFitem('\n# SCATTERING FACTOR INFO') |
|---|
| 713 | #WriteCIFitem('loop_ _atom_type_symbol') |
|---|
| 714 | #if histblk['Instrument Parameters'][0]['Type'][1][1] == 'X': |
|---|
| 715 | # WriteCIFitem(' _atom_type_scat_dispersion_real') |
|---|
| 716 | # WriteCIFitem(' _atom_type_scat_dispersion_imag') |
|---|
| 717 | # for lbl in ('a1','a2','a3', 'a4', 'b1', 'b2', 'b3', 'b4', 'c'): |
|---|
| 718 | # WriteCIFitem(' _atom_type_scat_Cromer_Mann_'+lbl) |
|---|
| 719 | #elif histblk['Instrument Parameters'][0]['Type'][1][1] == 'N': |
|---|
| 720 | # WriteCIFitem(' _atom_type_scat_length_neutron') |
|---|
| 721 | #WriteCIFitem(' _atom_type_scat_source') |
|---|
| 722 | |
|---|
| 723 | WriteCIFitem('_pd_proc_ls_background_function',FormatBackground(histblk['Background'])) |
|---|
| 724 | |
|---|
| 725 | #WriteCIFitem('_exptl_absorpt_process_details','?') |
|---|
| 726 | #WriteCIFitem('_exptl_absorpt_correction_T_min','?') |
|---|
| 727 | #WriteCIFitem('_exptl_absorpt_correction_T_max','?') |
|---|
| 728 | #C extinction |
|---|
| 729 | #WRITE(IUCIF,'(A)') '# Extinction correction' |
|---|
| 730 | #CALL WRVAL(IUCIF,'_gsas_exptl_extinct_corr_T_min',TEXT(1:10)) |
|---|
| 731 | #CALL WRVAL(IUCIF,'_gsas_exptl_extinct_corr_T_max',TEXT(11:20)) |
|---|
| 732 | |
|---|
| 733 | if not oneblock: # instrumental profile terms go here |
|---|
| 734 | WriteCIFitem('_pd_proc_ls_profile_function', |
|---|
| 735 | FormatInstProfile(histblk["Instrument Parameters"])) |
|---|
| 736 | |
|---|
| 737 | #refprx = '_refln.' # mm |
|---|
| 738 | refprx = '_refln_' # normal |
|---|
| 739 | WriteCIFitem('\n# STRUCTURE FACTOR TABLE') |
|---|
| 740 | # compute maximum intensity reflection |
|---|
| 741 | Imax = 0 |
|---|
| 742 | for phasenam in histblk['Reflection Lists']: |
|---|
| 743 | scale = self.Phases[phasenam]['Histograms'][histlbl]['Scale'][0] |
|---|
| 744 | Icorr = np.array([refl[13] for refl in histblk['Reflection Lists'][phasenam]]) |
|---|
| 745 | FO2 = np.array([refl[8] for refl in histblk['Reflection Lists'][phasenam]]) |
|---|
| 746 | I100 = scale*FO2*Icorr |
|---|
| 747 | Imax = max(Imax,max(I100)) |
|---|
| 748 | |
|---|
| 749 | WriteCIFitem('loop_') |
|---|
| 750 | if len(histblk['Reflection Lists'].keys()) > 1: |
|---|
| 751 | WriteCIFitem('\t_pd_refln_phase_id') |
|---|
| 752 | WriteCIFitem('\t' + refprx + 'index_h' + |
|---|
| 753 | '\n\t' + refprx + 'index_k' + |
|---|
| 754 | '\n\t' + refprx + 'index_l' + |
|---|
| 755 | # '\n\t_pd_refln_wavelength_id' + |
|---|
| 756 | # '\n\t' + refprx + 'status' + |
|---|
| 757 | '\n\t' + refprx + 'F_squared_meas' + |
|---|
| 758 | # '\n\t' + refprx + 'F_squared_sigma' + |
|---|
| 759 | '\n\t' + refprx + 'F_squared_calc' + |
|---|
| 760 | '\n\t' + refprx + 'phase_calc' + |
|---|
| 761 | '\n\t_pd_refln_d_spacing') |
|---|
| 762 | if Imax > 0: |
|---|
| 763 | WriteCIFitem('\t_gsas_i100_meas') |
|---|
| 764 | |
|---|
| 765 | refcount = 0 |
|---|
| 766 | hklmin = None |
|---|
| 767 | hklmax = None |
|---|
| 768 | dmax = None |
|---|
| 769 | dmin = None |
|---|
| 770 | for phasenam in histblk['Reflection Lists']: |
|---|
| 771 | scale = self.Phases[phasenam]['Histograms'][histlbl]['Scale'][0] |
|---|
| 772 | phaseid = self.Phases[phasenam]['pId'] |
|---|
| 773 | refcount += len(histblk['Reflection Lists'][phasenam]) |
|---|
| 774 | for ref in histblk['Reflection Lists'][phasenam]: |
|---|
| 775 | if DEBUG: |
|---|
| 776 | print 'DEBUG: skip reflection list' |
|---|
| 777 | break |
|---|
| 778 | if hklmin is None: |
|---|
| 779 | hklmin = ref[0:3] |
|---|
| 780 | hklmax = ref[0:3] |
|---|
| 781 | dmax = dmin = ref[4] |
|---|
| 782 | if len(histblk['Reflection Lists'].keys()) > 1: |
|---|
| 783 | s = PutInCol(phaseid,2) |
|---|
| 784 | else: |
|---|
| 785 | s = "" |
|---|
| 786 | for i,hkl in enumerate(ref[0:3]): |
|---|
| 787 | hklmax[i] = max(hkl,hklmax[i]) |
|---|
| 788 | hklmin[i] = min(hkl,hklmin[i]) |
|---|
| 789 | s += PutInCol(int(hkl),4) |
|---|
| 790 | for I in ref[8:10]: |
|---|
| 791 | s += PutInCol(G2mth.ValEsd(I,-0.0009),10) |
|---|
| 792 | s += PutInCol(G2mth.ValEsd(ref[10],-0.9),7) |
|---|
| 793 | dmax = max(dmax,ref[4]) |
|---|
| 794 | dmin = min(dmin,ref[4]) |
|---|
| 795 | s += PutInCol(G2mth.ValEsd(ref[4],-0.009),8) |
|---|
| 796 | if Imax > 0: |
|---|
| 797 | I100 = 100.*scale*ref[8]*ref[13]/Imax |
|---|
| 798 | s += PutInCol(G2mth.ValEsd(I100,-0.09),6) |
|---|
| 799 | WriteCIFitem(" "+s) |
|---|
| 800 | |
|---|
| 801 | WriteCIFitem('_reflns_number_total', str(refcount)) |
|---|
| 802 | if hklmin is not None and len(histblk['Reflection Lists']) == 1: # hkl range has no meaning with multiple phases |
|---|
| 803 | WriteCIFitem('_reflns_limit_h_min', str(int(hklmin[0]))) |
|---|
| 804 | WriteCIFitem('_reflns_limit_h_max', str(int(hklmax[0]))) |
|---|
| 805 | WriteCIFitem('_reflns_limit_k_min', str(int(hklmin[1]))) |
|---|
| 806 | WriteCIFitem('_reflns_limit_k_max', str(int(hklmax[1]))) |
|---|
| 807 | WriteCIFitem('_reflns_limit_l_min', str(int(hklmin[2]))) |
|---|
| 808 | WriteCIFitem('_reflns_limit_l_max', str(int(hklmax[2]))) |
|---|
| 809 | if hklmin is not None: |
|---|
| 810 | WriteCIFitem('_reflns_d_resolution_high', G2mth.ValEsd(dmin,-0.009)) |
|---|
| 811 | WriteCIFitem('_reflns_d_resolution_low', G2mth.ValEsd(dmax,-0.0009)) |
|---|
| 812 | |
|---|
| 813 | WriteCIFitem('\n# POWDER DATA TABLE') |
|---|
| 814 | # is data fixed step? If the step varies by <0.01% treat as fixed step |
|---|
| 815 | steps = histblk['Data'][0][1:] - histblk['Data'][0][:-1] |
|---|
| 816 | if abs(max(steps)-min(steps)) > abs(max(steps))/10000.: |
|---|
| 817 | fixedstep = False |
|---|
| 818 | else: |
|---|
| 819 | fixedstep = True |
|---|
| 820 | |
|---|
| 821 | if fixedstep: # and not TOF |
|---|
| 822 | WriteCIFitem('_pd_meas_2theta_range_min', G2mth.ValEsd(histblk['Data'][0][0],-0.00009)) |
|---|
| 823 | WriteCIFitem('_pd_meas_2theta_range_max', G2mth.ValEsd(histblk['Data'][0][-1],-0.00009)) |
|---|
| 824 | WriteCIFitem('_pd_meas_2theta_range_inc', G2mth.ValEsd(steps.sum()/len(steps),-0.00009)) |
|---|
| 825 | # zero correct, if defined |
|---|
| 826 | zero = None |
|---|
| 827 | zerolst = histblk['Instrument Parameters'][0].get('Zero') |
|---|
| 828 | if zerolst: zero = zerolst[1] |
|---|
| 829 | zero = self.parmDict.get('Zero',zero) |
|---|
| 830 | # TODO: Bob is zero added or subtracted? |
|---|
| 831 | if zero: |
|---|
| 832 | WriteCIFitem('_pd_proc_2theta_range_min', G2mth.ValEsd(histblk['Data'][0][0]-zero,-0.00009)) |
|---|
| 833 | WriteCIFitem('_pd_proc_2theta_range_max', G2mth.ValEsd(histblk['Data'][0][-1]-zero,-0.00009)) |
|---|
| 834 | WriteCIFitem('_pd_proc_2theta_range_inc', G2mth.ValEsd(steps.sum()/len(steps),-0.00009)) |
|---|
| 835 | |
|---|
| 836 | if zero: |
|---|
| 837 | WriteCIFitem('_pd_proc_number_of_points', str(len(histblk['Data'][0]))) |
|---|
| 838 | else: |
|---|
| 839 | WriteCIFitem('_pd_meas_number_of_points', str(len(histblk['Data'][0]))) |
|---|
| 840 | WriteCIFitem('\nloop_') |
|---|
| 841 | # WriteCIFitem('\t_pd_proc_d_spacing') # need easy way to get this |
|---|
| 842 | if not fixedstep: |
|---|
| 843 | if zero: |
|---|
| 844 | WriteCIFitem('\t_pd_proc_2theta_corrected') |
|---|
| 845 | else: |
|---|
| 846 | WriteCIFitem('\t_pd_meas_2theta_scan') |
|---|
| 847 | # at least for now, always report weights. TODO: Should they be multiplied by weights? |
|---|
| 848 | #if countsdata: |
|---|
| 849 | # WriteCIFitem('\t_pd_meas_counts_total') |
|---|
| 850 | #else: |
|---|
| 851 | WriteCIFitem('\t_pd_meas_intensity_total') |
|---|
| 852 | WriteCIFitem('\t_pd_calc_intensity_total') |
|---|
| 853 | WriteCIFitem('\t_pd_proc_intensity_bkg_calc') |
|---|
| 854 | WriteCIFitem('\t_pd_proc_ls_weight') |
|---|
| 855 | # TODO: are data excluded? |
|---|
| 856 | for x,yobs,yw,ycalc,ybkg in zip(histblk['Data'][0], |
|---|
| 857 | histblk['Data'][1], |
|---|
| 858 | histblk['Data'][2], |
|---|
| 859 | histblk['Data'][3], |
|---|
| 860 | histblk['Data'][4]): |
|---|
| 861 | if DEBUG: |
|---|
| 862 | print 'DEBUG: skip reflection list' |
|---|
| 863 | break |
|---|
| 864 | if fixedstep: |
|---|
| 865 | s = "" |
|---|
| 866 | else: |
|---|
| 867 | s = PutInCol(G2mth.ValEsd(x-zero,-0.00009),10) |
|---|
| 868 | s += PutInCol(G2mth.ValEsd(yobs,-0.00009),14) |
|---|
| 869 | s += PutInCol(G2mth.ValEsd(ycalc,-0.00009),14) |
|---|
| 870 | s += PutInCol(G2mth.ValEsd(ybkg,-0.00009),14) |
|---|
| 871 | s += PutInCol(G2mth.ValEsd(yw,-0.000009),14) |
|---|
| 872 | WriteCIFitem(" "+s) |
|---|
| 873 | |
|---|
| 874 | def WriteSingleXtalData(histlbl): |
|---|
| 875 | histblk = self.Histograms[histlbl] |
|---|
| 876 | print 'TODO: single xtal here data for',histblk["Instrument Parameters"][0]['InstrName'] |
|---|
| 877 | |
|---|
| 878 | #refprx = '_refln.' # mm |
|---|
| 879 | refprx = '_refln_' # normal |
|---|
| 880 | |
|---|
| 881 | print histblk.keys() |
|---|
| 882 | |
|---|
| 883 | WriteCIFitem('\n# STRUCTURE FACTOR TABLE') |
|---|
| 884 | WriteCIFitem('loop_' + |
|---|
| 885 | '\n\t' + refprx + 'index_h' + |
|---|
| 886 | '\n\t' + refprx + 'index_k' + |
|---|
| 887 | '\n\t' + refprx + 'index_l' + |
|---|
| 888 | '\n\t' + refprx + 'F_squared_meas' + |
|---|
| 889 | '\n\t' + refprx + 'F_squared_sigma' + |
|---|
| 890 | '\n\t' + refprx + 'F_squared_calc' + |
|---|
| 891 | '\n\t' + refprx + 'phase_calc' + |
|---|
| 892 | '\n\t_pd_refln_d_spacing' |
|---|
| 893 | ) |
|---|
| 894 | |
|---|
| 895 | hklmin = None |
|---|
| 896 | hklmax = None |
|---|
| 897 | dmax = None |
|---|
| 898 | dmin = None |
|---|
| 899 | refcount = len(histblk['Data']) |
|---|
| 900 | for ref in histblk['Data']: |
|---|
| 901 | s = " " |
|---|
| 902 | if hklmin is None: |
|---|
| 903 | hklmin = ref[0:3] |
|---|
| 904 | hklmax = ref[0:3] |
|---|
| 905 | dmax = dmin = ref[4] |
|---|
| 906 | for i,hkl in enumerate(ref[0:3]): |
|---|
| 907 | hklmax[i] = max(hkl,hklmax[i]) |
|---|
| 908 | hklmin[i] = min(hkl,hklmin[i]) |
|---|
| 909 | s += PutInCol(int(hkl),4) |
|---|
| 910 | sig = ref[6] * ref[8] / ref[5] |
|---|
| 911 | s += PutInCol(G2mth.ValEsd(ref[8],-abs(sig/10)),12) |
|---|
| 912 | s += PutInCol(G2mth.ValEsd(sig,-abs(sig)/10.),10) |
|---|
| 913 | s += PutInCol(G2mth.ValEsd(ref[9],-abs(sig/10)),12) |
|---|
| 914 | s += PutInCol(G2mth.ValEsd(ref[10],-0.9),7) |
|---|
| 915 | dmax = max(dmax,ref[4]) |
|---|
| 916 | dmin = min(dmin,ref[4]) |
|---|
| 917 | s += PutInCol(G2mth.ValEsd(ref[4],-0.009),8) |
|---|
| 918 | WriteCIFitem(s) |
|---|
| 919 | WriteCIFitem('_reflns_number_total', str(refcount)) |
|---|
| 920 | if hklmin is not None: |
|---|
| 921 | WriteCIFitem('_reflns_limit_h_min', str(int(hklmin[0]))) |
|---|
| 922 | WriteCIFitem('_reflns_limit_h_max', str(int(hklmax[0]))) |
|---|
| 923 | WriteCIFitem('_reflns_limit_k_min', str(int(hklmin[1]))) |
|---|
| 924 | WriteCIFitem('_reflns_limit_k_max', str(int(hklmax[1]))) |
|---|
| 925 | WriteCIFitem('_reflns_limit_l_min', str(int(hklmin[2]))) |
|---|
| 926 | WriteCIFitem('_reflns_limit_l_max', str(int(hklmax[2]))) |
|---|
| 927 | WriteCIFitem('_reflns_d_resolution_high', G2mth.ValEsd(dmin,-0.009)) |
|---|
| 928 | WriteCIFitem('_reflns_d_resolution_low', G2mth.ValEsd(dmax,-0.0009)) |
|---|
| 929 | |
|---|
| 930 | #============================================================ |
|---|
| 931 | # the export process starts here |
|---|
| 932 | # also load all of the tree into a set of dicts |
|---|
| 933 | self.loadTree() |
|---|
| 934 | #self.dumpTree() |
|---|
| 935 | # create a dict with refined values and their uncertainties |
|---|
| 936 | self.loadParmDict() |
|---|
| 937 | # |
|---|
| 938 | |
|---|
| 939 | # get restraint info |
|---|
| 940 | #restraintDict = self.OverallParms.get('Restraints',{}) |
|---|
| 941 | #for i in self.OverallParms['Constraints']: |
|---|
| 942 | # print i |
|---|
| 943 | # for j in self.OverallParms['Constraints'][i]: |
|---|
| 944 | # print j |
|---|
| 945 | #return |
|---|
| 946 | |
|---|
| 947 | self.CIFdate = dt.datetime.strftime(dt.datetime.now(),"%Y-%m-%dT%H:%M") |
|---|
| 948 | # count phases, powder and single crystal histograms |
|---|
| 949 | self.nphase = len(self.Phases) |
|---|
| 950 | self.powderDict = {} |
|---|
| 951 | self.xtalDict = {} |
|---|
| 952 | for hist in self.Histograms: |
|---|
| 953 | i = self.Histograms[hist]['hId'] |
|---|
| 954 | if hist.startswith("PWDR"): |
|---|
| 955 | self.powderDict[i] = hist |
|---|
| 956 | elif hist.startswith("HKLF"): |
|---|
| 957 | self.xtalDict[i] = hist |
|---|
| 958 | # is there anything to export? |
|---|
| 959 | if self.nphase + len(self.powderDict) + len(self.xtalDict) == 0: |
|---|
| 960 | self.G2frame.ErrorDialog( |
|---|
| 961 | 'Empty project', |
|---|
| 962 | 'No data or phases to include in CIF') |
|---|
| 963 | return |
|---|
| 964 | # is there a file name defined? |
|---|
| 965 | self.CIFname = os.path.splitext( |
|---|
| 966 | os.path.split(self.G2frame.GSASprojectfile)[1] |
|---|
| 967 | )[0] |
|---|
| 968 | self.CIFname = self.CIFname.replace(' ','') |
|---|
| 969 | if not self.CIFname: |
|---|
| 970 | self.G2frame.ErrorDialog( |
|---|
| 971 | 'No GPX name', |
|---|
| 972 | 'Please save the project to provide a name') |
|---|
| 973 | return |
|---|
| 974 | # test for quick CIF mode or no data |
|---|
| 975 | self.quickmode = False |
|---|
| 976 | phasenam = phasenum = None # include all phases |
|---|
| 977 | if mode != "full" or len(self.powderDict) + len(self.xtalDict) == 0: |
|---|
| 978 | self.quickmode = True |
|---|
| 979 | oneblock = True |
|---|
| 980 | if self.nphase == 0: |
|---|
| 981 | self.G2frame.ErrorDialog( |
|---|
| 982 | 'No phase present', |
|---|
| 983 | 'Cannot create a coordinates CIF with no phases') |
|---|
| 984 | return |
|---|
| 985 | elif self.nphase > 1: # quick mode: choose one phase |
|---|
| 986 | choices = sorted(self.Phases.keys()) |
|---|
| 987 | phasenum = G2gd.ItemSelector(choices,self.G2frame) |
|---|
| 988 | if phasenum is None: return |
|---|
| 989 | phasenam = choices[phasenum] |
|---|
| 990 | # will this require a multiblock CIF? |
|---|
| 991 | elif self.nphase > 1: |
|---|
| 992 | oneblock = False |
|---|
| 993 | elif len(self.powderDict) + len(self.xtalDict) > 1: |
|---|
| 994 | oneblock = False |
|---|
| 995 | else: # one phase, one dataset, Full CIF |
|---|
| 996 | oneblock = True |
|---|
| 997 | |
|---|
| 998 | # make sure needed infomation is present |
|---|
| 999 | # get CIF author name -- required for full CIFs |
|---|
| 1000 | try: |
|---|
| 1001 | self.author = self.OverallParms['Controls'].get("Author",'').strip() |
|---|
| 1002 | except KeyError: |
|---|
| 1003 | pass |
|---|
| 1004 | while not (self.author or self.quickmode): |
|---|
| 1005 | dlg = G2gd.SingleStringDialog(self.G2frame,'Get CIF Author','Provide CIF Author name (Last, First)') |
|---|
| 1006 | if not dlg.Show(): return # cancel was pressed |
|---|
| 1007 | self.author = dlg.GetValue() |
|---|
| 1008 | dlg.Destroy() |
|---|
| 1009 | try: |
|---|
| 1010 | self.OverallParms['Controls']["Author"] = self.author # save for future |
|---|
| 1011 | except KeyError: |
|---|
| 1012 | pass |
|---|
| 1013 | self.shortauthorname = self.author.replace(',','').replace(' ','')[:20] |
|---|
| 1014 | |
|---|
| 1015 | # check the instrument name for every histogram |
|---|
| 1016 | if not self.quickmode: |
|---|
| 1017 | dictlist = [] |
|---|
| 1018 | keylist = [] |
|---|
| 1019 | lbllist = [] |
|---|
| 1020 | invalid = 0 |
|---|
| 1021 | key3 = 'InstrName' |
|---|
| 1022 | for hist in self.Histograms: |
|---|
| 1023 | if hist.startswith("PWDR"): |
|---|
| 1024 | key2 = "Sample Parameters" |
|---|
| 1025 | d = self.Histograms[hist][key2] |
|---|
| 1026 | elif hist.startswith("HKLF"): |
|---|
| 1027 | key2 = "Instrument Parameters" |
|---|
| 1028 | d = self.Histograms[hist][key2][0] |
|---|
| 1029 | |
|---|
| 1030 | lbllist.append(hist) |
|---|
| 1031 | dictlist.append(d) |
|---|
| 1032 | keylist.append(key3) |
|---|
| 1033 | instrname = d.get(key3) |
|---|
| 1034 | if instrname is None: |
|---|
| 1035 | d[key3] = '' |
|---|
| 1036 | invalid += 1 |
|---|
| 1037 | elif instrname.strip() == '': |
|---|
| 1038 | invalid += 1 |
|---|
| 1039 | if invalid: |
|---|
| 1040 | msg = "" |
|---|
| 1041 | if invalid > 3: msg = ( |
|---|
| 1042 | "\n\nNote: it may be faster to set the name for\n" |
|---|
| 1043 | "one histogram for each instrument and use the\n" |
|---|
| 1044 | "File/Copy option to duplicate the name" |
|---|
| 1045 | ) |
|---|
| 1046 | if not G2gd.CallScrolledMultiEditor( |
|---|
| 1047 | self.G2frame,dictlist,keylist, |
|---|
| 1048 | prelbl=range(1,len(dictlist)+1), |
|---|
| 1049 | postlbl=lbllist, |
|---|
| 1050 | title='Instrument names', |
|---|
| 1051 | header="Edit instrument names. Note that a non-blank\nname is required for all histograms"+msg, |
|---|
| 1052 | ): return |
|---|
| 1053 | |
|---|
| 1054 | if oneblock and not self.quickmode: |
|---|
| 1055 | # select a dataset to use (there should only be one set in one block, |
|---|
| 1056 | # but take whatever comes 1st |
|---|
| 1057 | for hist in self.Histograms: |
|---|
| 1058 | histblk = self.Histograms[hist] |
|---|
| 1059 | if hist.startswith("PWDR"): |
|---|
| 1060 | instnam = histblk["Sample Parameters"]['InstrName'] |
|---|
| 1061 | break # ignore all but 1st data histogram |
|---|
| 1062 | elif hist.startswith("HKLF"): |
|---|
| 1063 | instnam = histblk["Instrument Parameters"][0]['InstrName'] |
|---|
| 1064 | break # ignore all but 1st data histogram |
|---|
| 1065 | #====================================================================== |
|---|
| 1066 | # Start writing the CIF - single block |
|---|
| 1067 | #====================================================================== |
|---|
| 1068 | if oneblock: |
|---|
| 1069 | WriteCIFitem('data_'+self.CIFname) |
|---|
| 1070 | if phasenam is None: # if not already selected, select the first phase (should be one) |
|---|
| 1071 | phasenam = self.Phases.keys()[0] |
|---|
| 1072 | #print 'phasenam',phasenam |
|---|
| 1073 | phaseblk = self.Phases[phasenam] # pointer to current phase info |
|---|
| 1074 | if not self.quickmode: |
|---|
| 1075 | instnam = instnam.replace(' ','') |
|---|
| 1076 | WriteCIFitem('_pd_block_id', |
|---|
| 1077 | str(self.CIFdate) + "|" + str(self.CIFname) + "|" + |
|---|
| 1078 | str(self.shortauthorname) + "|" + instnam) |
|---|
| 1079 | WriteAudit() |
|---|
| 1080 | WritePubTemplate() |
|---|
| 1081 | WriteOverall() |
|---|
| 1082 | WritePhaseTemplate() |
|---|
| 1083 | # report the phase info |
|---|
| 1084 | WritePhaseInfo(phasenam) |
|---|
| 1085 | if hist.startswith("PWDR") and not self.quickmode: |
|---|
| 1086 | # preferred orientation |
|---|
| 1087 | SH = FormatSH(phasenam) |
|---|
| 1088 | MD = FormatHAPpo(phasenam) |
|---|
| 1089 | if SH and MD: |
|---|
| 1090 | WriteCIFitem('_pd_proc_ls_pref_orient_corr', SH + '\n' + MD) |
|---|
| 1091 | elif SH or MD: |
|---|
| 1092 | WriteCIFitem('_pd_proc_ls_pref_orient_corr', SH + MD) |
|---|
| 1093 | else: |
|---|
| 1094 | WriteCIFitem('_pd_proc_ls_pref_orient_corr', 'none') |
|---|
| 1095 | # report profile, since one-block: include both histogram and phase info |
|---|
| 1096 | WriteCIFitem('_pd_proc_ls_profile_function', |
|---|
| 1097 | FormatInstProfile(histblk["Instrument Parameters"]) |
|---|
| 1098 | + '\n' + |
|---|
| 1099 | FormatPhaseProfile(phasenam)) |
|---|
| 1100 | WritePowderTemplate() |
|---|
| 1101 | WritePowderData(hist) |
|---|
| 1102 | elif hist.startswith("HKLF") and not self.quickmode: |
|---|
| 1103 | WriteSnglXtalTemplate() |
|---|
| 1104 | WriteSingleXtalData(hist) |
|---|
| 1105 | else: |
|---|
| 1106 | #====================================================================== |
|---|
| 1107 | # Start writing the CIF - multiblock |
|---|
| 1108 | #====================================================================== |
|---|
| 1109 | # publication info |
|---|
| 1110 | WriteCIFitem('\ndata_'+self.CIFname+'_publ') |
|---|
| 1111 | WriteAudit() |
|---|
| 1112 | WriteCIFitem('_pd_block_id', |
|---|
| 1113 | str(self.CIFdate) + "|" + str(self.CIFname) + "|" + |
|---|
| 1114 | str(self.shortauthorname) + "|Overall") |
|---|
| 1115 | WritePubTemplate() |
|---|
| 1116 | # overall info |
|---|
| 1117 | WriteCIFitem('data_'+str(self.CIFname)+'_overall') |
|---|
| 1118 | WriteOverall() |
|---|
| 1119 | #============================================================ |
|---|
| 1120 | WriteCIFitem('# POINTERS TO PHASE AND HISTOGRAM BLOCKS') |
|---|
| 1121 | datablockidDict = {} # save block names here -- N.B. check for conflicts between phase & hist names (unlikely!) |
|---|
| 1122 | # loop over phase blocks |
|---|
| 1123 | if self.nphase > 1: |
|---|
| 1124 | loopprefix = '' |
|---|
| 1125 | WriteCIFitem('loop_ _pd_phase_block_id') |
|---|
| 1126 | else: |
|---|
| 1127 | loopprefix = '_pd_phase_block_id' |
|---|
| 1128 | |
|---|
| 1129 | for phasenam in sorted(self.Phases.keys()): |
|---|
| 1130 | i = self.Phases[phasenam]['pId'] |
|---|
| 1131 | datablockidDict[phasenam] = (str(self.CIFdate) + "|" + str(self.CIFname) + "|" + |
|---|
| 1132 | 'phase_'+ str(i) + '|' + str(self.shortauthorname)) |
|---|
| 1133 | WriteCIFitem(loopprefix,datablockidDict[phasenam]) |
|---|
| 1134 | # loop over data blocks |
|---|
| 1135 | if len(self.powderDict) + len(self.xtalDict) > 1: |
|---|
| 1136 | loopprefix = '' |
|---|
| 1137 | WriteCIFitem('loop_ _pd_block_diffractogram_id') |
|---|
| 1138 | else: |
|---|
| 1139 | loopprefix = '_pd_block_diffractogram_id' |
|---|
| 1140 | for i in sorted(self.powderDict.keys()): |
|---|
| 1141 | hist = self.powderDict[i] |
|---|
| 1142 | histblk = self.Histograms[hist] |
|---|
| 1143 | instnam = histblk["Sample Parameters"]['InstrName'] |
|---|
| 1144 | instnam = instnam.replace(' ','') |
|---|
| 1145 | i = histblk['hId'] |
|---|
| 1146 | datablockidDict[hist] = (str(self.CIFdate) + "|" + str(self.CIFname) + "|" + |
|---|
| 1147 | str(self.shortauthorname) + "|" + |
|---|
| 1148 | instnam + "_hist_"+str(i)) |
|---|
| 1149 | WriteCIFitem(loopprefix,datablockidDict[hist]) |
|---|
| 1150 | for i in sorted(self.xtalDict.keys()): |
|---|
| 1151 | hist = self.xtalDict[i] |
|---|
| 1152 | histblk = self.Histograms[hist] |
|---|
| 1153 | instnam = histblk["Instrument Parameters"][0]['InstrName'] |
|---|
| 1154 | instnam = instnam.replace(' ','') |
|---|
| 1155 | i = histblk['hId'] |
|---|
| 1156 | datablockidDict[hist] = (str(self.CIFdate) + "|" + str(self.CIFname) + "|" + |
|---|
| 1157 | str(self.shortauthorname) + "|" + |
|---|
| 1158 | instnam + "_hist_"+str(i)) |
|---|
| 1159 | WriteCIFitem(loopprefix,datablockidDict[hist]) |
|---|
| 1160 | #============================================================ |
|---|
| 1161 | # loop over phases, exporting them |
|---|
| 1162 | phasebyhistDict = {} # create a cross-reference to phases by histogram |
|---|
| 1163 | for j,phasenam in enumerate(sorted(self.Phases.keys())): |
|---|
| 1164 | i = self.Phases[phasenam]['pId'] |
|---|
| 1165 | WriteCIFitem('\ndata_'+self.CIFname+"_phase_"+str(i)) |
|---|
| 1166 | print "debug, processing ",phasenam |
|---|
| 1167 | WriteCIFitem('# Information for phase '+str(i)) |
|---|
| 1168 | WriteCIFitem('_pd_block_id',datablockidDict[phasenam]) |
|---|
| 1169 | # report the phase |
|---|
| 1170 | WritePhaseTemplate() |
|---|
| 1171 | WritePhaseInfo(phasenam) |
|---|
| 1172 | # preferred orientation |
|---|
| 1173 | SH = FormatSH(phasenam) |
|---|
| 1174 | MD = FormatHAPpo(phasenam) |
|---|
| 1175 | if SH and MD: |
|---|
| 1176 | WriteCIFitem('_pd_proc_ls_pref_orient_corr', SH + '\n' + MD) |
|---|
| 1177 | elif SH or MD: |
|---|
| 1178 | WriteCIFitem('_pd_proc_ls_pref_orient_corr', SH + MD) |
|---|
| 1179 | else: |
|---|
| 1180 | WriteCIFitem('_pd_proc_ls_pref_orient_corr', 'none') |
|---|
| 1181 | # report sample profile terms |
|---|
| 1182 | PP = FormatPhaseProfile(phasenam) |
|---|
| 1183 | if PP: |
|---|
| 1184 | WriteCIFitem('_pd_proc_ls_profile_function',PP) |
|---|
| 1185 | |
|---|
| 1186 | #============================================================ |
|---|
| 1187 | # loop over histograms, exporting them |
|---|
| 1188 | for i in sorted(self.powderDict.keys()): |
|---|
| 1189 | hist = self.powderDict[i] |
|---|
| 1190 | histblk = self.Histograms[hist] |
|---|
| 1191 | if hist.startswith("PWDR"): |
|---|
| 1192 | WriteCIFitem('\ndata_'+self.CIFname+"_pwd_"+str(i)) |
|---|
| 1193 | #instnam = histblk["Sample Parameters"]['InstrName'] |
|---|
| 1194 | # report instrumental profile terms |
|---|
| 1195 | WriteCIFitem('_pd_proc_ls_profile_function', |
|---|
| 1196 | FormatInstProfile(histblk["Instrument Parameters"])) |
|---|
| 1197 | WriteCIFitem('# Information for histogram '+str(i)+': '+hist) |
|---|
| 1198 | WriteCIFitem('_pd_block_id',datablockidDict[hist]) |
|---|
| 1199 | WritePowderTemplate() |
|---|
| 1200 | WritePowderData(hist) |
|---|
| 1201 | for i in sorted(self.xtalDict.keys()): |
|---|
| 1202 | hist = self.xtalDict[i] |
|---|
| 1203 | histblk = self.Histograms[hist] |
|---|
| 1204 | if hist.startswith("HKLF"): |
|---|
| 1205 | WriteCIFitem('\ndata_'+self.CIFname+"_sx_"+str(i)) |
|---|
| 1206 | #instnam = histblk["Instrument Parameters"][0]['InstrName'] |
|---|
| 1207 | WriteCIFitem('# Information for histogram '+str(i)+': '+hist) |
|---|
| 1208 | WriteCIFitem('_pd_block_id',datablockidDict[hist]) |
|---|
| 1209 | WriteSnglXtalTemplate() |
|---|
| 1210 | WriteSingleXtalData(hist) |
|---|
| 1211 | |
|---|
| 1212 | WriteCIFitem('#--' + 15*'eof--' + '#') |
|---|
| 1213 | |
|---|
