Source code for G2sfact_CIF

# -*- coding: utf-8 -*-
########### SVN repository information ###################
# $Date: 2020-04-24 16:06:35 +0000 (Fri, 24 Apr 2020) $
# $Author: toby $
# $Revision: 4410 $
# $URL: https://subversion.xray.aps.anl.gov/pyGSAS/trunk/imports/G2sfact_CIF.py $
# $Id: G2sfact_CIF.py 4410 2020-04-24 16:06:35Z toby $
########### SVN repository information ###################
'''
*Module G2sfact_CIF: CIF import*
-----------------------------------
Read structure factors from a CIF reflection table.

'''
# routines to read in structure factors from a CIF
# 
from __future__ import division, print_function
import numpy as np
import os.path
import GSASIIobj as G2obj
import GSASIIpath
try:
    import GSASIIctrlGUI as G2G
except ImportError:
    pass
GSASIIpath.SetVersionNumber("$Revision: 4410 $")
import CifFile as cif # PyCifRW from James Hester

[docs]class CIFhklReader(G2obj.ImportStructFactor): 'Routines to import Phase information from a CIF file' def __init__(self): super(self.__class__,self).__init__( # fancy way to self-reference extensionlist = ('.CIF','.cif','.FCF','.fcf','.HKL','.hkl'), strictExtension = False, formatName = 'CIF', longFormatName = 'CIF format structure factor file (.cif or .hkl)' ) # Validate the contents
[docs] def ContentsValidator(self, filename): 'Use standard CIF validator' fp = open(filename,'r') return self.CIFValidator(fp) fp.close()
[docs] def Reader(self, filename, ParentFrame=None, **kwarg): '''Read single crystal data from a CIF. If multiple datasets are requested, use self.repeat and buffer caching. ''' hklitems = [('_refln_index_h','_refln_index_k','_refln_index_l','_refln_index_m_1'), ('_refln.index_h','_refln.index_k','_refln.index_l','_refln.index_m_1')] cellitems = [ ('_cell_length_a','_cell_length_b','_cell_length_c', '_cell_angle_alpha','_cell_angle_beta','_cell_angle_gamma',), ('_cell.length_a','_cell.length_b','_cell.length_c', '_cell.angle_alpha','_cell.angle_beta','_cell.angle_gamma',),] Fdatanames = ('_refln_f_meas','_refln.f_meas','_refln.f_meas_au', ) F2datanames = ('_refln_f_squared_meas','_refln.f_squared_meas', '_refln_intensity_meas','_refln.intensity_meas', ) # Idatanames = ('_refln_intensity_meas','_refln.intensity_meas', # ) # not used yet # # Isignames = ('_refln_intensity_meas_sigma','_refln.intensity_meas_sigma', # ) # not used yet Fcalcnames = ('_refln_f_calc','_refln.f_calc','_refln.f_calc_au', ) F2calcnames = ('_refln_f_squared_calc','_refln.f_squared_calc', ) Fsignames = ('_refln_f_meas_sigma','_refln.f_meas_sigma','_refln.f_meas_sigma_au', '_refln_f_sigma', ) F2signames = ('_refln_f_squared_meas_sigma','_refln.f_squared_meas_sigma', '_refln_f_squared_sigma','_refln.f_squared_sigma', '_refln_intensity_meas_sigma','_refln.intensity_meas_sigma', '_refln.intensity_sigma',) phasenames = ('_refln_phase_calc','_refln.phase_calc', ) SGdataname = ('_symmetry_space_group_name_H-M', '_symmetry.space_group_name_H-M') phasenamefields = ( '_chemical_name_common', '_pd_phase_name', '_chemical_formula_sum' ) rdbuffer = kwarg.get('buffer') cf = None if self.repeat and rdbuffer is not None: cf = rdbuffer.get('lastcif') print ('Reusing previously parsed CIF') if cf is None: cf = G2obj.ReadCIF(filename) # scan blocks for reflections self.errors = 'Error during scan of blocks for datasets' blklist = [] for blk in cf.keys(): # scan for reflections, F or F2 values and cell lengths. # Ignore blocks that do not have structure factors and a cell blkkeys = [k.lower() for k in cf[blk].keys()] gotFo = False im = 0 for i in range(2): if hklitems[i][3] in blkkeys: #Super lattice reflections h,k,l,m im = 1 if hklitems[i][0] in blkkeys and hklitems[i][1] in blkkeys and hklitems[i][2] in blkkeys: dnIndex = i break else: break # no reflections for dn in Fdatanames: if dn in blkkeys: blklist.append(blk) gotFo = True break if gotFo: break for dn in F2datanames: if dn in blkkeys: blklist.append(blk) break else: break if not blklist: selblk = None # no block to choose elif len(blklist) == 1: # only one choice selblk = 0 else: # choose from options choice = [] for blknm in blklist: choice.append('') # accumulate some info about this phase choice[-1] += blknm + ': ' for i in phasenamefields: # get a name for the phase name = cf[blknm].get(i) if name is None or name == '?' or name == '.': continue else: choice[-1] += name.strip()[:20] + ', ' break s = '' fmt = "%.2f," for i,key in enumerate(cellitems[dnIndex]): if i == 3: fmt = "%.f," if i == 5: fmt = "%.f" val = cf[blknm].get(key) if val is None: break s += fmt % cif.get_number_with_esd(val)[0] if s: choice[-1] += ', cell: ' + s for dn in SGdataname: sg = cf[blknm].get(dn) if sg: choice[-1] += ', (' + sg.strip() + ')' break choice.append('Import all of the above') if self.repeat: # we were called to repeat the read selblk = self.repeatcount self.repeatcount += 1 if self.repeatcount >= len(blklist): self.repeat = False else: selblk = G2G.BlockSelector( choice, ParentFrame=ParentFrame, title='Select a dataset from one the CIF data_ blocks below', size=(600,100), header='Dataset Selector') self.errors = 'Error during reading of selected block' if selblk is None: return False # no block selected or available if selblk >= len(blklist): # all blocks selected selblk = 0 self.repeat = True if rdbuffer is not None: rdbuffer['lastcif'] = cf # save the parsed cif for the next loop self.repeatcount = 1 blknm = blklist[selblk] blk = cf[blklist[selblk]] self.objname = os.path.basename(filename)+':'+str(blknm) self.errors = 'Error during reading of reflections' # read in reflections try: refloop = blk.GetLoop(hklitems[0][0]) dnIndex = 0 except KeyError: try: refloop = blk.GetLoop(hklitems[1][0]) dnIndex = 1 except KeyError: self.errors += "\nUnexpected: '_refln[-.]index_h not found!" return False itemkeys = {} # prepare an index to the CIF reflection loop for i,key in enumerate(refloop.keys()): itemkeys[key.lower()] = i # scan for obs & sig data names: F2dn = None Fdn = None F2cdn = None Fcdn = None F2sdn = None Fsdn = None Phdn = None for dn in F2datanames: if dn in itemkeys: F2dn = dn for dm in F2signames: if dm in itemkeys: F2sdn = dm break break else: for dn in Fdatanames: if dn in itemkeys: Fdn = dn for dm in Fsignames: if dm in itemkeys: Fsdn = dm break break else: msg = "\nno F or F2 loop value found in file\n" msg += "A CIF reflection file needs to have at least one of\n" for dn in F2datanames+Fdatanames: msg += dn + ', ' self.errors += msg return False # scan for calc data names - might be different! for dm in F2calcnames: if dm in itemkeys: F2cdn = dm break for dm in Fcalcnames: if dm in itemkeys: Fcdn = dm break for dn in phasenames: if dn in itemkeys: Phdn = dn break # loop over all reflections for item in refloop: F2c = 0.0 sigF2 = 0.0 HKL = [] try: for i in hklitems[dnIndex][:3+im]: # '_refln[._]index_[hkl]' num = itemkeys.get(i) try: HKL.append(int(item[num])) except: HKL.append('.') #h,k,l,tw,dsp,Fo2,sig,Fc2,Fot2,Fct2,phase,Ext if im: ref = HKL+[1,0,0,0,1, 0,0,0,0,0, 0,0] else: ref = HKL+[1,0,0,1,0, 0,0,0,0,0, 0] if F2dn: F2 = item[itemkeys[F2dn]] if '(' in F2: F2, sigF2 = cif.get_number_with_esd(F2) F2 = float(F2) sigF2 = float(sigF2) elif F2sdn: F2 = float(F2) sigF2 = float(item[itemkeys[F2sdn]]) else: F2 = float(F2) else: F = item[itemkeys[Fdn]] if '(' in F: F, sig = cif.get_number_with_esd(F) elif Fsdn: F = float(F) sig = float(item[itemkeys[Fsdn]]) else: F = float(F) sig = 0.0 F2 = F**2 sigF2 = 2.0*F*sig try: if F2cdn: F2c = float(item[itemkeys[F2cdn]]) except: pass try: if Fcdn: Fc = float(item[itemkeys[Fcdn]]) F2c = Fc*Fc except: pass ref[8+im] = F2 ref[5+im] = F2 ref[6+im] = sigF2 ref[9+im] = F2c ref[7+im] = F2c try: if Phdn: ref[10+im] = float(item[itemkeys[Phdn]]) except: pass except: continue # skip over incompletely parsed reflections self.RefDict['RefList'].append(ref) # self.RefDict['FF'].append({}) self.RefDict['RefList'] = np.array(self.RefDict['RefList']) self.errors = 'Error during reading of dataset parameters' Type = 'SXC' if blk.get('_diffrn_radiation_probe'): if blk['_diffrn_radiation_probe'] == 'neutron': Type = 'SNC' elif blk.get('_diffrn_radiation.probe'): if blk['_diffrn_radiation.probe'] == 'neutron': Type = 'SNC' self.RefDict['Type'] = Type self.RefDict['Super'] = im if blk.get('_diffrn_radiation_wavelength'): wave = float(blk['_diffrn_radiation_wavelength']) elif blk.get('_diffrn_radiation.wavelength'): wave = float(blk['_diffrn_radiation.wavelength']) else: wave = 0.70926 self.UpdateParameters(Type=Type,Wave=wave) # histogram type return True