| 1 | # -*- coding: utf-8 -*- |
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| 2 | ''' |
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| 3 | *GSASIIstrMath - structure math routines* |
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| 4 | ----------------------------------------- |
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| 5 | ''' |
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| 6 | ########### SVN repository information ################### |
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| 7 | # $Date: 2022-10-06 15:16:28 +0000 (Thu, 06 Oct 2022) $ |
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| 8 | # $Author: vondreele $ |
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| 9 | # $Revision: 5343 $ |
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| 10 | # $URL: trunk/GSASIIstrMath.py $ |
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| 11 | # $Id: GSASIIstrMath.py 5343 2022-10-06 15:16:28Z vondreele $ |
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| 12 | ########### SVN repository information ################### |
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| 13 | from __future__ import division, print_function |
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| 14 | import time |
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| 15 | import copy |
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| 16 | import numpy as np |
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| 17 | import numpy.ma as ma |
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| 18 | import numpy.linalg as nl |
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| 19 | import scipy.stats as st |
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| 20 | import multiprocessing as mp |
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| 21 | import pickle |
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| 22 | import GSASIIpath |
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| 23 | GSASIIpath.SetVersionNumber("$Revision: 5343 $") |
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| 24 | import GSASIIElem as G2el |
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| 25 | import GSASIIlattice as G2lat |
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| 26 | import GSASIIspc as G2spc |
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| 27 | import GSASIIpwd as G2pwd |
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| 28 | import GSASIImapvars as G2mv |
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| 29 | import GSASIImath as G2mth |
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| 30 | import GSASIIobj as G2obj |
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| 31 | import GSASIImpsubs as G2mp |
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| 32 | #G2mp.InitMP(False) # This disables multiprocessing |
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| 33 | |
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| 34 | sind = lambda x: np.sin(x*np.pi/180.) |
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| 35 | cosd = lambda x: np.cos(x*np.pi/180.) |
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| 36 | tand = lambda x: np.tan(x*np.pi/180.) |
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| 37 | asind = lambda x: 180.*np.arcsin(x)/np.pi |
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| 38 | acosd = lambda x: 180.*np.arccos(x)/np.pi |
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| 39 | atan2d = lambda y,x: 180.*np.arctan2(y,x)/np.pi |
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| 40 | |
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| 41 | try: # fails on doc build |
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| 42 | ateln2 = 8.0*np.log(2.0) |
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| 43 | twopi = 2.0*np.pi |
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| 44 | twopisq = 2.0*np.pi**2 |
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| 45 | except TypeError: |
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| 46 | pass |
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| 47 | nxs = np.newaxis |
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| 48 | |
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| 49 | ################################################################################ |
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| 50 | ##### Rigid Body Models |
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| 51 | ################################################################################ |
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| 52 | |
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| 53 | def ApplyRBModels(parmDict,Phases,rigidbodyDict,Update=False): |
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| 54 | ''' Takes RB info from RBModels in Phase and RB data in rigidbodyDict along with |
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| 55 | current RB values in parmDict & modifies atom contents (fxyz & Uij) of parmDict |
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| 56 | ''' |
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| 57 | atxIds = ['Ax:','Ay:','Az:'] |
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| 58 | atuIds = ['AU11:','AU22:','AU33:','AU12:','AU13:','AU23:'] |
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| 59 | RBIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]}) #these are lists of rbIds |
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| 60 | if not RBIds['Vector'] and not RBIds['Residue']: |
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| 61 | return |
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| 62 | VRBIds = RBIds['Vector'] |
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| 63 | RRBIds = RBIds['Residue'] |
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| 64 | if Update: |
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| 65 | RBData = rigidbodyDict |
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| 66 | else: |
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| 67 | RBData = copy.deepcopy(rigidbodyDict) # don't mess with original! |
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| 68 | if RBIds['Vector']: # first update the vector magnitudes |
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| 69 | VRBData = RBData['Vector'] |
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| 70 | for i,rbId in enumerate(VRBIds): |
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| 71 | if VRBData[rbId]['useCount']: |
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| 72 | for j in range(len(VRBData[rbId]['VectMag'])): |
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| 73 | name = '::RBV;'+str(j)+':'+str(i) |
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| 74 | VRBData[rbId]['VectMag'][j] = parmDict[name] |
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| 75 | for phase in Phases: |
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| 76 | Phase = Phases[phase] |
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| 77 | General = Phase['General'] |
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| 78 | cx,ct,cs,cia = General['AtomPtrs'] |
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| 79 | cell = General['Cell'][1:7] |
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| 80 | Amat,Bmat = G2lat.cell2AB(cell) |
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| 81 | AtLookup = G2mth.FillAtomLookUp(Phase['Atoms'],cia+8) |
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| 82 | pfx = str(Phase['pId'])+'::' |
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| 83 | if Update: |
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| 84 | RBModels = Phase['RBModels'] |
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| 85 | else: |
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| 86 | RBModels = copy.deepcopy(Phase['RBModels']) # again don't mess with original! |
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| 87 | for irb,RBObj in enumerate(RBModels.get('Vector',[])): |
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| 88 | jrb = VRBIds.index(RBObj['RBId']) |
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| 89 | rbsx = str(irb)+':'+str(jrb) |
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| 90 | for i,px in enumerate(['RBVPx:','RBVPy:','RBVPz:']): |
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| 91 | RBObj['Orig'][0][i] = parmDict[pfx+px+rbsx] |
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| 92 | for i,po in enumerate(['RBVOa:','RBVOi:','RBVOj:','RBVOk:']): |
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| 93 | RBObj['Orient'][0][i] = parmDict[pfx+po+rbsx] |
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| 94 | RBObj['Orient'][0] = G2mth.normQ(RBObj['Orient'][0]) |
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| 95 | RBObj['AtomFrac'][0] = parmDict[pfx+'RBVf:'+rbsx] |
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| 96 | TLS = RBObj['ThermalMotion'] |
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| 97 | if 'T' in TLS[0]: |
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| 98 | for i,pt in enumerate(['RBVT11:','RBVT22:','RBVT33:','RBVT12:','RBVT13:','RBVT23:']): |
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| 99 | TLS[1][i] = parmDict[pfx+pt+rbsx] |
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| 100 | if 'L' in TLS[0]: |
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| 101 | for i,pt in enumerate(['RBVL11:','RBVL22:','RBVL33:','RBVL12:','RBVL13:','RBVL23:']): |
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| 102 | TLS[1][i+6] = parmDict[pfx+pt+rbsx] |
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| 103 | if 'S' in TLS[0]: |
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| 104 | for i,pt in enumerate(['RBVS12:','RBVS13:','RBVS21:','RBVS23:','RBVS31:','RBVS32:','RBVSAA:','RBVSBB:']): |
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| 105 | TLS[1][i+12] = parmDict[pfx+pt+rbsx] |
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| 106 | if 'U' in TLS[0]: |
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| 107 | TLS[1][0] = parmDict[pfx+'RBVU:'+rbsx] |
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| 108 | XYZ,Cart = G2mth.UpdateRBXYZ(Bmat,RBObj,RBData,'Vector') |
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| 109 | UIJ = G2mth.UpdateRBUIJ(Bmat,Cart,RBObj) |
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| 110 | for i,x in enumerate(XYZ): |
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| 111 | atId = RBObj['Ids'][i] |
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| 112 | if parmDict[pfx+'Afrac:'+str(AtLookup[atId])]: |
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| 113 | parmDict[pfx+'Afrac:'+str(AtLookup[atId])] = RBObj['AtomFrac'][0] |
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| 114 | for j in [0,1,2]: |
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| 115 | parmDict[pfx+atxIds[j]+str(AtLookup[atId])] = x[j] |
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| 116 | if UIJ[i][0] == 'A': |
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| 117 | for j in range(6): |
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| 118 | parmDict[pfx+atuIds[j]+str(AtLookup[atId])] = UIJ[i][j+2] |
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| 119 | elif UIJ[i][0] == 'I': |
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| 120 | parmDict[pfx+'AUiso:'+str(AtLookup[atId])] = UIJ[i][1] |
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| 121 | |
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| 122 | for irb,RBObj in enumerate(RBModels.get('Residue',[])): |
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| 123 | jrb = RRBIds.index(RBObj['RBId']) |
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| 124 | rbsx = str(irb)+':'+str(jrb) |
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| 125 | for i,px in enumerate(['RBRPx:','RBRPy:','RBRPz:']): |
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| 126 | RBObj['Orig'][0][i] = parmDict[pfx+px+rbsx] |
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| 127 | for i,po in enumerate(['RBROa:','RBROi:','RBROj:','RBROk:']): |
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| 128 | RBObj['Orient'][0][i] = parmDict[pfx+po+rbsx] |
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| 129 | RBObj['Orient'][0] = G2mth.normQ(RBObj['Orient'][0]) |
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| 130 | RBObj['AtomFrac'][0] = parmDict[pfx+'RBRf:'+rbsx] |
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| 131 | TLS = RBObj['ThermalMotion'] |
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| 132 | if 'T' in TLS[0]: |
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| 133 | for i,pt in enumerate(['RBRT11:','RBRT22:','RBRT33:','RBRT12:','RBRT13:','RBRT23:']): |
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| 134 | RBObj['ThermalMotion'][1][i] = parmDict[pfx+pt+rbsx] |
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| 135 | if 'L' in TLS[0]: |
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| 136 | for i,pt in enumerate(['RBRL11:','RBRL22:','RBRL33:','RBRL12:','RBRL13:','RBRL23:']): |
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| 137 | RBObj['ThermalMotion'][1][i+6] = parmDict[pfx+pt+rbsx] |
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| 138 | if 'S' in TLS[0]: |
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| 139 | for i,pt in enumerate(['RBRS12:','RBRS13:','RBRS21:','RBRS23:','RBRS31:','RBRS32:','RBRSAA:','RBRSBB:']): |
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| 140 | RBObj['ThermalMotion'][1][i+12] = parmDict[pfx+pt+rbsx] |
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| 141 | if 'U' in TLS[0]: |
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| 142 | RBObj['ThermalMotion'][1][0] = parmDict[pfx+'RBRU:'+rbsx] |
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| 143 | for itors,tors in enumerate(RBObj['Torsions']): |
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| 144 | tors[0] = parmDict[pfx+'RBRTr;'+str(itors)+':'+rbsx] |
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| 145 | XYZ,Cart = G2mth.UpdateRBXYZ(Bmat,RBObj,RBData,'Residue') |
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| 146 | UIJ = G2mth.UpdateRBUIJ(Bmat,Cart,RBObj) |
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| 147 | for i,x in enumerate(XYZ): |
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| 148 | atId = RBObj['Ids'][i] |
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| 149 | if parmDict[pfx+'Afrac:'+str(AtLookup[atId])]: |
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| 150 | parmDict[pfx+'Afrac:'+str(AtLookup[atId])] = RBObj['AtomFrac'][0] |
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| 151 | for j in [0,1,2]: |
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| 152 | parmDict[pfx+atxIds[j]+str(AtLookup[atId])] = x[j] |
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| 153 | if UIJ[i][0] == 'A': |
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| 154 | for j in range(6): |
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| 155 | parmDict[pfx+atuIds[j]+str(AtLookup[atId])] = UIJ[i][j+2] |
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| 156 | elif UIJ[i][0] == 'I': |
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| 157 | parmDict[pfx+'AUiso:'+str(AtLookup[atId])] = UIJ[i][1] |
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| 158 | |
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| 159 | def ApplyRBModelDervs(dFdvDict,parmDict,rigidbodyDict,Phase): |
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| 160 | 'Computes rigid body derivatives' |
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| 161 | atxIds = ['dAx:','dAy:','dAz:'] |
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| 162 | atuIds = ['AU11:','AU22:','AU33:','AU12:','AU13:','AU23:'] |
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| 163 | OIds = ['Oa:','Oi:','Oj:','Ok:'] |
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| 164 | RBIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]}) #these are lists of rbIds |
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| 165 | if not RBIds['Vector'] and not RBIds['Residue']: |
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| 166 | return |
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| 167 | VRBIds = RBIds['Vector'] |
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| 168 | RRBIds = RBIds['Residue'] |
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| 169 | RBData = rigidbodyDict |
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| 170 | for item in parmDict: |
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| 171 | if 'RB' in item: |
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| 172 | dFdvDict[item] = 0. #NB: this is a vector which is no. refl. long & must be filled! |
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| 173 | General = Phase['General'] |
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| 174 | cx,ct,cs,cia = General['AtomPtrs'] |
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| 175 | cell = General['Cell'][1:7] |
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| 176 | Amat,Bmat = G2lat.cell2AB(cell) |
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| 177 | rpd = np.pi/180. |
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| 178 | rpd2 = rpd**2 |
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| 179 | g = nl.inv(np.inner(Bmat,Bmat)) |
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| 180 | gvec = np.sqrt(np.array([g[0][0]**2,g[1][1]**2,g[2][2]**2, |
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| 181 | g[0][0]*g[1][1],g[0][0]*g[2][2],g[1][1]*g[2][2]])) |
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| 182 | AtLookup = G2mth.FillAtomLookUp(Phase['Atoms'],cia+8) |
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| 183 | pfx = str(Phase['pId'])+'::' |
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| 184 | RBModels = Phase['RBModels'] |
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| 185 | |
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| 186 | for irb,RBObj in enumerate(RBModels.get('Vector',[])): |
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| 187 | symAxis = RBObj.get('symAxis') |
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| 188 | VModel = RBData['Vector'][RBObj['RBId']] |
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| 189 | Q = RBObj['Orient'][0] |
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| 190 | jrb = VRBIds.index(RBObj['RBId']) |
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| 191 | rbsx = str(irb)+':'+str(jrb) |
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| 192 | dXdv = [] |
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| 193 | for iv in range(len(VModel['VectMag'])): |
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| 194 | dCdv = [] |
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| 195 | for vec in VModel['rbVect'][iv]: |
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| 196 | dCdv.append(G2mth.prodQVQ(Q,vec)) |
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| 197 | dXdv.append(np.inner(Bmat,np.array(dCdv)).T) |
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| 198 | XYZ,Cart = G2mth.UpdateRBXYZ(Bmat,RBObj,RBData,'Vector') |
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| 199 | for ia,atId in enumerate(RBObj['Ids']): |
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| 200 | atNum = AtLookup[atId] |
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| 201 | if parmDict[pfx+'Afrac:'+str(AtLookup[atId])]: |
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| 202 | dFdvDict[pfx+'RBVf:'+rbsx] += dFdvDict[pfx+'Afrac:'+str(atNum)] |
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| 203 | dx = 0.00001 |
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| 204 | for iv in range(len(VModel['VectMag'])): |
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| 205 | for ix in [0,1,2]: |
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| 206 | dFdvDict['::RBV;'+str(iv)+':'+str(jrb)] += dXdv[iv][ia][ix]*dFdvDict[pfx+atxIds[ix]+str(atNum)] |
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| 207 | for i,name in enumerate(['RBVPx:','RBVPy:','RBVPz:']): |
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| 208 | dFdvDict[pfx+name+rbsx] += dFdvDict[pfx+atxIds[i]+str(atNum)] |
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| 209 | for iv in range(4): |
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| 210 | Q[iv] -= dx |
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| 211 | XYZ1 = G2mth.RotateRBXYZ(Bmat,Cart,G2mth.normQ(Q),symAxis) |
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| 212 | Q[iv] += 2.*dx |
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| 213 | XYZ2 = G2mth.RotateRBXYZ(Bmat,Cart,G2mth.normQ(Q),symAxis) |
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| 214 | Q[iv] -= dx |
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| 215 | dXdO = (XYZ2[ia]-XYZ1[ia])/(2.*dx) |
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| 216 | for ix in [0,1,2]: |
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| 217 | dFdvDict[pfx+'RBV'+OIds[iv]+rbsx] += dXdO[ix]*dFdvDict[pfx+atxIds[ix]+str(atNum)] |
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| 218 | X = G2mth.prodQVQ(Q,Cart[ia]) |
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| 219 | dFdu = np.array([dFdvDict[pfx+Uid+str(AtLookup[atId])] for Uid in atuIds]).T/gvec |
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| 220 | dFdu = G2lat.U6toUij(dFdu.T) |
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| 221 | dFdu = np.tensordot(Amat,np.tensordot(Amat,dFdu,([1,0])),([0,1])) |
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| 222 | dFdu = G2lat.UijtoU6(dFdu) |
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| 223 | atNum = AtLookup[atId] |
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| 224 | if 'T' in RBObj['ThermalMotion'][0]: |
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| 225 | for i,name in enumerate(['RBVT11:','RBVT22:','RBVT33:','RBVT12:','RBVT13:','RBVT23:']): |
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| 226 | dFdvDict[pfx+name+rbsx] += dFdu[i] |
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| 227 | if 'L' in RBObj['ThermalMotion'][0]: |
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| 228 | dFdvDict[pfx+'RBVL11:'+rbsx] += rpd2*(dFdu[1]*X[2]**2+dFdu[2]*X[1]**2-dFdu[5]*X[1]*X[2]) |
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| 229 | dFdvDict[pfx+'RBVL22:'+rbsx] += rpd2*(dFdu[0]*X[2]**2+dFdu[2]*X[0]**2-dFdu[4]*X[0]*X[2]) |
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| 230 | dFdvDict[pfx+'RBVL33:'+rbsx] += rpd2*(dFdu[0]*X[1]**2+dFdu[1]*X[0]**2-dFdu[3]*X[0]*X[1]) |
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| 231 | dFdvDict[pfx+'RBVL12:'+rbsx] += rpd2*(-dFdu[3]*X[2]**2-2.*dFdu[2]*X[0]*X[1]+ |
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| 232 | dFdu[4]*X[1]*X[2]+dFdu[5]*X[0]*X[2]) |
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| 233 | dFdvDict[pfx+'RBVL13:'+rbsx] += rpd2*(-dFdu[4]*X[1]**2-2.*dFdu[1]*X[0]*X[2]+ |
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| 234 | dFdu[3]*X[1]*X[2]+dFdu[5]*X[0]*X[1]) |
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| 235 | dFdvDict[pfx+'RBVL23:'+rbsx] += rpd2*(-dFdu[5]*X[0]**2-2.*dFdu[0]*X[1]*X[2]+ |
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| 236 | dFdu[3]*X[0]*X[2]+dFdu[4]*X[0]*X[1]) |
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| 237 | if 'S' in RBObj['ThermalMotion'][0]: |
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| 238 | dFdvDict[pfx+'RBVS12:'+rbsx] += rpd*(dFdu[5]*X[1]-2.*dFdu[1]*X[2]) |
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| 239 | dFdvDict[pfx+'RBVS13:'+rbsx] += rpd*(-dFdu[5]*X[2]+2.*dFdu[2]*X[1]) |
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| 240 | dFdvDict[pfx+'RBVS21:'+rbsx] += rpd*(-dFdu[4]*X[0]+2.*dFdu[0]*X[2]) |
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| 241 | dFdvDict[pfx+'RBVS23:'+rbsx] += rpd*(dFdu[4]*X[2]-2.*dFdu[2]*X[0]) |
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| 242 | dFdvDict[pfx+'RBVS31:'+rbsx] += rpd*(dFdu[3]*X[0]-2.*dFdu[0]*X[1]) |
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| 243 | dFdvDict[pfx+'RBVS32:'+rbsx] += rpd*(-dFdu[3]*X[1]+2.*dFdu[1]*X[0]) |
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| 244 | dFdvDict[pfx+'RBVSAA:'+rbsx] += rpd*(dFdu[4]*X[1]-dFdu[3]*X[2]) |
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| 245 | dFdvDict[pfx+'RBVSBB:'+rbsx] += rpd*(dFdu[5]*X[0]-dFdu[3]*X[2]) |
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| 246 | if 'U' in RBObj['ThermalMotion'][0]: |
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| 247 | dFdvDict[pfx+'RBVU:'+rbsx] += dFdvDict[pfx+'AUiso:'+str(AtLookup[atId])] |
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| 248 | |
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| 249 | for irb,RBObj in enumerate(RBModels.get('Residue',[])): |
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| 250 | symAxis = RBObj.get('symAxis') |
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| 251 | Q = RBObj['Orient'][0] |
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| 252 | jrb = RRBIds.index(RBObj['RBId']) |
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| 253 | torData = RBData['Residue'][RBObj['RBId']]['rbSeq'] |
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| 254 | rbsx = str(irb)+':'+str(jrb) |
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| 255 | XYZ,Cart = G2mth.UpdateRBXYZ(Bmat,RBObj,RBData,'Residue') |
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| 256 | for itors,tors in enumerate(RBObj['Torsions']): #derivative error? |
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| 257 | tname = pfx+'RBRTr;'+str(itors)+':'+rbsx |
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| 258 | orId,pvId = torData[itors][:2] |
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| 259 | pivotVec = Cart[orId]-Cart[pvId] |
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| 260 | QA = G2mth.AVdeg2Q(-0.001,pivotVec) |
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| 261 | QB = G2mth.AVdeg2Q(0.001,pivotVec) |
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| 262 | for ir in torData[itors][3]: |
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| 263 | atNum = AtLookup[RBObj['Ids'][ir]] |
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| 264 | rVec = Cart[ir]-Cart[pvId] |
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| 265 | dR = G2mth.prodQVQ(QB,rVec)-G2mth.prodQVQ(QA,rVec) |
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| 266 | dRdT = np.inner(Bmat,G2mth.prodQVQ(Q,dR))/.002 |
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| 267 | for ix in [0,1,2]: |
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| 268 | dFdvDict[tname] += dRdT[ix]*dFdvDict[pfx+atxIds[ix]+str(atNum)] |
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| 269 | for ia,atId in enumerate(RBObj['Ids']): |
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| 270 | atNum = AtLookup[atId] |
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| 271 | if parmDict[pfx+'Afrac:'+str(AtLookup[atId])]: |
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| 272 | dFdvDict[pfx+'RBRf:'+rbsx] += dFdvDict[pfx+'Afrac:'+str(atNum)] |
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| 273 | dx = 0.00001 |
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| 274 | for i,name in enumerate(['RBRPx:','RBRPy:','RBRPz:']): |
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| 275 | dFdvDict[pfx+name+rbsx] += dFdvDict[pfx+atxIds[i]+str(atNum)] |
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| 276 | for iv in range(4): |
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| 277 | Q[iv] -= dx |
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| 278 | XYZ1 = G2mth.RotateRBXYZ(Bmat,Cart,G2mth.normQ(Q),symAxis) |
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| 279 | Q[iv] += 2.*dx |
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| 280 | XYZ2 = G2mth.RotateRBXYZ(Bmat,Cart,G2mth.normQ(Q),symAxis) |
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| 281 | Q[iv] -= dx |
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| 282 | dXdO = (XYZ2[ia]-XYZ1[ia])/(2.*dx) |
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| 283 | for ix in [0,1,2]: |
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| 284 | dFdvDict[pfx+'RBR'+OIds[iv]+rbsx] += dXdO[ix]*dFdvDict[pfx+atxIds[ix]+str(atNum)] |
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| 285 | X = G2mth.prodQVQ(Q,Cart[ia]) |
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| 286 | dFdu = np.array([dFdvDict[pfx+Uid+str(AtLookup[atId])] for Uid in atuIds]).T/gvec |
|---|
| 287 | dFdu = G2lat.U6toUij(dFdu.T) |
|---|
| 288 | dFdu = np.tensordot(Amat.T,np.tensordot(Amat,dFdu,([1,0])),([0,1])) |
|---|
| 289 | dFdu = G2lat.UijtoU6(dFdu) |
|---|
| 290 | atNum = AtLookup[atId] |
|---|
| 291 | if 'T' in RBObj['ThermalMotion'][0]: |
|---|
| 292 | for i,name in enumerate(['RBRT11:','RBRT22:','RBRT33:','RBRT12:','RBRT13:','RBRT23:']): |
|---|
| 293 | dFdvDict[pfx+name+rbsx] += dFdu[i] |
|---|
| 294 | if 'L' in RBObj['ThermalMotion'][0]: |
|---|
| 295 | dFdvDict[pfx+'RBRL11:'+rbsx] += rpd2*(dFdu[1]*X[2]**2+dFdu[2]*X[1]**2-dFdu[5]*X[1]*X[2]) |
|---|
| 296 | dFdvDict[pfx+'RBRL22:'+rbsx] += rpd2*(dFdu[0]*X[2]**2+dFdu[2]*X[0]**2-dFdu[4]*X[0]*X[2]) |
|---|
| 297 | dFdvDict[pfx+'RBRL33:'+rbsx] += rpd2*(dFdu[0]*X[1]**2+dFdu[1]*X[0]**2-dFdu[3]*X[0]*X[1]) |
|---|
| 298 | dFdvDict[pfx+'RBRL12:'+rbsx] += rpd2*(-dFdu[3]*X[2]**2-2.*dFdu[2]*X[0]*X[1]+ |
|---|
| 299 | dFdu[4]*X[1]*X[2]+dFdu[5]*X[0]*X[2]) |
|---|
| 300 | dFdvDict[pfx+'RBRL13:'+rbsx] += rpd2*(dFdu[4]*X[1]**2-2.*dFdu[1]*X[0]*X[2]+ |
|---|
| 301 | dFdu[3]*X[1]*X[2]+dFdu[5]*X[0]*X[1]) |
|---|
| 302 | dFdvDict[pfx+'RBRL23:'+rbsx] += rpd2*(dFdu[5]*X[0]**2-2.*dFdu[0]*X[1]*X[2]+ |
|---|
| 303 | dFdu[3]*X[0]*X[2]+dFdu[4]*X[0]*X[1]) |
|---|
| 304 | if 'S' in RBObj['ThermalMotion'][0]: |
|---|
| 305 | dFdvDict[pfx+'RBRS12:'+rbsx] += rpd*(dFdu[5]*X[1]-2.*dFdu[1]*X[2]) |
|---|
| 306 | dFdvDict[pfx+'RBRS13:'+rbsx] += rpd*(-dFdu[5]*X[2]+2.*dFdu[2]*X[1]) |
|---|
| 307 | dFdvDict[pfx+'RBRS21:'+rbsx] += rpd*(-dFdu[4]*X[0]+2.*dFdu[0]*X[2]) |
|---|
| 308 | dFdvDict[pfx+'RBRS23:'+rbsx] += rpd*(dFdu[4]*X[2]-2.*dFdu[2]*X[0]) |
|---|
| 309 | dFdvDict[pfx+'RBRS31:'+rbsx] += rpd*(dFdu[3]*X[0]-2.*dFdu[0]*X[1]) |
|---|
| 310 | dFdvDict[pfx+'RBRS32:'+rbsx] += rpd*(-dFdu[3]*X[1]+2.*dFdu[1]*X[0]) |
|---|
| 311 | dFdvDict[pfx+'RBRSAA:'+rbsx] += rpd*(dFdu[4]*X[1]-dFdu[3]*X[2]) |
|---|
| 312 | dFdvDict[pfx+'RBRSBB:'+rbsx] += rpd*(dFdu[5]*X[0]-dFdu[3]*X[2]) |
|---|
| 313 | if 'U' in RBObj['ThermalMotion'][0]: |
|---|
| 314 | dFdvDict[pfx+'RBRU:'+rbsx] += dFdvDict[pfx+'AUiso:'+str(AtLookup[atId])] |
|---|
| 315 | |
|---|
| 316 | ################################################################################ |
|---|
| 317 | ##### Penalty & restraint functions |
|---|
| 318 | ################################################################################ |
|---|
| 319 | |
|---|
| 320 | def penaltyFxn(HistoPhases,calcControls,parmDict,varyList): |
|---|
| 321 | 'Compute user-supplied and built-in restraint functions' |
|---|
| 322 | Histograms,Phases,restraintDict,rigidbodyDict = HistoPhases |
|---|
| 323 | pNames = [] |
|---|
| 324 | pVals = [] |
|---|
| 325 | pWt = [] |
|---|
| 326 | negWt = {} |
|---|
| 327 | pWsum = {} |
|---|
| 328 | pWnum = {} |
|---|
| 329 | for phase in Phases: |
|---|
| 330 | pId = Phases[phase]['pId'] |
|---|
| 331 | negWt[pId] = Phases[phase]['General']['Pawley neg wt'] |
|---|
| 332 | General = Phases[phase]['General'] |
|---|
| 333 | cx,ct,cs,cia = General['AtomPtrs'] |
|---|
| 334 | textureData = General['SH Texture'] |
|---|
| 335 | SGData = General['SGData'] |
|---|
| 336 | Atoms = Phases[phase]['Atoms'] |
|---|
| 337 | AtLookup = G2mth.FillAtomLookUp(Phases[phase]['Atoms'],cia+8) |
|---|
| 338 | cell = General['Cell'][1:7] |
|---|
| 339 | Amat,Bmat = G2lat.cell2AB(cell) |
|---|
| 340 | if phase not in restraintDict: |
|---|
| 341 | continue |
|---|
| 342 | phaseRest = restraintDict[phase] |
|---|
| 343 | names = [['Bond','Bonds'],['Angle','Angles'],['Plane','Planes'], |
|---|
| 344 | ['Chiral','Volumes'],['Torsion','Torsions'],['Rama','Ramas'], |
|---|
| 345 | ['ChemComp','Sites'],['Texture','HKLs'],['General','General'],] |
|---|
| 346 | for name,rest in names: |
|---|
| 347 | pWsum[name] = 0. |
|---|
| 348 | pWnum[name] = 0 |
|---|
| 349 | if name not in phaseRest: |
|---|
| 350 | continue |
|---|
| 351 | itemRest = phaseRest[name] |
|---|
| 352 | if itemRest[rest] and itemRest['Use']: |
|---|
| 353 | wt = itemRest.get('wtFactor',1.) |
|---|
| 354 | if name in ['Bond','Angle','Plane','Chiral']: |
|---|
| 355 | for i,[indx,ops,obs,esd] in enumerate(itemRest[rest]): |
|---|
| 356 | pNames.append(str(pId)+':'+name+':'+str(i)) |
|---|
| 357 | XYZ = np.array(G2mth.GetAtomCoordsByID(pId,parmDict,AtLookup,indx)) |
|---|
| 358 | XYZ = G2mth.getSyXYZ(XYZ,ops,SGData) |
|---|
| 359 | if name == 'Bond': |
|---|
| 360 | calc = G2mth.getRestDist(XYZ,Amat) |
|---|
| 361 | elif name == 'Angle': |
|---|
| 362 | calc = G2mth.getRestAngle(XYZ,Amat) |
|---|
| 363 | elif name == 'Plane': |
|---|
| 364 | calc = G2mth.getRestPlane(XYZ,Amat) |
|---|
| 365 | elif name == 'Chiral': |
|---|
| 366 | calc = G2mth.getRestChiral(XYZ,Amat) |
|---|
| 367 | pVals.append(obs-calc) |
|---|
| 368 | pWt.append(wt/esd**2) |
|---|
| 369 | pWsum[name] += wt*((obs-calc)/esd)**2 |
|---|
| 370 | pWnum[name] += 1 |
|---|
| 371 | elif name in ['Torsion','Rama']: |
|---|
| 372 | coeffDict = itemRest['Coeff'] |
|---|
| 373 | for i,[indx,ops,cofName,esd] in enumerate(itemRest[rest]): |
|---|
| 374 | pNames.append(str(pId)+':'+name+':'+str(i)) |
|---|
| 375 | XYZ = np.array(G2mth.GetAtomCoordsByID(pId,parmDict,AtLookup,indx)) |
|---|
| 376 | XYZ = G2mth.getSyXYZ(XYZ,ops,SGData) |
|---|
| 377 | if name == 'Torsion': |
|---|
| 378 | tor = G2mth.getRestTorsion(XYZ,Amat) |
|---|
| 379 | restr,calc = G2mth.calcTorsionEnergy(tor,coeffDict[cofName]) |
|---|
| 380 | else: |
|---|
| 381 | phi,psi = G2mth.getRestRama(XYZ,Amat) |
|---|
| 382 | restr,calc = G2mth.calcRamaEnergy(phi,psi,coeffDict[cofName]) |
|---|
| 383 | pVals.append(restr) |
|---|
| 384 | pWt.append(wt/esd**2) |
|---|
| 385 | pWsum[name] += wt*(restr/esd)**2 |
|---|
| 386 | pWnum[name] += 1 |
|---|
| 387 | elif name == 'ChemComp': |
|---|
| 388 | for i,[indx,factors,obs,esd] in enumerate(itemRest[rest]): |
|---|
| 389 | pNames.append(str(pId)+':'+name+':'+str(i)) |
|---|
| 390 | mul = np.array(G2mth.GetAtomItemsById(Atoms,AtLookup,indx,cs+1)) |
|---|
| 391 | frac = np.array(G2mth.GetAtomFracByID(pId,parmDict,AtLookup,indx)) |
|---|
| 392 | calc = np.sum(mul*frac*factors) |
|---|
| 393 | pVals.append(obs-calc) |
|---|
| 394 | pWt.append(wt/esd**2) |
|---|
| 395 | pWsum[name] += wt*((obs-calc)/esd)**2 |
|---|
| 396 | pWnum[name] += 1 |
|---|
| 397 | elif name == 'Texture': |
|---|
| 398 | SHkeys = list(textureData['SH Coeff'][1].keys()) |
|---|
| 399 | SHCoef = G2mth.GetSHCoeff(pId,parmDict,SHkeys) |
|---|
| 400 | shModels = ['cylindrical','none','shear - 2/m','rolling - mmm'] |
|---|
| 401 | SamSym = dict(zip(shModels,['0','-1','2/m','mmm'])) |
|---|
| 402 | for i,[hkl,grid,esd1,ifesd2,esd2] in enumerate(itemRest[rest]): |
|---|
| 403 | PH = np.array(hkl) |
|---|
| 404 | phi,beta = G2lat.CrsAng(np.array(hkl),cell,SGData) |
|---|
| 405 | ODFln = G2lat.Flnh(False,SHCoef,phi,beta,SGData) |
|---|
| 406 | R,P,Z = G2mth.getRestPolefig(ODFln,SamSym[textureData['Model']],grid) |
|---|
| 407 | Z1 = ma.masked_greater(Z,0.0) #is this + or -? |
|---|
| 408 | IndZ1 = np.array(ma.nonzero(Z1)) |
|---|
| 409 | for ind in IndZ1.T: |
|---|
| 410 | pNames.append('%d:%s:%d:%.2f:%.2f'%(pId,name,i,R[ind[0],ind[1]],P[ind[0],ind[1]])) |
|---|
| 411 | pVals.append(Z1[ind[0]][ind[1]]) |
|---|
| 412 | pWt.append(wt/esd1**2) |
|---|
| 413 | pWsum[name] += wt*(-Z1[ind[0]][ind[1]]/esd1)**2 |
|---|
| 414 | pWnum[name] += 1 |
|---|
| 415 | if ifesd2: |
|---|
| 416 | Z2 = 1.-Z |
|---|
| 417 | for ind in np.ndindex(grid,grid): |
|---|
| 418 | pNames.append('%d:%s:%d:%.2f:%.2f'%(pId,name+'-unit',i,R[ind[0],ind[1]],P[ind[0],ind[1]])) |
|---|
| 419 | pVals.append(Z2[ind[0]][ind[1]]) |
|---|
| 420 | pWt.append(wt/esd2**2) |
|---|
| 421 | pWsum[name] += wt*(Z2/esd2)**2 |
|---|
| 422 | pWnum[name] += 1 |
|---|
| 423 | elif name == 'General': |
|---|
| 424 | for i,(eq,obs,esd) in enumerate(itemRest[rest]): |
|---|
| 425 | calcobj = G2obj.ExpressionCalcObj(eq) |
|---|
| 426 | calcobj.SetupCalc(parmDict) |
|---|
| 427 | calc = calcobj.EvalExpression() |
|---|
| 428 | try: |
|---|
| 429 | pVals.append(obs-calc) |
|---|
| 430 | pWt.append(wt/esd**2) |
|---|
| 431 | pWsum[name] += wt*((obs-calc)/esd)**2 |
|---|
| 432 | pWnum[name] += 1 |
|---|
| 433 | pNames.append(str(pId)+':'+name+':'+str(i)) |
|---|
| 434 | except: |
|---|
| 435 | print('Error computing General restraint #{}'.format(i+1)) |
|---|
| 436 | for phase in Phases: |
|---|
| 437 | name = 'SH-Pref.Ori.' |
|---|
| 438 | pId = Phases[phase]['pId'] |
|---|
| 439 | General = Phases[phase]['General'] |
|---|
| 440 | SGData = General['SGData'] |
|---|
| 441 | cell = General['Cell'][1:7] |
|---|
| 442 | pWsum[name] = 0.0 |
|---|
| 443 | pWnum[name] = 0 |
|---|
| 444 | for hist in Phases[phase]['Histograms']: |
|---|
| 445 | if not Phases[phase]['Histograms'][hist]['Use']: |
|---|
| 446 | continue |
|---|
| 447 | if hist in Histograms and 'PWDR' in hist: |
|---|
| 448 | hId = Histograms[hist]['hId'] |
|---|
| 449 | phfx = '%d:%d:'%(pId,hId) |
|---|
| 450 | if calcControls.get(phfx+'poType','') == 'SH': |
|---|
| 451 | toler = calcControls[phfx+'SHtoler'] |
|---|
| 452 | wt = 1./toler**2 |
|---|
| 453 | HKLs = np.array(calcControls[phfx+'SHhkl']) |
|---|
| 454 | SHnames = calcControls[phfx+'SHnames'] |
|---|
| 455 | SHcof = dict(zip(SHnames,[parmDict[phfx+cof] for cof in SHnames])) |
|---|
| 456 | for i,PH in enumerate(HKLs): |
|---|
| 457 | phi,beta = G2lat.CrsAng(PH,cell,SGData) |
|---|
| 458 | SH3Coef = {} |
|---|
| 459 | for item in SHcof: |
|---|
| 460 | L,N = eval(item.strip('C')) |
|---|
| 461 | SH3Coef['C%d,0,%d'%(L,N)] = SHcof[item] |
|---|
| 462 | ODFln = G2lat.Flnh(False,SH3Coef,phi,beta,SGData) |
|---|
| 463 | X = np.linspace(0,90.0,26) |
|---|
| 464 | Y = ma.masked_greater(G2lat.polfcal(ODFln,'0',X,0.0),0.0) #+ or -? |
|---|
| 465 | IndY = ma.nonzero(Y) |
|---|
| 466 | for ind in IndY[0]: |
|---|
| 467 | pNames.append('%d:%d:%s:%d:%.2f'%(pId,hId,name,i,X[ind])) |
|---|
| 468 | pVals.append(Y[ind]) |
|---|
| 469 | pWt.append(wt) |
|---|
| 470 | pWsum[name] += wt*(Y[ind])**2 |
|---|
| 471 | pWnum[name] += 1 |
|---|
| 472 | pWsum['PWLref'] = 0. |
|---|
| 473 | pWnum['PWLref'] = 0 |
|---|
| 474 | for item in varyList: |
|---|
| 475 | if 'PWLref' in item and parmDict[item] < 0.: |
|---|
| 476 | pId = int(item.split(':')[0]) |
|---|
| 477 | if negWt[pId]: |
|---|
| 478 | pNames.append(item) |
|---|
| 479 | pVals.append(parmDict[item]) |
|---|
| 480 | pWt.append(negWt[pId]) |
|---|
| 481 | pWsum['PWLref'] += negWt[pId]*(parmDict[item])**2 |
|---|
| 482 | pWnum['PWLref'] += 1 |
|---|
| 483 | pVals = np.array(pVals) |
|---|
| 484 | pWt = np.array(pWt) #should this be np.sqrt? |
|---|
| 485 | return pNames,pVals,pWt,pWsum,pWnum |
|---|
| 486 | |
|---|
| 487 | def penaltyDeriv(pNames,pVal,HistoPhases,calcControls,parmDict,varyList): |
|---|
| 488 | '''Compute derivatives on user-supplied and built-in restraint |
|---|
| 489 | (penalty) functions |
|---|
| 490 | |
|---|
| 491 | where pNames is list of restraint labels |
|---|
| 492 | |
|---|
| 493 | returns pDerv with partial derivatives by variable# in varList and |
|---|
| 494 | restraint# in pNames (pDerv[variable#][restraint#]) |
|---|
| 495 | ''' |
|---|
| 496 | Histograms,Phases,restraintDict,rigidbodyDict = HistoPhases |
|---|
| 497 | pDerv = np.zeros((len(varyList),len(pVal))) |
|---|
| 498 | for pName in pNames: # loop over restraints |
|---|
| 499 | if 'General' == pName.split(':')[1]: |
|---|
| 500 | # initialize for General restraint(s) here |
|---|
| 501 | parmDict0 = parmDict.copy() |
|---|
| 502 | # setup steps for each parameter |
|---|
| 503 | stepDict = {} |
|---|
| 504 | for parm in varyList: |
|---|
| 505 | stepDict[parm] = G2obj.getVarStep(parm,parmDict) |
|---|
| 506 | break |
|---|
| 507 | for phase in Phases: |
|---|
| 508 | # if phase not in restraintDict: |
|---|
| 509 | # continue |
|---|
| 510 | pId = Phases[phase]['pId'] |
|---|
| 511 | General = Phases[phase]['General'] |
|---|
| 512 | cx,ct,cs,cia = General['AtomPtrs'] |
|---|
| 513 | SGData = General['SGData'] |
|---|
| 514 | Atoms = Phases[phase]['Atoms'] |
|---|
| 515 | AtLookup = G2mth.FillAtomLookUp(Phases[phase]['Atoms'],cia+8) |
|---|
| 516 | cell = General['Cell'][1:7] |
|---|
| 517 | Amat,Bmat = G2lat.cell2AB(cell) |
|---|
| 518 | textureData = General['SH Texture'] |
|---|
| 519 | |
|---|
| 520 | SHkeys = list(textureData['SH Coeff'][1].keys()) |
|---|
| 521 | SHCoef = G2mth.GetSHCoeff(pId,parmDict,SHkeys) |
|---|
| 522 | shModels = ['cylindrical','none','shear - 2/m','rolling - mmm'] |
|---|
| 523 | SamSym = dict(zip(shModels,['0','-1','2/m','mmm'])) |
|---|
| 524 | sam = SamSym[textureData['Model']] |
|---|
| 525 | phaseRest = restraintDict.get(phase,{}) |
|---|
| 526 | names = {'Bond':'Bonds','Angle':'Angles','Plane':'Planes', |
|---|
| 527 | 'Chiral':'Volumes','Torsion':'Torsions','Rama':'Ramas', |
|---|
| 528 | 'ChemComp':'Sites','Texture':'HKLs'} |
|---|
| 529 | lasthkl = np.array([0,0,0]) |
|---|
| 530 | for ip,pName in enumerate(pNames): # loop over restraints |
|---|
| 531 | pnames = pName.split(':') |
|---|
| 532 | if pId == int(pnames[0]): |
|---|
| 533 | name = pnames[1] |
|---|
| 534 | if 'PWL' in pName: |
|---|
| 535 | pDerv[varyList.index(pName)][ip] += 1. |
|---|
| 536 | continue |
|---|
| 537 | elif 'SH-' in pName: |
|---|
| 538 | continue |
|---|
| 539 | Id = int(pnames[2]) |
|---|
| 540 | itemRest = phaseRest[name] |
|---|
| 541 | if name in ['Bond','Angle','Plane','Chiral']: |
|---|
| 542 | indx,ops,obs,esd = itemRest[names[name]][Id] |
|---|
| 543 | dNames = [] |
|---|
| 544 | for ind in indx: |
|---|
| 545 | dNames += [str(pId)+'::dA'+Xname+':'+str(AtLookup[ind]) for Xname in ['x','y','z']] |
|---|
| 546 | XYZ = np.array(G2mth.GetAtomCoordsByID(pId,parmDict,AtLookup,indx)) |
|---|
| 547 | if name == 'Bond': |
|---|
| 548 | deriv = G2mth.getRestDeriv(G2mth.getRestDist,XYZ,Amat,ops,SGData) |
|---|
| 549 | elif name == 'Angle': |
|---|
| 550 | deriv = G2mth.getRestDeriv(G2mth.getRestAngle,XYZ,Amat,ops,SGData) |
|---|
| 551 | elif name == 'Plane': |
|---|
| 552 | deriv = G2mth.getRestDeriv(G2mth.getRestPlane,XYZ,Amat,ops,SGData) |
|---|
| 553 | elif name == 'Chiral': |
|---|
| 554 | deriv = G2mth.getRestDeriv(G2mth.getRestChiral,XYZ,Amat,ops,SGData) |
|---|
| 555 | elif name in ['Torsion','Rama']: |
|---|
| 556 | coffDict = itemRest['Coeff'] |
|---|
| 557 | indx,ops,cofName,esd = itemRest[names[name]][Id] |
|---|
| 558 | dNames = [] |
|---|
| 559 | for ind in indx: |
|---|
| 560 | dNames += [str(pId)+'::dA'+Xname+':'+str(AtLookup[ind]) for Xname in ['x','y','z']] |
|---|
| 561 | XYZ = np.array(G2mth.GetAtomCoordsByID(pId,parmDict,AtLookup,indx)) |
|---|
| 562 | if name == 'Torsion': |
|---|
| 563 | deriv = G2mth.getTorsionDeriv(XYZ,Amat,coffDict[cofName]) |
|---|
| 564 | else: |
|---|
| 565 | deriv = G2mth.getRamaDeriv(XYZ,Amat,coffDict[cofName]) |
|---|
| 566 | elif name == 'ChemComp': |
|---|
| 567 | indx,factors,obs,esd = itemRest[names[name]][Id] |
|---|
| 568 | dNames = [] |
|---|
| 569 | for ind in indx: |
|---|
| 570 | dNames += [str(pId)+'::Afrac:'+str(AtLookup[ind])] |
|---|
| 571 | mul = np.array(G2mth.GetAtomItemsById(Atoms,AtLookup,indx,cs+1)) |
|---|
| 572 | deriv = mul*factors |
|---|
| 573 | elif 'Texture' in name: |
|---|
| 574 | deriv = [] |
|---|
| 575 | dNames = [] |
|---|
| 576 | hkl,grid,esd1,ifesd2,esd2 = itemRest[names[name]][Id] |
|---|
| 577 | hkl = np.array(hkl) |
|---|
| 578 | if np.any(lasthkl-hkl): |
|---|
| 579 | phi,beta = G2lat.CrsAng(np.array(hkl),cell,SGData) |
|---|
| 580 | ODFln = G2lat.Flnh(False,SHCoef,phi,beta,SGData) |
|---|
| 581 | lasthkl = copy.copy(hkl) |
|---|
| 582 | if 'unit' in name: |
|---|
| 583 | pass |
|---|
| 584 | else: |
|---|
| 585 | gam = float(pnames[3]) |
|---|
| 586 | psi = float(pnames[4]) |
|---|
| 587 | for SHname in ODFln: |
|---|
| 588 | l,m,n = eval(SHname[1:]) |
|---|
| 589 | Ksl = G2lat.GetKsl(l,m,sam,psi,gam)[0] |
|---|
| 590 | dNames += [str(pId)+'::'+SHname] |
|---|
| 591 | deriv.append(-ODFln[SHname][0]*Ksl/SHCoef[SHname]) |
|---|
| 592 | elif name == 'General': |
|---|
| 593 | deriv = [] |
|---|
| 594 | dNames = [] |
|---|
| 595 | eq,obs,esd = itemRest[name][Id] |
|---|
| 596 | calcobj = G2obj.ExpressionCalcObj(eq) |
|---|
| 597 | parmlist = list(eq.assgnVars.values()) # parameters used in this expression |
|---|
| 598 | for parm in parmlist: # expand list if any parms are determined by constraints |
|---|
| 599 | if parm in G2mv.GetDependentVars(): |
|---|
| 600 | parmlist += G2mv.GetIndependentVars() |
|---|
| 601 | break |
|---|
| 602 | for ind,var in enumerate(varyList): |
|---|
| 603 | drv = 0 |
|---|
| 604 | if var in parmlist: |
|---|
| 605 | step = stepDict.get(var,1e-5) |
|---|
| 606 | calc = [] |
|---|
| 607 | # apply step to parameter |
|---|
| 608 | oneparm = True |
|---|
| 609 | for s in -step,2*step: |
|---|
| 610 | parmDict[var] += s |
|---|
| 611 | # extend shift if needed to other parameters |
|---|
| 612 | if var in G2mv.independentVars: |
|---|
| 613 | G2mv.Dict2Map(parmDict) |
|---|
| 614 | oneparm = False |
|---|
| 615 | elif var in G2mv.dependentVars: |
|---|
| 616 | G2mv.Map2Dict(parmDict,[]) |
|---|
| 617 | oneparm = False |
|---|
| 618 | if 'RB' in var: |
|---|
| 619 | ApplyRBModels(parmDict,Phases,rigidbodyDict) |
|---|
| 620 | # test |
|---|
| 621 | oneparm = False |
|---|
| 622 | calcobj.SetupCalc(parmDict) |
|---|
| 623 | calc.append(calcobj.EvalExpression()) |
|---|
| 624 | drv = (calc[1]-calc[0])*.5/step |
|---|
| 625 | # restore the dict |
|---|
| 626 | if oneparm: |
|---|
| 627 | parmDict[var] = parmDict0[var] |
|---|
| 628 | else: |
|---|
| 629 | parmDict = parmDict0.copy() |
|---|
| 630 | else: |
|---|
| 631 | drv = 0 |
|---|
| 632 | pDerv[ind][ip] = drv |
|---|
| 633 | # Add derivatives into matrix, if needed |
|---|
| 634 | for dName,drv in zip(dNames,deriv): |
|---|
| 635 | try: |
|---|
| 636 | ind = varyList.index(dName) |
|---|
| 637 | pDerv[ind][ip] += drv |
|---|
| 638 | except ValueError: |
|---|
| 639 | pass |
|---|
| 640 | |
|---|
| 641 | lasthkl = np.array([0,0,0]) |
|---|
| 642 | for ip,pName in enumerate(pNames): |
|---|
| 643 | deriv = [] |
|---|
| 644 | dNames = [] |
|---|
| 645 | pnames = pName.split(':') |
|---|
| 646 | if 'SH-' in pName and pId == int(pnames[0]): |
|---|
| 647 | hId = int(pnames[1]) |
|---|
| 648 | phfx = '%d:%d:'%(pId,hId) |
|---|
| 649 | psi = float(pnames[4]) |
|---|
| 650 | HKLs = calcControls[phfx+'SHhkl'] |
|---|
| 651 | SHnames = calcControls[phfx+'SHnames'] |
|---|
| 652 | SHcof = dict(zip(SHnames,[parmDict[phfx+cof] for cof in SHnames])) |
|---|
| 653 | hkl = np.array(HKLs[int(pnames[3])]) |
|---|
| 654 | if np.any(lasthkl-hkl): |
|---|
| 655 | phi,beta = G2lat.CrsAng(np.array(hkl),cell,SGData) |
|---|
| 656 | SH3Coef = {} |
|---|
| 657 | for item in SHcof: |
|---|
| 658 | L,N = eval(item.strip('C')) |
|---|
| 659 | SH3Coef['C%d,0,%d'%(L,N)] = SHcof[item] |
|---|
| 660 | ODFln = G2lat.Flnh(False,SH3Coef,phi,beta,SGData) |
|---|
| 661 | lasthkl = copy.copy(hkl) |
|---|
| 662 | for SHname in SHnames: |
|---|
| 663 | l,n = eval(SHname[1:]) |
|---|
| 664 | SH3name = 'C%d,0,%d'%(l,n) |
|---|
| 665 | Ksl = G2lat.GetKsl(l,0,'0',psi,0.0)[0] |
|---|
| 666 | dNames += [phfx+SHname] |
|---|
| 667 | deriv.append(ODFln[SH3name][0]*Ksl/SHcof[SHname]) |
|---|
| 668 | for dName,drv in zip(dNames,deriv): |
|---|
| 669 | try: |
|---|
| 670 | ind = varyList.index(dName) |
|---|
| 671 | pDerv[ind][ip] += drv |
|---|
| 672 | except ValueError: |
|---|
| 673 | pass |
|---|
| 674 | return pDerv |
|---|
| 675 | |
|---|
| 676 | ################################################################################ |
|---|
| 677 | ##### Function & derivative calculations |
|---|
| 678 | ################################################################################ |
|---|
| 679 | |
|---|
| 680 | def GetAtomFXU(pfx,calcControls,parmDict): |
|---|
| 681 | 'Needs a doc string' |
|---|
| 682 | Natoms = calcControls['Natoms'][pfx] |
|---|
| 683 | Tdata = Natoms*[' ',] |
|---|
| 684 | Mdata = np.zeros(Natoms) |
|---|
| 685 | IAdata = Natoms*[' ',] |
|---|
| 686 | Fdata = np.zeros(Natoms) |
|---|
| 687 | Xdata = np.zeros((3,Natoms)) |
|---|
| 688 | dXdata = np.zeros((3,Natoms)) |
|---|
| 689 | Uisodata = np.zeros(Natoms) |
|---|
| 690 | Uijdata = np.zeros((6,Natoms)) |
|---|
| 691 | Gdata = np.zeros((3,Natoms)) |
|---|
| 692 | keys = {'Atype:':Tdata,'Amul:':Mdata,'Afrac:':Fdata,'AI/A:':IAdata, |
|---|
| 693 | 'dAx:':dXdata[0],'dAy:':dXdata[1],'dAz:':dXdata[2], |
|---|
| 694 | 'Ax:':Xdata[0],'Ay:':Xdata[1],'Az:':Xdata[2],'AUiso:':Uisodata, |
|---|
| 695 | 'AU11:':Uijdata[0],'AU22:':Uijdata[1],'AU33:':Uijdata[2], |
|---|
| 696 | 'AU12:':Uijdata[3],'AU13:':Uijdata[4],'AU23:':Uijdata[5], |
|---|
| 697 | 'AMx:':Gdata[0],'AMy:':Gdata[1],'AMz:':Gdata[2],} |
|---|
| 698 | for iatm in range(Natoms): |
|---|
| 699 | for key in keys: |
|---|
| 700 | parm = pfx+key+str(iatm) |
|---|
| 701 | if parm in parmDict: |
|---|
| 702 | keys[key][iatm] = parmDict[parm] |
|---|
| 703 | Fdata = np.where(Fdata,Fdata,1.e-8) #avoid divide by zero in derivative calc. |
|---|
| 704 | Gdata = np.where(Gdata,Gdata,1.e-8) #avoid divide by zero in derivative calc. |
|---|
| 705 | |
|---|
| 706 | return Tdata,Mdata,Fdata,Xdata,dXdata,IAdata,Uisodata,Uijdata,Gdata |
|---|
| 707 | |
|---|
| 708 | def GetAtomSSFXU(pfx,calcControls,parmDict): |
|---|
| 709 | 'Needs a doc string' |
|---|
| 710 | Natoms = calcControls['Natoms'][pfx] |
|---|
| 711 | maxSSwave = calcControls['maxSSwave'][pfx] |
|---|
| 712 | Nwave = {'F':maxSSwave['Sfrac'],'X':maxSSwave['Spos'],'Y':maxSSwave['Spos'],'Z':maxSSwave['Spos'], |
|---|
| 713 | 'U':maxSSwave['Sadp'],'M':maxSSwave['Smag'],'T':maxSSwave['Spos']} |
|---|
| 714 | XSSdata = np.zeros((6,maxSSwave['Spos'],Natoms)) |
|---|
| 715 | FSSdata = np.zeros((2,maxSSwave['Sfrac'],Natoms)) |
|---|
| 716 | USSdata = np.zeros((12,maxSSwave['Sadp'],Natoms)) |
|---|
| 717 | MSSdata = np.zeros((6,maxSSwave['Smag'],Natoms)) |
|---|
| 718 | waveTypes = [] |
|---|
| 719 | keys = {'Fsin:':FSSdata[0],'Fcos:':FSSdata[1],'Fzero:':FSSdata[0],'Fwid:':FSSdata[1], |
|---|
| 720 | 'Tmin:':XSSdata[0],'Tmax:':XSSdata[1],'Xmax:':XSSdata[2],'Ymax:':XSSdata[3],'Zmax:':XSSdata[4], |
|---|
| 721 | 'Xsin:':XSSdata[0],'Ysin:':XSSdata[1],'Zsin:':XSSdata[2],'Xcos:':XSSdata[3],'Ycos:':XSSdata[4],'Zcos:':XSSdata[5], |
|---|
| 722 | 'U11sin:':USSdata[0],'U22sin:':USSdata[1],'U33sin:':USSdata[2],'U12sin:':USSdata[3],'U13sin:':USSdata[4],'U23sin:':USSdata[5], |
|---|
| 723 | 'U11cos:':USSdata[6],'U22cos:':USSdata[7],'U33cos:':USSdata[8],'U12cos:':USSdata[9],'U13cos:':USSdata[10],'U23cos:':USSdata[11], |
|---|
| 724 | 'MXsin:':MSSdata[0],'MYsin:':MSSdata[1],'MZsin:':MSSdata[2],'MXcos:':MSSdata[3],'MYcos:':MSSdata[4],'MZcos:':MSSdata[5]} |
|---|
| 725 | for iatm in range(Natoms): |
|---|
| 726 | wavetype = [parmDict.get(pfx+kind+'waveType:'+str(iatm),'') for kind in ['F','P','A','M']] |
|---|
| 727 | waveTypes.append(wavetype) |
|---|
| 728 | for key in keys: |
|---|
| 729 | for m in range(Nwave[key[0]]): |
|---|
| 730 | parm = pfx+key+str(iatm)+':%d'%(m) |
|---|
| 731 | if parm in parmDict: |
|---|
| 732 | keys[key][m][iatm] = parmDict[parm] |
|---|
| 733 | return waveTypes,FSSdata,XSSdata,USSdata,MSSdata |
|---|
| 734 | |
|---|
| 735 | def StructureFactor2(refDict,G,hfx,pfx,SGData,calcControls,parmDict): |
|---|
| 736 | ''' Compute structure factors for all h,k,l for phase |
|---|
| 737 | puts the result, F^2, in each ref[8] in refList |
|---|
| 738 | operates on blocks of 100 reflections for speed |
|---|
| 739 | input: |
|---|
| 740 | |
|---|
| 741 | :param dict refDict: where |
|---|
| 742 | 'RefList' list where each ref = h,k,l,it,d,... |
|---|
| 743 | 'FF' dict of form factors - filed in below |
|---|
| 744 | :param np.array G: reciprocal metric tensor |
|---|
| 745 | :param str pfx: phase id string |
|---|
| 746 | :param dict SGData: space group info. dictionary output from SpcGroup |
|---|
| 747 | :param dict calcControls: |
|---|
| 748 | :param dict ParmDict: |
|---|
| 749 | |
|---|
| 750 | ''' |
|---|
| 751 | phfx = pfx.split(':')[0]+hfx |
|---|
| 752 | ast = np.sqrt(np.diag(G)) |
|---|
| 753 | Mast = twopisq*np.multiply.outer(ast,ast) |
|---|
| 754 | SGMT = np.array([ops[0].T for ops in SGData['SGOps']]) # must be ops[0].T |
|---|
| 755 | SGT = np.array([ops[1] for ops in SGData['SGOps']]) |
|---|
| 756 | FFtables = calcControls['FFtables'] |
|---|
| 757 | EFtables = calcControls['EFtables'] |
|---|
| 758 | BLtables = calcControls['BLtables'] |
|---|
| 759 | Amat,Bmat = G2lat.Gmat2AB(G) |
|---|
| 760 | Flack = 1.0 |
|---|
| 761 | if not SGData['SGInv'] and 'S' in calcControls[hfx+'histType'] and phfx+'Flack' in parmDict: |
|---|
| 762 | Flack = 1.-2.*parmDict[phfx+'Flack'] |
|---|
| 763 | TwinLaw = np.array([[[1,0,0],[0,1,0],[0,0,1]],]) |
|---|
| 764 | TwDict = refDict.get('TwDict',{}) |
|---|
| 765 | if 'S' in calcControls[hfx+'histType']: |
|---|
| 766 | NTL = calcControls[phfx+'NTL'] |
|---|
| 767 | NM = calcControls[phfx+'TwinNMN']+1 |
|---|
| 768 | TwinLaw = calcControls[phfx+'TwinLaw'] |
|---|
| 769 | TwinFr = np.array([parmDict[phfx+'TwinFr:'+str(i)] for i in range(len(TwinLaw))]) |
|---|
| 770 | TwinInv = list(np.where(calcControls[phfx+'TwinInv'],-1,1)) |
|---|
| 771 | Tdata,Mdata,Fdata,Xdata,dXdata,IAdata,Uisodata,Uijdata,Gdata = \ |
|---|
| 772 | GetAtomFXU(pfx,calcControls,parmDict) |
|---|
| 773 | if not Xdata.size: #no atoms in phase! |
|---|
| 774 | return |
|---|
| 775 | if 'NC' in calcControls[hfx+'histType'] or 'NB' in calcControls[hfx+'histType']: |
|---|
| 776 | FP,FPP = G2el.BlenResCW(Tdata,BLtables,parmDict[hfx+'Lam']) |
|---|
| 777 | elif 'X' in calcControls[hfx+'histType']: |
|---|
| 778 | FP = np.array([FFtables[El][hfx+'FP'] for El in Tdata]) |
|---|
| 779 | FPP = np.array([FFtables[El][hfx+'FPP'] for El in Tdata]) |
|---|
| 780 | elif 'SEC' in calcControls[hfx+'histType']: |
|---|
| 781 | FP = np.zeros(len(Tdata)) |
|---|
| 782 | FPP = np.zeros(len(Tdata)) |
|---|
| 783 | Uij = np.array(G2lat.U6toUij(Uijdata)) |
|---|
| 784 | bij = Mast*Uij.T |
|---|
| 785 | blkSize = 100 #no. of reflections in a block - size seems optimal |
|---|
| 786 | nRef = refDict['RefList'].shape[0] |
|---|
| 787 | SQ = 1./(2.*refDict['RefList'].T[4])**2 |
|---|
| 788 | if 'N' in calcControls[hfx+'histType']: |
|---|
| 789 | dat = G2el.getBLvalues(BLtables) |
|---|
| 790 | refDict['FF']['El'] = list(dat.keys()) |
|---|
| 791 | refDict['FF']['FF'] = np.ones((nRef,len(dat)))*list(dat.values()) |
|---|
| 792 | elif 'SEC' in calcControls[hfx+'histType']: |
|---|
| 793 | dat = G2el.getFFvalues(EFtables,0.) |
|---|
| 794 | refDict['FF']['El'] = list(dat.keys()) |
|---|
| 795 | refDict['FF']['FF'] = np.zeros((nRef,len(dat))) |
|---|
| 796 | for iel,El in enumerate(refDict['FF']['El']): |
|---|
| 797 | refDict['FF']['FF'].T[iel] = G2el.ScatFac(EFtables[El],SQ) |
|---|
| 798 | else: #'X' |
|---|
| 799 | dat = G2el.getFFvalues(FFtables,0.) |
|---|
| 800 | refDict['FF']['El'] = list(dat.keys()) |
|---|
| 801 | refDict['FF']['FF'] = np.zeros((nRef,len(dat))) |
|---|
| 802 | for iel,El in enumerate(refDict['FF']['El']): |
|---|
| 803 | refDict['FF']['FF'].T[iel] = G2el.ScatFac(FFtables[El],SQ) |
|---|
| 804 | #reflection processing begins here - big arrays! |
|---|
| 805 | iBeg = 0 |
|---|
| 806 | while iBeg < nRef: |
|---|
| 807 | iFin = min(iBeg+blkSize,nRef) |
|---|
| 808 | refl = refDict['RefList'][iBeg:iFin] #array(blkSize,nItems) |
|---|
| 809 | H = refl.T[:3] #array(blkSize,3) |
|---|
| 810 | H = np.squeeze(np.inner(H.T,TwinLaw)) #maybe array(blkSize,nTwins,3) or (blkSize,3) |
|---|
| 811 | TwMask = np.any(H,axis=-1) |
|---|
| 812 | if TwinLaw.shape[0] > 1 and TwDict: #need np.inner(TwinLaw[?],TwDict[iref][i])*TwinInv[i] |
|---|
| 813 | for ir in range(blkSize): |
|---|
| 814 | iref = ir+iBeg |
|---|
| 815 | if iref in TwDict: |
|---|
| 816 | for i in TwDict[iref]: |
|---|
| 817 | for n in range(NTL): |
|---|
| 818 | H[ir][i+n*NM] = np.inner(TwinLaw[n*NM],np.array(TwDict[iref][i])*TwinInv[i+n*NM]) |
|---|
| 819 | TwMask = np.any(H,axis=-1) |
|---|
| 820 | SQ = 1./(2.*refl.T[4])**2 #array(blkSize) |
|---|
| 821 | SQfactor = 4.0*SQ*twopisq #ditto prev. |
|---|
| 822 | if 'T' in calcControls[hfx+'histType']: |
|---|
| 823 | if 'P' in calcControls[hfx+'histType']: |
|---|
| 824 | FP,FPP = G2el.BlenResTOF(Tdata,BLtables,refl.T[14]) |
|---|
| 825 | else: |
|---|
| 826 | FP,FPP = G2el.BlenResTOF(Tdata,BLtables,refl.T[12]) |
|---|
| 827 | FP = np.repeat(FP.T,len(SGT)*len(TwinLaw),axis=0) |
|---|
| 828 | FPP = np.repeat(FPP.T,len(SGT)*len(TwinLaw),axis=0) |
|---|
| 829 | Uniq = np.inner(H,SGMT) |
|---|
| 830 | Phi = np.inner(H,SGT) |
|---|
| 831 | phase = twopi*(np.inner(Uniq,(dXdata+Xdata).T).T+Phi.T).T |
|---|
| 832 | sinp = np.sin(phase) |
|---|
| 833 | cosp = np.cos(phase) |
|---|
| 834 | biso = -SQfactor*Uisodata[:,nxs] |
|---|
| 835 | Tiso = np.repeat(np.where(biso<1.,np.exp(biso),1.0),len(SGT)*len(TwinLaw),axis=1).T |
|---|
| 836 | HbH = -np.sum(Uniq.T*np.swapaxes(np.inner(bij,Uniq),2,-1),axis=1) |
|---|
| 837 | # HbH = -np.sum(np.inner(Uniq,bij)*Uniq[:,:,nxs,:],axis=-1).T #doesn't work, but should! |
|---|
| 838 | Tuij = np.where(HbH<1.,np.exp(HbH),1.0).T |
|---|
| 839 | Tcorr = np.reshape(Tiso,Tuij.shape)*Tuij*Mdata*Fdata/len(SGMT) |
|---|
| 840 | Tindx = np.array([refDict['FF']['El'].index(El) for El in Tdata]) |
|---|
| 841 | FF = np.repeat(refDict['FF']['FF'][iBeg:iFin].T[Tindx].T,len(SGT)*len(TwinLaw),axis=0) |
|---|
| 842 | Bab = np.repeat(parmDict[phfx+'BabA']*np.exp(-parmDict[phfx+'BabU']*SQfactor),len(SGT)*len(TwinLaw)) |
|---|
| 843 | if 'T' in calcControls[hfx+'histType']: #fa,fb are 2 X blkSize X nTwin X nOps x nAtoms |
|---|
| 844 | fa = np.array([np.reshape(((FF+FP).T-Bab).T,cosp.shape)*cosp*Tcorr,-np.reshape(Flack*FPP,sinp.shape)*sinp*Tcorr]) |
|---|
| 845 | fb = np.array([np.reshape(((FF+FP).T-Bab).T,sinp.shape)*sinp*Tcorr,np.reshape(Flack*FPP,cosp.shape)*cosp*Tcorr]) |
|---|
| 846 | else: |
|---|
| 847 | fa = np.array([np.reshape(((FF+FP).T-Bab).T,cosp.shape)*cosp*Tcorr,-Flack*FPP*sinp*Tcorr]) |
|---|
| 848 | fb = np.array([np.reshape(((FF+FP).T-Bab).T,sinp.shape)*sinp*Tcorr,Flack*FPP*cosp*Tcorr]) |
|---|
| 849 | fas = np.sum(np.sum(fa,axis=-1),axis=-1) #real 2 x blkSize x nTwin; sum over atoms & uniq hkl |
|---|
| 850 | fbs = np.sum(np.sum(fb,axis=-1),axis=-1) #imag |
|---|
| 851 | if SGData['SGInv']: #centrosymmetric; B=0 |
|---|
| 852 | fbs[0] *= 0. |
|---|
| 853 | fas[1] *= 0. |
|---|
| 854 | if 'P' in calcControls[hfx+'histType']: #PXC, PNC & PNT: F^2 = A[0]^2 + A[1]^2 + B[0]^2 + B[1]^2 |
|---|
| 855 | refl.T[9] = np.sum(fas**2,axis=0)+np.sum(fbs**2,axis=0) #add fam**2 & fbm**2 here |
|---|
| 856 | refl.T[10] = atan2d(fbs[0],fas[0]) #ignore f' & f" |
|---|
| 857 | else: #HKLF: F^2 = (A[0]+A[1])^2 + (B[0]+B[1])^2 |
|---|
| 858 | if len(TwinLaw) > 1: |
|---|
| 859 | refl.T[9] = np.sum(fas[:,:,0],axis=0)**2+np.sum(fbs[:,:,0],axis=0)**2 #FcT from primary twin element |
|---|
| 860 | refl.T[7] = np.sum(TwinFr*TwMask*np.sum(fas,axis=0)**2,axis=-1)+ \ |
|---|
| 861 | np.sum(TwinFr*TwMask*np.sum(fbs,axis=0)**2,axis=-1) #Fc sum over twins |
|---|
| 862 | refl.T[10] = atan2d(fbs[0].T[0],fas[0].T[0]) #ignore f' & f" & use primary twin |
|---|
| 863 | else: # checked correct!! |
|---|
| 864 | refl.T[9] = np.sum(fas,axis=0)**2+np.sum(fbs,axis=0)**2 |
|---|
| 865 | refl.T[7] = np.copy(refl.T[9]) |
|---|
| 866 | refl.T[10] = atan2d(fbs[0],fas[0]) #ignore f' & f" |
|---|
| 867 | # refl.T[10] = atan2d(np.sum(fbs,axis=0),np.sum(fas,axis=0)) #include f' & f" |
|---|
| 868 | iBeg += blkSize |
|---|
| 869 | # print 'sf time %.4f, nref %d, blkSize %d'%(time.time()-time0,nRef,blkSize) |
|---|
| 870 | |
|---|
| 871 | def StructureFactorDerv2(refDict,G,hfx,pfx,SGData,calcControls,parmDict): |
|---|
| 872 | '''Compute structure factor derivatives on blocks of reflections - for powders/nontwins only |
|---|
| 873 | faster than StructureFactorDerv - correct for powders/nontwins!! |
|---|
| 874 | input: |
|---|
| 875 | |
|---|
| 876 | :param dict refDict: where |
|---|
| 877 | 'RefList' list where each ref = h,k,l,it,d,... |
|---|
| 878 | 'FF' dict of form factors - filled in below |
|---|
| 879 | :param np.array G: reciprocal metric tensor |
|---|
| 880 | :param str hfx: histogram id string |
|---|
| 881 | :param str pfx: phase id string |
|---|
| 882 | :param dict SGData: space group info. dictionary output from SpcGroup |
|---|
| 883 | :param dict calcControls: |
|---|
| 884 | :param dict parmDict: |
|---|
| 885 | |
|---|
| 886 | :returns: dict dFdvDict: dictionary of derivatives |
|---|
| 887 | ''' |
|---|
| 888 | phfx = pfx.split(':')[0]+hfx |
|---|
| 889 | ast = np.sqrt(np.diag(G)) |
|---|
| 890 | Mast = twopisq*np.multiply.outer(ast,ast) |
|---|
| 891 | SGMT = np.array([ops[0].T for ops in SGData['SGOps']]) # must be ops[0].T |
|---|
| 892 | SGT = np.array([ops[1] for ops in SGData['SGOps']]) |
|---|
| 893 | FFtables = calcControls['FFtables'] |
|---|
| 894 | BLtables = calcControls['BLtables'] |
|---|
| 895 | Amat,Bmat = G2lat.Gmat2AB(G) |
|---|
| 896 | nRef = len(refDict['RefList']) |
|---|
| 897 | Tdata,Mdata,Fdata,Xdata,dXdata,IAdata,Uisodata,Uijdata,Gdata = \ |
|---|
| 898 | GetAtomFXU(pfx,calcControls,parmDict) |
|---|
| 899 | if not Xdata.size: #no atoms in phase! |
|---|
| 900 | return {} |
|---|
| 901 | mSize = len(Mdata) |
|---|
| 902 | FF = np.zeros(len(Tdata)) |
|---|
| 903 | if 'NC' in calcControls[hfx+'histType'] or 'NB' in calcControls[hfx+'histType']: |
|---|
| 904 | FP,FPP = G2el.BlenResCW(Tdata,BLtables,parmDict[hfx+'Lam']) |
|---|
| 905 | elif 'X' in calcControls[hfx+'histType']: |
|---|
| 906 | FP = np.array([FFtables[El][hfx+'FP'] for El in Tdata]) |
|---|
| 907 | FPP = np.array([FFtables[El][hfx+'FPP'] for El in Tdata]) |
|---|
| 908 | elif 'SEC' in calcControls[hfx+'histType']: |
|---|
| 909 | FP = np.zeros(len(Tdata)) |
|---|
| 910 | FPP = np.zeros(len(Tdata)) |
|---|
| 911 | Uij = np.array(G2lat.U6toUij(Uijdata)) |
|---|
| 912 | bij = Mast*Uij.T |
|---|
| 913 | dFdvDict = {} |
|---|
| 914 | dFdfr = np.zeros((nRef,mSize)) |
|---|
| 915 | dFdx = np.zeros((nRef,mSize,3)) |
|---|
| 916 | dFdui = np.zeros((nRef,mSize)) |
|---|
| 917 | dFdua = np.zeros((nRef,mSize,6)) |
|---|
| 918 | dFdbab = np.zeros((nRef,2)) |
|---|
| 919 | dFdfl = np.zeros((nRef)) |
|---|
| 920 | Flack = 1.0 |
|---|
| 921 | if not SGData['SGInv'] and 'S' in calcControls[hfx+'histType'] and phfx+'Flack' in parmDict: |
|---|
| 922 | Flack = 1.-2.*parmDict[phfx+'Flack'] |
|---|
| 923 | # time0 = time.time() |
|---|
| 924 | #reflection processing begins here - big arrays! |
|---|
| 925 | iBeg = 0 |
|---|
| 926 | blkSize = 32 #no. of reflections in a block - optimized for speed |
|---|
| 927 | while iBeg < nRef: |
|---|
| 928 | iFin = min(iBeg+blkSize,nRef) |
|---|
| 929 | refl = refDict['RefList'][iBeg:iFin] #array(blkSize,nItems) |
|---|
| 930 | H = refl.T[:3].T |
|---|
| 931 | SQ = 1./(2.*refl.T[4])**2 # or (sin(theta)/lambda)**2 |
|---|
| 932 | SQfactor = 8.0*SQ*np.pi**2 |
|---|
| 933 | if 'T' in calcControls[hfx+'histType']: |
|---|
| 934 | if 'P' in calcControls[hfx+'histType']: |
|---|
| 935 | FP,FPP = G2el.BlenResTOF(Tdata,BLtables,refl.T[14]) |
|---|
| 936 | else: |
|---|
| 937 | FP,FPP = G2el.BlenResTOF(Tdata,BLtables,refl.T[12]) |
|---|
| 938 | FP = np.repeat(FP.T,len(SGT),axis=0) |
|---|
| 939 | FPP = np.repeat(FPP.T,len(SGT),axis=0) |
|---|
| 940 | dBabdA = np.exp(-parmDict[phfx+'BabU']*SQfactor) |
|---|
| 941 | Bab = np.repeat(parmDict[phfx+'BabA']*np.exp(-parmDict[phfx+'BabU']*SQfactor),len(SGT)) |
|---|
| 942 | Tindx = np.array([refDict['FF']['El'].index(El) for El in Tdata]) |
|---|
| 943 | FF = np.repeat(refDict['FF']['FF'][iBeg:iFin].T[Tindx].T,len(SGT),axis=0) |
|---|
| 944 | Uniq = np.inner(H,SGMT) # array(nSGOp,3) |
|---|
| 945 | Phi = np.inner(H,SGT) |
|---|
| 946 | phase = twopi*(np.inner(Uniq,(dXdata+Xdata).T).T+Phi.T).T |
|---|
| 947 | sinp = np.sin(phase) #refBlk x nOps x nAtoms |
|---|
| 948 | cosp = np.cos(phase) |
|---|
| 949 | occ = Mdata*Fdata/len(SGT) |
|---|
| 950 | biso = -SQfactor*Uisodata[:,nxs] |
|---|
| 951 | Tiso = np.repeat(np.where(biso<1.,np.exp(biso),1.0),len(SGT),axis=1).T |
|---|
| 952 | HbH = -np.sum(Uniq.T*np.swapaxes(np.inner(bij,Uniq),2,-1),axis=1) #Natm,Nops,Nref |
|---|
| 953 | # HbH = -np.sum(np.inner(Uniq,bij)*Uniq[:,:,nxs,:],axis=-1).T #doesn't work, but should! |
|---|
| 954 | Tuij = np.where(HbH<1.,np.exp(HbH),1.0).T #Nref,Nops,Natm |
|---|
| 955 | Tcorr = np.reshape(Tiso,Tuij.shape)*Tuij*Mdata*Fdata/len(SGMT) |
|---|
| 956 | Hij = np.array([Mast*np.multiply.outer(U,U) for U in np.reshape(Uniq,(-1,3))]) #Nref*Nops,3,3 |
|---|
| 957 | Hij = np.reshape(np.array([G2lat.UijtoU6(uij) for uij in Hij]),(-1,len(SGT),6)) #Nref,Nops,6 |
|---|
| 958 | fot = np.reshape(((FF+FP).T-Bab).T,cosp.shape)*Tcorr |
|---|
| 959 | if len(FPP.shape) > 1: |
|---|
| 960 | fotp = np.reshape(FPP,cosp.shape)*Tcorr |
|---|
| 961 | else: |
|---|
| 962 | fotp = FPP*Tcorr |
|---|
| 963 | if 'T' in calcControls[hfx+'histType']: |
|---|
| 964 | fa = np.array([fot*cosp,-np.reshape(Flack*FPP,sinp.shape)*sinp*Tcorr]) |
|---|
| 965 | fb = np.array([fot*sinp,np.reshape(Flack*FPP,cosp.shape)*cosp*Tcorr]) |
|---|
| 966 | else: |
|---|
| 967 | fa = np.array([fot*cosp,-Flack*FPP*sinp*Tcorr]) |
|---|
| 968 | fb = np.array([fot*sinp,Flack*FPP*cosp*Tcorr]) |
|---|
| 969 | fas = np.sum(np.sum(fa,axis=-1),axis=-1) #real sum over atoms & unique hkl array(2,refBlk,nTwins) |
|---|
| 970 | fbs = np.sum(np.sum(fb,axis=-1),axis=-1) #imag sum over atoms & uniq hkl |
|---|
| 971 | fax = np.array([-fot*sinp,-fotp*cosp]) #positions array(2,refBlk,nEqv,nAtoms) |
|---|
| 972 | fbx = np.array([fot*cosp,-fotp*sinp]) |
|---|
| 973 | #sum below is over Uniq |
|---|
| 974 | dfadfr = np.sum(fa/occ,axis=-2) #array(2,refBlk,nAtom) Fdata != 0 avoids /0. problem |
|---|
| 975 | dfadba = np.sum(-cosp*Tcorr,axis=-2) #array(refBlk,nAtom) |
|---|
| 976 | dfadx = np.sum(twopi*Uniq[nxs,:,nxs,:,:]*np.swapaxes(fax,-2,-1)[:,:,:,:,nxs],axis=-2) |
|---|
| 977 | dfadui = np.sum(-SQfactor[nxs,:,nxs,nxs]*fa,axis=-2) #array(Ops,refBlk,nAtoms) |
|---|
| 978 | dfadua = np.sum(-Hij[nxs,:,nxs,:,:]*np.swapaxes(fa,-2,-1)[:,:,:,:,nxs],axis=-2) |
|---|
| 979 | # array(2,refBlk,nAtom,3) & array(2,refBlk,nAtom,6) |
|---|
| 980 | if not SGData['SGInv']: |
|---|
| 981 | dfbdfr = np.sum(fb/occ,axis=-2) #Fdata != 0 avoids /0. problem |
|---|
| 982 | dfbdba = np.sum(-sinp*Tcorr,axis=-2) |
|---|
| 983 | dfadfl = np.sum(np.sum(-fotp*sinp,axis=-1),axis=-1) |
|---|
| 984 | dfbdfl = np.sum(np.sum(fotp*cosp,axis=-1),axis=-1) |
|---|
| 985 | dfbdx = np.sum(twopi*Uniq[nxs,:,nxs,:,:]*np.swapaxes(fbx,-2,-1)[:,:,:,:,nxs],axis=-2) |
|---|
| 986 | dfbdui = np.sum(-SQfactor[nxs,:,nxs,nxs]*fb,axis=-2) |
|---|
| 987 | dfbdua = np.sum(-Hij[nxs,:,nxs,:,:]*np.swapaxes(fb,-2,-1)[:,:,:,:,nxs],axis=-2) |
|---|
| 988 | else: |
|---|
| 989 | dfbdfr = np.zeros_like(dfadfr) |
|---|
| 990 | dfbdx = np.zeros_like(dfadx) |
|---|
| 991 | dfbdui = np.zeros_like(dfadui) |
|---|
| 992 | dfbdua = np.zeros_like(dfadua) |
|---|
| 993 | dfbdba = np.zeros_like(dfadba) |
|---|
| 994 | dfadfl = 0.0 |
|---|
| 995 | dfbdfl = 0.0 |
|---|
| 996 | #NB: the above have been checked against PA(1:10,1:2) in strfctr.for for Al2O3! |
|---|
| 997 | SA = fas[0]+fas[1] |
|---|
| 998 | SB = fbs[0]+fbs[1] |
|---|
| 999 | if 'P' in calcControls[hfx+'histType']: #checked perfect for centro & noncentro |
|---|
| 1000 | dFdfr[iBeg:iFin] = 2.*np.sum(fas[:,:,nxs]*dfadfr+fbs[:,:,nxs]*dfbdfr,axis=0)*Mdata/len(SGMT) |
|---|
| 1001 | dFdx[iBeg:iFin] = 2.*np.sum(fas[:,:,nxs,nxs]*dfadx+fbs[:,:,nxs,nxs]*dfbdx,axis=0) |
|---|
| 1002 | dFdui[iBeg:iFin] = 2.*np.sum(fas[:,:,nxs]*dfadui+fbs[:,:,nxs]*dfbdui,axis=0) |
|---|
| 1003 | dFdua[iBeg:iFin] = 2.*np.sum(fas[:,:,nxs,nxs]*dfadua+fbs[:,:,nxs,nxs]*dfbdua,axis=0) |
|---|
| 1004 | else: |
|---|
| 1005 | dFdfr[iBeg:iFin] = (2.*SA[:,nxs]*(dfadfr[0]+dfadfr[1])+2.*SB[:,nxs]*(dfbdfr[0]+dfbdfr[1]))*Mdata/len(SGMT) |
|---|
| 1006 | dFdx[iBeg:iFin] = 2.*SA[:,nxs,nxs]*(dfadx[0]+dfadx[1])+2.*SB[:,nxs,nxs]*(dfbdx[0]+dfbdx[1]) |
|---|
| 1007 | dFdui[iBeg:iFin] = 2.*SA[:,nxs]*(dfadui[0]+dfadui[1])+2.*SB[:,nxs]*(dfbdui[0]+dfbdui[1]) |
|---|
| 1008 | dFdua[iBeg:iFin] = 2.*SA[:,nxs,nxs]*(dfadua[0]+dfadua[1])+2.*SB[:,nxs,nxs]*(dfbdua[0]+dfbdua[1]) |
|---|
| 1009 | dFdfl[iBeg:iFin] = -SA*dfadfl-SB*dfbdfl #array(nRef,) |
|---|
| 1010 | dFdbab[iBeg:iFin] = 2.*(fas[0,nxs]*np.array([np.sum(dfadba.T*dBabdA,axis=0),np.sum(-dfadba.T*parmDict[phfx+'BabA']*SQfactor*dBabdA,axis=0)])+ \ |
|---|
| 1011 | fbs[0,nxs]*np.array([np.sum(dfbdba.T*dBabdA,axis=0),np.sum(-dfbdba.T*parmDict[phfx+'BabA']*SQfactor*dBabdA,axis=0)])).T |
|---|
| 1012 | iBeg += blkSize |
|---|
| 1013 | # print 'derv time %.4f, nref %d, blkSize %d'%(time.time()-time0,nRef,blkSize) |
|---|
| 1014 | #loop over atoms - each dict entry is list of derivatives for all the reflections |
|---|
| 1015 | for i in range(len(Mdata)): |
|---|
| 1016 | dFdvDict[pfx+'Afrac:'+str(i)] = dFdfr.T[i] |
|---|
| 1017 | dFdvDict[pfx+'dAx:'+str(i)] = dFdx.T[0][i] |
|---|
| 1018 | dFdvDict[pfx+'dAy:'+str(i)] = dFdx.T[1][i] |
|---|
| 1019 | dFdvDict[pfx+'dAz:'+str(i)] = dFdx.T[2][i] |
|---|
| 1020 | dFdvDict[pfx+'AUiso:'+str(i)] = dFdui.T[i] |
|---|
| 1021 | dFdvDict[pfx+'AU11:'+str(i)] = dFdua.T[0][i] |
|---|
| 1022 | dFdvDict[pfx+'AU22:'+str(i)] = dFdua.T[1][i] |
|---|
| 1023 | dFdvDict[pfx+'AU33:'+str(i)] = dFdua.T[2][i] |
|---|
| 1024 | dFdvDict[pfx+'AU12:'+str(i)] = dFdua.T[3][i] |
|---|
| 1025 | dFdvDict[pfx+'AU13:'+str(i)] = dFdua.T[4][i] |
|---|
| 1026 | dFdvDict[pfx+'AU23:'+str(i)] = dFdua.T[5][i] |
|---|
| 1027 | dFdvDict[phfx+'Flack'] = 4.*dFdfl.T |
|---|
| 1028 | dFdvDict[phfx+'BabA'] = dFdbab.T[0] |
|---|
| 1029 | dFdvDict[phfx+'BabU'] = dFdbab.T[1] |
|---|
| 1030 | return dFdvDict |
|---|
| 1031 | |
|---|
| 1032 | def MagStructureFactor2(refDict,G,hfx,pfx,SGData,calcControls,parmDict): |
|---|
| 1033 | ''' Compute neutron magnetic structure factors for all h,k,l for phase |
|---|
| 1034 | puts the result, F^2, in each ref[8] in refList |
|---|
| 1035 | operates on blocks of 100 reflections for speed |
|---|
| 1036 | input: |
|---|
| 1037 | |
|---|
| 1038 | :param dict refDict: where |
|---|
| 1039 | 'RefList' list where each ref = h,k,l,it,d,... |
|---|
| 1040 | 'FF' dict of form factors - filed in below |
|---|
| 1041 | :param np.array G: reciprocal metric tensor |
|---|
| 1042 | :param str pfx: phase id string |
|---|
| 1043 | :param dict SGData: space group info. dictionary output from SpcGroup |
|---|
| 1044 | :param dict calcControls: |
|---|
| 1045 | :param dict ParmDict: |
|---|
| 1046 | |
|---|
| 1047 | :returns: copy of new refList - used in calculating numerical derivatives |
|---|
| 1048 | |
|---|
| 1049 | ''' |
|---|
| 1050 | g = nl.inv(G) |
|---|
| 1051 | ast = np.sqrt(np.diag(G)) |
|---|
| 1052 | ainv = np.sqrt(np.diag(g)) |
|---|
| 1053 | GS = G/np.outer(ast,ast) |
|---|
| 1054 | Ginv = g/np.outer(ainv,ainv) |
|---|
| 1055 | uAmat = G2lat.Gmat2AB(GS)[0] |
|---|
| 1056 | Bmat = G2lat.Gmat2AB(G)[1] |
|---|
| 1057 | Mast = twopisq*np.multiply.outer(ast,ast) |
|---|
| 1058 | SGMT = np.array([ops[0].T for ops in SGData['SGOps']]) |
|---|
| 1059 | SGT = np.array([ops[1] for ops in SGData['SGOps']]) |
|---|
| 1060 | Ncen = len(SGData['SGCen']) |
|---|
| 1061 | Nops = len(SGMT)*Ncen |
|---|
| 1062 | if not SGData['SGFixed']: |
|---|
| 1063 | Nops *= (1+SGData['SGInv']) |
|---|
| 1064 | MFtables = calcControls['MFtables'] |
|---|
| 1065 | TwinLaw = np.ones(1) |
|---|
| 1066 | # TwinLaw = np.array([[[1,0,0],[0,1,0],[0,0,1]],]) |
|---|
| 1067 | # TwDict = refDict.get('TwDict',{}) |
|---|
| 1068 | # if 'S' in calcControls[hfx+'histType']: |
|---|
| 1069 | # NTL = calcControls[phfx+'NTL'] |
|---|
| 1070 | # NM = calcControls[phfx+'TwinNMN']+1 |
|---|
| 1071 | # TwinLaw = calcControls[phfx+'TwinLaw'] |
|---|
| 1072 | # TwinFr = np.array([parmDict[phfx+'TwinFr:'+str(i)] for i in range(len(TwinLaw))]) |
|---|
| 1073 | # TwinInv = list(np.where(calcControls[phfx+'TwinInv'],-1,1)) |
|---|
| 1074 | Tdata,Mdata,Fdata,Xdata,dXdata,IAdata,Uisodata,Uijdata,Gdata = \ |
|---|
| 1075 | GetAtomFXU(pfx,calcControls,parmDict) |
|---|
| 1076 | if not Xdata.size: #no atoms in phase! |
|---|
| 1077 | return |
|---|
| 1078 | Mag = np.array([np.sqrt(np.inner(mag,np.inner(mag,Ginv))) for mag in Gdata.T]) |
|---|
| 1079 | Gdata = np.inner(Gdata.T,np.swapaxes(SGMT,1,2)).T #apply sym. ops. |
|---|
| 1080 | if SGData['SGInv'] and not SGData['SGFixed']: |
|---|
| 1081 | Gdata = np.hstack((Gdata,-Gdata)) #inversion if any |
|---|
| 1082 | Gdata = np.hstack([Gdata for icen in range(Ncen)]) #dup over cell centering--> [Mxyz,nops,natms] |
|---|
| 1083 | Gdata = SGData['MagMom'][nxs,:,nxs]*Gdata #flip vectors according to spin flip * det(opM) |
|---|
| 1084 | Mag = np.tile(Mag[:,nxs],Nops).T #make Mag same length as Gdata |
|---|
| 1085 | Kdata = np.inner(Gdata.T,uAmat).T |
|---|
| 1086 | Kmean = np.mean(np.sqrt(np.sum(Kdata**2,axis=0)),axis=0) |
|---|
| 1087 | Kdata /= Kmean #Cartesian unit vectors |
|---|
| 1088 | Uij = np.array(G2lat.U6toUij(Uijdata)) |
|---|
| 1089 | bij = Mast*Uij.T |
|---|
| 1090 | blkSize = 100 #no. of reflections in a block - size seems optimal |
|---|
| 1091 | nRef = refDict['RefList'].shape[0] |
|---|
| 1092 | SQ = 1./(2.*refDict['RefList'].T[4])**2 |
|---|
| 1093 | refDict['FF']['El'] = list(MFtables.keys()) |
|---|
| 1094 | refDict['FF']['MF'] = np.zeros((nRef,len(MFtables))) |
|---|
| 1095 | for iel,El in enumerate(refDict['FF']['El']): |
|---|
| 1096 | refDict['FF']['MF'].T[iel] = G2el.MagScatFac(MFtables[El],SQ) |
|---|
| 1097 | #reflection processing begins here - big arrays! |
|---|
| 1098 | iBeg = 0 |
|---|
| 1099 | while iBeg < nRef: |
|---|
| 1100 | iFin = min(iBeg+blkSize,nRef) |
|---|
| 1101 | refl = refDict['RefList'][iBeg:iFin] #array(blkSize,nItems) |
|---|
| 1102 | H = refl.T[:3].T #array(blkSize,3) |
|---|
| 1103 | # H = np.squeeze(np.inner(H.T,TwinLaw)) #maybe array(blkSize,nTwins,3) or (blkSize,3) |
|---|
| 1104 | # TwMask = np.any(H,axis=-1) |
|---|
| 1105 | # if TwinLaw.shape[0] > 1 and TwDict: #need np.inner(TwinLaw[?],TwDict[iref][i])*TwinInv[i] |
|---|
| 1106 | # for ir in range(blkSize): |
|---|
| 1107 | # iref = ir+iBeg |
|---|
| 1108 | # if iref in TwDict: |
|---|
| 1109 | # for i in TwDict[iref]: |
|---|
| 1110 | # for n in range(NTL): |
|---|
| 1111 | # H[ir][i+n*NM] = np.inner(TwinLaw[n*NM],np.array(TwDict[iref][i])*TwinInv[i+n*NM]) |
|---|
| 1112 | # TwMask = np.any(H,axis=-1) |
|---|
| 1113 | SQ = 1./(2.*refl.T[4])**2 #array(blkSize) |
|---|
| 1114 | SQfactor = 4.0*SQ*twopisq #ditto prev. |
|---|
| 1115 | Uniq = np.inner(H,SGMT) |
|---|
| 1116 | Phi = np.inner(H,SGT) |
|---|
| 1117 | phase = twopi*(np.inner(Uniq,(dXdata+Xdata).T).T+Phi.T).T |
|---|
| 1118 | biso = -SQfactor*Uisodata[:,nxs] |
|---|
| 1119 | Tiso = np.repeat(np.where(biso<1.,np.exp(biso),1.0),len(SGT)*len(TwinLaw),axis=1).T |
|---|
| 1120 | HbH = -np.sum(Uniq.T*np.swapaxes(np.inner(bij,Uniq),2,-1),axis=1) |
|---|
| 1121 | Tuij = np.where(HbH<1.,np.exp(HbH),1.0).T |
|---|
| 1122 | Tindx = np.array([refDict['FF']['El'].index(El) for El in Tdata]) |
|---|
| 1123 | MF = refDict['FF']['MF'][iBeg:iFin].T[Tindx].T #Nref,Natm |
|---|
| 1124 | TMcorr = 0.539*(np.reshape(Tiso,Tuij.shape)*Tuij)[:,0,:]*Fdata*Mdata*MF/(2*Nops) #Nref,Natm |
|---|
| 1125 | if SGData['SGInv']: |
|---|
| 1126 | if not SGData['SGFixed']: |
|---|
| 1127 | mphase = np.hstack((phase,-phase)) #OK |
|---|
| 1128 | else: |
|---|
| 1129 | mphase = phase |
|---|
| 1130 | else: |
|---|
| 1131 | mphase = phase # |
|---|
| 1132 | mphase = np.array([mphase+twopi*np.inner(cen,H)[:,nxs,nxs] for cen in SGData['SGCen']]) |
|---|
| 1133 | mphase = np.concatenate(mphase,axis=1) #Nref,full Nop,Natm |
|---|
| 1134 | sinm = np.sin(mphase) #ditto - match magstrfc.for |
|---|
| 1135 | cosm = np.cos(mphase) #ditto |
|---|
| 1136 | HM = np.inner(Bmat,H) #put into cartesian space |
|---|
| 1137 | HM = HM/np.sqrt(np.sum(HM**2,axis=0)) #Kdata = MAGS & HM = UVEC in magstrfc.for both OK |
|---|
| 1138 | eDotK = np.sum(HM[:,:,nxs,nxs]*Kdata[:,nxs,:,:],axis=0) |
|---|
| 1139 | Q = HM[:,:,nxs,nxs]*eDotK[nxs,:,:,:]-Kdata[:,nxs,:,:] #xyz,Nref,Nop,Natm = BPM in magstrfc.for OK |
|---|
| 1140 | fam = Q*TMcorr[nxs,:,nxs,:]*cosm[nxs,:,:,:]*Mag[nxs,nxs,:,:] #ditto |
|---|
| 1141 | fbm = Q*TMcorr[nxs,:,nxs,:]*sinm[nxs,:,:,:]*Mag[nxs,nxs,:,:] #ditto |
|---|
| 1142 | fams = np.sum(np.sum(fam,axis=-1),axis=-1) #Mxyz,Nref Sum(sum(fam,atoms),ops) |
|---|
| 1143 | fbms = np.sum(np.sum(fbm,axis=-1),axis=-1) #ditto |
|---|
| 1144 | refl.T[9] = np.sum(fams**2,axis=0)+np.sum(fbms**2,axis=0) #Sum(fams**2,Mxyz) Re + Im |
|---|
| 1145 | refl.T[7] = np.copy(refl.T[9]) |
|---|
| 1146 | refl.T[10] = atan2d(fbms[0],fams[0]) #- what is phase for mag refl? |
|---|
| 1147 | # if 'P' in calcControls[hfx+'histType']: #PXC, PNC & PNT: F^2 = A[0]^2 + A[1]^2 + B[0]^2 + B[1]^2 |
|---|
| 1148 | # refl.T[9] = np.sum(fas**2,axis=0)+np.sum(fbs**2,axis=0) #add fam**2 & fbm**2 here |
|---|
| 1149 | # refl.T[10] = atan2d(fbs[0],fas[0]) #ignore f' & f" |
|---|
| 1150 | # else: #HKLF: F^2 = (A[0]+A[1])^2 + (B[0]+B[1])^2 |
|---|
| 1151 | # if len(TwinLaw) > 1: |
|---|
| 1152 | # refl.T[9] = np.sum(fas[:,:,0],axis=0)**2+np.sum(fbs[:,:,0],axis=0)**2 #FcT from primary twin element |
|---|
| 1153 | # refl.T[7] = np.sum(TwinFr*TwMask*np.sum(fas,axis=0)**2,axis=-1)+ \ |
|---|
| 1154 | # np.sum(TwinFr*TwMask*np.sum(fbs,axis=0)**2,axis=-1) #Fc sum over twins |
|---|
| 1155 | # refl.T[10] = atan2d(fbs[0].T[0],fas[0].T[0]) #ignore f' & f" & use primary twin |
|---|
| 1156 | # else: # checked correct!! |
|---|
| 1157 | # refl.T[9] = np.sum(fas,axis=0)**2+np.sum(fbs,axis=0)**2 |
|---|
| 1158 | # refl.T[7] = np.copy(refl.T[9]) |
|---|
| 1159 | # refl.T[10] = atan2d(fbs[0],fas[0]) #ignore f' & f" |
|---|
| 1160 | ## refl.T[10] = atan2d(np.sum(fbs,axis=0),np.sum(fas,axis=0)) #include f' & f" |
|---|
| 1161 | iBeg += blkSize |
|---|
| 1162 | # print 'sf time %.4f, nref %d, blkSize %d'%(time.time()-time0,nRef,blkSize) |
|---|
| 1163 | return copy.deepcopy(refDict['RefList']) |
|---|
| 1164 | |
|---|
| 1165 | def MagStructureFactorDerv2(refDict,G,hfx,pfx,SGData,calcControls,parmDict): |
|---|
| 1166 | '''Compute magnetic structure factor derivatives numerically - for powders/nontwins only |
|---|
| 1167 | input: |
|---|
| 1168 | |
|---|
| 1169 | :param dict refDict: where |
|---|
| 1170 | 'RefList' list where each ref = h,k,l,it,d,... |
|---|
| 1171 | 'FF' dict of form factors - filled in below |
|---|
| 1172 | :param np.array G: reciprocal metric tensor |
|---|
| 1173 | :param str hfx: histogram id string |
|---|
| 1174 | :param str pfx: phase id string |
|---|
| 1175 | :param dict SGData: space group info. dictionary output from SpcGroup |
|---|
| 1176 | :param dict calcControls: |
|---|
| 1177 | :param dict parmDict: |
|---|
| 1178 | |
|---|
| 1179 | :returns: dict dFdvDict: dictionary of magnetic derivatives |
|---|
| 1180 | ''' |
|---|
| 1181 | |
|---|
| 1182 | trefDict = copy.deepcopy(refDict) |
|---|
| 1183 | dM = 1.e-6 |
|---|
| 1184 | dFdvDict = {} |
|---|
| 1185 | for parm in parmDict: |
|---|
| 1186 | if 'AM' in parm: |
|---|
| 1187 | parmDict[parm] += dM |
|---|
| 1188 | prefList = MagStructureFactor2(trefDict,G,hfx,pfx,SGData,calcControls,parmDict) |
|---|
| 1189 | parmDict[parm] -= 2*dM |
|---|
| 1190 | mrefList = MagStructureFactor2(trefDict,G,hfx,pfx,SGData,calcControls,parmDict) |
|---|
| 1191 | parmDict[parm] += dM |
|---|
| 1192 | dFdvDict[parm] = (prefList[:,9]-mrefList[:,9])/(2.*dM) |
|---|
| 1193 | return dFdvDict |
|---|
| 1194 | |
|---|
| 1195 | def MagStructureFactorDerv(refDict,G,hfx,pfx,SGData,calcControls,parmDict): |
|---|
| 1196 | '''Compute nonmagnetic structure factor derivatives on blocks of reflections in magnetic structures - for powders/nontwins only |
|---|
| 1197 | input: |
|---|
| 1198 | |
|---|
| 1199 | :param dict refDict: where |
|---|
| 1200 | 'RefList' list where each ref = h,k,l,it,d,... |
|---|
| 1201 | 'FF' dict of form factors - filled in below |
|---|
| 1202 | :param np.array G: reciprocal metric tensor |
|---|
| 1203 | :param str hfx: histogram id string |
|---|
| 1204 | :param str pfx: phase id string |
|---|
| 1205 | :param dict SGData: space group info. dictionary output from SpcGroup |
|---|
| 1206 | :param dict calcControls: |
|---|
| 1207 | :param dict parmDict: |
|---|
| 1208 | |
|---|
| 1209 | :returns: dict dFdvDict: dictionary of derivatives |
|---|
| 1210 | ''' |
|---|
| 1211 | |
|---|
| 1212 | g = nl.inv(G) |
|---|
| 1213 | ast = np.sqrt(np.diag(G)) |
|---|
| 1214 | ainv = np.sqrt(np.diag(g)) |
|---|
| 1215 | GS = G/np.outer(ast,ast) |
|---|
| 1216 | Ginv = g/np.outer(ainv,ainv) |
|---|
| 1217 | uAmat = G2lat.Gmat2AB(GS)[0] |
|---|
| 1218 | Mast = twopisq*np.multiply.outer(ast,ast) |
|---|
| 1219 | SGMT = np.array([ops[0].T for ops in SGData['SGOps']]) |
|---|
| 1220 | SGT = np.array([ops[1] for ops in SGData['SGOps']]) |
|---|
| 1221 | Ncen = len(SGData['SGCen']) |
|---|
| 1222 | Nops = len(SGMT)*Ncen |
|---|
| 1223 | if not SGData['SGFixed']: |
|---|
| 1224 | Nops *= (1+SGData['SGInv']) |
|---|
| 1225 | Bmat = G2lat.Gmat2AB(G)[1] |
|---|
| 1226 | nRef = len(refDict['RefList']) |
|---|
| 1227 | Tdata,Mdata,Fdata,Xdata,dXdata,IAdata,Uisodata,Uijdata,Gdata = \ |
|---|
| 1228 | GetAtomFXU(pfx,calcControls,parmDict) |
|---|
| 1229 | if not Xdata.size: #no atoms in phase! |
|---|
| 1230 | return {} |
|---|
| 1231 | mSize = len(Mdata) |
|---|
| 1232 | Mag = np.array([np.sqrt(np.inner(mag,np.inner(mag,Ginv))) for mag in Gdata.T]) |
|---|
| 1233 | Gones = np.ones_like(Gdata) |
|---|
| 1234 | Gdata = np.inner(Gdata.T,np.swapaxes(SGMT,1,2)).T #apply sym. ops. |
|---|
| 1235 | Gones = np.inner(Gones.T,SGMT).T |
|---|
| 1236 | if SGData['SGInv'] and not SGData['SGFixed']: |
|---|
| 1237 | Gdata = np.hstack((Gdata,-Gdata)) #inversion if any |
|---|
| 1238 | Gones = np.hstack((Gones,-Gones)) #inversion if any |
|---|
| 1239 | Gdata = np.hstack([Gdata for icen in range(Ncen)]) #dup over cell centering |
|---|
| 1240 | Gones = np.hstack([Gones for icen in range(Ncen)]) #dup over cell centering |
|---|
| 1241 | Gdata = SGData['MagMom'][nxs,:,nxs]*Gdata #flip vectors according to spin flip |
|---|
| 1242 | Gones = SGData['MagMom'][nxs,:,nxs]*Gones #flip vectors according to spin flip |
|---|
| 1243 | Mag = np.tile(Mag[:,nxs],Nops).T #make Mag same length as Gdata |
|---|
| 1244 | Kdata = np.inner(Gdata.T,uAmat).T #Cartesian unit vectors |
|---|
| 1245 | Kmean = np.mean(np.sqrt(np.sum(Kdata**2,axis=0)),axis=0) |
|---|
| 1246 | Kdata /= Kmean |
|---|
| 1247 | Uij = np.array(G2lat.U6toUij(Uijdata)) |
|---|
| 1248 | bij = Mast*Uij.T |
|---|
| 1249 | dFdvDict = {} |
|---|
| 1250 | dFdfr = np.zeros((nRef,mSize)) |
|---|
| 1251 | dFdx = np.zeros((nRef,mSize,3)) |
|---|
| 1252 | dFdui = np.zeros((nRef,mSize)) |
|---|
| 1253 | dFdua = np.zeros((nRef,mSize,6)) |
|---|
| 1254 | time0 = time.time() |
|---|
| 1255 | #reflection processing begins here - big arrays! |
|---|
| 1256 | iBeg = 0 |
|---|
| 1257 | blkSize = 5 #no. of reflections in a block - optimized for speed |
|---|
| 1258 | while iBeg < nRef: |
|---|
| 1259 | iFin = min(iBeg+blkSize,nRef) |
|---|
| 1260 | refl = refDict['RefList'][iBeg:iFin] #array(blkSize,nItems) |
|---|
| 1261 | H = refl.T[:3].T |
|---|
| 1262 | SQ = 1./(2.*refl.T[4])**2 # or (sin(theta)/lambda)**2 |
|---|
| 1263 | SQfactor = 8.0*SQ*np.pi**2 |
|---|
| 1264 | Uniq = np.inner(H,SGMT) # array(nSGOp,3) |
|---|
| 1265 | Phi = np.inner(H,SGT) |
|---|
| 1266 | phase = twopi*(np.inner(Uniq,(dXdata+Xdata).T).T+Phi.T).T |
|---|
| 1267 | occ = Mdata*Fdata/Nops |
|---|
| 1268 | biso = -SQfactor*Uisodata[:,nxs] |
|---|
| 1269 | Tiso = np.repeat(np.where(biso<1.,np.exp(biso),1.0),len(SGT),axis=1).T |
|---|
| 1270 | HbH = -np.sum(Uniq.T*np.swapaxes(np.inner(bij,Uniq),2,-1),axis=1) |
|---|
| 1271 | Tuij = np.where(HbH<1.,np.exp(HbH),1.0).T |
|---|
| 1272 | Hij = np.array([Mast*np.multiply.outer(U,U) for U in np.reshape(Uniq,(-1,3))]) |
|---|
| 1273 | Hij = np.reshape(np.array([G2lat.UijtoU6(uij) for uij in Hij]),(-1,len(SGT),6)) |
|---|
| 1274 | Tindx = np.array([refDict['FF']['El'].index(El) for El in Tdata]) |
|---|
| 1275 | MF = refDict['FF']['MF'][iBeg:iFin].T[Tindx].T #Nref,Natm |
|---|
| 1276 | TMcorr = 0.539*(np.reshape(Tiso,Tuij.shape)*Tuij)[:,0,:]*Fdata*Mdata*MF/(2*Nops) #Nref,Natm |
|---|
| 1277 | if SGData['SGInv']: |
|---|
| 1278 | if not SGData['SGFixed']: |
|---|
| 1279 | mphase = np.hstack((phase,-phase)) #OK |
|---|
| 1280 | Uniq = np.hstack((Uniq,-Uniq)) #Nref,Nops,hkl |
|---|
| 1281 | Hij = np.hstack((Hij,Hij)) |
|---|
| 1282 | else: |
|---|
| 1283 | mphase = phase |
|---|
| 1284 | else: |
|---|
| 1285 | mphase = phase # |
|---|
| 1286 | Hij = np.concatenate(np.array([Hij for cen in SGData['SGCen']]),axis=1) |
|---|
| 1287 | Uniq = np.hstack([Uniq for cen in SGData['SGCen']]) |
|---|
| 1288 | mphase = np.array([mphase+twopi*np.inner(cen,H)[:,nxs,nxs] for cen in SGData['SGCen']]) |
|---|
| 1289 | mphase = np.concatenate(mphase,axis=1) #Nref,Nop,Natm |
|---|
| 1290 | sinm = np.sin(mphase) #ditto - match magstrfc.for |
|---|
| 1291 | cosm = np.cos(mphase) #ditto |
|---|
| 1292 | HM = np.inner(Bmat.T,H) #put into cartesian space |
|---|
| 1293 | HM = HM/np.sqrt(np.sum(HM**2,axis=0)) #unit cartesian vector for H |
|---|
| 1294 | eDotK = np.sum(HM[:,:,nxs,nxs]*Kdata[:,nxs,:,:],axis=0) |
|---|
| 1295 | Q = HM[:,:,nxs,nxs]*eDotK[nxs,:,:,:]-Kdata[:,nxs,:,:] #Mxyz,Nref,Nop,Natm = BPM in magstrfc.for OK |
|---|
| 1296 | |
|---|
| 1297 | fam = Q*TMcorr[nxs,:,nxs,:]*cosm[nxs,:,:,:]*Mag[nxs,nxs,:,:] #Mxyz,Nref,Nop,Natm |
|---|
| 1298 | fbm = Q*TMcorr[nxs,:,nxs,:]*sinm[nxs,:,:,:]*Mag[nxs,nxs,:,:] |
|---|
| 1299 | fams = np.sum(np.sum(fam,axis=-1),axis=-1) #Mxyz,Nref |
|---|
| 1300 | fbms = np.sum(np.sum(fbm,axis=-1),axis=-1) |
|---|
| 1301 | famx = -Q*TMcorr[nxs,:,nxs,:]*Mag[nxs,nxs,:,:]*sinm[nxs,:,:,:] #Mxyz,Nref,Nops,Natom |
|---|
| 1302 | fbmx = Q*TMcorr[nxs,:,nxs,:]*Mag[nxs,nxs,:,:]*cosm[nxs,:,:,:] |
|---|
| 1303 | #sums below are over Nops - real part |
|---|
| 1304 | dfadfr = np.sum(fam/occ,axis=2) #array(Mxyz,refBlk,nAtom) Fdata != 0 avoids /0. problem deriv OK |
|---|
| 1305 | dfadx = np.sum(twopi*Uniq[nxs,:,:,nxs,:]*famx[:,:,:,:,nxs],axis=2) #deriv OK |
|---|
| 1306 | dfadui = np.sum(-SQfactor[:,nxs,nxs]*fam,axis=2) #array(Ops,refBlk,nAtoms) deriv OK |
|---|
| 1307 | dfadua = np.sum(-Hij[nxs,:,:,nxs,:]*fam[:,:,:,:,nxs],axis=2) #deriv OK |
|---|
| 1308 | # imaginary part; array(3,refBlk,nAtom,3) & array(3,refBlk,nAtom,6) |
|---|
| 1309 | dfbdfr = np.sum(fbm/occ,axis=2) #array(mxyz,refBlk,nAtom) Fdata != 0 avoids /0. problem |
|---|
| 1310 | dfbdx = np.sum(twopi*Uniq[nxs,:,:,nxs,:]*fbmx[:,:,:,:,nxs],axis=2) |
|---|
| 1311 | dfbdui = np.sum(-SQfactor[:,nxs,nxs]*fbm,axis=2) #array(Ops,refBlk,nAtoms) |
|---|
| 1312 | dfbdua = np.sum(-Hij[nxs,:,:,nxs,:]*fbm[:,:,:,:,nxs],axis=2) |
|---|
| 1313 | #accumulate derivatives |
|---|
| 1314 | dFdfr[iBeg:iFin] = 2.*np.sum((fams[:,:,nxs]*dfadfr+fbms[:,:,nxs]*dfbdfr)*Mdata/Nops,axis=0) #ok |
|---|
| 1315 | dFdx[iBeg:iFin] = 2.*np.sum(fams[:,:,nxs,nxs]*dfadx+fbms[:,:,nxs,nxs]*dfbdx,axis=0) #ok |
|---|
| 1316 | dFdui[iBeg:iFin] = 2.*np.sum(fams[:,:,nxs]*dfadui+fbms[:,:,nxs]*dfbdui,axis=0) #ok |
|---|
| 1317 | dFdua[iBeg:iFin] = 2.*np.sum(fams[:,:,nxs,nxs]*dfadua+fbms[:,:,nxs,nxs]*dfbdua,axis=0) #ok |
|---|
| 1318 | iBeg += blkSize |
|---|
| 1319 | print (' %d derivative time %.4f\r'%(nRef,time.time()-time0)) |
|---|
| 1320 | #loop over atoms - each dict entry is list of derivatives for all the reflections |
|---|
| 1321 | for i in range(len(Mdata)): |
|---|
| 1322 | dFdvDict[pfx+'Afrac:'+str(i)] = dFdfr.T[i] |
|---|
| 1323 | dFdvDict[pfx+'dAx:'+str(i)] = dFdx.T[0][i] |
|---|
| 1324 | dFdvDict[pfx+'dAy:'+str(i)] = dFdx.T[1][i] |
|---|
| 1325 | dFdvDict[pfx+'dAz:'+str(i)] = dFdx.T[2][i] |
|---|
| 1326 | dFdvDict[pfx+'AUiso:'+str(i)] = dFdui.T[i] |
|---|
| 1327 | dFdvDict[pfx+'AU11:'+str(i)] = dFdua.T[0][i] |
|---|
| 1328 | dFdvDict[pfx+'AU22:'+str(i)] = dFdua.T[1][i] |
|---|
| 1329 | dFdvDict[pfx+'AU33:'+str(i)] = dFdua.T[2][i] |
|---|
| 1330 | dFdvDict[pfx+'AU12:'+str(i)] = dFdua.T[3][i] |
|---|
| 1331 | dFdvDict[pfx+'AU13:'+str(i)] = dFdua.T[4][i] |
|---|
| 1332 | dFdvDict[pfx+'AU23:'+str(i)] = dFdua.T[5][i] |
|---|
| 1333 | return dFdvDict |
|---|
| 1334 | |
|---|
| 1335 | def StructureFactorDervTw2(refDict,G,hfx,pfx,SGData,calcControls,parmDict): |
|---|
| 1336 | '''Compute structure factor derivatives on blocks of reflections - for twins only |
|---|
| 1337 | faster than StructureFactorDervTw |
|---|
| 1338 | input: |
|---|
| 1339 | |
|---|
| 1340 | :param dict refDict: where |
|---|
| 1341 | 'RefList' list where each ref = h,k,l,it,d,... |
|---|
| 1342 | 'FF' dict of form factors - filled in below |
|---|
| 1343 | :param np.array G: reciprocal metric tensor |
|---|
| 1344 | :param str hfx: histogram id string |
|---|
| 1345 | :param str pfx: phase id string |
|---|
| 1346 | :param dict SGData: space group info. dictionary output from SpcGroup |
|---|
| 1347 | :param dict calcControls: |
|---|
| 1348 | :param dict parmDict: |
|---|
| 1349 | |
|---|
| 1350 | :returns: dict dFdvDict: dictionary of derivatives |
|---|
| 1351 | ''' |
|---|
| 1352 | phfx = pfx.split(':')[0]+hfx |
|---|
| 1353 | ast = np.sqrt(np.diag(G)) |
|---|
| 1354 | Mast = twopisq*np.multiply.outer(ast,ast) |
|---|
| 1355 | SGMT = np.array([ops[0].T for ops in SGData['SGOps']]) |
|---|
| 1356 | SGT = np.array([ops[1] for ops in SGData['SGOps']]) |
|---|
| 1357 | FFtables = calcControls['FFtables'] |
|---|
| 1358 | BLtables = calcControls['BLtables'] |
|---|
| 1359 | TwDict = refDict.get('TwDict',{}) |
|---|
| 1360 | NTL = calcControls[phfx+'NTL'] |
|---|
| 1361 | NM = calcControls[phfx+'TwinNMN']+1 |
|---|
| 1362 | TwinLaw = calcControls[phfx+'TwinLaw'] |
|---|
| 1363 | TwinFr = np.array([parmDict[phfx+'TwinFr:'+str(i)] for i in range(len(TwinLaw))]) |
|---|
| 1364 | TwinInv = list(np.where(calcControls[phfx+'TwinInv'],-1,1)) |
|---|
| 1365 | nTwin = len(TwinLaw) |
|---|
| 1366 | nRef = len(refDict['RefList']) |
|---|
| 1367 | Tdata,Mdata,Fdata,Xdata,dXdata,IAdata,Uisodata,Uijdata,Gdata = \ |
|---|
| 1368 | GetAtomFXU(pfx,calcControls,parmDict) |
|---|
| 1369 | if not Xdata.size: #no atoms in phase! |
|---|
| 1370 | return {} |
|---|
| 1371 | mSize = len(Mdata) |
|---|
| 1372 | FF = np.zeros(len(Tdata)) |
|---|
| 1373 | if 'NC' in calcControls[hfx+'histType'] or 'NB' in calcControls[hfx+'histType']: |
|---|
| 1374 | FP,FPP = G2el.BlenResCW(Tdata,BLtables,parmDict[hfx+'Lam']) |
|---|
| 1375 | elif 'X' in calcControls[hfx+'histType']: |
|---|
| 1376 | FP = np.array([FFtables[El][hfx+'FP'] for El in Tdata]) |
|---|
| 1377 | FPP = np.array([FFtables[El][hfx+'FPP'] for El in Tdata]) |
|---|
| 1378 | elif 'SEC' in calcControls[hfx+'histType']: |
|---|
| 1379 | FP = np.zeros(len(Tdata)) |
|---|
| 1380 | FPP = np.zeros(len(Tdata)) |
|---|
| 1381 | |
|---|
| 1382 | Uij = np.array(G2lat.U6toUij(Uijdata)) |
|---|
| 1383 | bij = Mast*Uij.T |
|---|
| 1384 | dFdvDict = {} |
|---|
| 1385 | dFdfr = np.zeros((nRef,nTwin,mSize)) |
|---|
| 1386 | dFdx = np.zeros((nRef,nTwin,mSize,3)) |
|---|
| 1387 | dFdui = np.zeros((nRef,nTwin,mSize)) |
|---|
| 1388 | dFdua = np.zeros((nRef,nTwin,mSize,6)) |
|---|
| 1389 | dFdbab = np.zeros((nRef,nTwin,2)) |
|---|
| 1390 | dFdtw = np.zeros((nRef,nTwin)) |
|---|
| 1391 | time0 = time.time() |
|---|
| 1392 | #reflection processing begins here - big arrays! |
|---|
| 1393 | iBeg = 0 |
|---|
| 1394 | blkSize = 16 #no. of reflections in a block - optimized for speed |
|---|
| 1395 | while iBeg < nRef: |
|---|
| 1396 | iFin = min(iBeg+blkSize,nRef) |
|---|
| 1397 | refl = refDict['RefList'][iBeg:iFin] #array(blkSize,nItems) |
|---|
| 1398 | H = refl.T[:3] |
|---|
| 1399 | H = np.inner(H.T,TwinLaw) #array(3,nTwins) |
|---|
| 1400 | TwMask = np.any(H,axis=-1) |
|---|
| 1401 | for ir in range(blkSize): |
|---|
| 1402 | iref = ir+iBeg |
|---|
| 1403 | if iref in TwDict: |
|---|
| 1404 | for i in TwDict[iref]: |
|---|
| 1405 | for n in range(NTL): |
|---|
| 1406 | H[ir][i+n*NM] = np.inner(TwinLaw[n*NM],np.array(TwDict[iref][i])*TwinInv[i+n*NM]) |
|---|
| 1407 | TwMask = np.any(H,axis=-1) |
|---|
| 1408 | SQ = 1./(2.*refl.T[4])**2 # or (sin(theta)/lambda)**2 |
|---|
| 1409 | SQfactor = 8.0*SQ*np.pi**2 |
|---|
| 1410 | if 'T' in calcControls[hfx+'histType']: |
|---|
| 1411 | if 'P' in calcControls[hfx+'histType']: |
|---|
| 1412 | FP,FPP = G2el.BlenResTOF(Tdata,BLtables,refl.T[14]) |
|---|
| 1413 | else: |
|---|
| 1414 | FP,FPP = G2el.BlenResTOF(Tdata,BLtables,refl.T[12]) |
|---|
| 1415 | FP = np.repeat(FP.T,len(SGT)*len(TwinLaw),axis=0) |
|---|
| 1416 | FPP = np.repeat(FPP.T,len(SGT)*len(TwinLaw),axis=0) |
|---|
| 1417 | dBabdA = np.exp(-parmDict[phfx+'BabU']*SQfactor) |
|---|
| 1418 | Bab = np.repeat(parmDict[phfx+'BabA']*dBabdA,len(SGT)*nTwin) |
|---|
| 1419 | Tindx = np.array([refDict['FF']['El'].index(El) for El in Tdata]) |
|---|
| 1420 | FF = np.repeat(refDict['FF']['FF'][iBeg:iFin].T[Tindx].T,len(SGT)*len(TwinLaw),axis=0) |
|---|
| 1421 | Uniq = np.inner(H,SGMT) # (nTwin,nSGOp,3) |
|---|
| 1422 | Phi = np.inner(H,SGT) |
|---|
| 1423 | phase = twopi*(np.inner(Uniq,(dXdata+Xdata).T).T+Phi.T).T |
|---|
| 1424 | sinp = np.sin(phase) |
|---|
| 1425 | cosp = np.cos(phase) |
|---|
| 1426 | occ = Mdata*Fdata/len(SGT) |
|---|
| 1427 | biso = -SQfactor*Uisodata[:,nxs] |
|---|
| 1428 | Tiso = np.repeat(np.where(biso<1.,np.exp(biso),1.0),len(SGT)*nTwin,axis=1) |
|---|
| 1429 | HbH = -np.sum(Uniq.T*np.swapaxes(np.inner(bij,Uniq),2,-1),axis=1) |
|---|
| 1430 | Hij = np.array([Mast*np.multiply.outer(U,U) for U in np.reshape(Uniq,(-1,3))]) |
|---|
| 1431 | Hij = np.reshape(np.array([G2lat.UijtoU6(uij) for uij in Hij]),(-1,nTwin,len(SGT),6)) |
|---|
| 1432 | Tuij = np.where(HbH<1.,np.exp(HbH),1.0) |
|---|
| 1433 | Tcorr = (np.reshape(Tiso,Tuij.shape)*Tuij).T*Mdata*Fdata/len(SGMT) |
|---|
| 1434 | fot = np.reshape(((FF+FP).T-Bab).T,cosp.shape)*Tcorr |
|---|
| 1435 | fotp = FPP*Tcorr |
|---|
| 1436 | if 'T' in calcControls[hfx+'histType']: #fa,fb are 2 X blkSize X nTwin X nOps x nAtoms |
|---|
| 1437 | fa = np.array([np.reshape(((FF+FP).T-Bab).T,cosp.shape)*cosp*Tcorr,-np.reshape(FPP,sinp.shape)*sinp*Tcorr]) |
|---|
| 1438 | fb = np.array([np.reshape(((FF+FP).T-Bab).T,sinp.shape)*sinp*Tcorr,np.reshape(FPP,cosp.shape)*cosp*Tcorr]) |
|---|
| 1439 | else: |
|---|
| 1440 | fa = np.array([np.reshape(((FF+FP).T-Bab).T,cosp.shape)*cosp*Tcorr,-FPP*sinp*Tcorr]) |
|---|
| 1441 | fb = np.array([np.reshape(((FF+FP).T-Bab).T,sinp.shape)*sinp*Tcorr,FPP*cosp*Tcorr]) |
|---|
| 1442 | fas = np.sum(np.sum(fa,axis=-1),axis=-1) #real sum over atoms & unique hkl array(2,nTwins) |
|---|
| 1443 | fbs = np.sum(np.sum(fb,axis=-1),axis=-1) #imag sum over atoms & uniq hkl |
|---|
| 1444 | if SGData['SGInv']: #centrosymmetric; B=0 |
|---|
| 1445 | fbs[0] *= 0. |
|---|
| 1446 | fas[1] *= 0. |
|---|
| 1447 | fax = np.array([-fot*sinp,-fotp*cosp]) #positions array(2,nRef,ntwi,nEqv,nAtoms) |
|---|
| 1448 | fbx = np.array([fot*cosp,-fotp*sinp]) |
|---|
| 1449 | #sum below is over Uniq |
|---|
| 1450 | dfadfr = np.sum(np.sum(fa/occ,axis=-2),axis=0) #array(2,nRef,ntwin,nAtom) Fdata != 0 avoids /0. problem |
|---|
| 1451 | dfadba = np.sum(-cosp*Tcorr[:,nxs],axis=1) |
|---|
| 1452 | dfadui = np.sum(np.sum(-SQfactor[nxs,:,nxs,nxs,nxs]*fa,axis=-2),axis=0) |
|---|
| 1453 | dfadx = np.sum(np.sum(twopi*Uniq[nxs,:,:,:,nxs,:]*fax[:,:,:,:,:,nxs],axis=-3),axis=0) # nRef x nTwin x nAtoms x xyz; sum on ops & A,A' |
|---|
| 1454 | dfadua = np.sum(np.sum(-Hij[nxs,:,:,:,nxs,:]*fa[:,:,:,:,:,nxs],axis=-3),axis=0) |
|---|
| 1455 | if not SGData['SGInv']: |
|---|
| 1456 | dfbdfr = np.sum(np.sum(fb/occ,axis=-2),axis=0) #Fdata != 0 avoids /0. problem |
|---|
| 1457 | dfadba /= 2. |
|---|
| 1458 | # dfbdba = np.sum(-sinp*Tcorr[:,nxs],axis=1)/2. |
|---|
| 1459 | dfbdui = np.sum(np.sum(-SQfactor[nxs,:,nxs,nxs,nxs]*fb,axis=-2),axis=0) |
|---|
| 1460 | dfbdx = np.sum(np.sum(twopi*Uniq[nxs,:,:,:,nxs,:]*fbx[:,:,:,:,:,nxs],axis=-3),axis=0) |
|---|
| 1461 | dfbdua = np.sum(np.sum(-Hij[nxs,:,:,:,nxs,:]*fb[:,:,:,:,:,nxs],axis=-3),axis=0) |
|---|
| 1462 | else: |
|---|
| 1463 | dfbdfr = np.zeros_like(dfadfr) |
|---|
| 1464 | dfbdx = np.zeros_like(dfadx) |
|---|
| 1465 | dfbdui = np.zeros_like(dfadui) |
|---|
| 1466 | dfbdua = np.zeros_like(dfadua) |
|---|
| 1467 | # dfbdba = np.zeros_like(dfadba) |
|---|
| 1468 | SA = fas[0]+fas[1] |
|---|
| 1469 | SB = fbs[0]+fbs[1] |
|---|
| 1470 | dFdfr[iBeg:iFin] = ((2.*TwMask*SA)[:,:,nxs]*dfadfr+(2.*TwMask*SB)[:,:,nxs]*dfbdfr)*Mdata[nxs,nxs,:]/len(SGMT) |
|---|
| 1471 | dFdx[iBeg:iFin] = (2.*TwMask*SA)[:,:,nxs,nxs]*dfadx+(2.*TwMask*SB)[:,:,nxs,nxs]*dfbdx |
|---|
| 1472 | dFdui[iBeg:iFin] = (2.*TwMask*SA)[:,:,nxs]*dfadui+(2.*TwMask*SB)[:,:,nxs]*dfbdui |
|---|
| 1473 | dFdua[iBeg:iFin] = (2.*TwMask*SA)[:,:,nxs,nxs]*dfadua+(2.*TwMask*SB)[:,:,nxs,nxs]*dfbdua |
|---|
| 1474 | if SGData['SGInv']: #centrosymmetric; B=0 |
|---|
| 1475 | dFdtw[iBeg:iFin] = np.sum(TwMask[nxs,:]*fas,axis=0)**2 |
|---|
| 1476 | else: |
|---|
| 1477 | dFdtw[iBeg:iFin] = np.sum(TwMask[nxs,:]*fas,axis=0)**2+np.sum(TwMask[nxs,:]*fbs,axis=0)**2 |
|---|
| 1478 | # dFdbab[iBeg:iFin] = fas[0,:,nxs]*np.array([np.sum(dfadba*dBabdA),np.sum(-dfadba*parmDict[phfx+'BabA']*SQfactor*dBabdA)]).T+ \ |
|---|
| 1479 | # fbs[0,:,nxs]*np.array([np.sum(dfbdba*dBabdA),np.sum(-dfbdba*parmDict[phfx+'BabA']*SQfactor*dBabdA)]).T |
|---|
| 1480 | iBeg += blkSize |
|---|
| 1481 | print (' %d derivative time %.4f\r'%(len(refDict['RefList']),time.time()-time0)) |
|---|
| 1482 | #loop over atoms - each dict entry is list of derivatives for all the reflections |
|---|
| 1483 | for i in range(len(Mdata)): #these all OK |
|---|
| 1484 | dFdvDict[pfx+'Afrac:'+str(i)] = np.sum(dFdfr.T[i]*TwinFr[:,nxs],axis=0) |
|---|
| 1485 | dFdvDict[pfx+'dAx:'+str(i)] = np.sum(dFdx.T[0][i]*TwinFr[:,nxs],axis=0) |
|---|
| 1486 | dFdvDict[pfx+'dAy:'+str(i)] = np.sum(dFdx.T[1][i]*TwinFr[:,nxs],axis=0) |
|---|
| 1487 | dFdvDict[pfx+'dAz:'+str(i)] = np.sum(dFdx.T[2][i]*TwinFr[:,nxs],axis=0) |
|---|
| 1488 | dFdvDict[pfx+'AUiso:'+str(i)] = np.sum(dFdui.T[i]*TwinFr[:,nxs],axis=0) |
|---|
| 1489 | dFdvDict[pfx+'AU11:'+str(i)] = np.sum(dFdua.T[0][i]*TwinFr[:,nxs],axis=0) |
|---|
| 1490 | dFdvDict[pfx+'AU22:'+str(i)] = np.sum(dFdua.T[1][i]*TwinFr[:,nxs],axis=0) |
|---|
| 1491 | dFdvDict[pfx+'AU33:'+str(i)] = np.sum(dFdua.T[2][i]*TwinFr[:,nxs],axis=0) |
|---|
| 1492 | dFdvDict[pfx+'AU12:'+str(i)] = np.sum(dFdua.T[3][i]*TwinFr[:,nxs],axis=0) |
|---|
| 1493 | dFdvDict[pfx+'AU13:'+str(i)] = np.sum(dFdua.T[4][i]*TwinFr[:,nxs],axis=0) |
|---|
| 1494 | dFdvDict[pfx+'AU23:'+str(i)] = np.sum(dFdua.T[5][i]*TwinFr[:,nxs],axis=0) |
|---|
| 1495 | dFdvDict[phfx+'BabA'] = dFdbab.T[0] |
|---|
| 1496 | dFdvDict[phfx+'BabU'] = dFdbab.T[1] |
|---|
| 1497 | for i in range(nTwin): |
|---|
| 1498 | dFdvDict[phfx+'TwinFr:'+str(i)] = dFdtw.T[i] |
|---|
| 1499 | return dFdvDict |
|---|
| 1500 | |
|---|
| 1501 | def SStructureFactor(refDict,G,hfx,pfx,SGData,SSGData,calcControls,parmDict): |
|---|
| 1502 | ''' |
|---|
| 1503 | Compute super structure factors for all h,k,l,m for phase - no twins |
|---|
| 1504 | puts the result, F^2, in each ref[9] in refList |
|---|
| 1505 | works on blocks of 32 reflections for speed |
|---|
| 1506 | input: |
|---|
| 1507 | |
|---|
| 1508 | :param dict refDict: where |
|---|
| 1509 | 'RefList' list where each ref = h,k,l,m,it,d,... |
|---|
| 1510 | 'FF' dict of form factors - filed in below |
|---|
| 1511 | :param np.array G: reciprocal metric tensor |
|---|
| 1512 | :param str pfx: phase id string |
|---|
| 1513 | :param dict SGData: space group info. dictionary output from SpcGroup |
|---|
| 1514 | :param dict calcControls: |
|---|
| 1515 | :param dict ParmDict: |
|---|
| 1516 | |
|---|
| 1517 | ''' |
|---|
| 1518 | phfx = pfx.split(':')[0]+hfx |
|---|
| 1519 | ast = np.sqrt(np.diag(G)) |
|---|
| 1520 | GS = G/np.outer(ast,ast) |
|---|
| 1521 | uAmat,uBmat = G2lat.Gmat2AB(GS) |
|---|
| 1522 | Amat,Bmat = G2lat.Gmat2AB(G) |
|---|
| 1523 | Mast = twopisq*np.multiply.outer(ast,ast) |
|---|
| 1524 | SGInv = SGData['SGInv'] |
|---|
| 1525 | SGMT = np.array([ops[0].T for ops in SGData['SGOps']]) |
|---|
| 1526 | Nops = len(SGMT)*(1+SGData['SGInv']) |
|---|
| 1527 | if SGData['SGGray']: |
|---|
| 1528 | Nops *= 2 |
|---|
| 1529 | SSGMT = np.array([ops[0].T for ops in SSGData['SSGOps']]) |
|---|
| 1530 | GamI = np.array([ops[0][3,3] for ops in SSGData['SSGOps']]) |
|---|
| 1531 | if SGData['SGInv']: |
|---|
| 1532 | GamI = np.hstack((GamI,-GamI)) |
|---|
| 1533 | GamI = np.hstack([GamI for cen in SGData['SGCen']]) |
|---|
| 1534 | if SGData['SGGray']: |
|---|
| 1535 | GamI = np.hstack((GamI,GamI)) |
|---|
| 1536 | SSGT = np.array([ops[1] for ops in SSGData['SSGOps']]) |
|---|
| 1537 | SSCen = SSGData['SSGCen'] |
|---|
| 1538 | FFtables = calcControls['FFtables'] |
|---|
| 1539 | EFtables = calcControls['EFtables'] |
|---|
| 1540 | BLtables = calcControls['BLtables'] |
|---|
| 1541 | MFtables = calcControls['MFtables'] |
|---|
| 1542 | Flack = 1.0 |
|---|
| 1543 | if not SGData['SGInv'] and 'S' in calcControls[hfx+'histType'] and phfx+'Flack' in parmDict: |
|---|
| 1544 | Flack = 1.-2.*parmDict[phfx+'Flack'] |
|---|
| 1545 | Tdata,Mdata,Fdata,Xdata,dXdata,IAdata,Uisodata,Uijdata,Gdata = \ |
|---|
| 1546 | GetAtomFXU(pfx,calcControls,parmDict) |
|---|
| 1547 | if not Xdata.size: #no atoms in phase! |
|---|
| 1548 | return |
|---|
| 1549 | waveTypes,FSSdata,XSSdata,USSdata,MSSdata = GetAtomSSFXU(pfx,calcControls,parmDict) |
|---|
| 1550 | ngl,nWaves,Fmod,Xmod,Umod,Mmod,glTau,glWt = G2mth.makeWaves(waveTypes,FSSdata,XSSdata,USSdata,MSSdata,Mast) #NB: Mmod is ReIm,Mxyz,Ntau,Natm |
|---|
| 1551 | modQ = np.array([parmDict[pfx+'mV0'],parmDict[pfx+'mV1'],parmDict[pfx+'mV2']]) |
|---|
| 1552 | |
|---|
| 1553 | if parmDict[pfx+'isMag']: #This part correct for making modulated mag moments on equiv atoms - Mmod matched drawing & Bilbao drawings |
|---|
| 1554 | |
|---|
| 1555 | # mXYZ = np.array([[XYZ[0] for XYZ in list(G2spc.GenAtom(xyz,SGData,All=True,Move=True))] for xyz in (Xdata+dXdata).T]) #Natn,Nop,xyz |
|---|
| 1556 | # if SGData['SGGray']: |
|---|
| 1557 | # mXYZ = np.hstack((mXYZ,mXYZ)) |
|---|
| 1558 | |
|---|
| 1559 | # MmodAR,MmodBR,MmodAI,MmodBI = G2mth.MagMod(glTau,mXYZ,modQ,MSSdata,SGData,SSGData) #Ntau,Nops,Natm,Mxyz cos,sin parts sum matches drawing |
|---|
| 1560 | mXYZ,MmodAR,MmodBR,MmodAI,MmodBI = G2mth.MagMod2(glTau,Xdata+dXdata,modQ,MSSdata,SGData,SSGData) #Ntau,Nops,Natm,Mxyz cos,sin parts sum matches drawing |
|---|
| 1561 | #expand Mmod over mag symm ops. --> GSSdata |
|---|
| 1562 | if not SGData['SGGray']: #for fixed Mx,My,Mz |
|---|
| 1563 | GSdata = np.inner(Gdata.T,np.swapaxes(SGMT,1,2)) #apply sym. ops.--> Natm,Nops,Nxyz |
|---|
| 1564 | if SGData['SGInv'] and not SGData['SGFixed']: #inversion if any |
|---|
| 1565 | GSdata = np.hstack((GSdata,-GSdata)) |
|---|
| 1566 | GSdata = np.hstack([GSdata for cen in SSCen]) #dup over cell centering - Natm,Nops,Mxyz |
|---|
| 1567 | GSdata = SGData['MagMom'][nxs,:,nxs]*GSdata #flip vectors according to spin flip * det(opM) |
|---|
| 1568 | GSdata = np.swapaxes(GSdata,0,1) #Nop,Natm,Mxyz |
|---|
| 1569 | |
|---|
| 1570 | FF = np.zeros(len(Tdata)) |
|---|
| 1571 | if 'NC' in calcControls[hfx+'histType'] or 'NB' in calcControls[hfx+'histType']: |
|---|
| 1572 | FP,FPP = G2el.BlenResCW(Tdata,BLtables,parmDict[hfx+'Lam']) |
|---|
| 1573 | elif 'X' in calcControls[hfx+'histType']: |
|---|
| 1574 | FP = np.array([FFtables[El][hfx+'FP'] for El in Tdata]) |
|---|
| 1575 | FPP = np.array([FFtables[El][hfx+'FPP'] for El in Tdata]) |
|---|
| 1576 | elif 'SEC' in calcControls[hfx+'histType']: |
|---|
| 1577 | FP = np.zeros(len(Tdata)) |
|---|
| 1578 | FPP = np.zeros(len(Tdata)) |
|---|
| 1579 | Uij = np.array(G2lat.U6toUij(Uijdata)).T |
|---|
| 1580 | bij = Mast*Uij |
|---|
| 1581 | blkSize = 48 #no. of reflections in a block |
|---|
| 1582 | nRef = refDict['RefList'].shape[0] |
|---|
| 1583 | SQ = 1./(2.*refDict['RefList'].T[5])**2 |
|---|
| 1584 | if 'N' in calcControls[hfx+'histType']: |
|---|
| 1585 | dat = G2el.getBLvalues(BLtables) |
|---|
| 1586 | refDict['FF']['El'] = list(dat.keys()) |
|---|
| 1587 | refDict['FF']['FF'] = np.ones((nRef,len(dat)))*list(dat.values()) |
|---|
| 1588 | refDict['FF']['MF'] = np.zeros((nRef,len(dat))) |
|---|
| 1589 | for iel,El in enumerate(refDict['FF']['El']): |
|---|
| 1590 | if El in MFtables: |
|---|
| 1591 | refDict['FF']['MF'].T[iel] = G2el.MagScatFac(MFtables[El],SQ) |
|---|
| 1592 | elif 'SEC' in calcControls[hfx+'histType']: |
|---|
| 1593 | dat = G2el.getFFvalues(EFtables,0.) |
|---|
| 1594 | refDict['FF']['El'] = list(dat.keys()) |
|---|
| 1595 | refDict['FF']['FF'] = np.zeros((nRef,len(dat))) |
|---|
| 1596 | for iel,El in enumerate(refDict['FF']['El']): |
|---|
| 1597 | refDict['FF']['FF'].T[iel] = G2el.ScatFac(EFtables[El],SQ) |
|---|
| 1598 | else: |
|---|
| 1599 | dat = G2el.getFFvalues(FFtables,0.) |
|---|
| 1600 | refDict['FF']['El'] = list(dat.keys()) |
|---|
| 1601 | refDict['FF']['FF'] = np.zeros((nRef,len(dat))) |
|---|
| 1602 | for iel,El in enumerate(refDict['FF']['El']): |
|---|
| 1603 | refDict['FF']['FF'].T[iel] = G2el.ScatFac(FFtables[El],SQ) |
|---|
| 1604 | #reflection processing begins here - big arrays! |
|---|
| 1605 | iBeg = 0 |
|---|
| 1606 | while iBeg < nRef: |
|---|
| 1607 | iFin = min(iBeg+blkSize,nRef) |
|---|
| 1608 | mRef= iFin-iBeg |
|---|
| 1609 | refl = refDict['RefList'][iBeg:iFin] #array(blkSize,nItems) |
|---|
| 1610 | H = refl.T[:4] #array(blkSize,4) |
|---|
| 1611 | HP = H[:3]+modQ[:,nxs]*H[3:] #projected hklm to hkl |
|---|
| 1612 | SQ = 1./(2.*refl.T[5])**2 #array(blkSize) |
|---|
| 1613 | SQfactor = 4.0*SQ*twopisq #ditto prev. |
|---|
| 1614 | Uniq = np.inner(H.T,SSGMT) |
|---|
| 1615 | UniqP = np.inner(HP.T,SGMT) |
|---|
| 1616 | Phi = np.inner(H.T,SSGT) |
|---|
| 1617 | if SGInv and not SGData['SGFixed']: #if centro - expand HKL sets |
|---|
| 1618 | Uniq = np.hstack((Uniq,-Uniq)) |
|---|
| 1619 | Phi = np.hstack((Phi,-Phi)) |
|---|
| 1620 | UniqP = np.hstack((UniqP,-UniqP)) |
|---|
| 1621 | if 'T' in calcControls[hfx+'histType']: |
|---|
| 1622 | if 'P' in calcControls[hfx+'histType']: |
|---|
| 1623 | FP,FPP = G2el.BlenResTOF(Tdata,BLtables,refl.T[14]) |
|---|
| 1624 | else: |
|---|
| 1625 | FP,FPP = G2el.BlenResTOF(Tdata,BLtables,refl.T[12]) |
|---|
| 1626 | FP = np.repeat(FP.T,Uniq.shape[1],axis=0) |
|---|
| 1627 | FPP = np.repeat(FPP.T,Uniq.shape[1],axis=0) |
|---|
| 1628 | Bab = 0. |
|---|
| 1629 | if phfx+'BabA' in parmDict: |
|---|
| 1630 | Bab = np.repeat(parmDict[phfx+'BabA']*np.exp(-parmDict[phfx+'BabU']*SQfactor),Uniq.shape[1]) |
|---|
| 1631 | Tindx = np.array([refDict['FF']['El'].index(El) for El in Tdata]) |
|---|
| 1632 | FF = np.repeat(refDict['FF']['FF'][iBeg:iFin].T[Tindx].T,Uniq.shape[1],axis=0) |
|---|
| 1633 | phase = twopi*(np.inner(Uniq[:,:,:3],(dXdata.T+Xdata.T))-Phi[:,:,nxs]) |
|---|
| 1634 | sinp = np.sin(phase) |
|---|
| 1635 | cosp = np.cos(phase) |
|---|
| 1636 | biso = -SQfactor*Uisodata[:,nxs] |
|---|
| 1637 | Tiso = np.repeat(np.where(biso<1.,np.exp(biso),1.0),Uniq.shape[1],axis=1).T |
|---|
| 1638 | HbH = -np.sum(UniqP[:,:,nxs,:]*np.inner(UniqP[:,:,:],bij),axis=-1) #use hklt proj to hkl |
|---|
| 1639 | Tuij = np.where(HbH<1.,np.exp(HbH),1.0) |
|---|
| 1640 | Tcorr = np.reshape(Tiso,Tuij.shape)*Tuij*Mdata*Fdata/Uniq.shape[1] #refBlk x ops x atoms |
|---|
| 1641 | |
|---|
| 1642 | if 'N' in calcControls[hfx+'histType'] and parmDict[pfx+'isMag']: |
|---|
| 1643 | |
|---|
| 1644 | phasem = twopi*np.inner(mXYZ,HP.T).T #2pi(Q.r) |
|---|
| 1645 | cosm = np.cos(phasem) #Nref,nops,natm |
|---|
| 1646 | sinm = np.sin(phasem) |
|---|
| 1647 | MF = refDict['FF']['MF'][iBeg:iFin].T[Tindx].T #Nref,Natm |
|---|
| 1648 | TMcorr = 0.539*(np.reshape(Tiso,Tuij.shape)*Tuij)[:,0,:]*Mdata*Fdata*MF/(2*Nops) #Nref,Natm |
|---|
| 1649 | HM = np.inner(Bmat,HP.T) #put into cartesian space X||H,Z||H*L; Bmat.T correct Cart coordinates |
|---|
| 1650 | eM = (HM*refl.T[5]).T # normalize HP by d* Nref,hkl=Unit vectors || Q |
|---|
| 1651 | |
|---|
| 1652 | if not SGData['SGGray']: #correct -fixed Mx,My,Mz contribution |
|---|
| 1653 | fam0 = TMcorr[:,nxs,:,nxs]*GSdata[nxs,:,:,:]*cosm[:,:,:,nxs] #Nref,Nops,Natm,Mxyz |
|---|
| 1654 | fbm0 = TMcorr[:,nxs,:,nxs]*GSdata[nxs,:,:,:]*sinm[:,:,:,nxs] |
|---|
| 1655 | # calc mag. structure factors; Nref,Ntau,Nops,Natm,Mxyz |
|---|
| 1656 | fams = TMcorr[:,nxs,nxs,:,nxs]*SGData['MagMom'][nxs,nxs,:,nxs,nxs]*np.array([np.where(H[3,i]!=0,( |
|---|
| 1657 | (-MmodAR+H[3,i]*MmodBR)*cosm[i,nxs,:,:,nxs]+ |
|---|
| 1658 | GamI[nxs,:,nxs,nxs]*(MmodAI-H[3,i]*MmodBI)*sinm[i,nxs,:,:,nxs]), |
|---|
| 1659 | 0.) for i in range(mRef)])/2. #Nref,Ntau,Nops,Natm,Mxyz |
|---|
| 1660 | |
|---|
| 1661 | fbms = TMcorr[:,nxs,nxs,:,nxs]*SGData['MagMom'][nxs,nxs,:,nxs,nxs]*np.array([np.where(H[3,i]!=0,( |
|---|
| 1662 | (MmodAR-H[3,i]*MmodBR)*sinm[i,nxs,:,:,nxs]+ |
|---|
| 1663 | GamI[nxs,:,nxs,nxs]*(-MmodAI+H[3,i]*MmodBI)*cosm[i,nxs,:,:,nxs]), |
|---|
| 1664 | 0.) for i in range(mRef)])/2. #Nref,Ntau,Nops,Natm,Mxyz |
|---|
| 1665 | |
|---|
| 1666 | if not SGData['SGGray']: |
|---|
| 1667 | fams += fam0[:,nxs,:,:,:] |
|---|
| 1668 | fbms += fbm0[:,nxs,:,:,:] |
|---|
| 1669 | |
|---|
| 1670 | #sum ops & atms |
|---|
| 1671 | fasm = np.sum(np.sum(fams,axis=-2),axis=-2) #Nref,Ntau,Mxyz; sum ops & atoms |
|---|
| 1672 | fbsm = np.sum(np.sum(fbms,axis=-2),axis=-2) |
|---|
| 1673 | # #put into cartesian space |
|---|
| 1674 | facm = np.inner(fasm,uBmat) #uBmat best fit for DyMnGe; +,- & -,+ fams, fbms; Nref, Ntau, Mxyz |
|---|
| 1675 | fbcm = np.inner(fbsm,uBmat) #Nref,Ntau,Mxyz |
|---|
| 1676 | #form e.F dot product |
|---|
| 1677 | eDotFa = np.sum(eM[:,nxs,:]*facm,axis=-1) #Nref,Ntau |
|---|
| 1678 | eDotFb = np.sum(eM[:,nxs,:]*fbcm,axis=-1) |
|---|
| 1679 | #intensity Halpern & Johnson |
|---|
| 1680 | fass = np.sum((facm-eM[:,nxs,:]*eDotFa[:,:,nxs])**2,axis=-1) #Nref,Ntau |
|---|
| 1681 | fbss = np.sum((fbcm-eM[:,nxs,:]*eDotFb[:,:,nxs])**2,axis=-1) |
|---|
| 1682 | # gray *2 |
|---|
| 1683 | if SGData['SGGray']: |
|---|
| 1684 | fass *= 2. |
|---|
| 1685 | fbss *= 2. |
|---|
| 1686 | ## #do integration |
|---|
| 1687 | fas = np.sum(fass*glWt[nxs,:],axis=1) |
|---|
| 1688 | fbs = np.sum(fbss*glWt[nxs,:],axis=1) |
|---|
| 1689 | |
|---|
| 1690 | refl.T[10] = fas+fbs #Sum(fams**2,Mxyz) Re + Im |
|---|
| 1691 | refl.T[11] = atan2d(fbs,fas) |
|---|
| 1692 | |
|---|
| 1693 | else: |
|---|
| 1694 | GfpuA = G2mth.Modulation(Uniq,UniqP,nWaves,Fmod,Xmod,Umod,glTau,glWt) #2 x refBlk x sym X atoms |
|---|
| 1695 | if 'T' in calcControls[hfx+'histType']: |
|---|
| 1696 | fa = np.array([np.reshape(((FF+FP).T-Bab).T,cosp.shape)*cosp*Tcorr,-np.reshape(Flack*FPP,sinp.shape)*sinp*Tcorr]) |
|---|
| 1697 | fb = np.array([np.reshape(Flack*FPP,cosp.shape)*cosp*Tcorr,np.reshape(((FF+FP).T-Bab).T,sinp.shape)*sinp*Tcorr]) |
|---|
| 1698 | else: |
|---|
| 1699 | fa = np.array([np.reshape(((FF+FP).T-Bab).T,cosp.shape)*cosp*Tcorr,-Flack*FPP*sinp*Tcorr]) |
|---|
| 1700 | fb = np.array([Flack*FPP*cosp*Tcorr,np.reshape(((FF+FP).T-Bab).T,sinp.shape)*sinp*Tcorr]) |
|---|
| 1701 | fag = fa*GfpuA[0]-fb*GfpuA[1] #real; 2 x refBlk x sym x atoms |
|---|
| 1702 | fbg = fb*GfpuA[0]+fa*GfpuA[1] |
|---|
| 1703 | fas = np.sum(np.sum(fag,axis=-1),axis=-1) #2 x refBlk; sum sym & atoms |
|---|
| 1704 | fbs = np.sum(np.sum(fbg,axis=-1),axis=-1) |
|---|
| 1705 | |
|---|
| 1706 | refl.T[10] = np.sum(fas,axis=0)**2+np.sum(fbs,axis=0)**2 #square of sums |
|---|
| 1707 | refl.T[11] = atan2d(fbs[0],fas[0]) #use only tau=0; ignore f' & f" |
|---|
| 1708 | if 'P' not in calcControls[hfx+'histType']: |
|---|
| 1709 | refl.T[8] = np.copy(refl.T[10]) |
|---|
| 1710 | iBeg += blkSize |
|---|
| 1711 | return copy.deepcopy(refDict['RefList']) |
|---|
| 1712 | |
|---|
| 1713 | def SStructureFactorTw(refDict,G,hfx,pfx,SGData,SSGData,calcControls,parmDict): |
|---|
| 1714 | ''' |
|---|
| 1715 | Compute super structure factors for all h,k,l,m for phase - twins only |
|---|
| 1716 | puts the result, F^2, in each ref[8+im] in refList |
|---|
| 1717 | works on blocks of 32 reflections for speed |
|---|
| 1718 | input: |
|---|
| 1719 | |
|---|
| 1720 | :param dict refDict: where |
|---|
| 1721 | 'RefList' list where each ref = h,k,l,m,it,d,... |
|---|
| 1722 | 'FF' dict of form factors - filed in below |
|---|
| 1723 | :param np.array G: reciprocal metric tensor |
|---|
| 1724 | :param str pfx: phase id string |
|---|
| 1725 | :param dict SGData: space group info. dictionary output from SpcGroup |
|---|
| 1726 | :param dict calcControls: |
|---|
| 1727 | :param dict ParmDict: |
|---|
| 1728 | |
|---|
| 1729 | ''' |
|---|
| 1730 | phfx = pfx.split(':')[0]+hfx |
|---|
| 1731 | ast = np.sqrt(np.diag(G)) |
|---|
| 1732 | Mast = twopisq*np.multiply.outer(ast,ast) |
|---|
| 1733 | SGInv = SGData['SGInv'] |
|---|
| 1734 | SGMT = np.array([ops[0].T for ops in SGData['SGOps']]) |
|---|
| 1735 | SSGMT = np.array([ops[0].T for ops in SSGData['SSGOps']]) |
|---|
| 1736 | SSGT = np.array([ops[1] for ops in SSGData['SSGOps']]) |
|---|
| 1737 | FFtables = calcControls['FFtables'] |
|---|
| 1738 | EFtables = calcControls['EFtables'] |
|---|
| 1739 | BLtables = calcControls['BLtables'] |
|---|
| 1740 | MFtables = calcControls['MFtables'] |
|---|
| 1741 | Flack = 1.0 |
|---|
| 1742 | if not SGData['SGInv'] and 'S' in calcControls[hfx+'histType'] and phfx+'Flack' in parmDict: |
|---|
| 1743 | Flack = 1.-2.*parmDict[phfx+'Flack'] |
|---|
| 1744 | TwinLaw = np.array([[[1,0,0,0],[0,1,0,0],[0,0,1,0],[0,0,0,1]],]) #4D? |
|---|
| 1745 | TwDict = refDict.get('TwDict',{}) |
|---|
| 1746 | if 'S' in calcControls[hfx+'histType']: |
|---|
| 1747 | NTL = calcControls[phfx+'NTL'] |
|---|
| 1748 | NM = calcControls[phfx+'TwinNMN']+1 |
|---|
| 1749 | TwinLaw = calcControls[phfx+'TwinLaw'] #this'll have to be 4D also... |
|---|
| 1750 | TwinFr = np.array([parmDict[phfx+'TwinFr:'+str(i)] for i in range(len(TwinLaw))]) |
|---|
| 1751 | TwinInv = list(np.where(calcControls[phfx+'TwinInv'],-1,1)) |
|---|
| 1752 | Tdata,Mdata,Fdata,Xdata,dXdata,IAdata,Uisodata,Uijdata,Gdata = \ |
|---|
| 1753 | GetAtomFXU(pfx,calcControls,parmDict) |
|---|
| 1754 | if not Xdata.size: #no atoms in phase! |
|---|
| 1755 | return |
|---|
| 1756 | waveTypes,FSSdata,XSSdata,USSdata,MSSdata = GetAtomSSFXU(pfx,calcControls,parmDict) |
|---|
| 1757 | ngl,nWaves,Fmod,Xmod,Umod,Mmod,glTau,glWt = G2mth.makeWaves(waveTypes,FSSdata,XSSdata,USSdata,Mast) |
|---|
| 1758 | modQ = np.array([parmDict[pfx+'mV0'],parmDict[pfx+'mV1'],parmDict[pfx+'mV2']]) |
|---|
| 1759 | FF = np.zeros(len(Tdata)) |
|---|
| 1760 | if 'NC' in calcControls[hfx+'histType'] or 'NB' in calcControls[hfx+'histType']: |
|---|
| 1761 | FP,FPP = G2el.BlenResCW(Tdata,BLtables,parmDict[hfx+'Lam']) |
|---|
| 1762 | elif 'X' in calcControls[hfx+'histType']: |
|---|
| 1763 | FP = np.array([FFtables[El][hfx+'FP'] for El in Tdata]) |
|---|
| 1764 | FPP = np.array([FFtables[El][hfx+'FPP'] for El in Tdata]) |
|---|
| 1765 | elif 'SEC' in calcControls[hfx+'histType']: |
|---|
| 1766 | FP = np.zeros(len(Tdata)) |
|---|
| 1767 | FPP = np.zeros(len(Tdata)) |
|---|
| 1768 | Uij = np.array(G2lat.U6toUij(Uijdata)).T |
|---|
| 1769 | bij = Mast*Uij |
|---|
| 1770 | blkSize = 32 #no. of reflections in a block |
|---|
| 1771 | nRef = refDict['RefList'].shape[0] |
|---|
| 1772 | if not len(refDict['FF']): #no form factors - 1st time thru StructureFactor |
|---|
| 1773 | SQ = 1./(2.*refDict['RefList'].T[5])**2 |
|---|
| 1774 | if 'N' in calcControls[hfx+'histType']: |
|---|
| 1775 | dat = G2el.getBLvalues(BLtables) |
|---|
| 1776 | refDict['FF']['El'] = list(dat.keys()) |
|---|
| 1777 | refDict['FF']['FF'] = np.ones((nRef,len(dat)))*list(dat.values()) |
|---|
| 1778 | refDict['FF']['MF'] = np.zeros((nRef,len(dat))) |
|---|
| 1779 | for iel,El in enumerate(refDict['FF']['El']): |
|---|
| 1780 | if El in MFtables: |
|---|
| 1781 | refDict['FF']['MF'].T[iel] = G2el.MagScatFac(MFtables[El],SQ) |
|---|
| 1782 | elif 'SEC' in calcControls[hfx+'histType']: |
|---|
| 1783 | dat = G2el.getFFvalues(EFtables,0.) |
|---|
| 1784 | refDict['FF']['El'] = list(dat.keys()) |
|---|
| 1785 | refDict['FF']['FF'] = np.zeros((nRef,len(dat))) |
|---|
| 1786 | for iel,El in enumerate(refDict['FF']['El']): |
|---|
| 1787 | refDict['FF']['FF'].T[iel] = G2el.ScatFac(EFtables[El],SQ) |
|---|
| 1788 | else: |
|---|
| 1789 | dat = G2el.getFFvalues(FFtables,0.) |
|---|
| 1790 | refDict['FF']['El'] = list(dat.keys()) |
|---|
| 1791 | refDict['FF']['FF'] = np.zeros((nRef,len(dat))) |
|---|
| 1792 | for iel,El in enumerate(refDict['FF']['El']): |
|---|
| 1793 | refDict['FF']['FF'].T[iel] = G2el.ScatFac(FFtables[El],SQ) |
|---|
| 1794 | # time0 = time.time() |
|---|
| 1795 | #reflection processing begins here - big arrays! |
|---|
| 1796 | iBeg = 0 |
|---|
| 1797 | while iBeg < nRef: |
|---|
| 1798 | iFin = min(iBeg+blkSize,nRef) |
|---|
| 1799 | refl = refDict['RefList'][iBeg:iFin] #array(blkSize,nItems) |
|---|
| 1800 | H = refl[:,:4] #array(blkSize,4) |
|---|
| 1801 | H3 = refl[:,:3] |
|---|
| 1802 | HP = H[:,:3]+modQ[nxs,:]*H[:,3:] #projected hklm to hkl |
|---|
| 1803 | HP = np.inner(HP,TwinLaw) #array(blkSize,nTwins,4) |
|---|
| 1804 | H3 = np.inner(H3,TwinLaw) |
|---|
| 1805 | TwMask = np.any(HP,axis=-1) |
|---|
| 1806 | if TwinLaw.shape[0] > 1 and TwDict: #need np.inner(TwinLaw[?],TwDict[iref][i])*TwinInv[i] |
|---|
| 1807 | for ir in range(blkSize): |
|---|
| 1808 | iref = ir+iBeg |
|---|
| 1809 | if iref in TwDict: |
|---|
| 1810 | for i in TwDict[iref]: |
|---|
| 1811 | for n in range(NTL): |
|---|
| 1812 | HP[ir][i+n*NM] = np.inner(TwinLaw[n*NM],np.array(TwDict[iref][i])*TwinInv[i+n*NM]) |
|---|
| 1813 | H3[ir][i+n*NM] = np.inner(TwinLaw[n*NM],np.array(TwDict[iref][i])*TwinInv[i+n*NM]) |
|---|
| 1814 | TwMask = np.any(HP,axis=-1) |
|---|
| 1815 | SQ = 1./(2.*refl.T[5])**2 #array(blkSize) |
|---|
| 1816 | SQfactor = 4.0*SQ*twopisq #ditto prev. |
|---|
| 1817 | Uniq = np.inner(H,SSGMT) |
|---|
| 1818 | Uniq3 = np.inner(H3,SGMT) |
|---|
| 1819 | UniqP = np.inner(HP,SGMT) |
|---|
| 1820 | Phi = np.inner(H,SSGT) |
|---|
| 1821 | if SGInv: #if centro - expand HKL sets |
|---|
| 1822 | Uniq = np.hstack((Uniq,-Uniq)) |
|---|
| 1823 | Uniq3 = np.hstack((Uniq3,-Uniq3)) |
|---|
| 1824 | Phi = np.hstack((Phi,-Phi)) |
|---|
| 1825 | UniqP = np.hstack((UniqP,-UniqP)) |
|---|
| 1826 | if 'T' in calcControls[hfx+'histType']: |
|---|
| 1827 | if 'P' in calcControls[hfx+'histType']: |
|---|
| 1828 | FP,FPP = G2el.BlenResTOF(Tdata,BLtables,refl.T[14]) |
|---|
| 1829 | else: |
|---|
| 1830 | FP,FPP = G2el.BlenResTOF(Tdata,BLtables,refl.T[12]) |
|---|
| 1831 | FP = np.repeat(FP.T,Uniq.shape[1]*len(TwinLaw),axis=0) |
|---|
| 1832 | FPP = np.repeat(FPP.T,Uniq.shape[1]*len(TwinLaw),axis=0) |
|---|
| 1833 | Bab = np.repeat(parmDict[phfx+'BabA']*np.exp(-parmDict[phfx+'BabU']*SQfactor),Uniq.shape[1]*len(TwinLaw)) |
|---|
| 1834 | Tindx = np.array([refDict['FF']['El'].index(El) for El in Tdata]) |
|---|
| 1835 | FF = np.repeat(refDict['FF']['FF'][iBeg:iFin].T[Tindx].T,Uniq.shape[1]*len(TwinLaw),axis=0) |
|---|
| 1836 | phase = twopi*(np.inner(Uniq3,(dXdata.T+Xdata.T))-Phi[:,nxs,:,nxs]) |
|---|
| 1837 | sinp = np.sin(phase) |
|---|
| 1838 | cosp = np.cos(phase) |
|---|
| 1839 | biso = -SQfactor*Uisodata[:,nxs] |
|---|
| 1840 | Tiso = np.repeat(np.where(biso<1.,np.exp(biso),1.0),Uniq.shape[1]*len(TwinLaw),axis=1).T |
|---|
| 1841 | HbH = -np.sum(UniqP[:,:,:,nxs]*np.inner(UniqP[:,:,:],bij),axis=-1) #use hklt proj to hkl |
|---|
| 1842 | Tuij = np.where(HbH<1.,np.exp(HbH),1.0) |
|---|
| 1843 | Tcorr = np.reshape(Tiso,Tuij.shape)*Tuij*Mdata*Fdata/Uniq.shape[1] #refBlk x ops x atoms |
|---|
| 1844 | if 'T' in calcControls[hfx+'histType']: |
|---|
| 1845 | fa = np.array([np.reshape(((FF+FP).T-Bab).T,cosp.shape)*cosp*Tcorr,-np.reshape(Flack*FPP,sinp.shape)*sinp*Tcorr]) |
|---|
| 1846 | fb = np.array([np.reshape(Flack*FPP,cosp.shape)*cosp*Tcorr,np.reshape(((FF+FP).T-Bab).T,sinp.shape)*sinp*Tcorr]) |
|---|
| 1847 | else: |
|---|
| 1848 | fa = np.array([np.reshape(((FF+FP).T-Bab).T,cosp.shape)*cosp*Tcorr,-Flack*FPP*sinp*Tcorr]) |
|---|
| 1849 | fb = np.array([Flack*FPP*cosp*Tcorr,np.reshape(((FF+FP).T-Bab).T,sinp.shape)*sinp*Tcorr]) |
|---|
| 1850 | GfpuA = G2mth.ModulationTw(Uniq,UniqP,nWaves,Fmod,Xmod,Umod,glTau,glWt) #2 x refBlk x sym X atoms |
|---|
| 1851 | fag = fa*GfpuA[0]-fb*GfpuA[1] #real; 2 x refBlk x sym x atoms |
|---|
| 1852 | fbg = fb*GfpuA[0]+fa*GfpuA[1] |
|---|
| 1853 | fas = np.sum(np.sum(fag,axis=-1),axis=-1) #2 x refBlk; sum sym & atoms |
|---|
| 1854 | fbs = np.sum(np.sum(fbg,axis=-1),axis=-1) |
|---|
| 1855 | refl.T[10] = np.sum(fas[:,:,0],axis=0)**2+np.sum(fbs[:,:,0],axis=0)**2 #FcT from primary twin element |
|---|
| 1856 | refl.T[8] = np.sum(TwinFr*np.sum(TwMask[nxs,:,:]*fas,axis=0)**2,axis=-1)+ \ |
|---|
| 1857 | np.sum(TwinFr*np.sum(TwMask[nxs,:,:]*fbs,axis=0)**2,axis=-1) #Fc sum over twins |
|---|
| 1858 | refl.T[11] = atan2d(fbs[0].T[0],fas[0].T[0]) #ignore f' & f" |
|---|
| 1859 | iBeg += blkSize |
|---|
| 1860 | # print ('nRef %d time %.4f\r'%(nRef,time.time()-time0)) |
|---|
| 1861 | |
|---|
| 1862 | def SStructureFactorDerv(refDict,im,G,hfx,pfx,SGData,SSGData,calcControls,parmDict): |
|---|
| 1863 | ''' |
|---|
| 1864 | Compute super structure factor derivatives for all h,k,l,m for phase - no twins |
|---|
| 1865 | Only Fourier component are done analytically here |
|---|
| 1866 | input: |
|---|
| 1867 | |
|---|
| 1868 | :param dict refDict: where |
|---|
| 1869 | 'RefList' list where each ref = h,k,l,m,it,d,... |
|---|
| 1870 | 'FF' dict of form factors - filled in below |
|---|
| 1871 | :param int im: = 1 (could be eliminated) |
|---|
| 1872 | :param np.array G: reciprocal metric tensor |
|---|
| 1873 | :param str hfx: histogram id string |
|---|
| 1874 | :param str pfx: phase id string |
|---|
| 1875 | :param dict SGData: space group info. dictionary output from SpcGroup |
|---|
| 1876 | :param dict SSGData: super space group info. |
|---|
| 1877 | :param dict calcControls: |
|---|
| 1878 | :param dict ParmDict: |
|---|
| 1879 | |
|---|
| 1880 | :returns: dict dFdvDict: dictionary of derivatives |
|---|
| 1881 | ''' |
|---|
| 1882 | phfx = pfx.split(':')[0]+hfx |
|---|
| 1883 | ast = np.sqrt(np.diag(G)) |
|---|
| 1884 | Mast = twopisq*np.multiply.outer(ast,ast) |
|---|
| 1885 | SGInv = SGData['SGInv'] |
|---|
| 1886 | SGMT = np.array([ops[0].T for ops in SGData['SGOps']]) |
|---|
| 1887 | SSGMT = np.array([ops[0].T for ops in SSGData['SSGOps']]) |
|---|
| 1888 | SSGT = np.array([ops[1] for ops in SSGData['SSGOps']]) |
|---|
| 1889 | FFtables = calcControls['FFtables'] |
|---|
| 1890 | EFtables = calcControls['EFtables'] |
|---|
| 1891 | BLtables = calcControls['BLtables'] |
|---|
| 1892 | nRef = len(refDict['RefList']) |
|---|
| 1893 | Tdata,Mdata,Fdata,Xdata,dXdata,IAdata,Uisodata,Uijdata,Gdata = \ |
|---|
| 1894 | GetAtomFXU(pfx,calcControls,parmDict) |
|---|
| 1895 | if not Xdata.size: #no atoms in phase! |
|---|
| 1896 | return {} |
|---|
| 1897 | mSize = len(Mdata) #no. atoms |
|---|
| 1898 | waveTypes,FSSdata,XSSdata,USSdata,MSSdata = GetAtomSSFXU(pfx,calcControls,parmDict) |
|---|
| 1899 | ngl,nWaves,Fmod,Xmod,Umod,Mmod,glTau,glWt = G2mth.makeWaves(waveTypes,FSSdata,XSSdata,USSdata,MSSdata,Mast) |
|---|
| 1900 | waveShapes,SCtauF,SCtauX,SCtauU,UmodAB = G2mth.makeWavesDerv(ngl,waveTypes,FSSdata,XSSdata,USSdata,Mast) |
|---|
| 1901 | modQ = np.array([parmDict[pfx+'mV0'],parmDict[pfx+'mV1'],parmDict[pfx+'mV2']]) |
|---|
| 1902 | FF = np.zeros(len(Tdata)) |
|---|
| 1903 | if 'NC' in calcControls[hfx+'histType'] or 'NB' in calcControls[hfx+'histType']: |
|---|
| 1904 | FP,FPP = G2el.BlenResCW(Tdata,BLtables,parmDict[hfx+'Lam']) |
|---|
| 1905 | elif 'X' in calcControls[hfx+'histType']: |
|---|
| 1906 | FP = np.array([FFtables[El][hfx+'FP'] for El in Tdata]) |
|---|
| 1907 | FPP = np.array([FFtables[El][hfx+'FPP'] for El in Tdata]) |
|---|
| 1908 | elif 'SEC' in calcControls[hfx+'histType']: |
|---|
| 1909 | FP = np.zeros(len(Tdata)) |
|---|
| 1910 | FPP = np.zeros(len(Tdata)) |
|---|
| 1911 | Uij = np.array(G2lat.U6toUij(Uijdata)).T |
|---|
| 1912 | bij = Mast*Uij |
|---|
| 1913 | if not len(refDict['FF']): |
|---|
| 1914 | if 'N' in calcControls[hfx+'histType']: |
|---|
| 1915 | dat = G2el.getBLvalues(BLtables) #will need wave here for anom. neutron b's |
|---|
| 1916 | elif 'SEC' in calcControls[hfx+'histType']: |
|---|
| 1917 | dat = G2el.getFFvalues(EFtables,0.) |
|---|
| 1918 | else: |
|---|
| 1919 | dat = G2el.getFFvalues(FFtables,0.) |
|---|
| 1920 | refDict['FF']['El'] = list(dat.keys()) |
|---|
| 1921 | refDict['FF']['FF'] = np.zeros((len(refDict['RefList']),len(dat))) |
|---|
| 1922 | dFdvDict = {} |
|---|
| 1923 | dFdfr = np.zeros((nRef,mSize)) |
|---|
| 1924 | dFdx = np.zeros((nRef,mSize,3)) |
|---|
| 1925 | dFdui = np.zeros((nRef,mSize)) |
|---|
| 1926 | dFdua = np.zeros((nRef,mSize,6)) |
|---|
| 1927 | dFdbab = np.zeros((nRef,2)) |
|---|
| 1928 | dFdfl = np.zeros((nRef)) |
|---|
| 1929 | dFdGf = np.zeros((nRef,mSize,FSSdata.shape[1],2)) |
|---|
| 1930 | dFdGx = np.zeros((nRef,mSize,XSSdata.shape[1],6)) |
|---|
| 1931 | dFdGu = np.zeros((nRef,mSize,USSdata.shape[1],12)) |
|---|
| 1932 | Flack = 1.0 |
|---|
| 1933 | if not SGData['SGInv'] and 'S' in calcControls[hfx+'histType'] and phfx+'Flack' in parmDict: |
|---|
| 1934 | Flack = 1.-2.*parmDict[phfx+'Flack'] |
|---|
| 1935 | time0 = time.time() |
|---|
| 1936 | nRef = len(refDict['RefList'])/100 |
|---|
| 1937 | for iref,refl in enumerate(refDict['RefList']): |
|---|
| 1938 | if 'T' in calcControls[hfx+'histType']: |
|---|
| 1939 | FP,FPP = G2el.BlenResCW(Tdata,BLtables,refl.T[12+im]) |
|---|
| 1940 | H = np.array(refl[:4]) |
|---|
| 1941 | HP = H[:3]+modQ*H[3:] #projected hklm to hkl |
|---|
| 1942 | SQ = 1./(2.*refl[4+im])**2 # or (sin(theta)/lambda)**2 |
|---|
| 1943 | SQfactor = 8.0*SQ*np.pi**2 |
|---|
| 1944 | Bab = 0.0 |
|---|
| 1945 | if phfx+'BabA' in parmDict: |
|---|
| 1946 | dBabdA = np.exp(-parmDict[phfx+'BabU']*SQfactor) |
|---|
| 1947 | Bab = parmDict[phfx+'BabA']*dBabdA |
|---|
| 1948 | Tindx = np.array([refDict['FF']['El'].index(El) for El in Tdata]) |
|---|
| 1949 | FF = refDict['FF']['FF'][iref].T[Tindx] |
|---|
| 1950 | Uniq = np.inner(H,SSGMT) |
|---|
| 1951 | Phi = np.inner(H,SSGT) |
|---|
| 1952 | UniqP = np.inner(HP,SGMT) |
|---|
| 1953 | if SGInv: #if centro - expand HKL sets |
|---|
| 1954 | Uniq = np.vstack((Uniq,-Uniq)) |
|---|
| 1955 | Phi = np.hstack((Phi,-Phi)) |
|---|
| 1956 | UniqP = np.vstack((UniqP,-UniqP)) |
|---|
| 1957 | phase = twopi*(np.inner(Uniq[:,:3],(dXdata+Xdata).T)+Phi[:,nxs]) |
|---|
| 1958 | sinp = np.sin(phase) |
|---|
| 1959 | cosp = np.cos(phase) |
|---|
| 1960 | occ = Mdata*Fdata/Uniq.shape[0] |
|---|
| 1961 | biso = -SQfactor*Uisodata[:,nxs] |
|---|
| 1962 | Tiso = np.repeat(np.where(biso<1.,np.exp(biso),1.0),Uniq.shape[0],axis=1).T #ops x atoms |
|---|
| 1963 | HbH = -np.sum(UniqP[:,nxs,:3]*np.inner(UniqP[:,:3],bij),axis=-1) #ops x atoms |
|---|
| 1964 | Hij = np.array([Mast*np.multiply.outer(U[:3],U[:3]) for U in UniqP]) #atoms x 3x3 |
|---|
| 1965 | Hij = np.array([G2lat.UijtoU6(uij) for uij in Hij]) #atoms x 6 |
|---|
| 1966 | Tuij = np.where(HbH<1.,np.exp(HbH),1.0) #ops x atoms |
|---|
| 1967 | Tcorr = np.reshape(Tiso,Tuij.shape)*Tuij*Mdata*Fdata/Uniq.shape[0] #ops x atoms |
|---|
| 1968 | fot = (FF+FP-Bab)*Tcorr #ops x atoms |
|---|
| 1969 | fotp = FPP*Tcorr #ops x atoms |
|---|
| 1970 | GfpuA = G2mth.Modulation(Uniq,UniqP,nWaves,Fmod,Xmod,Umod,glTau,glWt) #2 x sym X atoms |
|---|
| 1971 | dGdf,dGdx,dGdu = G2mth.ModulationDerv(Uniq,UniqP,Hij,nWaves,waveShapes,Fmod,Xmod,UmodAB,SCtauF,SCtauX,SCtauU,glTau,glWt) |
|---|
| 1972 | # GfpuA is 2 x ops x atoms |
|---|
| 1973 | # derivs are: ops x atoms x waves x 2,6,12, or 5 parms as [real,imag] parts |
|---|
| 1974 | fa = np.array([((FF+FP).T-Bab).T*cosp*Tcorr,-Flack*FPP*sinp*Tcorr]) # array(2,nEqv,nAtoms) |
|---|
| 1975 | fb = np.array([((FF+FP).T-Bab).T*sinp*Tcorr,Flack*FPP*cosp*Tcorr]) #or array(2,nEqv,nAtoms) |
|---|
| 1976 | fag = fa*GfpuA[0]-fb*GfpuA[1] |
|---|
| 1977 | fbg = fb*GfpuA[0]+fa*GfpuA[1] |
|---|
| 1978 | |
|---|
| 1979 | fas = np.sum(np.sum(fag,axis=1),axis=1) # 2 x twin |
|---|
| 1980 | fbs = np.sum(np.sum(fbg,axis=1),axis=1) |
|---|
| 1981 | fax = np.array([-fot*sinp,-fotp*cosp]) #positions; 2 x ops x atoms |
|---|
| 1982 | fbx = np.array([fot*cosp,-fotp*sinp]) |
|---|
| 1983 | fax = fax*GfpuA[0]-fbx*GfpuA[1] |
|---|
| 1984 | fbx = fbx*GfpuA[0]+fax*GfpuA[1] |
|---|
| 1985 | #sum below is over Uniq |
|---|
| 1986 | dfadfr = np.sum(fag/occ,axis=1) #Fdata != 0 ever avoids /0. problem |
|---|
| 1987 | dfbdfr = np.sum(fbg/occ,axis=1) #Fdata != 0 avoids /0. problem |
|---|
| 1988 | dfadba = np.sum(-cosp*Tcorr[:,nxs],axis=1) |
|---|
| 1989 | dfbdba = np.sum(-sinp*Tcorr[:,nxs],axis=1) |
|---|
| 1990 | dfadui = np.sum(-SQfactor*fag,axis=1) |
|---|
| 1991 | dfbdui = np.sum(-SQfactor*fbg,axis=1) |
|---|
| 1992 | dfadx = np.sum(twopi*Uniq[:,:3]*np.swapaxes(fax,-2,-1)[:,:,:,nxs],axis=-2) #2 x nAtom x 3xyz; sum nOps |
|---|
| 1993 | dfbdx = np.sum(twopi*Uniq[:,:3]*np.swapaxes(fbx,-2,-1)[:,:,:,nxs],axis=-2) |
|---|
| 1994 | dfadua = np.sum(-Hij*np.swapaxes(fag,-2,-1)[:,:,:,nxs],axis=-2) #2 x nAtom x 6Uij; sum nOps |
|---|
| 1995 | dfbdua = np.sum(-Hij*np.swapaxes(fbg,-2,-1)[:,:,:,nxs],axis=-2) #these are correct also for twins above |
|---|
| 1996 | # array(2,nAtom,nWave,2) & array(2,nAtom,nWave,6) & array(2,nAtom,nWave,12); sum on nOps |
|---|
| 1997 | dfadGf = np.sum(fa[:,:,:,nxs,nxs]*dGdf[0][nxs,:,:,:,:]-fb[:,:,:,nxs,nxs]*dGdf[1][nxs,:,:,:,:],axis=1) |
|---|
| 1998 | dfbdGf = np.sum(fb[:,:,:,nxs,nxs]*dGdf[0][nxs,:,:,:,:]+fa[:,:,:,nxs,nxs]*dGdf[1][nxs,:,:,:,:],axis=1) |
|---|
| 1999 | dfadGx = np.sum(fa[:,:,:,nxs,nxs]*dGdx[0][nxs,:,:,:,:]-fb[:,:,:,nxs,nxs]*dGdx[1][nxs,:,:,:,:],axis=1) |
|---|
| 2000 | dfbdGx = np.sum(fb[:,:,:,nxs,nxs]*dGdx[0][nxs,:,:,:,:]+fa[:,:,:,nxs,nxs]*dGdx[1][nxs,:,:,:,:],axis=1) |
|---|
| 2001 | dfadGu = np.sum(fa[:,:,:,nxs,nxs]*dGdu[0][nxs,:,:,:,:]-fb[:,:,:,nxs,nxs]*dGdu[1][nxs,:,:,:,:],axis=1) |
|---|
| 2002 | dfbdGu = np.sum(fb[:,:,:,nxs,nxs]*dGdu[0][nxs,:,:,:,:]+fa[:,:,:,nxs,nxs]*dGdu[1][nxs,:,:,:,:],axis=1) |
|---|
| 2003 | if not SGData['SGInv']: #Flack derivative |
|---|
| 2004 | dfadfl = np.sum(-FPP*Tcorr*sinp) |
|---|
| 2005 | dfbdfl = np.sum(FPP*Tcorr*cosp) |
|---|
| 2006 | else: |
|---|
| 2007 | dfadfl = 1.0 |
|---|
| 2008 | dfbdfl = 1.0 |
|---|
| 2009 | SA = fas[0]+fas[1] #float = A+A' |
|---|
| 2010 | SB = fbs[0]+fbs[1] #float = B+B' |
|---|
| 2011 | if 'P' in calcControls[hfx+'histType']: #checked perfect for centro & noncentro? |
|---|
| 2012 | dFdfl[iref] = -SA*dfadfl-SB*dfbdfl #array(nRef,) |
|---|
| 2013 | dFdfr[iref] = 2.*(fas[0]*dfadfr[0]+fas[1]*dfadfr[1])*Mdata/len(Uniq)+ \ |
|---|
| 2014 | 2.*(fbs[0]*dfbdfr[0]-fbs[1]*dfbdfr[1])*Mdata/len(Uniq) |
|---|
| 2015 | dFdx[iref] = 2.*(fas[0]*dfadx[0]+fas[1]*dfadx[1])+ \ |
|---|
| 2016 | 2.*(fbs[0]*dfbdx[0]+fbs[1]*dfbdx[1]) |
|---|
| 2017 | dFdui[iref] = 2.*(fas[0]*dfadui[0]+fas[1]*dfadui[1])+ \ |
|---|
| 2018 | 2.*(fbs[0]*dfbdui[0]-fbs[1]*dfbdui[1]) |
|---|
| 2019 | dFdua[iref] = 2.*(fas[0]*dfadua[0]+fas[1]*dfadua[1])+ \ |
|---|
| 2020 | 2.*(fbs[0]*dfbdua[0]+fbs[1]*dfbdua[1]) |
|---|
| 2021 | dFdGf[iref] = 2.*(fas[0]*dfadGf[0]+fas[1]*dfadGf[1])+ \ |
|---|
| 2022 | 2.*(fbs[0]*dfbdGf[0]+fbs[1]*dfbdGf[1]) |
|---|
| 2023 | dFdGx[iref] = 2.*(fas[0]*dfadGx[0]+fas[1]*dfadGx[1])+ \ |
|---|
| 2024 | 2.*(fbs[0]*dfbdGx[0]-fbs[1]*dfbdGx[1]) |
|---|
| 2025 | dFdGu[iref] = 2.*(fas[0]*dfadGu[0]+fas[1]*dfadGu[1])+ \ |
|---|
| 2026 | 2.*(fbs[0]*dfbdGu[0]+fbs[1]*dfbdGu[1]) |
|---|
| 2027 | else: #OK, I think |
|---|
| 2028 | dFdfr[iref] = 2.*(SA*dfadfr[0]+SA*dfadfr[1]+SB*dfbdfr[0]+SB*dfbdfr[1])*Mdata/len(Uniq) #array(nRef,nAtom) |
|---|
| 2029 | dFdx[iref] = 2.*(SA*dfadx[0]+SA*dfadx[1]+SB*dfbdx[0]+SB*dfbdx[1]) #array(nRef,nAtom,3) |
|---|
| 2030 | dFdui[iref] = 2.*(SA*dfadui[0]+SA*dfadui[1]+SB*dfbdui[0]+SB*dfbdui[1]) #array(nRef,nAtom) |
|---|
| 2031 | dFdua[iref] = 2.*(SA*dfadua[0]+SA*dfadua[1]+SB*dfbdua[0]+SB*dfbdua[1]) #array(nRef,nAtom,6) |
|---|
| 2032 | dFdfl[iref] = -SA*dfadfl-SB*dfbdfl #array(nRef,) |
|---|
| 2033 | |
|---|
| 2034 | dFdGf[iref] = 2.*(SA*dfadGf[0]+SB*dfbdGf[1]) #array(nRef,natom,nwave,2) |
|---|
| 2035 | dFdGx[iref] = 2.*(SA*dfadGx[0]+SB*dfbdGx[1]) #array(nRef,natom,nwave,6) |
|---|
| 2036 | dFdGu[iref] = 2.*(SA*dfadGu[0]+SB*dfbdGu[1]) #array(nRef,natom,nwave,12) |
|---|
| 2037 | if phfx+'BabA' in parmDict: |
|---|
| 2038 | dFdbab[iref] = 2.*fas[0]*np.array([np.sum(dfadba*dBabdA),np.sum(-dfadba*parmDict[phfx+'BabA']*SQfactor*dBabdA)]).T+ \ |
|---|
| 2039 | 2.*fbs[0]*np.array([np.sum(dfbdba*dBabdA),np.sum(-dfbdba*parmDict[phfx+'BabA']*SQfactor*dBabdA)]).T |
|---|
| 2040 | #loop over atoms - each dict entry is list of derivatives for all the reflections |
|---|
| 2041 | if not iref%100 : |
|---|
| 2042 | print (' %d derivative time %.4f\r'%(iref,time.time()-time0),end='') |
|---|
| 2043 | for i in range(len(Mdata)): #loop over atoms |
|---|
| 2044 | dFdvDict[pfx+'Afrac:'+str(i)] = dFdfr.T[i] |
|---|
| 2045 | dFdvDict[pfx+'dAx:'+str(i)] = dFdx.T[0][i] |
|---|
| 2046 | dFdvDict[pfx+'dAy:'+str(i)] = dFdx.T[1][i] |
|---|
| 2047 | dFdvDict[pfx+'dAz:'+str(i)] = dFdx.T[2][i] |
|---|
| 2048 | dFdvDict[pfx+'AUiso:'+str(i)] = dFdui.T[i] |
|---|
| 2049 | dFdvDict[pfx+'AU11:'+str(i)] = dFdua.T[0][i] |
|---|
| 2050 | dFdvDict[pfx+'AU22:'+str(i)] = dFdua.T[1][i] |
|---|
| 2051 | dFdvDict[pfx+'AU33:'+str(i)] = dFdua.T[2][i] |
|---|
| 2052 | dFdvDict[pfx+'AU12:'+str(i)] = dFdua.T[3][i] |
|---|
| 2053 | dFdvDict[pfx+'AU13:'+str(i)] = dFdua.T[4][i] |
|---|
| 2054 | dFdvDict[pfx+'AU23:'+str(i)] = dFdua.T[5][i] |
|---|
| 2055 | for j in range(FSSdata.shape[1]): #loop over waves Fzero & Fwid? |
|---|
| 2056 | dFdvDict[pfx+'Fsin:'+str(i)+':'+str(j)] = dFdGf.T[0][j][i] |
|---|
| 2057 | dFdvDict[pfx+'Fcos:'+str(i)+':'+str(j)] = dFdGf.T[1][j][i] |
|---|
| 2058 | nx = 0 |
|---|
| 2059 | if waveTypes[i] in ['Block','ZigZag']: |
|---|
| 2060 | nx = 1 |
|---|
| 2061 | for j in range(XSSdata.shape[1]-nx): #loop over waves |
|---|
| 2062 | dFdvDict[pfx+'Xsin:'+str(i)+':'+str(j+nx)] = dFdGx.T[0][j][i] |
|---|
| 2063 | dFdvDict[pfx+'Ysin:'+str(i)+':'+str(j+nx)] = dFdGx.T[1][j][i] |
|---|
| 2064 | dFdvDict[pfx+'Zsin:'+str(i)+':'+str(j+nx)] = dFdGx.T[2][j][i] |
|---|
| 2065 | dFdvDict[pfx+'Xcos:'+str(i)+':'+str(j+nx)] = dFdGx.T[3][j][i] |
|---|
| 2066 | dFdvDict[pfx+'Ycos:'+str(i)+':'+str(j+nx)] = dFdGx.T[4][j][i] |
|---|
| 2067 | dFdvDict[pfx+'Zcos:'+str(i)+':'+str(j+nx)] = dFdGx.T[5][j][i] |
|---|
| 2068 | for j in range(USSdata.shape[1]): #loop over waves |
|---|
| 2069 | dFdvDict[pfx+'U11sin:'+str(i)+':'+str(j)] = dFdGu.T[0][j][i] |
|---|
| 2070 | dFdvDict[pfx+'U22sin:'+str(i)+':'+str(j)] = dFdGu.T[1][j][i] |
|---|
| 2071 | dFdvDict[pfx+'U33sin:'+str(i)+':'+str(j)] = dFdGu.T[2][j][i] |
|---|
| 2072 | dFdvDict[pfx+'U12sin:'+str(i)+':'+str(j)] = dFdGu.T[3][j][i] |
|---|
| 2073 | dFdvDict[pfx+'U13sin:'+str(i)+':'+str(j)] = dFdGu.T[4][j][i] |
|---|
| 2074 | dFdvDict[pfx+'U23sin:'+str(i)+':'+str(j)] = dFdGu.T[5][j][i] |
|---|
| 2075 | dFdvDict[pfx+'U11cos:'+str(i)+':'+str(j)] = dFdGu.T[6][j][i] |
|---|
| 2076 | dFdvDict[pfx+'U22cos:'+str(i)+':'+str(j)] = dFdGu.T[7][j][i] |
|---|
| 2077 | dFdvDict[pfx+'U33cos:'+str(i)+':'+str(j)] = dFdGu.T[8][j][i] |
|---|
| 2078 | dFdvDict[pfx+'U12cos:'+str(i)+':'+str(j)] = dFdGu.T[9][j][i] |
|---|
| 2079 | dFdvDict[pfx+'U13cos:'+str(i)+':'+str(j)] = dFdGu.T[10][j][i] |
|---|
| 2080 | dFdvDict[pfx+'U23cos:'+str(i)+':'+str(j)] = dFdGu.T[11][j][i] |
|---|
| 2081 | |
|---|
| 2082 | dFdvDict[phfx+'Flack'] = 4.*dFdfl.T |
|---|
| 2083 | dFdvDict[phfx+'BabA'] = dFdbab.T[0] |
|---|
| 2084 | dFdvDict[phfx+'BabU'] = dFdbab.T[1] |
|---|
| 2085 | return dFdvDict |
|---|
| 2086 | |
|---|
| 2087 | def SStructureFactorDerv2(refDict,im,G,hfx,pfx,SGData,SSGData,calcControls,parmDict): |
|---|
| 2088 | ''' |
|---|
| 2089 | Compute super structure factor derivatives for all h,k,l,m for phase - no twins |
|---|
| 2090 | input: |
|---|
| 2091 | |
|---|
| 2092 | :param dict refDict: where |
|---|
| 2093 | 'RefList' list where each ref = h,k,l,m,it,d,... |
|---|
| 2094 | 'FF' dict of form factors - filled in below |
|---|
| 2095 | :param int im: = 1 (could be eliminated) |
|---|
| 2096 | :param np.array G: reciprocal metric tensor |
|---|
| 2097 | :param str hfx: histogram id string |
|---|
| 2098 | :param str pfx: phase id string |
|---|
| 2099 | :param dict SGData: space group info. dictionary output from SpcGroup |
|---|
| 2100 | :param dict SSGData: super space group info. |
|---|
| 2101 | :param dict calcControls: |
|---|
| 2102 | :param dict ParmDict: |
|---|
| 2103 | |
|---|
| 2104 | :returns: dict dFdvDict: dictionary of derivatives |
|---|
| 2105 | ''' |
|---|
| 2106 | |
|---|
| 2107 | trefDict = copy.deepcopy(refDict) |
|---|
| 2108 | dM = 1.e-4 |
|---|
| 2109 | dFdvDict = {} |
|---|
| 2110 | for parm in parmDict: |
|---|
| 2111 | if ':' not in parm: |
|---|
| 2112 | continue |
|---|
| 2113 | if parm.split(':')[2] in ['Tmin','Tmax','Xmax','Ymax','Zmax','Fzero','Fwid', |
|---|
| 2114 | 'MXsin','MXcos','MYsin','MYcos','MZsin','MZcos','AMx','AMy','AMz',]: |
|---|
| 2115 | parmDict[parm] += dM |
|---|
| 2116 | prefList = SStructureFactor(trefDict,G,hfx,pfx,SGData,SSGData,calcControls,parmDict) |
|---|
| 2117 | parmDict[parm] -= 2*dM |
|---|
| 2118 | mrefList = SStructureFactor(trefDict,G,hfx,pfx,SGData,SSGData,calcControls,parmDict) |
|---|
| 2119 | parmDict[parm] += dM |
|---|
| 2120 | dFdvDict[parm] = (prefList[:,9+im]-mrefList[:,9+im])/(2.*dM) |
|---|
| 2121 | return dFdvDict |
|---|
| 2122 | |
|---|
| 2123 | def SStructureFactorDervTw(refDict,im,G,hfx,pfx,SGData,SSGData,calcControls,parmDict): |
|---|
| 2124 | 'Needs a doc string' |
|---|
| 2125 | phfx = pfx.split(':')[0]+hfx |
|---|
| 2126 | ast = np.sqrt(np.diag(G)) |
|---|
| 2127 | Mast = twopisq*np.multiply.outer(ast,ast) |
|---|
| 2128 | SGInv = SGData['SGInv'] |
|---|
| 2129 | SGMT = np.array([ops[0].T for ops in SGData['SGOps']]) |
|---|
| 2130 | SSGMT = np.array([ops[0].T for ops in SSGData['SSGOps']]) |
|---|
| 2131 | SSGT = np.array([ops[1] for ops in SSGData['SSGOps']]) |
|---|
| 2132 | FFtables = calcControls['FFtables'] |
|---|
| 2133 | EFtables = calcControls['EFtables'] |
|---|
| 2134 | BLtables = calcControls['BLtables'] |
|---|
| 2135 | TwinLaw = np.array([[[1,0,0,0],[0,1,0,0],[0,0,1,0],[0,0,0,1]],]) |
|---|
| 2136 | TwDict = refDict.get('TwDict',{}) |
|---|
| 2137 | if 'S' in calcControls[hfx+'histType']: |
|---|
| 2138 | NTL = calcControls[phfx+'NTL'] |
|---|
| 2139 | NM = calcControls[phfx+'TwinNMN']+1 |
|---|
| 2140 | TwinLaw = calcControls[phfx+'TwinLaw'] |
|---|
| 2141 | TwinInv = list(np.where(calcControls[phfx+'TwinInv'],-1,1)) |
|---|
| 2142 | nTwin = len(TwinLaw) |
|---|
| 2143 | nRef = len(refDict['RefList']) |
|---|
| 2144 | Tdata,Mdata,Fdata,Xdata,dXdata,IAdata,Uisodata,Uijdata,Gdata = \ |
|---|
| 2145 | GetAtomFXU(pfx,calcControls,parmDict) |
|---|
| 2146 | if not Xdata.size: #no atoms in phase! |
|---|
| 2147 | return {} |
|---|
| 2148 | mSize = len(Mdata) #no. atoms |
|---|
| 2149 | waveTypes,FSSdata,XSSdata,USSdata,MSSdata = GetAtomSSFXU(pfx,calcControls,parmDict) |
|---|
| 2150 | ngl,nWaves,Fmod,Xmod,Umod,Mmod,glTau,glWt = G2mth.makeWaves(waveTypes,FSSdata,XSSdata,USSdata,MSSdata,Mast) #NB: Mmod is ReIm,Mxyz,Ntau,Natm |
|---|
| 2151 | waveShapes,SCtauF,SCtauX,SCtauU,UmodAB = G2mth.makeWavesDerv(ngl,waveTypes,FSSdata,XSSdata,USSdata,Mast) |
|---|
| 2152 | modQ = np.array([parmDict[pfx+'mV0'],parmDict[pfx+'mV1'],parmDict[pfx+'mV2']]) |
|---|
| 2153 | FF = np.zeros(len(Tdata)) |
|---|
| 2154 | if 'NC' in calcControls[hfx+'histType'] or 'NB' in calcControls[hfx+'histType']: |
|---|
| 2155 | FP,FPP = G2el.BlenResCW(Tdata,BLtables,parmDict[hfx+'Lam']) |
|---|
| 2156 | elif 'X' in calcControls[hfx+'histType']: |
|---|
| 2157 | FP = np.array([FFtables[El][hfx+'FP'] for El in Tdata]) |
|---|
| 2158 | FPP = np.array([FFtables[El][hfx+'FPP'] for El in Tdata]) |
|---|
| 2159 | elif 'SEC' in calcControls[hfx+'histType']: |
|---|
| 2160 | FP = np.zeros(len(Tdata)) |
|---|
| 2161 | FPP = np.zeros(len(Tdata)) |
|---|
| 2162 | Uij = np.array(G2lat.U6toUij(Uijdata)).T |
|---|
| 2163 | bij = Mast*Uij |
|---|
| 2164 | if not len(refDict['FF']): |
|---|
| 2165 | if 'N' in calcControls[hfx+'histType']: |
|---|
| 2166 | dat = G2el.getBLvalues(BLtables) #will need wave here for anom. neutron b's |
|---|
| 2167 | elif 'SEC' in calcControls[hfx+'histType']: |
|---|
| 2168 | dat = G2el.getFFvalues(EFtables,0.) |
|---|
| 2169 | else: |
|---|
| 2170 | dat = G2el.getFFvalues(FFtables,0.) |
|---|
| 2171 | refDict['FF']['El'] = list(dat.keys()) |
|---|
| 2172 | refDict['FF']['FF'] = np.zeros((len(refDict['RefList']),len(dat))) |
|---|
| 2173 | dFdvDict = {} |
|---|
| 2174 | dFdfr = np.zeros((nRef,nTwin,mSize)) |
|---|
| 2175 | dFdx = np.zeros((nRef,nTwin,mSize,3)) |
|---|
| 2176 | dFdui = np.zeros((nRef,nTwin,mSize)) |
|---|
| 2177 | dFdua = np.zeros((nRef,nTwin,mSize,6)) |
|---|
| 2178 | dFdbab = np.zeros((nRef,nTwin,2)) |
|---|
| 2179 | dFdtw = np.zeros((nRef,nTwin)) |
|---|
| 2180 | dFdGf = np.zeros((nRef,nTwin,mSize,FSSdata.shape[1])) |
|---|
| 2181 | dFdGx = np.zeros((nRef,nTwin,mSize,XSSdata.shape[1],3)) |
|---|
| 2182 | dFdGz = np.zeros((nRef,nTwin,mSize,5)) |
|---|
| 2183 | dFdGu = np.zeros((nRef,nTwin,mSize,USSdata.shape[1],6)) |
|---|
| 2184 | Flack = 1.0 |
|---|
| 2185 | if not SGData['SGInv'] and 'S' in calcControls[hfx+'histType'] and phfx+'Flack' in parmDict: |
|---|
| 2186 | Flack = 1.-2.*parmDict[phfx+'Flack'] |
|---|
| 2187 | time0 = time.time() |
|---|
| 2188 | nRef = len(refDict['RefList'])/100 |
|---|
| 2189 | for iref,refl in enumerate(refDict['RefList']): |
|---|
| 2190 | if 'T' in calcControls[hfx+'histType']: |
|---|
| 2191 | FP,FPP = G2el.BlenResCW(Tdata,BLtables,refl.T[12+im]) |
|---|
| 2192 | H = np.array(refl[:4]) |
|---|
| 2193 | HP = H[:3]+modQ*H[3:] #projected hklm to hkl |
|---|
| 2194 | H = np.inner(H.T,TwinLaw) #maybe array(4,nTwins) or (4) |
|---|
| 2195 | TwMask = np.any(H,axis=-1) |
|---|
| 2196 | if TwinLaw.shape[0] > 1 and TwDict: |
|---|
| 2197 | if iref in TwDict: |
|---|
| 2198 | for i in TwDict[iref]: |
|---|
| 2199 | for n in range(NTL): |
|---|
| 2200 | H[i+n*NM] = np.inner(TwinLaw[n*NM],np.array(TwDict[iref][i])*TwinInv[i+n*NM]) |
|---|
| 2201 | TwMask = np.any(H,axis=-1) |
|---|
| 2202 | SQ = 1./(2.*refl[4+im])**2 # or (sin(theta)/lambda)**2 |
|---|
| 2203 | SQfactor = 8.0*SQ*np.pi**2 |
|---|
| 2204 | dBabdA = np.exp(-parmDict[phfx+'BabU']*SQfactor) |
|---|
| 2205 | Bab = parmDict[phfx+'BabA']*dBabdA |
|---|
| 2206 | Tindx = np.array([refDict['FF']['El'].index(El) for El in Tdata]) |
|---|
| 2207 | FF = refDict['FF']['FF'][iref].T[Tindx] |
|---|
| 2208 | Uniq = np.inner(H,SSGMT) |
|---|
| 2209 | Phi = np.inner(H,SSGT) |
|---|
| 2210 | UniqP = np.inner(HP,SGMT) |
|---|
| 2211 | if SGInv: #if centro - expand HKL sets |
|---|
| 2212 | Uniq = np.vstack((Uniq,-Uniq)) |
|---|
| 2213 | Phi = np.hstack((Phi,-Phi)) |
|---|
| 2214 | UniqP = np.vstack((UniqP,-UniqP)) |
|---|
| 2215 | phase = twopi*(np.inner(Uniq[:,:3],(dXdata+Xdata).T)+Phi[:,nxs]) |
|---|
| 2216 | sinp = np.sin(phase) |
|---|
| 2217 | cosp = np.cos(phase) |
|---|
| 2218 | occ = Mdata*Fdata/Uniq.shape[0] |
|---|
| 2219 | biso = -SQfactor*Uisodata[:,nxs] |
|---|
| 2220 | Tiso = np.repeat(np.where(biso<1.,np.exp(biso),1.0),Uniq.shape[0]*len(TwinLaw),axis=1).T #ops x atoms |
|---|
| 2221 | HbH = -np.sum(UniqP[:,nxs,:3]*np.inner(UniqP[:,:3],bij),axis=-1) #ops x atoms |
|---|
| 2222 | Hij = np.array([Mast*np.multiply.outer(U[:3],U[:3]) for U in UniqP]) #atoms x 3x3 |
|---|
| 2223 | Hij = np.squeeze(np.reshape(np.array([G2lat.UijtoU6(uij) for uij in Hij]),(nTwin,-1,6))) |
|---|
| 2224 | Tuij = np.where(HbH<1.,np.exp(HbH),1.0) #ops x atoms |
|---|
| 2225 | Tcorr = np.reshape(Tiso,Tuij.shape)*Tuij*Mdata*Fdata/Uniq.shape[0] #ops x atoms |
|---|
| 2226 | fot = (FF+FP-Bab)*Tcorr #ops x atoms |
|---|
| 2227 | fotp = FPP*Tcorr #ops x atoms |
|---|
| 2228 | GfpuA = G2mth.Modulation(Uniq,UniqP,nWaves,Fmod,Xmod,Umod,glTau,glWt) #2 x sym X atoms |
|---|
| 2229 | dGdf,dGdx,dGdu,dGdz = G2mth.ModulationDerv(Uniq,UniqP,Hij,nWaves,waveShapes,Fmod,Xmod,UmodAB,SCtauF,SCtauX,SCtauU,glTau,glWt) |
|---|
| 2230 | # GfpuA is 2 x ops x atoms |
|---|
| 2231 | # derivs are: ops x atoms x waves x 2,6,12, or 5 parms as [real,imag] parts |
|---|
| 2232 | fa = np.array([((FF+FP).T-Bab).T*cosp*Tcorr,-Flack*FPP*sinp*Tcorr]) # array(2,nTwin,nEqv,nAtoms) |
|---|
| 2233 | fb = np.array([((FF+FP).T-Bab).T*sinp*Tcorr,Flack*FPP*cosp*Tcorr]) #or array(2,nEqv,nAtoms) |
|---|
| 2234 | fag = fa*GfpuA[0]-fb*GfpuA[1] |
|---|
| 2235 | fbg = fb*GfpuA[0]+fa*GfpuA[1] |
|---|
| 2236 | |
|---|
| 2237 | fas = np.sum(np.sum(fag,axis=1),axis=1) # 2 x twin |
|---|
| 2238 | fbs = np.sum(np.sum(fbg,axis=1),axis=1) |
|---|
| 2239 | fax = np.array([-fot*sinp,-fotp*cosp]) #positions; 2 x twin x ops x atoms |
|---|
| 2240 | fbx = np.array([fot*cosp,-fotp*sinp]) |
|---|
| 2241 | fax = fax*GfpuA[0]-fbx*GfpuA[1] |
|---|
| 2242 | fbx = fbx*GfpuA[0]+fax*GfpuA[1] |
|---|
| 2243 | #sum below is over Uniq |
|---|
| 2244 | dfadfr = np.sum(fag/occ,axis=1) #Fdata != 0 ever avoids /0. problem |
|---|
| 2245 | dfbdfr = np.sum(fbg/occ,axis=1) #Fdata != 0 avoids /0. problem |
|---|
| 2246 | dfadba = np.sum(-cosp*Tcorr[:,nxs],axis=1) |
|---|
| 2247 | dfbdba = np.sum(-sinp*Tcorr[:,nxs],axis=1) |
|---|
| 2248 | dfadui = np.sum(-SQfactor*fag,axis=1) |
|---|
| 2249 | dfbdui = np.sum(-SQfactor*fbg,axis=1) |
|---|
| 2250 | dfadx = np.array([np.sum(twopi*Uniq[it,:,:3]*np.swapaxes(fax,-2,-1)[:,it,:,:,nxs],axis=-2) for it in range(nTwin)]) |
|---|
| 2251 | dfbdx = np.array([np.sum(twopi*Uniq[it,:,:3]*np.swapaxes(fbx,-2,-1)[:,it,:,:,nxs],axis=-2) for it in range(nTwin)]) |
|---|
| 2252 | dfadua = np.array([np.sum(-Hij[it]*np.swapaxes(fag,-2,-1)[:,it,:,:,nxs],axis=-2) for it in range(nTwin)]) |
|---|
| 2253 | dfbdua = np.array([np.sum(-Hij[it]*np.swapaxes(fbg,-2,-1)[:,it,:,:,nxs],axis=-2) for it in range(nTwin)]) |
|---|
| 2254 | # array(2,nTwin,nAtom,3) & array(2,nTwin,nAtom,6) & array(2,nTwin,nAtom,12) |
|---|
| 2255 | dfadGf = np.sum(fa[:,it,:,:,nxs,nxs]*dGdf[0][nxs,nxs,:,:,:,:]-fb[:,it,:,:,nxs,nxs]*dGdf[1][nxs,nxs,:,:,:,:],axis=1) |
|---|
| 2256 | dfbdGf = np.sum(fb[:,it,:,:,nxs,nxs]*dGdf[0][nxs,nxs,:,:,:,:]+fa[:,it,:,:,nxs,nxs]*dGdf[1][nxs,nxs,:,:,:,:],axis=1) |
|---|
| 2257 | dfadGx = np.sum(fa[:,it,:,:,nxs,nxs]*dGdx[0][nxs,nxs,:,:,:,:]-fb[:,it,:,:,nxs,nxs]*dGdx[1][nxs,nxs,:,:,:,:],axis=1) |
|---|
| 2258 | dfbdGx = np.sum(fb[:,it,:,:,nxs,nxs]*dGdx[0][nxs,nxs,:,:,:,:]+fa[:,it,:,:,nxs,nxs]*dGdx[1][nxs,nxs,:,:,:,:],axis=1) |
|---|
| 2259 | dfadGz = np.sum(fa[:,it,:,0,nxs,nxs]*dGdz[0][nxs,nxs,:,:,:]-fb[:,it,:,0,nxs,nxs]*dGdz[1][nxs,nxs,:,:,:],axis=1) |
|---|
| 2260 | dfbdGz = np.sum(fb[:,it,:,0,nxs,nxs]*dGdz[0][nxs,nxs,:,:,:]+fa[:,it,:,0,nxs,nxs]*dGdz[1][nxs,nxs,:,:,:],axis=1) |
|---|
| 2261 | dfadGu = np.sum(fa[:,it,:,:,nxs,nxs]*dGdu[0][nxs,nxs,:,:,:,:]-fb[:,it,:,:,nxs,nxs]*dGdu[1][nxs,nxs,:,:,:,:],axis=1) |
|---|
| 2262 | dfbdGu = np.sum(fb[:,it,:,:,nxs,nxs]*dGdu[0][nxs,nxs,:,:,:,:]+fa[:,it,:,:,nxs,nxs]*dGdu[1][nxs,nxs,:,:,:,:],axis=1) |
|---|
| 2263 | # GSASIIpath.IPyBreak() |
|---|
| 2264 | #NB: the above have been checked against PA(1:10,1:2) in strfctr.for for Al2O3! |
|---|
| 2265 | SA = fas[0]+fas[1] #float = A+A' (might be array[nTwin]) |
|---|
| 2266 | SB = fbs[0]+fbs[1] #float = B+B' (might be array[nTwin]) |
|---|
| 2267 | dFdfr[iref] = [2.*TwMask[it]*(SA[it]*dfadfr[0][it]+SA[it]*dfadfr[1][it]+SB[it]*dfbdfr[0][it]+SB[it]*dfbdfr[1][it])*Mdata/len(Uniq[it]) for it in range(nTwin)] |
|---|
| 2268 | dFdx[iref] = [2.*TwMask[it]*(SA[it]*dfadx[it][0]+SA[it]*dfadx[it][1]+SB[it]*dfbdx[it][0]+SB[it]*dfbdx[it][1]) for it in range(nTwin)] |
|---|
| 2269 | dFdui[iref] = [2.*TwMask[it]*(SA[it]*dfadui[it][0]+SA[it]*dfadui[it][1]+SB[it]*dfbdui[it][0]+SB[it]*dfbdui[it][1]) for it in range(nTwin)] |
|---|
| 2270 | dFdua[iref] = [2.*TwMask[it]*(SA[it]*dfadua[it][0]+SA[it]*dfadua[it][1]+SB[it]*dfbdua[it][0]+SB[it]*dfbdua[it][1]) for it in range(nTwin)] |
|---|
| 2271 | dFdtw[iref] = np.sum(TwMask*fas,axis=0)**2+np.sum(TwMask*fbs,axis=0)**2 |
|---|
| 2272 | |
|---|
| 2273 | dFdGf[iref] = [2.*TwMask[it]*(SA[it]*dfadGf[1]+SB[it]*dfbdGf[1]) for it in range(nTwin)] |
|---|
| 2274 | dFdGx[iref] = [2.*TwMask[it]*(SA[it]*dfadGx[1]+SB[it]*dfbdGx[1]) for it in range(nTwin)] |
|---|
| 2275 | dFdGz[iref] = [2.*TwMask[it]*(SA[it]*dfadGz[1]+SB[it]*dfbdGz[1]) for it in range(nTwin)] |
|---|
| 2276 | dFdGu[iref] = [2.*TwMask[it]*(SA[it]*dfadGu[1]+SB[it]*dfbdGu[1]) for it in range(nTwin)] |
|---|
| 2277 | # GSASIIpath.IPyBreak() |
|---|
| 2278 | dFdbab[iref] = 2.*fas[0]*np.array([np.sum(dfadba*dBabdA),np.sum(-dfadba*parmDict[phfx+'BabA']*SQfactor*dBabdA)]).T+ \ |
|---|
| 2279 | 2.*fbs[0]*np.array([np.sum(dfbdba*dBabdA),np.sum(-dfbdba*parmDict[phfx+'BabA']*SQfactor*dBabdA)]).T |
|---|
| 2280 | #loop over atoms - each dict entry is list of derivatives for all the reflections |
|---|
| 2281 | if not iref%100 : |
|---|
| 2282 | print (' %d derivative time %.4f\r'%(iref,time.time()-time0),end='') |
|---|
| 2283 | for i in range(len(Mdata)): #loop over atoms |
|---|
| 2284 | dFdvDict[pfx+'Afrac:'+str(i)] = dFdfr.T[i] |
|---|
| 2285 | dFdvDict[pfx+'dAx:'+str(i)] = dFdx.T[0][i] |
|---|
| 2286 | dFdvDict[pfx+'dAy:'+str(i)] = dFdx.T[1][i] |
|---|
| 2287 | dFdvDict[pfx+'dAz:'+str(i)] = dFdx.T[2][i] |
|---|
| 2288 | dFdvDict[pfx+'AUiso:'+str(i)] = dFdui.T[i] |
|---|
| 2289 | dFdvDict[pfx+'AU11:'+str(i)] = dFdua.T[0][i] |
|---|
| 2290 | dFdvDict[pfx+'AU22:'+str(i)] = dFdua.T[1][i] |
|---|
| 2291 | dFdvDict[pfx+'AU33:'+str(i)] = dFdua.T[2][i] |
|---|
| 2292 | dFdvDict[pfx+'AU12:'+str(i)] = dFdua.T[3][i] |
|---|
| 2293 | dFdvDict[pfx+'AU13:'+str(i)] = dFdua.T[4][i] |
|---|
| 2294 | dFdvDict[pfx+'AU23:'+str(i)] = dFdua.T[5][i] |
|---|
| 2295 | for j in range(FSSdata.shape[1]): #loop over waves Fzero & Fwid? |
|---|
| 2296 | dFdvDict[pfx+'Fsin:'+str(i)+':'+str(j)] = dFdGf.T[0][j][i] |
|---|
| 2297 | dFdvDict[pfx+'Fcos:'+str(i)+':'+str(j)] = dFdGf.T[1][j][i] |
|---|
| 2298 | nx = 0 |
|---|
| 2299 | if waveTypes[i] in ['Block','ZigZag']: |
|---|
| 2300 | nx = 1 |
|---|
| 2301 | dFdvDict[pfx+'Tmin:'+str(i)+':0'] = dFdGz.T[0][i] #ZigZag/Block waves (if any) |
|---|
| 2302 | dFdvDict[pfx+'Tmax:'+str(i)+':0'] = dFdGz.T[1][i] |
|---|
| 2303 | dFdvDict[pfx+'Xmax:'+str(i)+':0'] = dFdGz.T[2][i] |
|---|
| 2304 | dFdvDict[pfx+'Ymax:'+str(i)+':0'] = dFdGz.T[3][i] |
|---|
| 2305 | dFdvDict[pfx+'Zmax:'+str(i)+':0'] = dFdGz.T[4][i] |
|---|
| 2306 | for j in range(XSSdata.shape[1]-nx): #loop over waves |
|---|
| 2307 | dFdvDict[pfx+'Xsin:'+str(i)+':'+str(j+nx)] = dFdGx.T[0][j][i] |
|---|
| 2308 | dFdvDict[pfx+'Ysin:'+str(i)+':'+str(j+nx)] = dFdGx.T[1][j][i] |
|---|
| 2309 | dFdvDict[pfx+'Zsin:'+str(i)+':'+str(j+nx)] = dFdGx.T[2][j][i] |
|---|
| 2310 | dFdvDict[pfx+'Xcos:'+str(i)+':'+str(j+nx)] = dFdGx.T[3][j][i] |
|---|
| 2311 | dFdvDict[pfx+'Ycos:'+str(i)+':'+str(j+nx)] = dFdGx.T[4][j][i] |
|---|
| 2312 | dFdvDict[pfx+'Zcos:'+str(i)+':'+str(j+nx)] = dFdGx.T[5][j][i] |
|---|
| 2313 | for j in range(USSdata.shape[1]): #loop over waves |
|---|
| 2314 | dFdvDict[pfx+'U11sin:'+str(i)+':'+str(j)] = dFdGu.T[0][j][i] |
|---|
| 2315 | dFdvDict[pfx+'U22sin:'+str(i)+':'+str(j)] = dFdGu.T[1][j][i] |
|---|
| 2316 | dFdvDict[pfx+'U33sin:'+str(i)+':'+str(j)] = dFdGu.T[2][j][i] |
|---|
| 2317 | dFdvDict[pfx+'U12sin:'+str(i)+':'+str(j)] = dFdGu.T[3][j][i] |
|---|
| 2318 | dFdvDict[pfx+'U13sin:'+str(i)+':'+str(j)] = dFdGu.T[4][j][i] |
|---|
| 2319 | dFdvDict[pfx+'U23sin:'+str(i)+':'+str(j)] = dFdGu.T[5][j][i] |
|---|
| 2320 | dFdvDict[pfx+'U11cos:'+str(i)+':'+str(j)] = dFdGu.T[6][j][i] |
|---|
| 2321 | dFdvDict[pfx+'U22cos:'+str(i)+':'+str(j)] = dFdGu.T[7][j][i] |
|---|
| 2322 | dFdvDict[pfx+'U33cos:'+str(i)+':'+str(j)] = dFdGu.T[8][j][i] |
|---|
| 2323 | dFdvDict[pfx+'U12cos:'+str(i)+':'+str(j)] = dFdGu.T[9][j][i] |
|---|
| 2324 | dFdvDict[pfx+'U13cos:'+str(i)+':'+str(j)] = dFdGu.T[10][j][i] |
|---|
| 2325 | dFdvDict[pfx+'U23cos:'+str(i)+':'+str(j)] = dFdGu.T[11][j][i] |
|---|
| 2326 | |
|---|
| 2327 | # GSASIIpath.IPyBreak() |
|---|
| 2328 | dFdvDict[phfx+'BabA'] = dFdbab.T[0] |
|---|
| 2329 | dFdvDict[phfx+'BabU'] = dFdbab.T[1] |
|---|
| 2330 | return dFdvDict |
|---|
| 2331 | |
|---|
| 2332 | def SCExtinction(ref,im,phfx,hfx,pfx,calcControls,parmDict,varyList): |
|---|
| 2333 | ''' Single crystal extinction function; returns extinction & derivative |
|---|
| 2334 | ''' |
|---|
| 2335 | extCor = 1.0 |
|---|
| 2336 | dervDict = {} |
|---|
| 2337 | dervCor = 1.0 |
|---|
| 2338 | if calcControls[phfx+'EType'] != 'None': |
|---|
| 2339 | SQ = 1/(4.*ref[4+im]**2) |
|---|
| 2340 | if 'C' in parmDict[hfx+'Type']: |
|---|
| 2341 | cos2T = 1.0-2.*SQ*parmDict[hfx+'Lam']**2 #cos(2theta) |
|---|
| 2342 | else: #'T' |
|---|
| 2343 | cos2T = 1.0-2.*SQ*ref[12+im]**2 #cos(2theta) |
|---|
| 2344 | if 'SXC' in parmDict[hfx+'Type'] or 'SEC' in parmDict[hfx+'Type']: |
|---|
| 2345 | AV = 7.9406e5/parmDict[pfx+'Vol']**2 #is 7.9406e5 constant right for electroms? |
|---|
| 2346 | PL = np.sqrt(1.0-cos2T**2)/parmDict[hfx+'Lam'] |
|---|
| 2347 | P12 = (calcControls[phfx+'Cos2TM']+cos2T**4)/(calcControls[phfx+'Cos2TM']+cos2T**2) |
|---|
| 2348 | PLZ = AV*P12*ref[9+im]*parmDict[hfx+'Lam']**2 |
|---|
| 2349 | elif 'SNT' in parmDict[hfx+'Type']: |
|---|
| 2350 | AV = 1.e7/parmDict[pfx+'Vol']**2 |
|---|
| 2351 | PL = SQ |
|---|
| 2352 | PLZ = AV*ref[9+im]*ref[12+im]**2 |
|---|
| 2353 | elif 'SNC' in parmDict[hfx+'Type']: |
|---|
| 2354 | AV = 1.e7/parmDict[pfx+'Vol']**2 |
|---|
| 2355 | PL = np.sqrt(1.0-cos2T**2)/parmDict[hfx+'Lam'] |
|---|
| 2356 | PLZ = AV*ref[9+im]*parmDict[hfx+'Lam']**2 |
|---|
| 2357 | |
|---|
| 2358 | if 'Primary' in calcControls[phfx+'EType']: |
|---|
| 2359 | PLZ *= 1.5 |
|---|
| 2360 | else: |
|---|
| 2361 | if 'C' in parmDict[hfx+'Type']: |
|---|
| 2362 | PLZ *= calcControls[phfx+'Tbar'] |
|---|
| 2363 | else: #'T' |
|---|
| 2364 | PLZ *= ref[13+im] #t-bar |
|---|
| 2365 | if 'Primary' in calcControls[phfx+'EType']: |
|---|
| 2366 | PLZ *= 1.5 |
|---|
| 2367 | PSIG = parmDict[phfx+'Ep'] |
|---|
| 2368 | elif 'I & II' in calcControls[phfx+'EType']: |
|---|
| 2369 | PSIG = parmDict[phfx+'Eg']/np.sqrt(1.+(parmDict[phfx+'Es']*PL/parmDict[phfx+'Eg'])**2) |
|---|
| 2370 | elif 'Type II' in calcControls[phfx+'EType']: |
|---|
| 2371 | PSIG = parmDict[phfx+'Es'] |
|---|
| 2372 | else: # 'Secondary Type I' |
|---|
| 2373 | PSIG = parmDict[phfx+'Eg']/PL |
|---|
| 2374 | |
|---|
| 2375 | AG = 0.58+0.48*cos2T+0.24*cos2T**2 |
|---|
| 2376 | AL = 0.025+0.285*cos2T |
|---|
| 2377 | BG = 0.02-0.025*cos2T |
|---|
| 2378 | BL = 0.15-0.2*(0.75-cos2T)**2 |
|---|
| 2379 | if cos2T < 0.: |
|---|
| 2380 | BL = -0.45*cos2T |
|---|
| 2381 | CG = 2. |
|---|
| 2382 | CL = 2. |
|---|
| 2383 | PF = PLZ*PSIG |
|---|
| 2384 | |
|---|
| 2385 | if 'Gaussian' in calcControls[phfx+'EApprox']: |
|---|
| 2386 | PF4 = 1.+CG*PF+AG*PF**2/(1.+BG*PF) |
|---|
| 2387 | extCor = np.sqrt(PF4) |
|---|
| 2388 | PF3 = 0.5*(CG+2.*AG*PF/(1.+BG*PF)-AG*PF**2*BG/(1.+BG*PF)**2)/(PF4*extCor) |
|---|
| 2389 | else: |
|---|
| 2390 | PF4 = 1.+CL*PF+AL*PF**2/(1.+BL*PF) |
|---|
| 2391 | extCor = np.sqrt(PF4) |
|---|
| 2392 | PF3 = 0.5*(CL+2.*AL*PF/(1.+BL*PF)-AL*PF**2*BL/(1.+BL*PF)**2)/(PF4*extCor) |
|---|
| 2393 | |
|---|
| 2394 | dervCor = (1.+PF)*PF3 #extinction corr for other derivatives |
|---|
| 2395 | if 'Primary' in calcControls[phfx+'EType'] and phfx+'Ep' in varyList: |
|---|
| 2396 | dervDict[phfx+'Ep'] = -ref[7+im]*PLZ*PF3 |
|---|
| 2397 | if 'II' in calcControls[phfx+'EType'] and phfx+'Es' in varyList: |
|---|
| 2398 | dervDict[phfx+'Es'] = -ref[7+im]*PLZ*PF3*(PSIG/parmDict[phfx+'Es'])**3 |
|---|
| 2399 | if 'I' in calcControls[phfx+'EType'] and phfx+'Eg' in varyList: |
|---|
| 2400 | dervDict[phfx+'Eg'] = -ref[7+im]*PLZ*PF3*(PSIG/parmDict[phfx+'Eg'])**3*PL**2 |
|---|
| 2401 | |
|---|
| 2402 | return 1./extCor,dervDict,dervCor |
|---|
| 2403 | |
|---|
| 2404 | def Dict2Values(parmdict, varylist): |
|---|
| 2405 | '''Use before call to leastsq to setup list of values for the parameters |
|---|
| 2406 | in parmdict, as selected by key in varylist''' |
|---|
| 2407 | return [parmdict[key] for key in varylist] |
|---|
| 2408 | |
|---|
| 2409 | def Values2Dict(parmdict, varylist, values): |
|---|
| 2410 | ''' Use after call to leastsq to update the parameter dictionary with |
|---|
| 2411 | values corresponding to keys in varylist''' |
|---|
| 2412 | parmdict.update(zip(varylist,values)) |
|---|
| 2413 | |
|---|
| 2414 | def GetNewCellParms(parmDict,varyList): |
|---|
| 2415 | '''Compute unit cell tensor terms from varied Aij and Dij values. |
|---|
| 2416 | Terms are included in the dict only if Aij or Dij is varied. |
|---|
| 2417 | ''' |
|---|
| 2418 | newCellDict = {} |
|---|
| 2419 | Anames = ['A'+str(i) for i in range(6)] |
|---|
| 2420 | Ddict = dict(zip(['D11','D22','D33','D12','D13','D23'],Anames)) |
|---|
| 2421 | for item in varyList: |
|---|
| 2422 | keys = item.split(':') |
|---|
| 2423 | if keys[2] in Ddict: |
|---|
| 2424 | key = keys[0]+'::'+Ddict[keys[2]] #key is e.g. '0::A0' |
|---|
| 2425 | parm = keys[0]+'::'+keys[2] #parm is e.g. '0::D11' |
|---|
| 2426 | newCellDict[parm] = [key,parmDict[key]+parmDict[item]] |
|---|
| 2427 | return newCellDict # is e.g. {'0::D11':A0-D11} |
|---|
| 2428 | |
|---|
| 2429 | def ApplyXYZshifts(parmDict,varyList): |
|---|
| 2430 | ''' |
|---|
| 2431 | takes atom x,y,z shift and applies it to corresponding atom x,y,z value |
|---|
| 2432 | |
|---|
| 2433 | :param dict parmDict: parameter dictionary |
|---|
| 2434 | :param list varyList: list of variables (not used!) |
|---|
| 2435 | :returns: newAtomDict - dictionary of new atomic coordinate names & values; key is parameter shift name |
|---|
| 2436 | |
|---|
| 2437 | ''' |
|---|
| 2438 | newAtomDict = {} |
|---|
| 2439 | for item in parmDict: |
|---|
| 2440 | if 'dA' in item: |
|---|
| 2441 | parm = ''.join(item.split('d')) |
|---|
| 2442 | parmDict[parm] += parmDict[item] |
|---|
| 2443 | newAtomDict[item] = [parm,parmDict[parm]] |
|---|
| 2444 | return newAtomDict |
|---|
| 2445 | |
|---|
| 2446 | def SHTXcal(refl,im,g,pfx,hfx,SGData,calcControls,parmDict): |
|---|
| 2447 | 'Spherical harmonics texture' |
|---|
| 2448 | IFCoup = 'Bragg' in calcControls[hfx+'instType'] |
|---|
| 2449 | if 'T' in calcControls[hfx+'histType']: |
|---|
| 2450 | tth = parmDict[hfx+'2-theta'] |
|---|
| 2451 | else: |
|---|
| 2452 | tth = refl[5+im] |
|---|
| 2453 | odfCor = 1.0 |
|---|
| 2454 | H = refl[:3] |
|---|
| 2455 | cell = G2lat.Gmat2cell(g) |
|---|
| 2456 | Sangls = [parmDict[pfx+'SH omega'],parmDict[pfx+'SH chi'],parmDict[pfx+'SH phi']] |
|---|
| 2457 | Gangls = [parmDict[hfx+'Phi'],parmDict[hfx+'Chi'],parmDict[hfx+'Omega'],parmDict[hfx+'Azimuth']] |
|---|
| 2458 | phi,beta = G2lat.CrsAng(H,cell,SGData) |
|---|
| 2459 | psi,gam,x,x = G2lat.SamAng(tth/2.,Gangls,Sangls,IFCoup) #ignore 2 sets of angle derivs. |
|---|
| 2460 | SHnames = G2lat.GenSHCoeff(SGData['SGLaue'],parmDict[pfx+'SHmodel'],parmDict[pfx+'SHorder']) |
|---|
| 2461 | for item in SHnames: |
|---|
| 2462 | L,M,N = eval(item.strip('C')) |
|---|
| 2463 | Kcl = G2lat.GetKcl(L,N,SGData['SGLaue'],phi,beta) |
|---|
| 2464 | Ksl,x,x = G2lat.GetKsl(L,M,parmDict[pfx+'SHmodel'],psi,gam) |
|---|
| 2465 | Lnorm = G2lat.Lnorm(L) |
|---|
| 2466 | odfCor += parmDict[pfx+item]*Lnorm*Kcl*Ksl |
|---|
| 2467 | return odfCor |
|---|
| 2468 | |
|---|
| 2469 | def SHTXcalDerv(refl,im,g,pfx,hfx,SGData,calcControls,parmDict): |
|---|
| 2470 | 'Spherical harmonics texture derivatives' |
|---|
| 2471 | if 'T' in calcControls[hfx+'histType']: |
|---|
| 2472 | tth = parmDict[hfx+'2-theta'] |
|---|
| 2473 | else: |
|---|
| 2474 | tth = refl[5+im] |
|---|
| 2475 | IFCoup = 'Bragg' in calcControls[hfx+'instType'] |
|---|
| 2476 | odfCor = 1.0 |
|---|
| 2477 | dFdODF = {} |
|---|
| 2478 | dFdSA = [0,0,0] |
|---|
| 2479 | H = refl[:3] |
|---|
| 2480 | cell = G2lat.Gmat2cell(g) |
|---|
| 2481 | Sangls = [parmDict[pfx+'SH omega'],parmDict[pfx+'SH chi'],parmDict[pfx+'SH phi']] |
|---|
| 2482 | Gangls = [parmDict[hfx+'Phi'],parmDict[hfx+'Chi'],parmDict[hfx+'Omega'],parmDict[hfx+'Azimuth']] |
|---|
| 2483 | phi,beta = G2lat.CrsAng(H,cell,SGData) |
|---|
| 2484 | psi,gam,dPSdA,dGMdA = G2lat.SamAng(tth/2.,Gangls,Sangls,IFCoup) |
|---|
| 2485 | SHnames = G2lat.GenSHCoeff(SGData['SGLaue'],parmDict[pfx+'SHmodel'],parmDict[pfx+'SHorder']) |
|---|
| 2486 | for item in SHnames: |
|---|
| 2487 | L,M,N = eval(item.strip('C')) |
|---|
| 2488 | Kcl = G2lat.GetKcl(L,N,SGData['SGLaue'],phi,beta) |
|---|
| 2489 | Ksl,dKsdp,dKsdg = G2lat.GetKsl(L,M,parmDict[pfx+'SHmodel'],psi,gam) |
|---|
| 2490 | Lnorm = G2lat.Lnorm(L) |
|---|
| 2491 | odfCor += parmDict[pfx+item]*Lnorm*Kcl*Ksl |
|---|
| 2492 | dFdODF[pfx+item] = Lnorm*Kcl*Ksl |
|---|
| 2493 | for i in range(3): |
|---|
| 2494 | dFdSA[i] += parmDict[pfx+item]*Lnorm*Kcl*(dKsdp*dPSdA[i]+dKsdg*dGMdA[i]) |
|---|
| 2495 | return odfCor,dFdODF,dFdSA |
|---|
| 2496 | |
|---|
| 2497 | def SHPOcal(refl,im,g,phfx,hfx,SGData,calcControls,parmDict): |
|---|
| 2498 | 'spherical harmonics preferred orientation (cylindrical symmetry only)' |
|---|
| 2499 | if 'T' in calcControls[hfx+'histType']: |
|---|
| 2500 | tth = parmDict[hfx+'2-theta'] |
|---|
| 2501 | else: |
|---|
| 2502 | tth = refl[5+im] |
|---|
| 2503 | odfCor = 1.0 |
|---|
| 2504 | H = refl[:3] |
|---|
| 2505 | cell = G2lat.Gmat2cell(g) |
|---|
| 2506 | Sangls = [0.,0.,0.] |
|---|
| 2507 | if 'Bragg' in calcControls[hfx+'instType']: |
|---|
| 2508 | Gangls = [0.,90.,0.,parmDict[hfx+'Azimuth']] |
|---|
| 2509 | IFCoup = True |
|---|
| 2510 | else: |
|---|
| 2511 | Gangls = [parmDict[hfx+'Phi'],parmDict[hfx+'Chi'],parmDict[hfx+'Omega'],parmDict[hfx+'Azimuth']] |
|---|
| 2512 | IFCoup = False |
|---|
| 2513 | phi,beta = G2lat.CrsAng(H,cell,SGData) |
|---|
| 2514 | psi,gam,x,x = G2lat.SamAng(tth/2.,Gangls,Sangls,IFCoup) #ignore 2 sets of angle derivs. |
|---|
| 2515 | SHnames = calcControls[phfx+'SHnames'] |
|---|
| 2516 | for item in SHnames: |
|---|
| 2517 | L,N = eval(item.strip('C')) |
|---|
| 2518 | Kcl = G2lat.GetKcl(L,N,SGData['SGLaue'],phi,beta) |
|---|
| 2519 | Ksl,x,x = G2lat.GetKsl(L,0,'0',psi,gam) |
|---|
| 2520 | Lnorm = G2lat.Lnorm(L) |
|---|
| 2521 | odfCor += parmDict[phfx+item]*Lnorm*Kcl*Ksl |
|---|
| 2522 | return np.squeeze(odfCor) |
|---|
| 2523 | |
|---|
| 2524 | def SHPOcalDerv(refl,im,g,phfx,hfx,SGData,calcControls,parmDict): |
|---|
| 2525 | 'spherical harmonics preferred orientation derivatives (cylindrical symmetry only)' |
|---|
| 2526 | if 'T' in calcControls[hfx+'histType']: |
|---|
| 2527 | tth = parmDict[hfx+'2-theta'] |
|---|
| 2528 | else: |
|---|
| 2529 | tth = refl[5+im] |
|---|
| 2530 | odfCor = 1.0 |
|---|
| 2531 | dFdODF = {} |
|---|
| 2532 | H = refl[:3] |
|---|
| 2533 | cell = G2lat.Gmat2cell(g) |
|---|
| 2534 | Sangls = [0.,0.,0.] |
|---|
| 2535 | if 'Bragg' in calcControls[hfx+'instType']: |
|---|
| 2536 | Gangls = [0.,90.,0.,parmDict[hfx+'Azimuth']] |
|---|
| 2537 | IFCoup = True |
|---|
| 2538 | else: |
|---|
| 2539 | Gangls = [parmDict[hfx+'Phi'],parmDict[hfx+'Chi'],parmDict[hfx+'Omega'],parmDict[hfx+'Azimuth']] |
|---|
| 2540 | IFCoup = False |
|---|
| 2541 | phi,beta = G2lat.CrsAng(H,cell,SGData) |
|---|
| 2542 | psi,gam,x,x = G2lat.SamAng(tth/2.,Gangls,Sangls,IFCoup) #ignore 2 sets of angle derivs. |
|---|
| 2543 | SHnames = calcControls[phfx+'SHnames'] |
|---|
| 2544 | for item in SHnames: |
|---|
| 2545 | L,N = eval(item.strip('C')) |
|---|
| 2546 | Kcl = G2lat.GetKcl(L,N,SGData['SGLaue'],phi,beta) |
|---|
| 2547 | Ksl,x,x = G2lat.GetKsl(L,0,'0',psi,gam) |
|---|
| 2548 | Lnorm = G2lat.Lnorm(L) |
|---|
| 2549 | odfCor += parmDict[phfx+item]*Lnorm*Kcl*Ksl |
|---|
| 2550 | dFdODF[phfx+item] = Kcl*Ksl*Lnorm |
|---|
| 2551 | return odfCor,dFdODF |
|---|
| 2552 | |
|---|
| 2553 | def GetPrefOri(uniq,G,g,phfx,hfx,SGData,calcControls,parmDict): |
|---|
| 2554 | 'March-Dollase preferred orientation correction' |
|---|
| 2555 | POcorr = 1.0 |
|---|
| 2556 | MD = parmDict[phfx+'MD'] |
|---|
| 2557 | if MD != 1.0: |
|---|
| 2558 | MDAxis = calcControls[phfx+'MDAxis'] |
|---|
| 2559 | sumMD = 0 |
|---|
| 2560 | for H in uniq: |
|---|
| 2561 | cosP,sinP = G2lat.CosSinAngle(H,MDAxis,G) |
|---|
| 2562 | A = 1.0/np.sqrt((MD*cosP)**2+sinP**2/MD) |
|---|
| 2563 | sumMD += A**3 |
|---|
| 2564 | POcorr = sumMD/len(uniq) |
|---|
| 2565 | return POcorr |
|---|
| 2566 | |
|---|
| 2567 | def GetPrefOriDerv(refl,im,uniq,G,g,phfx,hfx,SGData,calcControls,parmDict): |
|---|
| 2568 | 'Needs a doc string' |
|---|
| 2569 | POcorr = 1.0 |
|---|
| 2570 | POderv = {} |
|---|
| 2571 | if calcControls[phfx+'poType'] == 'MD': |
|---|
| 2572 | MD = parmDict[phfx+'MD'] |
|---|
| 2573 | MDAxis = calcControls[phfx+'MDAxis'] |
|---|
| 2574 | sumMD = 0 |
|---|
| 2575 | sumdMD = 0 |
|---|
| 2576 | for H in uniq: |
|---|
| 2577 | cosP,sinP = G2lat.CosSinAngle(H,MDAxis,G) |
|---|
| 2578 | A = 1.0/np.sqrt((MD*cosP)**2+sinP**2/MD) |
|---|
| 2579 | sumMD += A**3 |
|---|
| 2580 | sumdMD -= (1.5*A**5)*(2.0*MD*cosP**2-(sinP/MD)**2) |
|---|
| 2581 | POcorr = sumMD/len(uniq) |
|---|
| 2582 | POderv[phfx+'MD'] = sumdMD/len(uniq) |
|---|
| 2583 | else: #spherical harmonics |
|---|
| 2584 | if calcControls[phfx+'SHord']: |
|---|
| 2585 | POcorr,POderv = SHPOcalDerv(refl,im,g,phfx,hfx,SGData,calcControls,parmDict) |
|---|
| 2586 | return POcorr,POderv |
|---|
| 2587 | |
|---|
| 2588 | def GetAbsorb(refl,im,hfx,calcControls,parmDict): |
|---|
| 2589 | 'Needs a doc string' |
|---|
| 2590 | if 'Debye' in calcControls[hfx+'instType']: |
|---|
| 2591 | if 'T' in calcControls[hfx+'histType']: |
|---|
| 2592 | return G2pwd.Absorb('Cylinder',parmDict[hfx+'Absorption']*refl[14+im],abs(parmDict[hfx+'2-theta']),0,0) |
|---|
| 2593 | else: |
|---|
| 2594 | return G2pwd.Absorb('Cylinder',parmDict[hfx+'Absorption'],refl[5+im],0,0) |
|---|
| 2595 | else: |
|---|
| 2596 | return G2pwd.SurfaceRough(parmDict[hfx+'SurfRoughA'],parmDict[hfx+'SurfRoughB'],refl[5+im]) |
|---|
| 2597 | |
|---|
| 2598 | def GetAbsorbDerv(refl,im,hfx,calcControls,parmDict): |
|---|
| 2599 | 'Needs a doc string' |
|---|
| 2600 | if 'Debye' in calcControls[hfx+'instType']: |
|---|
| 2601 | if 'T' in calcControls[hfx+'histType']: |
|---|
| 2602 | return G2pwd.AbsorbDerv('Cylinder',parmDict[hfx+'Absorption']*refl[14+im],abs(parmDict[hfx+'2-theta']),0,0) |
|---|
| 2603 | else: |
|---|
| 2604 | return G2pwd.AbsorbDerv('Cylinder',parmDict[hfx+'Absorption'],refl[5+im],0,0) |
|---|
| 2605 | else: |
|---|
| 2606 | return np.array(G2pwd.SurfaceRoughDerv(parmDict[hfx+'SurfRoughA'],parmDict[hfx+'SurfRoughB'],refl[5+im])) |
|---|
| 2607 | |
|---|
| 2608 | def GetPwdrExt(refl,im,pfx,phfx,hfx,calcControls,parmDict): |
|---|
| 2609 | 'Needs a doc string' |
|---|
| 2610 | coef = np.array([-0.5,0.25,-0.10416667,0.036458333,-0.0109375,2.8497409E-3]) |
|---|
| 2611 | pi2 = np.sqrt(2./np.pi) |
|---|
| 2612 | if 'T' in calcControls[hfx+'histType']: |
|---|
| 2613 | sth2 = sind(abs(parmDict[hfx+'2-theta'])/2.)**2 |
|---|
| 2614 | wave = refl[14+im] |
|---|
| 2615 | else: #'C'W |
|---|
| 2616 | sth2 = sind(refl[5+im]/2.)**2 |
|---|
| 2617 | wave = parmDict.get(hfx+'Lam',parmDict.get(hfx+'Lam1',1.0)) |
|---|
| 2618 | c2th = 1.-2.0*sth2 |
|---|
| 2619 | flv2 = refl[9+im]*(wave/parmDict[pfx+'Vol'])**2 |
|---|
| 2620 | if 'X' in calcControls[hfx+'histType']: |
|---|
| 2621 | flv2 *= 0.079411*(1.0+c2th**2)/2.0 |
|---|
| 2622 | xfac = flv2*parmDict[phfx+'Extinction'] |
|---|
| 2623 | exb = 1.0 |
|---|
| 2624 | if xfac > -1.: |
|---|
| 2625 | exb = 1./np.sqrt(1.+xfac) |
|---|
| 2626 | exl = 1.0 |
|---|
| 2627 | if 0 < xfac <= 1.: |
|---|
| 2628 | xn = np.array([xfac**(i+1) for i in range(6)]) |
|---|
| 2629 | exl += np.sum(xn*coef) |
|---|
| 2630 | elif xfac > 1.: |
|---|
| 2631 | xfac2 = 1./np.sqrt(xfac) |
|---|
| 2632 | exl = pi2*(1.-0.125/xfac)*xfac2 |
|---|
| 2633 | return exb*sth2+exl*(1.-sth2) |
|---|
| 2634 | |
|---|
| 2635 | def GetPwdrExtDerv(refl,im,pfx,phfx,hfx,calcControls,parmDict): |
|---|
| 2636 | 'Needs a doc string' |
|---|
| 2637 | coef = np.array([-0.5,0.25,-0.10416667,0.036458333,-0.0109375,2.8497409E-3]) |
|---|
| 2638 | pi2 = np.sqrt(2./np.pi) |
|---|
| 2639 | if 'T' in calcControls[hfx+'histType']: |
|---|
| 2640 | sth2 = sind(abs(parmDict[hfx+'2-theta'])/2.)**2 |
|---|
| 2641 | wave = refl[14+im] |
|---|
| 2642 | else: #'C'W |
|---|
| 2643 | sth2 = sind(refl[5+im]/2.)**2 |
|---|
| 2644 | wave = parmDict.get(hfx+'Lam',parmDict.get(hfx+'Lam1',1.0)) |
|---|
| 2645 | c2th = 1.-2.0*sth2 |
|---|
| 2646 | flv2 = refl[9+im]*(wave/parmDict[pfx+'Vol'])**2 |
|---|
| 2647 | if 'X' in calcControls[hfx+'histType']: |
|---|
| 2648 | flv2 *= 0.079411*(1.0+c2th**2)/2.0 |
|---|
| 2649 | xfac = flv2*parmDict[phfx+'Extinction'] |
|---|
| 2650 | dbde = -500.*flv2 |
|---|
| 2651 | if xfac > -1.: |
|---|
| 2652 | dbde = -0.5*flv2/np.sqrt(1.+xfac)**3 |
|---|
| 2653 | dlde = 0. |
|---|
| 2654 | if 0 < xfac <= 1.: |
|---|
| 2655 | xn = np.array([i*flv2*xfac**i for i in [1,2,3,4,5,6]]) |
|---|
| 2656 | dlde = np.sum(xn*coef)/xfac |
|---|
| 2657 | elif xfac > 1.: |
|---|
| 2658 | xfac2 = 1./np.sqrt(xfac) |
|---|
| 2659 | dlde = 0.5*flv2*pi2*xfac2*(-1./xfac+0.375/xfac**2) |
|---|
| 2660 | |
|---|
| 2661 | return dbde*sth2+dlde*(1.-sth2) |
|---|
| 2662 | |
|---|
| 2663 | def GetIntensityCorr(refl,im,uniq,G,g,pfx,phfx,hfx,SGData,calcControls,parmDict): |
|---|
| 2664 | 'Needs a doc string' #need powder extinction! |
|---|
| 2665 | parmDict[phfx+'Scale'] = max(1.e-12,parmDict[phfx+'Scale']) #put floor on phase fraction scale |
|---|
| 2666 | parmDict[hfx+'Scale'] = max(1.e-12,parmDict[hfx+'Scale']) #put floor on histogram scale |
|---|
| 2667 | Icorr = parmDict[phfx+'Scale']*parmDict[hfx+'Scale']*refl[3+im] #scale*multiplicity |
|---|
| 2668 | if 'XC' in parmDict[hfx+'Type']: |
|---|
| 2669 | Icorr *= G2pwd.Polarization(parmDict[hfx+'Polariz.'],refl[5+im],parmDict[hfx+'Azimuth'])[0] |
|---|
| 2670 | POcorr = 1.0 |
|---|
| 2671 | if pfx+'SHorder' in parmDict: #generalized spherical harmonics texture - takes precidence |
|---|
| 2672 | POcorr = SHTXcal(refl,im,g,pfx,hfx,SGData,calcControls,parmDict) |
|---|
| 2673 | elif calcControls[phfx+'poType'] == 'MD': #March-Dollase |
|---|
| 2674 | POcorr = GetPrefOri(uniq,G,g,phfx,hfx,SGData,calcControls,parmDict) |
|---|
| 2675 | elif calcControls[phfx+'SHord']: #cylindrical spherical harmonics |
|---|
| 2676 | POcorr = SHPOcal(refl,im,g,phfx,hfx,SGData,calcControls,parmDict) |
|---|
| 2677 | Icorr *= POcorr |
|---|
| 2678 | AbsCorr = 1.0 |
|---|
| 2679 | AbsCorr = GetAbsorb(refl,im,hfx,calcControls,parmDict) |
|---|
| 2680 | Icorr *= AbsCorr |
|---|
| 2681 | ExtCorr = GetPwdrExt(refl,im,pfx,phfx,hfx,calcControls,parmDict) |
|---|
| 2682 | Icorr *= ExtCorr |
|---|
| 2683 | return Icorr,POcorr,AbsCorr,ExtCorr |
|---|
| 2684 | |
|---|
| 2685 | def GetIntensityDerv(refl,im,wave,uniq,G,g,pfx,phfx,hfx,SGData,calcControls,parmDict): |
|---|
| 2686 | 'Needs a doc string' #need powder extinction derivs! |
|---|
| 2687 | dIdsh = 1./parmDict[hfx+'Scale'] |
|---|
| 2688 | dIdsp = 1./parmDict[phfx+'Scale'] |
|---|
| 2689 | if 'XC' in parmDict[hfx+'Type']: |
|---|
| 2690 | pola,dIdPola = G2pwd.Polarization(parmDict[hfx+'Polariz.'],refl[5+im],parmDict[hfx+'Azimuth']) |
|---|
| 2691 | dIdPola /= pola |
|---|
| 2692 | else: #'N' |
|---|
| 2693 | dIdPola = 0.0 |
|---|
| 2694 | dFdODF = {} |
|---|
| 2695 | dFdSA = [0,0,0] |
|---|
| 2696 | dIdPO = {} |
|---|
| 2697 | if pfx+'SHorder' in parmDict: |
|---|
| 2698 | odfCor,dFdODF,dFdSA = SHTXcalDerv(refl,im,g,pfx,hfx,SGData,calcControls,parmDict) |
|---|
| 2699 | for iSH in dFdODF: |
|---|
| 2700 | dFdODF[iSH] /= odfCor |
|---|
| 2701 | for i in range(3): |
|---|
| 2702 | dFdSA[i] /= odfCor |
|---|
| 2703 | elif calcControls[phfx+'poType'] == 'MD' or calcControls[phfx+'SHord']: |
|---|
| 2704 | POcorr,dIdPO = GetPrefOriDerv(refl,im,uniq,G,g,phfx,hfx,SGData,calcControls,parmDict) |
|---|
| 2705 | for iPO in dIdPO: |
|---|
| 2706 | dIdPO[iPO] /= POcorr |
|---|
| 2707 | if 'T' in parmDict[hfx+'Type']: |
|---|
| 2708 | dFdAb = GetAbsorbDerv(refl,im,hfx,calcControls,parmDict)*wave/refl[16+im] #wave/abs corr |
|---|
| 2709 | dFdEx = GetPwdrExtDerv(refl,im,pfx,phfx,hfx,calcControls,parmDict)/refl[17+im] #/ext corr |
|---|
| 2710 | else: |
|---|
| 2711 | dFdAb = GetAbsorbDerv(refl,im,hfx,calcControls,parmDict)*wave/refl[13+im] #wave/abs corr |
|---|
| 2712 | dFdEx = GetPwdrExtDerv(refl,im,pfx,phfx,hfx,calcControls,parmDict)/refl[14+im] #/ext corr |
|---|
| 2713 | return dIdsh,dIdsp,dIdPola,dIdPO,dFdODF,dFdSA,dFdAb,dFdEx |
|---|
| 2714 | |
|---|
| 2715 | def GetSampleSigGam(refl,im,wave,G,GB,SGData,hfx,phfx,calcControls,parmDict): |
|---|
| 2716 | 'Needs a doc string' |
|---|
| 2717 | if 'C' in calcControls[hfx+'histType'] or 'B' in calcControls[hfx+'histType']: #All checked & OK |
|---|
| 2718 | costh = cosd(refl[5+im]/2.) |
|---|
| 2719 | #crystallite size |
|---|
| 2720 | if calcControls[phfx+'SizeType'] == 'isotropic': |
|---|
| 2721 | Sgam = 1.8*wave/(np.pi*parmDict[phfx+'Size;i']*costh) |
|---|
| 2722 | elif calcControls[phfx+'SizeType'] == 'uniaxial': |
|---|
| 2723 | H = np.array(refl[:3]) |
|---|
| 2724 | P = np.array(calcControls[phfx+'SizeAxis']) |
|---|
| 2725 | cosP,sinP = G2lat.CosSinAngle(H,P,G) |
|---|
| 2726 | Sgam = (1.8*wave/np.pi)/(parmDict[phfx+'Size;i']*parmDict[phfx+'Size;a']*costh) |
|---|
| 2727 | Sgam *= np.sqrt((sinP*parmDict[phfx+'Size;a'])**2+(cosP*parmDict[phfx+'Size;i'])**2) |
|---|
| 2728 | else: #ellipsoidal crystallites |
|---|
| 2729 | Sij =[parmDict[phfx+'Size;%d'%(i)] for i in range(6)] |
|---|
| 2730 | H = np.array(refl[:3]) |
|---|
| 2731 | lenR = G2pwd.ellipseSize(H,Sij,GB) |
|---|
| 2732 | Sgam = 1.8*wave/(np.pi*costh*lenR) |
|---|
| 2733 | #microstrain |
|---|
| 2734 | if calcControls[phfx+'MustrainType'] == 'isotropic': |
|---|
| 2735 | Mgam = 0.018*parmDict[phfx+'Mustrain;i']*tand(refl[5+im]/2.)/np.pi |
|---|
| 2736 | elif calcControls[phfx+'MustrainType'] == 'uniaxial': |
|---|
| 2737 | H = np.array(refl[:3]) |
|---|
| 2738 | P = np.array(calcControls[phfx+'MustrainAxis']) |
|---|
| 2739 | cosP,sinP = G2lat.CosSinAngle(H,P,G) |
|---|
| 2740 | Si = parmDict[phfx+'Mustrain;i'] |
|---|
| 2741 | Sa = parmDict[phfx+'Mustrain;a'] |
|---|
| 2742 | Mgam = 0.018*Si*Sa*tand(refl[5+im]/2.)/(np.pi*np.sqrt((Si*cosP)**2+(Sa*sinP)**2)) |
|---|
| 2743 | else: #generalized - P.W. Stephens model |
|---|
| 2744 | Strms = G2spc.MustrainCoeff(refl[:3],SGData) |
|---|
| 2745 | Sum = 0 |
|---|
| 2746 | for i,strm in enumerate(Strms): |
|---|
| 2747 | Sum += parmDict[phfx+'Mustrain;'+str(i)]*strm |
|---|
| 2748 | Mgam = 0.018*refl[4+im]**2*tand(refl[5+im]/2.)*np.sqrt(Sum)/np.pi |
|---|
| 2749 | elif 'E' in calcControls[hfx+'histType']: |
|---|
| 2750 | return 0.,0. #wrong - fix later if wanted |
|---|
| 2751 | elif 'T' in calcControls[hfx+'histType']: #All checked & OK |
|---|
| 2752 | #crystallite size |
|---|
| 2753 | if calcControls[phfx+'SizeType'] == 'isotropic': #OK |
|---|
| 2754 | Sgam = 1.e-4*parmDict[hfx+'difC']*refl[4+im]**2/parmDict[phfx+'Size;i'] |
|---|
| 2755 | elif calcControls[phfx+'SizeType'] == 'uniaxial': #OK |
|---|
| 2756 | H = np.array(refl[:3]) |
|---|
| 2757 | P = np.array(calcControls[phfx+'SizeAxis']) |
|---|
| 2758 | cosP,sinP = G2lat.CosSinAngle(H,P,G) |
|---|
| 2759 | Sgam = 1.e-4*parmDict[hfx+'difC']*refl[4+im]**2/(parmDict[phfx+'Size;i']*parmDict[phfx+'Size;a']) |
|---|
| 2760 | Sgam *= np.sqrt((sinP*parmDict[phfx+'Size;a'])**2+(cosP*parmDict[phfx+'Size;i'])**2) |
|---|
| 2761 | else: #ellipsoidal crystallites #OK |
|---|
| 2762 | Sij =[parmDict[phfx+'Size;%d'%(i)] for i in range(6)] |
|---|
| 2763 | H = np.array(refl[:3]) |
|---|
| 2764 | lenR = G2pwd.ellipseSize(H,Sij,GB) |
|---|
| 2765 | Sgam = 1.e-4*parmDict[hfx+'difC']*refl[4+im]**2/lenR |
|---|
| 2766 | #microstrain |
|---|
| 2767 | if calcControls[phfx+'MustrainType'] == 'isotropic': #OK |
|---|
| 2768 | Mgam = 1.e-6*parmDict[hfx+'difC']*refl[4+im]*parmDict[phfx+'Mustrain;i'] |
|---|
| 2769 | elif calcControls[phfx+'MustrainType'] == 'uniaxial': #OK |
|---|
| 2770 | H = np.array(refl[:3]) |
|---|
| 2771 | P = np.array(calcControls[phfx+'MustrainAxis']) |
|---|
| 2772 | cosP,sinP = G2lat.CosSinAngle(H,P,G) |
|---|
| 2773 | Si = parmDict[phfx+'Mustrain;i'] |
|---|
| 2774 | Sa = parmDict[phfx+'Mustrain;a'] |
|---|
| 2775 | Mgam = 1.e-6*parmDict[hfx+'difC']*refl[4+im]*Si*Sa/np.sqrt((Si*cosP)**2+(Sa*sinP)**2) |
|---|
| 2776 | else: #generalized - P.W. Stephens model OK |
|---|
| 2777 | Strms = G2spc.MustrainCoeff(refl[:3],SGData) |
|---|
| 2778 | Sum = 0 |
|---|
| 2779 | for i,strm in enumerate(Strms): |
|---|
| 2780 | Sum += parmDict[phfx+'Mustrain;'+str(i)]*strm |
|---|
| 2781 | Mgam = 1.e-6*parmDict[hfx+'difC']*np.sqrt(Sum)*refl[4+im]**3 |
|---|
| 2782 | |
|---|
| 2783 | gam = Sgam*parmDict[phfx+'Size;mx']+Mgam*parmDict[phfx+'Mustrain;mx'] |
|---|
| 2784 | sig = (Sgam*(1.-parmDict[phfx+'Size;mx']))**2+(Mgam*(1.-parmDict[phfx+'Mustrain;mx']))**2 |
|---|
| 2785 | sig /= ateln2 |
|---|
| 2786 | return sig,gam |
|---|
| 2787 | |
|---|
| 2788 | def GetSampleSigGamDerv(refl,im,wave,G,GB,SGData,hfx,phfx,calcControls,parmDict): |
|---|
| 2789 | 'Needs a doc string' |
|---|
| 2790 | gamDict = {} |
|---|
| 2791 | sigDict = {} |
|---|
| 2792 | if 'C' in calcControls[hfx+'histType'] or 'B' in calcControls[hfx+'histType']: #All checked & OK |
|---|
| 2793 | costh = cosd(refl[5+im]/2.) |
|---|
| 2794 | tanth = tand(refl[5+im]/2.) |
|---|
| 2795 | #crystallite size derivatives |
|---|
| 2796 | if calcControls[phfx+'SizeType'] == 'isotropic': |
|---|
| 2797 | Sgam = 1.8*wave/(np.pi*costh*parmDict[phfx+'Size;i']) |
|---|
| 2798 | gamDict[phfx+'Size;i'] = -1.8*wave*parmDict[phfx+'Size;mx']/(np.pi*costh*parmDict[phfx+'Size;i']**2) |
|---|
| 2799 | sigDict[phfx+'Size;i'] = -3.6*Sgam*wave*(1.-parmDict[phfx+'Size;mx'])**2/(np.pi*costh*ateln2) |
|---|
| 2800 | elif calcControls[phfx+'SizeType'] == 'uniaxial': |
|---|
| 2801 | H = np.array(refl[:3]) |
|---|
| 2802 | P = np.array(calcControls[phfx+'SizeAxis']) |
|---|
| 2803 | cosP,sinP = G2lat.CosSinAngle(H,P,G) |
|---|
| 2804 | Si = parmDict[phfx+'Size;i'] |
|---|
| 2805 | Sa = parmDict[phfx+'Size;a'] |
|---|
| 2806 | gami = 1.8*wave/(costh*np.pi*Si*Sa) |
|---|
| 2807 | sqtrm = np.sqrt((sinP*Sa)**2+(cosP*Si)**2) |
|---|
| 2808 | Sgam = gami*sqtrm |
|---|
| 2809 | dsi = gami*Si*cosP**2/sqtrm-Sgam/Si |
|---|
| 2810 | dsa = gami*Sa*sinP**2/sqtrm-Sgam/Sa |
|---|
| 2811 | gamDict[phfx+'Size;i'] = dsi*parmDict[phfx+'Size;mx'] |
|---|
| 2812 | gamDict[phfx+'Size;a'] = dsa*parmDict[phfx+'Size;mx'] |
|---|
| 2813 | sigDict[phfx+'Size;i'] = 2.*dsi*Sgam*(1.-parmDict[phfx+'Size;mx'])**2/ateln2 |
|---|
| 2814 | sigDict[phfx+'Size;a'] = 2.*dsa*Sgam*(1.-parmDict[phfx+'Size;mx'])**2/ateln2 |
|---|
| 2815 | else: #ellipsoidal crystallites |
|---|
| 2816 | const = 1.8*wave/(np.pi*costh) |
|---|
| 2817 | Sij =[parmDict[phfx+'Size;%d'%(i)] for i in range(6)] |
|---|
| 2818 | H = np.array(refl[:3]) |
|---|
| 2819 | lenR,dRdS = G2pwd.ellipseSizeDerv(H,Sij,GB) |
|---|
| 2820 | Sgam = const/lenR |
|---|
| 2821 | for i,item in enumerate([phfx+'Size;%d'%(j) for j in range(6)]): |
|---|
| 2822 | gamDict[item] = -(const/lenR**2)*dRdS[i]*parmDict[phfx+'Size;mx'] |
|---|
| 2823 | sigDict[item] = -2.*Sgam*(const/lenR**2)*dRdS[i]*(1.-parmDict[phfx+'Size;mx'])**2/ateln2 |
|---|
| 2824 | gamDict[phfx+'Size;mx'] = Sgam |
|---|
| 2825 | sigDict[phfx+'Size;mx'] = -2.*Sgam**2*(1.-parmDict[phfx+'Size;mx'])/ateln2 |
|---|
| 2826 | |
|---|
| 2827 | #microstrain derivatives |
|---|
| 2828 | if calcControls[phfx+'MustrainType'] == 'isotropic': |
|---|
| 2829 | Mgam = 0.018*parmDict[phfx+'Mustrain;i']*tand(refl[5+im]/2.)/np.pi |
|---|
| 2830 | gamDict[phfx+'Mustrain;i'] = 0.018*tanth*parmDict[phfx+'Mustrain;mx']/np.pi |
|---|
| 2831 | sigDict[phfx+'Mustrain;i'] = 0.036*Mgam*tanth*(1.-parmDict[phfx+'Mustrain;mx'])**2/(np.pi*ateln2) |
|---|
| 2832 | elif calcControls[phfx+'MustrainType'] == 'uniaxial': |
|---|
| 2833 | H = np.array(refl[:3]) |
|---|
| 2834 | P = np.array(calcControls[phfx+'MustrainAxis']) |
|---|
| 2835 | cosP,sinP = G2lat.CosSinAngle(H,P,G) |
|---|
| 2836 | Si = parmDict[phfx+'Mustrain;i'] |
|---|
| 2837 | Sa = parmDict[phfx+'Mustrain;a'] |
|---|
| 2838 | gami = 0.018*Si*Sa*tanth/np.pi |
|---|
| 2839 | sqtrm = np.sqrt((Si*cosP)**2+(Sa*sinP)**2) |
|---|
| 2840 | Mgam = gami/sqtrm |
|---|
| 2841 | dsi = -gami*Si*cosP**2/sqtrm**3 |
|---|
| 2842 | dsa = -gami*Sa*sinP**2/sqtrm**3 |
|---|
| 2843 | gamDict[phfx+'Mustrain;i'] = (Mgam/Si+dsi)*parmDict[phfx+'Mustrain;mx'] |
|---|
| 2844 | gamDict[phfx+'Mustrain;a'] = (Mgam/Sa+dsa)*parmDict[phfx+'Mustrain;mx'] |
|---|
| 2845 | sigDict[phfx+'Mustrain;i'] = 2*(Mgam/Si+dsi)*Mgam*(1.-parmDict[phfx+'Mustrain;mx'])**2/ateln2 |
|---|
| 2846 | sigDict[phfx+'Mustrain;a'] = 2*(Mgam/Sa+dsa)*Mgam*(1.-parmDict[phfx+'Mustrain;mx'])**2/ateln2 |
|---|
| 2847 | else: #generalized - P.W. Stephens model |
|---|
| 2848 | const = 0.018*refl[4+im]**2*tanth/np.pi |
|---|
| 2849 | Strms = G2spc.MustrainCoeff(refl[:3],SGData) |
|---|
| 2850 | Sum = 0 |
|---|
| 2851 | for i,strm in enumerate(Strms): |
|---|
| 2852 | Sum += parmDict[phfx+'Mustrain;'+str(i)]*strm |
|---|
| 2853 | gamDict[phfx+'Mustrain;'+str(i)] = strm*parmDict[phfx+'Mustrain;mx']/2. |
|---|
| 2854 | sigDict[phfx+'Mustrain;'+str(i)] = strm*(1.-parmDict[phfx+'Mustrain;mx'])**2 |
|---|
| 2855 | Mgam = const*np.sqrt(Sum) |
|---|
| 2856 | for i in range(len(Strms)): |
|---|
| 2857 | gamDict[phfx+'Mustrain;'+str(i)] *= Mgam/Sum |
|---|
| 2858 | sigDict[phfx+'Mustrain;'+str(i)] *= const**2/ateln2 |
|---|
| 2859 | gamDict[phfx+'Mustrain;mx'] = Mgam |
|---|
| 2860 | sigDict[phfx+'Mustrain;mx'] = -2.*Mgam**2*(1.-parmDict[phfx+'Mustrain;mx'])/ateln2 |
|---|
| 2861 | elif 'E' in calcControls[hfx+'histType']: |
|---|
| 2862 | return {},{} #wrong - fix later if wanted |
|---|
| 2863 | else: #'T'OF - All checked & OK |
|---|
| 2864 | if calcControls[phfx+'SizeType'] == 'isotropic': #OK |
|---|
| 2865 | Sgam = 1.e-4*parmDict[hfx+'difC']*refl[4+im]**2/parmDict[phfx+'Size;i'] |
|---|
| 2866 | gamDict[phfx+'Size;i'] = -Sgam*parmDict[phfx+'Size;mx']/parmDict[phfx+'Size;i'] |
|---|
| 2867 | sigDict[phfx+'Size;i'] = -2.*Sgam**2*(1.-parmDict[phfx+'Size;mx'])**2/(ateln2*parmDict[phfx+'Size;i']) |
|---|
| 2868 | elif calcControls[phfx+'SizeType'] == 'uniaxial': #OK |
|---|
| 2869 | const = 1.e-4*parmDict[hfx+'difC']*refl[4+im]**2 |
|---|
| 2870 | H = np.array(refl[:3]) |
|---|
| 2871 | P = np.array(calcControls[phfx+'SizeAxis']) |
|---|
| 2872 | cosP,sinP = G2lat.CosSinAngle(H,P,G) |
|---|
| 2873 | Si = parmDict[phfx+'Size;i'] |
|---|
| 2874 | Sa = parmDict[phfx+'Size;a'] |
|---|
| 2875 | gami = const/(Si*Sa) |
|---|
| 2876 | sqtrm = np.sqrt((sinP*Sa)**2+(cosP*Si)**2) |
|---|
| 2877 | Sgam = gami*sqtrm |
|---|
| 2878 | dsi = gami*Si*cosP**2/sqtrm-Sgam/Si |
|---|
| 2879 | dsa = gami*Sa*sinP**2/sqtrm-Sgam/Sa |
|---|
| 2880 | gamDict[phfx+'Size;i'] = dsi*parmDict[phfx+'Size;mx'] |
|---|
| 2881 | gamDict[phfx+'Size;a'] = dsa*parmDict[phfx+'Size;mx'] |
|---|
| 2882 | sigDict[phfx+'Size;i'] = 2.*dsi*Sgam*(1.-parmDict[phfx+'Size;mx'])**2/ateln2 |
|---|
| 2883 | sigDict[phfx+'Size;a'] = 2.*dsa*Sgam*(1.-parmDict[phfx+'Size;mx'])**2/ateln2 |
|---|
| 2884 | else: #OK ellipsoidal crystallites |
|---|
| 2885 | const = 1.e-4*parmDict[hfx+'difC']*refl[4+im]**2 |
|---|
| 2886 | Sij =[parmDict[phfx+'Size;%d'%(i)] for i in range(6)] |
|---|
| 2887 | H = np.array(refl[:3]) |
|---|
| 2888 | lenR,dRdS = G2pwd.ellipseSizeDerv(H,Sij,GB) |
|---|
| 2889 | Sgam = const/lenR |
|---|
| 2890 | for i,item in enumerate([phfx+'Size;%d'%(j) for j in range(6)]): |
|---|
| 2891 | gamDict[item] = -(const/lenR**2)*dRdS[i]*parmDict[phfx+'Size;mx'] |
|---|
| 2892 | sigDict[item] = -2.*Sgam*(const/lenR**2)*dRdS[i]*(1.-parmDict[phfx+'Size;mx'])**2/ateln2 |
|---|
| 2893 | gamDict[phfx+'Size;mx'] = Sgam #OK |
|---|
| 2894 | sigDict[phfx+'Size;mx'] = -2.*Sgam**2*(1.-parmDict[phfx+'Size;mx'])/ateln2 #OK |
|---|
| 2895 | |
|---|
| 2896 | #microstrain derivatives |
|---|
| 2897 | if calcControls[phfx+'MustrainType'] == 'isotropic': |
|---|
| 2898 | Mgam = 1.e-6*parmDict[hfx+'difC']*refl[4+im]*parmDict[phfx+'Mustrain;i'] |
|---|
| 2899 | gamDict[phfx+'Mustrain;i'] = 1.e-6*refl[4+im]*parmDict[hfx+'difC']*parmDict[phfx+'Mustrain;mx'] #OK |
|---|
| 2900 | sigDict[phfx+'Mustrain;i'] = 2.*Mgam**2*(1.-parmDict[phfx+'Mustrain;mx'])**2/(ateln2*parmDict[phfx+'Mustrain;i']) |
|---|
| 2901 | elif calcControls[phfx+'MustrainType'] == 'uniaxial': |
|---|
| 2902 | H = np.array(refl[:3]) |
|---|
| 2903 | P = np.array(calcControls[phfx+'MustrainAxis']) |
|---|
| 2904 | cosP,sinP = G2lat.CosSinAngle(H,P,G) |
|---|
| 2905 | Si = parmDict[phfx+'Mustrain;i'] |
|---|
| 2906 | Sa = parmDict[phfx+'Mustrain;a'] |
|---|
| 2907 | gami = 1.e-6*parmDict[hfx+'difC']*refl[4+im]*Si*Sa |
|---|
| 2908 | sqtrm = np.sqrt((Si*cosP)**2+(Sa*sinP)**2) |
|---|
| 2909 | Mgam = gami/sqtrm |
|---|
| 2910 | dsi = -gami*Si*cosP**2/sqtrm**3 |
|---|
| 2911 | dsa = -gami*Sa*sinP**2/sqtrm**3 |
|---|
| 2912 | gamDict[phfx+'Mustrain;i'] = (Mgam/Si+dsi)*parmDict[phfx+'Mustrain;mx'] |
|---|
| 2913 | gamDict[phfx+'Mustrain;a'] = (Mgam/Sa+dsa)*parmDict[phfx+'Mustrain;mx'] |
|---|
| 2914 | sigDict[phfx+'Mustrain;i'] = 2*(Mgam/Si+dsi)*Mgam*(1.-parmDict[phfx+'Mustrain;mx'])**2/ateln2 |
|---|
| 2915 | sigDict[phfx+'Mustrain;a'] = 2*(Mgam/Sa+dsa)*Mgam*(1.-parmDict[phfx+'Mustrain;mx'])**2/ateln2 |
|---|
| 2916 | else: #generalized - P.W. Stephens model OK |
|---|
| 2917 | Strms = G2spc.MustrainCoeff(refl[:3],SGData) |
|---|
| 2918 | const = 1.e-6*parmDict[hfx+'difC']*refl[4+im]**3 |
|---|
| 2919 | Sum = 0 |
|---|
| 2920 | for i,strm in enumerate(Strms): |
|---|
| 2921 | Sum += parmDict[phfx+'Mustrain;'+str(i)]*strm |
|---|
| 2922 | gamDict[phfx+'Mustrain;'+str(i)] = strm*parmDict[phfx+'Mustrain;mx']/2. |
|---|
| 2923 | sigDict[phfx+'Mustrain;'+str(i)] = strm*(1.-parmDict[phfx+'Mustrain;mx'])**2 |
|---|
| 2924 | Mgam = const*np.sqrt(Sum) |
|---|
| 2925 | for i in range(len(Strms)): |
|---|
| 2926 | gamDict[phfx+'Mustrain;'+str(i)] *= Mgam/Sum |
|---|
| 2927 | sigDict[phfx+'Mustrain;'+str(i)] *= const**2/ateln2 |
|---|
| 2928 | gamDict[phfx+'Mustrain;mx'] = Mgam |
|---|
| 2929 | sigDict[phfx+'Mustrain;mx'] = -2.*Mgam**2*(1.-parmDict[phfx+'Mustrain;mx'])/ateln2 |
|---|
| 2930 | |
|---|
| 2931 | return sigDict,gamDict |
|---|
| 2932 | |
|---|
| 2933 | def GetReflPos(refl,im,wave,A,pfx,hfx,phfx,calcControls,parmDict): |
|---|
| 2934 | 'Needs a doc string' |
|---|
| 2935 | if im: |
|---|
| 2936 | h,k,l,m = refl[:4] |
|---|
| 2937 | vec = np.array([parmDict[pfx+'mV0'],parmDict[pfx+'mV1'],parmDict[pfx+'mV2']]) |
|---|
| 2938 | d = 1./np.sqrt(G2lat.calc_rDsqSS(np.array([h,k,l,m]),A,vec)) |
|---|
| 2939 | else: |
|---|
| 2940 | h,k,l = refl[:3] |
|---|
| 2941 | d = 1./np.sqrt(G2lat.calc_rDsq(np.array([h,k,l]),A)) |
|---|
| 2942 | refl[4+im] = d |
|---|
| 2943 | if 'C' in calcControls[hfx+'histType'] or 'B' in calcControls[hfx+'histType']: |
|---|
| 2944 | pos = 2.0*asind(wave/(2.0*d))+parmDict[hfx+'Zero'] |
|---|
| 2945 | const = 9.e-2/(np.pi*parmDict[hfx+'Gonio. radius']) #shifts in microns |
|---|
| 2946 | if 'Bragg' in calcControls[hfx+'instType']: |
|---|
| 2947 | pos -= const*(4.*parmDict[hfx+'Shift']*cosd(pos/2.0)+ \ |
|---|
| 2948 | parmDict[hfx+'Transparency']*sind(pos)*100.0) #trans(=1/mueff) in cm |
|---|
| 2949 | else: #Debye-Scherrer - simple but maybe not right |
|---|
| 2950 | pos -= const*(parmDict[hfx+'DisplaceX']*cosd(pos)+(parmDict[hfx+'DisplaceY']+parmDict[phfx+'LayerDisp'])*sind(pos)) |
|---|
| 2951 | elif 'E' in calcControls[hfx+'histType']: |
|---|
| 2952 | pos = 12.397639/(2.0*d*sind(parmDict[hfx+'2-theta']/2.0))+parmDict[hfx+'ZE']+parmDict[hfx+'YE']*d+parmDict[hfx+'XE']*d**2 |
|---|
| 2953 | elif 'T' in calcControls[hfx+'histType']: |
|---|
| 2954 | pos = parmDict[hfx+'difC']*d+parmDict[hfx+'difA']*d**2+parmDict[hfx+'difB']/d+parmDict[hfx+'Zero'] |
|---|
| 2955 | #do I need sample position effects - maybe? |
|---|
| 2956 | return pos |
|---|
| 2957 | |
|---|
| 2958 | def GetReflPosDerv(refl,im,wave,A,pfx,hfx,phfx,calcControls,parmDict): |
|---|
| 2959 | 'Needs a doc string' |
|---|
| 2960 | dpr = 180./np.pi |
|---|
| 2961 | if im: |
|---|
| 2962 | h,k,l,m = refl[:4] |
|---|
| 2963 | vec = np.array([parmDict[pfx+'mV0'],parmDict[pfx+'mV1'],parmDict[pfx+'mV2']]) |
|---|
| 2964 | dstsq = G2lat.calc_rDsqSS(np.array([h,k,l,m]),A,vec) |
|---|
| 2965 | h,k,l = [h+m*vec[0],k+m*vec[1],l+m*vec[2]] #do proj of hklm to hkl so dPdA & dPdV come out right |
|---|
| 2966 | else: |
|---|
| 2967 | m = 0 |
|---|
| 2968 | h,k,l = refl[:3] |
|---|
| 2969 | dstsq = G2lat.calc_rDsq(np.array([h,k,l]),A) |
|---|
| 2970 | dst = np.sqrt(dstsq) |
|---|
| 2971 | dsp = 1./dst |
|---|
| 2972 | if 'C' in calcControls[hfx+'histType'] or 'B' in calcControls[hfx+'histType']: |
|---|
| 2973 | pos = refl[5+im]-parmDict[hfx+'Zero'] |
|---|
| 2974 | const = dpr/np.sqrt(1.0-wave**2*dstsq/4.0) |
|---|
| 2975 | dpdw = const*dst |
|---|
| 2976 | dpdA = np.array([h**2,k**2,l**2,h*k,h*l,k*l])*const*wave/(2.0*dst) |
|---|
| 2977 | dpdZ = 1.0 |
|---|
| 2978 | dpdV = np.array([2.*h*A[0]+k*A[3]+l*A[4],2*k*A[1]+h*A[3]+l*A[5], |
|---|
| 2979 | 2*l*A[2]+h*A[4]+k*A[5]])*m*const*wave/(2.0*dst) |
|---|
| 2980 | shft = 9.e-2/(np.pi*parmDict[hfx+'Gonio. radius']) #shifts in microns |
|---|
| 2981 | if 'Bragg' in calcControls[hfx+'instType']: |
|---|
| 2982 | dpdSh = -4.*shft*cosd(pos/2.0) |
|---|
| 2983 | dpdTr = -shft*sind(pos)*100.0 |
|---|
| 2984 | return dpdA,dpdw,dpdZ,dpdSh,dpdTr,0.,0.,dpdV |
|---|
| 2985 | else: #Debye-Scherrer - simple but maybe not right |
|---|
| 2986 | dpdXd = -shft*cosd(pos) |
|---|
| 2987 | dpdYd = -shft*sind(pos) |
|---|
| 2988 | return dpdA,dpdw,dpdZ,0.,0.,dpdXd,dpdYd,dpdV |
|---|
| 2989 | elif 'E' in calcControls[hfx+'histType']: |
|---|
| 2990 | tth = parmDict[hfx+'2-theta']/2.0 |
|---|
| 2991 | dpdZE = 1.0 |
|---|
| 2992 | dpdYE = dsp |
|---|
| 2993 | dpdXE = dsp**2 |
|---|
| 2994 | dpdA = np.array([h**2,k**2,l**2,h*k,h*l,k*l])*refl[5+im]*dsp**2/2. |
|---|
| 2995 | dpdTTh = -12.397639*cosd(tth)/(dsp*sind(tth)**2) |
|---|
| 2996 | return dpdA,dpdTTh,dpdXE,dpdYE,dpdZE |
|---|
| 2997 | elif 'T' in calcControls[hfx+'histType']: |
|---|
| 2998 | dpdA = -np.array([h**2,k**2,l**2,h*k,h*l,k*l])*parmDict[hfx+'difC']*dsp**3/2. |
|---|
| 2999 | dpdZ = 1.0 |
|---|
| 3000 | dpdDC = dsp |
|---|
| 3001 | dpdDA = dsp**2 |
|---|
| 3002 | dpdDB = 1./dsp |
|---|
| 3003 | dpdV = np.array([2.*h*A[0]+k*A[3]+l*A[4],2*k*A[1]+h*A[3]+l*A[5], |
|---|
| 3004 | 2*l*A[2]+h*A[4]+k*A[5]])*m*parmDict[hfx+'difC']*dsp**3/2. |
|---|
| 3005 | return dpdA,dpdZ,dpdDC,dpdDA,dpdDB,dpdV |
|---|
| 3006 | |
|---|
| 3007 | def GetHStrainShift(refl,im,SGData,phfx,hfx,calcControls,parmDict): |
|---|
| 3008 | '''Computes the shifts in peak position due to the Hydrostatic strain |
|---|
| 3009 | (HStrain, Dij terms). |
|---|
| 3010 | This routine is not used anywhere |
|---|
| 3011 | ''' |
|---|
| 3012 | laue = SGData['SGLaue'] |
|---|
| 3013 | uniq = SGData['SGUniq'] |
|---|
| 3014 | h,k,l = refl[:3] |
|---|
| 3015 | if laue in ['m3','m3m']: |
|---|
| 3016 | hkl1 = (h**2+k**2+l**2) |
|---|
| 3017 | hkl2 = ((h*k)**2+(h*l)**2+(k*l)**2)/hkl1**2 |
|---|
| 3018 | Dij = parmDict[phfx+'D11']*hkl1+parmDict[phfx+'eA']*hkl2 |
|---|
| 3019 | elif laue in ['6/m','6/mmm','3m1','31m','3']: |
|---|
| 3020 | Dij = parmDict[phfx+'D11']*(h**2+k**2+h*k)+parmDict[phfx+'D33']*l**2 |
|---|
| 3021 | elif laue in ['3R','3mR']: |
|---|
| 3022 | Dij = parmDict[phfx+'D11']*(h**2+k**2+l**2)+parmDict[phfx+'D12']*(h*k+h*l+k*l) |
|---|
| 3023 | elif laue in ['4/m','4/mmm']: |
|---|
| 3024 | Dij = parmDict[phfx+'D11']*(h**2+k**2)+parmDict[phfx+'D33']*l**2 |
|---|
| 3025 | elif laue in ['mmm']: |
|---|
| 3026 | Dij = parmDict[phfx+'D11']*h**2+parmDict[phfx+'D22']*k**2+parmDict[phfx+'D33']*l**2 |
|---|
| 3027 | elif laue in ['2/m']: |
|---|
| 3028 | Dij = parmDict[phfx+'D11']*h**2+parmDict[phfx+'D22']*k**2+parmDict[phfx+'D33']*l**2 |
|---|
| 3029 | if uniq == 'a': |
|---|
| 3030 | Dij += parmDict[phfx+'D23']*k*l |
|---|
| 3031 | elif uniq == 'b': |
|---|
| 3032 | Dij += parmDict[phfx+'D13']*h*l |
|---|
| 3033 | elif uniq == 'c': |
|---|
| 3034 | Dij += parmDict[phfx+'D12']*h*k |
|---|
| 3035 | else: |
|---|
| 3036 | Dij = parmDict[phfx+'D11']*h**2+parmDict[phfx+'D22']*k**2+parmDict[phfx+'D33']*l**2+ \ |
|---|
| 3037 | parmDict[phfx+'D12']*h*k+parmDict[phfx+'D13']*h*l+parmDict[phfx+'D23']*k*l |
|---|
| 3038 | if 'C' in calcControls[hfx+'histType'] or 'B' in calcControls[hfx+'histType']: |
|---|
| 3039 | return -180.*Dij*refl[4+im]**2*tand(refl[5+im]/2.0)/np.pi |
|---|
| 3040 | elif 'E' in calcControls[hfx+'histType']: |
|---|
| 3041 | return Dij*refl[5+im]/refl[4+im]**2 |
|---|
| 3042 | else: |
|---|
| 3043 | return -Dij*parmDict[hfx+'difC']*0.5*refl[4+im]**2 |
|---|
| 3044 | |
|---|
| 3045 | def GetHStrainShiftDerv(refl,im,SGData,phfx,hfx,calcControls,parmDict): |
|---|
| 3046 | '''Computes the derivatives due to the shifts in peak position from Hydrostatic strain |
|---|
| 3047 | (HStrain, Dij terms). |
|---|
| 3048 | ''' |
|---|
| 3049 | laue = SGData['SGLaue'] |
|---|
| 3050 | uniq = SGData['SGUniq'] |
|---|
| 3051 | h,k,l = refl[:3] |
|---|
| 3052 | if laue in ['m3','m3m']: |
|---|
| 3053 | dDijDict = {phfx+'D11':h**2+k**2+l**2, |
|---|
| 3054 | phfx+'eA':((h*k)**2+(h*l)**2+(k*l)**2)/(h**2+k**2+l**2)**2} |
|---|
| 3055 | elif laue in ['6/m','6/mmm','3m1','31m','3']: |
|---|
| 3056 | dDijDict = {phfx+'D11':h**2+k**2+h*k,phfx+'D33':l**2} |
|---|
| 3057 | elif laue in ['3R','3mR']: |
|---|
| 3058 | dDijDict = {phfx+'D11':h**2+k**2+l**2,phfx+'D12':h*k+h*l+k*l} |
|---|
| 3059 | elif laue in ['4/m','4/mmm']: |
|---|
| 3060 | dDijDict = {phfx+'D11':h**2+k**2,phfx+'D33':l**2} |
|---|
| 3061 | elif laue in ['mmm']: |
|---|
| 3062 | dDijDict = {phfx+'D11':h**2,phfx+'D22':k**2,phfx+'D33':l**2} |
|---|
| 3063 | elif laue in ['2/m']: |
|---|
| 3064 | dDijDict = {phfx+'D11':h**2,phfx+'D22':k**2,phfx+'D33':l**2} |
|---|
| 3065 | if uniq == 'a': |
|---|
| 3066 | dDijDict[phfx+'D23'] = k*l |
|---|
| 3067 | elif uniq == 'b': |
|---|
| 3068 | dDijDict[phfx+'D13'] = h*l |
|---|
| 3069 | elif uniq == 'c': |
|---|
| 3070 | dDijDict[phfx+'D12'] = h*k |
|---|
| 3071 | else: |
|---|
| 3072 | dDijDict = {phfx+'D11':h**2,phfx+'D22':k**2,phfx+'D33':l**2, |
|---|
| 3073 | phfx+'D12':h*k,phfx+'D13':h*l,phfx+'D23':k*l} |
|---|
| 3074 | if 'C' in calcControls[hfx+'histType'] or 'B' in calcControls[hfx+'histType']: |
|---|
| 3075 | for item in dDijDict: |
|---|
| 3076 | dDijDict[item] *= 180.0*refl[4+im]**2*tand(refl[5+im]/2.0)/np.pi |
|---|
| 3077 | elif 'E' in calcControls[hfx+'histType']: |
|---|
| 3078 | for item in dDijDict: |
|---|
| 3079 | dDijDict[item] *= refl[5+im]/refl[4+im]**2 |
|---|
| 3080 | else: |
|---|
| 3081 | for item in dDijDict: |
|---|
| 3082 | dDijDict[item] *= -parmDict[hfx+'difC']*refl[4+im]**3/2. |
|---|
| 3083 | return dDijDict |
|---|
| 3084 | |
|---|
| 3085 | def GetDij(phfx,SGData,parmDict): |
|---|
| 3086 | HSvals = [parmDict[phfx+name] for name in G2spc.HStrainNames(SGData)] |
|---|
| 3087 | return G2spc.HStrainVals(HSvals,SGData) |
|---|
| 3088 | |
|---|
| 3089 | def GetFobsSq(Histograms,Phases,parmDict,calcControls): |
|---|
| 3090 | '''Compute the observed structure factors for Powder histograms and store in reflection array |
|---|
| 3091 | Multiprocessing support added |
|---|
| 3092 | ''' |
|---|
| 3093 | if GSASIIpath.GetConfigValue('Show_timing',False): |
|---|
| 3094 | starttime = time.time() #; print 'start GetFobsSq' |
|---|
| 3095 | histoList = list(Histograms.keys()) |
|---|
| 3096 | histoList.sort() |
|---|
| 3097 | Ka2 = shl = lamRatio = kRatio = None |
|---|
| 3098 | for histogram in histoList: |
|---|
| 3099 | if 'PWDR' in histogram[:4]: |
|---|
| 3100 | Histogram = Histograms[histogram] |
|---|
| 3101 | hId = Histogram['hId'] |
|---|
| 3102 | hfx = ':%d:'%(hId) |
|---|
| 3103 | Limits = calcControls[hfx+'Limits'] |
|---|
| 3104 | if 'C' in calcControls[hfx+'histType']: |
|---|
| 3105 | shl = max(parmDict[hfx+'SH/L'],0.0005) |
|---|
| 3106 | Ka2 = False |
|---|
| 3107 | kRatio = 0.0 |
|---|
| 3108 | if hfx+'Lam1' in list(parmDict.keys()): |
|---|
| 3109 | Ka2 = True |
|---|
| 3110 | lamRatio = 360*(parmDict[hfx+'Lam2']-parmDict[hfx+'Lam1'])/(np.pi*parmDict[hfx+'Lam1']) |
|---|
| 3111 | kRatio = parmDict[hfx+'I(L2)/I(L1)'] |
|---|
| 3112 | x,y,w,yc,yb,yd = Histogram['Data'] |
|---|
| 3113 | xMask = ma.getmaskarray(x) |
|---|
| 3114 | xB = np.searchsorted(x,Limits[0]) |
|---|
| 3115 | xF = np.searchsorted(x,Limits[1]) |
|---|
| 3116 | ymb = np.array(y-yb) |
|---|
| 3117 | ymb = np.where(ymb,ymb,1.0) |
|---|
| 3118 | ycmb = np.array(yc-yb) |
|---|
| 3119 | ratio = 1./np.where(ycmb,ycmb/ymb,1.e10) |
|---|
| 3120 | refLists = Histogram['Reflection Lists'] |
|---|
| 3121 | for phase in refLists: |
|---|
| 3122 | if phase not in Phases: #skips deleted or renamed phases silently! |
|---|
| 3123 | continue |
|---|
| 3124 | Phase = Phases[phase] |
|---|
| 3125 | if histogram not in Phase['Histograms']: |
|---|
| 3126 | continue |
|---|
| 3127 | im = 0 |
|---|
| 3128 | if Phase['General'].get('Modulated',False): |
|---|
| 3129 | im = 1 |
|---|
| 3130 | pId = Phase['pId'] |
|---|
| 3131 | phfx = '%d:%d:'%(pId,hId) |
|---|
| 3132 | refDict = refLists[phase] |
|---|
| 3133 | sumFo = 0.0 |
|---|
| 3134 | sumdF = 0.0 |
|---|
| 3135 | sumFosq = 0.0 |
|---|
| 3136 | sumdFsq = 0.0 |
|---|
| 3137 | sumInt = 0.0 |
|---|
| 3138 | nExcl = 0 |
|---|
| 3139 | # test to see if we are using multiprocessing below |
|---|
| 3140 | useMP,ncores = G2mp.InitMP() |
|---|
| 3141 | if len(refDict['RefList']) < 100: useMP = False |
|---|
| 3142 | if useMP: # multiprocessing: create a set of initialized Python processes |
|---|
| 3143 | MPpool = mp.Pool(G2mp.ncores,G2mp.InitFobsSqGlobals, |
|---|
| 3144 | [x,ratio,shl,xB,xF,im,lamRatio,kRatio,xMask,Ka2]) |
|---|
| 3145 | profArgs = [[] for i in range(G2mp.ncores)] |
|---|
| 3146 | else: |
|---|
| 3147 | G2mp.InitFobsSqGlobals(x,ratio,shl,xB,xF,im,lamRatio,kRatio,xMask,Ka2) |
|---|
| 3148 | if 'C' in calcControls[hfx+'histType']: |
|---|
| 3149 | # are we multiprocessing? |
|---|
| 3150 | for iref,refl in enumerate(refDict['RefList']): |
|---|
| 3151 | if useMP: |
|---|
| 3152 | profArgs[iref%G2mp.ncores].append((refl,iref)) |
|---|
| 3153 | else: |
|---|
| 3154 | icod = G2mp.ComputeFobsSqCW(refl,iref) |
|---|
| 3155 | if type(icod) is tuple: |
|---|
| 3156 | refl[8+im] = icod[0] |
|---|
| 3157 | sumInt += icod[1] |
|---|
| 3158 | if parmDict.get(phfx+'LeBail'): |
|---|
| 3159 | refl[9+im] = refl[8+im] |
|---|
| 3160 | elif icod == -1: |
|---|
| 3161 | refl[3+im] *= -1 |
|---|
| 3162 | nExcl += 1 |
|---|
| 3163 | elif icod == -2: |
|---|
| 3164 | break |
|---|
| 3165 | if useMP: |
|---|
| 3166 | for sInt,resList in MPpool.imap_unordered(G2mp.ComputeFobsSqCWbatch,profArgs): |
|---|
| 3167 | sumInt += sInt |
|---|
| 3168 | for refl8im,irefl in resList: |
|---|
| 3169 | if refl8im is None: |
|---|
| 3170 | refDict['RefList'][irefl][3+im] *= -1 |
|---|
| 3171 | nExcl += 1 |
|---|
| 3172 | else: |
|---|
| 3173 | refDict['RefList'][irefl][8+im] = refl8im |
|---|
| 3174 | if parmDict.get(phfx+'LeBail'): |
|---|
| 3175 | refDict['RefList'][irefl][9+im] = refDict['RefList'][irefl][8+im] |
|---|
| 3176 | elif 'T' in calcControls[hfx+'histType']: |
|---|
| 3177 | for iref,refl in enumerate(refDict['RefList']): |
|---|
| 3178 | if useMP: |
|---|
| 3179 | profArgs[iref%G2mp.ncores].append((refl,iref)) |
|---|
| 3180 | else: |
|---|
| 3181 | icod = G2mp.ComputeFobsSqTOF(refl,iref) |
|---|
| 3182 | if type(icod) is tuple: |
|---|
| 3183 | refl[8+im] = icod[0] |
|---|
| 3184 | sumInt += icod[1] |
|---|
| 3185 | if parmDict.get(phfx+'LeBail'): |
|---|
| 3186 | refl[9+im] = refl[8+im] |
|---|
| 3187 | elif icod == -1: |
|---|
| 3188 | refl[3+im] *= -1 |
|---|
| 3189 | nExcl += 1 |
|---|
| 3190 | elif icod == -2: |
|---|
| 3191 | break |
|---|
| 3192 | if useMP: |
|---|
| 3193 | for sInt,resList in MPpool.imap_unordered(G2mp.ComputeFobsSqTOFbatch,profArgs): |
|---|
| 3194 | sumInt += sInt |
|---|
| 3195 | for refl8im,irefl in resList: |
|---|
| 3196 | if refl8im is None: |
|---|
| 3197 | refDict['RefList'][irefl][3+im] *= -1 |
|---|
| 3198 | nExcl += 1 |
|---|
| 3199 | else: |
|---|
| 3200 | refDict['RefList'][irefl][8+im] = refl8im |
|---|
| 3201 | if parmDict.get(phfx+'LeBail'): |
|---|
| 3202 | refDict['RefList'][irefl][9+im] = refDict['RefList'][irefl][8+im] |
|---|
| 3203 | elif 'E' in calcControls[hfx+'histType']: |
|---|
| 3204 | for iref,refl in enumerate(refDict['RefList']): |
|---|
| 3205 | if useMP: |
|---|
| 3206 | profArgs[iref%G2mp.ncores].append((refl,iref)) |
|---|
| 3207 | else: |
|---|
| 3208 | icod = G2mp.ComputeFobsSqED(refl,iref) |
|---|
| 3209 | if type(icod) is tuple: |
|---|
| 3210 | refl[8+im] = icod[0] |
|---|
| 3211 | sumInt += icod[1] |
|---|
| 3212 | if parmDict.get(phfx+'LeBail'): |
|---|
| 3213 | refl[9+im] = refl[8+im] |
|---|
| 3214 | elif icod == -1: |
|---|
| 3215 | refl[3+im] *= -1 |
|---|
| 3216 | nExcl += 1 |
|---|
| 3217 | elif icod == -2: |
|---|
| 3218 | break |
|---|
| 3219 | if useMP: |
|---|
| 3220 | for sInt,resList in MPpool.imap_unordered(G2mp.ComputeFobsSqEDbatch,profArgs): |
|---|
| 3221 | sumInt += sInt |
|---|
| 3222 | for refl8im,irefl in resList: |
|---|
| 3223 | if refl8im is None: |
|---|
| 3224 | refDict['RefList'][irefl][3+im] *= -1 |
|---|
| 3225 | nExcl += 1 |
|---|
| 3226 | else: |
|---|
| 3227 | refDict['RefList'][irefl][8+im] = refl8im |
|---|
| 3228 | if parmDict.get(phfx+'LeBail'): |
|---|
| 3229 | refDict['RefList'][irefl][9+im] = refDict['RefList'][irefl][8+im] |
|---|
| 3230 | elif 'B' in calcControls[hfx+'histType']: |
|---|
| 3231 | for iref,refl in enumerate(refDict['RefList']): |
|---|
| 3232 | if useMP: |
|---|
| 3233 | profArgs[iref%G2mp.ncores].append((refl,iref)) |
|---|
| 3234 | else: |
|---|
| 3235 | icod = G2mp.ComputeFobsSqPink(refl,iref) |
|---|
| 3236 | if type(icod) is tuple: |
|---|
| 3237 | refl[8+im] = icod[0] |
|---|
| 3238 | sumInt += icod[1] |
|---|
| 3239 | if parmDict.get(phfx+'LeBail'): |
|---|
| 3240 | refl[9+im] = refl[8+im] |
|---|
| 3241 | elif icod == -1: |
|---|
| 3242 | refl[3+im] *= -1 |
|---|
| 3243 | nExcl += 1 |
|---|
| 3244 | elif icod == -2: |
|---|
| 3245 | break |
|---|
| 3246 | if useMP: |
|---|
| 3247 | for sInt,resList in MPpool.imap_unordered(G2mp.ComputeFobsSqPinkbatch,profArgs): |
|---|
| 3248 | sumInt += sInt |
|---|
| 3249 | for refl8im,irefl in resList: |
|---|
| 3250 | if refl8im is None: |
|---|
| 3251 | refDict['RefList'][irefl][3+im] *= -1 |
|---|
| 3252 | nExcl += 1 |
|---|
| 3253 | else: |
|---|
| 3254 | refDict['RefList'][irefl][8+im] = refl8im |
|---|
| 3255 | if parmDict.get(phfx+'LeBail'): |
|---|
| 3256 | refDict['RefList'][irefl][9+im] = refDict['RefList'][irefl][8+im] |
|---|
| 3257 | if useMP: MPpool.terminate() |
|---|
| 3258 | sumFo = 0.0 |
|---|
| 3259 | sumdF = 0.0 |
|---|
| 3260 | sumFosq = 0.0 |
|---|
| 3261 | sumdFsq = 0.0 |
|---|
| 3262 | for iref,refl in enumerate(refDict['RefList']): |
|---|
| 3263 | Fo = np.sqrt(np.abs(refl[8+im])) |
|---|
| 3264 | Fc = np.sqrt(np.abs(refl[9+im])) |
|---|
| 3265 | sumFo += Fo |
|---|
| 3266 | sumFosq += refl[8+im]**2 |
|---|
| 3267 | sumdF += np.abs(Fo-Fc) |
|---|
| 3268 | sumdFsq += (refl[8+im]-refl[9+im])**2 |
|---|
| 3269 | if sumFo: |
|---|
| 3270 | Histogram['Residuals'][phfx+'Rf'] = min(100.,(sumdF/sumFo)*100.) |
|---|
| 3271 | Histogram['Residuals'][phfx+'Rf^2'] = min(100.,np.sqrt(sumdFsq/sumFosq)*100.) |
|---|
| 3272 | else: |
|---|
| 3273 | Histogram['Residuals'][phfx+'Rf'] = 100. |
|---|
| 3274 | Histogram['Residuals'][phfx+'Rf^2'] = 100. |
|---|
| 3275 | Histogram['Residuals'][phfx+'sumInt'] = sumInt |
|---|
| 3276 | Histogram['Residuals'][phfx+'Nref'] = len(refDict['RefList'])-nExcl |
|---|
| 3277 | Histogram['Residuals']['hId'] = hId |
|---|
| 3278 | elif 'HKLF' in histogram[:4]: |
|---|
| 3279 | Histogram = Histograms[histogram] |
|---|
| 3280 | Histogram['Residuals']['hId'] = Histograms[histogram]['hId'] |
|---|
| 3281 | if GSASIIpath.GetConfigValue('Show_timing',False): |
|---|
| 3282 | print ('GetFobsSq t=',time.time()-starttime) |
|---|
| 3283 | |
|---|
| 3284 | def getPowderProfile(parmDict,x,varylist,Histogram,Phases,calcControls,pawleyLookup,histogram=None): |
|---|
| 3285 | 'Computes the powder pattern for a histogram based on contributions from all used phases' |
|---|
| 3286 | if GSASIIpath.GetConfigValue('Show_timing',False): starttime = time.time() |
|---|
| 3287 | |
|---|
| 3288 | def GetReflSigGamCW(refl,im,wave,G,GB,phfx,calcControls,parmDict): |
|---|
| 3289 | U = parmDict[hfx+'U'] |
|---|
| 3290 | V = parmDict[hfx+'V'] |
|---|
| 3291 | W = parmDict[hfx+'W'] |
|---|
| 3292 | X = parmDict[hfx+'X'] |
|---|
| 3293 | Y = parmDict[hfx+'Y'] |
|---|
| 3294 | Z = parmDict[hfx+'Z'] |
|---|
| 3295 | tanPos = tand(refl[5+im]/2.0) |
|---|
| 3296 | Ssig,Sgam = GetSampleSigGam(refl,im,wave,G,GB,SGData,hfx,phfx,calcControls,parmDict) |
|---|
| 3297 | sig = U*tanPos**2+V*tanPos+W+Ssig #save peak sigma |
|---|
| 3298 | sig = max(0.001,sig) |
|---|
| 3299 | gam = X/cosd(refl[5+im]/2.0)+Y*tanPos+Sgam+Z #save peak gamma |
|---|
| 3300 | gam = max(0.001,gam) |
|---|
| 3301 | return sig,gam |
|---|
| 3302 | |
|---|
| 3303 | def GetReflSigGamTOF(refl,im,G,GB,phfx,calcControls,parmDict): |
|---|
| 3304 | sig = parmDict[hfx+'sig-0']+parmDict[hfx+'sig-1']*refl[4+im]**2+ \ |
|---|
| 3305 | parmDict[hfx+'sig-2']*refl[4+im]**4+parmDict[hfx+'sig-q']*refl[4+im] |
|---|
| 3306 | gam = parmDict[hfx+'X']*refl[4+im]+parmDict[hfx+'Y']*refl[4+im]**2+parmDict[hfx+'Z'] |
|---|
| 3307 | Ssig,Sgam = GetSampleSigGam(refl,im,0.0,G,GB,SGData,hfx,phfx,calcControls,parmDict) |
|---|
| 3308 | sig += Ssig |
|---|
| 3309 | gam += Sgam |
|---|
| 3310 | return sig,gam |
|---|
| 3311 | |
|---|
| 3312 | def GetReflSigGamED(refl,im,G,GB,phfx,calcControls,parmDict): |
|---|
| 3313 | sig = parmDict[hfx+'A']*refl[5+im]**2+parmDict[hfx+'B']*refl[5+im]+parmDict[hfx+'C'] |
|---|
| 3314 | gam = 0.001 |
|---|
| 3315 | # Ssig,Sgam = GetSampleSigGam(refl,im,0.0,G,GB,SGData,hfx,phfx,calcControls,parmDict) |
|---|
| 3316 | # sig += Ssig |
|---|
| 3317 | # gam += Sgam |
|---|
| 3318 | return sig,gam |
|---|
| 3319 | |
|---|
| 3320 | def GetReflAlpBet(refl,im,hfx,parmDict): |
|---|
| 3321 | alp = parmDict[hfx+'alpha']/refl[4+im] |
|---|
| 3322 | bet = parmDict[hfx+'beta-0']+parmDict[hfx+'beta-1']/refl[4+im]**4+parmDict[hfx+'beta-q']/refl[4+im]**2 |
|---|
| 3323 | return alp,bet |
|---|
| 3324 | |
|---|
| 3325 | def GetPinkReflAlpBet(refl,im,hfx,parmDict): |
|---|
| 3326 | tanPos = tand(refl[5+im]/2.0) |
|---|
| 3327 | alp = max(0.1,parmDict[hfx+'alpha-0']+parmDict[hfx+'alpha-1']*tanPos) |
|---|
| 3328 | bet = max(0.001,parmDict[hfx+'beta-0']+parmDict[hfx+'beta-1']*tanPos) |
|---|
| 3329 | return alp,bet |
|---|
| 3330 | |
|---|
| 3331 | def SavePartial(phase,y): |
|---|
| 3332 | phPartialFP = open(phasePartials,'ab') # append to file |
|---|
| 3333 | pickle.dump(phase,phPartialFP) |
|---|
| 3334 | pickle.dump(y,phPartialFP) |
|---|
| 3335 | phPartialFP.close() |
|---|
| 3336 | |
|---|
| 3337 | hId = Histogram['hId'] |
|---|
| 3338 | hfx = ':%d:'%(hId) |
|---|
| 3339 | bakType = calcControls[hfx+'bakType'] |
|---|
| 3340 | fixback = Histogram['Background'][1].get('fixback',None) |
|---|
| 3341 | yb,Histogram['sumBk'] = G2pwd.getBackground(hfx,parmDict,bakType,calcControls[hfx+'histType'],x,fixback) |
|---|
| 3342 | yc = np.zeros_like(yb) |
|---|
| 3343 | cw = np.diff(ma.getdata(x)) |
|---|
| 3344 | cw = np.append(cw,cw[-1]) |
|---|
| 3345 | # set up for save of phase partials if triggered in GSASIIdataGUI.OnRefinePartials |
|---|
| 3346 | phasePartials = calcControls.get('PhasePartials',None) |
|---|
| 3347 | Nphase = len(Histogram['Reflection Lists']) #partials made ony if Nphase > 1 |
|---|
| 3348 | if phasePartials: |
|---|
| 3349 | |
|---|
| 3350 | phPartialFP = open(phasePartials,'ab') # create histogram header |
|---|
| 3351 | pickle.dump(None,phPartialFP) |
|---|
| 3352 | pickle.dump(hId,phPartialFP) |
|---|
| 3353 | if Nphase > 1: |
|---|
| 3354 | pickle.dump(x,phPartialFP) |
|---|
| 3355 | pickle.dump(yb,phPartialFP) |
|---|
| 3356 | else: |
|---|
| 3357 | pickle.dump(None,phPartialFP) |
|---|
| 3358 | pickle.dump(None,phPartialFP) |
|---|
| 3359 | phPartialFP.close() |
|---|
| 3360 | |
|---|
| 3361 | if 'C' in calcControls[hfx+'histType']: |
|---|
| 3362 | shl = max(parmDict[hfx+'SH/L'],0.002) |
|---|
| 3363 | Ka2 = False |
|---|
| 3364 | if hfx+'Lam1' in (parmDict.keys()): |
|---|
| 3365 | wave = parmDict[hfx+'Lam1'] |
|---|
| 3366 | Ka2 = True |
|---|
| 3367 | lamRatio = 360*(parmDict[hfx+'Lam2']-parmDict[hfx+'Lam1'])/(np.pi*parmDict[hfx+'Lam1']) |
|---|
| 3368 | kRatio = parmDict[hfx+'I(L2)/I(L1)'] |
|---|
| 3369 | else: |
|---|
| 3370 | wave = parmDict[hfx+'Lam'] |
|---|
| 3371 | elif 'B' in calcControls[hfx+'histType']: |
|---|
| 3372 | wave = parmDict[hfx+'Lam'] |
|---|
| 3373 | else: |
|---|
| 3374 | shl = 0. |
|---|
| 3375 | for phase in Histogram['Reflection Lists']: |
|---|
| 3376 | refDict = Histogram['Reflection Lists'][phase] |
|---|
| 3377 | if phase not in Phases: #skips deleted or renamed phases silently! |
|---|
| 3378 | continue |
|---|
| 3379 | Phase = Phases[phase] |
|---|
| 3380 | if histogram and not histogram in Phase['Histograms']: |
|---|
| 3381 | continue |
|---|
| 3382 | pId = Phase['pId'] |
|---|
| 3383 | pfx = '%d::'%(pId) |
|---|
| 3384 | phfx = '%d:%d:'%(pId,hId) |
|---|
| 3385 | hfx = ':%d:'%(hId) |
|---|
| 3386 | SGData = Phase['General']['SGData'] |
|---|
| 3387 | SGMT = np.array([ops[0].T for ops in SGData['SGOps']]) |
|---|
| 3388 | im = 0 |
|---|
| 3389 | if Phase['General'].get('Modulated',False): |
|---|
| 3390 | SSGData = Phase['General']['SSGData'] |
|---|
| 3391 | im = 1 #offset in SS reflection list |
|---|
| 3392 | Dij = GetDij(phfx,SGData,parmDict) |
|---|
| 3393 | A = [parmDict[pfx+'A%d'%(i)]+Dij[i] for i in range(6)] #TODO: need to do something if Dij << 0. |
|---|
| 3394 | G,g = G2lat.A2Gmat(A) #recip & real metric tensors |
|---|
| 3395 | if np.any(np.diag(G)<0.): |
|---|
| 3396 | msg = 'Invalid metric tensor for phase #{}\n ({})'.format( |
|---|
| 3397 | pId,Phase['General']['Name']) |
|---|
| 3398 | elif np.any(np.isnan(A)): |
|---|
| 3399 | msg = 'Infinite metric tensor for phase #{}\n ({})'.format( |
|---|
| 3400 | pId,Phase['General']['Name']) |
|---|
| 3401 | else: |
|---|
| 3402 | msg = None |
|---|
| 3403 | if msg: |
|---|
| 3404 | print('\nInvalid cell metric tensor for phase #{} ({})\n'.format( |
|---|
| 3405 | pId,Phase['General']['Name']),'values (A): {:.3f} {:.3f} {:.3f} {:.3f} {:.3f} {:.3f}\n'.format(*A)) |
|---|
| 3406 | raise G2obj.G2Exception('Error: '+msg+' See console.\nCheck for refinement of conflicting variables') |
|---|
| 3407 | GA,GB = G2lat.Gmat2AB(G) #Orthogonalization matrices |
|---|
| 3408 | Vst = np.sqrt(nl.det(G)) #V* |
|---|
| 3409 | if not Phase['General'].get('doPawley') and not parmDict.get(phfx+'LeBail'): |
|---|
| 3410 | if 'E' in calcControls[hfx+'histType']: |
|---|
| 3411 | print('\n\n**** Error: EDX data not suitable for Rietveld refinement ****\n\n') |
|---|
| 3412 | else: |
|---|
| 3413 | if im: |
|---|
| 3414 | SStructureFactor(refDict,G,hfx,pfx,SGData,SSGData,calcControls,parmDict) |
|---|
| 3415 | elif parmDict[pfx+'isMag'] and 'N' in calcControls[hfx+'histType']: |
|---|
| 3416 | MagStructureFactor2(refDict,G,hfx,pfx,SGData,calcControls,parmDict) |
|---|
| 3417 | else: |
|---|
| 3418 | StructureFactor2(refDict,G,hfx,pfx,SGData,calcControls,parmDict) |
|---|
| 3419 | badPeak = False |
|---|
| 3420 | # test to see if we are using multiprocessing here |
|---|
| 3421 | useMP,ncores = G2mp.InitMP() |
|---|
| 3422 | if len(refDict['RefList']) < 100: useMP = False |
|---|
| 3423 | if phasePartials: |
|---|
| 3424 | useMP = False |
|---|
| 3425 | ypartial = np.zeros_like(yb) |
|---|
| 3426 | if useMP: # multiprocessing: create a set of initialized Python processes |
|---|
| 3427 | MPpool = mp.Pool(ncores,G2mp.InitPwdrProfGlobals,[im,shl,x]) |
|---|
| 3428 | profArgs = [[] for i in range(ncores)] |
|---|
| 3429 | if 'C' in calcControls[hfx+'histType']: |
|---|
| 3430 | for iref,refl in enumerate(refDict['RefList']): |
|---|
| 3431 | if im: |
|---|
| 3432 | h,k,l,m = refl[:4] |
|---|
| 3433 | else: |
|---|
| 3434 | h,k,l = refl[:3] |
|---|
| 3435 | Uniq = np.inner(refl[:3],SGMT) |
|---|
| 3436 | refl[5+im] = GetReflPos(refl,im,wave,A,pfx,hfx,phfx,calcControls,parmDict) #corrected reflection position |
|---|
| 3437 | # refl[5+im] += GetHStrainShift(refl,im,SGData,phfx,hfx,calcControls,parmDict) #apply hydrostatic strain shift |
|---|
| 3438 | Lorenz = 1./(2.*sind(refl[5+im]/2.)**2*cosd(refl[5+im]/2.)) #Lorentz correction |
|---|
| 3439 | refl[6+im:8+im] = GetReflSigGamCW(refl,im,wave,G,GB,phfx,calcControls,parmDict) #peak sig & gam |
|---|
| 3440 | refl[11+im:15+im] = GetIntensityCorr(refl,im,Uniq,G,g,pfx,phfx,hfx,SGData,calcControls,parmDict) |
|---|
| 3441 | refl[11+im] *= Vst*Lorenz |
|---|
| 3442 | |
|---|
| 3443 | if Phase['General'].get('doPawley'): |
|---|
| 3444 | try: |
|---|
| 3445 | if im: |
|---|
| 3446 | pInd = pfx+'PWLref:%d'%(pawleyLookup[pfx+'%d,%d,%d,%d'%(h,k,l,m)]) |
|---|
| 3447 | else: |
|---|
| 3448 | pInd = pfx+'PWLref:%d'%(pawleyLookup[pfx+'%d,%d,%d'%(h,k,l)]) |
|---|
| 3449 | refl[9+im] = parmDict[pInd] |
|---|
| 3450 | except KeyError: |
|---|
| 3451 | # print ' ***Error %d,%d,%d missing from Pawley reflection list ***'%(h,k,l) |
|---|
| 3452 | continue |
|---|
| 3453 | Wd,fmin,fmax = G2pwd.getWidthsCW(refl[5+im],refl[6+im],refl[7+im],shl) |
|---|
| 3454 | iBeg = np.searchsorted(x,refl[5+im]-fmin) |
|---|
| 3455 | iFin = np.searchsorted(x,refl[5+im]+fmax) |
|---|
| 3456 | if not iBeg+iFin: #peak below low limit - skip peak |
|---|
| 3457 | continue |
|---|
| 3458 | elif not iBeg-iFin: #peak above high limit - done |
|---|
| 3459 | break |
|---|
| 3460 | elif iBeg > iFin: #bad peak coeff - skip |
|---|
| 3461 | badPeak = True |
|---|
| 3462 | continue |
|---|
| 3463 | if useMP: |
|---|
| 3464 | profArgs[iref%ncores].append((refl[5+im],refl,iBeg,iFin,1.)) |
|---|
| 3465 | else: |
|---|
| 3466 | fp = G2pwd.getFCJVoigt3(refl[5+im],refl[6+im],refl[7+im],shl,ma.getdata(x[iBeg:iFin]))[0] |
|---|
| 3467 | yc[iBeg:iFin] += refl[11+im]*refl[9+im]*fp #>90% of time spent here |
|---|
| 3468 | if phasePartials: ypartial[iBeg:iFin] += refl[11+im]*refl[9+im]*fp |
|---|
| 3469 | if Ka2: |
|---|
| 3470 | pos2 = refl[5+im]+lamRatio*tand(refl[5+im]/2.0) # + 360/pi * Dlam/lam * tan(th) |
|---|
| 3471 | Wd,fmin,fmax = G2pwd.getWidthsCW(pos2,refl[6+im],refl[7+im],shl) |
|---|
| 3472 | iBeg = np.searchsorted(x,pos2-fmin) |
|---|
| 3473 | iFin = np.searchsorted(x,pos2+fmax) |
|---|
| 3474 | if not iBeg+iFin: #peak below low limit - skip peak |
|---|
| 3475 | continue |
|---|
| 3476 | elif not iBeg-iFin: #peak above high limit - done |
|---|
| 3477 | return yc,yb |
|---|
| 3478 | elif iBeg > iFin: #bad peak coeff - skip |
|---|
| 3479 | continue |
|---|
| 3480 | if useMP: |
|---|
| 3481 | profArgs[iref%ncores].append((pos2,refl,iBeg,iFin,kRatio)) |
|---|
| 3482 | else: |
|---|
| 3483 | fp2 = G2pwd.getFCJVoigt3(pos2,refl[6+im],refl[7+im],shl,ma.getdata(x[iBeg:iFin]))[0] |
|---|
| 3484 | yc[iBeg:iFin] += refl[11+im]*refl[9+im]*kRatio*fp2 #and here |
|---|
| 3485 | if phasePartials: ypartial[iBeg:iFin] += refl[11+im]*refl[9+im]*kRatio*fp2 |
|---|
| 3486 | elif 'E' in calcControls[hfx+'histType']: |
|---|
| 3487 | |
|---|
| 3488 | for iref,refl in enumerate(refDict['RefList']): |
|---|
| 3489 | if im: |
|---|
| 3490 | h,k,l,m = refl[:4] |
|---|
| 3491 | else: |
|---|
| 3492 | h,k,l = refl[:3] |
|---|
| 3493 | Uniq = np.inner(refl[:3],SGMT) |
|---|
| 3494 | refl[5+im] = GetReflPos(refl,im,0.0,A,pfx,hfx,phfx,calcControls,parmDict) #corrected reflection position |
|---|
| 3495 | # refl[5+im] += GetHStrainShift(refl,im,SGData,phfx,hfx,calcControls,parmDict) #apply hydrostatic strain shift |
|---|
| 3496 | refl[6+im:8+im] = GetReflSigGamED(refl,im,G,GB,phfx,calcControls,parmDict) #peak sig & gam |
|---|
| 3497 | refl[11+im] = 1.0 #no intensity corrections; default = 1.0 |
|---|
| 3498 | |
|---|
| 3499 | if Phase['General'].get('doPawley'): |
|---|
| 3500 | try: |
|---|
| 3501 | if im: |
|---|
| 3502 | pInd = pfx+'PWLref:%d'%(pawleyLookup[pfx+'%d,%d,%d,%d'%(h,k,l,m)]) |
|---|
| 3503 | else: |
|---|
| 3504 | pInd = pfx+'PWLref:%d'%(pawleyLookup[pfx+'%d,%d,%d'%(h,k,l)]) |
|---|
| 3505 | refl[9+im] = parmDict[pInd] |
|---|
| 3506 | except KeyError: |
|---|
| 3507 | continue |
|---|
| 3508 | Wd,fmin,fmax = G2pwd.getWidthsED(refl[5+im],refl[6+im]) |
|---|
| 3509 | iBeg = np.searchsorted(x,refl[5+im]-fmin) |
|---|
| 3510 | iFin = np.searchsorted(x,refl[5+im]+fmax) |
|---|
| 3511 | if not iBeg+iFin: #peak below low limit - skip peak |
|---|
| 3512 | continue |
|---|
| 3513 | elif not iBeg-iFin: #peak above high limit - done |
|---|
| 3514 | break |
|---|
| 3515 | elif iBeg > iFin: #bad peak coeff - skip |
|---|
| 3516 | badPeak = True |
|---|
| 3517 | continue |
|---|
| 3518 | if useMP: |
|---|
| 3519 | profArgs[iref%ncores].append((refl[5+im],refl,iBeg,iFin,1.)) |
|---|
| 3520 | else: |
|---|
| 3521 | fp = G2pwd.getPsVoigt(refl[5+im],refl[6+im]*1.e4,.001,ma.getdata(x[iBeg:iFin]))[0] |
|---|
| 3522 | yc[iBeg:iFin] += refl[9+im]*fp |
|---|
| 3523 | if phasePartials: ypartial[iBeg:iFin] += refl[11+im]*refl[9+im]*fp |
|---|
| 3524 | |
|---|
| 3525 | elif 'B' in calcControls[hfx+'histType']: |
|---|
| 3526 | for iref,refl in enumerate(refDict['RefList']): |
|---|
| 3527 | if im: |
|---|
| 3528 | h,k,l,m = refl[:4] |
|---|
| 3529 | else: |
|---|
| 3530 | h,k,l = refl[:3] |
|---|
| 3531 | Uniq = np.inner(refl[:3],SGMT) |
|---|
| 3532 | refl[5+im] = GetReflPos(refl,im,wave,A,pfx,hfx,phfx,calcControls,parmDict) #corrected reflection position |
|---|
| 3533 | # refl[5+im] += GetHStrainShift(refl,im,SGData,phfx,hfx,calcControls,parmDict) #apply hydrostatic strain shift |
|---|
| 3534 | Lorenz = 1./(2.*sind(refl[5+im]/2.)**2*cosd(refl[5+im]/2.)) #Lorentz correction |
|---|
| 3535 | refl[6+im:8+im] = GetReflSigGamCW(refl,im,wave,G,GB,phfx,calcControls,parmDict) #peak sig & gam |
|---|
| 3536 | refl[12+im:14+im] = GetPinkReflAlpBet(refl,im,hfx,parmDict) |
|---|
| 3537 | refl[11+im],refl[14+im],refl[15+im],refl[16+im] = GetIntensityCorr(refl,im,Uniq,G,g,pfx,phfx,hfx,SGData,calcControls,parmDict) |
|---|
| 3538 | refl[11+im] *= Vst*Lorenz |
|---|
| 3539 | |
|---|
| 3540 | if Phase['General'].get('doPawley'): |
|---|
| 3541 | try: |
|---|
| 3542 | if im: |
|---|
| 3543 | pInd = pfx+'PWLref:%d'%(pawleyLookup[pfx+'%d,%d,%d,%d'%(h,k,l,m)]) |
|---|
| 3544 | else: |
|---|
| 3545 | pInd = pfx+'PWLref:%d'%(pawleyLookup[pfx+'%d,%d,%d'%(h,k,l)]) |
|---|
| 3546 | refl[9+im] = parmDict[pInd] |
|---|
| 3547 | except KeyError: |
|---|
| 3548 | continue |
|---|
| 3549 | Wd,fmin,fmax = G2pwd.getWidthsTOF(refl[5+im],refl[12+im],refl[13+im],refl[6+im]/1.e4,refl[7+im]/100.) |
|---|
| 3550 | iBeg = np.searchsorted(x,refl[5+im]-fmin) |
|---|
| 3551 | iFin = np.searchsorted(x,refl[5+im]+fmax) |
|---|
| 3552 | if not iBeg+iFin: #peak below low limit - skip peak |
|---|
| 3553 | continue |
|---|
| 3554 | elif not iBeg-iFin: #peak above high limit - done |
|---|
| 3555 | break |
|---|
| 3556 | elif iBeg > iFin: #bad peak coeff - skip |
|---|
| 3557 | badPeak = True |
|---|
| 3558 | continue |
|---|
| 3559 | if useMP: |
|---|
| 3560 | profArgs[iref%ncores].append((refl[5+im],refl,iBeg,iFin,1.)) |
|---|
| 3561 | else: |
|---|
| 3562 | fp = G2pwd.getEpsVoigt(refl[5+im],refl[12+im],refl[13+im],refl[6+im]/1.e4,refl[7+im]/100.,ma.getdata(x[iBeg:iFin]))[0] |
|---|
| 3563 | # if 'NB' in calcControls[hfx+'histType']: |
|---|
| 3564 | # yc[iBeg:iFin] += refl[11+im]*refl[9+im]*fp*.001/cw[iBeg:iFin] |
|---|
| 3565 | # else: |
|---|
| 3566 | # yc[iBeg:iFin] += refl[11+im]*refl[9+im]*fp |
|---|
| 3567 | yc[iBeg:iFin] += refl[11+im]*refl[9+im]*fp |
|---|
| 3568 | if phasePartials: ypartial[iBeg:iFin] += refl[11+im]*refl[9+im]*fp |
|---|
| 3569 | |
|---|
| 3570 | elif 'T' in calcControls[hfx+'histType']: |
|---|
| 3571 | for iref,refl in enumerate(refDict['RefList']): |
|---|
| 3572 | if im: |
|---|
| 3573 | h,k,l,m = refl[:4] |
|---|
| 3574 | else: |
|---|
| 3575 | h,k,l = refl[:3] |
|---|
| 3576 | Uniq = np.inner(refl[:3],SGMT) |
|---|
| 3577 | refl[5+im] = GetReflPos(refl,im,0.0,A,pfx,hfx,phfx,calcControls,parmDict) #corrected reflection position - #TODO - what about tabluated offset? |
|---|
| 3578 | Lorenz = sind(abs(parmDict[hfx+'2-theta'])/2)*refl[4+im]**4 #TOF Lorentz correction |
|---|
| 3579 | # refl[5+im] += GetHStrainShift(refl,im,SGData,phfx,hfx,calcControls,parmDict) #apply hydrostatic strain shift |
|---|
| 3580 | refl[6+im:8+im] = GetReflSigGamTOF(refl,im,G,GB,phfx,calcControls,parmDict) #peak sig & gam |
|---|
| 3581 | refl[12+im:14+im] = GetReflAlpBet(refl,im,hfx,parmDict) #TODO - skip if alp, bet tabulated? |
|---|
| 3582 | refl[11+im],refl[15+im],refl[16+im],refl[17+im] = GetIntensityCorr(refl,im,Uniq,G,g,pfx,phfx,hfx,SGData,calcControls,parmDict) |
|---|
| 3583 | refl[11+im] *= Vst*Lorenz |
|---|
| 3584 | if Phase['General'].get('doPawley'): |
|---|
| 3585 | try: |
|---|
| 3586 | if im: |
|---|
| 3587 | pInd =pfx+'PWLref:%d'%(pawleyLookup[pfx+'%d,%d,%d,%d'%(h,k,l,m)]) |
|---|
| 3588 | else: |
|---|
| 3589 | pInd =pfx+'PWLref:%d'%(pawleyLookup[pfx+'%d,%d,%d'%(h,k,l)]) |
|---|
| 3590 | refl[9+im] = parmDict[pInd] |
|---|
| 3591 | except KeyError: |
|---|
| 3592 | continue |
|---|
| 3593 | Wd,fmin,fmax = G2pwd.getWidthsTOF(refl[5+im],refl[12+im],refl[13+im],refl[6+im],refl[7+im]) |
|---|
| 3594 | iBeg = np.searchsorted(x,refl[5+im]-fmin) |
|---|
| 3595 | iFin = np.searchsorted(x,refl[5+im]+fmax) |
|---|
| 3596 | if not iBeg+iFin: #peak below low limit - skip peak |
|---|
| 3597 | continue |
|---|
| 3598 | elif not iBeg-iFin: #peak above high limit - done |
|---|
| 3599 | break |
|---|
| 3600 | elif iBeg > iFin: #bad peak coeff - skip |
|---|
| 3601 | badPeak = True |
|---|
| 3602 | continue |
|---|
| 3603 | if useMP: |
|---|
| 3604 | profArgs[iref%ncores].append((refl[5+im],refl,iBeg,iFin)) |
|---|
| 3605 | else: |
|---|
| 3606 | fp = G2pwd.getEpsVoigt(refl[5+im],refl[12+im],refl[13+im],refl[6+im],refl[7+im],ma.getdata(x[iBeg:iFin]))[0] |
|---|
| 3607 | yc[iBeg:iFin] += refl[11+im]*refl[9+im]*fp |
|---|
| 3608 | if phasePartials: ypartial[iBeg:iFin] += refl[11+im]*refl[9+im]*fp |
|---|
| 3609 | |
|---|
| 3610 | if phasePartials: #for all flavors of PWDR |
|---|
| 3611 | if Nphase > 1: |
|---|
| 3612 | SavePartial(phase,ypartial) |
|---|
| 3613 | else: |
|---|
| 3614 | SavePartial(phase,[]) |
|---|
| 3615 | |
|---|
| 3616 | # print 'profile calc time: %.3fs'%(time.time()-time0) |
|---|
| 3617 | if useMP and 'C' in calcControls[hfx+'histType']: |
|---|
| 3618 | for y in MPpool.imap_unordered(G2mp.ComputePwdrProfCW,profArgs): |
|---|
| 3619 | yc += y |
|---|
| 3620 | MPpool.terminate() |
|---|
| 3621 | elif useMP and 'T' in calcControls[hfx+'histType']: |
|---|
| 3622 | for y in MPpool.imap_unordered(G2mp.ComputePwdrProfTOF,profArgs): |
|---|
| 3623 | yc += y |
|---|
| 3624 | MPpool.terminate() |
|---|
| 3625 | elif useMP and 'B' in calcControls[hfx+'histType']: |
|---|
| 3626 | for y in MPpool.imap_unordered(G2mp.ComputePwdrProfPink,profArgs): |
|---|
| 3627 | yc += y |
|---|
| 3628 | MPpool.terminate() |
|---|
| 3629 | elif useMP and 'E' in calcControls[hfx+'histType']: |
|---|
| 3630 | for y in MPpool.imap_unordered(G2mp.ComputePwdrProfED,profArgs): |
|---|
| 3631 | yc += y |
|---|
| 3632 | MPpool.terminate() |
|---|
| 3633 | if badPeak: |
|---|
| 3634 | print ('ouch #7 bad profile coefficients yield negative peak width; some reflections skipped') |
|---|
| 3635 | if GSASIIpath.GetConfigValue('Show_timing',False): |
|---|
| 3636 | print ('getPowderProfile t=%.3f'%(time.time()-starttime)) |
|---|
| 3637 | return yc,yb |
|---|
| 3638 | |
|---|
| 3639 | def getPowderProfileDerv(args): |
|---|
| 3640 | '''Computes the derivatives of the computed powder pattern with respect to all |
|---|
| 3641 | refined parameters. |
|---|
| 3642 | Used for single processor & Multiprocessor versions |
|---|
| 3643 | ''' |
|---|
| 3644 | import pytexture as ptx |
|---|
| 3645 | ptx.pyqlmninit() #initialize fortran arrays for spherical harmonics for each processor |
|---|
| 3646 | parmDict,x,varylist,Histogram,Phases,rigidbodyDict,calcControls,pawleyLookup,dependentVars = args[:9] |
|---|
| 3647 | prc,tprc,histogram = 0,1,None |
|---|
| 3648 | if len(args) >= 10: prc=args[9] |
|---|
| 3649 | if len(args) >= 11: tprc=args[10] |
|---|
| 3650 | if len(args) >= 12: histogram=args[11] |
|---|
| 3651 | |
|---|
| 3652 | def cellVaryDerv(pfx,SGData,dpdA): |
|---|
| 3653 | if SGData['SGLaue'] in ['-1',]: |
|---|
| 3654 | return [[pfx+'A0',dpdA[0]],[pfx+'A1',dpdA[1]],[pfx+'A2',dpdA[2]], |
|---|
| 3655 | [pfx+'A3',dpdA[3]],[pfx+'A4',dpdA[4]],[pfx+'A5',dpdA[5]]] |
|---|
| 3656 | elif SGData['SGLaue'] in ['2/m',]: |
|---|
| 3657 | if SGData['SGUniq'] == 'a': |
|---|
| 3658 | return [[pfx+'A0',dpdA[0]],[pfx+'A1',dpdA[1]],[pfx+'A2',dpdA[2]],[pfx+'A5',dpdA[5]]] |
|---|
| 3659 | elif SGData['SGUniq'] == 'b': |
|---|
| 3660 | return [[pfx+'A0',dpdA[0]],[pfx+'A1',dpdA[1]],[pfx+'A2',dpdA[2]],[pfx+'A4',dpdA[4]]] |
|---|
| 3661 | else: |
|---|
| 3662 | return [[pfx+'A0',dpdA[0]],[pfx+'A1',dpdA[1]],[pfx+'A2',dpdA[2]],[pfx+'A3',dpdA[3]]] |
|---|
| 3663 | elif SGData['SGLaue'] in ['mmm',]: |
|---|
| 3664 | return [[pfx+'A0',dpdA[0]],[pfx+'A1',dpdA[1]],[pfx+'A2',dpdA[2]]] |
|---|
| 3665 | elif SGData['SGLaue'] in ['4/m','4/mmm']: |
|---|
| 3666 | return [[pfx+'A0',dpdA[0]],[pfx+'A2',dpdA[2]]] |
|---|
| 3667 | elif SGData['SGLaue'] in ['6/m','6/mmm','3m1', '31m', '3']: |
|---|
| 3668 | return [[pfx+'A0',dpdA[0]],[pfx+'A2',dpdA[2]]] |
|---|
| 3669 | elif SGData['SGLaue'] in ['3R', '3mR']: |
|---|
| 3670 | return [[pfx+'A0',dpdA[0]+dpdA[1]+dpdA[2]],[pfx+'A3',dpdA[3]+dpdA[4]+dpdA[5]]] |
|---|
| 3671 | elif SGData['SGLaue'] in ['m3m','m3']: |
|---|
| 3672 | return [[pfx+'A0',dpdA[0]]] |
|---|
| 3673 | |
|---|
| 3674 | # create a list of dependent variables and set up a dictionary to hold their derivatives |
|---|
| 3675 | # dependentVars = G2mv.GetDependentVars() |
|---|
| 3676 | depDerivDict = {} |
|---|
| 3677 | for j in dependentVars: |
|---|
| 3678 | depDerivDict[j] = np.zeros(shape=(len(x))) |
|---|
| 3679 | # print ('dependent vars',dependentVars) |
|---|
| 3680 | hId = Histogram['hId'] |
|---|
| 3681 | hfx = ':%d:'%(hId) |
|---|
| 3682 | bakType = calcControls[hfx+'bakType'] |
|---|
| 3683 | dMdv = np.zeros(shape=(len(varylist),len(x))) |
|---|
| 3684 | fixback = Histogram['Background'][1].get('fixback',None) |
|---|
| 3685 | dMdb,dMddb,dMdpk,dMdfb = G2pwd.getBackgroundDerv(hfx,parmDict,bakType,calcControls[hfx+'histType'],x,fixback) |
|---|
| 3686 | if prc == 0 and hfx+'Back;0' in varylist: # for now assume that Back;x vars to not appear in constraints |
|---|
| 3687 | bBpos = varylist.index(hfx+'Back;0') |
|---|
| 3688 | dMdv[bBpos:bBpos+len(dMdb)] += dMdb #TODO crash if bck parms tossed |
|---|
| 3689 | names = [hfx+'DebyeA',hfx+'DebyeR',hfx+'DebyeU'] |
|---|
| 3690 | for name in varylist: |
|---|
| 3691 | if prc == 0 and 'Debye' in name: |
|---|
| 3692 | Id = int(name.split(';')[-1]) |
|---|
| 3693 | parm = name[:int(name.rindex(';'))] |
|---|
| 3694 | if parm in names: #skips if bkg fxn not in current histogram |
|---|
| 3695 | ip = names.index(parm) |
|---|
| 3696 | dMdv[varylist.index(name)] += dMddb[3*Id+ip] |
|---|
| 3697 | names = [hfx+'BkPkpos',hfx+'BkPkint',hfx+'BkPksig',hfx+'BkPkgam'] |
|---|
| 3698 | for name in varylist: |
|---|
| 3699 | if prc == 0 and 'BkPk' in name: |
|---|
| 3700 | parm,Id = name.split(';') |
|---|
| 3701 | Id = int(Id) |
|---|
| 3702 | if parm in names: #skips if bkg fxn not in current histogram |
|---|
| 3703 | ip = names.index(parm) |
|---|
| 3704 | dMdv[varylist.index(name)] += dMdpk[4*Id+ip] |
|---|
| 3705 | if hfx+'BF mult' in varylist: |
|---|
| 3706 | dMdv[varylist.index(hfx+'BF mult')] += dMdfb |
|---|
| 3707 | cw = np.diff(ma.getdata(x)) |
|---|
| 3708 | cw = np.append(cw,cw[-1]) |
|---|
| 3709 | Ka2 = False #also for TOF! |
|---|
| 3710 | if 'C' in calcControls[hfx+'histType']: |
|---|
| 3711 | shl = max(parmDict[hfx+'SH/L'],0.002) |
|---|
| 3712 | if hfx+'Lam1' in (parmDict.keys()): |
|---|
| 3713 | wave = parmDict[hfx+'Lam1'] |
|---|
| 3714 | Ka2 = True |
|---|
| 3715 | lamRatio = 360*(parmDict[hfx+'Lam2']-parmDict[hfx+'Lam1'])/(np.pi*parmDict[hfx+'Lam1']) |
|---|
| 3716 | kRatio = parmDict[hfx+'I(L2)/I(L1)'] |
|---|
| 3717 | else: |
|---|
| 3718 | wave = parmDict[hfx+'Lam'] |
|---|
| 3719 | elif 'B' in calcControls[hfx+'histType']: |
|---|
| 3720 | wave = parmDict[hfx+'Lam'] |
|---|
| 3721 | for phase in Histogram['Reflection Lists']: |
|---|
| 3722 | refDict = Histogram['Reflection Lists'][phase] |
|---|
| 3723 | if phase not in Phases: #skips deleted or renamed phases silently! |
|---|
| 3724 | continue |
|---|
| 3725 | Phase = Phases[phase] |
|---|
| 3726 | if histogram and histogram not in Phase['Histograms']: |
|---|
| 3727 | continue |
|---|
| 3728 | SGData = Phase['General']['SGData'] |
|---|
| 3729 | SGMT = np.array([ops[0].T for ops in SGData['SGOps']]) |
|---|
| 3730 | im = 0 |
|---|
| 3731 | if Phase['General'].get('Modulated',False): |
|---|
| 3732 | SSGData = Phase['General']['SSGData'] |
|---|
| 3733 | im = 1 #offset in SS reflection list |
|---|
| 3734 | #?? |
|---|
| 3735 | pId = Phase['pId'] |
|---|
| 3736 | pfx = '%d::'%(pId) |
|---|
| 3737 | phfx = '%d:%d:'%(pId,hId) |
|---|
| 3738 | Dij = GetDij(phfx,SGData,parmDict) |
|---|
| 3739 | A = [parmDict[pfx+'A%d'%(i)]+Dij[i] for i in range(6)] |
|---|
| 3740 | G,g = G2lat.A2Gmat(A) #recip & real metric tensors |
|---|
| 3741 | GA,GB = G2lat.Gmat2AB(G) #Orthogonalization matricies |
|---|
| 3742 | if not Phase['General'].get('doPawley') and not parmDict.get(phfx+'LeBail') and 'E' not in calcControls[hfx+'histType']: |
|---|
| 3743 | if im: |
|---|
| 3744 | dFdvDict = SStructureFactorDerv(refDict,im,G,hfx,pfx,SGData,SSGData,calcControls,parmDict) |
|---|
| 3745 | dFdvDict.update(SStructureFactorDerv2(refDict,im,G,hfx,pfx,SGData,SSGData,calcControls,parmDict)) |
|---|
| 3746 | else: |
|---|
| 3747 | if Phase['General']['Type'] == 'magnetic': |
|---|
| 3748 | dFdvDict = MagStructureFactorDerv(refDict,G,hfx,pfx,SGData,calcControls,parmDict) |
|---|
| 3749 | dFdvDict.update(MagStructureFactorDerv2(refDict,G,hfx,pfx,SGData,calcControls,parmDict)) |
|---|
| 3750 | else: |
|---|
| 3751 | dFdvDict = StructureFactorDerv2(refDict,G,hfx,pfx,SGData,calcControls,parmDict) |
|---|
| 3752 | ApplyRBModelDervs(dFdvDict,parmDict,rigidbodyDict,Phase) |
|---|
| 3753 | # determine the parameters that will have derivatives computed only at end |
|---|
| 3754 | nonatomvarylist = [] |
|---|
| 3755 | for name in varylist: |
|---|
| 3756 | if '::RBV;' not in name: |
|---|
| 3757 | try: |
|---|
| 3758 | aname = name.split(pfx)[1][:2] |
|---|
| 3759 | if aname not in ['Af','dA','AU','RB','AM','Xs','Xc','Ys','Yc','Zs','Zc', \ |
|---|
| 3760 | 'Tm','Xm','Ym','Zm','U1','U2','U3','MX','MY','MZ']: continue # skip anything not an atom or rigid body param |
|---|
| 3761 | except IndexError: |
|---|
| 3762 | continue |
|---|
| 3763 | nonatomvarylist.append(name) |
|---|
| 3764 | nonatomdependentVars = [] |
|---|
| 3765 | for name in dependentVars: |
|---|
| 3766 | if '::RBV;' not in name: |
|---|
| 3767 | try: |
|---|
| 3768 | aname = name.split(pfx)[1][:2] |
|---|
| 3769 | if aname not in ['Af','dA','AU','RB','AM','Xs','Xc','Ys','Yc','Zs','Zc', \ |
|---|
| 3770 | 'Tm','Xm','Ym','Zm','U1','U2','U3','MX','MY','MZ']: continue # skip anything not an atom or rigid body param |
|---|
| 3771 | except IndexError: |
|---|
| 3772 | continue |
|---|
| 3773 | nonatomdependentVars.append(name) |
|---|
| 3774 | #========================================================================================== |
|---|
| 3775 | #========================================================================================== |
|---|
| 3776 | for iref in range(prc,len(refDict['RefList']),tprc): |
|---|
| 3777 | refl = refDict['RefList'][iref] |
|---|
| 3778 | if im: |
|---|
| 3779 | h,k,l,m = refl[:4] |
|---|
| 3780 | else: |
|---|
| 3781 | h,k,l = refl[:3] |
|---|
| 3782 | Uniq = np.inner(refl[:3],SGMT) |
|---|
| 3783 | if 'T' in calcControls[hfx+'histType']: |
|---|
| 3784 | wave = refl[14+im] |
|---|
| 3785 | if 'E' in calcControls[hfx+'histType']: |
|---|
| 3786 | dIdsh,dIdsp,dIdpola,dIdPO,dFdODF,dFdSA,dFdAb,dFdEx = [[],[],[],[],[],[],[],[]] |
|---|
| 3787 | else: |
|---|
| 3788 | dIdsh,dIdsp,dIdpola,dIdPO,dFdODF,dFdSA,dFdAb,dFdEx = GetIntensityDerv(refl,im,wave,Uniq,G,g,pfx,phfx,hfx,SGData,calcControls,parmDict) |
|---|
| 3789 | if 'C' in calcControls[hfx+'histType']: #CW powder |
|---|
| 3790 | Wd,fmin,fmax = G2pwd.getWidthsCW(refl[5+im],refl[6+im],refl[7+im],shl) |
|---|
| 3791 | elif 'T' in calcControls[hfx+'histType']: |
|---|
| 3792 | Wd,fmin,fmax = G2pwd.getWidthsTOF(refl[5+im],refl[12+im],refl[13+im],refl[6+im],refl[7+im]) |
|---|
| 3793 | elif 'B' in calcControls[hfx+'histType']: |
|---|
| 3794 | Wd,fmin,fmax = G2pwd.getWidthsTOF(refl[5+im],refl[12+im],refl[13+im],refl[6+im]/1.e4,refl[7+im]/100.) |
|---|
| 3795 | elif 'E' in calcControls[hfx+'histType']: |
|---|
| 3796 | Wd,fmin,fmax = G2pwd.getWidthsED(refl[5+im],refl[6+im]) |
|---|
| 3797 | iBeg = np.searchsorted(x,refl[5+im]-fmin) |
|---|
| 3798 | iFin = np.searchsorted(x,refl[5+im]+fmax) |
|---|
| 3799 | if not iBeg+iFin: #peak below low limit - skip peak |
|---|
| 3800 | continue |
|---|
| 3801 | elif not iBeg-iFin: #peak above high limit - done |
|---|
| 3802 | break |
|---|
| 3803 | pos = refl[5+im] |
|---|
| 3804 | if 'C' in calcControls[hfx+'histType']: |
|---|
| 3805 | tanth = tand(pos/2.0) |
|---|
| 3806 | costh = cosd(pos/2.0) |
|---|
| 3807 | lenBF = iFin-iBeg |
|---|
| 3808 | dMdpk = np.zeros(shape=(6,lenBF)) |
|---|
| 3809 | dMdipk = G2pwd.getdFCJVoigt3(refl[5+im],refl[6+im],refl[7+im],shl,ma.getdata(x[iBeg:iFin])) |
|---|
| 3810 | for i in range(5): |
|---|
| 3811 | dMdpk[i] += refl[11+im]*refl[9+im]*dMdipk[i] |
|---|
| 3812 | dervDict = {'int':dMdpk[0],'pos':dMdpk[1],'sig':dMdpk[2],'gam':dMdpk[3],'shl':dMdpk[4],'L1/L2':np.zeros_like(dMdpk[0])} |
|---|
| 3813 | if Ka2: |
|---|
| 3814 | pos2 = refl[5+im]+lamRatio*tanth # + 360/pi * Dlam/lam * tan(th) |
|---|
| 3815 | iBeg2 = np.searchsorted(x,pos2-fmin) |
|---|
| 3816 | iFin2 = np.searchsorted(x,pos2+fmax) |
|---|
| 3817 | if iBeg2-iFin2: |
|---|
| 3818 | lenBF2 = iFin2-iBeg2 |
|---|
| 3819 | dMdpk2 = np.zeros(shape=(6,lenBF2)) |
|---|
| 3820 | dMdipk2 = G2pwd.getdFCJVoigt3(pos2,refl[6+im],refl[7+im],shl,ma.getdata(x[iBeg2:iFin2])) |
|---|
| 3821 | for i in range(5): |
|---|
| 3822 | dMdpk2[i] = refl[11+im]*refl[9+im]*kRatio*dMdipk2[i] |
|---|
| 3823 | dMdpk2[5] = refl[11+im]*dMdipk2[0] |
|---|
| 3824 | dervDict2 = {'int':dMdpk2[0],'pos':dMdpk2[1],'sig':dMdpk2[2],'gam':dMdpk2[3],'shl':dMdpk2[4],'L1/L2':dMdpk2[5]*refl[9]} |
|---|
| 3825 | elif 'T' in calcControls[hfx+'histType']: |
|---|
| 3826 | lenBF = iFin-iBeg |
|---|
| 3827 | if lenBF < 0: #bad peak coeff |
|---|
| 3828 | break |
|---|
| 3829 | dMdpk = np.zeros(shape=(6,lenBF)) |
|---|
| 3830 | dMdipk = G2pwd.getdEpsVoigt(refl[5+im],refl[12+im],refl[13+im],refl[6+im],refl[7+im],ma.getdata(x[iBeg:iFin])) |
|---|
| 3831 | for i in range(6): |
|---|
| 3832 | dMdpk[i] += refl[11+im]*refl[9+im]*dMdipk[i] |
|---|
| 3833 | dervDict = {'int':dMdpk[0],'pos':dMdpk[1],'alp':dMdpk[2],'bet':dMdpk[3],'sig':dMdpk[4],'gam':dMdpk[5]} |
|---|
| 3834 | elif 'B' in calcControls[hfx+'histType']: |
|---|
| 3835 | tanth = tand(pos/2.0) |
|---|
| 3836 | costh = cosd(pos/2.0) |
|---|
| 3837 | lenBF = iFin-iBeg |
|---|
| 3838 | if lenBF < 0: #bad peak coeff |
|---|
| 3839 | break |
|---|
| 3840 | dMdpk = np.zeros(shape=(6,lenBF)) |
|---|
| 3841 | dMdipk = G2pwd.getdEpsVoigt(refl[5+im],refl[12+im],refl[13+im],refl[6+im]/1.e4,refl[7+im]/100.,ma.getdata(x[iBeg:iFin])) |
|---|
| 3842 | for i in range(6): |
|---|
| 3843 | dMdpk[i] = refl[11+im]*refl[9+im]*dMdipk[i] |
|---|
| 3844 | dervDict = {'int':dMdpk[0],'pos':dMdpk[1],'alp':dMdpk[2],'bet':dMdpk[3],'sig':dMdpk[4]/1.e4,'gam':dMdpk[5]/100.} |
|---|
| 3845 | elif 'E' in calcControls[hfx+'histType']: |
|---|
| 3846 | lenBF = iFin-iBeg |
|---|
| 3847 | if lenBF < 0: #bad peak coeff |
|---|
| 3848 | break |
|---|
| 3849 | dMdpk = np.zeros(shape=(4,lenBF)) |
|---|
| 3850 | dMdipk = G2pwd.getdPsVoigt(refl[5+im],refl[6+im]*10**4,0.001,ma.getdata(x[iBeg:iFin])) |
|---|
| 3851 | for i in range(4): |
|---|
| 3852 | dMdpk[i] = refl[9+im]*dMdipk[i] |
|---|
| 3853 | dervDict = {'int':dMdpk[0],'pos':-dMdpk[1],'sig':dMdpk[2]*1.e4} |
|---|
| 3854 | if Phase['General'].get('doPawley'): |
|---|
| 3855 | dMdpw = np.zeros(len(x)) |
|---|
| 3856 | try: |
|---|
| 3857 | if im: |
|---|
| 3858 | pIdx = pfx+'PWLref:'+str(pawleyLookup[pfx+'%d,%d,%d,%d'%(h,k,l,m)]) |
|---|
| 3859 | else: |
|---|
| 3860 | pIdx = pfx+'PWLref:'+str(pawleyLookup[pfx+'%d,%d,%d'%(h,k,l)]) |
|---|
| 3861 | idx = varylist.index(pIdx) |
|---|
| 3862 | dMdpw[iBeg:iFin] = dervDict['int']/refl[9+im] |
|---|
| 3863 | if Ka2: #not for TOF either |
|---|
| 3864 | dMdpw[iBeg2:iFin2] += dervDict2['int']/refl[9+im] |
|---|
| 3865 | dMdv[idx] = dMdpw |
|---|
| 3866 | except: # ValueError: |
|---|
| 3867 | pass |
|---|
| 3868 | if 'C' in calcControls[hfx+'histType']: |
|---|
| 3869 | dpdA,dpdw,dpdZ,dpdSh,dpdTr,dpdX,dpdY,dpdV = GetReflPosDerv(refl,im,wave,A,pfx,hfx,phfx,calcControls,parmDict) |
|---|
| 3870 | names = {hfx+'Scale':[dIdsh,'int'],hfx+'Polariz.':[dIdpola,'int'],phfx+'Scale':[dIdsp,'int'], |
|---|
| 3871 | hfx+'U':[tanth**2,'sig'],hfx+'V':[tanth,'sig'],hfx+'W':[1.0,'sig'], |
|---|
| 3872 | hfx+'X':[1.0/costh,'gam'],hfx+'Y':[tanth,'gam'],hfx+'Z':[1.0,'gam'],hfx+'SH/L':[1.0,'shl'], |
|---|
| 3873 | hfx+'I(L2)/I(L1)':[1.0,'L1/L2'],hfx+'Zero':[dpdZ,'pos'],hfx+'Lam':[dpdw,'pos'], |
|---|
| 3874 | hfx+'Shift':[dpdSh,'pos'],hfx+'Transparency':[dpdTr,'pos'],hfx+'DisplaceX':[dpdX,'pos'], |
|---|
| 3875 | hfx+'DisplaceY':[dpdY,'pos'],phfx+'Extinction':[dFdEx,'int'],phfx+'LayerDisp':[dpdY,'pos']} |
|---|
| 3876 | if 'Bragg' in calcControls[hfx+'instType']: |
|---|
| 3877 | names.update({hfx+'SurfRoughA':[dFdAb[0],'int'], |
|---|
| 3878 | hfx+'SurfRoughB':[dFdAb[1],'int'],}) |
|---|
| 3879 | else: |
|---|
| 3880 | names.update({hfx+'Absorption':[dFdAb,'int'],}) |
|---|
| 3881 | elif 'T' in calcControls[hfx+'histType']: #'T'OF |
|---|
| 3882 | dpdA,dpdZ,dpdDC,dpdDA,dpdDB,dpdV = GetReflPosDerv(refl,im,0.0,A,pfx,hfx,phfx,calcControls,parmDict) |
|---|
| 3883 | names = {hfx+'Scale':[dIdsh,'int'],phfx+'Scale':[dIdsp,'int'], |
|---|
| 3884 | hfx+'difC':[dpdDC,'pos'],hfx+'difA':[dpdDA,'pos'],hfx+'difB':[dpdDB,'pos'], |
|---|
| 3885 | hfx+'Zero':[dpdZ,'pos'],hfx+'X':[refl[4+im],'gam'],hfx+'Y':[refl[4+im]**2,'gam'],hfx+'Z':[1.0,'gam'], |
|---|
| 3886 | hfx+'alpha':[1./refl[4+im],'alp'],hfx+'beta-0':[1.0,'bet'],hfx+'beta-1':[1./refl[4+im]**4,'bet'], |
|---|
| 3887 | hfx+'beta-q':[1./refl[4+im]**2,'bet'],hfx+'sig-0':[1.0,'sig'],hfx+'sig-1':[refl[4+im]**2,'sig'], |
|---|
| 3888 | hfx+'sig-2':[refl[4+im]**4,'sig'],hfx+'sig-q':[refl[4+im],'sig'], |
|---|
| 3889 | hfx+'Absorption':[dFdAb,'int'],phfx+'Extinction':[dFdEx,'int'],} |
|---|
| 3890 | elif 'B' in calcControls[hfx+'histType']: |
|---|
| 3891 | dpdA,dpdw,dpdZ,dpdSh,dpdTr,dpdX,dpdY,dpdV = GetReflPosDerv(refl,im,wave,A,pfx,hfx,phfx,calcControls,parmDict) |
|---|
| 3892 | names = {hfx+'Scale':[dIdsh,'int'],phfx+'Scale':[dIdsp,'int'],hfx+'Lam':[dpdw,'pos'], |
|---|
| 3893 | hfx+'Zero':[dpdZ,'pos'],hfx+'X':[1.0/costh,'gam'],hfx+'Y':[tanth,'gam'],hfx+'Z':[1.0,'gam'], |
|---|
| 3894 | hfx+'U':[tanth**2,'sig'],hfx+'V':[tanth,'sig'],hfx+'W':[1.0,'sig'],hfx+'Polariz.':[dIdpola,'int'], |
|---|
| 3895 | hfx+'alpha-0':[1.0,'alp'],hfx+'alpha-1':[tanth,'alp'],hfx+'beta-0':[1.0,'bet'],hfx+'beta-1':[tanth,'bet'], |
|---|
| 3896 | hfx+'Absorption':[dFdAb,'int'],phfx+'Extinction':[dFdEx,'int'],hfx+'DisplaceX':[dpdX,'pos'],hfx+'DisplaceY':[dpdY,'pos']} |
|---|
| 3897 | elif 'E' in calcControls[hfx+'histType']: |
|---|
| 3898 | dpdA,dpdTTh,dpdXE,dpdYE,dpdZE = GetReflPosDerv(refl,im,0.0,A,pfx,hfx,phfx,calcControls,parmDict) |
|---|
| 3899 | names = {hfx+'Scale':[dIdsh,'int'],hfx+'2-theta':[dpdTTh,'pos'], |
|---|
| 3900 | hfx+'A':[refl[5+im]**2,'sig'],hfx+'B':[refl[5+im],'sig'],hfx+'C':[1.0,'sig'], |
|---|
| 3901 | hfx+'XE':[dpdXE,'pos'],hfx+'YE':[dpdYE,'pos'],hfx+'ZE':[dpdZE,'pos'] } |
|---|
| 3902 | for name in names: |
|---|
| 3903 | item = names[name] |
|---|
| 3904 | if name in varylist: |
|---|
| 3905 | dMdv[varylist.index(name)][iBeg:iFin] += item[0]*dervDict[item[1]] |
|---|
| 3906 | if Ka2 and iFin2-iBeg2: |
|---|
| 3907 | dMdv[varylist.index(name)][iBeg2:iFin2] += item[0]*dervDict2[item[1]] |
|---|
| 3908 | elif name in dependentVars: |
|---|
| 3909 | depDerivDict[name][iBeg:iFin] += item[0]*dervDict[item[1]] |
|---|
| 3910 | if Ka2 and iFin2-iBeg2: |
|---|
| 3911 | depDerivDict[name][iBeg2:iFin2] += item[0]*dervDict2[item[1]] |
|---|
| 3912 | for iPO in dIdPO: |
|---|
| 3913 | if iPO in varylist: |
|---|
| 3914 | dMdv[varylist.index(iPO)][iBeg:iFin] += dIdPO[iPO]*dervDict['int'] |
|---|
| 3915 | if Ka2 and iFin2-iBeg2: |
|---|
| 3916 | dMdv[varylist.index(iPO)][iBeg2:iFin2] += dIdPO[iPO]*dervDict2['int'] |
|---|
| 3917 | elif iPO in dependentVars: |
|---|
| 3918 | depDerivDict[iPO][iBeg:iFin] += dIdPO[iPO]*dervDict['int'] |
|---|
| 3919 | if Ka2 and iFin2-iBeg2: |
|---|
| 3920 | depDerivDict[iPO][iBeg2:iFin2] += dIdPO[iPO]*dervDict2['int'] |
|---|
| 3921 | for i,name in enumerate(['omega','chi','phi']): |
|---|
| 3922 | aname = pfx+'SH '+name |
|---|
| 3923 | if aname in varylist: |
|---|
| 3924 | dMdv[varylist.index(aname)][iBeg:iFin] += dFdSA[i]*dervDict['int'] |
|---|
| 3925 | if Ka2 and iFin2-iBeg2: |
|---|
| 3926 | dMdv[varylist.index(aname)][iBeg2:iFin2] += dFdSA[i]*dervDict2['int'] |
|---|
| 3927 | elif aname in dependentVars: |
|---|
| 3928 | depDerivDict[aname][iBeg:iFin] += dFdSA[i]*dervDict['int'] |
|---|
| 3929 | if Ka2 and iFin2-iBeg2: |
|---|
| 3930 | depDerivDict[aname][iBeg2:iFin2] += dFdSA[i]*dervDict2['int'] |
|---|
| 3931 | for iSH in dFdODF: |
|---|
| 3932 | if iSH in varylist: |
|---|
| 3933 | dMdv[varylist.index(iSH)][iBeg:iFin] += dFdODF[iSH]*dervDict['int'] |
|---|
| 3934 | if Ka2 and iFin2-iBeg2: |
|---|
| 3935 | dMdv[varylist.index(iSH)][iBeg2:iFin2] += dFdODF[iSH]*dervDict2['int'] |
|---|
| 3936 | elif iSH in dependentVars: |
|---|
| 3937 | depDerivDict[iSH][iBeg:iFin] += dFdODF[iSH]*dervDict['int'] |
|---|
| 3938 | if Ka2 and iFin2-iBeg2: |
|---|
| 3939 | depDerivDict[iSH][iBeg2:iFin2] += dFdODF[iSH]*dervDict2['int'] |
|---|
| 3940 | cellDervNames = cellVaryDerv(pfx,SGData,dpdA) |
|---|
| 3941 | for name,dpdA in cellDervNames: |
|---|
| 3942 | if name in varylist: |
|---|
| 3943 | dMdv[varylist.index(name)][iBeg:iFin] += dpdA*dervDict['pos'] |
|---|
| 3944 | if Ka2 and iFin2-iBeg2: |
|---|
| 3945 | dMdv[varylist.index(name)][iBeg2:iFin2] += dpdA*dervDict2['pos'] |
|---|
| 3946 | elif name in dependentVars: #need to scale for mixed phase constraints? |
|---|
| 3947 | depDerivDict[name][iBeg:iFin] += dpdA*dervDict['pos'] |
|---|
| 3948 | if Ka2 and iFin2-iBeg2: |
|---|
| 3949 | depDerivDict[name][iBeg2:iFin2] += dpdA*dervDict2['pos'] |
|---|
| 3950 | dDijDict = GetHStrainShiftDerv(refl,im,SGData,phfx,hfx,calcControls,parmDict) |
|---|
| 3951 | for name in dDijDict: |
|---|
| 3952 | if name in varylist: |
|---|
| 3953 | dMdv[varylist.index(name)][iBeg:iFin] += dDijDict[name]*dervDict['pos'] |
|---|
| 3954 | if Ka2 and iFin2-iBeg2: |
|---|
| 3955 | dMdv[varylist.index(name)][iBeg2:iFin2] += dDijDict[name]*dervDict2['pos'] |
|---|
| 3956 | elif name in dependentVars: |
|---|
| 3957 | depDerivDict[name][iBeg:iFin] += dDijDict[name]*dervDict['pos'] |
|---|
| 3958 | if Ka2 and iFin2-iBeg2: |
|---|
| 3959 | depDerivDict[name][iBeg2:iFin2] += dDijDict[name]*dervDict2['pos'] |
|---|
| 3960 | #TODO: need Layer Disp deriv here |
|---|
| 3961 | for i,name in enumerate([pfx+'mV0',pfx+'mV1',pfx+'mV2']): |
|---|
| 3962 | if name in varylist: |
|---|
| 3963 | dMdv[varylist.index(name)][iBeg:iFin] += dpdV[i]*dervDict['pos'] |
|---|
| 3964 | if Ka2 and iFin2-iBeg2: |
|---|
| 3965 | dMdv[varylist.index(name)][iBeg2:iFin2] += dpdV[i]*dervDict2['pos'] |
|---|
| 3966 | elif name in dependentVars: |
|---|
| 3967 | depDerivDict[name][iBeg:iFin] += dpdV[i]*dervDict['pos'] |
|---|
| 3968 | if Ka2 and iFin2-iBeg2: |
|---|
| 3969 | depDerivDict[name][iBeg2:iFin2] += dpdV[i]*dervDict2['pos'] |
|---|
| 3970 | if 'C' in calcControls[hfx+'histType'] or 'B' in calcControls[hfx+'histType']: |
|---|
| 3971 | sigDict,gamDict = GetSampleSigGamDerv(refl,im,wave,G,GB,SGData,hfx,phfx,calcControls,parmDict) |
|---|
| 3972 | elif 'T' in calcControls[hfx+'histType']: #'T'OF |
|---|
| 3973 | sigDict,gamDict = GetSampleSigGamDerv(refl,im,0.0,G,GB,SGData,hfx,phfx,calcControls,parmDict) |
|---|
| 3974 | else: #'E' |
|---|
| 3975 | sigDict = {} |
|---|
| 3976 | gamDict = {} |
|---|
| 3977 | for name in gamDict: |
|---|
| 3978 | if name in varylist: |
|---|
| 3979 | dMdv[varylist.index(name)][iBeg:iFin] += gamDict[name]*dervDict['gam'] |
|---|
| 3980 | if Ka2 and iFin2-iBeg2: |
|---|
| 3981 | dMdv[varylist.index(name)][iBeg2:iFin2] += gamDict[name]*dervDict2['gam'] |
|---|
| 3982 | elif name in dependentVars: |
|---|
| 3983 | depDerivDict[name][iBeg:iFin] += gamDict[name]*dervDict['gam'] |
|---|
| 3984 | if Ka2 and iFin2-iBeg2: |
|---|
| 3985 | depDerivDict[name][iBeg2:iFin2] += gamDict[name]*dervDict2['gam'] |
|---|
| 3986 | for name in sigDict: |
|---|
| 3987 | if name in varylist: |
|---|
| 3988 | dMdv[varylist.index(name)][iBeg:iFin] += sigDict[name]*dervDict['sig'] |
|---|
| 3989 | if Ka2 and iFin2-iBeg2: |
|---|
| 3990 | dMdv[varylist.index(name)][iBeg2:iFin2] += sigDict[name]*dervDict2['sig'] |
|---|
| 3991 | elif name in dependentVars: |
|---|
| 3992 | depDerivDict[name][iBeg:iFin] += sigDict[name]*dervDict['sig'] |
|---|
| 3993 | if Ka2 and iFin2-iBeg2: |
|---|
| 3994 | depDerivDict[name][iBeg2:iFin2] += sigDict[name]*dervDict2['sig'] |
|---|
| 3995 | for name in ['BabA','BabU']: |
|---|
| 3996 | if refl[9+im]: |
|---|
| 3997 | if phfx+name in varylist: |
|---|
| 3998 | dMdv[varylist.index(phfx+name)][iBeg:iFin] += parmDict[phfx+'Scale']*dFdvDict[phfx+name][iref]*dervDict['int']/refl[9+im] |
|---|
| 3999 | if Ka2 and iFin2-iBeg2: |
|---|
| 4000 | dMdv[varylist.index(phfx+name)][iBeg2:iFin2] += parmDict[phfx+'Scale']*dFdvDict[phfx+name][iref]*dervDict2['int']/refl[9+im] |
|---|
| 4001 | elif phfx+name in dependentVars: |
|---|
| 4002 | depDerivDict[phfx+name][iBeg:iFin] += parmDict[phfx+'Scale']*dFdvDict[phfx+name][iref]*dervDict['int']/refl[9+im] |
|---|
| 4003 | if Ka2 and iFin2-iBeg2: |
|---|
| 4004 | depDerivDict[phfx+name][iBeg2:iFin2] += parmDict[phfx+'Scale']*dFdvDict[phfx+name][iref]*dervDict2['int']/refl[9+im] |
|---|
| 4005 | if not Phase['General'].get('doPawley') and not parmDict.get(phfx+'LeBail') and 'E' not in calcControls[hfx+'histType']: |
|---|
| 4006 | #do atom derivatives - for RB,F,X & U so far - how do I scale mixed phase constraints? |
|---|
| 4007 | corr = 0. |
|---|
| 4008 | corr2 = 0. |
|---|
| 4009 | if refl[9+im]: |
|---|
| 4010 | corr = dervDict['int']/refl[9+im] |
|---|
| 4011 | if Ka2 and iFin2-iBeg2: |
|---|
| 4012 | corr2 = dervDict2['int']/refl[9+im] |
|---|
| 4013 | for name in nonatomvarylist: |
|---|
| 4014 | dMdv[varylist.index(name)][iBeg:iFin] += dFdvDict[name][iref]*corr |
|---|
| 4015 | if Ka2 and iFin2-iBeg2: |
|---|
| 4016 | dMdv[varylist.index(name)][iBeg2:iFin2] += dFdvDict[name][iref]*corr2 |
|---|
| 4017 | for name in nonatomdependentVars: |
|---|
| 4018 | depDerivDict[name][iBeg:iFin] += dFdvDict[name][iref]*corr |
|---|
| 4019 | if Ka2 and iFin2-iBeg2: |
|---|
| 4020 | depDerivDict[name][iBeg2:iFin2] += dFdvDict[name][iref]*corr2 |
|---|
| 4021 | # now process derivatives in constraints |
|---|
| 4022 | dMdv[:,ma.getmaskarray(x)] = 0. # instead of masking, zero out masked values |
|---|
| 4023 | #G2mv.Dict2Deriv(varylist,depDerivDict,dMdv) |
|---|
| 4024 | return dMdv,depDerivDict |
|---|
| 4025 | |
|---|
| 4026 | def UserRejectHKL(ref,im,userReject): |
|---|
| 4027 | if ref[5+im]/ref[6+im] < userReject['minF/sig']: |
|---|
| 4028 | return False |
|---|
| 4029 | elif userReject['MaxD'] < ref[4+im] > userReject['MinD']: |
|---|
| 4030 | return False |
|---|
| 4031 | elif ref[11+im] < userReject['MinExt']: |
|---|
| 4032 | return False |
|---|
| 4033 | elif abs(ref[5+im]-ref[7+im])/ref[6+im] > userReject['MaxDF/F']: |
|---|
| 4034 | return False |
|---|
| 4035 | return True |
|---|
| 4036 | |
|---|
| 4037 | def dervHKLF(Histogram,Phase,calcControls,varylist,parmDict,rigidbodyDict): |
|---|
| 4038 | '''Loop over reflections in a HKLF histogram and compute derivatives of the fitting |
|---|
| 4039 | model (M) with respect to all parameters. Independent and dependant dM/dp arrays |
|---|
| 4040 | are returned to either dervRefine or HessRefine. |
|---|
| 4041 | |
|---|
| 4042 | :returns: |
|---|
| 4043 | ''' |
|---|
| 4044 | hId = Histogram['hId'] |
|---|
| 4045 | hfx = ':%d:'%(hId) |
|---|
| 4046 | pfx = '%d::'%(Phase['pId']) |
|---|
| 4047 | phfx = '%d:%d:'%(Phase['pId'],hId) |
|---|
| 4048 | SGData = Phase['General']['SGData'] |
|---|
| 4049 | im = 0 |
|---|
| 4050 | if Phase['General'].get('Modulated',False): |
|---|
| 4051 | SSGData = Phase['General']['SSGData'] |
|---|
| 4052 | im = 1 #offset in SS reflection list |
|---|
| 4053 | A = [parmDict[pfx+'A%d'%(i)] for i in range(6)] |
|---|
| 4054 | G,g = G2lat.A2Gmat(A) #recip & real metric tensors |
|---|
| 4055 | TwinLaw = calcControls[phfx+'TwinLaw'] |
|---|
| 4056 | refDict = Histogram['Data'] |
|---|
| 4057 | if parmDict[phfx+'Scale'] < 0.: |
|---|
| 4058 | parmDict[phfx+'Scale'] = .001 |
|---|
| 4059 | if im: # split to nontwin/twin versions |
|---|
| 4060 | if len(TwinLaw) > 1: |
|---|
| 4061 | dFdvDict = SStructureFactorDervTw(refDict,im,G,hfx,pfx,SGData,SSGData,calcControls,parmDict) #not ok |
|---|
| 4062 | else: |
|---|
| 4063 | dFdvDict = SStructureFactorDerv(refDict,im,G,hfx,pfx,SGData,SSGData,calcControls,parmDict) #OK |
|---|
| 4064 | dFdvDict.update(SStructureFactorDerv2(refDict,im,G,hfx,pfx,SGData,SSGData,calcControls,parmDict)) |
|---|
| 4065 | else: |
|---|
| 4066 | if len(TwinLaw) > 1: |
|---|
| 4067 | dFdvDict = StructureFactorDervTw2(refDict,G,hfx,pfx,SGData,calcControls,parmDict) |
|---|
| 4068 | else: #correct!! |
|---|
| 4069 | if Phase['General']['Type'] == 'magnetic': |
|---|
| 4070 | dFdvDict = MagStructureFactorDerv(refDict,G,hfx,pfx,SGData,calcControls,parmDict) |
|---|
| 4071 | dFdvDict.update(MagStructureFactorDerv2(refDict,G,hfx,pfx,SGData,calcControls,parmDict)) |
|---|
| 4072 | else: |
|---|
| 4073 | dFdvDict = StructureFactorDerv2(refDict,G,hfx,pfx,SGData,calcControls,parmDict) |
|---|
| 4074 | ApplyRBModelDervs(dFdvDict,parmDict,rigidbodyDict,Phase) |
|---|
| 4075 | dMdvh = np.zeros((len(varylist),len(refDict['RefList']))) |
|---|
| 4076 | dependentVars = G2mv.GetDependentVars() |
|---|
| 4077 | depDerivDict = {} |
|---|
| 4078 | for j in dependentVars: |
|---|
| 4079 | depDerivDict[j] = np.zeros(shape=(len(refDict['RefList']))) |
|---|
| 4080 | wdf = np.zeros(len(refDict['RefList'])) |
|---|
| 4081 | if calcControls['F**2']: |
|---|
| 4082 | for iref,ref in enumerate(refDict['RefList']): |
|---|
| 4083 | if ref[6+im] > 0: |
|---|
| 4084 | dervDict,dervCor = SCExtinction(ref,im,phfx,hfx,pfx,calcControls,parmDict,varylist+dependentVars)[1:] |
|---|
| 4085 | w = 1.0/ref[6+im] |
|---|
| 4086 | if ref[3+im] > 0: |
|---|
| 4087 | wdf[iref] = w*(ref[5+im]-ref[7+im]) |
|---|
| 4088 | for j,var in enumerate(varylist): |
|---|
| 4089 | if var in dFdvDict: |
|---|
| 4090 | dMdvh[j][iref] = w*dFdvDict[var][iref]*parmDict[phfx+'Scale']*ref[11+im] |
|---|
| 4091 | for var in dependentVars: |
|---|
| 4092 | if var in dFdvDict: |
|---|
| 4093 | depDerivDict[var][iref] = w*dFdvDict[var][iref]*parmDict[phfx+'Scale']*ref[11+im] |
|---|
| 4094 | if phfx+'Scale' in varylist: |
|---|
| 4095 | dMdvh[varylist.index(phfx+'Scale')][iref] = w*ref[7+im]*ref[11+im]/parmDict[phfx+'Scale'] #OK |
|---|
| 4096 | elif phfx+'Scale' in dependentVars: |
|---|
| 4097 | depDerivDict[phfx+'Scale'][iref] = w*ref[7+im]*ref[11+im]/parmDict[phfx+'Scale'] #OK |
|---|
| 4098 | for item in ['Ep','Es','Eg']: |
|---|
| 4099 | if phfx+item in varylist and phfx+item in dervDict: |
|---|
| 4100 | dMdvh[varylist.index(phfx+item)][iref] = w*dervDict[phfx+item]/ref[11+im] #OK |
|---|
| 4101 | elif phfx+item in dependentVars and phfx+item in dervDict: |
|---|
| 4102 | depDerivDict[phfx+item][iref] = w*dervDict[phfx+item]/ref[11+im] #OK |
|---|
| 4103 | for item in ['BabA','BabU']: |
|---|
| 4104 | if phfx+item in varylist: |
|---|
| 4105 | dMdvh[varylist.index(phfx+item)][iref] = w*dFdvDict[phfx+item][iref]*parmDict[phfx+'Scale']*ref[11+im] |
|---|
| 4106 | elif phfx+item in dependentVars: |
|---|
| 4107 | depDerivDict[phfx+item][iref] = w*dFdvDict[phfx+item][iref]*parmDict[phfx+'Scale']*ref[11+im] |
|---|
| 4108 | else: #F refinement |
|---|
| 4109 | for iref,ref in enumerate(refDict['RefList']): |
|---|
| 4110 | if ref[5+im] > 0.: |
|---|
| 4111 | dervDict,dervCor = SCExtinction(ref,im,phfx,hfx,pfx,calcControls,parmDict,varylist+dependentVars)[1:] |
|---|
| 4112 | Fo = np.sqrt(ref[5+im]) |
|---|
| 4113 | Fc = np.sqrt(ref[7+im]) |
|---|
| 4114 | w = 1.0/ref[6+im] |
|---|
| 4115 | if ref[3+im] > 0: |
|---|
| 4116 | wdf[iref] = 2.0*Fc*w*(Fo-Fc) |
|---|
| 4117 | for j,var in enumerate(varylist): |
|---|
| 4118 | if var in dFdvDict: |
|---|
| 4119 | dMdvh[j][iref] = w*dFdvDict[var][iref]*parmDict[phfx+'Scale']*ref[11+im] |
|---|
| 4120 | for var in dependentVars: |
|---|
| 4121 | if var in dFdvDict: |
|---|
| 4122 | depDerivDict[var][iref] = w*dFdvDict[var][iref]*parmDict[phfx+'Scale']*ref[11+im] |
|---|
| 4123 | if phfx+'Scale' in varylist: |
|---|
| 4124 | dMdvh[varylist.index(phfx+'Scale')][iref] = w*ref[7+im]*ref[11+im]/parmDict[phfx+'Scale'] #OK |
|---|
| 4125 | elif phfx+'Scale' in dependentVars: |
|---|
| 4126 | depDerivDict[phfx+'Scale'][iref] = w*ref[7+im]*ref[11+im]/parmDict[phfx+'Scale'] #OK |
|---|
| 4127 | for item in ['Ep','Es','Eg']: #OK! |
|---|
| 4128 | if phfx+item in varylist and phfx+item in dervDict: |
|---|
| 4129 | dMdvh[varylist.index(phfx+item)][iref] = w*dervDict[phfx+item]/ref[11+im] |
|---|
| 4130 | elif phfx+item in dependentVars and phfx+item in dervDict: |
|---|
| 4131 | depDerivDict[phfx+item][iref] = w*dervDict[phfx+item]/ref[11+im] |
|---|
| 4132 | for item in ['BabA','BabU']: |
|---|
| 4133 | if phfx+item in varylist: |
|---|
| 4134 | dMdvh[varylist.index(phfx+item)][iref] = w*dFdvDict[phfx+item][iref]*parmDict[phfx+'Scale']*ref[11+im] |
|---|
| 4135 | elif phfx+item in dependentVars: |
|---|
| 4136 | depDerivDict[phfx+item][iref] = w*dFdvDict[phfx+item][iref]*parmDict[phfx+'Scale']*ref[11+im] |
|---|
| 4137 | return dMdvh,depDerivDict,wdf |
|---|
| 4138 | |
|---|
| 4139 | |
|---|
| 4140 | def dervRefine(values,HistoPhases,parmDict,varylist,calcControls,pawleyLookup,dlg): |
|---|
| 4141 | '''Loop over histograms and compute derivatives of the fitting |
|---|
| 4142 | model (M) with respect to all parameters. Results are returned in |
|---|
| 4143 | a Jacobian matrix (aka design matrix) of dimensions (n by m) where |
|---|
| 4144 | n is the number of parameters and m is the number of data |
|---|
| 4145 | points. This can exceed memory when m gets large. This routine is |
|---|
| 4146 | used when refinement derivatives are selected as "analtytic |
|---|
| 4147 | Jacobian" in Controls. |
|---|
| 4148 | |
|---|
| 4149 | :returns: Jacobian numpy.array dMdv for all histograms concatinated |
|---|
| 4150 | ''' |
|---|
| 4151 | parmDict.update(zip(varylist,values)) |
|---|
| 4152 | G2mv.Dict2Map(parmDict) |
|---|
| 4153 | Histograms,Phases,restraintDict,rigidbodyDict = HistoPhases |
|---|
| 4154 | dependentVars = G2mv.GetDependentVars() |
|---|
| 4155 | histoList = list(Histograms.keys()) |
|---|
| 4156 | histoList.sort() |
|---|
| 4157 | First = True |
|---|
| 4158 | for histogram in histoList: |
|---|
| 4159 | if 'PWDR' in histogram[:4]: |
|---|
| 4160 | Histogram = Histograms[histogram] |
|---|
| 4161 | hId = Histogram['hId'] |
|---|
| 4162 | hfx = ':%d:'%(hId) |
|---|
| 4163 | wtFactor = calcControls[hfx+'wtFactor'] |
|---|
| 4164 | Limits = calcControls[hfx+'Limits'] |
|---|
| 4165 | x,y,w,yc,yb,yd = Histogram['Data'] |
|---|
| 4166 | xB = np.searchsorted(x,Limits[0]) |
|---|
| 4167 | xF = np.searchsorted(x,Limits[1])+1 |
|---|
| 4168 | dMdv,depDerivDict = getPowderProfileDerv([parmDict,x[xB:xF], |
|---|
| 4169 | varylist,Histogram,Phases,rigidbodyDict,calcControls,pawleyLookup,dependentVars]) |
|---|
| 4170 | G2mv.Dict2Deriv(varylist,depDerivDict,dMdv) |
|---|
| 4171 | dMdvh = np.sqrt(w[xB:xF])*dMdv |
|---|
| 4172 | elif 'HKLF' in histogram[:4]: |
|---|
| 4173 | Histogram = Histograms[histogram] |
|---|
| 4174 | phase = Histogram['Reflection Lists'] |
|---|
| 4175 | Phase = Phases[phase] |
|---|
| 4176 | dMdvh,depDerivDict,wdf = dervHKLF(Histogram,Phase,calcControls,varylist,parmDict,rigidbodyDict) |
|---|
| 4177 | hfx = ':%d:'%(Histogram['hId']) |
|---|
| 4178 | wtFactor = calcControls[hfx+'wtFactor'] |
|---|
| 4179 | # now process derivatives in constraints |
|---|
| 4180 | G2mv.Dict2Deriv(varylist,depDerivDict,dMdvh) |
|---|
| 4181 | else: |
|---|
| 4182 | continue #skip non-histogram entries |
|---|
| 4183 | if First: |
|---|
| 4184 | dMdV = np.sqrt(wtFactor)*dMdvh |
|---|
| 4185 | First = False |
|---|
| 4186 | else: |
|---|
| 4187 | dMdV = np.concatenate((dMdV.T,np.sqrt(wtFactor)*dMdvh.T)).T |
|---|
| 4188 | |
|---|
| 4189 | GetFobsSq(Histograms,Phases,parmDict,calcControls) |
|---|
| 4190 | pNames,pVals,pWt,pWsum,pWnum = penaltyFxn(HistoPhases,calcControls,parmDict,varylist) |
|---|
| 4191 | if np.any(pVals): |
|---|
| 4192 | dpdv = penaltyDeriv(pNames,pVals,HistoPhases,calcControls,parmDict,varylist) |
|---|
| 4193 | dMdV = np.concatenate((dMdV.T,(np.sqrt(pWt)*dpdv).T)).T |
|---|
| 4194 | |
|---|
| 4195 | return dMdV |
|---|
| 4196 | |
|---|
| 4197 | def HessRefine(values,HistoPhases,parmDict,varylist,calcControls,pawleyLookup,dlg): |
|---|
| 4198 | '''Loop over histograms and compute derivatives of the fitting |
|---|
| 4199 | model (M) with respect to all parameters. For each histogram, the |
|---|
| 4200 | Jacobian matrix, dMdv, with dimensions (n by m) where n is the |
|---|
| 4201 | number of parameters and m is the number of data points *in the |
|---|
| 4202 | histogram*. The (n by n) Hessian is computed from each Jacobian |
|---|
| 4203 | and it is returned. This routine is used when refinement |
|---|
| 4204 | derivatives are selected as "analtytic Hessian" in Controls. |
|---|
| 4205 | |
|---|
| 4206 | :returns: Vec,Hess where Vec is the least-squares vector and Hess is the Hessian |
|---|
| 4207 | ''' |
|---|
| 4208 | parmDict.update(zip(varylist,values)) |
|---|
| 4209 | G2mv.Dict2Map(parmDict) |
|---|
| 4210 | Histograms,Phases,restraintDict,rigidbodyDict = HistoPhases |
|---|
| 4211 | dependentVars = G2mv.GetDependentVars() |
|---|
| 4212 | #fixup H atom positions here? |
|---|
| 4213 | ApplyRBModels(parmDict,Phases,rigidbodyDict) #,Update=True?? |
|---|
| 4214 | Hess = np.empty(0) |
|---|
| 4215 | Vec = np.empty(0) |
|---|
| 4216 | histoList = list(Histograms.keys()) |
|---|
| 4217 | histoList.sort() |
|---|
| 4218 | for histogram in histoList: |
|---|
| 4219 | if 'PWDR' in histogram[:4]: |
|---|
| 4220 | if hasattr(dlg,'SetHistogram'): dlg.SetHistogram(None,'Computing derivatives for '+histogram) |
|---|
| 4221 | Histogram = Histograms[histogram] |
|---|
| 4222 | hId = Histogram['hId'] |
|---|
| 4223 | hfx = ':%d:'%(hId) |
|---|
| 4224 | wtFactor = calcControls[hfx+'wtFactor'] |
|---|
| 4225 | Limits = calcControls[hfx+'Limits'] |
|---|
| 4226 | x,y,w,yc,yb,yd = Histogram['Data'] |
|---|
| 4227 | W = wtFactor*w |
|---|
| 4228 | dy = y-yc |
|---|
| 4229 | xB = np.searchsorted(x,Limits[0]) |
|---|
| 4230 | xF = np.searchsorted(x,Limits[1])+1 |
|---|
| 4231 | useMP,ncores = G2mp.InitMP() |
|---|
| 4232 | if GSASIIpath.GetConfigValue('Show_timing',False): starttime = time.time() |
|---|
| 4233 | if useMP: |
|---|
| 4234 | MPpool = mp.Pool(ncores) |
|---|
| 4235 | dMdvh = None |
|---|
| 4236 | depDerivDict = None |
|---|
| 4237 | # old approach, create all args prior to use |
|---|
| 4238 | # profArgs = [ |
|---|
| 4239 | # (parmDict,x[xB:xF],varylist,Histogram,Phases,rigidbodyDict,calcControls,pawleyLookup,dependentVars, |
|---|
| 4240 | # i,ncores,histogram) for i in range(ncores)] |
|---|
| 4241 | # for dmdv,depDerivs in MPpool.imap_unordered(getPowderProfileDerv,profArgs): |
|---|
| 4242 | # better, use a generator so arg is created as used |
|---|
| 4243 | profGenArgs = ( |
|---|
| 4244 | (parmDict,x[xB:xF],varylist,Histogram,Phases,rigidbodyDict,calcControls,pawleyLookup,dependentVars, |
|---|
| 4245 | i,ncores,histogram) for i in range(ncores)) |
|---|
| 4246 | for dmdv,depDerivs in MPpool.imap_unordered(getPowderProfileDerv,profGenArgs): |
|---|
| 4247 | if dMdvh is None: |
|---|
| 4248 | dMdvh = dmdv |
|---|
| 4249 | depDerivDict = depDerivs |
|---|
| 4250 | else: |
|---|
| 4251 | dMdvh += dmdv |
|---|
| 4252 | for key in depDerivs.keys(): depDerivDict[key] += depDerivs[key] |
|---|
| 4253 | MPpool.terminate() |
|---|
| 4254 | else: |
|---|
| 4255 | dMdvh,depDerivDict = getPowderProfileDerv([parmDict,x[xB:xF], |
|---|
| 4256 | varylist,Histogram,Phases,rigidbodyDict,calcControls,pawleyLookup,dependentVars,0,1,histogram]) |
|---|
| 4257 | #dMdvh = getPowderProfileDerv(parmDict,x[xB:xF], |
|---|
| 4258 | # varylist,Histogram,Phases,rigidbodyDict,calcControls,pawleyLookup,dependentVars) |
|---|
| 4259 | G2mv.Dict2Deriv(varylist,depDerivDict,dMdvh) |
|---|
| 4260 | if GSASIIpath.GetConfigValue('Show_timing',False): print ('getPowderProfileDerv t=%.3f'%(time.time()-starttime)) |
|---|
| 4261 | Wt = ma.sqrt(W[xB:xF])[nxs,:] |
|---|
| 4262 | Dy = dy[xB:xF][nxs,:] |
|---|
| 4263 | dMdvh *= Wt |
|---|
| 4264 | if dlg: |
|---|
| 4265 | GoOn = dlg.Update(Histogram['Residuals']['wR'],newmsg='Hessian for histogram %d\nAll data Rw=%8.3f%s'%(hId,Histogram['Residuals']['wR'],'%')) |
|---|
| 4266 | if type(GoOn) is tuple: |
|---|
| 4267 | if not GoOn[0]: |
|---|
| 4268 | raise G2obj.G2RefineCancel('Cancel pressed') |
|---|
| 4269 | elif not GoOn: |
|---|
| 4270 | raise G2obj.G2RefineCancel('Cancel pressed') |
|---|
| 4271 | #dlg.Raise() |
|---|
| 4272 | if len(Hess): |
|---|
| 4273 | Hess += np.inner(dMdvh,dMdvh) |
|---|
| 4274 | dMdvh *= Wt*Dy |
|---|
| 4275 | Vec += np.sum(dMdvh,axis=1) |
|---|
| 4276 | else: |
|---|
| 4277 | Hess = np.inner(dMdvh,dMdvh) |
|---|
| 4278 | dMdvh *= Wt*Dy |
|---|
| 4279 | Vec = np.sum(dMdvh,axis=1) |
|---|
| 4280 | elif 'HKLF' in histogram[:4]: |
|---|
| 4281 | if hasattr(dlg,'SetHistogram'): dlg.SetHistogram(None,'Computing derivatives for '+histogram) |
|---|
| 4282 | Histogram = Histograms[histogram] |
|---|
| 4283 | phase = Histogram['Reflection Lists'] |
|---|
| 4284 | Phase = Phases[phase] |
|---|
| 4285 | dMdvh,depDerivDict,wdf = dervHKLF(Histogram,Phase,calcControls,varylist,parmDict,rigidbodyDict) |
|---|
| 4286 | hId = Histogram['hId'] |
|---|
| 4287 | hfx = ':%d:'%(Histogram['hId']) |
|---|
| 4288 | wtFactor = calcControls[hfx+'wtFactor'] |
|---|
| 4289 | # now process derivatives in constraints |
|---|
| 4290 | G2mv.Dict2Deriv(varylist,depDerivDict,dMdvh) |
|---|
| 4291 | # print 'matrix build time: %.3f'%(time.time()-time0) |
|---|
| 4292 | |
|---|
| 4293 | if dlg: |
|---|
| 4294 | GoOn = dlg.Update(Histogram['Residuals']['wR'],newmsg='Hessian for histogram %d Rw=%8.3f%s'%(hId,Histogram['Residuals']['wR'],'%')) |
|---|
| 4295 | if type(GoOn) is tuple: |
|---|
| 4296 | if not GoOn[0]: |
|---|
| 4297 | raise G2obj.G2RefineCancel('Cancel pressed') |
|---|
| 4298 | elif not GoOn: |
|---|
| 4299 | raise G2obj.G2RefineCancel('Cancel pressed') |
|---|
| 4300 | #dlg.Raise() |
|---|
| 4301 | if len(Hess): |
|---|
| 4302 | Vec += wtFactor*np.sum(dMdvh*wdf,axis=1) |
|---|
| 4303 | Hess += wtFactor*np.inner(dMdvh,dMdvh) |
|---|
| 4304 | else: |
|---|
| 4305 | Vec = wtFactor*np.sum(dMdvh*wdf,axis=1) |
|---|
| 4306 | Hess = wtFactor*np.inner(dMdvh,dMdvh) |
|---|
| 4307 | else: |
|---|
| 4308 | continue #skip non-histogram entries |
|---|
| 4309 | GetFobsSq(Histograms,Phases,parmDict,calcControls) |
|---|
| 4310 | pNames,pVals,pWt,pWsum,pWnum = penaltyFxn(HistoPhases,calcControls,parmDict,varylist) |
|---|
| 4311 | if np.any(pVals): |
|---|
| 4312 | dpdv = penaltyDeriv(pNames,pVals,HistoPhases,calcControls,parmDict,varylist) |
|---|
| 4313 | Vec -= np.sum(dpdv*pWt*pVals,axis=1) |
|---|
| 4314 | Hess += np.inner(dpdv*pWt,dpdv) |
|---|
| 4315 | return Vec,Hess |
|---|
| 4316 | |
|---|
| 4317 | def errRefine(values,HistoPhases,parmDict,varylist,calcControls,pawleyLookup,dlg=None): |
|---|
| 4318 | '''Computes the point-by-point discrepancies between every data point in every histogram |
|---|
| 4319 | and the observed value. Used in the Jacobian, Hessian & numeric least-squares to compute function |
|---|
| 4320 | |
|---|
| 4321 | :returns: an np array of differences between observed and computed diffraction values. |
|---|
| 4322 | ''' |
|---|
| 4323 | Values2Dict(parmDict, varylist, values) |
|---|
| 4324 | if len(varylist): #skip if no variables; e.g. in a zero cycle LeBail refinement |
|---|
| 4325 | G2mv.Dict2Map(parmDict) |
|---|
| 4326 | Histograms,Phases,restraintDict,rigidbodyDict = HistoPhases |
|---|
| 4327 | M = np.empty(0) |
|---|
| 4328 | SumwYo = 0 |
|---|
| 4329 | Nobs = 0 |
|---|
| 4330 | Nrej = 0 |
|---|
| 4331 | Next = 0 |
|---|
| 4332 | ApplyRBModels(parmDict,Phases,rigidbodyDict) |
|---|
| 4333 | #fixup Hatom positions here.... |
|---|
| 4334 | histoList = list(Histograms.keys()) |
|---|
| 4335 | histoList.sort() |
|---|
| 4336 | phasePartials = calcControls.get('PhasePartials',None) |
|---|
| 4337 | if phasePartials: |
|---|
| 4338 | print('Storing intensity by phase in',phasePartials) |
|---|
| 4339 | phPartialFP = open(phasePartials,'wb') # create/clear partials file |
|---|
| 4340 | phPartialFP.close() |
|---|
| 4341 | for histogram in histoList: |
|---|
| 4342 | if 'PWDR' in histogram[:4]: |
|---|
| 4343 | Histogram = Histograms[histogram] |
|---|
| 4344 | hId = Histogram['hId'] |
|---|
| 4345 | if hasattr(dlg,'SetHistogram'): dlg.SetHistogram(hId,histogram) |
|---|
| 4346 | hfx = ':%d:'%(hId) |
|---|
| 4347 | wtFactor = calcControls[hfx+'wtFactor'] |
|---|
| 4348 | Limits = calcControls[hfx+'Limits'] |
|---|
| 4349 | x,y,w,yc,yb,yd = Histogram['Data'] |
|---|
| 4350 | yc *= 0.0 #zero full calcd profiles |
|---|
| 4351 | yb *= 0.0 |
|---|
| 4352 | yd *= 0.0 |
|---|
| 4353 | xB = np.searchsorted(x,Limits[0]) |
|---|
| 4354 | xF = np.searchsorted(x,Limits[1])+1 |
|---|
| 4355 | yc[xB:xF],yb[xB:xF] = getPowderProfile(parmDict,x[xB:xF], |
|---|
| 4356 | varylist,Histogram,Phases,calcControls,pawleyLookup,histogram) |
|---|
| 4357 | yc[xB:xF] += yb[xB:xF] |
|---|
| 4358 | if not np.any(y): #fill dummy data |
|---|
| 4359 | try: |
|---|
| 4360 | rv = st.poisson(yc[xB:xF]) |
|---|
| 4361 | y[xB:xF] = rv.rvs() |
|---|
| 4362 | except ValueError: |
|---|
| 4363 | y[xB:xF] = yc[xB:xF] |
|---|
| 4364 | Z = np.ones_like(yc[xB:xF]) |
|---|
| 4365 | Z[1::2] *= -1 |
|---|
| 4366 | y[xB:xF] = yc[xB:xF]+np.abs(y[xB:xF]-yc[xB:xF])*Z |
|---|
| 4367 | w[xB:xF] = np.where(y[xB:xF]>0.,1./y[xB:xF],1.0) |
|---|
| 4368 | yd[xB:xF] = y[xB:xF]-yc[xB:xF] |
|---|
| 4369 | W = wtFactor*w |
|---|
| 4370 | wdy = -ma.sqrt(w[xB:xF])*(yd[xB:xF]) |
|---|
| 4371 | Histogram['Residuals']['Durbin-Watson'] = ma.sum(ma.diff(wdy)**2)/ma.sum(wdy**2) |
|---|
| 4372 | wdy *= np.sqrt(wtFactor) |
|---|
| 4373 | Histogram['Residuals']['Nobs'] = ma.count(x[xB:xF]) |
|---|
| 4374 | Nobs += Histogram['Residuals']['Nobs'] |
|---|
| 4375 | Histogram['Residuals']['sumwYo'] = ma.sum(W[xB:xF]*y[xB:xF]**2) |
|---|
| 4376 | SumwYo += Histogram['Residuals']['sumwYo'] |
|---|
| 4377 | Histogram['Residuals']['R'] = min(100.,ma.sum(ma.abs(yd[xB:xF]))/ma.sum(y[xB:xF])*100.) |
|---|
| 4378 | Histogram['Residuals']['wR'] = min(100.,ma.sqrt(ma.sum(wdy**2)/Histogram['Residuals']['sumwYo'])*100.) |
|---|
| 4379 | sumYmB = ma.sum(ma.where(yc[xB:xF]!=yb[xB:xF],ma.abs(y[xB:xF]-yb[xB:xF]),0.)) |
|---|
| 4380 | sumwYmB2 = ma.sum(ma.where(yc[xB:xF]!=yb[xB:xF],W[xB:xF]*(y[xB:xF]-yb[xB:xF])**2,0.)) |
|---|
| 4381 | sumYB = ma.sum(ma.where(yc[xB:xF]!=yb[xB:xF],ma.abs(y[xB:xF]-yc[xB:xF])*ma.abs(y[xB:xF]-yb[xB:xF])/y[xB:xF],0.)) |
|---|
| 4382 | sumwYB2 = ma.sum(ma.where(yc[xB:xF]!=yb[xB:xF],W[xB:xF]*(ma.abs(y[xB:xF]-yc[xB:xF])*ma.abs(y[xB:xF]-yb[xB:xF])/y[xB:xF])**2,0.)) |
|---|
| 4383 | Histogram['Residuals']['Rb'] = min(100.,100.*sumYB/sumYmB) |
|---|
| 4384 | Histogram['Residuals']['wRb'] = min(100.,100.*ma.sqrt(sumwYB2/sumwYmB2)) |
|---|
| 4385 | Histogram['Residuals']['wRmin'] = min(100.,100.*ma.sqrt(Histogram['Residuals']['Nobs']/Histogram['Residuals']['sumwYo'])) |
|---|
| 4386 | if dlg: |
|---|
| 4387 | GoOn = dlg.Update(Histogram['Residuals']['wR'],newmsg='For histogram %d Rw=%8.3f%s'%(hId,Histogram['Residuals']['wR'],'%')) |
|---|
| 4388 | if type(GoOn) is tuple: |
|---|
| 4389 | if not GoOn[0]: |
|---|
| 4390 | raise G2obj.G2RefineCancel('Cancel pressed') |
|---|
| 4391 | elif not GoOn: |
|---|
| 4392 | raise G2obj.G2RefineCancel('Cancel pressed') |
|---|
| 4393 | #dlg.Raise() |
|---|
| 4394 | M = np.concatenate((M,wdy)) |
|---|
| 4395 | #end of PWDR processing |
|---|
| 4396 | elif 'HKLF' in histogram[:4]: |
|---|
| 4397 | Histogram = Histograms[histogram] |
|---|
| 4398 | hId = Histogram['hId'] |
|---|
| 4399 | if hasattr(dlg,'SetHistogram'): dlg.SetHistogram(hId,histogram) |
|---|
| 4400 | Histogram['Residuals'] = {} |
|---|
| 4401 | phase = Histogram['Reflection Lists'] |
|---|
| 4402 | Phase = Phases[phase] |
|---|
| 4403 | hfx = ':%d:'%(hId) |
|---|
| 4404 | wtFactor = calcControls[hfx+'wtFactor'] |
|---|
| 4405 | pfx = '%d::'%(Phase['pId']) |
|---|
| 4406 | phfx = '%d:%d:'%(Phase['pId'],hId) |
|---|
| 4407 | SGData = Phase['General']['SGData'] |
|---|
| 4408 | TwinLaw = calcControls[phfx+'TwinLaw'] |
|---|
| 4409 | im = 0 |
|---|
| 4410 | if parmDict[phfx+'Scale'] < 0.: |
|---|
| 4411 | parmDict[phfx+'Scale'] = .001 |
|---|
| 4412 | if Phase['General'].get('Modulated',False): |
|---|
| 4413 | SSGData = Phase['General']['SSGData'] |
|---|
| 4414 | im = 1 #offset in SS reflection list |
|---|
| 4415 | A = [parmDict[pfx+'A%d'%(i)] for i in range(6)] |
|---|
| 4416 | G,g = G2lat.A2Gmat(A) #recip & real metric tensors |
|---|
| 4417 | refDict = Histogram['Data'] |
|---|
| 4418 | if im: |
|---|
| 4419 | if len(TwinLaw) > 1: |
|---|
| 4420 | SStructureFactorTw(refDict,G,hfx,pfx,SGData,SSGData,calcControls,parmDict) |
|---|
| 4421 | else: |
|---|
| 4422 | SStructureFactor(refDict,G,hfx,pfx,SGData,SSGData,calcControls,parmDict) |
|---|
| 4423 | else: |
|---|
| 4424 | StructureFactor2(refDict,G,hfx,pfx,SGData,calcControls,parmDict) |
|---|
| 4425 | # print 'sf-calc time: %.3f'%(time.time()-time0) |
|---|
| 4426 | df = np.zeros(len(refDict['RefList'])) |
|---|
| 4427 | sumwYo = 0 |
|---|
| 4428 | sumFo = 0 |
|---|
| 4429 | sumFo2 = 0 |
|---|
| 4430 | sumFc2 = 0 |
|---|
| 4431 | sumdF = 0 |
|---|
| 4432 | sumdF2 = 0 |
|---|
| 4433 | if im: |
|---|
| 4434 | sumSSFo = np.zeros(10) |
|---|
| 4435 | sumSSFo2 = np.zeros(10) |
|---|
| 4436 | sumSSdF = np.zeros(10) |
|---|
| 4437 | sumSSdF2 = np.zeros(10) |
|---|
| 4438 | sumSSwYo = np.zeros(10) |
|---|
| 4439 | sumSSwdf2 = np.zeros(10) |
|---|
| 4440 | SSnobs = np.zeros(10) |
|---|
| 4441 | nobs = 0 |
|---|
| 4442 | nrej = 0 |
|---|
| 4443 | next = 0 |
|---|
| 4444 | maxH = 0 |
|---|
| 4445 | if calcControls['F**2']: |
|---|
| 4446 | for i,ref in enumerate(refDict['RefList']): |
|---|
| 4447 | if ref[6+im] > 0: |
|---|
| 4448 | ref[11+im] = SCExtinction(ref,im,phfx,hfx,pfx,calcControls,parmDict,varylist)[0] |
|---|
| 4449 | w = 1.0/ref[6+im] # 1/sig(F^2) |
|---|
| 4450 | ref[7+im] *= parmDict[phfx+'Scale']*ref[11+im] #correct Fc^2 for extinction |
|---|
| 4451 | ref[8+im] = ref[5+im]/(parmDict[phfx+'Scale']*ref[11+im]) |
|---|
| 4452 | if UserRejectHKL(ref,im,calcControls['UsrReject']) and ref[3+im]: #skip sp.gp. absences (mul=0) |
|---|
| 4453 | ref[3+im] = abs(ref[3+im]) #mark as allowed |
|---|
| 4454 | Fo = np.sqrt(ref[5+im]) |
|---|
| 4455 | sumFo += Fo |
|---|
| 4456 | sumFo2 += ref[5+im] |
|---|
| 4457 | sumFc2 += ref[7+im] |
|---|
| 4458 | sumdF += abs(Fo-np.sqrt(ref[7+im])) |
|---|
| 4459 | sumdF2 += abs(ref[5+im]-ref[7+im]) |
|---|
| 4460 | nobs += 1 |
|---|
| 4461 | df[i] = -w*(ref[5+im]-ref[7+im]) |
|---|
| 4462 | sumwYo += (w*ref[5+im])**2 #w*Fo^2 |
|---|
| 4463 | if im: #accumulate super lattice sums |
|---|
| 4464 | ind = int(abs(ref[3])) |
|---|
| 4465 | sumSSFo[ind] += Fo |
|---|
| 4466 | sumSSFo2[ind] += ref[5+im] |
|---|
| 4467 | sumSSdF[ind] += abs(Fo-np.sqrt(ref[7+im])) |
|---|
| 4468 | sumSSdF2[ind] += abs(ref[5+im]-ref[7+im]) |
|---|
| 4469 | sumSSwYo[ind] += (w*ref[5+im])**2 #w*Fo^2 |
|---|
| 4470 | sumSSwdf2[ind] += df[i]**2 |
|---|
| 4471 | SSnobs[ind] += 1 |
|---|
| 4472 | maxH = max(maxH,ind) |
|---|
| 4473 | else: |
|---|
| 4474 | if ref[3+im]: |
|---|
| 4475 | ref[3+im] = -abs(ref[3+im]) #mark as rejected |
|---|
| 4476 | nrej += 1 |
|---|
| 4477 | else: #sp.gp.extinct |
|---|
| 4478 | next += 1 |
|---|
| 4479 | else: |
|---|
| 4480 | for i,ref in enumerate(refDict['RefList']): |
|---|
| 4481 | if ref[5+im] > 0.: |
|---|
| 4482 | ref[11+im] = SCExtinction(ref,im,phfx,hfx,pfx,calcControls,parmDict,varylist)[0] |
|---|
| 4483 | ref[7+im] *= parmDict[phfx+'Scale']*ref[11+im] #correct Fc^2 for extinction |
|---|
| 4484 | ref[8+im] = ref[5+im]/(parmDict[phfx+'Scale']*ref[11+im]) |
|---|
| 4485 | Fo = np.sqrt(ref[5+im]) |
|---|
| 4486 | Fc = np.sqrt(ref[7+im]) |
|---|
| 4487 | w = 2.0*Fo/ref[6+im] # 1/sig(F)? |
|---|
| 4488 | if UserRejectHKL(ref,im,calcControls['UsrReject']) and ref[3+im]: #skip sp.gp. absences (mul=0) |
|---|
| 4489 | ref[3+im] = abs(ref[3+im]) #mark as allowed |
|---|
| 4490 | sumFo += Fo |
|---|
| 4491 | sumFo2 += ref[5+im] |
|---|
| 4492 | sumFc2 += ref[7+im] |
|---|
| 4493 | sumdF += abs(Fo-Fc) |
|---|
| 4494 | sumdF2 += abs(ref[5+im]-ref[7+im]) |
|---|
| 4495 | nobs += 1 |
|---|
| 4496 | df[i] = -w*(Fo-Fc) |
|---|
| 4497 | sumwYo += (w*Fo)**2 |
|---|
| 4498 | if im: |
|---|
| 4499 | ind = int(abs(ref[3])) |
|---|
| 4500 | sumSSFo[ind] += Fo |
|---|
| 4501 | sumSSFo2[ind] += ref[5+im] |
|---|
| 4502 | sumSSdF[ind] += abs(Fo-Fc) |
|---|
| 4503 | sumSSdF2[ind] += abs(ref[5+im]-ref[7+im]) |
|---|
| 4504 | sumSSwYo[ind] += (w*Fo)**2 |
|---|
| 4505 | sumSSwdf2[ind] += df[i]**2 |
|---|
| 4506 | SSnobs[ind] += 1 |
|---|
| 4507 | maxH = max(maxH,ind) |
|---|
| 4508 | else: |
|---|
| 4509 | if ref[3+im]: |
|---|
| 4510 | ref[3+im] = -abs(ref[3+im]) #mark as rejected |
|---|
| 4511 | nrej += 1 |
|---|
| 4512 | else: #sp.gp.extinct |
|---|
| 4513 | next += 1 |
|---|
| 4514 | Scale = sumFo2/sumFc2 |
|---|
| 4515 | if (Scale < 0.8 or Scale > 1.2) and phfx+'Scale' in varylist: |
|---|
| 4516 | print ('New scale: %.4f'%(Scale*parmDict[phfx+'Scale'])) |
|---|
| 4517 | indx = varylist.index(phfx+'Scale') |
|---|
| 4518 | values[indx] = Scale*parmDict[phfx+'Scale'] |
|---|
| 4519 | Histogram['Residuals']['Nobs'] = nobs |
|---|
| 4520 | Histogram['Residuals']['sumwYo'] = sumwYo |
|---|
| 4521 | SumwYo += sumwYo |
|---|
| 4522 | Histogram['Residuals']['wR'] = min(100.,np.sqrt(np.sum(df**2)/sumwYo)*100.) |
|---|
| 4523 | Histogram['Residuals'][phfx+'Rf'] = 100.*sumdF/sumFo |
|---|
| 4524 | Histogram['Residuals'][phfx+'Rf^2'] = 100.*sumdF2/sumFo2 |
|---|
| 4525 | Histogram['Residuals'][phfx+'Nref'] = nobs |
|---|
| 4526 | Histogram['Residuals'][phfx+'Nrej'] = nrej |
|---|
| 4527 | Histogram['Residuals'][phfx+'Next'] = next |
|---|
| 4528 | if im: |
|---|
| 4529 | Histogram['Residuals'][phfx+'SSRf'] = 100.*sumSSdF[:maxH+1]/sumSSFo[:maxH+1] |
|---|
| 4530 | Histogram['Residuals'][phfx+'SSRf^2'] = 100.*sumSSdF2[:maxH+1]/sumSSFo2[:maxH+1] |
|---|
| 4531 | Histogram['Residuals'][phfx+'SSNref'] = SSnobs[:maxH+1] |
|---|
| 4532 | Histogram['Residuals']['SSwR'] = np.sqrt(sumSSwdf2[:maxH+1]/sumSSwYo[:maxH+1])*100. |
|---|
| 4533 | Nobs += nobs |
|---|
| 4534 | Nrej += nrej |
|---|
| 4535 | Next += next |
|---|
| 4536 | if dlg: |
|---|
| 4537 | GoOn = dlg.Update(Histogram['Residuals']['wR'],newmsg='For histogram %d Rw=%8.3f%s'%(hId,Histogram['Residuals']['wR'],'%')) |
|---|
| 4538 | if type(GoOn) is tuple: |
|---|
| 4539 | if not GoOn[0]: |
|---|
| 4540 | raise G2obj.G2RefineCancel('Cancel pressed') |
|---|
| 4541 | elif not GoOn: |
|---|
| 4542 | raise G2obj.G2RefineCancel('Cancel pressed') |
|---|
| 4543 | #dlg.Raise() |
|---|
| 4544 | M = np.concatenate((M,wtFactor*df)) |
|---|
| 4545 | # end of HKLF processing |
|---|
| 4546 | # GetFobsSq(Histograms,Phases,parmDict,calcControls) |
|---|
| 4547 | Histograms['sumwYo'] = SumwYo |
|---|
| 4548 | Histograms['Nobs'] = Nobs |
|---|
| 4549 | Histograms['Nrej'] = Nrej |
|---|
| 4550 | Histograms['Next'] = Next |
|---|
| 4551 | Rw = min(100.,np.sqrt(np.sum(M**2)/SumwYo)*100.) |
|---|
| 4552 | if dlg: |
|---|
| 4553 | if hasattr(dlg,'SetHistogram'): dlg.SetHistogram(-1,'overall') |
|---|
| 4554 | GoOn = dlg.Update(Rw,newmsg='%s%8.3f%s'%('All data Rw =',Rw,'%')) |
|---|
| 4555 | if type(GoOn) is tuple: |
|---|
| 4556 | if not GoOn[0]: |
|---|
| 4557 | parmDict['saved values'] = values |
|---|
| 4558 | raise G2obj.G2RefineCancel('Cancel pressed') |
|---|
| 4559 | elif not GoOn: |
|---|
| 4560 | parmDict['saved values'] = values |
|---|
| 4561 | raise G2obj.G2RefineCancel('Cancel pressed') |
|---|
| 4562 | #dlg.Raise() |
|---|
| 4563 | pDict,pVals,pWt,pWsum,pWnum = penaltyFxn(HistoPhases,calcControls,parmDict,varylist) |
|---|
| 4564 | if len(pVals): |
|---|
| 4565 | pSum = np.sum(pWt*pVals**2) |
|---|
| 4566 | for name in pWsum: |
|---|
| 4567 | if pWsum[name]: |
|---|
| 4568 | print (' Penalty function for %5d %8ss = %12.5g'%(pWnum[name],name,pWsum[name])) |
|---|
| 4569 | print ('Total penalty function: %12.5g on %d terms'%(pSum,len(pVals))) |
|---|
| 4570 | if hasattr(dlg,'SetHistogram'): dlg.SetHistogram(-2,'Restraints') |
|---|
| 4571 | Nobs += len(pVals) |
|---|
| 4572 | M = np.concatenate((M,np.sqrt(pWt)*pVals)) |
|---|
| 4573 | GoOn = dlg.Update(100*pSum/np.sum(M**2),newmsg='Restraints') |
|---|
| 4574 | return M |
|---|
| 4575 | |
|---|
| 4576 | def calcMassFracs(varyList,covMatrix,Phases,hist,hId): |
|---|
| 4577 | '''Compute mass fractions and their uncertainties for all |
|---|
| 4578 | phases in a histogram. Computed using the covariance matrix, |
|---|
| 4579 | along with the derivatives for the mass fraction equations. |
|---|
| 4580 | |
|---|
| 4581 | :param list varyList: list of varied parameters |
|---|
| 4582 | :param np.array covMatrix: covariance matrix, order of rows and columns |
|---|
| 4583 | must match varyList |
|---|
| 4584 | :param dict Phases: data structure (from tree or .gpx) with all |
|---|
| 4585 | phase information |
|---|
| 4586 | :param str hist: name of selected histogram |
|---|
| 4587 | :param int hId: number of current histogram |
|---|
| 4588 | :returns: valDict,sigDict which contain the mass fraction values and |
|---|
| 4589 | sigmas, keyed by "ph:h:WgtFrac" |
|---|
| 4590 | ''' |
|---|
| 4591 | # Compute mass normalizer & assemble list of refined PF terms |
|---|
| 4592 | wtSum = 0.0 |
|---|
| 4593 | mass = {} |
|---|
| 4594 | phFr = {} |
|---|
| 4595 | used = {} |
|---|
| 4596 | for phase in Phases: |
|---|
| 4597 | if Phases[phase]['General']['Type'] == 'magnetic': continue |
|---|
| 4598 | if Phases[phase]['General']['doPawley']: continue |
|---|
| 4599 | if hist not in Phases[phase]['Histograms']: continue |
|---|
| 4600 | if not Phases[phase]['Histograms'][hist]['Use']: continue |
|---|
| 4601 | pId = Phases[phase]['pId'] |
|---|
| 4602 | mass[pId] = Phases[phase]['General']['Mass'] |
|---|
| 4603 | phFr[pId] = Phases[phase]['Histograms'][hist]['Scale'][0] |
|---|
| 4604 | wtSum += mass[pId]*phFr[pId] |
|---|
| 4605 | # Is this PF refined? |
|---|
| 4606 | var = "{}:{}:Scale".format(pId,hId) |
|---|
| 4607 | if var in varyList: # yes, save it |
|---|
| 4608 | used[varyList.index(var)] = pId |
|---|
| 4609 | elif var in G2mv.GetDependentVars(): |
|---|
| 4610 | for v,m in zip(*G2mv.getInvConstraintEq(var,varyList)): |
|---|
| 4611 | if v not in varyList: continue |
|---|
| 4612 | i = varyList.index(v) |
|---|
| 4613 | if i not in used: used[i] = {} |
|---|
| 4614 | used[i][pId] = m |
|---|
| 4615 | valDict = {} |
|---|
| 4616 | sigDict = {} |
|---|
| 4617 | for phasej in Phases: |
|---|
| 4618 | if Phases[phasej]['General']['Type'] == 'magnetic': continue |
|---|
| 4619 | if Phases[phase]['General']['doPawley']: continue |
|---|
| 4620 | if hist not in Phases[phasej]['Histograms']: continue |
|---|
| 4621 | if not Phases[phasej]['Histograms'][hist]['Use']: continue |
|---|
| 4622 | if wtSum < 1.0: continue #no atoms; probable LeBail |
|---|
| 4623 | pId_j = Phases[phasej]['pId'] |
|---|
| 4624 | var = "{}:{}:WgtFrac".format(pId_j,hId) |
|---|
| 4625 | valDict[var] = mass[pId_j] * phFr[pId_j] / wtSum |
|---|
| 4626 | Avec = np.zeros(len(varyList)) |
|---|
| 4627 | for i in used: |
|---|
| 4628 | if type(used[i]) is dict: |
|---|
| 4629 | for pId_i in used[i]: |
|---|
| 4630 | if pId_i == pId_j: |
|---|
| 4631 | deriv = (mass[pId_j]/wtSum) - (mass[pId_j]**2 * phFr[pId_j]/wtSum**2) |
|---|
| 4632 | else: |
|---|
| 4633 | deriv = -mass[pId_j]* mass[pId_i] * phFr[pId_j]/wtSum**2 |
|---|
| 4634 | Avec[i] += used[i][pId_i] * deriv # dot product |
|---|
| 4635 | else: |
|---|
| 4636 | pId_i = used[i] |
|---|
| 4637 | if pId_i == pId_j: |
|---|
| 4638 | Avec[i] = (mass[pId_j]/wtSum) - (mass[pId_j]**2 * phFr[pId_j]/wtSum**2) |
|---|
| 4639 | else: |
|---|
| 4640 | Avec[i] = -mass[pId_j]* mass[pId_i] * phFr[pId_j]/wtSum**2 |
|---|
| 4641 | sigDict[var] = np.sqrt(np.inner(Avec.T,np.inner(covMatrix,Avec))) |
|---|
| 4642 | if len(valDict) == 1: return {},{} # don't add where only a single phase is present |
|---|
| 4643 | return valDict,sigDict |
|---|
