Source code for GSASIIstrIO

# -*- coding: utf-8 -*-
########### SVN repository information ###################
# $Date: 2021-06-24 21:32:34 +0000 (Thu, 24 Jun 2021) $
# $Author: vondreele $
# $Revision: 4974 $
# $URL: https://subversion.xray.aps.anl.gov/pyGSAS/trunk/GSASIIstrIO.py $
# $Id: GSASIIstrIO.py 4974 2021-06-24 21:32:34Z vondreele $
########### SVN repository information ###################
'''
*GSASIIstrIO: structure I/O routines*
-------------------------------------

Contains routines for reading from GPX files and printing to the .LST file. 
Used for refinements and in G2scriptable. 

Should not contain any wxpython references as this should be able to be used
in non-GUI settings. 

'''
from __future__ import division, print_function
import platform
import os
import os.path as ospath
import time
import math
import copy
if '2' in platform.python_version_tuple()[0]:
    import cPickle
else:
    import pickle as cPickle
import numpy as np
import numpy.ma as ma
import GSASIIpath
GSASIIpath.SetVersionNumber("$Revision: 4974 $")
import GSASIIElem as G2el
import GSASIIlattice as G2lat
import GSASIIspc as G2spc
import GSASIIobj as G2obj
import GSASIImapvars as G2mv
import GSASIImath as G2mth
import GSASIIfiles as G2fil
import GSASIIpy3 as G2py3

sind = lambda x: np.sin(x*np.pi/180.)
cosd = lambda x: np.cos(x*np.pi/180.)
tand = lambda x: np.tan(x*np.pi/180.)
asind = lambda x: 180.*np.arcsin(x)/np.pi
acosd = lambda x: 180.*np.arccos(x)/np.pi
atan2d = lambda y,x: 180.*np.arctan2(y,x)/np.pi
    
ateln2 = 8.0*math.log(2.0)

#===============================================================================
# Support for GPX file reading
#===============================================================================
def cPickleLoad(fp):
    if '2' in platform.python_version_tuple()[0]:
        return cPickle.load(fp)
    else:
       return cPickle.load(fp,encoding='latin-1')

gpxIndex = {}; gpxNamelist = []; gpxSize = -1
'''Global variables used in :func:`IndexGPX` to see if file has changed 
(gpxSize) and to index where to find each 1st-level tree item in the file.
'''

[docs]def GetFullGPX(GPXfile): ''' Returns complete contents of GSASII gpx file. Used in :func:`GSASIIscriptable.LoadDictFromProjFile`. :param str GPXfile: full .gpx file name :returns: Project,nameList, where * Project (dict) is a representation of gpx file following the GSAS-II tree structure for each item: key = tree name (e.g. 'Controls', 'Restraints', etc.), data is dict * nameList (list) has names of main tree entries & subentries used to reconstruct project file ''' return IndexGPX(GPXfile,read=True)
[docs]def IndexGPX(GPXfile,read=False): '''Create an index to a GPX file, optionally the file into memory. The byte size of the GPX file is saved. If this routine is called again, and if this size does not change, indexing is not repeated since it is assumed the file has not changed (this can be overriden by setting read=True). :param str GPXfile: full .gpx file name :returns: Project,nameList if read=, where * Project (dict) is a representation of gpx file following the GSAS-II tree structure for each item: key = tree name (e.g. 'Controls', 'Restraints', etc.), data is dict * nameList (list) has names of main tree entries & subentries used to reconstruct project file ''' global gpxSize if gpxSize == os.path.getsize(GPXfile) and not read: return global gpxIndex gpxIndex = {} global gpxNamelist gpxNamelist = [] if GSASIIpath.GetConfigValue('debug'): print("DBG: Indexing GPX file") gpxSize = os.path.getsize(GPXfile) fp = open(GPXfile,'rb') Project = {} try: while True: pos = fp.tell() data = cPickleLoad(fp) datum = data[0] gpxIndex[datum[0]] = pos if read: Project[datum[0]] = {'data':datum[1]} gpxNamelist.append([datum[0],]) for datus in data[1:]: if read: Project[datum[0]][datus[0]] = datus[1] gpxNamelist[-1].append(datus[0]) # print('project load successful') except EOFError: pass except Exception as msg: G2fil.G2Print('Read Error:',msg) raise Exception("Error reading file "+str(GPXfile)+". This is not a GSAS-II .gpx file") finally: fp.close() if read: return Project,gpxNamelist
[docs]def GetControls(GPXfile): ''' Returns dictionary of control items found in GSASII gpx file :param str GPXfile: full .gpx file name :return: dictionary of control items ''' Controls = copy.deepcopy(G2obj.DefaultControls) IndexGPX(GPXfile) pos = gpxIndex.get('Controls') if pos is None: G2fil.G2Print('Warning: Controls not found in gpx file {}'.format(GPXfile)) return Controls fp = open(GPXfile,'rb') fp.seek(pos) datum = cPickleLoad(fp)[0] fp.close() Controls.update(datum[1]) return Controls
[docs]def GetConstraints(GPXfile): '''Read the constraints from the GPX file and interpret them called in :func:`ReadCheckConstraints`, :func:`GSASIIstrMain.Refine` and :func:`GSASIIstrMain.SeqRefine`. ''' IndexGPX(GPXfile) fl = open(GPXfile,'rb') pos = gpxIndex.get('Constraints') if pos is None: raise Exception("No constraints in GPX file") fl.seek(pos) datum = cPickleLoad(fl)[0] fl.close() constList = [] for item in datum[1]: if item.startswith('_'): continue constList += datum[1][item] constDict,fixedList,ignored = ProcessConstraints(constList) if ignored: G2fil.G2Print ('Warning: {} Constraints were rejected. Was a constrained phase, histogram or atom deleted?'.format(ignored)) return constDict,fixedList
[docs]def ProcessConstraints(constList): """Interpret the constraints in the constList input into a dictionary, etc. All :class:`GSASIIobj.G2VarObj` objects are mapped to the appropriate phase/hist/atoms based on the object internals (random Ids). If this can't be done (if a phase has been deleted, etc.), the variable is ignored. If the constraint cannot be used due to too many dropped variables, it is counted as ignored. NB: this processing does not include symmetry imposed constraints :param list constList: a list of lists where each item in the outer list specifies a constraint of some form, as described in the :mod:`GSASIIobj` :ref:`Constraint definition <Constraint_definitions_table>`. :returns: a tuple of (constDict,fixedList,ignored) where: * constDict (list of dicts) contains the constraint relationships * fixedList (list) contains the fixed values for each type of constraint. * ignored (int) counts the number of invalid constraint items (should always be zero!) """ constDict = [] fixedList = [] ignored = 0 namedVarList = [] for item in constList: if item[-1] == 'h': # process a hold fixedList.append('0') var = str(item[0][1]) if '?' not in var: constDict.append({var:0.0}) else: ignored += 1 elif item[-1] == 'f': # process a new variable fixedList.append(None) D = {} varyFlag = item[-2] varname = item[-3] for term in item[:-3]: var = str(term[1]) if '?' not in var: D[var] = term[0] if len(D) > 1: # add extra dict terms for input variable name and vary flag if varname is not None: varname = str(varname) # in case this is a G2VarObj if varname.startswith(':'): D['_name'] = varname else: D['_name'] = '::nv-' + varname D['_name'] = G2obj.MakeUniqueLabel(D['_name'],namedVarList) D['_vary'] = varyFlag == True # force to bool constDict.append(D) else: ignored += 1 #constFlag[-1] = ['Vary'] elif item[-1] == 'c': # process a contraint relationship D = {} for term in item[:-3]: var = str(term[1]) if '?' not in var: D[var] = term[0] if len(D) >= 1: fixedList.append(str(item[-3])) constDict.append(D) else: ignored += 1 elif item[-1] == 'e': # process an equivalence firstmult = None eqlist = [] for term in item[:-3]: if term[0] == 0: term[0] = 1.0 var = str(term[1]) if '?' in var: continue if firstmult is None: firstmult = term[0] firstvar = var else: eqlist.append([var,firstmult/term[0]]) if len(eqlist) > 0: G2mv.StoreEquivalence(firstvar,eqlist,False) else: ignored += 1 else: ignored += 1 return constDict,fixedList,ignored
[docs]def ReadCheckConstraints(GPXfile, seqHist=None): '''Load constraints and related info and return any error or warning messages This is done from the GPX file rather than the tree. :param dict seqHist: defines a specific histogram to be loaded for a sequential refinement, if None (default) all are loaded. ''' # init constraints G2mv.InitVars() # get variables Histograms,Phases = GetUsedHistogramsAndPhases(GPXfile) if not Phases: return 'Error: No phases or no histograms in phases!','' if not Histograms: return 'Error: no diffraction data','' constrDict,fixedList = GetConstraints(GPXfile) # load user constraints before internally generated ones if seqHist: Histograms = {seqHist:Histograms[seqHist]} # sequential fit: only need one histogram rigidbodyDict = GetRigidBodies(GPXfile) rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]}) rbVary,rbDict = GetRigidBodyModels(rigidbodyDict,Print=False) Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables,MFtables,maxSSwave = \ GetPhaseData(Phases,RestraintDict=None,rbIds=rbIds,Print=False) # generates atom symmetry constraints hapVary,hapDict,controlDict = GetHistogramPhaseData(Phases,Histograms,Print=False,resetRefList=False) histVary,histDict,controlDict = GetHistogramData(Histograms,Print=False) varyList = rbVary+phaseVary+hapVary+histVary msg = G2mv.EvaluateMultipliers(constrDict,phaseDict,hapDict,histDict) if msg: return 'Unable to interpret multiplier(s): '+msg,'' errmsg, warnmsg = G2mv.CheckConstraints(varyList,constrDict,fixedList) if errmsg: # print some diagnostic info on the constraints G2fil.G2Print('Error in constraints:\n'+errmsg+ '\nRefinement not possible due to conflict in constraints, see below:\n') G2fil.G2Print(G2mv.VarRemapShow(varyList,True),mode='error') return errmsg, warnmsg
def makeTwinFrConstr(Phases,Histograms,hapVary): TwConstr = [] TwFixed = [] for Phase in Phases: pId = Phases[Phase]['pId'] for Histogram in Phases[Phase]['Histograms']: try: hId = Histograms[Histogram]['hId'] phfx = '%d:%d:'%(pId,hId) if phfx+'TwinFr:0' in hapVary: TwFixed.append('1.0') #constraint value nTwin = len(Phases[Phase]['Histograms'][Histogram]['Twins']) TwConstr.append({phfx+'TwinFr:'+str(i):'1.0' for i in range(nTwin)}) except KeyError: #unused histograms? pass return TwConstr,TwFixed
[docs]def GetRestraints(GPXfile): '''Read the restraints from the GPX file. Throws an exception if not found in the .GPX file ''' IndexGPX(GPXfile) fl = open(GPXfile,'rb') pos = gpxIndex.get('Restraints') if pos is None: raise Exception("No Restraints in GPX file") fl.seek(pos) datum = cPickleLoad(fl)[0] fl.close() return datum[1]
[docs]def GetRigidBodies(GPXfile): '''Read the rigid body models from the GPX file ''' IndexGPX(GPXfile) fl = open(GPXfile,'rb') pos = gpxIndex.get('Rigid bodies') if pos is None: raise Exception("No Rigid bodies in GPX file") fl.seek(pos) datum = cPickleLoad(fl)[0] fl.close() return datum[1]
[docs]def GetFprime(controlDict,Histograms): 'Needs a doc string' FFtables = controlDict['FFtables'] if not FFtables: return histoList = list(Histograms.keys()) histoList.sort() for histogram in histoList: if histogram[:4] in ['PWDR','HKLF']: Histogram = Histograms[histogram] hId = Histogram['hId'] hfx = ':%d:'%(hId) if 'X' in controlDict[hfx+'histType']: keV = controlDict[hfx+'keV'] for El in FFtables: Orbs = G2el.GetXsectionCoeff(El.split('+')[0].split('-')[0]) FP,FPP,Mu = G2el.FPcalc(Orbs, keV) FFtables[El][hfx+'FP'] = FP FFtables[El][hfx+'FPP'] = FPP
def PrintFprime(FFtables,pfx,pFile): pFile.write('\n Resonant form factors:(ref: D.T. Cromer & D.A. Liberman (1981), Acta Cryst. A37, 267-268.)\n') Elstr = ' Element:' FPstr = " f' :" FPPstr = ' f" :' for El in FFtables: Elstr += ' %8s'%(El) FPstr += ' %8.3f'%(FFtables[El][pfx+'FP']) FPPstr += ' %8.3f'%(FFtables[El][pfx+'FPP']) pFile.write(Elstr+'\n') pFile.write(FPstr+'\n') pFile.write(FPPstr+'\n') def PrintBlength(BLtables,wave,pFile): pFile.write('\n Resonant neutron scattering lengths:\n') Elstr = ' Element:' FPstr = " b' :" FPPstr = ' b" :' for El in BLtables: BP,BPP = G2el.BlenResCW([El,],BLtables,wave) Elstr += ' %8s'%(El) FPstr += ' %8.3f'%(BP) FPPstr += ' %8.3f'%(BPP) pFile.write(Elstr+'\n') pFile.write(FPstr+'\n') pFile.write(FPPstr+'\n')
[docs]def PrintISOmodes(pFile,Phases,parmDict,sigDict): '''Prints the values for the ISODISTORT modes into the project's .lst file after a refinement. ''' for phase in Phases: if 'ISODISTORT' not in Phases[phase]: continue data = Phases[phase] ISO = data['ISODISTORT'] if 'G2VarList' in ISO: deltaList = [] for gv,Ilbl in zip(ISO['G2VarList'],ISO['IsoVarList']): dvar = gv.varname() var = dvar.replace('::dA','::A') albl = Ilbl[:Ilbl.rfind('_')] v = Ilbl[Ilbl.rfind('_')+1:] pval = ISO['ParentStructure'][albl][['dx','dy','dz'].index(v)] if var in parmDict: cval = parmDict[var] else: print('PrintISOmodes Error: Atom not found',"No value found for parameter "+str(var)) return deltaList.append(cval-pval) modeVals = np.inner(ISO['Var2ModeMatrix'],deltaList) if 'G2OccVarList' in ISO: deltaOccList = [] for gv,Ilbl in zip(ISO['G2OccVarList'],ISO['OccVarList']): var = gv.varname() albl = Ilbl[:Ilbl.rfind('_')] pval = ISO['BaseOcc'][albl] if var in parmDict: cval = parmDict[var] else: print('PrintISOmodes Error: Atom not found',"No value found for parameter "+str(var)) return deltaOccList.append(cval-pval) modeOccVals = np.inner(ISO['Var2OccMatrix'],deltaOccList) if 'G2VarList' in ISO: pFile.write('\n ISODISTORT Displacive Modes for phase {}\n'.format(data['General'].get('Name',''))) l = str(max([len(i) for i in ISO['IsoModeList']])+3) fmt = ' {:'+l+'}{}' for var,val,norm,G2mode in zip( ISO['IsoModeList'],modeVals,ISO['NormList'],ISO['G2ModeList'] ): try: value = G2py3.FormatSigFigs(val/norm) if str(G2mode) in sigDict: value = G2mth.ValEsd(val/norm,sigDict[str(G2mode)]/norm) except TypeError: value = '?' pFile.write(fmt.format(var,value)+'\n') if 'G2OccVarList' in ISO: pFile.write('\n ISODISTORT Occupancy Modes for phase {}\n'.format(data['General'].get('Name',''))) l = str(max([len(i) for i in ISO['OccModeList']])+3) fmt = ' {:'+l+'}{}' for var,val,norm,G2mode in zip( ISO['OccModeList'],modeOccVals,ISO['OccNormList'],ISO['G2OccModeList'] ): try: value = G2py3.FormatSigFigs(val/norm) if str(G2mode) in sigDict: value = G2mth.ValEsd(val/norm,sigDict[str(G2mode)]/norm) except TypeError: value = '?' pFile.write(fmt.format(var,value)+'\n')
[docs]def GetPhaseNames(GPXfile): ''' Returns a list of phase names found under 'Phases' in GSASII gpx file :param str GPXfile: full .gpx file name :return: list of phase names ''' IndexGPX(GPXfile) fl = open(GPXfile,'rb') pos = gpxIndex.get('Phases') if pos is None: raise Exception("No Phases in GPX file") fl.seek(pos) data = cPickleLoad(fl) fl.close() return [datus[0] for datus in data[1:]]
[docs]def GetAllPhaseData(GPXfile,PhaseName): ''' Returns the entire dictionary for PhaseName from GSASII gpx file :param str GPXfile: full .gpx file name :param str PhaseName: phase name :return: phase dictionary or None if PhaseName is not present ''' IndexGPX(GPXfile) fl = open(GPXfile,'rb') pos = gpxIndex.get('Phases') if pos is None: raise Exception("No Phases in GPX file") fl.seek(pos) data = cPickleLoad(fl) fl.close() for datus in data[1:]: if datus[0] == PhaseName: return datus[1]
[docs]def GetHistograms(GPXfile,hNames): """ Returns a dictionary of histograms found in GSASII gpx file :param str GPXfile: full .gpx file name :param str hNames: list of histogram names :return: dictionary of histograms (types = PWDR & HKLF) """ IndexGPX(GPXfile) fl = open(GPXfile,'rb') Histograms = {} for hist in hNames: pos = gpxIndex.get(hist) if pos is None: raise Exception("Histogram {} not found in GPX file".format(hist)) fl.seek(pos) data = cPickleLoad(fl) datum = data[0] if 'PWDR' in hist[:4]: PWDRdata = {} PWDRdata.update(datum[1][0]) #weight factor PWDRdata['Data'] = ma.array(ma.getdata(datum[1][1])) #masked powder data arrays/clear previous masks PWDRdata[data[2][0]] = data[2][1] #Limits & excluded regions (if any) PWDRdata[data[3][0]] = data[3][1] #Background PWDRdata[data[4][0]] = data[4][1] #Instrument parameters PWDRdata[data[5][0]] = data[5][1] #Sample parameters try: PWDRdata[data[9][0]] = data[9][1] #Reflection lists might be missing except IndexError: PWDRdata['Reflection Lists'] = {} PWDRdata['Residuals'] = {} Histograms[hist] = PWDRdata elif 'HKLF' in hist[:4]: HKLFdata = {} HKLFdata.update(datum[1][0]) #weight factor #patch if 'list' in str(type(datum[1][1])): #if isinstance(datum[1][1],list): RefData = {'RefList':[],'FF':{}} for ref in datum[1][1]: RefData['RefList'].append(ref[:11]+[ref[13],]) RefData['RefList'] = np.array(RefData['RefList']) datum[1][1] = RefData #end patch datum[1][1]['FF'] = {} HKLFdata['Data'] = datum[1][1] HKLFdata['Instrument Parameters'] = dict(data)['Instrument Parameters'] HKLFdata['Reflection Lists'] = None HKLFdata['Residuals'] = {} Histograms[hist] = HKLFdata fl.close() return Histograms
[docs]def GetHistogramNames(GPXfile,hTypes): """ Returns a list of histogram names found in a GSAS-II .gpx file that match specifed histogram types. Names are returned in the order they appear in the file. :param str GPXfile: full .gpx file name :param str hTypes: list of histogram types :return: list of histogram names (types = PWDR & HKLF) """ IndexGPX(GPXfile) return [n[0] for n in gpxNamelist if n[0][:4] in hTypes]
[docs]def GetUsedHistogramsAndPhases(GPXfile): ''' Returns all histograms that are found in any phase and any phase that uses a histogram. This also assigns numbers to used phases and histograms by the order they appear in the file. :param str GPXfile: full .gpx file name :returns: (Histograms,Phases) * Histograms = dictionary of histograms as {name:data,...} * Phases = dictionary of phases that use histograms ''' phaseNames = GetPhaseNames(GPXfile) histoList = GetHistogramNames(GPXfile,['PWDR','HKLF']) allHistograms = GetHistograms(GPXfile,histoList) phaseData = {} for name in phaseNames: phaseData[name] = GetAllPhaseData(GPXfile,name) Histograms = {} Phases = {} for phase in phaseData: Phase = phaseData[phase] if Phase['General']['Type'] == 'faulted': continue #don't use faulted phases! if Phase['Histograms']: for hist in Phase['Histograms']: if 'Use' not in Phase['Histograms'][hist]: #patch Phase['Histograms'][hist]['Use'] = True if Phase['Histograms'][hist]['Use'] and phase not in Phases: pId = phaseNames.index(phase) Phase['pId'] = pId Phases[phase] = Phase if hist not in Histograms and Phase['Histograms'][hist]['Use']: try: Histograms[hist] = allHistograms[hist] hId = histoList.index(hist) Histograms[hist]['hId'] = hId except KeyError: # would happen if a referenced histogram were # renamed or deleted G2fil.G2Print('Warning: For phase "'+phase+ '" unresolved reference to histogram "'+hist+'"') # load the fix background info into the histograms for hist in Histograms: if 'Background' not in Histograms[hist]: continue fixedBkg = Histograms[hist]['Background'][1].get('background PWDR') if fixedBkg: if not fixedBkg[0]: continue # patch: add refinement flag, if needed if len(fixedBkg) == 2: fixedBkg += [False] h = Histograms[hist]['Background'][1] try: Limits = Histograms[hist]['Limits'][1] x = Histograms[hist]['Data'][0] xB = np.searchsorted(x,Limits[0]) xF = np.searchsorted(x,Limits[1])+1 h['fixback'] = allHistograms[fixedBkg[0]]['Data'][1][xB:xF] except KeyError: # would happen if a referenced histogram were renamed or deleted G2fil.G2Print('Warning: For hist "{}" unresolved background reference to hist "{}"' .format(hist,fixedBkg[0])) G2obj.IndexAllIds(Histograms=Histograms,Phases=Phases) return Histograms,Phases
[docs]def getBackupName(GPXfile,makeBack): ''' Get the name for the backup .gpx file name :param str GPXfile: full .gpx file name :param bool makeBack: if True the name of a new file is returned, if False the name of the last file that exists is returned :returns: the name of a backup file ''' GPXpath,GPXname = ospath.split(GPXfile) if GPXpath == '': GPXpath = '.' Name = ospath.splitext(GPXname)[0] files = os.listdir(GPXpath) last = 0 for name in files: name = name.split('.') if len(name) == 3 and name[0] == Name and 'bak' in name[1]: if makeBack: last = max(last,int(name[1].strip('bak'))+1) else: last = max(last,int(name[1].strip('bak'))) GPXback = ospath.join(GPXpath,ospath.splitext(GPXname)[0]+'.bak'+str(last)+'.gpx') return GPXback
[docs]def GPXBackup(GPXfile,makeBack=True): ''' makes a backup of the specified .gpx file :param str GPXfile: full .gpx file name :param bool makeBack: if True (default), the backup is written to a new file; if False, the last backup is overwritten :returns: the name of the backup file that was written ''' import distutils.file_util as dfu GPXback = getBackupName(GPXfile,makeBack) tries = 0 while True: try: dfu.copy_file(GPXfile,GPXback) break except: tries += 1 if tries > 10: return GPXfile #failed! time.sleep(1) #just wait a second! return GPXback
[docs]def SetUsedHistogramsAndPhases(GPXfile,Histograms,Phases,RigidBodies,CovData,parmFrozenList,makeBack=True): ''' Updates gpxfile from all histograms that are found in any phase and any phase that used a histogram. Also updates rigid body definitions. This is used for non-sequential fits, but not for sequential fitting. :param str GPXfile: full .gpx file name :param dict Histograms: dictionary of histograms as {name:data,...} :param dict Phases: dictionary of phases that use histograms :param dict RigidBodies: dictionary of rigid bodies :param dict CovData: dictionary of refined variables, varyList, & covariance matrix :param list parmFrozenList: list of parameters (as str) that are frozen due to limits; converted to :class:`GSASIIobj.G2VarObj` objects. :param bool makeBack: True if new backup of .gpx file is to be made; else use the last one made ''' import distutils.file_util as dfu GPXback = GPXBackup(GPXfile,makeBack) G2fil.G2Print ('Read from file:'+GPXback) G2fil.G2Print ('Save to file :'+GPXfile) infile = open(GPXback,'rb') outfile = open(GPXfile,'wb') while True: try: data = cPickleLoad(infile) except EOFError: break datum = data[0] # print 'read: ',datum[0] if datum[0] == 'Phases': for iphase in range(len(data)): if data[iphase][0] in Phases: phaseName = data[iphase][0] data[iphase][1].update(Phases[phaseName]) elif datum[0] == 'Covariance': data[0][1] = CovData elif datum[0] == 'Rigid bodies': data[0][1] = RigidBodies elif datum[0] == 'Controls': Controls = data[0][1] if 'parmFrozen' not in Controls: Controls['parmFrozen'] = {} Controls['parmFrozen']['FrozenList'] = [ i if type(i) is G2obj.G2VarObj else G2obj.G2VarObj(i) for i in parmFrozenList] try: histogram = Histograms[datum[0]] # print 'found ',datum[0] data[0][1][1] = histogram['Data'] data[0][1][0].update(histogram['Residuals']) for datus in data[1:]: # print ' read: ',datus[0] if datus[0] in ['Instrument Parameters','Sample Parameters','Reflection Lists']: datus[1] = histogram[datus[0]] if datus[0] == 'Background': # remove fixed background from file d1 = {key:histogram['Background'][1][key] for key in histogram['Background'][1] if not key.startswith('_fixed')} datus[1] = copy.deepcopy(histogram['Background']) datus[1][1] = d1 except KeyError: pass try: cPickle.dump(data,outfile,1) except AttributeError: G2fil.G2Print ('ERROR - bad data in least squares result') infile.close() outfile.close() dfu.copy_file(GPXback,GPXfile) G2fil.G2Print ('GPX file save failed - old version retained',mode='error') return infile.close() outfile.close() G2fil.G2Print ('GPX file save successful')
[docs]def GetSeqResult(GPXfile): ''' Returns the sequential results table information from a GPX file. Called at the beginning of :meth:`GSASIIstrMain.SeqRefine` :param str GPXfile: full .gpx file name :returns: a dict containing the sequential results table ''' IndexGPX(GPXfile) pos = gpxIndex.get('Sequential results') if pos is None: return {} fl = open(GPXfile,'rb') fl.seek(pos) datum = cPickleLoad(fl)[0] fl.close() return datum[1]
[docs]def SetupSeqSavePhases(GPXfile): '''Initialize the files used to save intermediate results from sequential fits. ''' IndexGPX(GPXfile) # load initial Phase results from GPX fl = open(GPXfile,'rb') pos = gpxIndex.get('Phases') if pos is None: raise Exception("No Phases in GPX file") fl.seek(pos) data = cPickleLoad(fl) fl.close() # create GPX-like file to store latest Phase info; init with start vals GPXphase = os.path.splitext(GPXfile)[0]+'.seqPhase' fp = open(GPXphase,'wb') cPickle.dump(data,fp,1) fp.close() # create empty file for histogram info GPXhist = os.path.splitext(GPXfile)[0]+'.seqHist' fp = open(GPXhist,'wb') fp.close()
[docs]def SaveUpdatedHistogramsAndPhases(GPXfile,Histograms,Phases,RigidBodies,CovData,parmFrozen): ''' Save phase and histogram information into "pseudo-gpx" files. The phase information is overwritten each time this is called, but histogram information is appended after each sequential step. :param str GPXfile: full .gpx file name :param dict Histograms: dictionary of histograms as {name:data,...} :param dict Phases: dictionary of phases that use histograms :param dict RigidBodies: dictionary of rigid bodies :param dict CovData: dictionary of refined variables, varyList, & covariance matrix :param dict parmFrozen: dict with frozen parameters for all phases and histograms (specified as str values) ''' GPXphase = os.path.splitext(GPXfile)[0]+'.seqPhase' fp = open(GPXphase,'rb') data = cPickleLoad(fp) # first block in file should be Phases if data[0][0] != 'Phases': raise Exception('Unexpected block in {} file. How did this happen?' .format(GPXphase)) fp.close() # update previous phase info for datum in data[1:]: if datum[0] in Phases: datum[1].update(Phases[datum[0]]) # save latest Phase/refinement info fp = open(GPXphase,'wb') cPickle.dump(data,fp,1) cPickle.dump([['Covariance',CovData]],fp,1) cPickle.dump([['Rigid bodies',RigidBodies]],fp,1) cPickle.dump([['parmFrozen',parmFrozen]],fp,1) fp.close() # create an entry that looks like a PWDR tree item for key in Histograms: if key.startswith('PWDR '): break else: raise Exception('No PWDR entry in Histogram dict!') histname = key hist = copy.deepcopy(Histograms[key]) xfer_dict = {'Index Peak List': [[], []], 'Comments': [], 'Unit Cells List': [], 'Peak List': {'peaks': [], 'sigDict': {}}, } histData = hist['Data'] del hist['Data'] for key in ('Limits','Background','Instrument Parameters', 'Sample Parameters','Reflection Lists'): xfer_dict[key] = hist[key] if key == 'Background': # remove fixed background from file xfer_dict['Background'][1] = {k:hist['Background'][1][k] for k in hist['Background'][1] if not k.startswith('_fixed')} del hist[key] # xform into a gpx-type entry data = [] data.append([histname,[hist,histData,histname]]) for key in ['Comments','Limits','Background','Instrument Parameters', 'Sample Parameters','Peak List','Index Peak List', 'Unit Cells List','Reflection Lists']: data.append([key,xfer_dict[key]]) # append histogram to histogram info GPXhist = os.path.splitext(GPXfile)[0]+'.seqHist' fp = open(GPXhist,'ab') cPickle.dump(data,fp,1) fp.close() return
[docs]def SetSeqResult(GPXfile,Histograms,SeqResult): ''' Places the sequential results information into a GPX file after a refinement has been completed. Called at the end of :meth:`GSASIIstrMain.SeqRefine` :param str GPXfile: full .gpx file name ''' GPXback = GPXBackup(GPXfile) G2fil.G2Print ('Read from file:'+GPXback) G2fil.G2Print ('Save to file :'+GPXfile) GPXphase = os.path.splitext(GPXfile)[0]+'.seqPhase' fp = open(GPXphase,'rb') data = cPickleLoad(fp) # first block in file should be Phases if data[0][0] != 'Phases': raise Exception('Unexpected block in {} file. How did this happen?'.format(GPXphase)) Phases = {} for name,vals in data[1:]: Phases[name] = vals name,CovData = cPickleLoad(fp)[0] # 2nd block in file should be Covariance name,RigidBodies = cPickleLoad(fp)[0] # 3rd block in file should be Rigid Bodies name,parmFrozenDict = cPickleLoad(fp)[0] # 4th block in file should be frozen parameters fp.close() GPXhist = os.path.splitext(GPXfile)[0]+'.seqHist' hist = open(GPXhist,'rb') # build an index to the GPXhist file histIndex = {} while True: loc = hist.tell() try: datum = cPickleLoad(hist)[0] except EOFError: break histIndex[datum[0]] = loc infile = open(GPXback,'rb') outfile = open(GPXfile,'wb') while True: try: data = cPickleLoad(infile) except EOFError: break datum = data[0] if datum[0] == 'Sequential results': data[0][1] = SeqResult elif datum[0] == 'Phases': for pdata in data[1:]: if pdata[0] in Phases: pdata[1].update(Phases[pdata[0]]) elif datum[0] == 'Covariance': data[0][1] = CovData elif datum[0] == 'Rigid bodies': data[0][1] = RigidBodies elif datum[0] == 'Controls': # reset the Copy Next flag after a sequential fit Controls = data[0][1] Controls['Copy2Next'] = False for key in parmFrozenDict: Controls['parmFrozen'][key] = [ i if type(i) is G2obj.G2VarObj else G2obj.G2VarObj(i) for i in parmFrozenDict[key]] elif datum[0] in histIndex: hist.seek(histIndex[datum[0]]) hdata = cPickleLoad(hist) if data[0][0] != hdata[0][0]: G2fil.G2Print('Error! Updating {} with {}'.format(data[0][0],hdata[0][0])) data[0] = hdata[0] xferItems = ['Background','Instrument Parameters','Sample Parameters','Reflection Lists'] hItems = {name:j+1 for j,(name,val) in enumerate(hdata[1:]) if name in xferItems} for j,(name,val) in enumerate(data[1:]): if name not in xferItems: continue data[j+1][1] = hdata[hItems[name]][1] cPickle.dump(data,outfile,1) hist.close() infile.close() outfile.close() # clean up tmp files try: os.remove(GPXphase) except: G2fil.G2Print('Warning: unable to delete {}'.format(GPXphase)) try: os.remove(GPXhist) except: G2fil.G2Print('Warning: unable to delete {}'.format(GPXhist)) G2fil.G2Print ('GPX file merge completed')
#============================================================================== # Refinement routines #==============================================================================
[docs]def ShowBanner(pFile=None): 'Print authorship, copyright and citation notice' pFile.write(80*'*'+'\n') pFile.write(' General Structure Analysis System-II Crystal Structure Refinement\n') pFile.write(' by Robert B. Von Dreele & Brian H. Toby\n') pFile.write(' Argonne National Laboratory(C), 2010\n') pFile.write(' This product includes software developed by the UChicago Argonne, LLC,\n') pFile.write(' as Operator of Argonne National Laboratory.\n') pFile.write(' Please cite:\n') pFile.write(' B.H. Toby & R.B. Von Dreele, J. Appl. Cryst. 46, 544-549 (2013)\n') pFile.write(80*'*'+'\n')
[docs]def ShowControls(Controls,pFile=None,SeqRef=False,preFrozenCount=0): 'Print controls information' pFile.write(' Least squares controls:\n') pFile.write(' Refinement type: %s\n'%Controls['deriv type']) if 'Hessian' in Controls['deriv type']: pFile.write(' Maximum number of cycles: %d\n'%Controls['max cyc']) else: pFile.write(' Minimum delta-M/M for convergence: %.2g\n'%(Controls['min dM/M'])) pFile.write(' Regularize hydrogens (if any): %s\n'%Controls.get('HatomFix',False)) pFile.write(' Initial shift factor: %.3f\n'%(Controls['shift factor'])) if SeqRef: pFile.write(' Sequential refinement controls:\n') pFile.write(' Copy of histogram results to next: %s\n'%(Controls['Copy2Next'])) pFile.write(' Process histograms in reverse order: %s\n'%(Controls['Reverse Seq'])) if preFrozenCount: pFile.write('\n Starting refinement with {} Frozen variables\n\n'.format(preFrozenCount))
[docs]def GetPawleyConstr(SGLaue,PawleyRef,im,pawleyVary): 'needs a doc string' # if SGLaue in ['-1','2/m','mmm']: # return #no Pawley symmetry required constraints eqvDict = {} for i,varyI in enumerate(pawleyVary): eqvDict[varyI] = [] refI = int(varyI.split(':')[-1]) ih,ik,il = PawleyRef[refI][:3] dspI = PawleyRef[refI][4+im] for varyJ in pawleyVary[i+1:]: refJ = int(varyJ.split(':')[-1]) jh,jk,jl = PawleyRef[refJ][:3] dspJ = PawleyRef[refJ][4+im] if SGLaue in ['4/m','4/mmm']: isum = ih**2+ik**2 jsum = jh**2+jk**2 if abs(il) == abs(jl) and isum == jsum: eqvDict[varyI].append(varyJ) elif SGLaue in ['3R','3mR']: isum = ih**2+ik**2+il**2 jsum = jh**2+jk**2+jl**2 isum2 = ih*ik+ih*il+ik*il jsum2 = jh*jk+jh*jl+jk*jl if isum == jsum and isum2 == jsum2: eqvDict[varyI].append(varyJ) elif SGLaue in ['3','3m1','31m','6/m','6/mmm']: isum = ih**2+ik**2+ih*ik jsum = jh**2+jk**2+jh*jk if abs(il) == abs(jl) and isum == jsum: eqvDict[varyI].append(varyJ) elif SGLaue in ['m3','m3m']: isum = ih**2+ik**2+il**2 jsum = jh**2+jk**2+jl**2 if isum == jsum: eqvDict[varyI].append(varyJ) elif abs(dspI-dspJ)/dspI < 1.e-4: eqvDict[varyI].append(varyJ) for item in pawleyVary: if eqvDict[item]: for item2 in pawleyVary: if item2 in eqvDict[item]: eqvDict[item2] = [] G2mv.StoreEquivalence(item,eqvDict[item])
[docs]def cellVary(pfx,SGData): '''Creates equivalences for a phase based on the Laue class. Returns a list of A tensor terms that are non-zero. ''' if SGData['SGLaue'] in ['-1',]: return [pfx+'A0',pfx+'A1',pfx+'A2',pfx+'A3',pfx+'A4',pfx+'A5'] elif SGData['SGLaue'] in ['2/m',]: if SGData['SGUniq'] == 'a': return [pfx+'A0',pfx+'A1',pfx+'A2',pfx+'A5'] elif SGData['SGUniq'] == 'b': return [pfx+'A0',pfx+'A1',pfx+'A2',pfx+'A4'] else: return [pfx+'A0',pfx+'A1',pfx+'A2',pfx+'A3'] elif SGData['SGLaue'] in ['mmm',]: return [pfx+'A0',pfx+'A1',pfx+'A2'] elif SGData['SGLaue'] in ['4/m','4/mmm']: G2mv.StoreEquivalence(pfx+'A0',(pfx+'A1',)) return [pfx+'A0',pfx+'A1',pfx+'A2'] elif SGData['SGLaue'] in ['6/m','6/mmm','3m1', '31m', '3']: G2mv.StoreEquivalence(pfx+'A0',(pfx+'A1',pfx+'A3',)) return [pfx+'A0',pfx+'A1',pfx+'A2',pfx+'A3'] elif SGData['SGLaue'] in ['3R', '3mR']: G2mv.StoreEquivalence(pfx+'A0',(pfx+'A1',pfx+'A2',)) G2mv.StoreEquivalence(pfx+'A3',(pfx+'A4',pfx+'A5',)) return [pfx+'A0',pfx+'A1',pfx+'A2',pfx+'A3',pfx+'A4',pfx+'A5'] elif SGData['SGLaue'] in ['m3m','m3']: G2mv.StoreEquivalence(pfx+'A0',(pfx+'A1',pfx+'A2',)) return [pfx+'A0',pfx+'A1',pfx+'A2']
def modVary(pfx,SSGData): vary = [] for i,item in enumerate(SSGData['modSymb']): if item in ['a','b','g']: vary.append(pfx+'mV%d'%(i)) return vary ################################################################################ ##### Rigid Body Models and not General.get('doPawley') ################################################################################
[docs]def GetRigidBodyModels(rigidbodyDict,Print=True,pFile=None): 'Get Rigid body info from tree entry and print it to .LST file' def PrintResRBModel(RBModel): pFile.write('Residue RB name: %s no.atoms: %d, No. times used: %d\n'% (RBModel['RBname'],len(RBModel['rbTypes']),RBModel['useCount'])) for i in WriteResRBModel(RBModel): pFile.write(i) def PrintVecRBModel(RBModel): pFile.write('Vector RB name: %s no.atoms: %d No. times used: %d\n'% (RBModel['RBname'],len(RBModel['rbTypes']),RBModel['useCount'])) for i in WriteVecRBModel(RBModel): pFile.write(i) pFile.write('Orientation defined by: atom %s -> atom %s & atom %s -> atom %s\n'% (RBModel['rbRef'][0],RBModel['rbRef'][1],RBModel['rbRef'][0],RBModel['rbRef'][2])) if Print and pFile is None: raise Exception("specify pFile or Print=False") rbVary = [] rbDict = {} rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]}) if len(rbIds['Vector']): for irb,item in enumerate(rbIds['Vector']): if rigidbodyDict['Vector'][item]['useCount']: RBmags = rigidbodyDict['Vector'][item]['VectMag'] RBrefs = rigidbodyDict['Vector'][item]['VectRef'] for i,[mag,ref] in enumerate(zip(RBmags,RBrefs)): pid = '::RBV;'+str(i)+':'+str(irb) rbDict[pid] = mag if ref: rbVary.append(pid) if Print: pFile.write('\nVector rigid body model:\n') PrintVecRBModel(rigidbodyDict['Vector'][item]) if len(rbIds['Residue']): for item in rbIds['Residue']: if rigidbodyDict['Residue'][item]['useCount']: if Print: pFile.write('\nResidue rigid body model:\n') PrintResRBModel(rigidbodyDict['Residue'][item]) return rbVary,rbDict
[docs]def SetRigidBodyModels(parmDict,sigDict,rigidbodyDict,pFile=None): 'needs a doc string' def PrintRBVectandSig(VectRB,VectSig): pFile.write('\n Rigid body vector magnitudes for %s:\n'%VectRB['RBname']) namstr = ' names :' valstr = ' values:' sigstr = ' esds :' for i,[val,sig] in enumerate(zip(VectRB['VectMag'],VectSig)): namstr += '%12s'%('Vect '+str(i)) valstr += '%12.4f'%(val) if sig: sigstr += '%12.4f'%(sig) else: sigstr += 12*' ' pFile.write(namstr+'\n') pFile.write(valstr+'\n') pFile.write(sigstr+'\n') RBIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]}) #these are lists of rbIds if not RBIds['Vector']: return for irb,item in enumerate(RBIds['Vector']): if rigidbodyDict['Vector'][item]['useCount']: VectSig = [] RBmags = rigidbodyDict['Vector'][item]['VectMag'] for i,mag in enumerate(RBmags): name = '::RBV;'+str(i)+':'+str(irb) if name in sigDict: VectSig.append(sigDict[name]) PrintRBVectandSig(rigidbodyDict['Vector'][item],VectSig)
################################################################################ ##### Phase data ################################################################################
[docs]def GetPhaseData(PhaseData,RestraintDict={},rbIds={},Print=True,pFile=None, seqRef=False,symHold=None): '''Setup the phase information for a structural refinement, used for regular and sequential refinements, optionally printing information to the .lst file (if Print is True) ''' def PrintFFtable(FFtable): pFile.write('\n X-ray scattering factors:\n') pFile.write(' Symbol fa fb fc\n') pFile.write(99*'-'+'\n') for Ename in FFtable: ffdata = FFtable[Ename] fa = ffdata['fa'] fb = ffdata['fb'] pFile.write(' %8s %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f\n'% (Ename.ljust(8),fa[0],fa[1],fa[2],fa[3],fb[0],fb[1],fb[2],fb[3],ffdata['fc'])) def PrintMFtable(MFtable): pFile.write('\n <j0> Magnetic scattering factors:\n') pFile.write(' Symbol mfa mfb mfc\n') pFile.write(99*'-'+'\n') for Ename in MFtable: mfdata = MFtable[Ename] fa = mfdata['mfa'] fb = mfdata['mfb'] pFile.write(' %8s %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f\n'% (Ename.ljust(8),fa[0],fa[1],fa[2],fa[3],fb[0],fb[1],fb[2],fb[3],mfdata['mfc'])) pFile.write('\n <j2> Magnetic scattering factors:\n') pFile.write(' Symbol nfa nfb nfc\n') pFile.write(99*'-'+'\n') for Ename in MFtable: mfdata = MFtable[Ename] fa = mfdata['nfa'] fb = mfdata['nfb'] pFile.write(' %8s %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f\n'% (Ename.ljust(8),fa[0],fa[1],fa[2],fa[3],fb[0],fb[1],fb[2],fb[3],mfdata['nfc'])) def PrintBLtable(BLtable): pFile.write('\n Neutron scattering factors:\n') pFile.write(' Symbol isotope mass b resonant terms\n') pFile.write(99*'-'+'\n') for Ename in BLtable: bldata = BLtable[Ename] isotope = bldata[0] mass = bldata[1]['Mass'] if 'BW-LS' in bldata[1]: bres = bldata[1]['BW-LS'] blen = 0 else: blen = bldata[1]['SL'][0] bres = [] line = ' %8s%11s %10.3f %8.3f'%(Ename.ljust(8),isotope.center(11),mass,blen) for item in bres: line += '%10.5g'%(item) pFile.write(line+'\n') def PrintRBObjects(resRBData,vecRBData): def PrintRBThermals(): tlstr = ['11','22','33','12','13','23'] sstr = ['12','13','21','23','31','32','AA','BB'] TLS = RB['ThermalMotion'][1] TLSvar = RB['ThermalMotion'][2] if 'T' in RB['ThermalMotion'][0]: pFile.write('TLS data\n') text = '' for i in range(6): text += 'T'+tlstr[i]+' %8.4f %s '%(TLS[i],str(TLSvar[i])[0]) pFile.write(text+'\n') if 'L' in RB['ThermalMotion'][0]: text = '' for i in range(6,12): text += 'L'+tlstr[i-6]+' %8.2f %s '%(TLS[i],str(TLSvar[i])[0]) pFile.write(text+'\n') if 'S' in RB['ThermalMotion'][0]: text = '' for i in range(12,20): text += 'S'+sstr[i-12]+' %8.3f %s '%(TLS[i],str(TLSvar[i])[0]) pFile.write(text+'\n') if 'U' in RB['ThermalMotion'][0]: pFile.write('Uiso data\n') text = 'Uiso'+' %10.3f %s'%(TLS[0],str(TLSvar[0])[0]) pFile.write(text+'\n') if len(resRBData): for RB in resRBData: Oxyz = RB['Orig'][0] Qrijk = RB['Orient'][0] Angle = 2.0*acosd(Qrijk[0]) pFile.write('\nRBObject %s at %10.4f %10.4f %10.4f Refine? %s\n'% (RB['RBname'],Oxyz[0],Oxyz[1],Oxyz[2],RB['Orig'][1])) pFile.write('Orientation angle,vector: %10.3f %10.4f %10.4f %10.4f Refine? %s\n'% (Angle,Qrijk[1],Qrijk[2],Qrijk[3],RB['Orient'][1])) pFile.write('Atom site frac: %10.3f Refine? %s\n'%(RB['AtomFrac'][0],RB['AtomFrac'][1])) Torsions = RB['Torsions'] if len(Torsions): text = 'Torsions: ' for torsion in Torsions: text += '%10.4f Refine? %s'%(torsion[0],torsion[1]) pFile.write(text+'\n') PrintRBThermals() if len(vecRBData): for RB in vecRBData: Oxyz = RB['Orig'][0] Qrijk = RB['Orient'][0] Angle = 2.0*acosd(Qrijk[0]) pFile.write('\nRBObject %s at %10.4f %10.4f %10.4f Refine? %s\n'% (RB['RBname'],Oxyz[0],Oxyz[1],Oxyz[2],RB['Orig'][1])) pFile.write('Orientation angle,vector: %10.3f %10.4f %10.4f %10.4f Refine? %s\n'% (Angle,Qrijk[1],Qrijk[2],Qrijk[3],RB['Orient'][1])) pFile.write('Atom site frac: %10.3f Refine? %s\n'%(RB['AtomFrac'][0],RB['AtomFrac'][1])) PrintRBThermals() def PrintAtoms(General,Atoms): cx,ct,cs,cia = General['AtomPtrs'] pFile.write('\n Atoms:\n') line = ' name type refine? x y z '+ \ ' frac site sym mult I/A Uiso U11 U22 U33 U12 U13 U23' if General['Type'] == 'macromolecular': line = ' res no residue chain'+line pFile.write(line+'\n') if General['Type'] in ['nuclear','magnetic','faulted',]: pFile.write(135*'-'+'\n') for i,at in enumerate(Atoms): line = '%7s'%(at[ct-1])+'%7s'%(at[ct])+'%7s'%(at[ct+1])+'%10.5f'%(at[cx])+'%10.5f'%(at[cx+1])+ \ '%10.5f'%(at[cx+2])+'%8.3f'%(at[cx+3])+'%7s'%(at[cs])+'%5d'%(at[cs+1])+'%5s'%(at[cia]) if at[cia] == 'I': line += '%8.5f'%(at[cia+1])+48*' ' else: line += 8*' ' for j in range(6): line += '%8.5f'%(at[cia+2+j]) pFile.write(line+'\n') elif General['Type'] == 'macromolecular': pFile.write(135*'-'+'\n') for i,at in enumerate(Atoms): line = '%7s'%(at[0])+'%7s'%(at[1])+'%7s'%(at[2])+'%7s'%(at[ct-1])+'%7s'%(at[ct])+'%7s'%(at[ct+1])+'%10.5f'%(at[cx])+'%10.5f'%(at[cx+1])+ \ '%10.5f'%(at[cx+2])+'%8.3f'%(at[cx+3])+'%7s'%(at[cs])+'%5d'%(at[cs+1])+'%5s'%(at[cia]) if at[cia] == 'I': line += '%8.4f'%(at[cia+1])+48*' ' else: line += 8*' ' for j in range(6): line += '%8.4f'%(at[cia+2+j]) pFile.write(line+'\n') def PrintMoments(General,Atoms): cx,ct,cs,cia = General['AtomPtrs'] cmx = cx+4 AtInfo = dict(zip(General['AtomTypes'],General['Lande g'])) pFile.write('\n Magnetic moments:\n') line = ' name type refine? Mx My Mz ' pFile.write(line+'\n') pFile.write(135*'-'+'\n') for i,at in enumerate(Atoms): if AtInfo[at[ct]]: line = '%7s'%(at[ct-1])+'%7s'%(at[ct])+'%7s'%(at[ct+1])+'%10.5f'%(at[cmx])+'%10.5f'%(at[cmx+1])+ \ '%10.5f'%(at[cmx+2]) pFile.write(line+'\n') def PrintWaves(General,Atoms): cx,ct,cs,cia = General['AtomPtrs'] pFile.write('\n Modulation waves\n') names = {'Sfrac':['Fsin','Fcos','Fzero','Fwid'],'Spos':['Xsin','Ysin','Zsin','Xcos','Ycos','Zcos','Tmin','Tmax','Xmax','Ymax','Zmax'], 'Sadp':['U11sin','U22sin','U33sin','U12sin','U13sin','U23sin','U11cos','U22cos', 'U33cos','U12cos','U13cos','U23cos'],'Smag':['MXsin','MYsin','MZsin','MXcos','MYcos','MZcos']} pFile.write(135*'-'+'\n') for i,at in enumerate(Atoms): AtomSS = at[-1]['SS1'] for Stype in ['Sfrac','Spos','Sadp','Smag']: Waves = AtomSS[Stype] if len(Waves): pFile.write(' atom: %s, site sym: %s, type: %s wave type: %s:\n'% (at[ct-1],at[cs],Stype,Waves[0])) else: continue for iw,wave in enumerate(Waves[1:]): line = '' if Waves[0] in ['Block','ZigZag'] and Stype == 'Spos' and not iw: for item in names[Stype][6:]: line += '%8s '%(item) else: if Stype == 'Spos': for item in names[Stype][:6]: line += '%8s '%(item) else: for item in names[Stype]: line += '%8s '%(item) pFile.write(line+'\n') line = '' for item in wave[0]: line += '%8.4f '%(item) line += ' Refine? '+str(wave[1]) pFile.write(line+'\n') def PrintTexture(textureData): topstr = '\n Spherical harmonics texture: Order:' + \ str(textureData['Order']) if textureData['Order']: pFile.write('%s Refine? %s\n'%(topstr,textureData['SH Coeff'][0])) else: pFile.write(topstr+'\n') return names = ['omega','chi','phi'] line = '\n' for name in names: line += ' SH '+name+':'+'%12.4f'%(textureData['Sample '+name][1])+' Refine? '+str(textureData['Sample '+name][0]) pFile.write(line+'\n') pFile.write('\n Texture coefficients:\n') SHcoeff = textureData['SH Coeff'][1] SHkeys = list(SHcoeff.keys()) nCoeff = len(SHcoeff) nBlock = nCoeff//10+1 iBeg = 0 iFin = min(iBeg+10,nCoeff) for block in range(nBlock): ptlbls = ' names :' ptstr = ' values:' for item in SHkeys[iBeg:iFin]: ptlbls += '%12s'%(item) ptstr += '%12.4f'%(SHcoeff[item]) pFile.write(ptlbls+'\n') pFile.write(ptstr+'\n') iBeg += 10 iFin = min(iBeg+10,nCoeff) def MakeRBParms(rbKey,phaseVary,phaseDict): #### patch 2/24/21 BHT: new param, AtomFrac in RB if 'AtomFrac' not in RB: raise Exception('out of date RB: edit in RB Models') # end patch rbid = str(rbids.index(RB['RBId'])) pfxRB = pfx+'RB'+rbKey+'P' pstr = ['x','y','z'] ostr = ['a','i','j','k'] Sytsym = G2spc.SytSym(RB['Orig'][0],SGData)[0] xId,xCoef = G2spc.GetCSxinel(Sytsym) # gen origin site sym equivs = {1:[],2:[],3:[]} for i in range(3): name = pfxRB+pstr[i]+':'+str(iRB)+':'+rbid phaseDict[name] = RB['Orig'][0][i] if RB['Orig'][1]: if xId[i] > 0: phaseVary += [name,] equivs[xId[i]].append([name,xCoef[i]]) elif symHold is not None: #variable is held due to symmetry symHold.append(name) for equiv in equivs: if len(equivs[equiv]) > 1: name = equivs[equiv][0][0] coef = equivs[equiv][0][1] for eqv in equivs[equiv][1:]: eqv[1] /= coef G2mv.StoreEquivalence(name,(eqv,)) pfxRB = pfx+'RB'+rbKey+'O' A,V = G2mth.Q2AV(RB['Orig'][0]) fixAxis = [0, np.abs(V).argmax()+1] for i in range(4): name = pfxRB+ostr[i]+':'+str(iRB)+':'+rbid phaseDict[name] = RB['Orient'][0][i] if RB['Orient'][1] == 'AV' and i: phaseVary += [name,] elif RB['Orient'][1] == 'A' and not i: phaseVary += [name,] elif RB['Orient'][1] == 'V' and i not in fixAxis: phaseVary += [name,] name = pfx+'RB'+rbKey+'f:'+str(iRB)+':'+rbid phaseDict[name] = RB['AtomFrac'][0] if RB['AtomFrac'][1]: phaseVary += [name,] def MakeRBThermals(rbKey,phaseVary,phaseDict): rbid = str(rbids.index(RB['RBId'])) tlstr = ['11','22','33','12','13','23'] sstr = ['12','13','21','23','31','32','AA','BB'] if 'T' in RB['ThermalMotion'][0]: pfxRB = pfx+'RB'+rbKey+'T' for i in range(6): name = pfxRB+tlstr[i]+':'+str(iRB)+':'+rbid phaseDict[name] = RB['ThermalMotion'][1][i] if RB['ThermalMotion'][2][i]: phaseVary += [name,] if 'L' in RB['ThermalMotion'][0]: pfxRB = pfx+'RB'+rbKey+'L' for i in range(6): name = pfxRB+tlstr[i]+':'+str(iRB)+':'+rbid phaseDict[name] = RB['ThermalMotion'][1][i+6] if RB['ThermalMotion'][2][i+6]: phaseVary += [name,] if 'S' in RB['ThermalMotion'][0]: pfxRB = pfx+'RB'+rbKey+'S' for i in range(8): name = pfxRB+sstr[i]+':'+str(iRB)+':'+rbid phaseDict[name] = RB['ThermalMotion'][1][i+12] if RB['ThermalMotion'][2][i+12]: phaseVary += [name,] if 'U' in RB['ThermalMotion'][0]: name = pfx+'RB'+rbKey+'U:'+str(iRB)+':'+rbid phaseDict[name] = RB['ThermalMotion'][1][0] if RB['ThermalMotion'][2][0]: phaseVary += [name,] def MakeRBTorsions(rbKey,phaseVary,phaseDict): rbid = str(rbids.index(RB['RBId'])) pfxRB = pfx+'RB'+rbKey+'Tr;' for i,torsion in enumerate(RB['Torsions']): name = pfxRB+str(i)+':'+str(iRB)+':'+rbid phaseDict[name] = torsion[0] if torsion[1]: phaseVary += [name,] if Print and pFile is None: raise Exception("specify pFile or Print=False") if Print: pFile.write('\n Phases:\n') phaseVary = [] phaseDict = {} pawleyLookup = {} FFtables = {} #scattering factors - xrays MFtables = {} #Mag. form factors BLtables = {} # neutrons Natoms = {} maxSSwave = {} shModels = ['cylindrical','none','shear - 2/m','rolling - mmm'] SamSym = dict(zip(shModels,['0','-1','2/m','mmm'])) atomIndx = {} for name in PhaseData: General = PhaseData[name]['General'] pId = PhaseData[name]['pId'] pfx = str(pId)+'::' FFtable = G2el.GetFFtable(General['AtomTypes']) BLtable = G2el.GetBLtable(General) FFtables.update(FFtable) BLtables.update(BLtable) phaseDict[pfx+'isMag'] = False SGData = General['SGData'] SGtext,SGtable = G2spc.SGPrint(SGData) if General['Type'] == 'magnetic': MFtable = G2el.GetMFtable(General['AtomTypes'],General['Lande g']) MFtables.update(MFtable) phaseDict[pfx+'isMag'] = True SpnFlp = SGData['SpnFlp'] Atoms = PhaseData[name]['Atoms'] if Atoms and not General.get('doPawley'): cx,ct,cs,cia = General['AtomPtrs'] AtLookup = G2mth.FillAtomLookUp(Atoms,cia+8) PawleyRef = PhaseData[name].get('Pawley ref',[]) cell = General['Cell'] A = G2lat.cell2A(cell[1:7]) phaseDict.update({pfx+'A0':A[0],pfx+'A1':A[1],pfx+'A2':A[2], pfx+'A3':A[3],pfx+'A4':A[4],pfx+'A5':A[5],pfx+'Vol':G2lat.calc_V(A)}) if cell[0]: phaseVary += cellVary(pfx,SGData) #also fills in symmetry required constraints SSGtext = [] #no superstructure im = 0 if General.get('Modulated',False): im = 1 #refl offset Vec,vRef,maxH = General['SuperVec'] phaseDict.update({pfx+'mV0':Vec[0],pfx+'mV1':Vec[1],pfx+'mV2':Vec[2]}) SSGData = General['SSGData'] SSGtext,SSGtable = G2spc.SSGPrint(SGData,SSGData) if vRef: phaseVary += modVary(pfx,SSGData) resRBData = PhaseData[name]['RBModels'].get('Residue',[]) if resRBData: rbids = rbIds['Residue'] #NB: used in the MakeRB routines for iRB,RB in enumerate(resRBData): MakeRBParms('R',phaseVary,phaseDict) MakeRBThermals('R',phaseVary,phaseDict) MakeRBTorsions('R',phaseVary,phaseDict) vecRBData = PhaseData[name]['RBModels'].get('Vector',[]) if vecRBData: rbids = rbIds['Vector'] #NB: used in the MakeRB routines for iRB,RB in enumerate(vecRBData): MakeRBParms('V',phaseVary,phaseDict) MakeRBThermals('V',phaseVary,phaseDict) Natoms[pfx] = 0 maxSSwave[pfx] = {'Sfrac':0,'Spos':0,'Sadp':0,'Smag':0} if Atoms and not General.get('doPawley'): cx,ct,cs,cia = General['AtomPtrs'] Natoms[pfx] = len(Atoms) for i,at in enumerate(Atoms): atomIndx[at[cia+8]] = [pfx,i] #lookup table for restraints phaseDict.update({pfx+'Atype:'+str(i):at[ct],pfx+'Afrac:'+str(i):at[cx+3],pfx+'Amul:'+str(i):at[cs+1], pfx+'Ax:'+str(i):at[cx],pfx+'Ay:'+str(i):at[cx+1],pfx+'Az:'+str(i):at[cx+2], pfx+'dAx:'+str(i):0.,pfx+'dAy:'+str(i):0.,pfx+'dAz:'+str(i):0., #refined shifts for x,y,z pfx+'AI/A:'+str(i):at[cia],}) if at[cia] == 'I': phaseDict[pfx+'AUiso:'+str(i)] = at[cia+1] else: phaseDict.update({pfx+'AU11:'+str(i):at[cia+2],pfx+'AU22:'+str(i):at[cia+3],pfx+'AU33:'+str(i):at[cia+4], pfx+'AU12:'+str(i):at[cia+5],pfx+'AU13:'+str(i):at[cia+6],pfx+'AU23:'+str(i):at[cia+7]}) if General['Type'] == 'magnetic': phaseDict.update({pfx+'AMx:'+str(i):at[cx+4],pfx+'AMy:'+str(i):at[cx+5],pfx+'AMz:'+str(i):at[cx+6]}) if 'F' in at[ct+1]: phaseVary.append(pfx+'Afrac:'+str(i)) if 'X' in at[ct+1]: try: #patch for sytsym name changes xId,xCoef = G2spc.GetCSxinel(at[cs]) except KeyError: Sytsym = G2spc.SytSym(at[cx:cx+3],SGData)[0] at[cs] = Sytsym xId,xCoef = G2spc.GetCSxinel(at[cs]) names = [pfx+'dAx:'+str(i),pfx+'dAy:'+str(i),pfx+'dAz:'+str(i)] equivs = {1:[],2:[],3:[]} for j in range(3): if xId[j] > 0: phaseVary.append(names[j]) equivs[xId[j]].append([names[j],xCoef[j]]) elif symHold is not None: #variable is held due to symmetry symHold.append(names[j]) for equiv in equivs: if len(equivs[equiv]) > 1: name = equivs[equiv][0][0] coef = equivs[equiv][0][1] for eqv in equivs[equiv][1:]: eqv[1] /= coef G2mv.StoreEquivalence(name,(eqv,)) if 'U' in at[ct+1]: if at[cia] == 'I': phaseVary.append(pfx+'AUiso:'+str(i)) else: try: #patch for sytsym name changes uId,uCoef = G2spc.GetCSuinel(at[cs])[:2] except KeyError: Sytsym = G2spc.SytSym(at[cx:cx+3],SGData)[0] at[cs] = Sytsym uId,uCoef = G2spc.GetCSuinel(at[cs])[:2] names = [pfx+'AU11:'+str(i),pfx+'AU22:'+str(i),pfx+'AU33:'+str(i), pfx+'AU12:'+str(i),pfx+'AU13:'+str(i),pfx+'AU23:'+str(i)] equivs = {1:[],2:[],3:[],4:[],5:[],6:[]} for j in range(6): if uId[j] > 0: phaseVary.append(names[j]) equivs[uId[j]].append([names[j],uCoef[j]]) for equiv in equivs: if len(equivs[equiv]) > 1: name = equivs[equiv][0][0] coef = equivs[equiv][0][1] for eqv in equivs[equiv][1:]: eqv[1] /= coef G2mv.StoreEquivalence(name,(eqv,)) if 'M' in at[ct+1]: SytSym,Mul,Nop,dupDir = G2spc.SytSym(at[cx:cx+3],SGData) mId,mCoef = G2spc.GetCSpqinel(SpnFlp,dupDir) names = [pfx+'AMx:'+str(i),pfx+'AMy:'+str(i),pfx+'AMz:'+str(i)] equivs = {1:[],2:[],3:[]} for j in range(3): if mId[j] > 0: phaseVary.append(names[j]) equivs[mId[j]].append([names[j],mCoef[j]]) for equiv in equivs: if len(equivs[equiv]) > 1: name = equivs[equiv][0][0] coef = equivs[equiv][0][1] for eqv in equivs[equiv][1:]: eqv[1] /= coef G2mv.StoreEquivalence(name,(eqv,)) if General.get('Modulated',False): AtomSS = at[-1]['SS1'] for Stype in ['Sfrac','Spos','Sadp','Smag']: Waves = AtomSS[Stype] if len(Waves): waveType = Waves[0] else: continue phaseDict[pfx+Stype[1].upper()+'waveType:'+str(i)] = waveType nx = 0 for iw,wave in enumerate(Waves[1:]): if not iw: if waveType in ['ZigZag','Block']: nx = 1 CSI = G2spc.GetSSfxuinel(waveType,Stype,1,at[cx:cx+3],SGData,SSGData) else: CSI = G2spc.GetSSfxuinel('Fourier',Stype,iw+1-nx,at[cx:cx+3],SGData,SSGData) uId,uCoef = CSI[0] stiw = str(i)+':'+str(iw) if Stype == 'Spos': if waveType in ['ZigZag','Block',] and not iw: names = [pfx+'Tmin:'+stiw,pfx+'Tmax:'+stiw,pfx+'Xmax:'+stiw,pfx+'Ymax:'+stiw,pfx+'Zmax:'+stiw] equivs = {1:[],2:[], 3:[],4:[],5:[]} else: names = [pfx+'Xsin:'+stiw,pfx+'Ysin:'+stiw,pfx+'Zsin:'+stiw, pfx+'Xcos:'+stiw,pfx+'Ycos:'+stiw,pfx+'Zcos:'+stiw] equivs = {1:[],2:[],3:[], 4:[],5:[],6:[]} elif Stype == 'Sadp': names = [pfx+'U11sin:'+stiw,pfx+'U22sin:'+stiw,pfx+'U33sin:'+stiw, pfx+'U12sin:'+stiw,pfx+'U13sin:'+stiw,pfx+'U23sin:'+stiw, pfx+'U11cos:'+stiw,pfx+'U22cos:'+stiw,pfx+'U33cos:'+stiw, pfx+'U12cos:'+stiw,pfx+'U13cos:'+stiw,pfx+'U23cos:'+stiw] equivs = {1:[],2:[],3:[],4:[],5:[],6:[], 7:[],8:[],9:[],10:[],11:[],12:[]} elif Stype == 'Sfrac': equivs = {1:[],2:[]} if 'Crenel' in waveType and not iw: names = [pfx+'Fzero:'+stiw,pfx+'Fwid:'+stiw] else: names = [pfx+'Fsin:'+stiw,pfx+'Fcos:'+stiw] elif Stype == 'Smag': equivs = {1:[],2:[],3:[], 4:[],5:[],6:[]} names = [pfx+'MXsin:'+stiw,pfx+'MYsin:'+stiw,pfx+'MZsin:'+stiw, pfx+'MXcos:'+stiw,pfx+'MYcos:'+stiw,pfx+'MZcos:'+stiw] phaseDict.update(dict(zip(names,wave[0]))) if wave[1]: #what do we do here for multiple terms in modulation constraints? for j in range(len(equivs)): if uId[j][0] > 0: phaseVary.append(names[j]) equivs[uId[j][0]].append([names[j],uCoef[j][0]]) for equiv in equivs: if len(equivs[equiv]) > 1: name = equivs[equiv][0][0] coef = equivs[equiv][0][1] for eqv in equivs[equiv][1:]: eqv[1] /= coef G2mv.StoreEquivalence(name,(eqv,)) maxSSwave[pfx][Stype] = max(maxSSwave[pfx][Stype],iw+1) textureData = General['SH Texture'] if textureData['Order'] and not seqRef: phaseDict[pfx+'SHorder'] = textureData['Order'] phaseDict[pfx+'SHmodel'] = SamSym[textureData['Model']] for item in ['omega','chi','phi']: phaseDict[pfx+'SH '+item] = textureData['Sample '+item][1] if textureData['Sample '+item][0]: phaseVary.append(pfx+'SH '+item) for item in textureData['SH Coeff'][1]: phaseDict[pfx+item] = textureData['SH Coeff'][1][item] if textureData['SH Coeff'][0]: phaseVary.append(pfx+item) if Print: pFile.write('\n Phase name: %s\n'%General['Name']) pFile.write(135*'='+'\n') PrintFFtable(FFtable) PrintBLtable(BLtable) if General['Type'] == 'magnetic': PrintMFtable(MFtable) pFile.write('\n') #how do we print magnetic symmetry table? TBD if len(SSGtext): #if superstructure for line in SSGtext: pFile.write(line+'\n') if len(SSGtable): for item in SSGtable: line = ' %s '%(item) pFile.write(line+'\n') else: pFile.write(' ( 1) %s\n'%(SSGtable[0])) else: for line in SGtext: pFile.write(line+'\n') if len(SGtable): for item in SGtable: line = ' %s '%(item) pFile.write(line+'\n') else: pFile.write(' ( 1) %s\n'%(SGtable[0])) PrintRBObjects(resRBData,vecRBData) PrintAtoms(General,Atoms) if General['Type'] == 'magnetic': PrintMoments(General,Atoms) if General.get('Modulated',False): PrintWaves(General,Atoms) pFile.write('\n Unit cell: a = %.5f b = %.5f c = %.5f alpha = %.3f beta = %.3f gamma = %.3f volume = %.3f Refine? %s\n'% (cell[1],cell[2],cell[3],cell[4],cell[5],cell[6],cell[7],cell[0])) if len(SSGtext): #if superstructure pFile.write('\n Modulation vector: mV0 = %.4f mV1 = %.4f mV2 = %.4f max mod. index = %d Refine? %s\n'% (Vec[0],Vec[1],Vec[2],maxH,vRef)) if not seqRef: PrintTexture(textureData) if name in RestraintDict: PrintRestraints(cell[1:7],SGData,General['AtomPtrs'],Atoms,AtLookup, textureData,RestraintDict[name],pFile) elif PawleyRef: if Print: pFile.write('\n Phase name: %s\n'%General['Name']) pFile.write(135*'='+'\n') pFile.write('\n') if len(SSGtext): #if superstructure for line in SSGtext: pFile.write(line+'\n') if len(SSGtable): for item in SSGtable: line = ' %s '%(item) pFile.write(line+'\n') else: pFile.write(' ( 1) %s\n'%SSGtable[0]) else: for line in SGtext: pFile.write(line+'\n') if len(SGtable): for item in SGtable: line = ' %s '%(item) pFile.write(line+'\n') else: pFile.write(' ( 1) %s\n'%(SGtable[0])) pFile.write('\n Unit cell: a = %.5f b = %.5f c = %.5f alpha = %.3f beta = %.3f gamma = %.3f volume = %.3f Refine? %s\n'% (cell[1],cell[2],cell[3],cell[4],cell[5],cell[6],cell[7],cell[0])) if len(SSGtext): #if superstructure pFile.write('\n Modulation vector: mV0 = %.4f mV1 = %.4f mV2 = %.4f max mod. index = %d Refine? %s\n'% (Vec[0],Vec[1],Vec[2],maxH,vRef)) pawleyVary = [] for i,refl in enumerate(PawleyRef): phaseDict[pfx+'PWLref:'+str(i)] = refl[6+im] if im: pawleyLookup[pfx+'%d,%d,%d,%d'%(refl[0],refl[1],refl[2],refl[3])] = i else: pawleyLookup[pfx+'%d,%d,%d'%(refl[0],refl[1],refl[2])] = i if refl[5+im]: pawleyVary.append(pfx+'PWLref:'+str(i)) GetPawleyConstr(SGData['SGLaue'],PawleyRef,im,pawleyVary) #does G2mv.StoreEquivalence phaseVary += pawleyVary return Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables,MFtables,maxSSwave
[docs]def cellFill(pfx,SGData,parmDict,sigDict): '''Returns the filled-out reciprocal cell (A) terms and their uncertainties from the parameter and sig dictionaries. :param str pfx: parameter prefix ("n::", where n is a phase number) :param dict SGdata: a symmetry object :param dict parmDict: a dictionary of parameters :param dict sigDict: a dictionary of uncertainties on parameters :returns: A,sigA where each is a list of six terms with the A terms ''' if SGData['SGLaue'] in ['-1',]: A = [parmDict[pfx+'A0'],parmDict[pfx+'A1'],parmDict[pfx+'A2'], parmDict[pfx+'A3'],parmDict[pfx+'A4'],parmDict[pfx+'A5']] elif SGData['SGLaue'] in ['2/m',]: if SGData['SGUniq'] == 'a': A = [parmDict[pfx+'A0'],parmDict[pfx+'A1'],parmDict[pfx+'A2'], 0,0,parmDict[pfx+'A5']] elif SGData['SGUniq'] == 'b': A = [parmDict[pfx+'A0'],parmDict[pfx+'A1'],parmDict[pfx+'A2'], 0,parmDict[pfx+'A4'],0] else: A = [parmDict[pfx+'A0'],parmDict[pfx+'A1'],parmDict[pfx+'A2'], parmDict[pfx+'A3'],0,0] elif SGData['SGLaue'] in ['mmm',]: A = [parmDict[pfx+'A0'],parmDict[pfx+'A1'],parmDict[pfx+'A2'],0,0,0] elif SGData['SGLaue'] in ['4/m','4/mmm']: A = [parmDict[pfx+'A0'],parmDict[pfx+'A0'],parmDict[pfx+'A2'],0,0,0] elif SGData['SGLaue'] in ['6/m','6/mmm','3m1', '31m', '3']: A = [parmDict[pfx+'A0'],parmDict[pfx+'A0'],parmDict[pfx+'A2'], parmDict[pfx+'A0'],0,0] elif SGData['SGLaue'] in ['3R', '3mR']: A = [parmDict[pfx+'A0'],parmDict[pfx+'A0'],parmDict[pfx+'A0'], parmDict[pfx+'A3'],parmDict[pfx+'A3'],parmDict[pfx+'A3']] elif SGData['SGLaue'] in ['m3m','m3']: A = [parmDict[pfx+'A0'],parmDict[pfx+'A0'],parmDict[pfx+'A0'],0,0,0] try: if SGData['SGLaue'] in ['-1',]: sigA = [sigDict[pfx+'A0'],sigDict[pfx+'A1'],sigDict[pfx+'A2'], sigDict[pfx+'A3'],sigDict[pfx+'A4'],sigDict[pfx+'A5']] elif SGData['SGLaue'] in ['2/m',]: if SGData['SGUniq'] == 'a': sigA = [sigDict[pfx+'A0'],sigDict[pfx+'A1'],sigDict[pfx+'A2'], 0,0,sigDict[pfx+'A5']] elif SGData['SGUniq'] == 'b': sigA = [sigDict[pfx+'A0'],sigDict[pfx+'A1'],sigDict[pfx+'A2'], 0,sigDict[pfx+'A4'],0] else: sigA = [sigDict[pfx+'A0'],sigDict[pfx+'A1'],sigDict[pfx+'A2'], sigDict[pfx+'A3'],0,0] elif SGData['SGLaue'] in ['mmm',]: sigA = [sigDict[pfx+'A0'],sigDict[pfx+'A1'],sigDict[pfx+'A2'],0,0,0] elif SGData['SGLaue'] in ['4/m','4/mmm']: sigA = [sigDict[pfx+'A0'],0,sigDict[pfx+'A2'],0,0,0] elif SGData['SGLaue'] in ['6/m','6/mmm','3m1', '31m', '3']: sigA = [sigDict[pfx+'A0'],0,sigDict[pfx+'A2'],0,0,0] elif SGData['SGLaue'] in ['3R', '3mR']: sigA = [sigDict[pfx+'A0'],0,0,sigDict[pfx+'A3'],0,0] elif SGData['SGLaue'] in ['m3m','m3']: sigA = [sigDict[pfx+'A0'],0,0,0,0,0] except KeyError: sigA = [0,0,0,0,0,0] return A,sigA
[docs]def PrintRestraints(cell,SGData,AtPtrs,Atoms,AtLookup,textureData,phaseRest,pFile): 'needs a doc string' if phaseRest: Amat = G2lat.cell2AB(cell)[0] cx,ct,cs = AtPtrs[:3] names = [['Bond','Bonds'],['Angle','Angles'],['Plane','Planes'], ['Chiral','Volumes'],['Torsion','Torsions'],['Rama','Ramas'], ['ChemComp','Sites'],['Texture','HKLs']] for name,rest in names: itemRest = phaseRest[name] if rest in itemRest and itemRest[rest] and itemRest['Use']: pFile.write('\n %s restraint weight factor %10.3f Use: %s\n'%(name,itemRest['wtFactor'],str(itemRest['Use']))) if name in ['Bond','Angle','Plane','Chiral']: pFile.write(' calc obs sig delt/sig atoms(symOp): \n') for indx,ops,obs,esd in itemRest[rest]: try: AtNames = G2mth.GetAtomItemsById(Atoms,AtLookup,indx,ct-1) AtName = '' for i,Aname in enumerate(AtNames): AtName += Aname if ops[i] == '1': AtName += '-' else: AtName += '+('+ops[i]+')-' XYZ = np.array(G2mth.GetAtomItemsById(Atoms,AtLookup,indx,cx,3)) XYZ = G2mth.getSyXYZ(XYZ,ops,SGData) if name == 'Bond': calc = G2mth.getRestDist(XYZ,Amat) elif name == 'Angle': calc = G2mth.getRestAngle(XYZ,Amat) elif name == 'Plane': calc = G2mth.getRestPlane(XYZ,Amat) elif name == 'Chiral': calc = G2mth.getRestChiral(XYZ,Amat) pFile.write(' %9.3f %9.3f %8.3f %8.3f %s\n'%(calc,obs,esd,(obs-calc)/esd,AtName[:-1])) except KeyError: del itemRest[rest] elif name in ['Torsion','Rama']: pFile.write(' atoms(symOp) calc obs sig delt/sig torsions: \n') coeffDict = itemRest['Coeff'] for indx,ops,cofName,esd in itemRest[rest]: AtNames = G2mth.GetAtomItemsById(Atoms,AtLookup,indx,ct-1) AtName = '' for i,Aname in enumerate(AtNames): AtName += Aname+'+('+ops[i]+')-' XYZ = np.array(G2mth.GetAtomItemsById(Atoms,AtLookup,indx,cx,3)) XYZ = G2mth.getSyXYZ(XYZ,ops,SGData) if name == 'Torsion': tor = G2mth.getRestTorsion(XYZ,Amat) restr,calc = G2mth.calcTorsionEnergy(tor,coeffDict[cofName]) pFile.write(' %8.3f %8.3f %.3f %8.3f %8.3f %s\n'%(calc,obs,esd,(obs-calc)/esd,tor,AtName[:-1])) else: phi,psi = G2mth.getRestRama(XYZ,Amat) restr,calc = G2mth.calcRamaEnergy(phi,psi,coeffDict[cofName]) pFile.write(' %8.3f %8.3f %8.3f %8.3f %8.3f %8.3f %s\n'%(calc,obs,esd,(obs-calc)/esd,phi,psi,AtName[:-1])) elif name == 'ChemComp': pFile.write(' atoms mul*frac factor prod\n') for indx,factors,obs,esd in itemRest[rest]: try: atoms = G2mth.GetAtomItemsById(Atoms,AtLookup,indx,ct-1) mul = np.array(G2mth.GetAtomItemsById(Atoms,AtLookup,indx,cs+1)) frac = np.array(G2mth.GetAtomItemsById(Atoms,AtLookup,indx,cs-1)) mulfrac = mul*frac calcs = mul*frac*factors for iatm,[atom,mf,fr,clc] in enumerate(zip(atoms,mulfrac,factors,calcs)): pFile.write(' %10s %8.3f %8.3f %8.3f\n'%(atom,mf,fr,clc)) pFile.write(' Sum: calc: %8.3f obs: %8.3f esd: %8.3f\n'%(np.sum(calcs),obs,esd)) except KeyError: del itemRest[rest] elif name == 'Texture' and textureData['Order']: Start = False SHCoef = textureData['SH Coeff'][1] shModels = ['cylindrical','none','shear - 2/m','rolling - mmm'] SamSym = dict(zip(shModels,['0','-1','2/m','mmm'])) pFile.write (' HKL grid neg esd sum neg num neg use unit? unit esd \n') for hkl,grid,esd1,ifesd2,esd2 in itemRest[rest]: phi,beta = G2lat.CrsAng(np.array(hkl),cell,SGData) ODFln = G2lat.Flnh(Start,SHCoef,phi,beta,SGData) R,P,Z = G2mth.getRestPolefig(ODFln,SamSym[textureData['Model']],grid) Z = ma.masked_greater(Z,0.0) num = ma.count(Z) sum = 0 if num: sum = np.sum(Z) pFile.write (' %d %d %d %d %8.3f %8.3f %8d %s %8.3f\n'%(hkl[0],hkl[1],hkl[2],grid,esd1,sum,num,str(ifesd2),esd2))
[docs]def getCellEsd(pfx,SGData,A,covData): '''Compute the standard uncertainty on cell parameters :param str pfx: prefix of form p\:\: :param SGdata: space group information :param list A: Reciprocal cell Ai terms :param dict covData: covariance tree item ''' rVsq = G2lat.calc_rVsq(A) G,g = G2lat.A2Gmat(A) #get recip. & real metric tensors RMnames = [pfx+'A0',pfx+'A1',pfx+'A2',pfx+'A3',pfx+'A4',pfx+'A5'] varyList = covData['varyList'] covMatrix = covData['covMatrix'] if len(covMatrix): vcov = G2mth.getVCov(RMnames,varyList,covMatrix) if SGData['SGLaue'] in ['3', '3m1', '31m', '6/m', '6/mmm']: vcov[1,1] = vcov[3,3] = vcov[0,1] = vcov[1,0] = vcov[0,0] vcov[1,3] = vcov[3,1] = vcov[0,3] = vcov[3,0] = vcov[0,0] vcov[1,2] = vcov[2,1] = vcov[2,3] = vcov[3,2] = vcov[0,2] elif SGData['SGLaue'] in ['m3','m3m']: vcov[0:3,0:3] = vcov[0,0] elif SGData['SGLaue'] in ['4/m', '4/mmm']: vcov[0:2,0:2] = vcov[0,0] vcov[1,2] = vcov[2,1] = vcov[0,2] elif SGData['SGLaue'] in ['3R','3mR']: vcov[0:3,0:3] = vcov[0,0] # vcov[4,4] = vcov[5,5] = vcov[3,3] vcov[3:6,3:6] = vcov[3,3] vcov[0:3,3:6] = vcov[0,3] vcov[3:6,0:3] = vcov[3,0] else: vcov = np.eye(6) delt = 1.e-9 drVdA = np.zeros(6) for i in range(6): A[i] += delt drVdA[i] = G2lat.calc_rVsq(A) A[i] -= 2*delt drVdA[i] -= G2lat.calc_rVsq(A) A[i] += delt drVdA /= 2.*delt srcvlsq = np.inner(drVdA,np.inner(drVdA,vcov)) Vol = 1/np.sqrt(rVsq) sigVol = Vol**3*np.sqrt(srcvlsq)/2. #ok - checks with GSAS dcdA = np.zeros((6,6)) for i in range(6): pdcdA =np.zeros(6) A[i] += delt pdcdA += G2lat.A2cell(A) A[i] -= 2*delt pdcdA -= G2lat.A2cell(A) A[i] += delt dcdA[i] = pdcdA/(2.*delt) sigMat = np.inner(dcdA,np.inner(dcdA,vcov)) var = np.diag(sigMat) CS = np.where(var>0.,np.sqrt(var),0.) if SGData['SGLaue'] in ['3', '3m1', '31m', '6/m', '6/mmm','m3','m3m','4/m','4/mmm']: CS[3:6] = 0.0 return [CS[0],CS[1],CS[2],CS[5],CS[4],CS[3],sigVol]
[docs]def getCellSU(pId,hId,SGData,parmDict,covData): '''Compute the unit cell parameters and standard uncertainties where lattice parameters and Hstrain (Dij) may be refined :param pId: phase index :param hId: histogram index :param SGdata: space group information :param dict parmDict: parameter dict, must have all non-zero Dij and Ai terms :param dict covData: covariance tree item ''' Dnames = ['{}:{}:D{}'.format(pId,hId,i) for i in ['11','22','33','12','13','23']] Anames = ['{}::A{}'.format(pId,i) for i in range(6)] Ai = [parmDict[i] for i in Anames] Dij = [parmDict.get(i,0.) for i in Dnames] A = np.array(Ai) + np.array(Dij) cell = list(G2lat.A2cell(A)) + [G2lat.calc_V(A)] rVsq = G2lat.calc_rVsq(A) G,g = G2lat.A2Gmat(A) #get recip. & real metric tensors varyList = covData['varyList'] covMatrix = covData['covMatrix'] if len(covMatrix): vcov = G2mth.getVCov(Anames+Dnames,varyList,covMatrix) for i in [0,6]: for j in [0,6]: if SGData['SGLaue'] in ['3', '3m1', '31m', '6/m', '6/mmm']: vcov[1+i,1+j] = vcov[3+i,3+j] = vcov[i,1+j] = vcov[1+i,j] = vcov[i,j] vcov[1+i,3+j] = vcov[3+i,1+j] = vcov[i,3+j] = vcov[3+i,j] = vcov[i,j] vcov[1+i,2+j] = vcov[2+i,1+j] = vcov[2+i,3+j] = vcov[3+i,2+j] = vcov[i,2+j] elif SGData['SGLaue'] in ['m3','m3m']: vcov[i:3+i,j:3+j] = vcov[i,j] elif SGData['SGLaue'] in ['4/m', '4/mmm']: vcov[i:2+i,j:2+j] = vcov[i,j] vcov[1+i,2+j] = vcov[2+i,1+j] = vcov[i,2+j] elif SGData['SGLaue'] in ['3R','3mR']: vcov[i:3+j,i:3+j] = vcov[i,j] # vcov[4,4] = vcov[5,5] = vcov[3,3] vcov[3+i:6+i,3+j:6+j] = vcov[3,3+j] vcov[i:3+i,3+j:6+j] = vcov[i,3+j] vcov[3+i:6+i,j:3+j] = vcov[3+i,j] else: vcov = np.eye(12) delt = 1.e-9 drVdA = np.zeros(12) for i in range(12): A[i%6] += delt drVdA[i] = G2lat.calc_rVsq(A) A[i%6] -= 2*delt drVdA[i] -= G2lat.calc_rVsq(A) A[i%6] += delt drVdA /= 2.*delt srcvlsq = np.inner(drVdA,np.inner(drVdA,vcov)) Vol = 1/np.sqrt(rVsq) sigVol = Vol**3*np.sqrt(srcvlsq)/2. #ok - checks with GSAS dcdA = np.zeros((12,12)) for i in range(12): pdcdA =np.zeros(12) A[i%6] += delt pdcdA += G2lat.A2cell(A)+G2lat.A2cell(A) A[i%6] -= 2*delt pdcdA -= G2lat.A2cell(A)+G2lat.A2cell(A) A[i%6] += delt dcdA[i] = pdcdA/(2.*delt) sigMat = np.inner(dcdA,np.inner(dcdA,vcov)) var = np.diag(sigMat) CS = np.where(var>0.,np.sqrt(var),0.) if SGData['SGLaue'] in ['3', '3m1', '31m', '6/m', '6/mmm','m3','m3m','4/m','4/mmm']: CS[3:6] = 0.0 return cell,[CS[0],CS[1],CS[2],CS[5],CS[4],CS[3],sigVol]
[docs]def SetPhaseData(parmDict,sigDict,Phases,RBIds,covData,RestraintDict=None,pFile=None): '''Called after a refinement to transfer parameters from the parameter dict to the phase(s) information read from a GPX file. Also prints values to the .lst file ''' def PrintAtomsAndSig(General,Atoms,atomsSig): pFile.write('\n Atoms:\n') line = ' name x y z frac Uiso U11 U22 U33 U12 U13 U23' if General['Type'] == 'macromolecular': line = ' res no residue chain '+line cx,ct,cs,cia = General['AtomPtrs'] pFile.write(line+'\n') pFile.write(135*'-'+'\n') fmt = {0:'%7s',ct:'%7s',cx:'%10.5f',cx+1:'%10.5f',cx+2:'%10.5f',cx+3:'%8.3f',cia+1:'%8.5f', cia+2:'%8.5f',cia+3:'%8.5f',cia+4:'%8.5f',cia+5:'%8.5f',cia+6:'%8.5f',cia+7:'%8.5f'} noFXsig = {cx:[10*' ','%10s'],cx+1:[10*' ','%10s'],cx+2:[10*' ','%10s'],cx+3:[8*' ','%8s']} for atyp in General['AtomTypes']: #zero composition General['NoAtoms'][atyp] = 0. for i,at in enumerate(Atoms): General['NoAtoms'][at[ct]] += at[cx+3]*float(at[cx+5]) #new composition if General['Type'] == 'macromolecular': name = ' %s %s %s %s:'%(at[0],at[1],at[2],at[3]) valstr = ' values: ' sigstr = ' sig : ' else: name = fmt[0]%(at[ct-1])+fmt[1]%(at[ct])+':' valstr = ' values:' sigstr = ' sig :' for ind in range(cx,cx+4): sigind = str(i)+':'+str(ind) valstr += fmt[ind]%(at[ind]) if sigind in atomsSig: sigstr += fmt[ind]%(atomsSig[sigind]) else: sigstr += noFXsig[ind][1]%(noFXsig[ind][0]) if at[cia] == 'I': valstr += fmt[cia+1]%(at[cia+1]) if '%d:%d'%(i,cia+1) in atomsSig: sigstr += fmt[cia+1]%(atomsSig['%d:%d'%(i,cia+1)]) else: sigstr += 8*' ' else: valstr += 8*' ' sigstr += 8*' ' for ind in range(cia+2,cia+8): sigind = str(i)+':'+str(ind) valstr += fmt[ind]%(at[ind]) if sigind in atomsSig: sigstr += fmt[ind]%(atomsSig[sigind]) else: sigstr += 8*' ' pFile.write(name+'\n') pFile.write(valstr+'\n') pFile.write(sigstr+'\n') def PrintMomentsAndSig(General,Atoms,atomsSig): cell = General['Cell'][1:7] G = G2lat.fillgmat(cell) ast = np.sqrt(np.diag(G)) GS = G/np.outer(ast,ast) pFile.write('\n Magnetic Moments:\n') #add magnitude & angle, etc.? TBD line = ' name Mx My Mz |Mag|' cx,ct,cs,cia = General['AtomPtrs'] cmx = cx+4 AtInfo = dict(zip(General['AtomTypes'],General['Lande g'])) pFile.write(line+'\n') pFile.write(135*'-'+'\n') fmt = {0:'%7s',ct:'%7s',cmx:'%10.3f',cmx+1:'%10.3f',cmx+2:'%10.3f'} noFXsig = {cmx:[10*' ','%10s'],cmx+1:[10*' ','%10s'],cmx+2:[10*' ','%10s']} for i,at in enumerate(Atoms): if AtInfo[at[ct]]: name = fmt[0]%(at[ct-1])+fmt[1]%(at[ct])+':' valstr = ' values:' sigstr = ' sig :' for ind in range(cmx,cmx+3): sigind = str(i)+':'+str(ind) valstr += fmt[ind]%(at[ind]) if sigind in atomsSig: sigstr += fmt[ind]%(atomsSig[sigind]) else: sigstr += noFXsig[ind][1]%(noFXsig[ind][0]) mag = np.array(at[cmx:cmx+3]) Mag = np.sqrt(np.inner(mag,np.inner(mag,GS))) valstr += '%10.3f'%Mag sigstr += 10*' ' pFile.write(name+'\n') pFile.write(valstr+'\n') pFile.write(sigstr+'\n') def PrintWavesAndSig(General,Atoms,wavesSig): cx,ct,cs,cia = General['AtomPtrs'] pFile.write('\n Modulation waves\n') names = {'Sfrac':['Fsin','Fcos','Fzero','Fwid'],'Spos':['Xsin','Ysin','Zsin','Xcos','Ycos','Zcos','Tmin','Tmax','Xmax','Ymax','Zmax'], 'Sadp':['U11sin','U22sin','U33sin','U12sin','U13sin','U23sin','U11cos','U22cos', 'U33cos','U12cos','U13cos','U23cos'],'Smag':['MXsin','MYsin','MZsin','MXcos','MYcos','MZcos']} pFile.write(135*'-'+'\n') for i,at in enumerate(Atoms): AtomSS = at[-1]['SS1'] for Stype in ['Sfrac','Spos','Sadp','Smag']: Waves = AtomSS[Stype] if len(Waves) > 1: waveType = Waves[0] else: continue if len(Waves): pFile.write(' atom: %s, site sym: %s, type: %s wave type: %s:\n'% (at[ct-1],at[cs],Stype,waveType)) for iw,wave in enumerate(Waves[1:]): stiw = ':'+str(i)+':'+str(iw) namstr = ' names :' valstr = ' values:' sigstr = ' esds :' if Stype == 'Spos': nt = 6 ot = 0 if waveType in ['ZigZag','Block',] and not iw: nt = 5 ot = 6 for j in range(nt): name = names['Spos'][j+ot] namstr += '%12s'%(name) valstr += '%12.4f'%(wave[0][j]) if name+stiw in wavesSig: sigstr += '%12.4f'%(wavesSig[name+stiw]) else: sigstr += 12*' ' elif Stype == 'Sfrac': ot = 0 if 'Crenel' in waveType and not iw: ot = 2 for j in range(2): name = names['Sfrac'][j+ot] namstr += '%12s'%(names['Sfrac'][j+ot]) valstr += '%12.4f'%(wave[0][j]) if name+stiw in wavesSig: sigstr += '%12.4f'%(wavesSig[name+stiw]) else: sigstr += 12*' ' elif Stype == 'Sadp': for j in range(12): name = names['Sadp'][j] namstr += '%10s'%(names['Sadp'][j]) valstr += '%10.6f'%(wave[0][j]) if name+stiw in wavesSig: sigstr += '%10.6f'%(wavesSig[name+stiw]) else: sigstr += 10*' ' elif Stype == 'Smag': for j in range(6): name = names['Smag'][j] namstr += '%12s'%(names['Smag'][j]) valstr += '%12.4f'%(wave[0][j]) if name+stiw in wavesSig: sigstr += '%12.4f'%(wavesSig[name+stiw]) else: sigstr += 12*' ' pFile.write(namstr+'\n') pFile.write(valstr+'\n') pFile.write(sigstr+'\n') def PrintRBObjPOAndSig(rbfx,rbsx): for i in WriteRBObjPOAndSig(pfx,rbfx,rbsx,parmDict,sigDict): pFile.write(i+'\n') def PrintRBObjTLSAndSig(rbfx,rbsx,TLS): for i in WriteRBObjTLSAndSig(pfx,rbfx,rbsx,TLS,parmDict,sigDict): pFile.write(i) def PrintRBObjTorAndSig(rbsx): nTors = len(RBObj['Torsions']) if nTors: for i in WriteRBObjTorAndSig(pfx,rbsx,parmDict,sigDict,nTors): pFile.write(i) def PrintSHtextureAndSig(textureData,SHtextureSig): Tindx = 1.0 Tvar = 0.0 pFile.write('\n Spherical harmonics texture: Order: %d\n'%textureData['Order']) names = ['omega','chi','phi'] namstr = ' names :' ptstr = ' values:' sigstr = ' esds :' for name in names: namstr += '%12s'%(name) ptstr += '%12.3f'%(textureData['Sample '+name][1]) if 'Sample '+name in SHtextureSig: sigstr += '%12.3f'%(SHtextureSig['Sample '+name]) else: sigstr += 12*' ' pFile.write(namstr+'\n') pFile.write(ptstr+'\n') pFile.write(sigstr+'\n') pFile.write('\n Texture coefficients:\n') SHcoeff = textureData['SH Coeff'][1] SHkeys = list(SHcoeff.keys()) nCoeff = len(SHcoeff) nBlock = nCoeff//10+1 iBeg = 0 iFin = min(iBeg+10,nCoeff) for block in range(nBlock): namstr = ' names :' ptstr = ' values:' sigstr = ' esds :' for name in SHkeys[iBeg:iFin]: namstr += '%12s'%(name) ptstr += '%12.3f'%(SHcoeff[name]) l = 2.0*eval(name.strip('C'))[0]+1 Tindx += SHcoeff[name]**2/l if name in SHtextureSig: Tvar += (2.*SHcoeff[name]*SHtextureSig[name]/l)**2 sigstr += '%12.3f'%(SHtextureSig[name]) else: sigstr += 12*' ' pFile.write(namstr+'\n') pFile.write(ptstr+'\n') pFile.write(sigstr+'\n') iBeg += 10 iFin = min(iBeg+10,nCoeff) pFile.write(' Texture index J = %.3f(%d)'%(Tindx,int(1000*np.sqrt(Tvar)))) ########################################################################## # SetPhaseData starts here if pFile: pFile.write('\n Phases:\n') for phase in Phases: if pFile: pFile.write(' Result for phase: %s\n'%phase) if pFile: pFile.write(135*'='+'\n') Phase = Phases[phase] General = Phase['General'] SGData = General['SGData'] Atoms = Phase['Atoms'] AtLookup = [] if Atoms and not General.get('doPawley'): cx,ct,cs,cia = General['AtomPtrs'] AtLookup = G2mth.FillAtomLookUp(Atoms,cia+8) cell = General['Cell'] pId = Phase['pId'] pfx = str(pId)+'::' if cell[0]: A,sigA = cellFill(pfx,SGData,parmDict,sigDict) cellSig = getCellEsd(pfx,SGData,A,covData) #includes sigVol if pFile: pFile.write(' Reciprocal metric tensor: \n') ptfmt = "%15.9f" names = ['A11','A22','A33','A12','A13','A23'] namstr = ' names :' ptstr = ' values:' sigstr = ' esds :' for name,a,siga in zip(names,A,sigA): namstr += '%15s'%(name) ptstr += ptfmt%(a) if siga: sigstr += ptfmt%(siga) else: sigstr += 15*' ' if pFile: pFile.write(namstr+'\n') if pFile: pFile.write(ptstr+'\n') if pFile: pFile.write(sigstr+'\n') cell[1:7] = G2lat.A2cell(A) cell[7] = G2lat.calc_V(A) if pFile: pFile.write(' New unit cell:\n') ptfmt = ["%12.6f","%12.6f","%12.6f","%12.4f","%12.4f","%12.4f","%12.3f"] names = ['a','b','c','alpha','beta','gamma','Volume'] namstr = ' names :' ptstr = ' values:' sigstr = ' esds :' for name,fmt,a,siga in zip(names,ptfmt,cell[1:8],cellSig): namstr += '%12s'%(name) ptstr += fmt%(a) if siga: sigstr += fmt%(siga) else: sigstr += 12*' ' if pFile: pFile.write(namstr+'\n') if pFile: pFile.write(ptstr+'\n') if pFile: pFile.write(sigstr+'\n') ik = 6 #for Pawley stuff below if General.get('Modulated',False): ik = 7 Vec,vRef,maxH = General['SuperVec'] if vRef: if pFile: pFile.write(' New modulation vector:\n') namstr = ' names :' ptstr = ' values:' sigstr = ' esds :' for iv,var in enumerate(['mV0','mV1','mV2']): namstr += '%12s'%(pfx+var) ptstr += '%12.6f'%(parmDict[pfx+var]) if pfx+var in sigDict: Vec[iv] = parmDict[pfx+var] sigstr += '%12.6f'%(sigDict[pfx+var]) else: sigstr += 12*' ' if pFile: pFile.write(namstr+'\n') if pFile: pFile.write(ptstr+'\n') if pFile: pFile.write(sigstr+'\n') General['Mass'] = 0. if Phase['General'].get('doPawley'): pawleyRef = Phase['Pawley ref'] for i,refl in enumerate(pawleyRef): key = pfx+'PWLref:'+str(i) refl[ik] = parmDict[key] if key in sigDict: refl[ik+1] = sigDict[key] else: refl[ik+1] = 0 else: VRBIds = RBIds['Vector'] RRBIds = RBIds['Residue'] RBModels = Phase['RBModels'] if pFile: for irb,RBObj in enumerate(RBModels.get('Vector',[])): jrb = VRBIds.index(RBObj['RBId']) rbsx = str(irb)+':'+str(jrb) pFile.write(' Vector rigid body parameters:\n') PrintRBObjPOAndSig('RBV',rbsx) PrintRBObjTLSAndSig('RBV',rbsx,RBObj['ThermalMotion'][0]) for irb,RBObj in enumerate(RBModels.get('Residue',[])): jrb = RRBIds.index(RBObj['RBId']) rbsx = str(irb)+':'+str(jrb) pFile.write(' Residue rigid body parameters:\n') PrintRBObjPOAndSig('RBR',rbsx) PrintRBObjTLSAndSig('RBR',rbsx,RBObj['ThermalMotion'][0]) PrintRBObjTorAndSig(rbsx) atomsSig = {} wavesSig = {} cx,ct,cs,cia = General['AtomPtrs'] for i,at in enumerate(Atoms): names = {cx:pfx+'Ax:'+str(i),cx+1:pfx+'Ay:'+str(i),cx+2:pfx+'Az:'+str(i),cx+3:pfx+'Afrac:'+str(i), cia+1:pfx+'AUiso:'+str(i),cia+2:pfx+'AU11:'+str(i),cia+3:pfx+'AU22:'+str(i),cia+4:pfx+'AU33:'+str(i), cia+5:pfx+'AU12:'+str(i),cia+6:pfx+'AU13:'+str(i),cia+7:pfx+'AU23:'+str(i), cx+4:pfx+'AMx:'+str(i),cx+5:pfx+'AMy:'+str(i),cx+6:pfx+'AMz:'+str(i)} for ind in range(cx,cx+4): at[ind] = parmDict[names[ind]] if ind in range(cx,cx+3): name = names[ind].replace('A','dA') else: name = names[ind] if name in sigDict: atomsSig[str(i)+':'+str(ind)] = sigDict[name] if at[cia] == 'I': at[cia+1] = parmDict[names[cia+1]] if names[cia+1] in sigDict: atomsSig['%d:%d'%(i,cia+1)] = sigDict[names[cia+1]] else: for ind in range(cia+2,cia+8): at[ind] = parmDict[names[ind]] if names[ind] in sigDict: atomsSig[str(i)+':'+str(ind)] = sigDict[names[ind]] if General['Type'] == 'magnetic': for ind in range(cx+4,cx+7): at[ind] = parmDict[names[ind]] if names[ind] in sigDict: atomsSig[str(i)+':'+str(ind)] = sigDict[names[ind]] ind = General['AtomTypes'].index(at[ct]) General['Mass'] += General['AtomMass'][ind]*at[cx+3]*at[cx+5] if General.get('Modulated',False): AtomSS = at[-1]['SS1'] for Stype in ['Sfrac','Spos','Sadp','Smag']: Waves = AtomSS[Stype] if len(Waves): waveType = Waves[0] else: continue for iw,wave in enumerate(Waves[1:]): stiw = str(i)+':'+str(iw) if Stype == 'Spos': if waveType in ['ZigZag','Block',] and not iw: names = ['Tmin:'+stiw,'Tmax:'+stiw,'Xmax:'+stiw,'Ymax:'+stiw,'Zmax:'+stiw] else: names = ['Xsin:'+stiw,'Ysin:'+stiw,'Zsin:'+stiw, 'Xcos:'+stiw,'Ycos:'+stiw,'Zcos:'+stiw] elif Stype == 'Sadp': names = ['U11sin:'+stiw,'U22sin:'+stiw,'U33sin:'+stiw, 'U12sin:'+stiw,'U13sin:'+stiw,'U23sin:'+stiw, 'U11cos:'+stiw,'U22cos:'+stiw,'U33cos:'+stiw, 'U12cos:'+stiw,'U13cos:'+stiw,'U23cos:'+stiw] elif Stype == 'Sfrac': if 'Crenel' in waveType and not iw: names = ['Fzero:'+stiw,'Fwid:'+stiw] else: names = ['Fsin:'+stiw,'Fcos:'+stiw] elif Stype == 'Smag': names = ['MXsin:'+stiw,'MYsin:'+stiw,'MZsin:'+stiw, 'MXcos:'+stiw,'MYcos:'+stiw,'MZcos:'+stiw] for iname,name in enumerate(names): AtomSS[Stype][iw+1][0][iname] = parmDict[pfx+name] if pfx+name in sigDict: wavesSig[name] = sigDict[pfx+name] if pFile: PrintAtomsAndSig(General,Atoms,atomsSig) if pFile and General['Type'] == 'magnetic': PrintMomentsAndSig(General,Atoms,atomsSig) if pFile and General.get('Modulated',False): PrintWavesAndSig(General,Atoms,wavesSig) density = G2mth.getDensity(General)[0] if pFile: pFile.write('\n Density: {:.4f} g/cm**3\n'.format(density)) textureData = General['SH Texture'] if textureData['Order']: SHtextureSig = {} for name in ['omega','chi','phi']: aname = pfx+'SH '+name textureData['Sample '+name][1] = parmDict[aname] if aname in sigDict: SHtextureSig['Sample '+name] = sigDict[aname] for name in textureData['SH Coeff'][1]: aname = pfx+name textureData['SH Coeff'][1][name] = parmDict[aname] if aname in sigDict: SHtextureSig[name] = sigDict[aname] PrintSHtextureAndSig(textureData,SHtextureSig) if phase in RestraintDict and not Phase['General'].get('doPawley'): PrintRestraints(cell[1:7],SGData,General['AtomPtrs'],Atoms,AtLookup, textureData,RestraintDict[phase],pFile)
################################################################################ ##### Histogram & Phase data ################################################################################
[docs]def GetHistogramPhaseData(Phases,Histograms,Print=True,pFile=None,resetRefList=True): '''Loads the HAP histogram/phase information into dicts :param dict Phases: phase information :param dict Histograms: Histogram information :param bool Print: prints information as it is read :param file pFile: file object to print to (the default, None causes printing to the console) :param bool resetRefList: Should the contents of the Reflection List be initialized on loading. The default, True, initializes the Reflection List as it is loaded. :returns: (hapVary,hapDict,controlDict) * hapVary: list of refined variables * hapDict: dict with refined variables and their values * controlDict: dict with fixed parameters ''' def PrintSize(hapData): if hapData[0] in ['isotropic','uniaxial']: line = '\n Size model : %9s'%(hapData[0]) line += ' equatorial:'+'%12.3f'%(hapData[1][0])+' Refine? '+str(hapData[2][0]) if hapData[0] == 'uniaxial': line += ' axial:'+'%12.3f'%(hapData[1][1])+' Refine? '+str(hapData[2][1]) line += '\n\t LG mixing coeff.: %12.4f'%(hapData[1][2])+' Refine? '+str(hapData[2][2]) pFile.write(line+'\n') else: pFile.write('\n Size model : %s\n\t LG mixing coeff.:%12.4f Refine? %s\n'% (hapData[0],hapData[1][2],hapData[2][2])) Snames = ['S11','S22','S33','S12','S13','S23'] ptlbls = ' names :' ptstr = ' values:' varstr = ' refine:' for i,name in enumerate(Snames): ptlbls += '%12s' % (name) ptstr += '%12.3f' % (hapData[4][i]) varstr += '%12s' % (str(hapData[5][i])) pFile.write(ptlbls+'\n') pFile.write(ptstr+'\n') pFile.write(varstr+'\n') def PrintMuStrain(hapData,SGData): if hapData[0] in ['isotropic','uniaxial']: line = '\n Mustrain model: %9s'%(hapData[0]) line += ' equatorial:'+'%12.1f'%(hapData[1][0])+' Refine? '+str(hapData[2][0]) if hapData[0] == 'uniaxial': line += ' axial:'+'%12.1f'%(hapData[1][1])+' Refine? '+str(hapData[2][1]) line +='\n\t LG mixing coeff.:%12.4f'%(hapData[1][2])+' Refine? '+str(hapData[2][2]) pFile.write(line+'\n') else: pFile.write('\n Mustrain model: %s\n\t LG mixing coeff.:%12.4f Refine? %s\n'% (hapData[0],hapData[1][2],hapData[2][2])) Snames = G2spc.MustrainNames(SGData) ptlbls = ' names :' ptstr = ' values:' varstr = ' refine:' for i,name in enumerate(Snames): ptlbls += '%12s' % (name) ptstr += '%12.1f' % (hapData[4][i]) varstr += '%12s' % (str(hapData[5][i])) pFile.write(ptlbls+'\n') pFile.write(ptstr+'\n') pFile.write(varstr+'\n') def PrintHStrain(hapData,SGData): pFile.write('\n Hydrostatic/elastic strain:\n') Hsnames = G2spc.HStrainNames(SGData) ptlbls = ' names :' ptstr = ' values:' varstr = ' refine:' for i,name in enumerate(Hsnames): ptlbls += '%12s' % (name) ptstr += '%12.4g' % (hapData[0][i]) varstr += '%12s' % (str(hapData[1][i])) pFile.write(ptlbls+'\n') pFile.write(ptstr+'\n') pFile.write(varstr+'\n') def PrintSHPO(hapData): pFile.write('\n Spherical harmonics preferred orientation: Order: %d Refine? %s\n'%(hapData[4],hapData[2])) ptlbls = ' names :' ptstr = ' values:' for item in hapData[5]: ptlbls += '%12s'%(item) ptstr += '%12.3f'%(hapData[5][item]) pFile.write(ptlbls+'\n') pFile.write(ptstr+'\n') def PrintBabinet(hapData): pFile.write('\n Babinet form factor modification:\n') ptlbls = ' names :' ptstr = ' values:' varstr = ' refine:' for name in ['BabA','BabU']: ptlbls += '%12s' % (name) ptstr += '%12.6f' % (hapData[name][0]) varstr += '%12s' % (str(hapData[name][1])) pFile.write(ptlbls+'\n') pFile.write(ptstr+'\n') pFile.write(varstr+'\n') hapDict = {} hapVary = [] controlDict = {} for phase in Phases: HistoPhase = Phases[phase]['Histograms'] SGData = Phases[phase]['General']['SGData'] cell = Phases[phase]['General']['Cell'][1:7] A = G2lat.cell2A(cell) if Phases[phase]['General'].get('Modulated',False): SSGData = Phases[phase]['General']['SSGData'] Vec,x,maxH = Phases[phase]['General']['SuperVec'] pId = Phases[phase]['pId'] for histogram in Histograms: if histogram not in HistoPhase and phase in Histograms[histogram]['Reflection Lists']: #remove previously created reflection list if histogram is removed from phase #print("removing ",phase,"from",histogram) del Histograms[histogram]['Reflection Lists'][phase] histoList = list(HistoPhase.keys()) histoList.sort() for histogram in histoList: try: Histogram = Histograms[histogram] except KeyError: #skip if histogram not included e.g. in a sequential refinement continue if not HistoPhase[histogram]['Use']: #remove previously created & now unused phase reflection list if phase in Histograms[histogram]['Reflection Lists']: del Histograms[histogram]['Reflection Lists'][phase] continue hapData = HistoPhase[histogram] hId = Histogram['hId'] if 'PWDR' in histogram: limits = Histogram['Limits'][1] inst = Histogram['Instrument Parameters'][0] #TODO - grab table here if present if 'C' in inst['Type'][1]: try: wave = inst['Lam'][1] except KeyError: wave = inst['Lam1'][1] dmin = wave/(2.0*sind(limits[1]/2.0)) elif 'T' in inst['Type'][0]: dmin = limits[0]/inst['difC'][1] else: wave = inst['Lam'][1] dmin = wave/(2.0*sind(limits[1]/2.0)) pfx = str(pId)+':'+str(hId)+':' if Phases[phase]['General']['doPawley']: hapDict[pfx+'LeBail'] = False #Pawley supercedes LeBail hapDict[pfx+'newLeBail'] = True Tmin = G2lat.Dsp2pos(inst,dmin) if 'T' in inst['Type'][1]: limits[0] = max(limits[0],Tmin) else: limits[1] = min(limits[1],Tmin) else: hapDict[pfx+'LeBail'] = hapData.get('LeBail',False) hapDict[pfx+'newLeBail'] = hapData.get('newLeBail',True) if Phases[phase]['General']['Type'] == 'magnetic': dmin = max(dmin,Phases[phase]['General'].get('MagDmin',0.)) for item in ['Scale','Extinction']: hapDict[pfx+item] = hapData[item][0] if hapData[item][1] and not hapDict[pfx+'LeBail']: hapVary.append(pfx+item) names = G2spc.HStrainNames(SGData) HSvals = [] for i,name in enumerate(names): hapDict[pfx+name] = hapData['HStrain'][0][i] HSvals.append(hapDict[pfx+name]) if hapData['HStrain'][1][i]: hapVary.append(pfx+name) if 'Layer Disp' in hapData: hapDict[pfx+'LayerDisp'] = hapData['Layer Disp'][0] if hapData['Layer Disp'][1]: hapVary.append(pfx+'LayerDisp') else: hapDict[pfx+'LayerDisp'] = 0.0 controlDict[pfx+'poType'] = hapData['Pref.Ori.'][0] if hapData['Pref.Ori.'][0] == 'MD': hapDict[pfx+'MD'] = hapData['Pref.Ori.'][1] controlDict[pfx+'MDAxis'] = hapData['Pref.Ori.'][3] if hapData['Pref.Ori.'][2] and not hapDict[pfx+'LeBail']: hapVary.append(pfx+'MD') else: #'SH' spherical harmonics controlDict[pfx+'SHord'] = hapData['Pref.Ori.'][4] controlDict[pfx+'SHncof'] = len(hapData['Pref.Ori.'][5]) controlDict[pfx+'SHnames'] = G2lat.GenSHCoeff(SGData['SGLaue'],'0',controlDict[pfx+'SHord'],False) controlDict[pfx+'SHhkl'] = [] try: #patch for old Pref.Ori. items controlDict[pfx+'SHtoler'] = 0.1 if hapData['Pref.Ori.'][6][0] != '': controlDict[pfx+'SHhkl'] = [eval(a.replace(' ',',')) for a in hapData['Pref.Ori.'][6]] controlDict[pfx+'SHtoler'] = hapData['Pref.Ori.'][7] except IndexError: pass for item in hapData['Pref.Ori.'][5]: hapDict[pfx+item] = hapData['Pref.Ori.'][5][item] if hapData['Pref.Ori.'][2] and not hapDict[pfx+'LeBail']: hapVary.append(pfx+item) for item in ['Mustrain','Size']: controlDict[pfx+item+'Type'] = hapData[item][0] hapDict[pfx+item+';mx'] = hapData[item][1][2] if hapData[item][2][2]: hapVary.append(pfx+item+';mx') if hapData[item][0] in ['isotropic','uniaxial']: hapDict[pfx+item+';i'] = hapData[item][1][0] if hapData[item][2][0]: hapVary.append(pfx+item+';i') if hapData[item][0] == 'uniaxial': controlDict[pfx+item+'Axis'] = hapData[item][3] hapDict[pfx+item+';a'] = hapData[item][1][1] if hapData[item][2][1]: hapVary.append(pfx+item+';a') else: #generalized for mustrain or ellipsoidal for size Nterms = len(hapData[item][4]) if item == 'Mustrain': names = G2spc.MustrainNames(SGData) pwrs = [] for name in names: h,k,l = name[1:] pwrs.append([int(h),int(k),int(l)]) controlDict[pfx+'MuPwrs'] = pwrs for i in range(Nterms): sfx = ';'+str(i) hapDict[pfx+item+sfx] = hapData[item][4][i] if hapData[item][5][i]: hapVary.append(pfx+item+sfx) if Phases[phase]['General']['Type'] != 'magnetic': for bab in ['BabA','BabU']: hapDict[pfx+bab] = hapData['Babinet'][bab][0] if hapData['Babinet'][bab][1] and not hapDict[pfx+'LeBail']: hapVary.append(pfx+bab) if Print: pFile.write('\n Phase: %s in histogram: %s\n'%(phase,histogram)) pFile.write(135*'='+'\n') if hapDict[pfx+'LeBail']: pFile.write(' Perform LeBail extraction\n') else: pFile.write(' Phase fraction : %10.4g Refine? %s\n'%(hapData['Scale'][0],hapData['Scale'][1])) pFile.write(' Extinction coeff: %10.4f Refine? %s\n'%(hapData['Extinction'][0],hapData['Extinction'][1])) if hapData['Pref.Ori.'][0] == 'MD': Ax = hapData['Pref.Ori.'][3] pFile.write(' March-Dollase PO: %10.4f Refine? %s Axis: %d %d %d\n'% (hapData['Pref.Ori.'][1],hapData['Pref.Ori.'][2],Ax[0],Ax[1],Ax[2])) else: #'SH' for spherical harmonics PrintSHPO(hapData['Pref.Ori.']) pFile.write(' Penalty hkl list: %s tolerance: %.2f\n'%(controlDict[pfx+'SHhkl'],controlDict[pfx+'SHtoler'])) PrintSize(hapData['Size']) PrintMuStrain(hapData['Mustrain'],SGData) PrintHStrain(hapData['HStrain'],SGData) if 'Layer Disp' in hapData: pFile.write(' Layer Displacement: %10.3f Refine? %s\n'%(hapData['Layer Disp'][0],hapData['Layer Disp'][1])) if Phases[phase]['General']['Type'] != 'magnetic': if hapData['Babinet']['BabA'][0]: PrintBabinet(hapData['Babinet']) if phase in Histogram['Reflection Lists'] and 'RefList' not in Histogram['Reflection Lists'][phase] and hapData.get('LeBail',False): hapData['newLeBail'] = True if resetRefList and (not hapDict[pfx+'LeBail'] or (hapData.get('LeBail',False) and hapData['newLeBail'])): if hapData.get('LeBail',True): #stop regeneating reflections for LeBail hapData['newLeBail'] = False refList = [] # Uniq = [] # Phi = [] useExt = 'magnetic' in Phases[phase]['General']['Type'] and 'N' in inst['Type'][0] if Phases[phase]['General'].get('Modulated',False): ifSuper = True HKLd = np.array(G2lat.GenSSHLaue(dmin,SGData,SSGData,Vec,maxH,A)) HKLd = G2mth.sortArray(HKLd,4,reverse=True) for h,k,l,m,d in HKLd: ext,mul,uniq,phi = G2spc.GenHKLf([h,k,l],SGData) mul *= 2 # for powder overlap of Friedel pairs if m or not ext or useExt: if 'C' in inst['Type'][0]: pos = G2lat.Dsp2pos(inst,d) if limits[0] < pos < limits[1]: refList.append([h,k,l,m,mul,d, pos,0.0,0.0,0.0,1., 0.0,0.0,1.0,1.0,1.0]) #... sig,gam,fotsq,fctsq, phase,icorr,prfo,abs,ext # Uniq.append(uniq) # Phi.append(phi) elif 'T' in inst['Type'][0]: pos = G2lat.Dsp2pos(inst,d) if limits[0] < pos < limits[1]: wave = inst['difC'][1]*d/(252.816*inst['fltPath'][0]) refList.append([h,k,l,m,mul,d, pos,0.0,0.0,0.0,1., 0.0,0.0,0.0,0.0,wave, 1.0,1.0,1.0]) # ... sig,gam,fotsq,fctsq, phase,icorr,alp,bet,wave, prfo,abs,ext #TODO - if tabulated put alp & bet in here # Uniq.append(uniq) # Phi.append(phi) elif 'B' in inst['Type'][0]: pos = G2lat.Dsp2pos(inst,d) if limits[0] < pos < limits[1]: refList.append([h,k,l,m,mul,d, pos,0.0,0.0,0.0,1., 0.0,0.0,0.0,0.0, 1.0,1.0,1.0]) # ... sig,gam,fotsq,fctsq, phase,icorr,alp,bet, prfo,abs,ext else: ifSuper = False HKLd = np.array(G2lat.GenHLaue(dmin,SGData,A)) HKLd = G2mth.sortArray(HKLd,3,reverse=True) for h,k,l,d in HKLd: ext,mul,uniq,phi = G2spc.GenHKLf([h,k,l],SGData) if ext and 'N' in inst['Type'][0] and 'MagSpGrp' in SGData: ext = G2spc.checkMagextc([h,k,l],SGData) mul *= 2 # for powder overlap of Friedel pairs if ext and not useExt: continue if 'C' in inst['Type'][0]: pos = G2lat.Dsp2pos(inst,d) if limits[0] < pos < limits[1]: refList.append([h,k,l,mul,d, pos,0.0,0.0,0.0,1., 0.0,0.0,1.0,1.0,1.0]) #... sig,gam,fotsq,fctsq, phase,icorr,prfo,abs,ext # Uniq.append(uniq) # Phi.append(phi) elif 'T' in inst['Type'][0]: pos = G2lat.Dsp2pos(inst,d) if limits[0] < pos < limits[1]: wave = inst['difC'][1]*d/(252.816*inst['fltPath'][0]) refList.append([h,k,l,mul,d, pos,0.0,0.0,0.0,1., 0.0,0.0,0.0,0.0,wave, 1.0,1.0,1.0]) # ... sig,gam,fotsq,fctsq, phase,icorr,alp,bet,wave, prfo,abs,ext # Uniq.append(uniq) # Phi.append(phi) elif 'B' in inst['Type'][0]: pos = G2lat.Dsp2pos(inst,d) if limits[0] < pos < limits[1]: refList.append([h,k,l,mul,d, pos,0.0,0.0,0.0,1., 0.0,0.0,0.0,0.0, 1.0,1.0,1.0]) # ... sig,gam,fotsq,fctsq, phase,icorr,alp,bet, prfo,abs,ext Histogram['Reflection Lists'][phase] = {'RefList':np.array(refList),'FF':{},'Type':inst['Type'][0],'Super':ifSuper} elif 'HKLF' in histogram: inst = Histogram['Instrument Parameters'][0] hId = Histogram['hId'] hfx = ':%d:'%(hId) for item in inst: if type(inst) is not list and item != 'Type': continue # skip over non-refined items (such as InstName) hapDict[hfx+item] = inst[item][1] pfx = str(pId)+':'+str(hId)+':' hapDict[pfx+'Scale'] = hapData['Scale'][0] if hapData['Scale'][1]: hapVary.append(pfx+'Scale') extApprox,extType,extParms = hapData['Extinction'] controlDict[pfx+'EType'] = extType controlDict[pfx+'EApprox'] = extApprox if 'C' in inst['Type'][0]: controlDict[pfx+'Tbar'] = extParms['Tbar'] controlDict[pfx+'Cos2TM'] = extParms['Cos2TM'] if 'Primary' in extType: Ekey = ['Ep',] elif 'I & II' in extType: Ekey = ['Eg','Es'] elif 'Secondary Type II' == extType: Ekey = ['Es',] elif 'Secondary Type I' == extType: Ekey = ['Eg',] else: #'None' Ekey = [] for eKey in Ekey: hapDict[pfx+eKey] = extParms[eKey][0] if extParms[eKey][1]: hapVary.append(pfx+eKey) for bab in ['BabA','BabU']: hapDict[pfx+bab] = hapData['Babinet'][bab][0] if hapData['Babinet'][bab][1]: hapVary.append(pfx+bab) Twins = hapData.get('Twins',[[np.array([[1,0,0],[0,1,0],[0,0,1]]),[1.0,False,0]],]) if len(Twins) == 1: hapDict[pfx+'Flack'] = hapData.get('Flack',[0.,False])[0] if hapData.get('Flack',[0,False])[1]: hapVary.append(pfx+'Flack') sumTwFr = 0. controlDict[pfx+'TwinLaw'] = [] controlDict[pfx+'TwinInv'] = [] NTL = 0 for it,twin in enumerate(Twins): if 'bool' in str(type(twin[0])): controlDict[pfx+'TwinInv'].append(twin[0]) controlDict[pfx+'TwinLaw'].append(np.zeros((3,3))) else: NTL += 1 controlDict[pfx+'TwinInv'].append(False) controlDict[pfx+'TwinLaw'].append(twin[0]) if it: hapDict[pfx+'TwinFr:'+str(it)] = twin[1] sumTwFr += twin[1] else: hapDict[pfx+'TwinFr:0'] = twin[1][0] controlDict[pfx+'TwinNMN'] = twin[1][1] if Twins[0][1][1]: hapVary.append(pfx+'TwinFr:'+str(it)) controlDict[pfx+'NTL'] = NTL #need to make constraint on TwinFr controlDict[pfx+'TwinLaw'] = np.array(controlDict[pfx+'TwinLaw']) if len(Twins) > 1: #force sum to unity hapDict[pfx+'TwinFr:0'] = 1.-sumTwFr if Print: pFile.write('\n Phase: %s in histogram: %s\n'%(phase,histogram)) pFile.write(135*'='+'\n') pFile.write(' Scale factor : %10.4g Refine? %s\n'%(hapData['Scale'][0],hapData['Scale'][1])) if extType != 'None': pFile.write(' Extinction Type: %15s approx: %10s\n'%(extType,extApprox)) text = ' Parameters :' for eKey in Ekey: text += ' %4s : %10.3e Refine? '%(eKey,extParms[eKey][0])+str(extParms[eKey][1]) pFile.write(text+'\n') if hapData['Babinet']['BabA'][0]: PrintBabinet(hapData['Babinet']) if not SGData['SGInv'] and len(Twins) == 1: pFile.write(' Flack parameter: %10.3f Refine? %s\n'%(hapData['Flack'][0],hapData['Flack'][1])) if len(Twins) > 1: for it,twin in enumerate(Twins): if 'bool' in str(type(twin[0])): pFile.write(' Nonmerohedral twin fr.: %5.3f Inv? %s Refine? %s\n'% (hapDict[pfx+'TwinFr:'+str(it)],str(controlDict[pfx+'TwinInv'][it]),str(Twins[0][1][1]))) else: pFile.write(' Twin law: %s Twin fr.: %5.3f Refine? %s\n'% (str(twin[0]).replace('\n',','),hapDict[pfx+'TwinFr:'+str(it)],str(Twins[0][1][1]))) Histogram['Reflection Lists'] = phase return hapVary,hapDict,controlDict
[docs]def SetHistogramPhaseData(parmDict,sigDict,Phases,Histograms,calcControls,Print=True,pFile=None): 'needs a doc string' def PrintSizeAndSig(hapData,sizeSig): line = '\n Size model: %9s'%(hapData[0]) refine = False if hapData[0] in ['isotropic','uniaxial']: line += ' equatorial:%12.5f'%(hapData[1][0]) if sizeSig[0][0]: line += ', sig:%8.4f'%(sizeSig[0][0]) refine = True if hapData[0] == 'uniaxial': line += ' axial:%12.4f'%(hapData[1][1]) if sizeSig[0][1]: refine = True line += ', sig:%8.4f'%(sizeSig[0][1]) line += ' LG mix coeff.:%12.4f'%(hapData[1][2]) if sizeSig[0][2]: refine = True line += ', sig:%8.4f'%(sizeSig[0][2]) if refine: pFile.write(line+'\n') else: line += ' LG mix coeff.:%12.4f'%(hapData[1][2]) if sizeSig[0][2]: refine = True line += ', sig:%8.4f'%(sizeSig[0][2]) Snames = ['S11','S22','S33','S12','S13','S23'] ptlbls = ' name :' ptstr = ' value :' sigstr = ' sig :' for i,name in enumerate(Snames): ptlbls += '%12s' % (name) ptstr += '%12.6f' % (hapData[4][i]) if sizeSig[1][i]: refine = True sigstr += '%12.6f' % (sizeSig[1][i]) else: sigstr += 12*' ' if refine: pFile.write(line+'\n') pFile.write(ptlbls+'\n') pFile.write(ptstr+'\n') pFile.write(sigstr+'\n') def PrintMuStrainAndSig(hapData,mustrainSig,SGData): line = '\n Mustrain model: %9s\n'%(hapData[0]) refine = False if hapData[0] in ['isotropic','uniaxial']: line += ' equatorial:%12.1f'%(hapData[1][0]) if mustrainSig[0][0]: line += ', sig:%8.1f'%(mustrainSig[0][0]) refine = True if hapData[0] == 'uniaxial': line += ' axial:%12.1f'%(hapData[1][1]) if mustrainSig[0][1]: line += ', sig:%8.1f'%(mustrainSig[0][1]) line += ' LG mix coeff.:%12.4f'%(hapData[1][2]) if mustrainSig[0][2]: refine = True line += ', sig:%8.3f'%(mustrainSig[0][2]) if refine: pFile.write(line+'\n') else: line += ' LG mix coeff.:%12.4f'%(hapData[1][2]) if mustrainSig[0][2]: refine = True line += ', sig:%8.3f'%(mustrainSig[0][2]) Snames = G2spc.MustrainNames(SGData) ptlbls = ' name :' ptstr = ' value :' sigstr = ' sig :' for i,name in enumerate(Snames): ptlbls += '%12s' % (name) ptstr += '%12.1f' % (hapData[4][i]) if mustrainSig[1][i]: refine = True sigstr += '%12.1f' % (mustrainSig[1][i]) else: sigstr += 12*' ' if refine: pFile.write(line+'\n') pFile.write(ptlbls+'\n') pFile.write(ptstr+'\n') pFile.write(sigstr+'\n') def PrintHStrainAndSig(hapData,strainSig,SGData): Hsnames = G2spc.HStrainNames(SGData) ptlbls = ' name :' ptstr = ' value :' sigstr = ' sig :' refine = False for i,name in enumerate(Hsnames): ptlbls += '%12s' % (name) ptstr += '%12.4g' % (hapData[0][i]) if name in strainSig: refine = True sigstr += '%12.4g' % (strainSig[name]) else: sigstr += 12*' ' if refine: pFile.write('\n Hydrostatic/elastic strain:\n') pFile.write(ptlbls+'\n') pFile.write(ptstr+'\n') pFile.write(sigstr+'\n') def PrintSHPOAndSig(pfx,hapData,POsig): Tindx = 1.0 Tvar = 0.0 pFile.write('\n Spherical harmonics preferred orientation: Order: %d\n'%hapData[4]) ptlbls = ' names :' ptstr = ' values:' sigstr = ' sig :' for item in hapData[5]: ptlbls += '%12s'%(item) ptstr += '%12.3f'%(hapData[5][item]) l = 2.0*eval(item.strip('C'))[0]+1 Tindx += hapData[5][item]**2/l if pfx+item in POsig: Tvar += (2.*hapData[5][item]*POsig[pfx+item]/l)**2 sigstr += '%12.3f'%(POsig[pfx+item]) else: sigstr += 12*' ' pFile.write(ptlbls+'\n') pFile.write(ptstr+'\n') pFile.write(sigstr+'\n') pFile.write('\n Texture index J = %.3f(%d)\n'%(Tindx,int(1000*np.sqrt(Tvar)))) def PrintExtAndSig(pfx,hapData,ScalExtSig): pFile.write('\n Single crystal extinction: Type: %s Approx: %s\n'%(hapData[0],hapData[1])) text = '' for item in hapData[2]: if pfx+item in ScalExtSig: text += ' %s: '%(item) text += '%12.2e'%(hapData[2][item][0]) if pfx+item in ScalExtSig: text += ' sig: %12.2e'%(ScalExtSig[pfx+item]) pFile.write(text+'\n') def PrintBabinetAndSig(pfx,hapData,BabSig): pFile.write('\n Babinet form factor modification:\n') ptlbls = ' names :' ptstr = ' values:' sigstr = ' sig :' for item in hapData: ptlbls += '%12s'%(item) ptstr += '%12.3f'%(hapData[item][0]) if pfx+item in BabSig: sigstr += '%12.3f'%(BabSig[pfx+item]) else: sigstr += 12*' ' pFile.write(ptlbls+'\n') pFile.write(ptstr+'\n') pFile.write(sigstr+'\n') def PrintTwinsAndSig(pfx,twinData,TwinSig): pFile.write('\n Twin Law fractions :\n') ptlbls = ' names :' ptstr = ' values:' sigstr = ' sig :' for it,item in enumerate(twinData): ptlbls += ' twin #%d'%(it) if it: ptstr += '%12.3f'%(item[1]) else: ptstr += '%12.3f'%(item[1][0]) if pfx+'TwinFr:'+str(it) in TwinSig: sigstr += '%12.3f'%(TwinSig[pfx+'TwinFr:'+str(it)]) else: sigstr += 12*' ' pFile.write(ptlbls+'\n') pFile.write(ptstr+'\n') pFile.write(sigstr+'\n') PhFrExtPOSig = {} SizeMuStrSig = {} ScalExtSig = {} BabSig = {} TwinFrSig = {} wtFrSum = {} for phase in Phases: HistoPhase = Phases[phase]['Histograms'] General = Phases[phase]['General'] SGData = General['SGData'] pId = Phases[phase]['pId'] histoList = list(HistoPhase.keys()) histoList.sort() for histogram in histoList: try: Histogram = Histograms[histogram] except KeyError: #skip if histogram not included e.g. in a sequential refinement continue if not Phases[phase]['Histograms'][histogram]['Use']: #skip if phase absent from this histogram continue hapData = HistoPhase[histogram] hId = Histogram['hId'] pfx = str(pId)+':'+str(hId)+':' if hId not in wtFrSum: wtFrSum[hId] = 0. if 'PWDR' in histogram: parmDict[pfx+'Scale'] = max(1.e-12,parmDict[pfx+'Scale']) for item in ['Scale','Extinction']: hapData[item][0] = parmDict[pfx+item] if pfx+item in sigDict and not parmDict[pfx+'LeBail']: PhFrExtPOSig.update({pfx+item:sigDict[pfx+item],}) wtFrSum[hId] += hapData['Scale'][0]*General['Mass'] if hapData['Pref.Ori.'][0] == 'MD': hapData['Pref.Ori.'][1] = parmDict[pfx+'MD'] if pfx+'MD' in sigDict and not parmDict[pfx+'LeBail']: PhFrExtPOSig.update({pfx+'MD':sigDict[pfx+'MD'],}) else: #'SH' spherical harmonics for item in hapData['Pref.Ori.'][5]: hapData['Pref.Ori.'][5][item] = parmDict[pfx+item] if pfx+item in sigDict and not parmDict[pfx+'LeBail']: PhFrExtPOSig.update({pfx+item:sigDict[pfx+item],}) SizeMuStrSig.update({pfx+'Mustrain':[[0,0,0],[0 for i in range(len(hapData['Mustrain'][4]))]], pfx+'Size':[[0,0,0],[0 for i in range(len(hapData['Size'][4]))]], pfx+'HStrain':{}}) for item in ['Mustrain','Size']: hapData[item][1][2] = parmDict[pfx+item+';mx'] # hapData[item][1][2] = min(1.,max(0.,hapData[item][1][2])) if pfx+item+';mx' in sigDict: SizeMuStrSig[pfx+item][0][2] = sigDict[pfx+item+';mx'] if hapData[item][0] in ['isotropic','uniaxial']: hapData[item][1][0] = parmDict[pfx+item+';i'] if item == 'Size': hapData[item][1][0] = min(10.,max(0.001,hapData[item][1][0])) if pfx+item+';i' in sigDict: SizeMuStrSig[pfx+item][0][0] = sigDict[pfx+item+';i'] if hapData[item][0] == 'uniaxial': hapData[item][1][1] = parmDict[pfx+item+';a'] if item == 'Size': hapData[item][1][1] = min(10.,max(0.001,hapData[item][1][1])) if pfx+item+';a' in sigDict: SizeMuStrSig[pfx+item][0][1] = sigDict[pfx+item+';a'] else: #generalized for mustrain or ellipsoidal for size Nterms = len(hapData[item][4]) for i in range(Nterms): sfx = ';'+str(i) hapData[item][4][i] = parmDict[pfx+item+sfx] if pfx+item+sfx in sigDict: SizeMuStrSig[pfx+item][1][i] = sigDict[pfx+item+sfx] names = G2spc.HStrainNames(SGData) for i,name in enumerate(names): hapData['HStrain'][0][i] = parmDict[pfx+name] if pfx+name in sigDict: SizeMuStrSig[pfx+'HStrain'][name] = sigDict[pfx+name] if 'Layer Disp' in hapData: hapData['Layer Disp'][0] = parmDict[pfx+'LayerDisp'] if pfx+'LayerDisp' in sigDict: SizeMuStrSig[pfx+'LayerDisp'] = sigDict[pfx+'LayerDisp'] if Phases[phase]['General']['Type'] != 'magnetic': for name in ['BabA','BabU']: hapData['Babinet'][name][0] = parmDict[pfx+name] if pfx+name in sigDict and not parmDict[pfx+'LeBail']: BabSig[pfx+name] = sigDict[pfx+name] elif 'HKLF' in histogram: for item in ['Scale','Flack']: if parmDict.get(pfx+item): hapData[item][0] = parmDict[pfx+item] if pfx+item in sigDict: ScalExtSig[pfx+item] = sigDict[pfx+item] for item in ['Ep','Eg','Es']: if parmDict.get(pfx+item): hapData['Extinction'][2][item][0] = parmDict[pfx+item] if pfx+item in sigDict: ScalExtSig[pfx+item] = sigDict[pfx+item] for item in ['BabA','BabU']: hapData['Babinet'][item][0] = parmDict[pfx+item] if pfx+item in sigDict: BabSig[pfx+item] = sigDict[pfx+item] if 'Twins' in hapData: it = 1 sumTwFr = 0. while True: try: hapData['Twins'][it][1] = parmDict[pfx+'TwinFr:'+str(it)] if pfx+'TwinFr:'+str(it) in sigDict: TwinFrSig[pfx+'TwinFr:'+str(it)] = sigDict[pfx+'TwinFr:'+str(it)] if it: sumTwFr += hapData['Twins'][it][1] it += 1 except KeyError: break hapData['Twins'][0][1][0] = 1.-sumTwFr if Print: for phase in Phases: HistoPhase = Phases[phase]['Histograms'] General = Phases[phase]['General'] SGData = General['SGData'] pId = Phases[phase]['pId'] histoList = list(HistoPhase.keys()) histoList.sort() for histogram in histoList: try: Histogram = Histograms[histogram] except KeyError: #skip if histogram not included e.g. in a sequential refinement continue hapData = HistoPhase[histogram] hId = Histogram['hId'] Histogram['Residuals'][str(pId)+'::Name'] = phase pfx = str(pId)+':'+str(hId)+':' hfx = ':%s:'%(hId) if pfx+'Nref' not in Histogram['Residuals']: #skip not used phase in histogram continue pFile.write('\n Phase: %s in histogram: %s\n'%(phase,histogram)) pFile.write(135*'='+'\n') Inst = Histogram['Instrument Parameters'][0] if 'PWDR' in histogram: pFile.write(' Final refinement RF, RF^2 = %.2f%%, %.2f%% on %d reflections\n'% (Histogram['Residuals'][pfx+'Rf'],Histogram['Residuals'][pfx+'Rf^2'],Histogram['Residuals'][pfx+'Nref'])) pFile.write(' Durbin-Watson statistic = %.3f\n'%(Histogram['Residuals']['Durbin-Watson'])) pFile.write(' Bragg intensity sum = %.3g\n'%(Histogram['Residuals'][pfx+'sumInt'])) if parmDict[pfx+'LeBail']: pFile.write(' Performed LeBail extraction for phase %s in histogram %s\n'%(phase,histogram)) else: # if calcControls != None: #skipped in seqRefine # if 'X'in Inst['Type'][0]: # PrintFprime(calcControls['FFtables'],hfx,pFile) # elif 'NC' in Inst['Type'][0]: # PrintBlength(calcControls['BLtables'],Inst['Lam'][1],pFile) if pfx+'Scale' in PhFrExtPOSig: wtFr = hapData['Scale'][0]*General['Mass']/wtFrSum[hId] sigwtFr = PhFrExtPOSig[pfx+'Scale']*wtFr/hapData['Scale'][0] pFile.write(' Phase fraction : %10.5g, sig %10.5g Weight fraction : %8.5f, sig %10.5f\n'% (hapData['Scale'][0],PhFrExtPOSig[pfx+'Scale'],wtFr,sigwtFr)) if pfx+'Extinction' in PhFrExtPOSig: pFile.write(' Extinction coeff: %10.4f, sig %10.4f\n'%(hapData['Extinction'][0],PhFrExtPOSig[pfx+'Extinction'])) if hapData['Pref.Ori.'][0] == 'MD': if pfx+'MD' in PhFrExtPOSig: pFile.write(' March-Dollase PO: %10.4f, sig %10.4f\n'%(hapData['Pref.Ori.'][1],PhFrExtPOSig[pfx+'MD'])) else: PrintSHPOAndSig(pfx,hapData['Pref.Ori.'],PhFrExtPOSig) PrintSizeAndSig(hapData['Size'],SizeMuStrSig[pfx+'Size']) PrintMuStrainAndSig(hapData['Mustrain'],SizeMuStrSig[pfx+'Mustrain'],SGData) PrintHStrainAndSig(hapData['HStrain'],SizeMuStrSig[pfx+'HStrain'],SGData) if pfx+'LayerDisp' in SizeMuStrSig: pFile.write(' Layer displacement : %10.3f, sig %10.3f\n'%(hapData['Layer Disp'][0],SizeMuStrSig[pfx+'LayerDisp'])) if Phases[phase]['General']['Type'] != 'magnetic' and not parmDict[pfx+'LeBail']: if len(BabSig): PrintBabinetAndSig(pfx,hapData['Babinet'],BabSig) elif 'HKLF' in histogram: pFile.write(' Final refinement RF, RF^2 = %.2f%%, %.2f%% on %d reflections (%d user rejected, %d sp.gp.extinct)\n'% (Histogram['Residuals'][pfx+'Rf'],Histogram['Residuals'][pfx+'Rf^2'],Histogram['Residuals'][pfx+'Nref'], Histogram['Residuals'][pfx+'Nrej'],Histogram['Residuals'][pfx+'Next'])) if calcControls != None: #skipped in seqRefine if 'X'in Inst['Type'][0]: PrintFprime(calcControls['FFtables'],hfx,pFile) elif 'NC' in Inst['Type'][0]: PrintBlength(calcControls['BLtables'],Inst['Lam'][1],pFile) pFile.write(' HKLF histogram weight factor = %.3f\n'%(Histogram['wtFactor'])) if pfx+'Scale' in ScalExtSig: pFile.write(' Scale factor : %10.4g, sig %10.4g\n'%(hapData['Scale'][0],ScalExtSig[pfx+'Scale'])) if hapData['Extinction'][0] != 'None': PrintExtAndSig(pfx,hapData['Extinction'],ScalExtSig) if len(BabSig): PrintBabinetAndSig(pfx,hapData['Babinet'],BabSig) if pfx+'Flack' in ScalExtSig: pFile.write(' Flack parameter : %10.3f, sig %10.3f\n'%(hapData['Flack'][0],ScalExtSig[pfx+'Flack'])) if len(TwinFrSig): PrintTwinsAndSig(pfx,hapData['Twins'],TwinFrSig)
################################################################################ ##### Histogram data ################################################################################
[docs]def GetHistogramData(Histograms,Print=True,pFile=None): 'needs a doc string' def GetBackgroundParms(hId,Background): Back = Background[0] DebyePeaks = Background[1] bakType,bakFlag = Back[:2] backVals = Back[3:] backNames = [':'+str(hId)+':Back;'+str(i) for i in range(len(backVals))] backDict = dict(zip(backNames,backVals)) backVary = [] if bakFlag: backVary = backNames backDict[':'+str(hId)+':nDebye'] = DebyePeaks['nDebye'] backDict[':'+str(hId)+':nPeaks'] = DebyePeaks['nPeaks'] debyeDict = {} debyeList = [] for i in range(DebyePeaks['nDebye']): debyeNames = [':'+str(hId)+':DebyeA;'+str(i),':'+str(hId)+':DebyeR;'+str(i),':'+str(hId)+':DebyeU;'+str(i)] debyeDict.update(dict(zip(debyeNames,DebyePeaks['debyeTerms'][i][::2]))) debyeList += zip(debyeNames,DebyePeaks['debyeTerms'][i][1::2]) debyeVary = [] for item in debyeList: if item[1]: debyeVary.append(item[0]) backDict.update(debyeDict) backVary += debyeVary peakDict = {} peakList = [] for i in range(DebyePeaks['nPeaks']): peakNames = [':'+str(hId)+':BkPkpos;'+str(i),':'+str(hId)+ \ ':BkPkint;'+str(i),':'+str(hId)+':BkPksig;'+str(i),':'+str(hId)+':BkPkgam;'+str(i)] peakDict.update(dict(zip(peakNames,DebyePeaks['peaksList'][i][::2]))) peakList += zip(peakNames,DebyePeaks['peaksList'][i][1::2]) peakVary = [] for item in peakList: if item[1]: peakVary.append(item[0]) backDict.update(peakDict) backVary += peakVary if 'background PWDR' in Background[1]: backDict[':'+str(hId)+':Back File'] = Background[1]['background PWDR'][0] backDict[':'+str(hId)+':BF mult'] = Background[1]['background PWDR'][1] try: if Background[1]['background PWDR'][0] and Background[1]['background PWDR'][2]: backVary.append(':'+str(hId)+':BF mult') except IndexError: # old version without refine flag pass return bakType,backDict,backVary def GetInstParms(hId,Inst): #patch if 'Z' not in Inst: Inst['Z'] = [0.0,0.0,False] dataType = Inst['Type'][0] instDict = {} insVary = [] pfx = ':'+str(hId)+':' insKeys = list(Inst.keys()) insKeys.sort() for item in insKeys: if item in 'Azimuth': continue insName = pfx+item instDict[insName] = Inst[item][1] if len(Inst[item]) > 2 and Inst[item][2]: insVary.append(insName) if 'C' in dataType: instDict[pfx+'SH/L'] = max(instDict[pfx+'SH/L'],0.0005) elif 'T' in dataType: #trap zero alp, bet coeff. if not instDict[pfx+'alpha']: instDict[pfx+'alpha'] = 1.0 if not instDict[pfx+'beta-0'] and not instDict[pfx+'beta-1']: instDict[pfx+'beta-1'] = 1.0 elif 'B' in dataType: #trap zero alp, bet coeff. if not instDict[pfx+'alpha-0'] and not instDict[pfx+'alpha-1']: instDict[pfx+'alpha-1'] = 1.0 if not instDict[pfx+'beta-0'] and not instDict[pfx+'beta-1']: instDict[pfx+'beta-1'] = 1.0 return dataType,instDict,insVary def GetSampleParms(hId,Sample): sampVary = [] hfx = ':'+str(hId)+':' sampDict = {hfx+'Gonio. radius':Sample['Gonio. radius'],hfx+'Omega':Sample['Omega'], hfx+'Chi':Sample['Chi'],hfx+'Phi':Sample['Phi'],hfx+'Azimuth':Sample['Azimuth']} for key in ('Temperature','Pressure','FreePrm1','FreePrm2','FreePrm3'): if key in Sample: sampDict[hfx+key] = Sample[key] Type = Sample['Type'] if 'Bragg' in Type: #Bragg-Brentano for item in ['Scale','Shift','Transparency','SurfRoughA','SurfRoughB']: sampDict[hfx+item] = Sample[item][0] if Sample[item][1]: sampVary.append(hfx+item) elif 'Debye' in Type: #Debye-Scherrer for item in ['Scale','Absorption','DisplaceX','DisplaceY']: sampDict[hfx+item] = Sample[item][0] if Sample[item][1]: sampVary.append(hfx+item) return Type,sampDict,sampVary def PrintBackground(Background): Back = Background[0] DebyePeaks = Background[1] pFile.write('\n Background function: %s Refine? %s\n'%(Back[0],Back[1])) line = ' Coefficients: ' for i,back in enumerate(Back[3:]): line += '%10.3f'%(back) if i and not i%10: line += '\n'+15*' ' pFile.write(line+'\n') if DebyePeaks['nDebye']: pFile.write('\n Debye diffuse scattering coefficients\n') parms = ['DebyeA','DebyeR','DebyeU'] line = ' names : ' for parm in parms: line += '%8s refine?'%(parm) pFile.write(line+'\n') for j,term in enumerate(DebyePeaks['debyeTerms']): line = ' term'+'%2d'%(j)+':' for i in range(3): line += '%10.3f %5s'%(term[2*i],bool(term[2*i+1])) pFile.write(line+'\n') if DebyePeaks['nPeaks']: pFile.write('\n Single peak coefficients\n') parms = ['BkPkpos','BkPkint','BkPksig','BkPkgam'] line = ' names : ' for parm in parms: line += '%8s refine?'%(parm) pFile.write(line+'\n') for j,term in enumerate(DebyePeaks['peaksList']): line = ' peak'+'%2d'%(j)+':' for i in range(4): line += '%12.3f %5s'%(term[2*i],bool(term[2*i+1])) pFile.write(line+'\n') if 'background PWDR' in DebyePeaks: try: pFile.write(' Fixed background file: %s; mult: %.3f Refine? %s\n'%(DebyePeaks['background PWDR'][0], DebyePeaks['background PWDR'][1],DebyePeaks['background PWDR'][2])) except IndexError: #old version without refine flag pass def PrintInstParms(Inst): pFile.write('\n Instrument Parameters:\n') insKeys = list(Inst.keys()) insKeys.sort() iBeg = 0 Ok = True while Ok: ptlbls = ' name :' ptstr = ' value :' varstr = ' refine:' iFin = min(iBeg+9,len(insKeys)) for item in insKeys[iBeg:iFin]: if item not in ['Type','Source']: ptlbls += '%12s' % (item) ptstr += '%12.6f' % (Inst[item][1]) if item in ['Lam1','Lam2','Azimuth','fltPath','2-theta',]: varstr += 12*' ' else: varstr += '%12s' % (str(bool(Inst[item][2]))) pFile.write(ptlbls+'\n') pFile.write(ptstr+'\n') pFile.write(varstr+'\n') iBeg = iFin if iBeg == len(insKeys): Ok = False else: pFile.write('\n') def PrintSampleParms(Sample): pFile.write('\n Sample Parameters:\n') pFile.write(' Goniometer omega = %.2f, chi = %.2f, phi = %.2f\n'% (Sample['Omega'],Sample['Chi'],Sample['Phi'])) ptlbls = ' name :' ptstr = ' value :' varstr = ' refine:' if 'Bragg' in Sample['Type']: for item in ['Scale','Shift','Transparency','SurfRoughA','SurfRoughB']: ptlbls += '%14s'%(item) ptstr += '%14.4f'%(Sample[item][0]) varstr += '%14s'%(str(bool(Sample[item][1]))) elif 'Debye' in Type: #Debye-Scherrer for item in ['Scale','Absorption','DisplaceX','DisplaceY']: ptlbls += '%14s'%(item) ptstr += '%14.4f'%(Sample[item][0]) varstr += '%14s'%(str(bool(Sample[item][1]))) pFile.write(ptlbls+'\n') pFile.write(ptstr+'\n') pFile.write(varstr+'\n') histDict = {} histVary = [] controlDict = {} histoList = list(Histograms.keys()) histoList.sort() for histogram in histoList: if 'PWDR' in histogram: Histogram = Histograms[histogram] hId = Histogram['hId'] pfx = ':'+str(hId)+':' controlDict[pfx+'wtFactor'] = Histogram['wtFactor'] controlDict[pfx+'Limits'] = Histogram['Limits'][1] controlDict[pfx+'Exclude'] = Histogram['Limits'][2:] for excl in controlDict[pfx+'Exclude']: Histogram['Data'][0] = ma.masked_inside(Histogram['Data'][0],excl[0],excl[1]) if controlDict[pfx+'Exclude']: ma.mask_rows(Histogram['Data']) Background = Histogram['Background'] Type,bakDict,bakVary = GetBackgroundParms(hId,Background) controlDict[pfx+'bakType'] = Type histDict.update(bakDict) histVary += bakVary Inst = Histogram['Instrument Parameters'] #TODO ? ignores tabulated alp,bet & delt for TOF if 'T' in Type and len(Inst[1]): #patch - back-to-back exponential contribution to TOF line shape is removed G2fil.G2Print ('Warning: tabulated profile coefficients are ignored') Type,instDict,insVary = GetInstParms(hId,Inst[0]) controlDict[pfx+'histType'] = Type if 'XC' in Type or 'XB' in Type: if pfx+'Lam1' in instDict: controlDict[pfx+'keV'] = 12.397639/instDict[pfx+'Lam1'] else: controlDict[pfx+'keV'] = 12.397639/instDict[pfx+'Lam'] histDict.update(instDict) histVary += insVary Sample = Histogram['Sample Parameters'] Type,sampDict,sampVary = GetSampleParms(hId,Sample) controlDict[pfx+'instType'] = Type histDict.update(sampDict) histVary += sampVary if Print: pFile.write('\n Histogram: %s histogram Id: %d\n'%(histogram,hId)) pFile.write(135*'='+'\n') Units = {'C':' deg','T':' msec','B':' deg'} units = Units[controlDict[pfx+'histType'][2]] Limits = controlDict[pfx+'Limits'] pFile.write(' Instrument type: %s\n'%Sample['Type']) pFile.write(' Histogram limits: %8.2f%s to %8.2f%s\n'%(Limits[0],units,Limits[1],units)) if len(controlDict[pfx+'Exclude']): excls = controlDict[pfx+'Exclude'] for excl in excls: pFile.write(' Excluded region: %8.2f%s to %8.2f%s\n'%(excl[0],units,excl[1],units)) PrintSampleParms(Sample) PrintInstParms(Inst[0]) PrintBackground(Background) elif 'HKLF' in histogram: Histogram = Histograms[histogram] hId = Histogram['hId'] pfx = ':'+str(hId)+':' controlDict[pfx+'wtFactor'] = Histogram['wtFactor'] Inst = Histogram['Instrument Parameters'][0] controlDict[pfx+'histType'] = Inst['Type'][0] if 'X' in Inst['Type'][0]: histDict[pfx+'Lam'] = Inst['Lam'][1] controlDict[pfx+'keV'] = 12.397639/histDict[pfx+'Lam'] elif 'NC' in Inst['Type'][0] or 'NB' in Inst['Type'][0]: histDict[pfx+'Lam'] = Inst['Lam'][1] return histVary,histDict,controlDict
[docs]def SetHistogramData(parmDict,sigDict,Histograms,calcControls,Print=True,pFile=None,seq=False): 'Shows histogram data after a refinement' def SetBackgroundParms(pfx,Background,parmDict,sigDict): Back = Background[0] DebyePeaks = Background[1] lenBack = len(Back[3:]) backSig = [0 for i in range(lenBack+3*DebyePeaks['nDebye']+4*DebyePeaks['nPeaks'])] for i in range(lenBack): Back[3+i] = parmDict[pfx+'Back;'+str(i)] if pfx+'Back;'+str(i) in sigDict: backSig[i] = sigDict[pfx+'Back;'+str(i)] if DebyePeaks['nDebye']: for i in range(DebyePeaks['nDebye']): names = [pfx+'DebyeA;'+str(i),pfx+'DebyeR;'+str(i),pfx+'DebyeU;'+str(i)] for j,name in enumerate(names): DebyePeaks['debyeTerms'][i][2*j] = parmDict[name] if name in sigDict: backSig[lenBack+3*i+j] = sigDict[name] if DebyePeaks['nPeaks']: for i in range(DebyePeaks['nPeaks']): names = [pfx+'BkPkpos;'+str(i),pfx+'BkPkint;'+str(i), pfx+'BkPksig;'+str(i),pfx+'BkPkgam;'+str(i)] for j,name in enumerate(names): DebyePeaks['peaksList'][i][2*j] = parmDict[name] if name in sigDict: backSig[lenBack+3*DebyePeaks['nDebye']+4*i+j] = sigDict[name] if pfx+'BF mult' in sigDict: DebyePeaks['background PWDR'][1] = parmDict[pfx+'BF mult'] backSig.append(sigDict[pfx+'BF mult']) return backSig def SetInstParms(pfx,Inst,parmDict,sigDict): instSig = {} insKeys = list(Inst.keys()) insKeys.sort() for item in insKeys: insName = pfx+item Inst[item][1] = parmDict[insName] if insName in sigDict: instSig[item] = sigDict[insName] else: instSig[item] = 0 return instSig def SetSampleParms(pfx,Sample,parmDict,sigDict): if 'Bragg' in Sample['Type']: #Bragg-Brentano sampSig = [0 for i in range(5)] for i,item in enumerate(['Scale','Shift','Transparency','SurfRoughA','SurfRoughB']): Sample[item][0] = parmDict[pfx+item] if pfx+item in sigDict: sampSig[i] = sigDict[pfx+item] elif 'Debye' in Sample['Type']: #Debye-Scherrer sampSig = [0 for i in range(4)] for i,item in enumerate(['Scale','Absorption','DisplaceX','DisplaceY']): Sample[item][0] = parmDict[pfx+item] if pfx+item in sigDict: sampSig[i] = sigDict[pfx+item] return sampSig def PrintBackgroundSig(Background,backSig): Back = Background[0] DebyePeaks = Background[1] valstr = ' value : ' sigstr = ' sig : ' refine = False for i,back in enumerate(Back[3:]): valstr += '%10.4g'%(back) if Back[1]: refine = True sigstr += '%10.4g'%(backSig[i]) else: sigstr += 10*' ' if refine: pFile.write('\n Background function: %s\n'%Back[0]) pFile.write(valstr+'\n') pFile.write(sigstr+'\n') if DebyePeaks['nDebye']: ifAny = False ptfmt = "%12.3f" names = ' names :' ptstr = ' values:' sigstr = ' esds :' for item in sigDict: if 'Debye' in item: ifAny = True names += '%12s'%(item) ptstr += ptfmt%(parmDict[item]) sigstr += ptfmt%(sigDict[item]) if ifAny: pFile.write('\n Debye diffuse scattering coefficients\n') pFile.write(names+'\n') pFile.write(ptstr+'\n') pFile.write(sigstr+'\n') if DebyePeaks['nPeaks']: pFile.write('\n Single peak coefficients:\n') parms = ['BkPkpos','BkPkint','BkPksig','BkPkgam'] line = ' peak no. ' for parm in parms: line += '%14s%12s'%(parm.center(14),'esd'.center(12)) pFile.write(line+'\n') for ip in range(DebyePeaks['nPeaks']): ptstr = ' %4d '%(ip) for parm in parms: fmt = '%14.3f' efmt = '%12.3f' if parm == 'BkPkpos': fmt = '%14.4f' efmt = '%12.4f' name = pfx+parm+';%d'%(ip) ptstr += fmt%(parmDict[name]) if name in sigDict: ptstr += efmt%(sigDict[name]) else: ptstr += 12*' ' pFile.write(ptstr+'\n') if ('background PWDR' in DebyePeaks and len(DebyePeaks['background PWDR']) >= 3 and DebyePeaks['background PWDR'][2]): pFile.write(' Fixed background scale: %.3f(%d)\n'%(DebyePeaks['background PWDR'][1],int(1000*backSig[-1]))) sumBk = np.array(Histogram['sumBk']) pFile.write(' Background sums: empirical %.3g, Debye %.3g, peaks %.3g, Total %.3g\n'% (sumBk[0],sumBk[1],sumBk[2],np.sum(sumBk))) def PrintInstParmsSig(Inst,instSig): refine = False insKeys = list(instSig.keys()) insKeys.sort() iBeg = 0 Ok = True while Ok: ptlbls = ' names :' ptstr = ' value :' sigstr = ' sig :' iFin = min(iBeg+9,len(insKeys)) for name in insKeys[iBeg:iFin]: if name not in ['Type','Lam1','Lam2','Azimuth','Source','fltPath']: ptlbls += '%12s' % (name) ptstr += '%12.6f' % (Inst[name][1]) if instSig[name]: refine = True sigstr += '%12.6f' % (instSig[name]) else: sigstr += 12*' ' if refine: pFile.write('\n Instrument Parameters:\n') pFile.write(ptlbls+'\n') pFile.write(ptstr+'\n') pFile.write(sigstr+'\n') iBeg = iFin if iBeg == len(insKeys): Ok = False def PrintSampleParmsSig(Sample,sampleSig): ptlbls = ' names :' ptstr = ' values:' sigstr = ' sig :' refine = False if 'Bragg' in Sample['Type']: for i,item in enumerate(['Scale','Shift','Transparency','SurfRoughA','SurfRoughB']): ptlbls += '%14s'%(item) ptstr += '%14.4f'%(Sample[item][0]) if sampleSig[i]: refine = True sigstr += '%14.4f'%(sampleSig[i]) else: sigstr += 14*' ' elif 'Debye' in Sample['Type']: #Debye-Scherrer for i,item in enumerate(['Scale','Absorption','DisplaceX','DisplaceY']): ptlbls += '%14s'%(item) ptstr += '%14.4f'%(Sample[item][0]) if sampleSig[i]: refine = True sigstr += '%14.4f'%(sampleSig[i]) else: sigstr += 14*' ' if refine: pFile.write('\n Sample Parameters:\n') pFile.write(ptlbls+'\n') pFile.write(ptstr+'\n') pFile.write(sigstr+'\n') histoList = list(Histograms.keys()) histoList.sort() for histogram in histoList: if 'PWDR' in histogram: Histogram = Histograms[histogram] hId = Histogram['hId'] pfx = ':'+str(hId)+':' Background = Histogram['Background'] backSig = SetBackgroundParms(pfx,Background,parmDict,sigDict) Inst = Histogram['Instrument Parameters'][0] instSig = SetInstParms(pfx,Inst,parmDict,sigDict) Sample = Histogram['Sample Parameters'] parmDict[pfx+'Scale'] = max(1.e-12,parmDict[pfx+'Scale']) #put floor on phase fraction scale sampSig = SetSampleParms(pfx,Sample,parmDict,sigDict) if Print and not seq: pFile.write('\n Histogram: %s histogram Id: %d\n'%(histogram,hId)) pFile.write(135*'='+'\n') if Print: pFile.write(' PWDR histogram weight factor = '+'%.3f\n'%(Histogram['wtFactor'])) pFile.write(' Final refinement wR = %.2f%% on %d observations in this histogram\n'% (Histogram['Residuals']['wR'],Histogram['Residuals']['Nobs'])) pFile.write(' Other residuals: R = %.2f%%, R-bkg = %.2f%%, wR-bkg = %.2f%% wRmin = %.2f%%\n'% (Histogram['Residuals']['R'],Histogram['Residuals']['Rb'],Histogram['Residuals']['wR'],Histogram['Residuals']['wRmin'])) pFile.write(' Instrument type: %s\n'%Sample['Type']) if calcControls != None: #skipped in seqRefine if 'X' in Inst['Type'][0]: PrintFprime(calcControls['FFtables'],pfx,pFile) elif 'NC' in Inst['Type'][0]: PrintBlength(calcControls['BLtables'],Inst['Lam'][1],pFile) PrintSampleParmsSig(Sample,sampSig) PrintInstParmsSig(Inst,instSig) PrintBackgroundSig(Background,backSig)
[docs]def WriteRBObjPOAndSig(pfx,rbfx,rbsx,parmDict,sigDict): '''Cribbed version of PrintRBObjPOAndSig but returns lists of strings. Moved so it can be used in ExportCIF ''' namstr = ' names :' valstr = ' values:' sigstr = ' esds :' for i,px in enumerate(['Px:','Py:','Pz:']): name = pfx+rbfx+px+rbsx namstr += '%12s'%('Pos '+px[1]) valstr += '%12.5f'%(parmDict[name]) if name in sigDict: sigstr += '%12.5f'%(sigDict[name]) else: sigstr += 12*' ' for i,po in enumerate(['Oa:','Oi:','Oj:','Ok:']): name = pfx+rbfx+po+rbsx namstr += '%12s'%('Ori '+po[1]) valstr += '%12.5f'%(parmDict[name]) if name in sigDict: sigstr += '%12.5f'%(sigDict[name]) else: sigstr += 12*' ' name = pfx+rbfx+'f:'+rbsx namstr += '%12s'%('Frac') valstr += '%12.5f'%(parmDict[name]) if name in sigDict: sigstr += '%12.5f'%(sigDict[name]) else: sigstr += 12*' ' return (namstr,valstr,sigstr)
[docs]def WriteRBObjTLSAndSig(pfx,rbfx,rbsx,TLS,parmDict,sigDict): '''Cribbed version of PrintRBObjTLSAndSig but returns lists of strings. Moved so it can be used in ExportCIF ''' out = [] namstr = ' names :' valstr = ' values:' sigstr = ' esds :' if 'N' not in TLS: out.append(' Thermal motion:\n') if 'T' in TLS: for i,pt in enumerate(['T11:','T22:','T33:','T12:','T13:','T23:']): name = pfx+rbfx+pt+rbsx namstr += '%12s'%(pt[:3]) valstr += '%12.5f'%(parmDict[name]) if name in sigDict: sigstr += '%12.5f'%(sigDict[name]) else: sigstr += 12*' ' out.append(namstr+'\n') out.append(valstr+'\n') out.append(sigstr+'\n') if 'L' in TLS: namstr = ' names :' valstr = ' values:' sigstr = ' esds :' for i,pt in enumerate(['L11:','L22:','L33:','L12:','L13:','L23:']): name = pfx+rbfx+pt+rbsx namstr += '%12s'%(pt[:3]) valstr += '%12.3f'%(parmDict[name]) if name in sigDict: sigstr += '%12.3f'%(sigDict[name]) else: sigstr += 12*' ' out.append(namstr+'\n') out.append(valstr+'\n') out.append(sigstr+'\n') if 'S' in TLS: namstr = ' names :' valstr = ' values:' sigstr = ' esds :' for i,pt in enumerate(['S12:','S13:','S21:','S23:','S31:','S32:','SAA:','SBB:']): name = pfx+rbfx+pt+rbsx namstr += '%12s'%(pt[:3]) valstr += '%12.4f'%(parmDict[name]) if name in sigDict: sigstr += '%12.4f'%(sigDict[name]) else: sigstr += 12*' ' out.append(namstr+'\n') out.append(valstr+'\n') out.append(sigstr+'\n') if 'U' in TLS: name = pfx+rbfx+'U:'+rbsx namstr = ' names :'+'%12s'%('Uiso') valstr = ' values:'+'%12.5f'%(parmDict[name]) if name in sigDict: sigstr = ' esds :'+'%12.5f'%(sigDict[name]) else: sigstr = ' esds :'+12*' ' out.append(namstr+'\n') out.append(valstr+'\n') out.append(sigstr+'\n') return out
[docs]def WriteRBObjTorAndSig(pfx,rbsx,parmDict,sigDict,nTors): '''Cribbed version of PrintRBObjTorAndSig but returns lists of strings. Moved so it can be used in ExportCIF ''' out = [] namstr = ' names :' valstr = ' values:' sigstr = ' esds :' out.append(' Torsions:\n') for it in range(nTors): name = pfx+'RBRTr;'+str(it)+':'+rbsx namstr += '%12s'%('Tor'+str(it)) valstr += '%12.4f'%(parmDict[name]) if name in sigDict: sigstr += '%12.4f'%(sigDict[name]) out.append(namstr+'\n') out.append(valstr+'\n') out.append(sigstr+'\n') return out
[docs]def WriteResRBModel(RBModel): '''Write description of a residue rigid body. Code shifted from PrintResRBModel to make usable from G2export_CIF ''' out = [] atNames = RBModel['atNames'] rbRef = RBModel['rbRef'] rbSeq = RBModel['rbSeq'] out.append(' At name x y z\n') for name,xyz in zip(atNames,RBModel['rbXYZ']): out.append(' %8s %10.4f %10.4f %10.4f\n'%(name,xyz[0],xyz[1],xyz[2])) out.append(' Orientation defined by: %s -> %s & %s -> %s\n'% (atNames[rbRef[0]],atNames[rbRef[1]],atNames[rbRef[0]],atNames[rbRef[2]])) if rbSeq: for i,rbseq in enumerate(rbSeq): # nameLst = [atNames[i] for i in rbseq[3]] out.append(' Torsion sequence %d Bond: %s - %s riding: %s\n'% (i,atNames[rbseq[0]],atNames[rbseq[1]],str([atNames[i] for i in rbseq[3]]))) return out
[docs]def WriteVecRBModel(RBModel,sigDict={},irb=None): '''Write description of a vector rigid body. Code shifted from PrintVecRBModel to make usable from G2export_CIF ''' out = [] rbRef = RBModel['rbRef'] atTypes = RBModel['rbTypes'] for i in range(len(RBModel['VectMag'])): if sigDict and irb is not None: name = '::RBV;'+str(i)+':'+str(irb) s = G2mth.ValEsd(RBModel['VectMag'][i],sigDict.get(name,-.0001)) out.append('Vector no.: %d Magnitude: %s\n'%(i,s)) else: out.append('Vector no.: %d Magnitude: %8.4f Refine? %s\n'% (i,RBModel['VectMag'][i],RBModel['VectRef'][i])) out.append(' No. Type vx vy vz\n') for j,[name,xyz] in enumerate(zip(atTypes,RBModel['rbVect'][i])): out.append(' %d %2s %10.4f %10.4f %10.4f\n'%(j,name,xyz[0],xyz[1],xyz[2])) out.append(' No. Type x y z\n') for i,[name,xyz] in enumerate(zip(atTypes,RBModel['rbXYZ'])): out.append(' %d %2s %10.4f %10.4f %10.4f\n'%(i,name,xyz[0],xyz[1],xyz[2])) return out