| 1 | # -*- coding: utf-8 -*- |
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| 2 | ########### SVN repository information ################### |
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| 3 | # $Date: 2016-12-06 18:52:55 +0000 (Tue, 06 Dec 2016) $ |
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| 4 | # $Author: vondreele $ |
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| 5 | # $Revision: 2562 $ |
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| 6 | # $URL: trunk/GSASIIstrIO.py $ |
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| 7 | # $Id: GSASIIstrIO.py 2562 2016-12-06 18:52:55Z vondreele $ |
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| 8 | ########### SVN repository information ################### |
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| 9 | ''' |
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| 10 | *GSASIIstrIO: structure I/O routines* |
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| 11 | ------------------------------------- |
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| 12 | |
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| 13 | ''' |
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| 14 | import os |
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| 15 | import os.path as ospath |
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| 16 | import time |
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| 17 | import math |
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| 18 | import copy |
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| 19 | import cPickle |
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| 20 | import numpy as np |
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| 21 | import numpy.ma as ma |
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| 22 | import GSASIIpath |
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| 23 | GSASIIpath.SetVersionNumber("$Revision: 2562 $") |
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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 GSASIIobj as G2obj |
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| 28 | import GSASIImapvars as G2mv |
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| 29 | import GSASIImath as G2mth |
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| 30 | |
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| 31 | sind = lambda x: np.sin(x*np.pi/180.) |
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| 32 | cosd = lambda x: np.cos(x*np.pi/180.) |
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| 33 | tand = lambda x: np.tan(x*np.pi/180.) |
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| 34 | asind = lambda x: 180.*np.arcsin(x)/np.pi |
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| 35 | acosd = lambda x: 180.*np.arccos(x)/np.pi |
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| 36 | atan2d = lambda y,x: 180.*np.arctan2(y,x)/np.pi |
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| 37 | |
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| 38 | ateln2 = 8.0*math.log(2.0) |
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| 39 | |
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| 40 | def GetControls(GPXfile): |
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| 41 | ''' Returns dictionary of control items found in GSASII gpx file |
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| 42 | |
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| 43 | :param str GPXfile: full .gpx file name |
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| 44 | :return: dictionary of control items |
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| 45 | ''' |
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| 46 | Controls = copy.copy(G2obj.DefaultControls) |
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| 47 | fl = open(GPXfile,'rb') |
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| 48 | while True: |
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| 49 | try: |
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| 50 | data = cPickle.load(fl) |
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| 51 | except EOFError: |
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| 52 | break |
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| 53 | datum = data[0] |
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| 54 | if datum[0] == 'Controls': |
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| 55 | Controls.update(datum[1]) |
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| 56 | fl.close() |
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| 57 | return Controls |
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| 58 | |
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| 59 | def GetConstraints(GPXfile): |
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| 60 | '''Read the constraints from the GPX file and interpret them |
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| 61 | |
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| 62 | called in :func:`ReadCheckConstraints`, :func:`GSASIIstrMain.Refine` |
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| 63 | and :func:`GSASIIstrMain.SeqRefine`. |
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| 64 | ''' |
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| 65 | fl = open(GPXfile,'rb') |
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| 66 | while True: |
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| 67 | try: |
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| 68 | data = cPickle.load(fl) |
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| 69 | except EOFError: |
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| 70 | break |
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| 71 | datum = data[0] |
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| 72 | if datum[0] == 'Constraints': |
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| 73 | constList = [] |
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| 74 | for item in datum[1]: |
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| 75 | if item.startswith('_'): continue |
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| 76 | constList += datum[1][item] |
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| 77 | fl.close() |
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| 78 | constDict,fixedList,ignored = ProcessConstraints(constList) |
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| 79 | if ignored: |
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| 80 | print ignored,'Constraints were rejected. Was a constrained phase, histogram or atom deleted?' |
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| 81 | return constDict,fixedList |
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| 82 | fl.close() |
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| 83 | raise Exception,"No constraints in GPX file" |
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| 84 | |
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| 85 | def ProcessConstraints(constList): |
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| 86 | """Interpret the constraints in the constList input into a dictionary, etc. |
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| 87 | All :class:`GSASIIobj.G2VarObj` objects are mapped to the appropriate |
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| 88 | phase/hist/atoms based on the object internals (random Ids). If this can't be |
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| 89 | done (if a phase has been deleted, etc.), the variable is ignored. |
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| 90 | If the constraint cannot be used due to too many dropped variables, |
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| 91 | it is counted as ignored. |
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| 92 | |
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| 93 | :param list constList: a list of lists where each item in the outer list |
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| 94 | specifies a constraint of some form, as described in the :mod:`GSASIIobj` |
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| 95 | :ref:`Constraint definition <Constraint_definitions_table>`. |
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| 96 | |
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| 97 | :returns: a tuple of (constDict,fixedList,ignored) where: |
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| 98 | |
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| 99 | * constDict (list of dicts) contains the constraint relationships |
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| 100 | * fixedList (list) contains the fixed values for each type |
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| 101 | of constraint. |
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| 102 | * ignored (int) counts the number of invalid constraint items |
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| 103 | (should always be zero!) |
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| 104 | """ |
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| 105 | constDict = [] |
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| 106 | fixedList = [] |
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| 107 | ignored = 0 |
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| 108 | for item in constList: |
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| 109 | if item[-1] == 'h': |
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| 110 | # process a hold |
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| 111 | fixedList.append('0') |
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| 112 | var = str(item[0][1]) |
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| 113 | if '?' not in var: |
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| 114 | constDict.append({var:0.0}) |
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| 115 | else: |
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| 116 | ignored += 1 |
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| 117 | elif item[-1] == 'f': |
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| 118 | # process a new variable |
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| 119 | fixedList.append(None) |
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| 120 | D = {} |
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| 121 | varyFlag = item[-2] |
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| 122 | varname = item[-3] |
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| 123 | for term in item[:-3]: |
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| 124 | var = str(term[1]) |
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| 125 | if '?' not in var: |
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| 126 | D[var] = term[0] |
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| 127 | if len(D) > 1: |
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| 128 | # add extra dict terms for input variable name and vary flag |
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| 129 | if varname is not None: |
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| 130 | if varname.startswith('::'): |
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| 131 | varname = varname[2:].replace(':',';') |
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| 132 | else: |
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| 133 | varname = varname.replace(':',';') |
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| 134 | D['_name'] = '::' + varname |
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| 135 | D['_vary'] = varyFlag == True # force to bool |
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| 136 | constDict.append(D) |
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| 137 | else: |
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| 138 | ignored += 1 |
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| 139 | #constFlag[-1] = ['Vary'] |
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| 140 | elif item[-1] == 'c': |
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| 141 | # process a contraint relationship |
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| 142 | D = {} |
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| 143 | for term in item[:-3]: |
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| 144 | var = str(term[1]) |
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| 145 | if '?' not in var: |
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| 146 | D[var] = term[0] |
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| 147 | if len(D) >= 1: |
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| 148 | fixedList.append(str(item[-3])) |
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| 149 | constDict.append(D) |
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| 150 | else: |
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| 151 | ignored += 1 |
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| 152 | elif item[-1] == 'e': |
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| 153 | # process an equivalence |
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| 154 | firstmult = None |
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| 155 | eqlist = [] |
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| 156 | for term in item[:-3]: |
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| 157 | if term[0] == 0: term[0] = 1.0 |
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| 158 | var = str(term[1]) |
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| 159 | if '?' in var: continue |
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| 160 | if firstmult is None: |
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| 161 | firstmult = term[0] |
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| 162 | firstvar = var |
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| 163 | else: |
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| 164 | eqlist.append([var,firstmult/term[0]]) |
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| 165 | if len(eqlist) > 0: |
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| 166 | G2mv.StoreEquivalence(firstvar,eqlist) |
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| 167 | else: |
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| 168 | ignored += 1 |
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| 169 | else: |
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| 170 | ignored += 1 |
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| 171 | return constDict,fixedList,ignored |
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| 172 | |
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| 173 | def ReadCheckConstraints(GPXfile): |
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| 174 | '''Load constraints and related info and return any error or warning messages''' |
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| 175 | # init constraints |
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| 176 | G2mv.InitVars() |
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| 177 | # get variables |
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| 178 | Histograms,Phases = GetUsedHistogramsAndPhases(GPXfile) |
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| 179 | if not Phases: |
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| 180 | return 'Error: No phases or no histograms in phases!','' |
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| 181 | if not Histograms: |
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| 182 | return 'Error: no diffraction data','' |
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| 183 | constrDict,fixedList = GetConstraints(GPXfile) # load user constraints before internally generated ones |
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| 184 | rigidbodyDict = GetRigidBodies(GPXfile) |
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| 185 | rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]}) |
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| 186 | rbVary,rbDict = GetRigidBodyModels(rigidbodyDict,Print=False) |
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| 187 | Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables,MFtables,maxSSwave = \ |
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| 188 | GetPhaseData(Phases,RestraintDict=None,rbIds=rbIds,Print=False) # generates atom symmetry constraints |
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| 189 | hapVary,hapDict,controlDict = GetHistogramPhaseData(Phases,Histograms,Print=False) |
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| 190 | histVary,histDict,controlDict = GetHistogramData(Histograms,Print=False) |
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| 191 | varyList = rbVary+phaseVary+hapVary+histVary |
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| 192 | errmsg, warnmsg = G2mv.CheckConstraints(varyList,constrDict,fixedList) |
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| 193 | if errmsg: |
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| 194 | # print some diagnostic info on the constraints |
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| 195 | print('Error in constraints:\n'+errmsg+ |
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| 196 | '\nRefinement not possible due to conflict in constraints, see below:\n') |
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| 197 | print G2mv.VarRemapShow(varyList,True) |
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| 198 | return errmsg, warnmsg |
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| 199 | |
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| 200 | def makeTwinFrConstr(Phases,Histograms,hapVary): |
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| 201 | TwConstr = [] |
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| 202 | TwFixed = [] |
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| 203 | for Phase in Phases: |
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| 204 | pId = Phases[Phase]['pId'] |
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| 205 | for Histogram in Phases[Phase]['Histograms']: |
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| 206 | try: |
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| 207 | hId = Histograms[Histogram]['hId'] |
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| 208 | phfx = '%d:%d:'%(pId,hId) |
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| 209 | if phfx+'TwinFr:0' in hapVary: |
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| 210 | TwFixed.append('1.0') #constraint value |
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| 211 | nTwin = len(Phases[Phase]['Histograms'][Histogram]['Twins']) |
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| 212 | TwConstr.append({phfx+'TwinFr:'+str(i):'1.0' for i in range(nTwin)}) |
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| 213 | except KeyError: #unused histograms? |
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| 214 | pass |
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| 215 | return TwConstr,TwFixed |
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| 216 | |
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| 217 | def GetRestraints(GPXfile): |
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| 218 | '''Read the restraints from the GPX file. |
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| 219 | Throws an exception if not found in the .GPX file |
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| 220 | ''' |
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| 221 | fl = open(GPXfile,'rb') |
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| 222 | while True: |
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| 223 | try: |
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| 224 | data = cPickle.load(fl) |
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| 225 | except EOFError: |
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| 226 | break |
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| 227 | datum = data[0] |
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| 228 | if datum[0] == 'Restraints': |
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| 229 | restraintDict = datum[1] |
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| 230 | fl.close() |
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| 231 | return restraintDict |
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| 232 | |
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| 233 | def GetRigidBodies(GPXfile): |
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| 234 | '''Read the rigid body models from the GPX file |
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| 235 | ''' |
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| 236 | fl = open(GPXfile,'rb') |
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| 237 | while True: |
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| 238 | try: |
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| 239 | data = cPickle.load(fl) |
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| 240 | except EOFError: |
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| 241 | break |
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| 242 | datum = data[0] |
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| 243 | if datum[0] == 'Rigid bodies': |
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| 244 | rigidbodyDict = datum[1] |
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| 245 | fl.close() |
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| 246 | return rigidbodyDict |
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| 247 | |
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| 248 | def GetFprime(controlDict,Histograms): |
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| 249 | 'Needs a doc string' |
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| 250 | FFtables = controlDict['FFtables'] |
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| 251 | if not FFtables: |
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| 252 | return |
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| 253 | histoList = Histograms.keys() |
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| 254 | histoList.sort() |
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| 255 | for histogram in histoList: |
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| 256 | if histogram[:4] in ['PWDR','HKLF']: |
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| 257 | Histogram = Histograms[histogram] |
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| 258 | hId = Histogram['hId'] |
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| 259 | hfx = ':%d:'%(hId) |
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| 260 | if 'X' in controlDict[hfx+'histType']: |
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| 261 | keV = controlDict[hfx+'keV'] |
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| 262 | for El in FFtables: |
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| 263 | Orbs = G2el.GetXsectionCoeff(El.split('+')[0].split('-')[0]) |
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| 264 | FP,FPP,Mu = G2el.FPcalc(Orbs, keV) |
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| 265 | FFtables[El][hfx+'FP'] = FP |
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| 266 | FFtables[El][hfx+'FPP'] = FPP |
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| 267 | |
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| 268 | def PrintFprime(FFtables,pfx,pFile): |
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| 269 | print >>pFile,'\n Resonant form factors:' |
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| 270 | Elstr = ' Element:' |
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| 271 | FPstr = " f' :" |
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| 272 | FPPstr = ' f" :' |
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| 273 | for El in FFtables: |
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| 274 | Elstr += ' %8s'%(El) |
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| 275 | FPstr += ' %8.3f'%(FFtables[El][pfx+'FP']) |
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| 276 | FPPstr += ' %8.3f'%(FFtables[El][pfx+'FPP']) |
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| 277 | print >>pFile,Elstr |
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| 278 | print >>pFile,FPstr |
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| 279 | print >>pFile,FPPstr |
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| 280 | |
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| 281 | def GetPhaseNames(GPXfile): |
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| 282 | ''' Returns a list of phase names found under 'Phases' in GSASII gpx file |
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| 283 | |
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| 284 | :param str GPXfile: full .gpx file name |
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| 285 | :return: list of phase names |
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| 286 | ''' |
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| 287 | fl = open(GPXfile,'rb') |
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| 288 | PhaseNames = [] |
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| 289 | while True: |
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| 290 | try: |
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| 291 | data = cPickle.load(fl) |
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| 292 | except EOFError: |
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| 293 | break |
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| 294 | datum = data[0] |
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| 295 | if 'Phases' == datum[0]: |
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| 296 | for datus in data[1:]: |
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| 297 | PhaseNames.append(datus[0]) |
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| 298 | fl.close() |
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| 299 | return PhaseNames |
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| 300 | |
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| 301 | def GetAllPhaseData(GPXfile,PhaseName): |
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| 302 | ''' Returns the entire dictionary for PhaseName from GSASII gpx file |
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| 303 | |
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| 304 | :param str GPXfile: full .gpx file name |
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| 305 | :param str PhaseName: phase name |
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| 306 | :return: phase dictionary |
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| 307 | ''' |
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| 308 | fl = open(GPXfile,'rb') |
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| 309 | while True: |
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| 310 | try: |
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| 311 | data = cPickle.load(fl) |
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| 312 | except EOFError: |
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| 313 | break |
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| 314 | datum = data[0] |
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| 315 | if 'Phases' == datum[0]: |
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| 316 | for datus in data[1:]: |
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| 317 | if datus[0] == PhaseName: |
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| 318 | break |
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| 319 | fl.close() |
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| 320 | return datus[1] |
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| 321 | |
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| 322 | def GetHistograms(GPXfile,hNames): |
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| 323 | """ Returns a dictionary of histograms found in GSASII gpx file |
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| 324 | |
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| 325 | :param str GPXfile: full .gpx file name |
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| 326 | :param str hNames: list of histogram names |
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| 327 | :return: dictionary of histograms (types = PWDR & HKLF) |
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| 328 | |
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| 329 | """ |
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| 330 | fl = open(GPXfile,'rb') |
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| 331 | Histograms = {} |
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| 332 | while True: |
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| 333 | try: |
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| 334 | data = cPickle.load(fl) |
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| 335 | except EOFError: |
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| 336 | break |
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| 337 | datum = data[0] |
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| 338 | hist = datum[0] |
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| 339 | if hist in hNames: |
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| 340 | if 'PWDR' in hist[:4]: |
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| 341 | PWDRdata = {} |
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| 342 | PWDRdata.update(datum[1][0]) #weight factor |
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| 343 | PWDRdata['Data'] = ma.array(ma.getdata(datum[1][1])) #masked powder data arrays/clear previous masks |
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| 344 | PWDRdata[data[2][0]] = data[2][1] #Limits & excluded regions (if any) |
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| 345 | PWDRdata[data[3][0]] = data[3][1] #Background |
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| 346 | PWDRdata[data[4][0]] = data[4][1] #Instrument parameters |
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| 347 | PWDRdata[data[5][0]] = data[5][1] #Sample parameters |
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| 348 | try: |
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| 349 | PWDRdata[data[9][0]] = data[9][1] #Reflection lists might be missing |
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| 350 | except IndexError: |
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| 351 | PWDRdata['Reflection Lists'] = {} |
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| 352 | PWDRdata['Residuals'] = {} |
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| 353 | |
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| 354 | Histograms[hist] = PWDRdata |
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| 355 | elif 'HKLF' in hist[:4]: |
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| 356 | HKLFdata = {} |
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| 357 | HKLFdata.update(datum[1][0]) #weight factor |
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| 358 | #patch |
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| 359 | if 'list' in str(type(datum[1][1])): |
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| 360 | #if isinstance(datum[1][1],list): |
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| 361 | RefData = {'RefList':[],'FF':{}} |
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| 362 | for ref in datum[1][1]: |
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| 363 | RefData['RefList'].append(ref[:11]+[ref[13],]) |
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| 364 | RefData['RefList'] = np.array(RefData['RefList']) |
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| 365 | datum[1][1] = RefData |
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| 366 | #end patch |
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| 367 | datum[1][1]['FF'] = {} |
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| 368 | HKLFdata['Data'] = datum[1][1] |
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| 369 | HKLFdata[data[1][0]] = data[1][1] #Instrument parameters |
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| 370 | HKLFdata['Reflection Lists'] = None |
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| 371 | HKLFdata['Residuals'] = {} |
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| 372 | Histograms[hist] = HKLFdata |
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| 373 | fl.close() |
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| 374 | return Histograms |
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| 375 | |
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| 376 | def GetHistogramNames(GPXfile,hType): |
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| 377 | """ Returns a list of histogram names found in GSASII gpx file |
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| 378 | |
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| 379 | :param str GPXfile: full .gpx file name |
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| 380 | :param str hType: list of histogram types |
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| 381 | :return: list of histogram names (types = PWDR & HKLF) |
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| 382 | |
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| 383 | """ |
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| 384 | fl = open(GPXfile,'rb') |
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| 385 | HistogramNames = [] |
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| 386 | while True: |
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| 387 | try: |
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| 388 | data = cPickle.load(fl) |
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| 389 | except EOFError: |
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| 390 | break |
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| 391 | datum = data[0] |
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| 392 | if datum[0][:4] in hType: |
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| 393 | HistogramNames.append(datum[0]) |
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| 394 | fl.close() |
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| 395 | return HistogramNames |
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| 396 | |
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| 397 | def GetUsedHistogramsAndPhases(GPXfile): |
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| 398 | ''' Returns all histograms that are found in any phase |
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| 399 | and any phase that uses a histogram. This also |
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| 400 | assigns numbers to used phases and histograms by the |
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| 401 | order they appear in the file. |
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| 402 | |
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| 403 | :param str GPXfile: full .gpx file name |
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| 404 | :returns: (Histograms,Phases) |
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| 405 | |
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| 406 | * Histograms = dictionary of histograms as {name:data,...} |
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| 407 | * Phases = dictionary of phases that use histograms |
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| 408 | |
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| 409 | ''' |
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| 410 | phaseNames = GetPhaseNames(GPXfile) |
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| 411 | histoList = GetHistogramNames(GPXfile,['PWDR','HKLF']) |
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| 412 | allHistograms = GetHistograms(GPXfile,histoList) |
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| 413 | phaseData = {} |
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| 414 | for name in phaseNames: |
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| 415 | phaseData[name] = GetAllPhaseData(GPXfile,name) |
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| 416 | Histograms = {} |
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| 417 | Phases = {} |
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| 418 | for phase in phaseData: |
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| 419 | Phase = phaseData[phase] |
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| 420 | if Phase['General']['Type'] == 'faulted': continue #don't use faulted phases! |
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| 421 | if Phase['Histograms']: |
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| 422 | if phase not in Phases: |
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| 423 | pId = phaseNames.index(phase) |
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| 424 | Phase['pId'] = pId |
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| 425 | Phases[phase] = Phase |
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| 426 | for hist in Phase['Histograms']: |
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| 427 | if 'Use' not in Phase['Histograms'][hist]: #patch |
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| 428 | Phase['Histograms'][hist]['Use'] = True |
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| 429 | if hist not in Histograms and Phase['Histograms'][hist]['Use']: |
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| 430 | try: |
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| 431 | Histograms[hist] = allHistograms[hist] |
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| 432 | hId = histoList.index(hist) |
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| 433 | Histograms[hist]['hId'] = hId |
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| 434 | except KeyError: # would happen if a referenced histogram were |
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| 435 | # renamed or deleted |
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| 436 | print('For phase "'+str(phase)+ |
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| 437 | '" unresolved reference to histogram "'+str(hist)+'"') |
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| 438 | G2obj.IndexAllIds(Histograms=Histograms,Phases=Phases) |
|---|
| 439 | return Histograms,Phases |
|---|
| 440 | |
|---|
| 441 | def getBackupName(GPXfile,makeBack): |
|---|
| 442 | ''' |
|---|
| 443 | Get the name for the backup .gpx file name |
|---|
| 444 | |
|---|
| 445 | :param str GPXfile: full .gpx file name |
|---|
| 446 | :param bool makeBack: if True the name of a new file is returned, if |
|---|
| 447 | False the name of the last file that exists is returned |
|---|
| 448 | :returns: the name of a backup file |
|---|
| 449 | |
|---|
| 450 | ''' |
|---|
| 451 | GPXpath,GPXname = ospath.split(GPXfile) |
|---|
| 452 | if GPXpath == '': GPXpath = '.' |
|---|
| 453 | Name = ospath.splitext(GPXname)[0] |
|---|
| 454 | files = os.listdir(GPXpath) |
|---|
| 455 | last = 0 |
|---|
| 456 | for name in files: |
|---|
| 457 | name = name.split('.') |
|---|
| 458 | if len(name) == 3 and name[0] == Name and 'bak' in name[1]: |
|---|
| 459 | if makeBack: |
|---|
| 460 | last = max(last,int(name[1].strip('bak'))+1) |
|---|
| 461 | else: |
|---|
| 462 | last = max(last,int(name[1].strip('bak'))) |
|---|
| 463 | GPXback = ospath.join(GPXpath,ospath.splitext(GPXname)[0]+'.bak'+str(last)+'.gpx') |
|---|
| 464 | return GPXback |
|---|
| 465 | |
|---|
| 466 | def GPXBackup(GPXfile,makeBack=True): |
|---|
| 467 | ''' |
|---|
| 468 | makes a backup of the current .gpx file (?) |
|---|
| 469 | |
|---|
| 470 | :param str GPXfile: full .gpx file name |
|---|
| 471 | :param bool makeBack: if True (default), the backup is written to |
|---|
| 472 | a new file; if False, the last backup is overwritten |
|---|
| 473 | :returns: the name of the backup file that was written |
|---|
| 474 | ''' |
|---|
| 475 | import distutils.file_util as dfu |
|---|
| 476 | GPXback = getBackupName(GPXfile,makeBack) |
|---|
| 477 | tries = 0 |
|---|
| 478 | while True: |
|---|
| 479 | try: |
|---|
| 480 | dfu.copy_file(GPXfile,GPXback) |
|---|
| 481 | break |
|---|
| 482 | except: |
|---|
| 483 | tries += 1 |
|---|
| 484 | if tries > 10: |
|---|
| 485 | return GPXfile #failed! |
|---|
| 486 | time.sleep(1) #just wait a second! |
|---|
| 487 | return GPXback |
|---|
| 488 | |
|---|
| 489 | def SetUsedHistogramsAndPhases(GPXfile,Histograms,Phases,RigidBodies,CovData,makeBack=True): |
|---|
| 490 | ''' Updates gpxfile from all histograms that are found in any phase |
|---|
| 491 | and any phase that used a histogram. Also updates rigid body definitions. |
|---|
| 492 | |
|---|
| 493 | |
|---|
| 494 | :param str GPXfile: full .gpx file name |
|---|
| 495 | :param dict Histograms: dictionary of histograms as {name:data,...} |
|---|
| 496 | :param dict Phases: dictionary of phases that use histograms |
|---|
| 497 | :param dict RigidBodies: dictionary of rigid bodies |
|---|
| 498 | :param dict CovData: dictionary of refined variables, varyList, & covariance matrix |
|---|
| 499 | :param bool makeBack: True if new backup of .gpx file is to be made; else use the last one made |
|---|
| 500 | |
|---|
| 501 | ''' |
|---|
| 502 | |
|---|
| 503 | import distutils.file_util as dfu |
|---|
| 504 | GPXback = GPXBackup(GPXfile,makeBack) |
|---|
| 505 | print 'Read from file:',GPXback |
|---|
| 506 | print 'Save to file :',GPXfile |
|---|
| 507 | infile = open(GPXback,'rb') |
|---|
| 508 | outfile = open(GPXfile,'wb') |
|---|
| 509 | while True: |
|---|
| 510 | try: |
|---|
| 511 | data = cPickle.load(infile) |
|---|
| 512 | except EOFError: |
|---|
| 513 | break |
|---|
| 514 | datum = data[0] |
|---|
| 515 | # print 'read: ',datum[0] |
|---|
| 516 | if datum[0] == 'Phases': |
|---|
| 517 | for iphase in range(len(data)): |
|---|
| 518 | if data[iphase][0] in Phases: |
|---|
| 519 | phaseName = data[iphase][0] |
|---|
| 520 | data[iphase][1].update(Phases[phaseName]) |
|---|
| 521 | elif datum[0] == 'Covariance': |
|---|
| 522 | data[0][1] = CovData |
|---|
| 523 | elif datum[0] == 'Rigid bodies': |
|---|
| 524 | data[0][1] = RigidBodies |
|---|
| 525 | try: |
|---|
| 526 | histogram = Histograms[datum[0]] |
|---|
| 527 | # print 'found ',datum[0] |
|---|
| 528 | data[0][1][1] = histogram['Data'] |
|---|
| 529 | data[0][1][0].update(histogram['Residuals']) |
|---|
| 530 | for datus in data[1:]: |
|---|
| 531 | # print ' read: ',datus[0] |
|---|
| 532 | if datus[0] in ['Background','Instrument Parameters','Sample Parameters','Reflection Lists']: |
|---|
| 533 | datus[1] = histogram[datus[0]] |
|---|
| 534 | except KeyError: |
|---|
| 535 | pass |
|---|
| 536 | try: |
|---|
| 537 | cPickle.dump(data,outfile,1) |
|---|
| 538 | except AttributeError: |
|---|
| 539 | print 'ERROR - bad data in least squares result' |
|---|
| 540 | infile.close() |
|---|
| 541 | outfile.close() |
|---|
| 542 | dfu.copy_file(GPXback,GPXfile) |
|---|
| 543 | print 'GPX file save failed - old version retained' |
|---|
| 544 | return |
|---|
| 545 | |
|---|
| 546 | print 'GPX file save successful' |
|---|
| 547 | |
|---|
| 548 | def SetSeqResult(GPXfile,Histograms,SeqResult): |
|---|
| 549 | ''' |
|---|
| 550 | Needs doc string |
|---|
| 551 | |
|---|
| 552 | :param str GPXfile: full .gpx file name |
|---|
| 553 | ''' |
|---|
| 554 | GPXback = GPXBackup(GPXfile) |
|---|
| 555 | print 'Read from file:',GPXback |
|---|
| 556 | print 'Save to file :',GPXfile |
|---|
| 557 | infile = open(GPXback,'rb') |
|---|
| 558 | outfile = open(GPXfile,'wb') |
|---|
| 559 | while True: |
|---|
| 560 | try: |
|---|
| 561 | data = cPickle.load(infile) |
|---|
| 562 | except EOFError: |
|---|
| 563 | break |
|---|
| 564 | datum = data[0] |
|---|
| 565 | if datum[0] == 'Sequential results': |
|---|
| 566 | data[0][1] = SeqResult |
|---|
| 567 | # reset the Copy Next flag, since it should not be needed twice in a row |
|---|
| 568 | if datum[0] == 'Controls': |
|---|
| 569 | data[0][1]['Copy2Next'] = False |
|---|
| 570 | try: |
|---|
| 571 | histogram = Histograms[datum[0]] |
|---|
| 572 | data[0][1][1] = list(histogram['Data']) |
|---|
| 573 | for datus in data[1:]: |
|---|
| 574 | if datus[0] in ['Background','Instrument Parameters','Sample Parameters','Reflection Lists']: |
|---|
| 575 | datus[1] = histogram[datus[0]] |
|---|
| 576 | except KeyError: |
|---|
| 577 | pass |
|---|
| 578 | |
|---|
| 579 | cPickle.dump(data,outfile,1) |
|---|
| 580 | infile.close() |
|---|
| 581 | outfile.close() |
|---|
| 582 | print 'GPX file save successful' |
|---|
| 583 | |
|---|
| 584 | def ShowBanner(pFile=None): |
|---|
| 585 | 'Print authorship, copyright and citation notice' |
|---|
| 586 | print >>pFile,80*'*' |
|---|
| 587 | print >>pFile,' General Structure Analysis System-II Crystal Structure Refinement' |
|---|
| 588 | print >>pFile,' by Robert B. Von Dreele & Brian H. Toby' |
|---|
| 589 | print >>pFile,' Argonne National Laboratory(C), 2010' |
|---|
| 590 | print >>pFile,' This product includes software developed by the UChicago Argonne, LLC,' |
|---|
| 591 | print >>pFile,' as Operator of Argonne National Laboratory.' |
|---|
| 592 | print >>pFile,' Please cite:' |
|---|
| 593 | print >>pFile,' B.H. Toby & R.B. Von Dreele, J. Appl. Cryst. 46, 544-549 (2013)' |
|---|
| 594 | |
|---|
| 595 | print >>pFile,80*'*','\n' |
|---|
| 596 | |
|---|
| 597 | def ShowControls(Controls,pFile=None,SeqRef=False): |
|---|
| 598 | 'Print controls information' |
|---|
| 599 | print >>pFile,' Least squares controls:' |
|---|
| 600 | print >>pFile,' Refinement type: ',Controls['deriv type'] |
|---|
| 601 | if 'Hessian' in Controls['deriv type']: |
|---|
| 602 | print >>pFile,' Maximum number of cycles:',Controls['max cyc'] |
|---|
| 603 | else: |
|---|
| 604 | print >>pFile,' Minimum delta-M/M for convergence: ','%.2g'%(Controls['min dM/M']) |
|---|
| 605 | print >>pFile,' Regularize hydrogens (if any):',Controls.get('HatomFix',False) |
|---|
| 606 | print >>pFile,' Initial shift factor: ','%.3f'%(Controls['shift factor']) |
|---|
| 607 | if SeqRef: |
|---|
| 608 | print >>pFile,' Sequential refinement controls:' |
|---|
| 609 | print >>pFile,' Copy of histogram results to next: ',Controls['Copy2Next'] |
|---|
| 610 | print >>pFile,' Process histograms in reverse order: ',Controls['Reverse Seq'] |
|---|
| 611 | |
|---|
| 612 | def GetPawleyConstr(SGLaue,PawleyRef,im,pawleyVary): |
|---|
| 613 | 'needs a doc string' |
|---|
| 614 | # if SGLaue in ['-1','2/m','mmm']: |
|---|
| 615 | # return #no Pawley symmetry required constraints |
|---|
| 616 | eqvDict = {} |
|---|
| 617 | for i,varyI in enumerate(pawleyVary): |
|---|
| 618 | eqvDict[varyI] = [] |
|---|
| 619 | refI = int(varyI.split(':')[-1]) |
|---|
| 620 | ih,ik,il = PawleyRef[refI][:3] |
|---|
| 621 | dspI = PawleyRef[refI][4+im] |
|---|
| 622 | for varyJ in pawleyVary[i+1:]: |
|---|
| 623 | refJ = int(varyJ.split(':')[-1]) |
|---|
| 624 | jh,jk,jl = PawleyRef[refJ][:3] |
|---|
| 625 | dspJ = PawleyRef[refJ][4+im] |
|---|
| 626 | if SGLaue in ['4/m','4/mmm']: |
|---|
| 627 | isum = ih**2+ik**2 |
|---|
| 628 | jsum = jh**2+jk**2 |
|---|
| 629 | if abs(il) == abs(jl) and isum == jsum: |
|---|
| 630 | eqvDict[varyI].append(varyJ) |
|---|
| 631 | elif SGLaue in ['3R','3mR']: |
|---|
| 632 | isum = ih**2+ik**2+il**2 |
|---|
| 633 | jsum = jh**2+jk**2+jl**2 |
|---|
| 634 | isum2 = ih*ik+ih*il+ik*il |
|---|
| 635 | jsum2 = jh*jk+jh*jl+jk*jl |
|---|
| 636 | if isum == jsum and isum2 == jsum2: |
|---|
| 637 | eqvDict[varyI].append(varyJ) |
|---|
| 638 | elif SGLaue in ['3','3m1','31m','6/m','6/mmm']: |
|---|
| 639 | isum = ih**2+ik**2+ih*ik |
|---|
| 640 | jsum = jh**2+jk**2+jh*jk |
|---|
| 641 | if abs(il) == abs(jl) and isum == jsum: |
|---|
| 642 | eqvDict[varyI].append(varyJ) |
|---|
| 643 | elif SGLaue in ['m3','m3m']: |
|---|
| 644 | isum = ih**2+ik**2+il**2 |
|---|
| 645 | jsum = jh**2+jk**2+jl**2 |
|---|
| 646 | if isum == jsum: |
|---|
| 647 | eqvDict[varyI].append(varyJ) |
|---|
| 648 | elif abs(dspI-dspJ)/dspI < 1.e-4: |
|---|
| 649 | eqvDict[varyI].append(varyJ) |
|---|
| 650 | for item in pawleyVary: |
|---|
| 651 | if eqvDict[item]: |
|---|
| 652 | for item2 in pawleyVary: |
|---|
| 653 | if item2 in eqvDict[item]: |
|---|
| 654 | eqvDict[item2] = [] |
|---|
| 655 | G2mv.StoreEquivalence(item,eqvDict[item]) |
|---|
| 656 | |
|---|
| 657 | def cellVary(pfx,SGData): |
|---|
| 658 | 'needs a doc string' |
|---|
| 659 | if SGData['SGLaue'] in ['-1',]: |
|---|
| 660 | return [pfx+'A0',pfx+'A1',pfx+'A2',pfx+'A3',pfx+'A4',pfx+'A5'] |
|---|
| 661 | elif SGData['SGLaue'] in ['2/m',]: |
|---|
| 662 | if SGData['SGUniq'] == 'a': |
|---|
| 663 | return [pfx+'A0',pfx+'A1',pfx+'A2',pfx+'A5'] |
|---|
| 664 | elif SGData['SGUniq'] == 'b': |
|---|
| 665 | return [pfx+'A0',pfx+'A1',pfx+'A2',pfx+'A4'] |
|---|
| 666 | else: |
|---|
| 667 | return [pfx+'A0',pfx+'A1',pfx+'A2',pfx+'A3'] |
|---|
| 668 | elif SGData['SGLaue'] in ['mmm',]: |
|---|
| 669 | return [pfx+'A0',pfx+'A1',pfx+'A2'] |
|---|
| 670 | elif SGData['SGLaue'] in ['4/m','4/mmm']: |
|---|
| 671 | G2mv.StoreEquivalence(pfx+'A0',(pfx+'A1',)) |
|---|
| 672 | return [pfx+'A0',pfx+'A1',pfx+'A2'] |
|---|
| 673 | elif SGData['SGLaue'] in ['6/m','6/mmm','3m1', '31m', '3']: |
|---|
| 674 | G2mv.StoreEquivalence(pfx+'A0',(pfx+'A1',pfx+'A3',)) |
|---|
| 675 | return [pfx+'A0',pfx+'A1',pfx+'A2',pfx+'A3'] |
|---|
| 676 | elif SGData['SGLaue'] in ['3R', '3mR']: |
|---|
| 677 | G2mv.StoreEquivalence(pfx+'A0',(pfx+'A1',pfx+'A2',)) |
|---|
| 678 | G2mv.StoreEquivalence(pfx+'A3',(pfx+'A4',pfx+'A5',)) |
|---|
| 679 | return [pfx+'A0',pfx+'A1',pfx+'A2',pfx+'A3',pfx+'A4',pfx+'A5'] |
|---|
| 680 | elif SGData['SGLaue'] in ['m3m','m3']: |
|---|
| 681 | G2mv.StoreEquivalence(pfx+'A0',(pfx+'A1',pfx+'A2',)) |
|---|
| 682 | return [pfx+'A0',pfx+'A1',pfx+'A2'] |
|---|
| 683 | |
|---|
| 684 | def modVary(pfx,SSGData): |
|---|
| 685 | vary = [] |
|---|
| 686 | for i,item in enumerate(SSGData['modSymb']): |
|---|
| 687 | if item in ['a','b','g']: |
|---|
| 688 | vary.append(pfx+'mV%d'%(i)) |
|---|
| 689 | return vary |
|---|
| 690 | |
|---|
| 691 | ################################################################################ |
|---|
| 692 | ##### Rigid Body Models and not General.get('doPawley') |
|---|
| 693 | ################################################################################ |
|---|
| 694 | |
|---|
| 695 | def GetRigidBodyModels(rigidbodyDict,Print=True,pFile=None): |
|---|
| 696 | 'needs a doc string' |
|---|
| 697 | |
|---|
| 698 | def PrintResRBModel(RBModel): |
|---|
| 699 | atNames = RBModel['atNames'] |
|---|
| 700 | rbRef = RBModel['rbRef'] |
|---|
| 701 | rbSeq = RBModel['rbSeq'] |
|---|
| 702 | print >>pFile,'Residue RB name: ',RBModel['RBname'],' no.atoms: ',len(RBModel['rbTypes']), \ |
|---|
| 703 | 'No. times used: ',RBModel['useCount'] |
|---|
| 704 | print >>pFile,' At name x y z' |
|---|
| 705 | for name,xyz in zip(atNames,RBModel['rbXYZ']): |
|---|
| 706 | print >>pFile,' %8s %10.4f %10.4f %10.4f'%(name,xyz[0],xyz[1],xyz[2]) |
|---|
| 707 | print >>pFile,'Orientation defined by:',atNames[rbRef[0]],' -> ',atNames[rbRef[1]], \ |
|---|
| 708 | ' & ',atNames[rbRef[0]],' -> ',atNames[rbRef[2]] |
|---|
| 709 | if rbSeq: |
|---|
| 710 | for i,rbseq in enumerate(rbSeq): |
|---|
| 711 | print >>pFile,'Torsion sequence ',i,' Bond: '+atNames[rbseq[0]],' - ', \ |
|---|
| 712 | atNames[rbseq[1]],' riding: ',[atNames[i] for i in rbseq[3]] |
|---|
| 713 | |
|---|
| 714 | def PrintVecRBModel(RBModel): |
|---|
| 715 | rbRef = RBModel['rbRef'] |
|---|
| 716 | atTypes = RBModel['rbTypes'] |
|---|
| 717 | print >>pFile,'Vector RB name: ',RBModel['RBname'],' no.atoms: ',len(RBModel['rbTypes']), \ |
|---|
| 718 | 'No. times used: ',RBModel['useCount'] |
|---|
| 719 | for i in range(len(RBModel['VectMag'])): |
|---|
| 720 | print >>pFile,'Vector no.: ',i,' Magnitude: ', \ |
|---|
| 721 | '%8.4f'%(RBModel['VectMag'][i]),' Refine? ',RBModel['VectRef'][i] |
|---|
| 722 | print >>pFile,' No. Type vx vy vz' |
|---|
| 723 | for j,[name,xyz] in enumerate(zip(atTypes,RBModel['rbVect'][i])): |
|---|
| 724 | print >>pFile,' %d %2s %10.4f %10.4f %10.4f'%(j,name,xyz[0],xyz[1],xyz[2]) |
|---|
| 725 | print >>pFile,' No. Type x y z' |
|---|
| 726 | for i,[name,xyz] in enumerate(zip(atTypes,RBModel['rbXYZ'])): |
|---|
| 727 | print >>pFile,' %d %2s %10.4f %10.4f %10.4f'%(i,name,xyz[0],xyz[1],xyz[2]) |
|---|
| 728 | print >>pFile,'Orientation defined by: atom ',rbRef[0],' -> atom ',rbRef[1], \ |
|---|
| 729 | ' & atom ',rbRef[0],' -> atom ',rbRef[2] |
|---|
| 730 | rbVary = [] |
|---|
| 731 | rbDict = {} |
|---|
| 732 | rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]}) |
|---|
| 733 | if len(rbIds['Vector']): |
|---|
| 734 | for irb,item in enumerate(rbIds['Vector']): |
|---|
| 735 | if rigidbodyDict['Vector'][item]['useCount']: |
|---|
| 736 | RBmags = rigidbodyDict['Vector'][item]['VectMag'] |
|---|
| 737 | RBrefs = rigidbodyDict['Vector'][item]['VectRef'] |
|---|
| 738 | for i,[mag,ref] in enumerate(zip(RBmags,RBrefs)): |
|---|
| 739 | pid = '::RBV;'+str(i)+':'+str(irb) |
|---|
| 740 | rbDict[pid] = mag |
|---|
| 741 | if ref: |
|---|
| 742 | rbVary.append(pid) |
|---|
| 743 | if Print: |
|---|
| 744 | print >>pFile,'\nVector rigid body model:' |
|---|
| 745 | PrintVecRBModel(rigidbodyDict['Vector'][item]) |
|---|
| 746 | if len(rbIds['Residue']): |
|---|
| 747 | for item in rbIds['Residue']: |
|---|
| 748 | if rigidbodyDict['Residue'][item]['useCount']: |
|---|
| 749 | if Print: |
|---|
| 750 | print >>pFile,'\nResidue rigid body model:' |
|---|
| 751 | PrintResRBModel(rigidbodyDict['Residue'][item]) |
|---|
| 752 | return rbVary,rbDict |
|---|
| 753 | |
|---|
| 754 | def SetRigidBodyModels(parmDict,sigDict,rigidbodyDict,pFile=None): |
|---|
| 755 | 'needs a doc string' |
|---|
| 756 | |
|---|
| 757 | def PrintRBVectandSig(VectRB,VectSig): |
|---|
| 758 | print >>pFile,'\n Rigid body vector magnitudes for '+VectRB['RBname']+':' |
|---|
| 759 | namstr = ' names :' |
|---|
| 760 | valstr = ' values:' |
|---|
| 761 | sigstr = ' esds :' |
|---|
| 762 | for i,[val,sig] in enumerate(zip(VectRB['VectMag'],VectSig)): |
|---|
| 763 | namstr += '%12s'%('Vect '+str(i)) |
|---|
| 764 | valstr += '%12.4f'%(val) |
|---|
| 765 | if sig: |
|---|
| 766 | sigstr += '%12.4f'%(sig) |
|---|
| 767 | else: |
|---|
| 768 | sigstr += 12*' ' |
|---|
| 769 | print >>pFile,namstr |
|---|
| 770 | print >>pFile,valstr |
|---|
| 771 | print >>pFile,sigstr |
|---|
| 772 | |
|---|
| 773 | RBIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]}) #these are lists of rbIds |
|---|
| 774 | if not RBIds['Vector']: |
|---|
| 775 | return |
|---|
| 776 | for irb,item in enumerate(RBIds['Vector']): |
|---|
| 777 | if rigidbodyDict['Vector'][item]['useCount']: |
|---|
| 778 | VectSig = [] |
|---|
| 779 | RBmags = rigidbodyDict['Vector'][item]['VectMag'] |
|---|
| 780 | for i,mag in enumerate(RBmags): |
|---|
| 781 | name = '::RBV;'+str(i)+':'+str(irb) |
|---|
| 782 | if name in sigDict: |
|---|
| 783 | VectSig.append(sigDict[name]) |
|---|
| 784 | PrintRBVectandSig(rigidbodyDict['Vector'][item],VectSig) |
|---|
| 785 | |
|---|
| 786 | ################################################################################ |
|---|
| 787 | ##### Phase data |
|---|
| 788 | ################################################################################ |
|---|
| 789 | |
|---|
| 790 | def GetPhaseData(PhaseData,RestraintDict={},rbIds={},Print=True,pFile=None,seqRef=False): |
|---|
| 791 | 'needs a doc string' |
|---|
| 792 | |
|---|
| 793 | def PrintFFtable(FFtable): |
|---|
| 794 | print >>pFile,'\n X-ray scattering factors:' |
|---|
| 795 | print >>pFile,' Symbol fa fb fc' |
|---|
| 796 | print >>pFile,99*'-' |
|---|
| 797 | for Ename in FFtable: |
|---|
| 798 | ffdata = FFtable[Ename] |
|---|
| 799 | fa = ffdata['fa'] |
|---|
| 800 | fb = ffdata['fb'] |
|---|
| 801 | print >>pFile,' %8s %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f' % \ |
|---|
| 802 | (Ename.ljust(8),fa[0],fa[1],fa[2],fa[3],fb[0],fb[1],fb[2],fb[3],ffdata['fc']) |
|---|
| 803 | |
|---|
| 804 | def PrintMFtable(MFtable): |
|---|
| 805 | print >>pFile,'\n <j0> Magnetic scattering factors:' |
|---|
| 806 | print >>pFile,' Symbol mfa mfb mfc' |
|---|
| 807 | print >>pFile,99*'-' |
|---|
| 808 | for Ename in MFtable: |
|---|
| 809 | mfdata = MFtable[Ename] |
|---|
| 810 | fa = mfdata['mfa'] |
|---|
| 811 | fb = mfdata['mfb'] |
|---|
| 812 | print >>pFile,' %8s %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f' % \ |
|---|
| 813 | (Ename.ljust(8),fa[0],fa[1],fa[2],fa[3],fb[0],fb[1],fb[2],fb[3],mfdata['mfc']) |
|---|
| 814 | print >>pFile,'\n <j2> Magnetic scattering factors:' |
|---|
| 815 | print >>pFile,' Symbol nfa nfb nfc' |
|---|
| 816 | print >>pFile,99*'-' |
|---|
| 817 | for Ename in MFtable: |
|---|
| 818 | mfdata = MFtable[Ename] |
|---|
| 819 | fa = mfdata['nfa'] |
|---|
| 820 | fb = mfdata['nfb'] |
|---|
| 821 | print >>pFile,' %8s %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f' % \ |
|---|
| 822 | (Ename.ljust(8),fa[0],fa[1],fa[2],fa[3],fb[0],fb[1],fb[2],fb[3],mfdata['nfc']) |
|---|
| 823 | |
|---|
| 824 | def PrintBLtable(BLtable): |
|---|
| 825 | print >>pFile,'\n Neutron scattering factors:' |
|---|
| 826 | print >>pFile,' Symbol isotope mass b resonant terms' |
|---|
| 827 | print >>pFile,99*'-' |
|---|
| 828 | for Ename in BLtable: |
|---|
| 829 | bldata = BLtable[Ename] |
|---|
| 830 | isotope = bldata[0] |
|---|
| 831 | mass = bldata[1]['Mass'] |
|---|
| 832 | if 'SL' in bldata[1]: |
|---|
| 833 | blen = bldata[1]['SL'][0] |
|---|
| 834 | bres = [] |
|---|
| 835 | else: |
|---|
| 836 | blen = 0 |
|---|
| 837 | bres = bldata[1]['BW-LS'] |
|---|
| 838 | line = ' %8s%11s %10.3f %8.3f'%(Ename.ljust(8),isotope.center(11),mass,blen) |
|---|
| 839 | for item in bres: |
|---|
| 840 | line += '%10.5g'%(item) |
|---|
| 841 | print >>pFile,line |
|---|
| 842 | |
|---|
| 843 | def PrintRBObjects(resRBData,vecRBData): |
|---|
| 844 | |
|---|
| 845 | def PrintRBThermals(): |
|---|
| 846 | tlstr = ['11','22','33','12','13','23'] |
|---|
| 847 | sstr = ['12','13','21','23','31','32','AA','BB'] |
|---|
| 848 | TLS = RB['ThermalMotion'][1] |
|---|
| 849 | TLSvar = RB['ThermalMotion'][2] |
|---|
| 850 | if 'T' in RB['ThermalMotion'][0]: |
|---|
| 851 | print >>pFile,'TLS data' |
|---|
| 852 | text = '' |
|---|
| 853 | for i in range(6): |
|---|
| 854 | text += 'T'+tlstr[i]+' %8.4f %s '%(TLS[i],str(TLSvar[i])[0]) |
|---|
| 855 | print >>pFile,text |
|---|
| 856 | if 'L' in RB['ThermalMotion'][0]: |
|---|
| 857 | text = '' |
|---|
| 858 | for i in range(6,12): |
|---|
| 859 | text += 'L'+tlstr[i-6]+' %8.2f %s '%(TLS[i],str(TLSvar[i])[0]) |
|---|
| 860 | print >>pFile,text |
|---|
| 861 | if 'S' in RB['ThermalMotion'][0]: |
|---|
| 862 | text = '' |
|---|
| 863 | for i in range(12,20): |
|---|
| 864 | text += 'S'+sstr[i-12]+' %8.3f %s '%(TLS[i],str(TLSvar[i])[0]) |
|---|
| 865 | print >>pFile,text |
|---|
| 866 | if 'U' in RB['ThermalMotion'][0]: |
|---|
| 867 | print >>pFile,'Uiso data' |
|---|
| 868 | text = 'Uiso'+' %10.3f %s'%(TLS[0],str(TLSvar[0])[0]) |
|---|
| 869 | |
|---|
| 870 | if len(resRBData): |
|---|
| 871 | for RB in resRBData: |
|---|
| 872 | Oxyz = RB['Orig'][0] |
|---|
| 873 | Qrijk = RB['Orient'][0] |
|---|
| 874 | Angle = 2.0*acosd(Qrijk[0]) |
|---|
| 875 | print >>pFile,'\nRBObject ',RB['RBname'],' at ', \ |
|---|
| 876 | '%10.4f %10.4f %10.4f'%(Oxyz[0],Oxyz[1],Oxyz[2]),' Refine?',RB['Orig'][1] |
|---|
| 877 | print >>pFile,'Orientation angle,vector:', \ |
|---|
| 878 | '%10.3f %10.4f %10.4f %10.4f'%(Angle,Qrijk[1],Qrijk[2],Qrijk[3]),' Refine? ',RB['Orient'][1] |
|---|
| 879 | Torsions = RB['Torsions'] |
|---|
| 880 | if len(Torsions): |
|---|
| 881 | text = 'Torsions: ' |
|---|
| 882 | for torsion in Torsions: |
|---|
| 883 | text += '%10.4f Refine? %s'%(torsion[0],torsion[1]) |
|---|
| 884 | print >>pFile,text |
|---|
| 885 | PrintRBThermals() |
|---|
| 886 | if len(vecRBData): |
|---|
| 887 | for RB in vecRBData: |
|---|
| 888 | Oxyz = RB['Orig'][0] |
|---|
| 889 | Qrijk = RB['Orient'][0] |
|---|
| 890 | Angle = 2.0*acosd(Qrijk[0]) |
|---|
| 891 | print >>pFile,'\nRBObject ',RB['RBname'],' at ', \ |
|---|
| 892 | '%10.4f %10.4f %10.4f'%(Oxyz[0],Oxyz[1],Oxyz[2]),' Refine?',RB['Orig'][1] |
|---|
| 893 | print >>pFile,'Orientation angle,vector:', \ |
|---|
| 894 | '%10.3f %10.4f %10.4f %10.4f'%(Angle,Qrijk[1],Qrijk[2],Qrijk[3]),' Refine? ',RB['Orient'][1] |
|---|
| 895 | PrintRBThermals() |
|---|
| 896 | |
|---|
| 897 | def PrintAtoms(General,Atoms): |
|---|
| 898 | cx,ct,cs,cia = General['AtomPtrs'] |
|---|
| 899 | print >>pFile,'\n Atoms:' |
|---|
| 900 | line = ' name type refine? x y z '+ \ |
|---|
| 901 | ' frac site sym mult I/A Uiso U11 U22 U33 U12 U13 U23' |
|---|
| 902 | if General['Type'] == 'macromolecular': |
|---|
| 903 | line = ' res no residue chain'+line |
|---|
| 904 | print >>pFile,line |
|---|
| 905 | if General['Type'] in ['nuclear','magnetic','faulted',]: |
|---|
| 906 | print >>pFile,135*'-' |
|---|
| 907 | for i,at in enumerate(Atoms): |
|---|
| 908 | line = '%7s'%(at[ct-1])+'%7s'%(at[ct])+'%7s'%(at[ct+1])+'%10.5f'%(at[cx])+'%10.5f'%(at[cx+1])+ \ |
|---|
| 909 | '%10.5f'%(at[cx+2])+'%8.3f'%(at[cx+3])+'%7s'%(at[cs])+'%5d'%(at[cs+1])+'%5s'%(at[cia]) |
|---|
| 910 | if at[cia] == 'I': |
|---|
| 911 | line += '%8.5f'%(at[cia+1])+48*' ' |
|---|
| 912 | else: |
|---|
| 913 | line += 8*' ' |
|---|
| 914 | for j in range(6): |
|---|
| 915 | line += '%8.5f'%(at[cia+2+j]) |
|---|
| 916 | print >>pFile,line |
|---|
| 917 | elif General['Type'] == 'macromolecular': |
|---|
| 918 | print >>pFile,135*'-' |
|---|
| 919 | for i,at in enumerate(Atoms): |
|---|
| 920 | line = '%7s'%(at[0])+'%7s'%(at[1])+'%7s'%(at[2])+'%7s'%(at[ct-1])+'%7s'%(at[ct])+'%7s'%(at[ct+1])+'%10.5f'%(at[cx])+'%10.5f'%(at[cx+1])+ \ |
|---|
| 921 | '%10.5f'%(at[cx+2])+'%8.3f'%(at[cx+3])+'%7s'%(at[cs])+'%5d'%(at[cs+1])+'%5s'%(at[cia]) |
|---|
| 922 | if at[cia] == 'I': |
|---|
| 923 | line += '%8.4f'%(at[cia+1])+48*' ' |
|---|
| 924 | else: |
|---|
| 925 | line += 8*' ' |
|---|
| 926 | for j in range(6): |
|---|
| 927 | line += '%8.4f'%(at[cia+2+j]) |
|---|
| 928 | print >>pFile,line |
|---|
| 929 | |
|---|
| 930 | def PrintMoments(General,Atoms): |
|---|
| 931 | cx,ct,cs,cia = General['AtomPtrs'] |
|---|
| 932 | cmx = cx+4 |
|---|
| 933 | AtInfo = dict(zip(General['AtomTypes'],General['Lande g'])) |
|---|
| 934 | print >>pFile,'\n Magnetic moments:' |
|---|
| 935 | line = ' name type refine? Mx My Mz ' |
|---|
| 936 | print >>pFile,line |
|---|
| 937 | print >>pFile,135*'-' |
|---|
| 938 | for i,at in enumerate(Atoms): |
|---|
| 939 | if AtInfo[at[ct]]: |
|---|
| 940 | line = '%7s'%(at[ct-1])+'%7s'%(at[ct])+'%7s'%(at[ct+1])+'%10.5f'%(at[cmx])+'%10.5f'%(at[cmx+1])+ \ |
|---|
| 941 | '%10.5f'%(at[cmx+2]) |
|---|
| 942 | print >>pFile,line |
|---|
| 943 | |
|---|
| 944 | |
|---|
| 945 | def PrintWaves(General,Atoms): |
|---|
| 946 | cx,ct,cs,cia = General['AtomPtrs'] |
|---|
| 947 | print >>pFile,'\n Modulation waves' |
|---|
| 948 | names = {'Sfrac':['Fsin','Fcos','Fzero','Fwid'],'Spos':['Xsin','Ysin','Zsin','Xcos','Ycos','Zcos','Tmin','Tmax','Xmax','Ymax','Zmax'], |
|---|
| 949 | 'Sadp':['U11sin','U22sin','U33sin','U12sin','U13sin','U23sin','U11cos','U22cos', |
|---|
| 950 | 'U33cos','U12cos','U13cos','U23cos'],'Smag':['MXsin','MYsin','MZsin','MXcos','MYcos','MZcos']} |
|---|
| 951 | print >>pFile,135*'-' |
|---|
| 952 | for i,at in enumerate(Atoms): |
|---|
| 953 | AtomSS = at[-1]['SS1'] |
|---|
| 954 | for Stype in ['Sfrac','Spos','Sadp','Smag']: |
|---|
| 955 | Waves = AtomSS[Stype] |
|---|
| 956 | if len(Waves): |
|---|
| 957 | print >>pFile,' atom: %s, site sym: %s, type: %s wave type: %s:' \ |
|---|
| 958 | %(at[ct-1],at[cs],Stype,AtomSS['waveType']) |
|---|
| 959 | for iw,wave in enumerate(Waves): |
|---|
| 960 | line = '' |
|---|
| 961 | if AtomSS['waveType'] in ['Block','ZigZag'] and Stype == 'Spos' and not iw: |
|---|
| 962 | for item in names[Stype][6:]: |
|---|
| 963 | line += '%8s '%(item) |
|---|
| 964 | else: |
|---|
| 965 | if Stype == 'Spos': |
|---|
| 966 | for item in names[Stype][:6]: |
|---|
| 967 | line += '%8s '%(item) |
|---|
| 968 | else: |
|---|
| 969 | for item in names[Stype]: |
|---|
| 970 | line += '%8s '%(item) |
|---|
| 971 | print >>pFile,line |
|---|
| 972 | line = '' |
|---|
| 973 | for item in wave[0]: |
|---|
| 974 | line += '%8.4f '%(item) |
|---|
| 975 | line += ' Refine? '+str(wave[1]) |
|---|
| 976 | print >>pFile,line |
|---|
| 977 | |
|---|
| 978 | def PrintTexture(textureData): |
|---|
| 979 | topstr = '\n Spherical harmonics texture: Order:' + \ |
|---|
| 980 | str(textureData['Order']) |
|---|
| 981 | if textureData['Order']: |
|---|
| 982 | print >>pFile,topstr+' Refine? '+str(textureData['SH Coeff'][0]) |
|---|
| 983 | else: |
|---|
| 984 | print >>pFile,topstr |
|---|
| 985 | return |
|---|
| 986 | names = ['omega','chi','phi'] |
|---|
| 987 | line = '\n' |
|---|
| 988 | for name in names: |
|---|
| 989 | line += ' SH '+name+':'+'%12.4f'%(textureData['Sample '+name][1])+' Refine? '+str(textureData['Sample '+name][0]) |
|---|
| 990 | print >>pFile,line |
|---|
| 991 | print >>pFile,'\n Texture coefficients:' |
|---|
| 992 | SHcoeff = textureData['SH Coeff'][1] |
|---|
| 993 | SHkeys = SHcoeff.keys() |
|---|
| 994 | nCoeff = len(SHcoeff) |
|---|
| 995 | nBlock = nCoeff/10+1 |
|---|
| 996 | iBeg = 0 |
|---|
| 997 | iFin = min(iBeg+10,nCoeff) |
|---|
| 998 | for block in range(nBlock): |
|---|
| 999 | ptlbls = ' names :' |
|---|
| 1000 | ptstr = ' values:' |
|---|
| 1001 | for item in SHkeys[iBeg:iFin]: |
|---|
| 1002 | ptlbls += '%12s'%(item) |
|---|
| 1003 | ptstr += '%12.4f'%(SHcoeff[item]) |
|---|
| 1004 | print >>pFile,ptlbls |
|---|
| 1005 | print >>pFile,ptstr |
|---|
| 1006 | iBeg += 10 |
|---|
| 1007 | iFin = min(iBeg+10,nCoeff) |
|---|
| 1008 | |
|---|
| 1009 | def MakeRBParms(rbKey,phaseVary,phaseDict): |
|---|
| 1010 | rbid = str(rbids.index(RB['RBId'])) |
|---|
| 1011 | pfxRB = pfx+'RB'+rbKey+'P' |
|---|
| 1012 | pstr = ['x','y','z'] |
|---|
| 1013 | ostr = ['a','i','j','k'] |
|---|
| 1014 | for i in range(3): |
|---|
| 1015 | name = pfxRB+pstr[i]+':'+str(iRB)+':'+rbid |
|---|
| 1016 | phaseDict[name] = RB['Orig'][0][i] |
|---|
| 1017 | if RB['Orig'][1]: |
|---|
| 1018 | phaseVary += [name,] |
|---|
| 1019 | pfxRB = pfx+'RB'+rbKey+'O' |
|---|
| 1020 | for i in range(4): |
|---|
| 1021 | name = pfxRB+ostr[i]+':'+str(iRB)+':'+rbid |
|---|
| 1022 | phaseDict[name] = RB['Orient'][0][i] |
|---|
| 1023 | if RB['Orient'][1] == 'AV' and i: |
|---|
| 1024 | phaseVary += [name,] |
|---|
| 1025 | elif RB['Orient'][1] == 'A' and not i: |
|---|
| 1026 | phaseVary += [name,] |
|---|
| 1027 | |
|---|
| 1028 | def MakeRBThermals(rbKey,phaseVary,phaseDict): |
|---|
| 1029 | rbid = str(rbids.index(RB['RBId'])) |
|---|
| 1030 | tlstr = ['11','22','33','12','13','23'] |
|---|
| 1031 | sstr = ['12','13','21','23','31','32','AA','BB'] |
|---|
| 1032 | if 'T' in RB['ThermalMotion'][0]: |
|---|
| 1033 | pfxRB = pfx+'RB'+rbKey+'T' |
|---|
| 1034 | for i in range(6): |
|---|
| 1035 | name = pfxRB+tlstr[i]+':'+str(iRB)+':'+rbid |
|---|
| 1036 | phaseDict[name] = RB['ThermalMotion'][1][i] |
|---|
| 1037 | if RB['ThermalMotion'][2][i]: |
|---|
| 1038 | phaseVary += [name,] |
|---|
| 1039 | if 'L' in RB['ThermalMotion'][0]: |
|---|
| 1040 | pfxRB = pfx+'RB'+rbKey+'L' |
|---|
| 1041 | for i in range(6): |
|---|
| 1042 | name = pfxRB+tlstr[i]+':'+str(iRB)+':'+rbid |
|---|
| 1043 | phaseDict[name] = RB['ThermalMotion'][1][i+6] |
|---|
| 1044 | if RB['ThermalMotion'][2][i+6]: |
|---|
| 1045 | phaseVary += [name,] |
|---|
| 1046 | if 'S' in RB['ThermalMotion'][0]: |
|---|
| 1047 | pfxRB = pfx+'RB'+rbKey+'S' |
|---|
| 1048 | for i in range(8): |
|---|
| 1049 | name = pfxRB+sstr[i]+':'+str(iRB)+':'+rbid |
|---|
| 1050 | phaseDict[name] = RB['ThermalMotion'][1][i+12] |
|---|
| 1051 | if RB['ThermalMotion'][2][i+12]: |
|---|
| 1052 | phaseVary += [name,] |
|---|
| 1053 | if 'U' in RB['ThermalMotion'][0]: |
|---|
| 1054 | name = pfx+'RB'+rbKey+'U:'+str(iRB)+':'+rbid |
|---|
| 1055 | phaseDict[name] = RB['ThermalMotion'][1][0] |
|---|
| 1056 | if RB['ThermalMotion'][2][0]: |
|---|
| 1057 | phaseVary += [name,] |
|---|
| 1058 | |
|---|
| 1059 | def MakeRBTorsions(rbKey,phaseVary,phaseDict): |
|---|
| 1060 | rbid = str(rbids.index(RB['RBId'])) |
|---|
| 1061 | pfxRB = pfx+'RB'+rbKey+'Tr;' |
|---|
| 1062 | for i,torsion in enumerate(RB['Torsions']): |
|---|
| 1063 | name = pfxRB+str(i)+':'+str(iRB)+':'+rbid |
|---|
| 1064 | phaseDict[name] = torsion[0] |
|---|
| 1065 | if torsion[1]: |
|---|
| 1066 | phaseVary += [name,] |
|---|
| 1067 | |
|---|
| 1068 | if Print: |
|---|
| 1069 | print >>pFile,'\n Phases:' |
|---|
| 1070 | phaseVary = [] |
|---|
| 1071 | phaseDict = {} |
|---|
| 1072 | pawleyLookup = {} |
|---|
| 1073 | FFtables = {} #scattering factors - xrays |
|---|
| 1074 | MFtables = {} #Mag. form factors |
|---|
| 1075 | BLtables = {} # neutrons |
|---|
| 1076 | Natoms = {} |
|---|
| 1077 | maxSSwave = {} |
|---|
| 1078 | shModels = ['cylindrical','none','shear - 2/m','rolling - mmm'] |
|---|
| 1079 | SamSym = dict(zip(shModels,['0','-1','2/m','mmm'])) |
|---|
| 1080 | atomIndx = {} |
|---|
| 1081 | for name in PhaseData: |
|---|
| 1082 | General = PhaseData[name]['General'] |
|---|
| 1083 | pId = PhaseData[name]['pId'] |
|---|
| 1084 | pfx = str(pId)+'::' |
|---|
| 1085 | FFtable = G2el.GetFFtable(General['AtomTypes']) |
|---|
| 1086 | BLtable = G2el.GetBLtable(General) |
|---|
| 1087 | FFtables.update(FFtable) |
|---|
| 1088 | BLtables.update(BLtable) |
|---|
| 1089 | phaseDict[pfx+'isMag'] = False |
|---|
| 1090 | SGData = General['SGData'] |
|---|
| 1091 | SGtext,SGtable = G2spc.SGPrint(SGData) |
|---|
| 1092 | if General['Type'] == 'magnetic': |
|---|
| 1093 | MFtable = G2el.GetMFtable(General['AtomTypes'],General['Lande g']) |
|---|
| 1094 | MFtables.update(MFtable) |
|---|
| 1095 | phaseDict[pfx+'isMag'] = True |
|---|
| 1096 | SpnFlp = SGData['SpnFlp'] |
|---|
| 1097 | Atoms = PhaseData[name]['Atoms'] |
|---|
| 1098 | if Atoms and not General.get('doPawley'): |
|---|
| 1099 | cx,ct,cs,cia = General['AtomPtrs'] |
|---|
| 1100 | AtLookup = G2mth.FillAtomLookUp(Atoms,cia+8) |
|---|
| 1101 | PawleyRef = PhaseData[name].get('Pawley ref',[]) |
|---|
| 1102 | cell = General['Cell'] |
|---|
| 1103 | A = G2lat.cell2A(cell[1:7]) |
|---|
| 1104 | phaseDict.update({pfx+'A0':A[0],pfx+'A1':A[1],pfx+'A2':A[2], |
|---|
| 1105 | pfx+'A3':A[3],pfx+'A4':A[4],pfx+'A5':A[5],pfx+'Vol':G2lat.calc_V(A)}) |
|---|
| 1106 | if cell[0]: |
|---|
| 1107 | phaseVary += cellVary(pfx,SGData) #also fills in symmetry required constraints |
|---|
| 1108 | SSGtext = [] #no superstructure |
|---|
| 1109 | im = 0 |
|---|
| 1110 | if General.get('Modulated',False): |
|---|
| 1111 | im = 1 #refl offset |
|---|
| 1112 | Vec,vRef,maxH = General['SuperVec'] |
|---|
| 1113 | phaseDict.update({pfx+'mV0':Vec[0],pfx+'mV1':Vec[1],pfx+'mV2':Vec[2]}) |
|---|
| 1114 | SSGData = General['SSGData'] |
|---|
| 1115 | SSGtext,SSGtable = G2spc.SSGPrint(SGData,SSGData) |
|---|
| 1116 | if vRef: |
|---|
| 1117 | phaseVary += modVary(pfx,SSGData) |
|---|
| 1118 | resRBData = PhaseData[name]['RBModels'].get('Residue',[]) |
|---|
| 1119 | if resRBData: |
|---|
| 1120 | rbids = rbIds['Residue'] #NB: used in the MakeRB routines |
|---|
| 1121 | for iRB,RB in enumerate(resRBData): |
|---|
| 1122 | MakeRBParms('R',phaseVary,phaseDict) |
|---|
| 1123 | MakeRBThermals('R',phaseVary,phaseDict) |
|---|
| 1124 | MakeRBTorsions('R',phaseVary,phaseDict) |
|---|
| 1125 | |
|---|
| 1126 | vecRBData = PhaseData[name]['RBModels'].get('Vector',[]) |
|---|
| 1127 | if vecRBData: |
|---|
| 1128 | rbids = rbIds['Vector'] #NB: used in the MakeRB routines |
|---|
| 1129 | for iRB,RB in enumerate(vecRBData): |
|---|
| 1130 | MakeRBParms('V',phaseVary,phaseDict) |
|---|
| 1131 | MakeRBThermals('V',phaseVary,phaseDict) |
|---|
| 1132 | |
|---|
| 1133 | Natoms[pfx] = 0 |
|---|
| 1134 | maxSSwave[pfx] = {'Sfrac':0,'Spos':0,'Sadp':0,'Smag':0} |
|---|
| 1135 | if Atoms and not General.get('doPawley'): |
|---|
| 1136 | cx,ct,cs,cia = General['AtomPtrs'] |
|---|
| 1137 | Natoms[pfx] = len(Atoms) |
|---|
| 1138 | for i,at in enumerate(Atoms): |
|---|
| 1139 | atomIndx[at[cia+8]] = [pfx,i] #lookup table for restraints |
|---|
| 1140 | phaseDict.update({pfx+'Atype:'+str(i):at[ct],pfx+'Afrac:'+str(i):at[cx+3],pfx+'Amul:'+str(i):at[cs+1], |
|---|
| 1141 | pfx+'Ax:'+str(i):at[cx],pfx+'Ay:'+str(i):at[cx+1],pfx+'Az:'+str(i):at[cx+2], |
|---|
| 1142 | pfx+'dAx:'+str(i):0.,pfx+'dAy:'+str(i):0.,pfx+'dAz:'+str(i):0., #refined shifts for x,y,z |
|---|
| 1143 | pfx+'AI/A:'+str(i):at[cia],}) |
|---|
| 1144 | if at[cia] == 'I': |
|---|
| 1145 | phaseDict[pfx+'AUiso:'+str(i)] = at[cia+1] |
|---|
| 1146 | else: |
|---|
| 1147 | phaseDict.update({pfx+'AU11:'+str(i):at[cia+2],pfx+'AU22:'+str(i):at[cia+3],pfx+'AU33:'+str(i):at[cia+4], |
|---|
| 1148 | pfx+'AU12:'+str(i):at[cia+5],pfx+'AU13:'+str(i):at[cia+6],pfx+'AU23:'+str(i):at[cia+7]}) |
|---|
| 1149 | if General['Type'] == 'magnetic': |
|---|
| 1150 | phaseDict.update({pfx+'AMx:'+str(i):at[cx+4],pfx+'AMy:'+str(i):at[cx+5],pfx+'AMz:'+str(i):at[cx+6]}) |
|---|
| 1151 | if 'F' in at[ct+1]: |
|---|
| 1152 | phaseVary.append(pfx+'Afrac:'+str(i)) |
|---|
| 1153 | if 'X' in at[ct+1]: |
|---|
| 1154 | try: #patch for sytsym name changes |
|---|
| 1155 | xId,xCoef = G2spc.GetCSxinel(at[cs]) |
|---|
| 1156 | except KeyError: |
|---|
| 1157 | Sytsym = G2spc.SytSym(at[cx:cx+3],SGData)[0] |
|---|
| 1158 | at[cs] = Sytsym |
|---|
| 1159 | xId,xCoef = G2spc.GetCSxinel(at[cs]) |
|---|
| 1160 | xId,xCoef = G2spc.GetCSxinel(at[cs]) |
|---|
| 1161 | names = [pfx+'dAx:'+str(i),pfx+'dAy:'+str(i),pfx+'dAz:'+str(i)] |
|---|
| 1162 | equivs = [[],[],[]] |
|---|
| 1163 | for j in range(3): |
|---|
| 1164 | if xId[j] > 0: |
|---|
| 1165 | phaseVary.append(names[j]) |
|---|
| 1166 | equivs[xId[j]-1].append([names[j],xCoef[j]]) |
|---|
| 1167 | for equiv in equivs: |
|---|
| 1168 | if len(equiv) > 1: |
|---|
| 1169 | name = equiv[0][0] |
|---|
| 1170 | coef = equiv[0][1] |
|---|
| 1171 | for eqv in equiv[1:]: |
|---|
| 1172 | eqv[1] /= coef |
|---|
| 1173 | G2mv.StoreEquivalence(name,(eqv,)) |
|---|
| 1174 | if 'U' in at[ct+1]: |
|---|
| 1175 | if at[cia] == 'I': |
|---|
| 1176 | phaseVary.append(pfx+'AUiso:'+str(i)) |
|---|
| 1177 | else: |
|---|
| 1178 | try: #patch for sytsym name changes |
|---|
| 1179 | uId,uCoef = G2spc.GetCSuinel(at[cs])[:2] |
|---|
| 1180 | except KeyError: |
|---|
| 1181 | Sytsym = G2spc.SytSym(at[cx:cx+3],SGData)[0] |
|---|
| 1182 | at[cs] = Sytsym |
|---|
| 1183 | uId,uCoef = G2spc.GetCSuinel(at[cs])[:2] |
|---|
| 1184 | uId,uCoef = G2spc.GetCSuinel(at[cs])[:2] |
|---|
| 1185 | names = [pfx+'AU11:'+str(i),pfx+'AU22:'+str(i),pfx+'AU33:'+str(i), |
|---|
| 1186 | pfx+'AU12:'+str(i),pfx+'AU13:'+str(i),pfx+'AU23:'+str(i)] |
|---|
| 1187 | equivs = [[],[],[],[],[],[]] |
|---|
| 1188 | for j in range(6): |
|---|
| 1189 | if uId[j] > 0: |
|---|
| 1190 | phaseVary.append(names[j]) |
|---|
| 1191 | equivs[uId[j]-1].append([names[j],uCoef[j]]) |
|---|
| 1192 | for equiv in equivs: |
|---|
| 1193 | if len(equiv) > 1: |
|---|
| 1194 | name = equiv[0][0] |
|---|
| 1195 | coef = equiv[0][1] |
|---|
| 1196 | for eqv in equiv[1:]: |
|---|
| 1197 | eqv[1] /= coef |
|---|
| 1198 | G2mv.StoreEquivalence(name,equiv[1:]) |
|---|
| 1199 | if 'M' in at[ct+1]: |
|---|
| 1200 | SytSym,Mul,Nop,dupDir = G2spc.SytSym(at[cx:cx+3],SGData) |
|---|
| 1201 | mId,mCoef = G2spc.GetCSpqinel(SytSym,SpnFlp,dupDir) |
|---|
| 1202 | names = [pfx+'AMx:'+str(i),pfx+'AMy:'+str(i),pfx+'AMz:'+str(i)] |
|---|
| 1203 | equivs = [[],[],[]] |
|---|
| 1204 | for j in range(3): |
|---|
| 1205 | if mId[j] > 0: |
|---|
| 1206 | phaseVary.append(names[j]) |
|---|
| 1207 | equivs[mId[j]-1].append([names[j],mCoef[j]]) |
|---|
| 1208 | for equiv in equivs: |
|---|
| 1209 | if len(equiv) > 1: |
|---|
| 1210 | name = equiv[0][0] |
|---|
| 1211 | coef = equiv[0][1] |
|---|
| 1212 | for eqv in equiv[1:]: |
|---|
| 1213 | eqv[1] /= coef |
|---|
| 1214 | G2mv.StoreEquivalence(name,(eqv,)) |
|---|
| 1215 | if General.get('Modulated',False): |
|---|
| 1216 | AtomSS = at[-1]['SS1'] |
|---|
| 1217 | waveType = AtomSS['waveType'] |
|---|
| 1218 | phaseDict[pfx+'waveType:'+str(i)] = waveType |
|---|
| 1219 | for Stype in ['Sfrac','Spos','Sadp','Smag']: |
|---|
| 1220 | Waves = AtomSS[Stype] |
|---|
| 1221 | nx = 0 |
|---|
| 1222 | for iw,wave in enumerate(Waves): |
|---|
| 1223 | if not iw: |
|---|
| 1224 | if waveType in ['ZigZag','Block']: |
|---|
| 1225 | nx = 1 |
|---|
| 1226 | CSI = G2spc.GetSSfxuinel(waveType,1,at[cx:cx+3],SGData,SSGData) |
|---|
| 1227 | else: |
|---|
| 1228 | CSI = G2spc.GetSSfxuinel('Fourier',iw+1-nx,at[cx:cx+3],SGData,SSGData) |
|---|
| 1229 | uId,uCoef = CSI[Stype] |
|---|
| 1230 | stiw = str(i)+':'+str(iw) |
|---|
| 1231 | if Stype == 'Spos': |
|---|
| 1232 | if waveType in ['ZigZag','Block',] and not iw: |
|---|
| 1233 | names = [pfx+'Tmin:'+stiw,pfx+'Tmax:'+stiw,pfx+'Xmax:'+stiw,pfx+'Ymax:'+stiw,pfx+'Zmax:'+stiw] |
|---|
| 1234 | equivs = [[],[], [],[],[]] |
|---|
| 1235 | else: |
|---|
| 1236 | names = [pfx+'Xsin:'+stiw,pfx+'Ysin:'+stiw,pfx+'Zsin:'+stiw, |
|---|
| 1237 | pfx+'Xcos:'+stiw,pfx+'Ycos:'+stiw,pfx+'Zcos:'+stiw] |
|---|
| 1238 | equivs = [[],[],[], [],[],[]] |
|---|
| 1239 | elif Stype == 'Sadp': |
|---|
| 1240 | names = [pfx+'U11sin:'+stiw,pfx+'U22sin:'+stiw,pfx+'U33sin:'+stiw, |
|---|
| 1241 | pfx+'U12sin:'+stiw,pfx+'U13sin:'+stiw,pfx+'U23sin:'+stiw, |
|---|
| 1242 | pfx+'U11cos:'+stiw,pfx+'U22cos:'+stiw,pfx+'U33cos:'+stiw, |
|---|
| 1243 | pfx+'U12cos:'+stiw,pfx+'U13cos:'+stiw,pfx+'U23cos:'+stiw] |
|---|
| 1244 | equivs = [[],[],[],[],[],[], [],[],[],[],[],[]] |
|---|
| 1245 | elif Stype == 'Sfrac': |
|---|
| 1246 | equivs = [[],[]] |
|---|
| 1247 | if 'Crenel' in waveType and not iw: |
|---|
| 1248 | names = [pfx+'Fzero:'+stiw,pfx+'Fwid:'+stiw] |
|---|
| 1249 | else: |
|---|
| 1250 | names = [pfx+'Fsin:'+stiw,pfx+'Fcos:'+stiw] |
|---|
| 1251 | elif Stype == 'Smag': |
|---|
| 1252 | equivs = [[],[],[], [],[],[]] |
|---|
| 1253 | names = [pfx+'MXsin:'+stiw,pfx+'MYsin:'+stiw,pfx+'MZsin:'+stiw, |
|---|
| 1254 | pfx+'MXcos:'+stiw,pfx+'MYcos:'+stiw,pfx+'MZcos:'+stiw] |
|---|
| 1255 | phaseDict.update(dict(zip(names,wave[0]))) |
|---|
| 1256 | if wave[1]: #what do we do here for multiple terms in modulation constraints? |
|---|
| 1257 | for j in range(len(equivs)): |
|---|
| 1258 | if uId[j][0] > 0: |
|---|
| 1259 | phaseVary.append(names[j]) |
|---|
| 1260 | equivs[uId[j][0]-1].append([names[j],uCoef[j][0]]) |
|---|
| 1261 | for equiv in equivs: |
|---|
| 1262 | if len(equiv) > 1: |
|---|
| 1263 | name = equiv[0][0] |
|---|
| 1264 | coef = equiv[0][1] |
|---|
| 1265 | for eqv in equiv[1:]: |
|---|
| 1266 | eqv[1] /= coef |
|---|
| 1267 | G2mv.StoreEquivalence(name,equiv[1:]) |
|---|
| 1268 | maxSSwave[pfx][Stype] = max(maxSSwave[pfx][Stype],iw+1) |
|---|
| 1269 | textureData = General['SH Texture'] |
|---|
| 1270 | if textureData['Order'] and not seqRef: |
|---|
| 1271 | phaseDict[pfx+'SHorder'] = textureData['Order'] |
|---|
| 1272 | phaseDict[pfx+'SHmodel'] = SamSym[textureData['Model']] |
|---|
| 1273 | for item in ['omega','chi','phi']: |
|---|
| 1274 | phaseDict[pfx+'SH '+item] = textureData['Sample '+item][1] |
|---|
| 1275 | if textureData['Sample '+item][0]: |
|---|
| 1276 | phaseVary.append(pfx+'SH '+item) |
|---|
| 1277 | for item in textureData['SH Coeff'][1]: |
|---|
| 1278 | phaseDict[pfx+item] = textureData['SH Coeff'][1][item] |
|---|
| 1279 | if textureData['SH Coeff'][0]: |
|---|
| 1280 | phaseVary.append(pfx+item) |
|---|
| 1281 | |
|---|
| 1282 | if Print: |
|---|
| 1283 | print >>pFile,'\n Phase name: ',General['Name'] |
|---|
| 1284 | print >>pFile,135*'=' |
|---|
| 1285 | PrintFFtable(FFtable) |
|---|
| 1286 | PrintBLtable(BLtable) |
|---|
| 1287 | if General['Type'] == 'magnetic': |
|---|
| 1288 | PrintMFtable(MFtable) |
|---|
| 1289 | print >>pFile,'' |
|---|
| 1290 | #how do we print magnetic symmetry table? TBD |
|---|
| 1291 | if len(SSGtext): #if superstructure |
|---|
| 1292 | for line in SSGtext: print >>pFile,line |
|---|
| 1293 | if len(SSGtable): |
|---|
| 1294 | for item in SSGtable: |
|---|
| 1295 | line = ' %s '%(item) |
|---|
| 1296 | print >>pFile,line |
|---|
| 1297 | else: |
|---|
| 1298 | print >>pFile,' ( 1) %s'%(SSGtable[0]) |
|---|
| 1299 | else: |
|---|
| 1300 | for line in SGtext: print >>pFile,line |
|---|
| 1301 | if len(SGtable): |
|---|
| 1302 | for item in SGtable: |
|---|
| 1303 | line = ' %s '%(item) |
|---|
| 1304 | print >>pFile,line |
|---|
| 1305 | else: |
|---|
| 1306 | print >>pFile,' ( 1) %s'%(SGtable[0]) |
|---|
| 1307 | PrintRBObjects(resRBData,vecRBData) |
|---|
| 1308 | PrintAtoms(General,Atoms) |
|---|
| 1309 | if General['Type'] == 'magnetic': |
|---|
| 1310 | PrintMoments(General,Atoms) |
|---|
| 1311 | if General.get('Modulated',False): |
|---|
| 1312 | PrintWaves(General,Atoms) |
|---|
| 1313 | print >>pFile,'\n Unit cell: a = %.5f'%(cell[1]),' b = %.5f'%(cell[2]),' c = %.5f'%(cell[3]), \ |
|---|
| 1314 | ' alpha = %.3f'%(cell[4]),' beta = %.3f'%(cell[5]),' gamma = %.3f'%(cell[6]), \ |
|---|
| 1315 | ' volume = %.3f'%(cell[7]),' Refine?',cell[0] |
|---|
| 1316 | if len(SSGtext): #if superstructure |
|---|
| 1317 | print >>pFile,'\n Modulation vector: mV0 = %.4f'%(Vec[0]),' mV1 = %.4f'%(Vec[1]), \ |
|---|
| 1318 | ' mV2 = %.4f'%(Vec[2]),' max mod. index = %d'%(maxH),' Refine?',vRef |
|---|
| 1319 | if not seqRef: |
|---|
| 1320 | PrintTexture(textureData) |
|---|
| 1321 | if name in RestraintDict: |
|---|
| 1322 | PrintRestraints(cell[1:7],SGData,General['AtomPtrs'],Atoms,AtLookup, |
|---|
| 1323 | textureData,RestraintDict[name],pFile) |
|---|
| 1324 | |
|---|
| 1325 | elif PawleyRef: |
|---|
| 1326 | if Print: |
|---|
| 1327 | print >>pFile,'\n Phase name: ',General['Name'] |
|---|
| 1328 | print >>pFile,135*'=' |
|---|
| 1329 | print >>pFile,'' |
|---|
| 1330 | if len(SSGtext): #if superstructure |
|---|
| 1331 | for line in SSGtext: print >>pFile,line |
|---|
| 1332 | if len(SSGtable): |
|---|
| 1333 | for item in SSGtable: |
|---|
| 1334 | line = ' %s '%(item) |
|---|
| 1335 | print >>pFile,line |
|---|
| 1336 | else: |
|---|
| 1337 | print >>pFile,' ( 1) %s'%(SSGtable[0]) |
|---|
| 1338 | else: |
|---|
| 1339 | for line in SGtext: print >>pFile,line |
|---|
| 1340 | if len(SGtable): |
|---|
| 1341 | for item in SGtable: |
|---|
| 1342 | line = ' %s '%(item) |
|---|
| 1343 | print >>pFile,line |
|---|
| 1344 | else: |
|---|
| 1345 | print >>pFile,' ( 1) %s'%(SGtable[0]) |
|---|
| 1346 | print >>pFile,'\n Unit cell: a = %.5f'%(cell[1]),' b = %.5f'%(cell[2]),' c = %.5f'%(cell[3]), \ |
|---|
| 1347 | ' alpha = %.3f'%(cell[4]),' beta = %.3f'%(cell[5]),' gamma = %.3f'%(cell[6]), \ |
|---|
| 1348 | ' volume = %.3f'%(cell[7]),' Refine?',cell[0] |
|---|
| 1349 | if len(SSGtext): #if superstructure |
|---|
| 1350 | print >>pFile,'\n Modulation vector: mV0 = %.4f'%(Vec[0]),' mV1 = %.4f'%(Vec[1]), \ |
|---|
| 1351 | ' mV2 = %.4f'%(Vec[2]),' max mod. index = %d'%(maxH),' Refine?',vRef |
|---|
| 1352 | pawleyVary = [] |
|---|
| 1353 | for i,refl in enumerate(PawleyRef): |
|---|
| 1354 | phaseDict[pfx+'PWLref:'+str(i)] = refl[6+im] |
|---|
| 1355 | if im: |
|---|
| 1356 | pawleyLookup[pfx+'%d,%d,%d,%d'%(refl[0],refl[1],refl[2],refl[3])] = i |
|---|
| 1357 | else: |
|---|
| 1358 | pawleyLookup[pfx+'%d,%d,%d'%(refl[0],refl[1],refl[2])] = i |
|---|
| 1359 | if refl[5+im]: |
|---|
| 1360 | pawleyVary.append(pfx+'PWLref:'+str(i)) |
|---|
| 1361 | GetPawleyConstr(SGData['SGLaue'],PawleyRef,im,pawleyVary) #does G2mv.StoreEquivalence |
|---|
| 1362 | phaseVary += pawleyVary |
|---|
| 1363 | |
|---|
| 1364 | return Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables,MFtables,maxSSwave |
|---|
| 1365 | |
|---|
| 1366 | def cellFill(pfx,SGData,parmDict,sigDict): |
|---|
| 1367 | '''Returns the filled-out reciprocal cell (A) terms and their uncertainties |
|---|
| 1368 | from the parameter and sig dictionaries. |
|---|
| 1369 | |
|---|
| 1370 | :param str pfx: parameter prefix ("n::", where n is a phase number) |
|---|
| 1371 | :param dict SGdata: a symmetry object |
|---|
| 1372 | :param dict parmDict: a dictionary of parameters |
|---|
| 1373 | :param dict sigDict: a dictionary of uncertainties on parameters |
|---|
| 1374 | |
|---|
| 1375 | :returns: A,sigA where each is a list of six terms with the A terms |
|---|
| 1376 | ''' |
|---|
| 1377 | if SGData['SGLaue'] in ['-1',]: |
|---|
| 1378 | A = [parmDict[pfx+'A0'],parmDict[pfx+'A1'],parmDict[pfx+'A2'], |
|---|
| 1379 | parmDict[pfx+'A3'],parmDict[pfx+'A4'],parmDict[pfx+'A5']] |
|---|
| 1380 | elif SGData['SGLaue'] in ['2/m',]: |
|---|
| 1381 | if SGData['SGUniq'] == 'a': |
|---|
| 1382 | A = [parmDict[pfx+'A0'],parmDict[pfx+'A1'],parmDict[pfx+'A2'], |
|---|
| 1383 | 0,0,parmDict[pfx+'A5']] |
|---|
| 1384 | elif SGData['SGUniq'] == 'b': |
|---|
| 1385 | A = [parmDict[pfx+'A0'],parmDict[pfx+'A1'],parmDict[pfx+'A2'], |
|---|
| 1386 | 0,parmDict[pfx+'A4'],0] |
|---|
| 1387 | else: |
|---|
| 1388 | A = [parmDict[pfx+'A0'],parmDict[pfx+'A1'],parmDict[pfx+'A2'], |
|---|
| 1389 | parmDict[pfx+'A3'],0,0] |
|---|
| 1390 | elif SGData['SGLaue'] in ['mmm',]: |
|---|
| 1391 | A = [parmDict[pfx+'A0'],parmDict[pfx+'A1'],parmDict[pfx+'A2'],0,0,0] |
|---|
| 1392 | elif SGData['SGLaue'] in ['4/m','4/mmm']: |
|---|
| 1393 | A = [parmDict[pfx+'A0'],parmDict[pfx+'A0'],parmDict[pfx+'A2'],0,0,0] |
|---|
| 1394 | elif SGData['SGLaue'] in ['6/m','6/mmm','3m1', '31m', '3']: |
|---|
| 1395 | A = [parmDict[pfx+'A0'],parmDict[pfx+'A0'],parmDict[pfx+'A2'], |
|---|
| 1396 | parmDict[pfx+'A0'],0,0] |
|---|
| 1397 | elif SGData['SGLaue'] in ['3R', '3mR']: |
|---|
| 1398 | A = [parmDict[pfx+'A0'],parmDict[pfx+'A0'],parmDict[pfx+'A0'], |
|---|
| 1399 | parmDict[pfx+'A3'],parmDict[pfx+'A3'],parmDict[pfx+'A3']] |
|---|
| 1400 | elif SGData['SGLaue'] in ['m3m','m3']: |
|---|
| 1401 | A = [parmDict[pfx+'A0'],parmDict[pfx+'A0'],parmDict[pfx+'A0'],0,0,0] |
|---|
| 1402 | |
|---|
| 1403 | try: |
|---|
| 1404 | if SGData['SGLaue'] in ['-1',]: |
|---|
| 1405 | sigA = [sigDict[pfx+'A0'],sigDict[pfx+'A1'],sigDict[pfx+'A2'], |
|---|
| 1406 | sigDict[pfx+'A3'],sigDict[pfx+'A4'],sigDict[pfx+'A5']] |
|---|
| 1407 | elif SGData['SGLaue'] in ['2/m',]: |
|---|
| 1408 | if SGData['SGUniq'] == 'a': |
|---|
| 1409 | sigA = [sigDict[pfx+'A0'],sigDict[pfx+'A1'],sigDict[pfx+'A2'], |
|---|
| 1410 | 0,0,sigDict[pfx+'A5']] |
|---|
| 1411 | elif SGData['SGUniq'] == 'b': |
|---|
| 1412 | sigA = [sigDict[pfx+'A0'],sigDict[pfx+'A1'],sigDict[pfx+'A2'], |
|---|
| 1413 | 0,sigDict[pfx+'A4'],0] |
|---|
| 1414 | else: |
|---|
| 1415 | sigA = [sigDict[pfx+'A0'],sigDict[pfx+'A1'],sigDict[pfx+'A2'], |
|---|
| 1416 | sigDict[pfx+'A3'],0,0] |
|---|
| 1417 | elif SGData['SGLaue'] in ['mmm',]: |
|---|
| 1418 | sigA = [sigDict[pfx+'A0'],sigDict[pfx+'A1'],sigDict[pfx+'A2'],0,0,0] |
|---|
| 1419 | elif SGData['SGLaue'] in ['4/m','4/mmm']: |
|---|
| 1420 | sigA = [sigDict[pfx+'A0'],0,sigDict[pfx+'A2'],0,0,0] |
|---|
| 1421 | elif SGData['SGLaue'] in ['6/m','6/mmm','3m1', '31m', '3']: |
|---|
| 1422 | sigA = [sigDict[pfx+'A0'],0,sigDict[pfx+'A2'],0,0,0] |
|---|
| 1423 | elif SGData['SGLaue'] in ['3R', '3mR']: |
|---|
| 1424 | sigA = [sigDict[pfx+'A0'],0,0,sigDict[pfx+'A3'],0,0] |
|---|
| 1425 | elif SGData['SGLaue'] in ['m3m','m3']: |
|---|
| 1426 | sigA = [sigDict[pfx+'A0'],0,0,0,0,0] |
|---|
| 1427 | except KeyError: |
|---|
| 1428 | sigA = [0,0,0,0,0,0] |
|---|
| 1429 | return A,sigA |
|---|
| 1430 | |
|---|
| 1431 | def PrintRestraints(cell,SGData,AtPtrs,Atoms,AtLookup,textureData,phaseRest,pFile): |
|---|
| 1432 | 'needs a doc string' |
|---|
| 1433 | if phaseRest: |
|---|
| 1434 | Amat = G2lat.cell2AB(cell)[0] |
|---|
| 1435 | cx,ct,cs = AtPtrs[:3] |
|---|
| 1436 | names = [['Bond','Bonds'],['Angle','Angles'],['Plane','Planes'], |
|---|
| 1437 | ['Chiral','Volumes'],['Torsion','Torsions'],['Rama','Ramas'], |
|---|
| 1438 | ['ChemComp','Sites'],['Texture','HKLs']] |
|---|
| 1439 | for name,rest in names: |
|---|
| 1440 | itemRest = phaseRest[name] |
|---|
| 1441 | if itemRest[rest] and itemRest['Use']: |
|---|
| 1442 | print >>pFile,'\n %s %10.3f Use: %s'%(name+' restraint weight factor',itemRest['wtFactor'],str(itemRest['Use'])) |
|---|
| 1443 | if name in ['Bond','Angle','Plane','Chiral']: |
|---|
| 1444 | print >>pFile,' calc obs sig delt/sig atoms(symOp): ' |
|---|
| 1445 | for indx,ops,obs,esd in itemRest[rest]: |
|---|
| 1446 | try: |
|---|
| 1447 | AtNames = G2mth.GetAtomItemsById(Atoms,AtLookup,indx,ct-1) |
|---|
| 1448 | AtName = '' |
|---|
| 1449 | for i,Aname in enumerate(AtNames): |
|---|
| 1450 | AtName += Aname |
|---|
| 1451 | if ops[i] == '1': |
|---|
| 1452 | AtName += '-' |
|---|
| 1453 | else: |
|---|
| 1454 | AtName += '+('+ops[i]+')-' |
|---|
| 1455 | XYZ = np.array(G2mth.GetAtomItemsById(Atoms,AtLookup,indx,cx,3)) |
|---|
| 1456 | XYZ = G2mth.getSyXYZ(XYZ,ops,SGData) |
|---|
| 1457 | if name == 'Bond': |
|---|
| 1458 | calc = G2mth.getRestDist(XYZ,Amat) |
|---|
| 1459 | elif name == 'Angle': |
|---|
| 1460 | calc = G2mth.getRestAngle(XYZ,Amat) |
|---|
| 1461 | elif name == 'Plane': |
|---|
| 1462 | calc = G2mth.getRestPlane(XYZ,Amat) |
|---|
| 1463 | elif name == 'Chiral': |
|---|
| 1464 | calc = G2mth.getRestChiral(XYZ,Amat) |
|---|
| 1465 | print >>pFile,' %9.3f %9.3f %8.3f %8.3f %s'%(calc,obs,esd,(obs-calc)/esd,AtName[:-1]) |
|---|
| 1466 | except KeyError: |
|---|
| 1467 | del itemRest[rest] |
|---|
| 1468 | elif name in ['Torsion','Rama']: |
|---|
| 1469 | print >>pFile,' atoms(symOp) calc obs sig delt/sig torsions: ' |
|---|
| 1470 | coeffDict = itemRest['Coeff'] |
|---|
| 1471 | for indx,ops,cofName,esd in itemRest[rest]: |
|---|
| 1472 | AtNames = G2mth.GetAtomItemsById(Atoms,AtLookup,indx,ct-1) |
|---|
| 1473 | AtName = '' |
|---|
| 1474 | for i,Aname in enumerate(AtNames): |
|---|
| 1475 | AtName += Aname+'+('+ops[i]+')-' |
|---|
| 1476 | XYZ = np.array(G2mth.GetAtomItemsById(Atoms,AtLookup,indx,cx,3)) |
|---|
| 1477 | XYZ = G2mth.getSyXYZ(XYZ,ops,SGData) |
|---|
| 1478 | if name == 'Torsion': |
|---|
| 1479 | tor = G2mth.getRestTorsion(XYZ,Amat) |
|---|
| 1480 | restr,calc = G2mth.calcTorsionEnergy(tor,coeffDict[cofName]) |
|---|
| 1481 | print >>pFile,' %8.3f %8.3f %.3f %8.3f %8.3f %s'%(calc,obs,esd,(obs-calc)/esd,tor,AtName[:-1]) |
|---|
| 1482 | else: |
|---|
| 1483 | phi,psi = G2mth.getRestRama(XYZ,Amat) |
|---|
| 1484 | restr,calc = G2mth.calcRamaEnergy(phi,psi,coeffDict[cofName]) |
|---|
| 1485 | print >>pFile,' %8.3f %8.3f %8.3f %8.3f %8.3f %8.3f %s'%(calc,obs,esd,(obs-calc)/esd,phi,psi,AtName[:-1]) |
|---|
| 1486 | elif name == 'ChemComp': |
|---|
| 1487 | print >>pFile,' atoms mul*frac factor prod' |
|---|
| 1488 | for indx,factors,obs,esd in itemRest[rest]: |
|---|
| 1489 | try: |
|---|
| 1490 | atoms = G2mth.GetAtomItemsById(Atoms,AtLookup,indx,ct-1) |
|---|
| 1491 | mul = np.array(G2mth.GetAtomItemsById(Atoms,AtLookup,indx,cs+1)) |
|---|
| 1492 | frac = np.array(G2mth.GetAtomItemsById(Atoms,AtLookup,indx,cs-1)) |
|---|
| 1493 | mulfrac = mul*frac |
|---|
| 1494 | calcs = mul*frac*factors |
|---|
| 1495 | for iatm,[atom,mf,fr,clc] in enumerate(zip(atoms,mulfrac,factors,calcs)): |
|---|
| 1496 | print >>pFile,' %10s %8.3f %8.3f %8.3f'%(atom,mf,fr,clc) |
|---|
| 1497 | print >>pFile,' Sum: calc: %8.3f obs: %8.3f esd: %8.3f'%(np.sum(calcs),obs,esd) |
|---|
| 1498 | except KeyError: |
|---|
| 1499 | del itemRest[rest] |
|---|
| 1500 | elif name == 'Texture' and textureData['Order']: |
|---|
| 1501 | Start = False |
|---|
| 1502 | SHCoef = textureData['SH Coeff'][1] |
|---|
| 1503 | shModels = ['cylindrical','none','shear - 2/m','rolling - mmm'] |
|---|
| 1504 | SamSym = dict(zip(shModels,['0','-1','2/m','mmm'])) |
|---|
| 1505 | print ' HKL grid neg esd sum neg num neg use unit? unit esd ' |
|---|
| 1506 | for hkl,grid,esd1,ifesd2,esd2 in itemRest[rest]: |
|---|
| 1507 | phi,beta = G2lat.CrsAng(np.array(hkl),cell,SGData) |
|---|
| 1508 | ODFln = G2lat.Flnh(Start,SHCoef,phi,beta,SGData) |
|---|
| 1509 | R,P,Z = G2mth.getRestPolefig(ODFln,SamSym[textureData['Model']],grid) |
|---|
| 1510 | Z = ma.masked_greater(Z,0.0) |
|---|
| 1511 | num = ma.count(Z) |
|---|
| 1512 | sum = 0 |
|---|
| 1513 | if num: |
|---|
| 1514 | sum = np.sum(Z) |
|---|
| 1515 | print ' %d %d %d %d %8.3f %8.3f %8d %s %8.3f'%(hkl[0],hkl[1],hkl[2],grid,esd1,sum,num,str(ifesd2),esd2) |
|---|
| 1516 | |
|---|
| 1517 | def getCellEsd(pfx,SGData,A,covData): |
|---|
| 1518 | 'needs a doc string' |
|---|
| 1519 | dpr = 180./np.pi |
|---|
| 1520 | rVsq = G2lat.calc_rVsq(A) |
|---|
| 1521 | G,g = G2lat.A2Gmat(A) #get recip. & real metric tensors |
|---|
| 1522 | cell = np.array(G2lat.Gmat2cell(g)) #real cell |
|---|
| 1523 | cellst = np.array(G2lat.Gmat2cell(G)) #recip. cell |
|---|
| 1524 | scos = cosd(cellst[3:6]) |
|---|
| 1525 | ssin = sind(cellst[3:6]) |
|---|
| 1526 | scot = scos/ssin |
|---|
| 1527 | rcos = cosd(cell[3:6]) |
|---|
| 1528 | rsin = sind(cell[3:6]) |
|---|
| 1529 | rcot = rcos/rsin |
|---|
| 1530 | RMnames = [pfx+'A0',pfx+'A1',pfx+'A2',pfx+'A3',pfx+'A4',pfx+'A5'] |
|---|
| 1531 | varyList = covData['varyList'] |
|---|
| 1532 | covMatrix = covData['covMatrix'] |
|---|
| 1533 | vcov = G2mth.getVCov(RMnames,varyList,covMatrix) |
|---|
| 1534 | if SGData['SGLaue'] in ['3', '3m1', '31m', '6/m', '6/mmm']: |
|---|
| 1535 | vcov[1,1] = vcov[3,3] = vcov[1,3] = vcov[3,1] = vcov[0,0] |
|---|
| 1536 | vcov[0,1] = vcov[1,0] = vcov[0,3] = vcov[3,0] = vcov[0,0] |
|---|
| 1537 | vcov[1,2] = vcov[2,1] = vcov[2,3] = vcov[3,2] = vcov[0,2] |
|---|
| 1538 | elif SGData['SGLaue'] in ['m3','m3m']: |
|---|
| 1539 | vcov[0:3,0:3] = vcov[0,0] |
|---|
| 1540 | elif SGData['SGLaue'] in ['4/m', '4/mmm']: |
|---|
| 1541 | vcov[0:2,0:2] = vcov[0,0] |
|---|
| 1542 | vcov[1,2] = vcov[2,1] = vcov[0,2] |
|---|
| 1543 | elif SGData['SGLaue'] in ['3R','3mR']: |
|---|
| 1544 | vcov[0:2,0:2] = vcov[0,0] |
|---|
| 1545 | vcov[4,4] = vcov[5,5] = vcov[3,3] |
|---|
| 1546 | vcov[0:3,3:6] = vcov[0,3] |
|---|
| 1547 | vcov[3:6,0:3] = vcov[3,0] |
|---|
| 1548 | Ax = np.array(A) |
|---|
| 1549 | Ax[3:] /= 2. |
|---|
| 1550 | drVdA = np.array([ |
|---|
| 1551 | Ax[1]*Ax[2]-Ax[5]**2, |
|---|
| 1552 | Ax[0]*Ax[2]-Ax[4]**2, |
|---|
| 1553 | Ax[0]*Ax[1]-Ax[3]**2, |
|---|
| 1554 | Ax[4]*Ax[5]-Ax[2]*Ax[3], |
|---|
| 1555 | Ax[3]*Ax[5]-Ax[1]*Ax[4], |
|---|
| 1556 | Ax[3]*Ax[4]-Ax[0]*Ax[5]]) |
|---|
| 1557 | srcvlsq = np.inner(drVdA,np.inner(drVdA,vcov)) |
|---|
| 1558 | Vol = 1/np.sqrt(rVsq) |
|---|
| 1559 | sigVol = Vol**3*np.sqrt(srcvlsq)/2. #ok - checks with GSAS |
|---|
| 1560 | |
|---|
| 1561 | R123 = Ax[0]*Ax[1]*Ax[2] |
|---|
| 1562 | dsasdg = np.zeros((3,6)) |
|---|
| 1563 | dadg = np.zeros((6,6)) |
|---|
| 1564 | for i0 in range(3): #0 1 2 |
|---|
| 1565 | i1 = (i0+1)%3 #1 2 0 |
|---|
| 1566 | i2 = (i1+1)%3 #2 0 1 |
|---|
| 1567 | i3 = 5-i2 #3 5 4 |
|---|
| 1568 | i4 = 5-i1 #4 3 5 |
|---|
| 1569 | i5 = 5-i0 #5 4 3 |
|---|
| 1570 | dsasdg[i0][i1] = 0.5*scot[i0]*scos[i0]/Ax[i1] |
|---|
| 1571 | dsasdg[i0][i2] = 0.5*scot[i0]*scos[i0]/Ax[i2] |
|---|
| 1572 | dsasdg[i0][i5] = -scot[i0]/np.sqrt(Ax[i1]*Ax[i2]) |
|---|
| 1573 | denmsq = Ax[i0]*(R123-Ax[i1]*Ax[i4]**2-Ax[i2]*Ax[i3]**2+(Ax[i4]*Ax[i3])**2) |
|---|
| 1574 | denom = np.sqrt(denmsq) |
|---|
| 1575 | dadg[i5][i0] = -Ax[i5]/denom-rcos[i0]/denmsq*(R123-0.5*Ax[i1]*Ax[i4]**2-0.5*Ax[i2]*Ax[i3]**2) |
|---|
| 1576 | dadg[i5][i1] = -0.5*rcos[i0]/denmsq*(Ax[i0]**2*Ax[i2]-Ax[i0]*Ax[i4]**2) |
|---|
| 1577 | dadg[i5][i2] = -0.5*rcos[i0]/denmsq*(Ax[i0]**2*Ax[i1]-Ax[i0]*Ax[i3]**2) |
|---|
| 1578 | dadg[i5][i3] = Ax[i4]/denom+rcos[i0]/denmsq*(Ax[i0]*Ax[i2]*Ax[i3]-Ax[i3]*Ax[i4]**2) |
|---|
| 1579 | dadg[i5][i4] = Ax[i3]/denom+rcos[i0]/denmsq*(Ax[i0]*Ax[i1]*Ax[i4]-Ax[i3]**2*Ax[i4]) |
|---|
| 1580 | dadg[i5][i5] = -Ax[i0]/denom |
|---|
| 1581 | for i0 in range(3): |
|---|
| 1582 | i1 = (i0+1)%3 |
|---|
| 1583 | i2 = (i1+1)%3 |
|---|
| 1584 | i3 = 5-i2 |
|---|
| 1585 | for ij in range(6): |
|---|
| 1586 | dadg[i0][ij] = cell[i0]*(rcot[i2]*dadg[i3][ij]/rsin[i2]-dsasdg[i1][ij]/ssin[i1]) |
|---|
| 1587 | if ij == i0: |
|---|
| 1588 | dadg[i0][ij] = dadg[i0][ij]-0.5*cell[i0]/Ax[i0] |
|---|
| 1589 | dadg[i3][ij] = -dadg[i3][ij]*rsin[2-i0]*dpr |
|---|
| 1590 | # GSASIIpath.IPyBreak() |
|---|
| 1591 | sigMat = np.inner(dadg,np.inner(dadg,vcov)) |
|---|
| 1592 | var = np.diag(sigMat) |
|---|
| 1593 | CS = np.where(var>0.,np.sqrt(var),0.) |
|---|
| 1594 | return [CS[0],CS[1],CS[2],CS[5],CS[4],CS[3],sigVol] |
|---|
| 1595 | |
|---|
| 1596 | def SetPhaseData(parmDict,sigDict,Phases,RBIds,covData,RestraintDict=None,pFile=None): |
|---|
| 1597 | 'needs a doc string' |
|---|
| 1598 | |
|---|
| 1599 | def PrintAtomsAndSig(General,Atoms,atomsSig): |
|---|
| 1600 | print >>pFile,'\n Atoms:' |
|---|
| 1601 | line = ' name x y z frac Uiso U11 U22 U33 U12 U13 U23' |
|---|
| 1602 | if General['Type'] == 'macromolecular': |
|---|
| 1603 | line = ' res no residue chain '+line |
|---|
| 1604 | cx,ct,cs,cia = General['AtomPtrs'] |
|---|
| 1605 | print >>pFile,line |
|---|
| 1606 | print >>pFile,135*'-' |
|---|
| 1607 | fmt = {0:'%7s',ct:'%7s',cx:'%10.5f',cx+1:'%10.5f',cx+2:'%10.5f',cx+3:'%8.3f',cia+1:'%8.5f', |
|---|
| 1608 | cia+2:'%8.5f',cia+3:'%8.5f',cia+4:'%8.5f',cia+5:'%8.5f',cia+6:'%8.5f',cia+7:'%8.5f'} |
|---|
| 1609 | noFXsig = {cx:[10*' ','%10s'],cx+1:[10*' ','%10s'],cx+2:[10*' ','%10s'],cx+3:[8*' ','%8s']} |
|---|
| 1610 | for atyp in General['AtomTypes']: #zero composition |
|---|
| 1611 | General['NoAtoms'][atyp] = 0. |
|---|
| 1612 | for i,at in enumerate(Atoms): |
|---|
| 1613 | General['NoAtoms'][at[ct]] += at[cx+3]*float(at[cx+5]) #new composition |
|---|
| 1614 | if General['Type'] == 'macromolecular': |
|---|
| 1615 | name = ' %s %s %s %s:'%(at[0],at[1],at[2],at[3]) |
|---|
| 1616 | valstr = ' values: ' |
|---|
| 1617 | sigstr = ' sig : ' |
|---|
| 1618 | else: |
|---|
| 1619 | name = fmt[0]%(at[ct-1])+fmt[1]%(at[ct])+':' |
|---|
| 1620 | valstr = ' values:' |
|---|
| 1621 | sigstr = ' sig :' |
|---|
| 1622 | for ind in range(cx,cx+4): |
|---|
| 1623 | sigind = str(i)+':'+str(ind) |
|---|
| 1624 | valstr += fmt[ind]%(at[ind]) |
|---|
| 1625 | if sigind in atomsSig: |
|---|
| 1626 | sigstr += fmt[ind]%(atomsSig[sigind]) |
|---|
| 1627 | else: |
|---|
| 1628 | sigstr += noFXsig[ind][1]%(noFXsig[ind][0]) |
|---|
| 1629 | if at[cia] == 'I': |
|---|
| 1630 | valstr += fmt[cia+1]%(at[cia+1]) |
|---|
| 1631 | if '%d:%d'%(i,cia+1) in atomsSig: |
|---|
| 1632 | sigstr += fmt[cia+1]%(atomsSig['%d:%d'%(i,cia+1)]) |
|---|
| 1633 | else: |
|---|
| 1634 | sigstr += 8*' ' |
|---|
| 1635 | else: |
|---|
| 1636 | valstr += 8*' ' |
|---|
| 1637 | sigstr += 8*' ' |
|---|
| 1638 | for ind in range(cia+2,cia+8): |
|---|
| 1639 | sigind = str(i)+':'+str(ind) |
|---|
| 1640 | valstr += fmt[ind]%(at[ind]) |
|---|
| 1641 | if sigind in atomsSig: |
|---|
| 1642 | sigstr += fmt[ind]%(atomsSig[sigind]) |
|---|
| 1643 | else: |
|---|
| 1644 | sigstr += 8*' ' |
|---|
| 1645 | print >>pFile,name |
|---|
| 1646 | print >>pFile,valstr |
|---|
| 1647 | print >>pFile,sigstr |
|---|
| 1648 | |
|---|
| 1649 | def PrintMomentsAndSig(General,Atoms,atomsSig): |
|---|
| 1650 | print >>pFile,'\n Magnetic Moments:' #add magnitude & angle, etc.? TBD |
|---|
| 1651 | line = ' name Mx My Mz' |
|---|
| 1652 | cx,ct,cs,cia = General['AtomPtrs'] |
|---|
| 1653 | cmx = cx+4 |
|---|
| 1654 | AtInfo = dict(zip(General['AtomTypes'],General['Lande g'])) |
|---|
| 1655 | print >>pFile,line |
|---|
| 1656 | print >>pFile,135*'-' |
|---|
| 1657 | fmt = {0:'%7s',ct:'%7s',cmx:'%10.5f',cmx+1:'%10.5f',cmx+2:'%10.5f'} |
|---|
| 1658 | noFXsig = {cmx:[10*' ','%10s'],cmx+1:[10*' ','%10s'],cmx+2:[10*' ','%10s']} |
|---|
| 1659 | for i,at in enumerate(Atoms): |
|---|
| 1660 | if AtInfo[at[ct]]: |
|---|
| 1661 | name = fmt[0]%(at[ct-1])+fmt[1]%(at[ct])+':' |
|---|
| 1662 | valstr = ' values:' |
|---|
| 1663 | sigstr = ' sig :' |
|---|
| 1664 | for ind in range(cmx,cmx+3): |
|---|
| 1665 | sigind = str(i)+':'+str(ind) |
|---|
| 1666 | valstr += fmt[ind]%(at[ind]) |
|---|
| 1667 | if sigind in atomsSig: |
|---|
| 1668 | sigstr += fmt[ind]%(atomsSig[sigind]) |
|---|
| 1669 | else: |
|---|
| 1670 | sigstr += noFXsig[ind][1]%(noFXsig[ind][0]) |
|---|
| 1671 | print >>pFile,name |
|---|
| 1672 | print >>pFile,valstr |
|---|
| 1673 | print >>pFile,sigstr |
|---|
| 1674 | |
|---|
| 1675 | def PrintWavesAndSig(General,Atoms,wavesSig): |
|---|
| 1676 | cx,ct,cs,cia = General['AtomPtrs'] |
|---|
| 1677 | print >>pFile,'\n Modulation waves' |
|---|
| 1678 | names = {'Sfrac':['Fsin','Fcos','Fzero','Fwid'],'Spos':['Xsin','Ysin','Zsin','Xcos','Ycos','Zcos','Tmin','Tmax','Xmax','Ymax','Zmax'], |
|---|
| 1679 | 'Sadp':['U11sin','U22sin','U33sin','U12sin','U13sin','U23sin','U11cos','U22cos', |
|---|
| 1680 | 'U33cos','U12cos','U13cos','U23cos'],'Smag':['MXsin','MYsin','MZsin','MXcos','MYcos','MZcos']} |
|---|
| 1681 | print >>pFile,135*'-' |
|---|
| 1682 | for i,at in enumerate(Atoms): |
|---|
| 1683 | AtomSS = at[-1]['SS1'] |
|---|
| 1684 | waveType = AtomSS['waveType'] |
|---|
| 1685 | for Stype in ['Sfrac','Spos','Sadp','Smag']: |
|---|
| 1686 | Waves = AtomSS[Stype] |
|---|
| 1687 | if len(Waves): |
|---|
| 1688 | print >>pFile,' atom: %s, site sym: %s, type: %s wave type: %s:' \ |
|---|
| 1689 | %(at[ct-1],at[cs],Stype,waveType) |
|---|
| 1690 | for iw,wave in enumerate(Waves): |
|---|
| 1691 | stiw = ':'+str(i)+':'+str(iw) |
|---|
| 1692 | namstr = ' names :' |
|---|
| 1693 | valstr = ' values:' |
|---|
| 1694 | sigstr = ' esds :' |
|---|
| 1695 | if Stype == 'Spos': |
|---|
| 1696 | nt = 6 |
|---|
| 1697 | ot = 0 |
|---|
| 1698 | if waveType in ['ZigZag','Block',] and not iw: |
|---|
| 1699 | nt = 5 |
|---|
| 1700 | ot = 6 |
|---|
| 1701 | for j in range(nt): |
|---|
| 1702 | name = names['Spos'][j+ot] |
|---|
| 1703 | namstr += '%12s'%(name) |
|---|
| 1704 | valstr += '%12.4f'%(wave[0][j]) |
|---|
| 1705 | if name+stiw in wavesSig: |
|---|
| 1706 | sigstr += '%12.4f'%(wavesSig[name+stiw]) |
|---|
| 1707 | else: |
|---|
| 1708 | sigstr += 12*' ' |
|---|
| 1709 | elif Stype == 'Sfrac': |
|---|
| 1710 | ot = 0 |
|---|
| 1711 | if 'Crenel' in waveType and not iw: |
|---|
| 1712 | ot = 2 |
|---|
| 1713 | for j in range(2): |
|---|
| 1714 | name = names['Sfrac'][j+ot] |
|---|
| 1715 | namstr += '%12s'%(names['Sfrac'][j+ot]) |
|---|
| 1716 | valstr += '%12.4f'%(wave[0][j]) |
|---|
| 1717 | if name+stiw in wavesSig: |
|---|
| 1718 | sigstr += '%12.4f'%(wavesSig[name+stiw]) |
|---|
| 1719 | else: |
|---|
| 1720 | sigstr += 12*' ' |
|---|
| 1721 | elif Stype == 'Sadp': |
|---|
| 1722 | for j in range(12): |
|---|
| 1723 | name = names['Sadp'][j] |
|---|
| 1724 | namstr += '%10s'%(names['Sadp'][j]) |
|---|
| 1725 | valstr += '%10.6f'%(wave[0][j]) |
|---|
| 1726 | if name+stiw in wavesSig: |
|---|
| 1727 | sigstr += '%10.6f'%(wavesSig[name+stiw]) |
|---|
| 1728 | else: |
|---|
| 1729 | sigstr += 10*' ' |
|---|
| 1730 | elif Stype == 'Smag': |
|---|
| 1731 | for j in range(6): |
|---|
| 1732 | name = names['Smag'][j] |
|---|
| 1733 | namstr += '%12s'%(names['Smag'][j]) |
|---|
| 1734 | valstr += '%12.4f'%(wave[0][j]) |
|---|
| 1735 | if name+stiw in wavesSig: |
|---|
| 1736 | sigstr += '%12.4f'%(wavesSig[name+stiw]) |
|---|
| 1737 | else: |
|---|
| 1738 | sigstr += 12*' ' |
|---|
| 1739 | |
|---|
| 1740 | print >>pFile,namstr |
|---|
| 1741 | print >>pFile,valstr |
|---|
| 1742 | print >>pFile,sigstr |
|---|
| 1743 | |
|---|
| 1744 | |
|---|
| 1745 | def PrintRBObjPOAndSig(rbfx,rbsx): |
|---|
| 1746 | namstr = ' names :' |
|---|
| 1747 | valstr = ' values:' |
|---|
| 1748 | sigstr = ' esds :' |
|---|
| 1749 | for i,px in enumerate(['Px:','Py:','Pz:']): |
|---|
| 1750 | name = pfx+rbfx+px+rbsx |
|---|
| 1751 | namstr += '%12s'%('Pos '+px[1]) |
|---|
| 1752 | valstr += '%12.5f'%(parmDict[name]) |
|---|
| 1753 | if name in sigDict: |
|---|
| 1754 | sigstr += '%12.5f'%(sigDict[name]) |
|---|
| 1755 | else: |
|---|
| 1756 | sigstr += 12*' ' |
|---|
| 1757 | for i,po in enumerate(['Oa:','Oi:','Oj:','Ok:']): |
|---|
| 1758 | name = pfx+rbfx+po+rbsx |
|---|
| 1759 | namstr += '%12s'%('Ori '+po[1]) |
|---|
| 1760 | valstr += '%12.5f'%(parmDict[name]) |
|---|
| 1761 | if name in sigDict: |
|---|
| 1762 | sigstr += '%12.5f'%(sigDict[name]) |
|---|
| 1763 | else: |
|---|
| 1764 | sigstr += 12*' ' |
|---|
| 1765 | print >>pFile,namstr |
|---|
| 1766 | print >>pFile,valstr |
|---|
| 1767 | print >>pFile,sigstr |
|---|
| 1768 | |
|---|
| 1769 | def PrintRBObjTLSAndSig(rbfx,rbsx,TLS): |
|---|
| 1770 | namstr = ' names :' |
|---|
| 1771 | valstr = ' values:' |
|---|
| 1772 | sigstr = ' esds :' |
|---|
| 1773 | if 'N' not in TLS: |
|---|
| 1774 | print >>pFile,' Thermal motion:' |
|---|
| 1775 | if 'T' in TLS: |
|---|
| 1776 | for i,pt in enumerate(['T11:','T22:','T33:','T12:','T13:','T23:']): |
|---|
| 1777 | name = pfx+rbfx+pt+rbsx |
|---|
| 1778 | namstr += '%12s'%(pt[:3]) |
|---|
| 1779 | valstr += '%12.5f'%(parmDict[name]) |
|---|
| 1780 | if name in sigDict: |
|---|
| 1781 | sigstr += '%12.5f'%(sigDict[name]) |
|---|
| 1782 | else: |
|---|
| 1783 | sigstr += 12*' ' |
|---|
| 1784 | print >>pFile,namstr |
|---|
| 1785 | print >>pFile,valstr |
|---|
| 1786 | print >>pFile,sigstr |
|---|
| 1787 | if 'L' in TLS: |
|---|
| 1788 | namstr = ' names :' |
|---|
| 1789 | valstr = ' values:' |
|---|
| 1790 | sigstr = ' esds :' |
|---|
| 1791 | for i,pt in enumerate(['L11:','L22:','L33:','L12:','L13:','L23:']): |
|---|
| 1792 | name = pfx+rbfx+pt+rbsx |
|---|
| 1793 | namstr += '%12s'%(pt[:3]) |
|---|
| 1794 | valstr += '%12.3f'%(parmDict[name]) |
|---|
| 1795 | if name in sigDict: |
|---|
| 1796 | sigstr += '%12.3f'%(sigDict[name]) |
|---|
| 1797 | else: |
|---|
| 1798 | sigstr += 12*' ' |
|---|
| 1799 | print >>pFile,namstr |
|---|
| 1800 | print >>pFile,valstr |
|---|
| 1801 | print >>pFile,sigstr |
|---|
| 1802 | if 'S' in TLS: |
|---|
| 1803 | namstr = ' names :' |
|---|
| 1804 | valstr = ' values:' |
|---|
| 1805 | sigstr = ' esds :' |
|---|
| 1806 | for i,pt in enumerate(['S12:','S13:','S21:','S23:','S31:','S32:','SAA:','SBB:']): |
|---|
| 1807 | name = pfx+rbfx+pt+rbsx |
|---|
| 1808 | namstr += '%12s'%(pt[:3]) |
|---|
| 1809 | valstr += '%12.4f'%(parmDict[name]) |
|---|
| 1810 | if name in sigDict: |
|---|
| 1811 | sigstr += '%12.4f'%(sigDict[name]) |
|---|
| 1812 | else: |
|---|
| 1813 | sigstr += 12*' ' |
|---|
| 1814 | print >>pFile,namstr |
|---|
| 1815 | print >>pFile,valstr |
|---|
| 1816 | print >>pFile,sigstr |
|---|
| 1817 | if 'U' in TLS: |
|---|
| 1818 | name = pfx+rbfx+'U:'+rbsx |
|---|
| 1819 | namstr = ' names :'+'%12s'%('Uiso') |
|---|
| 1820 | valstr = ' values:'+'%12.5f'%(parmDict[name]) |
|---|
| 1821 | if name in sigDict: |
|---|
| 1822 | sigstr = ' esds :'+'%12.5f'%(sigDict[name]) |
|---|
| 1823 | else: |
|---|
| 1824 | sigstr = ' esds :'+12*' ' |
|---|
| 1825 | print >>pFile,namstr |
|---|
| 1826 | print >>pFile,valstr |
|---|
| 1827 | print >>pFile,sigstr |
|---|
| 1828 | |
|---|
| 1829 | def PrintRBObjTorAndSig(rbsx): |
|---|
| 1830 | namstr = ' names :' |
|---|
| 1831 | valstr = ' values:' |
|---|
| 1832 | sigstr = ' esds :' |
|---|
| 1833 | nTors = len(RBObj['Torsions']) |
|---|
| 1834 | if nTors: |
|---|
| 1835 | print >>pFile,' Torsions:' |
|---|
| 1836 | for it in range(nTors): |
|---|
| 1837 | name = pfx+'RBRTr;'+str(it)+':'+rbsx |
|---|
| 1838 | namstr += '%12s'%('Tor'+str(it)) |
|---|
| 1839 | valstr += '%12.4f'%(parmDict[name]) |
|---|
| 1840 | if name in sigDict: |
|---|
| 1841 | sigstr += '%12.4f'%(sigDict[name]) |
|---|
| 1842 | print >>pFile,namstr |
|---|
| 1843 | print >>pFile,valstr |
|---|
| 1844 | print >>pFile,sigstr |
|---|
| 1845 | |
|---|
| 1846 | def PrintSHtextureAndSig(textureData,SHtextureSig): |
|---|
| 1847 | print >>pFile,'\n Spherical harmonics texture: Order:' + str(textureData['Order']) |
|---|
| 1848 | names = ['omega','chi','phi'] |
|---|
| 1849 | namstr = ' names :' |
|---|
| 1850 | ptstr = ' values:' |
|---|
| 1851 | sigstr = ' esds :' |
|---|
| 1852 | for name in names: |
|---|
| 1853 | namstr += '%12s'%(name) |
|---|
| 1854 | ptstr += '%12.3f'%(textureData['Sample '+name][1]) |
|---|
| 1855 | if 'Sample '+name in SHtextureSig: |
|---|
| 1856 | sigstr += '%12.3f'%(SHtextureSig['Sample '+name]) |
|---|
| 1857 | else: |
|---|
| 1858 | sigstr += 12*' ' |
|---|
| 1859 | print >>pFile,namstr |
|---|
| 1860 | print >>pFile,ptstr |
|---|
| 1861 | print >>pFile,sigstr |
|---|
| 1862 | print >>pFile,'\n Texture coefficients:' |
|---|
| 1863 | SHcoeff = textureData['SH Coeff'][1] |
|---|
| 1864 | SHkeys = SHcoeff.keys() |
|---|
| 1865 | nCoeff = len(SHcoeff) |
|---|
| 1866 | nBlock = nCoeff/10+1 |
|---|
| 1867 | iBeg = 0 |
|---|
| 1868 | iFin = min(iBeg+10,nCoeff) |
|---|
| 1869 | for block in range(nBlock): |
|---|
| 1870 | namstr = ' names :' |
|---|
| 1871 | ptstr = ' values:' |
|---|
| 1872 | sigstr = ' esds :' |
|---|
| 1873 | for name in SHkeys[iBeg:iFin]: |
|---|
| 1874 | namstr += '%12s'%(name) |
|---|
| 1875 | ptstr += '%12.3f'%(SHcoeff[name]) |
|---|
| 1876 | if name in SHtextureSig: |
|---|
| 1877 | sigstr += '%12.3f'%(SHtextureSig[name]) |
|---|
| 1878 | else: |
|---|
| 1879 | sigstr += 12*' ' |
|---|
| 1880 | print >>pFile,namstr |
|---|
| 1881 | print >>pFile,ptstr |
|---|
| 1882 | print >>pFile,sigstr |
|---|
| 1883 | iBeg += 10 |
|---|
| 1884 | iFin = min(iBeg+10,nCoeff) |
|---|
| 1885 | |
|---|
| 1886 | print >>pFile,'\n Phases:' |
|---|
| 1887 | for phase in Phases: |
|---|
| 1888 | print >>pFile,' Result for phase: ',phase |
|---|
| 1889 | print >>pFile,135*'=' |
|---|
| 1890 | Phase = Phases[phase] |
|---|
| 1891 | General = Phase['General'] |
|---|
| 1892 | SGData = General['SGData'] |
|---|
| 1893 | Atoms = Phase['Atoms'] |
|---|
| 1894 | if Atoms and not General.get('doPawley'): |
|---|
| 1895 | cx,ct,cs,cia = General['AtomPtrs'] |
|---|
| 1896 | AtLookup = G2mth.FillAtomLookUp(Atoms,cia+8) |
|---|
| 1897 | cell = General['Cell'] |
|---|
| 1898 | pId = Phase['pId'] |
|---|
| 1899 | pfx = str(pId)+'::' |
|---|
| 1900 | if cell[0]: |
|---|
| 1901 | A,sigA = cellFill(pfx,SGData,parmDict,sigDict) |
|---|
| 1902 | cellSig = getCellEsd(pfx,SGData,A,covData) #includes sigVol |
|---|
| 1903 | print >>pFile,' Reciprocal metric tensor: ' |
|---|
| 1904 | ptfmt = "%15.9f" |
|---|
| 1905 | names = ['A11','A22','A33','A12','A13','A23'] |
|---|
| 1906 | namstr = ' names :' |
|---|
| 1907 | ptstr = ' values:' |
|---|
| 1908 | sigstr = ' esds :' |
|---|
| 1909 | for name,a,siga in zip(names,A,sigA): |
|---|
| 1910 | namstr += '%15s'%(name) |
|---|
| 1911 | ptstr += ptfmt%(a) |
|---|
| 1912 | if siga: |
|---|
| 1913 | sigstr += ptfmt%(siga) |
|---|
| 1914 | else: |
|---|
| 1915 | sigstr += 15*' ' |
|---|
| 1916 | print >>pFile,namstr |
|---|
| 1917 | print >>pFile,ptstr |
|---|
| 1918 | print >>pFile,sigstr |
|---|
| 1919 | cell[1:7] = G2lat.A2cell(A) |
|---|
| 1920 | cell[7] = G2lat.calc_V(A) |
|---|
| 1921 | print >>pFile,' New unit cell:' |
|---|
| 1922 | ptfmt = ["%12.6f","%12.6f","%12.6f","%12.4f","%12.4f","%12.4f","%12.3f"] |
|---|
| 1923 | names = ['a','b','c','alpha','beta','gamma','Volume'] |
|---|
| 1924 | namstr = ' names :' |
|---|
| 1925 | ptstr = ' values:' |
|---|
| 1926 | sigstr = ' esds :' |
|---|
| 1927 | for name,fmt,a,siga in zip(names,ptfmt,cell[1:8],cellSig): |
|---|
| 1928 | namstr += '%12s'%(name) |
|---|
| 1929 | ptstr += fmt%(a) |
|---|
| 1930 | if siga: |
|---|
| 1931 | sigstr += fmt%(siga) |
|---|
| 1932 | else: |
|---|
| 1933 | sigstr += 12*' ' |
|---|
| 1934 | print >>pFile,namstr |
|---|
| 1935 | print >>pFile,ptstr |
|---|
| 1936 | print >>pFile,sigstr |
|---|
| 1937 | ik = 6 #for Pawley stuff below |
|---|
| 1938 | if General.get('Modulated',False): |
|---|
| 1939 | ik = 7 |
|---|
| 1940 | Vec,vRef,maxH = General['SuperVec'] |
|---|
| 1941 | if vRef: |
|---|
| 1942 | print >>pFile,' New modulation vector:' |
|---|
| 1943 | namstr = ' names :' |
|---|
| 1944 | ptstr = ' values:' |
|---|
| 1945 | sigstr = ' esds :' |
|---|
| 1946 | for var in ['mV0','mV1','mV2']: |
|---|
| 1947 | namstr += '%12s'%(pfx+var) |
|---|
| 1948 | ptstr += '%12.6f'%(parmDict[pfx+var]) |
|---|
| 1949 | if pfx+var in sigDict: |
|---|
| 1950 | sigstr += '%12.6f'%(sigDict[pfx+var]) |
|---|
| 1951 | else: |
|---|
| 1952 | sigstr += 12*' ' |
|---|
| 1953 | print >>pFile,namstr |
|---|
| 1954 | print >>pFile,ptstr |
|---|
| 1955 | print >>pFile,sigstr |
|---|
| 1956 | |
|---|
| 1957 | General['Mass'] = 0. |
|---|
| 1958 | if Phase['General'].get('doPawley'): |
|---|
| 1959 | pawleyRef = Phase['Pawley ref'] |
|---|
| 1960 | for i,refl in enumerate(pawleyRef): |
|---|
| 1961 | key = pfx+'PWLref:'+str(i) |
|---|
| 1962 | refl[ik] = parmDict[key] |
|---|
| 1963 | if key in sigDict: |
|---|
| 1964 | refl[ik+1] = sigDict[key] |
|---|
| 1965 | else: |
|---|
| 1966 | refl[ik+1] = 0 |
|---|
| 1967 | else: |
|---|
| 1968 | VRBIds = RBIds['Vector'] |
|---|
| 1969 | RRBIds = RBIds['Residue'] |
|---|
| 1970 | RBModels = Phase['RBModels'] |
|---|
| 1971 | for irb,RBObj in enumerate(RBModels.get('Vector',[])): |
|---|
| 1972 | jrb = VRBIds.index(RBObj['RBId']) |
|---|
| 1973 | rbsx = str(irb)+':'+str(jrb) |
|---|
| 1974 | print >>pFile,' Vector rigid body parameters:' |
|---|
| 1975 | PrintRBObjPOAndSig('RBV',rbsx) |
|---|
| 1976 | PrintRBObjTLSAndSig('RBV',rbsx,RBObj['ThermalMotion'][0]) |
|---|
| 1977 | for irb,RBObj in enumerate(RBModels.get('Residue',[])): |
|---|
| 1978 | jrb = RRBIds.index(RBObj['RBId']) |
|---|
| 1979 | rbsx = str(irb)+':'+str(jrb) |
|---|
| 1980 | print >>pFile,' Residue rigid body parameters:' |
|---|
| 1981 | PrintRBObjPOAndSig('RBR',rbsx) |
|---|
| 1982 | PrintRBObjTLSAndSig('RBR',rbsx,RBObj['ThermalMotion'][0]) |
|---|
| 1983 | PrintRBObjTorAndSig(rbsx) |
|---|
| 1984 | atomsSig = {} |
|---|
| 1985 | wavesSig = {} |
|---|
| 1986 | cx,ct,cs,cia = General['AtomPtrs'] |
|---|
| 1987 | for i,at in enumerate(Atoms): |
|---|
| 1988 | names = {cx:pfx+'Ax:'+str(i),cx+1:pfx+'Ay:'+str(i),cx+2:pfx+'Az:'+str(i),cx+3:pfx+'Afrac:'+str(i), |
|---|
| 1989 | cia+1:pfx+'AUiso:'+str(i),cia+2:pfx+'AU11:'+str(i),cia+3:pfx+'AU22:'+str(i),cia+4:pfx+'AU33:'+str(i), |
|---|
| 1990 | cia+5:pfx+'AU12:'+str(i),cia+6:pfx+'AU13:'+str(i),cia+7:pfx+'AU23:'+str(i), |
|---|
| 1991 | cx+4:pfx+'AMx:'+str(i),cx+5:pfx+'AMy:'+str(i),cx+6:pfx+'AMz:'+str(i)} |
|---|
| 1992 | for ind in range(cx,cx+4): |
|---|
| 1993 | at[ind] = parmDict[names[ind]] |
|---|
| 1994 | if ind in range(cx,cx+3): |
|---|
| 1995 | name = names[ind].replace('A','dA') |
|---|
| 1996 | else: |
|---|
| 1997 | name = names[ind] |
|---|
| 1998 | if name in sigDict: |
|---|
| 1999 | atomsSig[str(i)+':'+str(ind)] = sigDict[name] |
|---|
| 2000 | if at[cia] == 'I': |
|---|
| 2001 | at[cia+1] = parmDict[names[cia+1]] |
|---|
| 2002 | if names[cia+1] in sigDict: |
|---|
| 2003 | atomsSig['%d:%d'%(i,cia+1)] = sigDict[names[cia+1]] |
|---|
| 2004 | else: |
|---|
| 2005 | for ind in range(cia+2,cia+8): |
|---|
| 2006 | at[ind] = parmDict[names[ind]] |
|---|
| 2007 | if names[ind] in sigDict: |
|---|
| 2008 | atomsSig[str(i)+':'+str(ind)] = sigDict[names[ind]] |
|---|
| 2009 | if General['Type'] == 'magnetic': |
|---|
| 2010 | for ind in range(cx+4,cx+7): |
|---|
| 2011 | at[ind] = parmDict[names[ind]] |
|---|
| 2012 | if names[ind] in sigDict: |
|---|
| 2013 | atomsSig[str(i)+':'+str(ind)] = sigDict[names[ind]] |
|---|
| 2014 | ind = General['AtomTypes'].index(at[ct]) |
|---|
| 2015 | General['Mass'] += General['AtomMass'][ind]*at[cx+3]*at[cx+5] |
|---|
| 2016 | if General.get('Modulated',False): |
|---|
| 2017 | AtomSS = at[-1]['SS1'] |
|---|
| 2018 | waveType = AtomSS['waveType'] |
|---|
| 2019 | for Stype in ['Sfrac','Spos','Sadp','Smag']: |
|---|
| 2020 | Waves = AtomSS[Stype] |
|---|
| 2021 | for iw,wave in enumerate(Waves): |
|---|
| 2022 | stiw = str(i)+':'+str(iw) |
|---|
| 2023 | if Stype == 'Spos': |
|---|
| 2024 | if waveType in ['ZigZag','Block',] and not iw: |
|---|
| 2025 | names = ['Tmin:'+stiw,'Tmax:'+stiw,'Xmax:'+stiw,'Ymax:'+stiw,'Zmax:'+stiw] |
|---|
| 2026 | else: |
|---|
| 2027 | names = ['Xsin:'+stiw,'Ysin:'+stiw,'Zsin:'+stiw, |
|---|
| 2028 | 'Xcos:'+stiw,'Ycos:'+stiw,'Zcos:'+stiw] |
|---|
| 2029 | elif Stype == 'Sadp': |
|---|
| 2030 | names = ['U11sin:'+stiw,'U22sin:'+stiw,'U33sin:'+stiw, |
|---|
| 2031 | 'U12sin:'+stiw,'U13sin:'+stiw,'U23sin:'+stiw, |
|---|
| 2032 | 'U11cos:'+stiw,'U22cos:'+stiw,'U33cos:'+stiw, |
|---|
| 2033 | 'U12cos:'+stiw,'U13cos:'+stiw,'U23cos:'+stiw] |
|---|
| 2034 | elif Stype == 'Sfrac': |
|---|
| 2035 | if 'Crenel' in waveType and not iw: |
|---|
| 2036 | names = ['Fzero:'+stiw,'Fwid:'+stiw] |
|---|
| 2037 | else: |
|---|
| 2038 | names = ['Fsin:'+stiw,'Fcos:'+stiw] |
|---|
| 2039 | elif Stype == 'Smag': |
|---|
| 2040 | names = ['MXsin:'+stiw,'MYsin:'+stiw,'MZsin:'+stiw, |
|---|
| 2041 | 'MXcos:'+stiw,'MYcos:'+stiw,'MZcos:'+stiw] |
|---|
| 2042 | for iname,name in enumerate(names): |
|---|
| 2043 | AtomSS[Stype][iw][0][iname] = parmDict[pfx+name] |
|---|
| 2044 | if pfx+name in sigDict: |
|---|
| 2045 | wavesSig[name] = sigDict[pfx+name] |
|---|
| 2046 | |
|---|
| 2047 | PrintAtomsAndSig(General,Atoms,atomsSig) |
|---|
| 2048 | if General['Type'] == 'magnetic': |
|---|
| 2049 | PrintMomentsAndSig(General,Atoms,atomsSig) |
|---|
| 2050 | if General.get('Modulated',False): |
|---|
| 2051 | PrintWavesAndSig(General,Atoms,wavesSig) |
|---|
| 2052 | |
|---|
| 2053 | |
|---|
| 2054 | textureData = General['SH Texture'] |
|---|
| 2055 | if textureData['Order']: |
|---|
| 2056 | SHtextureSig = {} |
|---|
| 2057 | for name in ['omega','chi','phi']: |
|---|
| 2058 | aname = pfx+'SH '+name |
|---|
| 2059 | textureData['Sample '+name][1] = parmDict[aname] |
|---|
| 2060 | if aname in sigDict: |
|---|
| 2061 | SHtextureSig['Sample '+name] = sigDict[aname] |
|---|
| 2062 | for name in textureData['SH Coeff'][1]: |
|---|
| 2063 | aname = pfx+name |
|---|
| 2064 | textureData['SH Coeff'][1][name] = parmDict[aname] |
|---|
| 2065 | if aname in sigDict: |
|---|
| 2066 | SHtextureSig[name] = sigDict[aname] |
|---|
| 2067 | PrintSHtextureAndSig(textureData,SHtextureSig) |
|---|
| 2068 | if phase in RestraintDict and not Phase['General'].get('doPawley'): |
|---|
| 2069 | PrintRestraints(cell[1:7],SGData,General['AtomPtrs'],Atoms,AtLookup, |
|---|
| 2070 | textureData,RestraintDict[phase],pFile) |
|---|
| 2071 | |
|---|
| 2072 | ################################################################################ |
|---|
| 2073 | ##### Histogram & Phase data |
|---|
| 2074 | ################################################################################ |
|---|
| 2075 | |
|---|
| 2076 | def GetHistogramPhaseData(Phases,Histograms,Print=True,pFile=None,resetRefList=True): |
|---|
| 2077 | '''Loads the HAP histogram/phase information into dicts |
|---|
| 2078 | |
|---|
| 2079 | :param dict Phases: phase information |
|---|
| 2080 | :param dict Histograms: Histogram information |
|---|
| 2081 | :param bool Print: prints information as it is read |
|---|
| 2082 | :param file pFile: file object to print to (the default, None causes printing to the console) |
|---|
| 2083 | :param bool resetRefList: Should the contents of the Reflection List be initialized |
|---|
| 2084 | on loading. The default, True, initializes the Reflection List as it is loaded. |
|---|
| 2085 | |
|---|
| 2086 | :returns: (hapVary,hapDict,controlDict) |
|---|
| 2087 | * hapVary: list of refined variables |
|---|
| 2088 | * hapDict: dict with refined variables and their values |
|---|
| 2089 | * controlDict: dict with fixed parameters |
|---|
| 2090 | ''' |
|---|
| 2091 | |
|---|
| 2092 | def PrintSize(hapData): |
|---|
| 2093 | if hapData[0] in ['isotropic','uniaxial']: |
|---|
| 2094 | line = '\n Size model : %9s'%(hapData[0]) |
|---|
| 2095 | line += ' equatorial:'+'%12.5f'%(hapData[1][0])+' Refine? '+str(hapData[2][0]) |
|---|
| 2096 | if hapData[0] == 'uniaxial': |
|---|
| 2097 | line += ' axial:'+'%12.5f'%(hapData[1][1])+' Refine? '+str(hapData[2][1]) |
|---|
| 2098 | line += '\n\t LG mixing coeff.: %12.4f'%(hapData[1][2])+' Refine? '+str(hapData[2][2]) |
|---|
| 2099 | print >>pFile,line |
|---|
| 2100 | else: |
|---|
| 2101 | print >>pFile,'\n Size model : %s'%(hapData[0])+ \ |
|---|
| 2102 | '\n\t LG mixing coeff.:%12.4f'%(hapData[1][2])+' Refine? '+str(hapData[2][2]) |
|---|
| 2103 | Snames = ['S11','S22','S33','S12','S13','S23'] |
|---|
| 2104 | ptlbls = ' names :' |
|---|
| 2105 | ptstr = ' values:' |
|---|
| 2106 | varstr = ' refine:' |
|---|
| 2107 | for i,name in enumerate(Snames): |
|---|
| 2108 | ptlbls += '%12s' % (name) |
|---|
| 2109 | ptstr += '%12.6f' % (hapData[4][i]) |
|---|
| 2110 | varstr += '%12s' % (str(hapData[5][i])) |
|---|
| 2111 | print >>pFile,ptlbls |
|---|
| 2112 | print >>pFile,ptstr |
|---|
| 2113 | print >>pFile,varstr |
|---|
| 2114 | |
|---|
| 2115 | def PrintMuStrain(hapData,SGData): |
|---|
| 2116 | if hapData[0] in ['isotropic','uniaxial']: |
|---|
| 2117 | line = '\n Mustrain model: %9s'%(hapData[0]) |
|---|
| 2118 | line += ' equatorial:'+'%12.1f'%(hapData[1][0])+' Refine? '+str(hapData[2][0]) |
|---|
| 2119 | if hapData[0] == 'uniaxial': |
|---|
| 2120 | line += ' axial:'+'%12.1f'%(hapData[1][1])+' Refine? '+str(hapData[2][1]) |
|---|
| 2121 | line +='\n\t LG mixing coeff.:%12.4f'%(hapData[1][2])+' Refine? '+str(hapData[2][2]) |
|---|
| 2122 | print >>pFile,line |
|---|
| 2123 | else: |
|---|
| 2124 | print >>pFile,'\n Mustrain model: %s'%(hapData[0])+ \ |
|---|
| 2125 | '\n\t LG mixing coeff.:%12.4f'%(hapData[1][2])+' Refine? '+str(hapData[2][2]) |
|---|
| 2126 | Snames = G2spc.MustrainNames(SGData) |
|---|
| 2127 | ptlbls = ' names :' |
|---|
| 2128 | ptstr = ' values:' |
|---|
| 2129 | varstr = ' refine:' |
|---|
| 2130 | for i,name in enumerate(Snames): |
|---|
| 2131 | ptlbls += '%12s' % (name) |
|---|
| 2132 | ptstr += '%12.6f' % (hapData[4][i]) |
|---|
| 2133 | varstr += '%12s' % (str(hapData[5][i])) |
|---|
| 2134 | print >>pFile,ptlbls |
|---|
| 2135 | print >>pFile,ptstr |
|---|
| 2136 | print >>pFile,varstr |
|---|
| 2137 | |
|---|
| 2138 | def PrintHStrain(hapData,SGData): |
|---|
| 2139 | print >>pFile,'\n Hydrostatic/elastic strain: ' |
|---|
| 2140 | Hsnames = G2spc.HStrainNames(SGData) |
|---|
| 2141 | ptlbls = ' names :' |
|---|
| 2142 | ptstr = ' values:' |
|---|
| 2143 | varstr = ' refine:' |
|---|
| 2144 | for i,name in enumerate(Hsnames): |
|---|
| 2145 | ptlbls += '%12s' % (name) |
|---|
| 2146 | ptstr += '%12.4g' % (hapData[0][i]) |
|---|
| 2147 | varstr += '%12s' % (str(hapData[1][i])) |
|---|
| 2148 | print >>pFile,ptlbls |
|---|
| 2149 | print >>pFile,ptstr |
|---|
| 2150 | print >>pFile,varstr |
|---|
| 2151 | |
|---|
| 2152 | def PrintSHPO(hapData): |
|---|
| 2153 | print >>pFile,'\n Spherical harmonics preferred orientation: Order:' + \ |
|---|
| 2154 | str(hapData[4])+' Refine? '+str(hapData[2]) |
|---|
| 2155 | ptlbls = ' names :' |
|---|
| 2156 | ptstr = ' values:' |
|---|
| 2157 | for item in hapData[5]: |
|---|
| 2158 | ptlbls += '%12s'%(item) |
|---|
| 2159 | ptstr += '%12.3f'%(hapData[5][item]) |
|---|
| 2160 | print >>pFile,ptlbls |
|---|
| 2161 | print >>pFile,ptstr |
|---|
| 2162 | |
|---|
| 2163 | def PrintBabinet(hapData): |
|---|
| 2164 | print >>pFile,'\n Babinet form factor modification: ' |
|---|
| 2165 | ptlbls = ' names :' |
|---|
| 2166 | ptstr = ' values:' |
|---|
| 2167 | varstr = ' refine:' |
|---|
| 2168 | for name in ['BabA','BabU']: |
|---|
| 2169 | ptlbls += '%12s' % (name) |
|---|
| 2170 | ptstr += '%12.6f' % (hapData[name][0]) |
|---|
| 2171 | varstr += '%12s' % (str(hapData[name][1])) |
|---|
| 2172 | print >>pFile,ptlbls |
|---|
| 2173 | print >>pFile,ptstr |
|---|
| 2174 | print >>pFile,varstr |
|---|
| 2175 | |
|---|
| 2176 | hapDict = {} |
|---|
| 2177 | hapVary = [] |
|---|
| 2178 | controlDict = {} |
|---|
| 2179 | |
|---|
| 2180 | for phase in Phases: |
|---|
| 2181 | HistoPhase = Phases[phase]['Histograms'] |
|---|
| 2182 | SGData = Phases[phase]['General']['SGData'] |
|---|
| 2183 | cell = Phases[phase]['General']['Cell'][1:7] |
|---|
| 2184 | A = G2lat.cell2A(cell) |
|---|
| 2185 | if Phases[phase]['General'].get('Modulated',False): |
|---|
| 2186 | SSGData = Phases[phase]['General']['SSGData'] |
|---|
| 2187 | Vec,x,maxH = Phases[phase]['General']['SuperVec'] |
|---|
| 2188 | pId = Phases[phase]['pId'] |
|---|
| 2189 | histoList = HistoPhase.keys() |
|---|
| 2190 | histoList.sort() |
|---|
| 2191 | for histogram in histoList: |
|---|
| 2192 | try: |
|---|
| 2193 | Histogram = Histograms[histogram] |
|---|
| 2194 | except KeyError: |
|---|
| 2195 | #skip if histogram not included e.g. in a sequential refinement |
|---|
| 2196 | continue |
|---|
| 2197 | hapData = HistoPhase[histogram] |
|---|
| 2198 | hId = Histogram['hId'] |
|---|
| 2199 | if 'PWDR' in histogram: |
|---|
| 2200 | limits = Histogram['Limits'][1] |
|---|
| 2201 | inst = Histogram['Instrument Parameters'][0] |
|---|
| 2202 | if 'C' in inst['Type'][1]: |
|---|
| 2203 | try: |
|---|
| 2204 | wave = inst['Lam'][1] |
|---|
| 2205 | except KeyError: |
|---|
| 2206 | wave = inst['Lam1'][1] |
|---|
| 2207 | dmin = wave/(2.0*sind(limits[1]/2.0)) |
|---|
| 2208 | elif 'T' in inst['Type'][0]: |
|---|
| 2209 | dmin = limits[0]/inst['difC'][1] |
|---|
| 2210 | if Phases[phase]['General']['Type'] == 'magnetic': |
|---|
| 2211 | dmin = max(dmin,Phases[phase]['General']['MagDmin']) |
|---|
| 2212 | pfx = str(pId)+':'+str(hId)+':' |
|---|
| 2213 | for item in ['Scale','Extinction']: |
|---|
| 2214 | hapDict[pfx+item] = hapData[item][0] |
|---|
| 2215 | if hapData[item][1]: |
|---|
| 2216 | hapVary.append(pfx+item) |
|---|
| 2217 | names = G2spc.HStrainNames(SGData) |
|---|
| 2218 | HSvals = [] |
|---|
| 2219 | for i,name in enumerate(names): |
|---|
| 2220 | hapDict[pfx+name] = hapData['HStrain'][0][i] |
|---|
| 2221 | HSvals.append(hapDict[pfx+name]) |
|---|
| 2222 | if hapData['HStrain'][1][i]: |
|---|
| 2223 | hapVary.append(pfx+name) |
|---|
| 2224 | controlDict[pfx+'poType'] = hapData['Pref.Ori.'][0] |
|---|
| 2225 | if hapData['Pref.Ori.'][0] == 'MD': |
|---|
| 2226 | hapDict[pfx+'MD'] = hapData['Pref.Ori.'][1] |
|---|
| 2227 | controlDict[pfx+'MDAxis'] = hapData['Pref.Ori.'][3] |
|---|
| 2228 | if hapData['Pref.Ori.'][2]: |
|---|
| 2229 | hapVary.append(pfx+'MD') |
|---|
| 2230 | else: #'SH' spherical harmonics |
|---|
| 2231 | controlDict[pfx+'SHord'] = hapData['Pref.Ori.'][4] |
|---|
| 2232 | controlDict[pfx+'SHncof'] = len(hapData['Pref.Ori.'][5]) |
|---|
| 2233 | controlDict[pfx+'SHnames'] = G2lat.GenSHCoeff(SGData['SGLaue'],'0',controlDict[pfx+'SHord'],False) |
|---|
| 2234 | controlDict[pfx+'SHhkl'] = [] |
|---|
| 2235 | try: #patch for old Pref.Ori. items |
|---|
| 2236 | controlDict[pfx+'SHtoler'] = 0.1 |
|---|
| 2237 | if hapData['Pref.Ori.'][6][0] != '': |
|---|
| 2238 | controlDict[pfx+'SHhkl'] = [eval(a.replace(' ',',')) for a in hapData['Pref.Ori.'][6]] |
|---|
| 2239 | controlDict[pfx+'SHtoler'] = hapData['Pref.Ori.'][7] |
|---|
| 2240 | except IndexError: |
|---|
| 2241 | pass |
|---|
| 2242 | for item in hapData['Pref.Ori.'][5]: |
|---|
| 2243 | hapDict[pfx+item] = hapData['Pref.Ori.'][5][item] |
|---|
| 2244 | if hapData['Pref.Ori.'][2]: |
|---|
| 2245 | hapVary.append(pfx+item) |
|---|
| 2246 | for item in ['Mustrain','Size']: |
|---|
| 2247 | controlDict[pfx+item+'Type'] = hapData[item][0] |
|---|
| 2248 | hapDict[pfx+item+';mx'] = hapData[item][1][2] |
|---|
| 2249 | if hapData[item][2][2]: |
|---|
| 2250 | hapVary.append(pfx+item+';mx') |
|---|
| 2251 | if hapData[item][0] in ['isotropic','uniaxial']: |
|---|
| 2252 | hapDict[pfx+item+';i'] = hapData[item][1][0] |
|---|
| 2253 | if hapData[item][2][0]: |
|---|
| 2254 | hapVary.append(pfx+item+';i') |
|---|
| 2255 | if hapData[item][0] == 'uniaxial': |
|---|
| 2256 | controlDict[pfx+item+'Axis'] = hapData[item][3] |
|---|
| 2257 | hapDict[pfx+item+';a'] = hapData[item][1][1] |
|---|
| 2258 | if hapData[item][2][1]: |
|---|
| 2259 | hapVary.append(pfx+item+';a') |
|---|
| 2260 | else: #generalized for mustrain or ellipsoidal for size |
|---|
| 2261 | Nterms = len(hapData[item][4]) |
|---|
| 2262 | if item == 'Mustrain': |
|---|
| 2263 | names = G2spc.MustrainNames(SGData) |
|---|
| 2264 | pwrs = [] |
|---|
| 2265 | for name in names: |
|---|
| 2266 | h,k,l = name[1:] |
|---|
| 2267 | pwrs.append([int(h),int(k),int(l)]) |
|---|
| 2268 | controlDict[pfx+'MuPwrs'] = pwrs |
|---|
| 2269 | for i in range(Nterms): |
|---|
| 2270 | sfx = ';'+str(i) |
|---|
| 2271 | hapDict[pfx+item+sfx] = hapData[item][4][i] |
|---|
| 2272 | if hapData[item][5][i]: |
|---|
| 2273 | hapVary.append(pfx+item+sfx) |
|---|
| 2274 | if Phases[phase]['General']['Type'] != 'magnetic': |
|---|
| 2275 | for bab in ['BabA','BabU']: |
|---|
| 2276 | hapDict[pfx+bab] = hapData['Babinet'][bab][0] |
|---|
| 2277 | if hapData['Babinet'][bab][1]: |
|---|
| 2278 | hapVary.append(pfx+bab) |
|---|
| 2279 | |
|---|
| 2280 | if Print: |
|---|
| 2281 | print >>pFile,'\n Phase: ',phase,' in histogram: ',histogram |
|---|
| 2282 | print >>pFile,135*'=' |
|---|
| 2283 | print >>pFile,' Phase fraction : %10.4f'%(hapData['Scale'][0]),' Refine?',hapData['Scale'][1] |
|---|
| 2284 | print >>pFile,' Extinction coeff: %10.4f'%(hapData['Extinction'][0]),' Refine?',hapData['Extinction'][1] |
|---|
| 2285 | if hapData['Pref.Ori.'][0] == 'MD': |
|---|
| 2286 | Ax = hapData['Pref.Ori.'][3] |
|---|
| 2287 | print >>pFile,' March-Dollase PO: %10.4f'%(hapData['Pref.Ori.'][1]),' Refine?',hapData['Pref.Ori.'][2], \ |
|---|
| 2288 | ' Axis: %d %d %d'%(Ax[0],Ax[1],Ax[2]) |
|---|
| 2289 | else: #'SH' for spherical harmonics |
|---|
| 2290 | PrintSHPO(hapData['Pref.Ori.']) |
|---|
| 2291 | print >>pFile,' Penalty hkl list: '+str(controlDict[pfx+'SHhkl'])+' tolerance: %.2f'%(controlDict[pfx+'SHtoler']) |
|---|
| 2292 | PrintSize(hapData['Size']) |
|---|
| 2293 | PrintMuStrain(hapData['Mustrain'],SGData) |
|---|
| 2294 | PrintHStrain(hapData['HStrain'],SGData) |
|---|
| 2295 | if Phases[phase]['General']['Type'] != 'magnetic': |
|---|
| 2296 | if hapData['Babinet']['BabA'][0]: |
|---|
| 2297 | PrintBabinet(hapData['Babinet']) |
|---|
| 2298 | if resetRefList: |
|---|
| 2299 | refList = [] |
|---|
| 2300 | Uniq = [] |
|---|
| 2301 | Phi = [] |
|---|
| 2302 | useExt = 'magnetic' in Phases[phase]['General']['Type'] and 'N' in inst['Type'][0] |
|---|
| 2303 | if Phases[phase]['General'].get('Modulated',False): |
|---|
| 2304 | ifSuper = True |
|---|
| 2305 | HKLd = np.array(G2lat.GenSSHLaue(dmin,SGData,SSGData,Vec,maxH,A)) |
|---|
| 2306 | HKLd = G2mth.sortArray(HKLd,4,reverse=True) |
|---|
| 2307 | for h,k,l,m,d in HKLd: |
|---|
| 2308 | ext,mul,uniq,phi = G2spc.GenHKLf([h,k,l],SGData) |
|---|
| 2309 | mul *= 2 # for powder overlap of Friedel pairs |
|---|
| 2310 | if m or not ext or useExt: |
|---|
| 2311 | if 'C' in inst['Type'][0]: |
|---|
| 2312 | pos = G2lat.Dsp2pos(inst,d) |
|---|
| 2313 | if limits[0] < pos < limits[1]: |
|---|
| 2314 | refList.append([h,k,l,m,mul,d, pos,0.0,0.0,0.0,0.0, 0.0,0.0,1.0,1.0,1.0]) |
|---|
| 2315 | #... sig,gam,fotsq,fctsq, phase,icorr,prfo,abs,ext |
|---|
| 2316 | Uniq.append(uniq) |
|---|
| 2317 | Phi.append(phi) |
|---|
| 2318 | elif 'T' in inst['Type'][0]: |
|---|
| 2319 | pos = G2lat.Dsp2pos(inst,d) |
|---|
| 2320 | if limits[0] < pos < limits[1]: |
|---|
| 2321 | wave = inst['difC'][1]*d/(252.816*inst['fltPath'][0]) |
|---|
| 2322 | refList.append([h,k,l,m,mul,d, pos,0.0,0.0,0.0,0.0, 0.0,0.0,0.0,0.0,wave, 1.0,1.0,1.0]) |
|---|
| 2323 | # ... sig,gam,fotsq,fctsq, phase,icorr,alp,bet,wave, prfo,abs,ext |
|---|
| 2324 | Uniq.append(uniq) |
|---|
| 2325 | Phi.append(phi) |
|---|
| 2326 | else: |
|---|
| 2327 | ifSuper = False |
|---|
| 2328 | HKLd = np.array(G2lat.GenHLaue(dmin,SGData,A)) |
|---|
| 2329 | HKLd = G2mth.sortArray(HKLd,3,reverse=True) |
|---|
| 2330 | for h,k,l,d in HKLd: |
|---|
| 2331 | ext,mul,uniq,phi = G2spc.GenHKLf([h,k,l],SGData) |
|---|
| 2332 | mul *= 2 # for powder overlap of Friedel pairs |
|---|
| 2333 | if ext and not useExt: |
|---|
| 2334 | continue |
|---|
| 2335 | if 'C' in inst['Type'][0]: |
|---|
| 2336 | pos = G2lat.Dsp2pos(inst,d) |
|---|
| 2337 | if limits[0] < pos < limits[1]: |
|---|
| 2338 | refList.append([h,k,l,mul,d, pos,0.0,0.0,0.0,0.0, 0.0,0.0,1.0,1.0,1.0]) |
|---|
| 2339 | #... sig,gam,fotsq,fctsq, phase,icorr,prfo,abs,ext |
|---|
| 2340 | Uniq.append(uniq) |
|---|
| 2341 | Phi.append(phi) |
|---|
| 2342 | elif 'T' in inst['Type'][0]: |
|---|
| 2343 | pos = G2lat.Dsp2pos(inst,d) |
|---|
| 2344 | if limits[0] < pos < limits[1]: |
|---|
| 2345 | wave = inst['difC'][1]*d/(252.816*inst['fltPath'][0]) |
|---|
| 2346 | refList.append([h,k,l,mul,d, pos,0.0,0.0,0.0,0.0, 0.0,0.0,0.0,0.0,wave, 1.0,1.0,1.0]) |
|---|
| 2347 | # ... sig,gam,fotsq,fctsq, phase,icorr,alp,bet,wave, prfo,abs,ext |
|---|
| 2348 | Uniq.append(uniq) |
|---|
| 2349 | Phi.append(phi) |
|---|
| 2350 | Histogram['Reflection Lists'][phase] = {'RefList':np.array(refList),'FF':{},'Type':inst['Type'][0],'Super':ifSuper} |
|---|
| 2351 | elif 'HKLF' in histogram: |
|---|
| 2352 | inst = Histogram['Instrument Parameters'][0] |
|---|
| 2353 | hId = Histogram['hId'] |
|---|
| 2354 | hfx = ':%d:'%(hId) |
|---|
| 2355 | for item in inst: |
|---|
| 2356 | if type(inst) is not list and item != 'Type': continue # skip over non-refined items (such as InstName) |
|---|
| 2357 | hapDict[hfx+item] = inst[item][1] |
|---|
| 2358 | pfx = str(pId)+':'+str(hId)+':' |
|---|
| 2359 | hapDict[pfx+'Scale'] = hapData['Scale'][0] |
|---|
| 2360 | if hapData['Scale'][1]: |
|---|
| 2361 | hapVary.append(pfx+'Scale') |
|---|
| 2362 | |
|---|
| 2363 | extApprox,extType,extParms = hapData['Extinction'] |
|---|
| 2364 | controlDict[pfx+'EType'] = extType |
|---|
| 2365 | controlDict[pfx+'EApprox'] = extApprox |
|---|
| 2366 | if 'C' in inst['Type'][0]: |
|---|
| 2367 | controlDict[pfx+'Tbar'] = extParms['Tbar'] |
|---|
| 2368 | controlDict[pfx+'Cos2TM'] = extParms['Cos2TM'] |
|---|
| 2369 | if 'Primary' in extType: |
|---|
| 2370 | Ekey = ['Ep',] |
|---|
| 2371 | elif 'I & II' in extType: |
|---|
| 2372 | Ekey = ['Eg','Es'] |
|---|
| 2373 | elif 'Secondary Type II' == extType: |
|---|
| 2374 | Ekey = ['Es',] |
|---|
| 2375 | elif 'Secondary Type I' == extType: |
|---|
| 2376 | Ekey = ['Eg',] |
|---|
| 2377 | else: #'None' |
|---|
| 2378 | Ekey = [] |
|---|
| 2379 | for eKey in Ekey: |
|---|
| 2380 | hapDict[pfx+eKey] = extParms[eKey][0] |
|---|
| 2381 | if extParms[eKey][1]: |
|---|
| 2382 | hapVary.append(pfx+eKey) |
|---|
| 2383 | for bab in ['BabA','BabU']: |
|---|
| 2384 | hapDict[pfx+bab] = hapData['Babinet'][bab][0] |
|---|
| 2385 | if hapData['Babinet'][bab][1]: |
|---|
| 2386 | hapVary.append(pfx+bab) |
|---|
| 2387 | Twins = hapData.get('Twins',[[np.array([[1,0,0],[0,1,0],[0,0,1]]),[1.0,False,0]],]) |
|---|
| 2388 | if len(Twins) == 1: |
|---|
| 2389 | hapDict[pfx+'Flack'] = hapData.get('Flack',[0.,False])[0] |
|---|
| 2390 | if hapData.get('Flack',[0,False])[1]: |
|---|
| 2391 | hapVary.append(pfx+'Flack') |
|---|
| 2392 | sumTwFr = 0. |
|---|
| 2393 | controlDict[pfx+'TwinLaw'] = [] |
|---|
| 2394 | controlDict[pfx+'TwinInv'] = [] |
|---|
| 2395 | NTL = 0 |
|---|
| 2396 | for it,twin in enumerate(Twins): |
|---|
| 2397 | if 'bool' in str(type(twin[0])): |
|---|
| 2398 | controlDict[pfx+'TwinInv'].append(twin[0]) |
|---|
| 2399 | controlDict[pfx+'TwinLaw'].append(np.zeros((3,3))) |
|---|
| 2400 | else: |
|---|
| 2401 | NTL += 1 |
|---|
| 2402 | controlDict[pfx+'TwinInv'].append(False) |
|---|
| 2403 | controlDict[pfx+'TwinLaw'].append(twin[0]) |
|---|
| 2404 | if it: |
|---|
| 2405 | hapDict[pfx+'TwinFr:'+str(it)] = twin[1] |
|---|
| 2406 | sumTwFr += twin[1] |
|---|
| 2407 | else: |
|---|
| 2408 | hapDict[pfx+'TwinFr:0'] = twin[1][0] |
|---|
| 2409 | controlDict[pfx+'TwinNMN'] = twin[1][1] |
|---|
| 2410 | if Twins[0][1][1]: |
|---|
| 2411 | hapVary.append(pfx+'TwinFr:'+str(it)) |
|---|
| 2412 | controlDict[pfx+'NTL'] = NTL |
|---|
| 2413 | #need to make constraint on TwinFr |
|---|
| 2414 | controlDict[pfx+'TwinLaw'] = np.array(controlDict[pfx+'TwinLaw']) |
|---|
| 2415 | if len(Twins) > 1: #force sum to unity |
|---|
| 2416 | hapDict[pfx+'TwinFr:0'] = 1.-sumTwFr |
|---|
| 2417 | if Print: |
|---|
| 2418 | print >>pFile,'\n Phase: ',phase,' in histogram: ',histogram |
|---|
| 2419 | print >>pFile,135*'=' |
|---|
| 2420 | print >>pFile,' Scale factor : %10.4f'%(hapData['Scale'][0]),' Refine?',hapData['Scale'][1] |
|---|
| 2421 | if extType != 'None': |
|---|
| 2422 | print >>pFile,' Extinction Type: %15s'%(extType),' approx: %10s'%(extApprox) |
|---|
| 2423 | text = ' Parameters :' |
|---|
| 2424 | for eKey in Ekey: |
|---|
| 2425 | text += ' %4s : %10.3e Refine? '%(eKey,extParms[eKey][0])+str(extParms[eKey][1]) |
|---|
| 2426 | print >>pFile,text |
|---|
| 2427 | if hapData['Babinet']['BabA'][0]: |
|---|
| 2428 | PrintBabinet(hapData['Babinet']) |
|---|
| 2429 | if not SGData['SGInv'] and len(Twins) == 1: |
|---|
| 2430 | print >>pFile,' Flack parameter: %10.3f'%(hapData['Flack'][0]),' Refine?',hapData['Flack'][1] |
|---|
| 2431 | if len(Twins) > 1: |
|---|
| 2432 | for it,twin in enumerate(Twins): |
|---|
| 2433 | if 'bool' in str(type(twin[0])): |
|---|
| 2434 | print >>pFile,' Nonmerohedral twin fr.: %5.3f Inv? %s Refine? '%(hapDict[pfx+'TwinFr:'+str(it)],str(controlDict[pfx+'TwinInv'][it])),Twins[0][1][1] |
|---|
| 2435 | else: |
|---|
| 2436 | print >>pFile,' Twin law: %s'%(str(twin[0]).replace('\n',',')),' Twin fr.: %5.3f Refine? '%(hapDict[pfx+'TwinFr:'+str(it)]),Twins[0][1][1] |
|---|
| 2437 | |
|---|
| 2438 | Histogram['Reflection Lists'] = phase |
|---|
| 2439 | |
|---|
| 2440 | return hapVary,hapDict,controlDict |
|---|
| 2441 | |
|---|
| 2442 | def SetHistogramPhaseData(parmDict,sigDict,Phases,Histograms,FFtables,Print=True,pFile=None): |
|---|
| 2443 | 'needs a doc string' |
|---|
| 2444 | |
|---|
| 2445 | def PrintSizeAndSig(hapData,sizeSig): |
|---|
| 2446 | line = '\n Size model: %9s'%(hapData[0]) |
|---|
| 2447 | refine = False |
|---|
| 2448 | if hapData[0] in ['isotropic','uniaxial']: |
|---|
| 2449 | line += ' equatorial:%12.5f'%(hapData[1][0]) |
|---|
| 2450 | if sizeSig[0][0]: |
|---|
| 2451 | line += ', sig:%8.4f'%(sizeSig[0][0]) |
|---|
| 2452 | refine = True |
|---|
| 2453 | if hapData[0] == 'uniaxial': |
|---|
| 2454 | line += ' axial:%12.4f'%(hapData[1][1]) |
|---|
| 2455 | if sizeSig[0][1]: |
|---|
| 2456 | refine = True |
|---|
| 2457 | line += ', sig:%8.4f'%(sizeSig[0][1]) |
|---|
| 2458 | line += ' LG mix coeff.:%12.4f'%(hapData[1][2]) |
|---|
| 2459 | if sizeSig[0][2]: |
|---|
| 2460 | refine = True |
|---|
| 2461 | line += ', sig:%8.4f'%(sizeSig[0][2]) |
|---|
| 2462 | if refine: |
|---|
| 2463 | print >>pFile,line |
|---|
| 2464 | else: |
|---|
| 2465 | line += ' LG mix coeff.:%12.4f'%(hapData[1][2]) |
|---|
| 2466 | if sizeSig[0][2]: |
|---|
| 2467 | refine = True |
|---|
| 2468 | line += ', sig:%8.4f'%(sizeSig[0][2]) |
|---|
| 2469 | Snames = ['S11','S22','S33','S12','S13','S23'] |
|---|
| 2470 | ptlbls = ' name :' |
|---|
| 2471 | ptstr = ' value :' |
|---|
| 2472 | sigstr = ' sig :' |
|---|
| 2473 | for i,name in enumerate(Snames): |
|---|
| 2474 | ptlbls += '%12s' % (name) |
|---|
| 2475 | ptstr += '%12.6f' % (hapData[4][i]) |
|---|
| 2476 | if sizeSig[1][i]: |
|---|
| 2477 | refine = True |
|---|
| 2478 | sigstr += '%12.6f' % (sizeSig[1][i]) |
|---|
| 2479 | else: |
|---|
| 2480 | sigstr += 12*' ' |
|---|
| 2481 | if refine: |
|---|
| 2482 | print >>pFile,line |
|---|
| 2483 | print >>pFile,ptlbls |
|---|
| 2484 | print >>pFile,ptstr |
|---|
| 2485 | print >>pFile,sigstr |
|---|
| 2486 | |
|---|
| 2487 | def PrintMuStrainAndSig(hapData,mustrainSig,SGData): |
|---|
| 2488 | line = '\n Mustrain model: %9s'%(hapData[0]) |
|---|
| 2489 | refine = False |
|---|
| 2490 | if hapData[0] in ['isotropic','uniaxial']: |
|---|
| 2491 | line += ' equatorial:%12.1f'%(hapData[1][0]) |
|---|
| 2492 | if mustrainSig[0][0]: |
|---|
| 2493 | line += ', sig:%8.1f'%(mustrainSig[0][0]) |
|---|
| 2494 | refine = True |
|---|
| 2495 | if hapData[0] == 'uniaxial': |
|---|
| 2496 | line += ' axial:%12.1f'%(hapData[1][1]) |
|---|
| 2497 | if mustrainSig[0][1]: |
|---|
| 2498 | line += ', sig:%8.1f'%(mustrainSig[0][1]) |
|---|
| 2499 | line += ' LG mix coeff.:%12.4f'%(hapData[1][2]) |
|---|
| 2500 | if mustrainSig[0][2]: |
|---|
| 2501 | refine = True |
|---|
| 2502 | line += ', sig:%8.3f'%(mustrainSig[0][2]) |
|---|
| 2503 | if refine: |
|---|
| 2504 | print >>pFile,line |
|---|
| 2505 | else: |
|---|
| 2506 | line += ' LG mix coeff.:%12.4f'%(hapData[1][2]) |
|---|
| 2507 | if mustrainSig[0][2]: |
|---|
| 2508 | refine = True |
|---|
| 2509 | line += ', sig:%8.3f'%(mustrainSig[0][2]) |
|---|
| 2510 | Snames = G2spc.MustrainNames(SGData) |
|---|
| 2511 | ptlbls = ' name :' |
|---|
| 2512 | ptstr = ' value :' |
|---|
| 2513 | sigstr = ' sig :' |
|---|
| 2514 | for i,name in enumerate(Snames): |
|---|
| 2515 | ptlbls += '%12s' % (name) |
|---|
| 2516 | ptstr += '%12.1f' % (hapData[4][i]) |
|---|
| 2517 | if mustrainSig[1][i]: |
|---|
| 2518 | refine = True |
|---|
| 2519 | sigstr += '%12.1f' % (mustrainSig[1][i]) |
|---|
| 2520 | else: |
|---|
| 2521 | sigstr += 12*' ' |
|---|
| 2522 | if refine: |
|---|
| 2523 | print >>pFile,line |
|---|
| 2524 | print >>pFile,ptlbls |
|---|
| 2525 | print >>pFile,ptstr |
|---|
| 2526 | print >>pFile,sigstr |
|---|
| 2527 | |
|---|
| 2528 | def PrintHStrainAndSig(hapData,strainSig,SGData): |
|---|
| 2529 | Hsnames = G2spc.HStrainNames(SGData) |
|---|
| 2530 | ptlbls = ' name :' |
|---|
| 2531 | ptstr = ' value :' |
|---|
| 2532 | sigstr = ' sig :' |
|---|
| 2533 | refine = False |
|---|
| 2534 | for i,name in enumerate(Hsnames): |
|---|
| 2535 | ptlbls += '%12s' % (name) |
|---|
| 2536 | ptstr += '%12.4g' % (hapData[0][i]) |
|---|
| 2537 | if name in strainSig: |
|---|
| 2538 | refine = True |
|---|
| 2539 | sigstr += '%12.4g' % (strainSig[name]) |
|---|
| 2540 | else: |
|---|
| 2541 | sigstr += 12*' ' |
|---|
| 2542 | if refine: |
|---|
| 2543 | print >>pFile,'\n Hydrostatic/elastic strain: ' |
|---|
| 2544 | print >>pFile,ptlbls |
|---|
| 2545 | print >>pFile,ptstr |
|---|
| 2546 | print >>pFile,sigstr |
|---|
| 2547 | |
|---|
| 2548 | def PrintSHPOAndSig(pfx,hapData,POsig): |
|---|
| 2549 | print >>pFile,'\n Spherical harmonics preferred orientation: Order:'+str(hapData[4]) |
|---|
| 2550 | ptlbls = ' names :' |
|---|
| 2551 | ptstr = ' values:' |
|---|
| 2552 | sigstr = ' sig :' |
|---|
| 2553 | for item in hapData[5]: |
|---|
| 2554 | ptlbls += '%12s'%(item) |
|---|
| 2555 | ptstr += '%12.3f'%(hapData[5][item]) |
|---|
| 2556 | if pfx+item in POsig: |
|---|
| 2557 | sigstr += '%12.3f'%(POsig[pfx+item]) |
|---|
| 2558 | else: |
|---|
| 2559 | sigstr += 12*' ' |
|---|
| 2560 | print >>pFile,ptlbls |
|---|
| 2561 | print >>pFile,ptstr |
|---|
| 2562 | print >>pFile,sigstr |
|---|
| 2563 | |
|---|
| 2564 | def PrintExtAndSig(pfx,hapData,ScalExtSig): |
|---|
| 2565 | print >>pFile,'\n Single crystal extinction: Type: ',hapData[0],' Approx: ',hapData[1] |
|---|
| 2566 | text = '' |
|---|
| 2567 | for item in hapData[2]: |
|---|
| 2568 | if pfx+item in ScalExtSig: |
|---|
| 2569 | text += ' %s: '%(item) |
|---|
| 2570 | text += '%12.2e'%(hapData[2][item][0]) |
|---|
| 2571 | if pfx+item in ScalExtSig: |
|---|
| 2572 | text += ' sig: %12.2e'%(ScalExtSig[pfx+item]) |
|---|
| 2573 | print >>pFile,text |
|---|
| 2574 | |
|---|
| 2575 | def PrintBabinetAndSig(pfx,hapData,BabSig): |
|---|
| 2576 | print >>pFile,'\n Babinet form factor modification: ' |
|---|
| 2577 | ptlbls = ' names :' |
|---|
| 2578 | ptstr = ' values:' |
|---|
| 2579 | sigstr = ' sig :' |
|---|
| 2580 | for item in hapData: |
|---|
| 2581 | ptlbls += '%12s'%(item) |
|---|
| 2582 | ptstr += '%12.3f'%(hapData[item][0]) |
|---|
| 2583 | if pfx+item in BabSig: |
|---|
| 2584 | sigstr += '%12.3f'%(BabSig[pfx+item]) |
|---|
| 2585 | else: |
|---|
| 2586 | sigstr += 12*' ' |
|---|
| 2587 | print >>pFile,ptlbls |
|---|
| 2588 | print >>pFile,ptstr |
|---|
| 2589 | print >>pFile,sigstr |
|---|
| 2590 | |
|---|
| 2591 | def PrintTwinsAndSig(pfx,twinData,TwinSig): |
|---|
| 2592 | print >>pFile,'\n Twin Law fractions : ' |
|---|
| 2593 | ptlbls = ' names :' |
|---|
| 2594 | ptstr = ' values:' |
|---|
| 2595 | sigstr = ' sig :' |
|---|
| 2596 | for it,item in enumerate(twinData): |
|---|
| 2597 | ptlbls += ' twin #%d'%(it) |
|---|
| 2598 | if it: |
|---|
| 2599 | ptstr += '%12.3f'%(item[1]) |
|---|
| 2600 | else: |
|---|
| 2601 | ptstr += '%12.3f'%(item[1][0]) |
|---|
| 2602 | if pfx+'TwinFr:'+str(it) in TwinSig: |
|---|
| 2603 | sigstr += '%12.3f'%(TwinSig[pfx+'TwinFr:'+str(it)]) |
|---|
| 2604 | else: |
|---|
| 2605 | sigstr += 12*' ' |
|---|
| 2606 | print >>pFile,ptlbls |
|---|
| 2607 | print >>pFile,ptstr |
|---|
| 2608 | print >>pFile,sigstr |
|---|
| 2609 | |
|---|
| 2610 | |
|---|
| 2611 | PhFrExtPOSig = {} |
|---|
| 2612 | SizeMuStrSig = {} |
|---|
| 2613 | ScalExtSig = {} |
|---|
| 2614 | BabSig = {} |
|---|
| 2615 | TwinFrSig = {} |
|---|
| 2616 | wtFrSum = {} |
|---|
| 2617 | for phase in Phases: |
|---|
| 2618 | HistoPhase = Phases[phase]['Histograms'] |
|---|
| 2619 | General = Phases[phase]['General'] |
|---|
| 2620 | SGData = General['SGData'] |
|---|
| 2621 | pId = Phases[phase]['pId'] |
|---|
| 2622 | histoList = HistoPhase.keys() |
|---|
| 2623 | histoList.sort() |
|---|
| 2624 | for histogram in histoList: |
|---|
| 2625 | try: |
|---|
| 2626 | Histogram = Histograms[histogram] |
|---|
| 2627 | except KeyError: |
|---|
| 2628 | #skip if histogram not included e.g. in a sequential refinement |
|---|
| 2629 | continue |
|---|
| 2630 | hapData = HistoPhase[histogram] |
|---|
| 2631 | hId = Histogram['hId'] |
|---|
| 2632 | pfx = str(pId)+':'+str(hId)+':' |
|---|
| 2633 | if hId not in wtFrSum: |
|---|
| 2634 | wtFrSum[hId] = 0. |
|---|
| 2635 | if 'PWDR' in histogram: |
|---|
| 2636 | for item in ['Scale','Extinction']: |
|---|
| 2637 | hapData[item][0] = parmDict[pfx+item] |
|---|
| 2638 | if pfx+item in sigDict: |
|---|
| 2639 | PhFrExtPOSig.update({pfx+item:sigDict[pfx+item],}) |
|---|
| 2640 | wtFrSum[hId] += hapData['Scale'][0]*General['Mass'] |
|---|
| 2641 | if hapData['Pref.Ori.'][0] == 'MD': |
|---|
| 2642 | hapData['Pref.Ori.'][1] = parmDict[pfx+'MD'] |
|---|
| 2643 | if pfx+'MD' in sigDict: |
|---|
| 2644 | PhFrExtPOSig.update({pfx+'MD':sigDict[pfx+'MD'],}) |
|---|
| 2645 | else: #'SH' spherical harmonics |
|---|
| 2646 | for item in hapData['Pref.Ori.'][5]: |
|---|
| 2647 | hapData['Pref.Ori.'][5][item] = parmDict[pfx+item] |
|---|
| 2648 | if pfx+item in sigDict: |
|---|
| 2649 | PhFrExtPOSig.update({pfx+item:sigDict[pfx+item],}) |
|---|
| 2650 | SizeMuStrSig.update({pfx+'Mustrain':[[0,0,0],[0 for i in range(len(hapData['Mustrain'][4]))]], |
|---|
| 2651 | pfx+'Size':[[0,0,0],[0 for i in range(len(hapData['Size'][4]))]], |
|---|
| 2652 | pfx+'HStrain':{}}) |
|---|
| 2653 | for item in ['Mustrain','Size']: |
|---|
| 2654 | hapData[item][1][2] = parmDict[pfx+item+';mx'] |
|---|
| 2655 | # hapData[item][1][2] = min(1.,max(0.,hapData[item][1][2])) |
|---|
| 2656 | if pfx+item+';mx' in sigDict: |
|---|
| 2657 | SizeMuStrSig[pfx+item][0][2] = sigDict[pfx+item+';mx'] |
|---|
| 2658 | if hapData[item][0] in ['isotropic','uniaxial']: |
|---|
| 2659 | hapData[item][1][0] = parmDict[pfx+item+';i'] |
|---|
| 2660 | if item == 'Size': |
|---|
| 2661 | hapData[item][1][0] = min(10.,max(0.001,hapData[item][1][0])) |
|---|
| 2662 | if pfx+item+';i' in sigDict: |
|---|
| 2663 | SizeMuStrSig[pfx+item][0][0] = sigDict[pfx+item+';i'] |
|---|
| 2664 | if hapData[item][0] == 'uniaxial': |
|---|
| 2665 | hapData[item][1][1] = parmDict[pfx+item+';a'] |
|---|
| 2666 | if item == 'Size': |
|---|
| 2667 | hapData[item][1][1] = min(10.,max(0.001,hapData[item][1][1])) |
|---|
| 2668 | if pfx+item+';a' in sigDict: |
|---|
| 2669 | SizeMuStrSig[pfx+item][0][1] = sigDict[pfx+item+';a'] |
|---|
| 2670 | else: #generalized for mustrain or ellipsoidal for size |
|---|
| 2671 | Nterms = len(hapData[item][4]) |
|---|
| 2672 | for i in range(Nterms): |
|---|
| 2673 | sfx = ';'+str(i) |
|---|
| 2674 | hapData[item][4][i] = parmDict[pfx+item+sfx] |
|---|
| 2675 | if pfx+item+sfx in sigDict: |
|---|
| 2676 | SizeMuStrSig[pfx+item][1][i] = sigDict[pfx+item+sfx] |
|---|
| 2677 | names = G2spc.HStrainNames(SGData) |
|---|
| 2678 | for i,name in enumerate(names): |
|---|
| 2679 | hapData['HStrain'][0][i] = parmDict[pfx+name] |
|---|
| 2680 | if pfx+name in sigDict: |
|---|
| 2681 | SizeMuStrSig[pfx+'HStrain'][name] = sigDict[pfx+name] |
|---|
| 2682 | if Phases[phase]['General']['Type'] != 'magnetic': |
|---|
| 2683 | for name in ['BabA','BabU']: |
|---|
| 2684 | hapData['Babinet'][name][0] = parmDict[pfx+name] |
|---|
| 2685 | if pfx+name in sigDict: |
|---|
| 2686 | BabSig[pfx+name] = sigDict[pfx+name] |
|---|
| 2687 | |
|---|
| 2688 | elif 'HKLF' in histogram: |
|---|
| 2689 | for item in ['Scale','Flack']: |
|---|
| 2690 | if parmDict.get(pfx+item): |
|---|
| 2691 | hapData[item][0] = parmDict[pfx+item] |
|---|
| 2692 | if pfx+item in sigDict: |
|---|
| 2693 | ScalExtSig[pfx+item] = sigDict[pfx+item] |
|---|
| 2694 | for item in ['Ep','Eg','Es']: |
|---|
| 2695 | if parmDict.get(pfx+item): |
|---|
| 2696 | hapData['Extinction'][2][item][0] = parmDict[pfx+item] |
|---|
| 2697 | if pfx+item in sigDict: |
|---|
| 2698 | ScalExtSig[pfx+item] = sigDict[pfx+item] |
|---|
| 2699 | for item in ['BabA','BabU']: |
|---|
| 2700 | hapData['Babinet'][item][0] = parmDict[pfx+item] |
|---|
| 2701 | if pfx+item in sigDict: |
|---|
| 2702 | BabSig[pfx+item] = sigDict[pfx+item] |
|---|
| 2703 | if 'Twins' in hapData: |
|---|
| 2704 | it = 1 |
|---|
| 2705 | sumTwFr = 0. |
|---|
| 2706 | while True: |
|---|
| 2707 | try: |
|---|
| 2708 | hapData['Twins'][it][1] = parmDict[pfx+'TwinFr:'+str(it)] |
|---|
| 2709 | if pfx+'TwinFr:'+str(it) in sigDict: |
|---|
| 2710 | TwinFrSig[pfx+'TwinFr:'+str(it)] = sigDict[pfx+'TwinFr:'+str(it)] |
|---|
| 2711 | if it: |
|---|
| 2712 | sumTwFr += hapData['Twins'][it][1] |
|---|
| 2713 | it += 1 |
|---|
| 2714 | except KeyError: |
|---|
| 2715 | break |
|---|
| 2716 | hapData['Twins'][0][1][0] = 1.-sumTwFr |
|---|
| 2717 | |
|---|
| 2718 | if Print: |
|---|
| 2719 | for phase in Phases: |
|---|
| 2720 | HistoPhase = Phases[phase]['Histograms'] |
|---|
| 2721 | General = Phases[phase]['General'] |
|---|
| 2722 | SGData = General['SGData'] |
|---|
| 2723 | pId = Phases[phase]['pId'] |
|---|
| 2724 | histoList = HistoPhase.keys() |
|---|
| 2725 | histoList.sort() |
|---|
| 2726 | for histogram in histoList: |
|---|
| 2727 | try: |
|---|
| 2728 | Histogram = Histograms[histogram] |
|---|
| 2729 | except KeyError: |
|---|
| 2730 | #skip if histogram not included e.g. in a sequential refinement |
|---|
| 2731 | continue |
|---|
| 2732 | print >>pFile,'\n Phase: ',phase,' in histogram: ',histogram |
|---|
| 2733 | print >>pFile,135*'=' |
|---|
| 2734 | hapData = HistoPhase[histogram] |
|---|
| 2735 | hId = Histogram['hId'] |
|---|
| 2736 | Histogram['Residuals'][str(pId)+'::Name'] = phase |
|---|
| 2737 | pfx = str(pId)+':'+str(hId)+':' |
|---|
| 2738 | hfx = ':%s:'%(hId) |
|---|
| 2739 | if 'PWDR' in histogram: |
|---|
| 2740 | print >>pFile,' Final refinement RF, RF^2 = %.2f%%, %.2f%% on %d reflections' \ |
|---|
| 2741 | %(Histogram['Residuals'][pfx+'Rf'],Histogram['Residuals'][pfx+'Rf^2'],Histogram['Residuals'][pfx+'Nref']) |
|---|
| 2742 | print >>pFile,' Bragg intensity sum = %.3g'%(Histogram['Residuals'][pfx+'sumInt']) |
|---|
| 2743 | |
|---|
| 2744 | if pfx+'Scale' in PhFrExtPOSig: |
|---|
| 2745 | wtFr = hapData['Scale'][0]*General['Mass']/wtFrSum[hId] |
|---|
| 2746 | sigwtFr = PhFrExtPOSig[pfx+'Scale']*wtFr/hapData['Scale'][0] |
|---|
| 2747 | print >>pFile,' Phase fraction : %10.5f, sig %10.5f Weight fraction : %8.5f, sig %10.5f' \ |
|---|
| 2748 | %(hapData['Scale'][0],PhFrExtPOSig[pfx+'Scale'],wtFr,sigwtFr) |
|---|
| 2749 | if pfx+'Extinction' in PhFrExtPOSig: |
|---|
| 2750 | print >>pFile,' Extinction coeff: %10.4f, sig %10.4f'%(hapData['Extinction'][0],PhFrExtPOSig[pfx+'Extinction']) |
|---|
| 2751 | if hapData['Pref.Ori.'][0] == 'MD': |
|---|
| 2752 | if pfx+'MD' in PhFrExtPOSig: |
|---|
| 2753 | print >>pFile,' March-Dollase PO: %10.4f, sig %10.4f'%(hapData['Pref.Ori.'][1],PhFrExtPOSig[pfx+'MD']) |
|---|
| 2754 | else: |
|---|
| 2755 | PrintSHPOAndSig(pfx,hapData['Pref.Ori.'],PhFrExtPOSig) |
|---|
| 2756 | PrintSizeAndSig(hapData['Size'],SizeMuStrSig[pfx+'Size']) |
|---|
| 2757 | PrintMuStrainAndSig(hapData['Mustrain'],SizeMuStrSig[pfx+'Mustrain'],SGData) |
|---|
| 2758 | PrintHStrainAndSig(hapData['HStrain'],SizeMuStrSig[pfx+'HStrain'],SGData) |
|---|
| 2759 | if Phases[phase]['General']['Type'] != 'magnetic': |
|---|
| 2760 | if len(BabSig): |
|---|
| 2761 | PrintBabinetAndSig(pfx,hapData['Babinet'],BabSig) |
|---|
| 2762 | |
|---|
| 2763 | elif 'HKLF' in histogram: |
|---|
| 2764 | Inst = Histogram['Instrument Parameters'][0] |
|---|
| 2765 | print >>pFile,' Final refinement RF, RF^2 = %.2f%%, %.2f%% on %d reflections (%d user rejected, %d sp.gp.extinct)' \ |
|---|
| 2766 | %(Histogram['Residuals'][pfx+'Rf'],Histogram['Residuals'][pfx+'Rf^2'],Histogram['Residuals'][pfx+'Nref'], |
|---|
| 2767 | Histogram['Residuals'][pfx+'Nrej'],Histogram['Residuals'][pfx+'Next']) |
|---|
| 2768 | if FFtables != None and 'N' not in Inst['Type'][0]: |
|---|
| 2769 | PrintFprime(FFtables,hfx,pFile) |
|---|
| 2770 | print >>pFile,' HKLF histogram weight factor = ','%.3f'%(Histogram['wtFactor']) |
|---|
| 2771 | if pfx+'Scale' in ScalExtSig: |
|---|
| 2772 | print >>pFile,' Scale factor : %10.4f, sig %10.4f'%(hapData['Scale'][0],ScalExtSig[pfx+'Scale']) |
|---|
| 2773 | if hapData['Extinction'][0] != 'None': |
|---|
| 2774 | PrintExtAndSig(pfx,hapData['Extinction'],ScalExtSig) |
|---|
| 2775 | if len(BabSig): |
|---|
| 2776 | PrintBabinetAndSig(pfx,hapData['Babinet'],BabSig) |
|---|
| 2777 | if pfx+'Flack' in ScalExtSig: |
|---|
| 2778 | print >>pFile,' Flack parameter : %10.3f, sig %10.3f'%(hapData['Flack'][0],ScalExtSig[pfx+'Flack']) |
|---|
| 2779 | if len(TwinFrSig): |
|---|
| 2780 | PrintTwinsAndSig(pfx,hapData['Twins'],TwinFrSig) |
|---|
| 2781 | |
|---|
| 2782 | ################################################################################ |
|---|
| 2783 | ##### Histogram data |
|---|
| 2784 | ################################################################################ |
|---|
| 2785 | |
|---|
| 2786 | def GetHistogramData(Histograms,Print=True,pFile=None): |
|---|
| 2787 | 'needs a doc string' |
|---|
| 2788 | |
|---|
| 2789 | def GetBackgroundParms(hId,Background): |
|---|
| 2790 | Back = Background[0] |
|---|
| 2791 | DebyePeaks = Background[1] |
|---|
| 2792 | bakType,bakFlag = Back[:2] |
|---|
| 2793 | backVals = Back[3:] |
|---|
| 2794 | backNames = [':'+str(hId)+':Back;'+str(i) for i in range(len(backVals))] |
|---|
| 2795 | backDict = dict(zip(backNames,backVals)) |
|---|
| 2796 | backVary = [] |
|---|
| 2797 | if bakFlag: |
|---|
| 2798 | backVary = backNames |
|---|
| 2799 | backDict[':'+str(hId)+':nDebye'] = DebyePeaks['nDebye'] |
|---|
| 2800 | backDict[':'+str(hId)+':nPeaks'] = DebyePeaks['nPeaks'] |
|---|
| 2801 | debyeDict = {} |
|---|
| 2802 | debyeList = [] |
|---|
| 2803 | for i in range(DebyePeaks['nDebye']): |
|---|
| 2804 | debyeNames = [':'+str(hId)+':DebyeA;'+str(i),':'+str(hId)+':DebyeR;'+str(i),':'+str(hId)+':DebyeU;'+str(i)] |
|---|
| 2805 | debyeDict.update(dict(zip(debyeNames,DebyePeaks['debyeTerms'][i][::2]))) |
|---|
| 2806 | debyeList += zip(debyeNames,DebyePeaks['debyeTerms'][i][1::2]) |
|---|
| 2807 | debyeVary = [] |
|---|
| 2808 | for item in debyeList: |
|---|
| 2809 | if item[1]: |
|---|
| 2810 | debyeVary.append(item[0]) |
|---|
| 2811 | backDict.update(debyeDict) |
|---|
| 2812 | backVary += debyeVary |
|---|
| 2813 | peakDict = {} |
|---|
| 2814 | peakList = [] |
|---|
| 2815 | for i in range(DebyePeaks['nPeaks']): |
|---|
| 2816 | peakNames = [':'+str(hId)+':BkPkpos;'+str(i),':'+str(hId)+ \ |
|---|
| 2817 | ':BkPkint;'+str(i),':'+str(hId)+':BkPksig;'+str(i),':'+str(hId)+':BkPkgam;'+str(i)] |
|---|
| 2818 | peakDict.update(dict(zip(peakNames,DebyePeaks['peaksList'][i][::2]))) |
|---|
| 2819 | peakList += zip(peakNames,DebyePeaks['peaksList'][i][1::2]) |
|---|
| 2820 | peakVary = [] |
|---|
| 2821 | for item in peakList: |
|---|
| 2822 | if item[1]: |
|---|
| 2823 | peakVary.append(item[0]) |
|---|
| 2824 | backDict.update(peakDict) |
|---|
| 2825 | backVary += peakVary |
|---|
| 2826 | return bakType,backDict,backVary |
|---|
| 2827 | |
|---|
| 2828 | def GetInstParms(hId,Inst): |
|---|
| 2829 | dataType = Inst['Type'][0] |
|---|
| 2830 | instDict = {} |
|---|
| 2831 | insVary = [] |
|---|
| 2832 | pfx = ':'+str(hId)+':' |
|---|
| 2833 | insKeys = Inst.keys() |
|---|
| 2834 | insKeys.sort() |
|---|
| 2835 | for item in insKeys: |
|---|
| 2836 | insName = pfx+item |
|---|
| 2837 | instDict[insName] = Inst[item][1] |
|---|
| 2838 | if len(Inst[item]) > 2 and Inst[item][2]: |
|---|
| 2839 | insVary.append(insName) |
|---|
| 2840 | if 'C' in dataType: |
|---|
| 2841 | instDict[pfx+'SH/L'] = max(instDict[pfx+'SH/L'],0.0005) |
|---|
| 2842 | return dataType,instDict,insVary |
|---|
| 2843 | |
|---|
| 2844 | def GetSampleParms(hId,Sample): |
|---|
| 2845 | sampVary = [] |
|---|
| 2846 | hfx = ':'+str(hId)+':' |
|---|
| 2847 | sampDict = {hfx+'Gonio. radius':Sample['Gonio. radius'],hfx+'Omega':Sample['Omega'], |
|---|
| 2848 | hfx+'Chi':Sample['Chi'],hfx+'Phi':Sample['Phi']} |
|---|
| 2849 | for key in ('Temperature','Pressure','FreePrm1','FreePrm2','FreePrm3'): |
|---|
| 2850 | if key in Sample: |
|---|
| 2851 | sampDict[hfx+key] = Sample[key] |
|---|
| 2852 | Type = Sample['Type'] |
|---|
| 2853 | if 'Bragg' in Type: #Bragg-Brentano |
|---|
| 2854 | for item in ['Scale','Shift','Transparency','SurfRoughA','SurfRoughB']: |
|---|
| 2855 | sampDict[hfx+item] = Sample[item][0] |
|---|
| 2856 | if Sample[item][1]: |
|---|
| 2857 | sampVary.append(hfx+item) |
|---|
| 2858 | elif 'Debye' in Type: #Debye-Scherrer |
|---|
| 2859 | for item in ['Scale','Absorption','DisplaceX','DisplaceY']: |
|---|
| 2860 | sampDict[hfx+item] = Sample[item][0] |
|---|
| 2861 | if Sample[item][1]: |
|---|
| 2862 | sampVary.append(hfx+item) |
|---|
| 2863 | return Type,sampDict,sampVary |
|---|
| 2864 | |
|---|
| 2865 | def PrintBackground(Background): |
|---|
| 2866 | Back = Background[0] |
|---|
| 2867 | DebyePeaks = Background[1] |
|---|
| 2868 | print >>pFile,'\n Background function: ',Back[0],' Refine?',bool(Back[1]) |
|---|
| 2869 | line = ' Coefficients: ' |
|---|
| 2870 | for i,back in enumerate(Back[3:]): |
|---|
| 2871 | line += '%10.3f'%(back) |
|---|
| 2872 | if i and not i%10: |
|---|
| 2873 | line += '\n'+15*' ' |
|---|
| 2874 | print >>pFile,line |
|---|
| 2875 | if DebyePeaks['nDebye']: |
|---|
| 2876 | print >>pFile,'\n Debye diffuse scattering coefficients' |
|---|
| 2877 | parms = ['DebyeA','DebyeR','DebyeU'] |
|---|
| 2878 | line = ' names : ' |
|---|
| 2879 | for parm in parms: |
|---|
| 2880 | line += '%8s refine?'%(parm) |
|---|
| 2881 | print >>pFile,line |
|---|
| 2882 | for j,term in enumerate(DebyePeaks['debyeTerms']): |
|---|
| 2883 | line = ' term'+'%2d'%(j)+':' |
|---|
| 2884 | for i in range(3): |
|---|
| 2885 | line += '%10.3f %5s'%(term[2*i],bool(term[2*i+1])) |
|---|
| 2886 | print >>pFile,line |
|---|
| 2887 | if DebyePeaks['nPeaks']: |
|---|
| 2888 | print >>pFile,'\n Single peak coefficients' |
|---|
| 2889 | parms = ['BkPkpos','BkPkint','BkPksig','BkPkgam'] |
|---|
| 2890 | line = ' names : ' |
|---|
| 2891 | for parm in parms: |
|---|
| 2892 | line += '%8s refine?'%(parm) |
|---|
| 2893 | print >>pFile,line |
|---|
| 2894 | for j,term in enumerate(DebyePeaks['peaksList']): |
|---|
| 2895 | line = ' peak'+'%2d'%(j)+':' |
|---|
| 2896 | for i in range(4): |
|---|
| 2897 | line += '%12.3f %5s'%(term[2*i],bool(term[2*i+1])) |
|---|
| 2898 | print >>pFile,line |
|---|
| 2899 | |
|---|
| 2900 | def PrintInstParms(Inst): |
|---|
| 2901 | print >>pFile,'\n Instrument Parameters:' |
|---|
| 2902 | insKeys = Inst.keys() |
|---|
| 2903 | insKeys.sort() |
|---|
| 2904 | iBeg = 0 |
|---|
| 2905 | Ok = True |
|---|
| 2906 | while Ok: |
|---|
| 2907 | ptlbls = ' name :' |
|---|
| 2908 | ptstr = ' value :' |
|---|
| 2909 | varstr = ' refine:' |
|---|
| 2910 | iFin = min(iBeg+9,len(insKeys)) |
|---|
| 2911 | for item in insKeys[iBeg:iFin]: |
|---|
| 2912 | if item not in ['Type','Source']: |
|---|
| 2913 | ptlbls += '%12s' % (item) |
|---|
| 2914 | ptstr += '%12.6f' % (Inst[item][1]) |
|---|
| 2915 | if item in ['Lam1','Lam2','Azimuth','fltPath','2-theta',]: |
|---|
| 2916 | varstr += 12*' ' |
|---|
| 2917 | else: |
|---|
| 2918 | varstr += '%12s' % (str(bool(Inst[item][2]))) |
|---|
| 2919 | print >>pFile,ptlbls |
|---|
| 2920 | print >>pFile,ptstr |
|---|
| 2921 | print >>pFile,varstr |
|---|
| 2922 | iBeg = iFin |
|---|
| 2923 | if iBeg == len(insKeys): |
|---|
| 2924 | Ok = False |
|---|
| 2925 | else: |
|---|
| 2926 | print >>pFile,'\n' |
|---|
| 2927 | |
|---|
| 2928 | def PrintSampleParms(Sample): |
|---|
| 2929 | print >>pFile,'\n Sample Parameters:' |
|---|
| 2930 | print >>pFile,' Goniometer omega = %.2f, chi = %.2f, phi = %.2f'% \ |
|---|
| 2931 | (Sample['Omega'],Sample['Chi'],Sample['Phi']) |
|---|
| 2932 | ptlbls = ' name :' |
|---|
| 2933 | ptstr = ' value :' |
|---|
| 2934 | varstr = ' refine:' |
|---|
| 2935 | if 'Bragg' in Sample['Type']: |
|---|
| 2936 | for item in ['Scale','Shift','Transparency','SurfRoughA','SurfRoughB']: |
|---|
| 2937 | ptlbls += '%14s'%(item) |
|---|
| 2938 | ptstr += '%14.4f'%(Sample[item][0]) |
|---|
| 2939 | varstr += '%14s'%(str(bool(Sample[item][1]))) |
|---|
| 2940 | |
|---|
| 2941 | elif 'Debye' in Type: #Debye-Scherrer |
|---|
| 2942 | for item in ['Scale','Absorption','DisplaceX','DisplaceY']: |
|---|
| 2943 | ptlbls += '%14s'%(item) |
|---|
| 2944 | ptstr += '%14.4f'%(Sample[item][0]) |
|---|
| 2945 | varstr += '%14s'%(str(bool(Sample[item][1]))) |
|---|
| 2946 | |
|---|
| 2947 | print >>pFile,ptlbls |
|---|
| 2948 | print >>pFile,ptstr |
|---|
| 2949 | print >>pFile,varstr |
|---|
| 2950 | |
|---|
| 2951 | histDict = {} |
|---|
| 2952 | histVary = [] |
|---|
| 2953 | controlDict = {} |
|---|
| 2954 | histoList = Histograms.keys() |
|---|
| 2955 | histoList.sort() |
|---|
| 2956 | for histogram in histoList: |
|---|
| 2957 | if 'PWDR' in histogram: |
|---|
| 2958 | Histogram = Histograms[histogram] |
|---|
| 2959 | hId = Histogram['hId'] |
|---|
| 2960 | pfx = ':'+str(hId)+':' |
|---|
| 2961 | controlDict[pfx+'wtFactor'] = Histogram['wtFactor'] |
|---|
| 2962 | controlDict[pfx+'Limits'] = Histogram['Limits'][1] |
|---|
| 2963 | controlDict[pfx+'Exclude'] = Histogram['Limits'][2:] |
|---|
| 2964 | for excl in controlDict[pfx+'Exclude']: |
|---|
| 2965 | Histogram['Data'][0] = ma.masked_inside(Histogram['Data'][0],excl[0],excl[1]) |
|---|
| 2966 | if controlDict[pfx+'Exclude']: |
|---|
| 2967 | ma.mask_rows(Histogram['Data']) |
|---|
| 2968 | Background = Histogram['Background'] |
|---|
| 2969 | Type,bakDict,bakVary = GetBackgroundParms(hId,Background) |
|---|
| 2970 | controlDict[pfx+'bakType'] = Type |
|---|
| 2971 | histDict.update(bakDict) |
|---|
| 2972 | histVary += bakVary |
|---|
| 2973 | |
|---|
| 2974 | Inst = Histogram['Instrument Parameters'][0] |
|---|
| 2975 | Type,instDict,insVary = GetInstParms(hId,Inst) |
|---|
| 2976 | controlDict[pfx+'histType'] = Type |
|---|
| 2977 | if 'XC' in Type: |
|---|
| 2978 | if pfx+'Lam1' in instDict: |
|---|
| 2979 | controlDict[pfx+'keV'] = 12.397639/instDict[pfx+'Lam1'] |
|---|
| 2980 | else: |
|---|
| 2981 | controlDict[pfx+'keV'] = 12.397639/instDict[pfx+'Lam'] |
|---|
| 2982 | histDict.update(instDict) |
|---|
| 2983 | histVary += insVary |
|---|
| 2984 | |
|---|
| 2985 | Sample = Histogram['Sample Parameters'] |
|---|
| 2986 | Type,sampDict,sampVary = GetSampleParms(hId,Sample) |
|---|
| 2987 | controlDict[pfx+'instType'] = Type |
|---|
| 2988 | histDict.update(sampDict) |
|---|
| 2989 | histVary += sampVary |
|---|
| 2990 | |
|---|
| 2991 | |
|---|
| 2992 | if Print: |
|---|
| 2993 | print >>pFile,'\n Histogram: ',histogram,' histogram Id: ',hId |
|---|
| 2994 | print >>pFile,135*'=' |
|---|
| 2995 | Units = {'C':' deg','T':' msec'} |
|---|
| 2996 | units = Units[controlDict[pfx+'histType'][2]] |
|---|
| 2997 | Limits = controlDict[pfx+'Limits'] |
|---|
| 2998 | print >>pFile,' Instrument type: ',Sample['Type'] |
|---|
| 2999 | print >>pFile,' Histogram limits: %8.2f%s to %8.2f%s'%(Limits[0],units,Limits[1],units) |
|---|
| 3000 | if len(controlDict[pfx+'Exclude']): |
|---|
| 3001 | excls = controlDict[pfx+'Exclude'] |
|---|
| 3002 | for excl in excls: |
|---|
| 3003 | print >>pFile,' Excluded region: %8.2f%s to %8.2f%s'%(excl[0],units,excl[1],units) |
|---|
| 3004 | PrintSampleParms(Sample) |
|---|
| 3005 | PrintInstParms(Inst) |
|---|
| 3006 | PrintBackground(Background) |
|---|
| 3007 | elif 'HKLF' in histogram: |
|---|
| 3008 | Histogram = Histograms[histogram] |
|---|
| 3009 | hId = Histogram['hId'] |
|---|
| 3010 | pfx = ':'+str(hId)+':' |
|---|
| 3011 | controlDict[pfx+'wtFactor'] = Histogram['wtFactor'] |
|---|
| 3012 | Inst = Histogram['Instrument Parameters'][0] |
|---|
| 3013 | controlDict[pfx+'histType'] = Inst['Type'][0] |
|---|
| 3014 | if 'X' in Inst['Type'][0]: |
|---|
| 3015 | histDict[pfx+'Lam'] = Inst['Lam'][1] |
|---|
| 3016 | controlDict[pfx+'keV'] = 12.397639/histDict[pfx+'Lam'] |
|---|
| 3017 | return histVary,histDict,controlDict |
|---|
| 3018 | |
|---|
| 3019 | def SetHistogramData(parmDict,sigDict,Histograms,FFtables,Print=True,pFile=None): |
|---|
| 3020 | 'needs a doc string' |
|---|
| 3021 | |
|---|
| 3022 | def SetBackgroundParms(pfx,Background,parmDict,sigDict): |
|---|
| 3023 | Back = Background[0] |
|---|
| 3024 | DebyePeaks = Background[1] |
|---|
| 3025 | lenBack = len(Back[3:]) |
|---|
| 3026 | backSig = [0 for i in range(lenBack+3*DebyePeaks['nDebye']+4*DebyePeaks['nPeaks'])] |
|---|
| 3027 | for i in range(lenBack): |
|---|
| 3028 | Back[3+i] = parmDict[pfx+'Back;'+str(i)] |
|---|
| 3029 | if pfx+'Back;'+str(i) in sigDict: |
|---|
| 3030 | backSig[i] = sigDict[pfx+'Back;'+str(i)] |
|---|
| 3031 | if DebyePeaks['nDebye']: |
|---|
| 3032 | for i in range(DebyePeaks['nDebye']): |
|---|
| 3033 | names = [pfx+'DebyeA;'+str(i),pfx+'DebyeR;'+str(i),pfx+'DebyeU;'+str(i)] |
|---|
| 3034 | for j,name in enumerate(names): |
|---|
| 3035 | DebyePeaks['debyeTerms'][i][2*j] = parmDict[name] |
|---|
| 3036 | if name in sigDict: |
|---|
| 3037 | backSig[lenBack+3*i+j] = sigDict[name] |
|---|
| 3038 | if DebyePeaks['nPeaks']: |
|---|
| 3039 | for i in range(DebyePeaks['nPeaks']): |
|---|
| 3040 | names = [pfx+'BkPkpos;'+str(i),pfx+'BkPkint;'+str(i), |
|---|
| 3041 | pfx+'BkPksig;'+str(i),pfx+'BkPkgam;'+str(i)] |
|---|
| 3042 | for j,name in enumerate(names): |
|---|
| 3043 | DebyePeaks['peaksList'][i][2*j] = parmDict[name] |
|---|
| 3044 | if name in sigDict: |
|---|
| 3045 | backSig[lenBack+3*DebyePeaks['nDebye']+4*i+j] = sigDict[name] |
|---|
| 3046 | return backSig |
|---|
| 3047 | |
|---|
| 3048 | def SetInstParms(pfx,Inst,parmDict,sigDict): |
|---|
| 3049 | instSig = {} |
|---|
| 3050 | insKeys = Inst.keys() |
|---|
| 3051 | insKeys.sort() |
|---|
| 3052 | for item in insKeys: |
|---|
| 3053 | insName = pfx+item |
|---|
| 3054 | Inst[item][1] = parmDict[insName] |
|---|
| 3055 | if insName in sigDict: |
|---|
| 3056 | instSig[item] = sigDict[insName] |
|---|
| 3057 | else: |
|---|
| 3058 | instSig[item] = 0 |
|---|
| 3059 | return instSig |
|---|
| 3060 | |
|---|
| 3061 | def SetSampleParms(pfx,Sample,parmDict,sigDict): |
|---|
| 3062 | if 'Bragg' in Sample['Type']: #Bragg-Brentano |
|---|
| 3063 | sampSig = [0 for i in range(5)] |
|---|
| 3064 | for i,item in enumerate(['Scale','Shift','Transparency','SurfRoughA','SurfRoughB']): |
|---|
| 3065 | Sample[item][0] = parmDict[pfx+item] |
|---|
| 3066 | if pfx+item in sigDict: |
|---|
| 3067 | sampSig[i] = sigDict[pfx+item] |
|---|
| 3068 | elif 'Debye' in Sample['Type']: #Debye-Scherrer |
|---|
| 3069 | sampSig = [0 for i in range(4)] |
|---|
| 3070 | for i,item in enumerate(['Scale','Absorption','DisplaceX','DisplaceY']): |
|---|
| 3071 | Sample[item][0] = parmDict[pfx+item] |
|---|
| 3072 | if pfx+item in sigDict: |
|---|
| 3073 | sampSig[i] = sigDict[pfx+item] |
|---|
| 3074 | return sampSig |
|---|
| 3075 | |
|---|
| 3076 | def PrintBackgroundSig(Background,backSig): |
|---|
| 3077 | Back = Background[0] |
|---|
| 3078 | DebyePeaks = Background[1] |
|---|
| 3079 | valstr = ' value : ' |
|---|
| 3080 | sigstr = ' sig : ' |
|---|
| 3081 | refine = False |
|---|
| 3082 | for i,back in enumerate(Back[3:]): |
|---|
| 3083 | valstr += '%10.4g'%(back) |
|---|
| 3084 | if Back[1]: |
|---|
| 3085 | refine = True |
|---|
| 3086 | sigstr += '%10.4g'%(backSig[i]) |
|---|
| 3087 | else: |
|---|
| 3088 | sigstr += 10*' ' |
|---|
| 3089 | if refine: |
|---|
| 3090 | print >>pFile,'\n Background function: ',Back[0] |
|---|
| 3091 | print >>pFile,valstr |
|---|
| 3092 | print >>pFile,sigstr |
|---|
| 3093 | if DebyePeaks['nDebye']: |
|---|
| 3094 | ifAny = False |
|---|
| 3095 | ptfmt = "%12.3f" |
|---|
| 3096 | names = ' names :' |
|---|
| 3097 | ptstr = ' values:' |
|---|
| 3098 | sigstr = ' esds :' |
|---|
| 3099 | for item in sigDict: |
|---|
| 3100 | if 'Debye' in item: |
|---|
| 3101 | ifAny = True |
|---|
| 3102 | names += '%12s'%(item) |
|---|
| 3103 | ptstr += ptfmt%(parmDict[item]) |
|---|
| 3104 | sigstr += ptfmt%(sigDict[item]) |
|---|
| 3105 | if ifAny: |
|---|
| 3106 | print >>pFile,'\n Debye diffuse scattering coefficients' |
|---|
| 3107 | print >>pFile,names |
|---|
| 3108 | print >>pFile,ptstr |
|---|
| 3109 | print >>pFile,sigstr |
|---|
| 3110 | if DebyePeaks['nPeaks']: |
|---|
| 3111 | print >>pFile,'\n Single peak coefficients:' |
|---|
| 3112 | parms = ['BkPkpos','BkPkint','BkPksig','BkPkgam'] |
|---|
| 3113 | line = ' peak no. ' |
|---|
| 3114 | for parm in parms: |
|---|
| 3115 | line += '%14s%12s'%(parm.center(14),'esd'.center(12)) |
|---|
| 3116 | print >>pFile,line |
|---|
| 3117 | for ip in range(DebyePeaks['nPeaks']): |
|---|
| 3118 | ptstr = ' %4d '%(ip) |
|---|
| 3119 | for parm in parms: |
|---|
| 3120 | fmt = '%14.3f' |
|---|
| 3121 | efmt = '%12.3f' |
|---|
| 3122 | if parm == 'BkPkpos': |
|---|
| 3123 | fmt = '%14.4f' |
|---|
| 3124 | efmt = '%12.4f' |
|---|
| 3125 | name = pfx+parm+';%d'%(ip) |
|---|
| 3126 | ptstr += fmt%(parmDict[name]) |
|---|
| 3127 | if name in sigDict: |
|---|
| 3128 | ptstr += efmt%(sigDict[name]) |
|---|
| 3129 | else: |
|---|
| 3130 | ptstr += 12*' ' |
|---|
| 3131 | print >>pFile,ptstr |
|---|
| 3132 | sumBk = np.array(Histogram['sumBk']) |
|---|
| 3133 | print >>pFile,' Background sums: empirical %.3g, Debye %.3g, peaks %.3g, Total %.3g' \ |
|---|
| 3134 | %(sumBk[0],sumBk[1],sumBk[2],np.sum(sumBk)) |
|---|
| 3135 | |
|---|
| 3136 | def PrintInstParmsSig(Inst,instSig): |
|---|
| 3137 | refine = False |
|---|
| 3138 | insKeys = instSig.keys() |
|---|
| 3139 | insKeys.sort() |
|---|
| 3140 | iBeg = 0 |
|---|
| 3141 | Ok = True |
|---|
| 3142 | while Ok: |
|---|
| 3143 | ptlbls = ' names :' |
|---|
| 3144 | ptstr = ' value :' |
|---|
| 3145 | sigstr = ' sig :' |
|---|
| 3146 | iFin = min(iBeg+9,len(insKeys)) |
|---|
| 3147 | for name in insKeys[iBeg:iFin]: |
|---|
| 3148 | if name not in ['Type','Lam1','Lam2','Azimuth','Source','fltPath']: |
|---|
| 3149 | ptlbls += '%12s' % (name) |
|---|
| 3150 | ptstr += '%12.6f' % (Inst[name][1]) |
|---|
| 3151 | if instSig[name]: |
|---|
| 3152 | refine = True |
|---|
| 3153 | sigstr += '%12.6f' % (instSig[name]) |
|---|
| 3154 | else: |
|---|
| 3155 | sigstr += 12*' ' |
|---|
| 3156 | if refine: |
|---|
| 3157 | print >>pFile,'\n Instrument Parameters:' |
|---|
| 3158 | print >>pFile,ptlbls |
|---|
| 3159 | print >>pFile,ptstr |
|---|
| 3160 | print >>pFile,sigstr |
|---|
| 3161 | iBeg = iFin |
|---|
| 3162 | if iBeg == len(insKeys): |
|---|
| 3163 | Ok = False |
|---|
| 3164 | |
|---|
| 3165 | def PrintSampleParmsSig(Sample,sampleSig): |
|---|
| 3166 | ptlbls = ' names :' |
|---|
| 3167 | ptstr = ' values:' |
|---|
| 3168 | sigstr = ' sig :' |
|---|
| 3169 | refine = False |
|---|
| 3170 | if 'Bragg' in Sample['Type']: |
|---|
| 3171 | for i,item in enumerate(['Scale','Shift','Transparency','SurfRoughA','SurfRoughB']): |
|---|
| 3172 | ptlbls += '%14s'%(item) |
|---|
| 3173 | ptstr += '%14.4f'%(Sample[item][0]) |
|---|
| 3174 | if sampleSig[i]: |
|---|
| 3175 | refine = True |
|---|
| 3176 | sigstr += '%14.4f'%(sampleSig[i]) |
|---|
| 3177 | else: |
|---|
| 3178 | sigstr += 14*' ' |
|---|
| 3179 | |
|---|
| 3180 | elif 'Debye' in Sample['Type']: #Debye-Scherrer |
|---|
| 3181 | for i,item in enumerate(['Scale','Absorption','DisplaceX','DisplaceY']): |
|---|
| 3182 | ptlbls += '%14s'%(item) |
|---|
| 3183 | ptstr += '%14.4f'%(Sample[item][0]) |
|---|
| 3184 | if sampleSig[i]: |
|---|
| 3185 | refine = True |
|---|
| 3186 | sigstr += '%14.4f'%(sampleSig[i]) |
|---|
| 3187 | else: |
|---|
| 3188 | sigstr += 14*' ' |
|---|
| 3189 | |
|---|
| 3190 | if refine: |
|---|
| 3191 | print >>pFile,'\n Sample Parameters:' |
|---|
| 3192 | print >>pFile,ptlbls |
|---|
| 3193 | print >>pFile,ptstr |
|---|
| 3194 | print >>pFile,sigstr |
|---|
| 3195 | |
|---|
| 3196 | histoList = Histograms.keys() |
|---|
| 3197 | histoList.sort() |
|---|
| 3198 | for histogram in histoList: |
|---|
| 3199 | if 'PWDR' in histogram: |
|---|
| 3200 | Histogram = Histograms[histogram] |
|---|
| 3201 | hId = Histogram['hId'] |
|---|
| 3202 | pfx = ':'+str(hId)+':' |
|---|
| 3203 | Background = Histogram['Background'] |
|---|
| 3204 | backSig = SetBackgroundParms(pfx,Background,parmDict,sigDict) |
|---|
| 3205 | |
|---|
| 3206 | Inst = Histogram['Instrument Parameters'][0] |
|---|
| 3207 | instSig = SetInstParms(pfx,Inst,parmDict,sigDict) |
|---|
| 3208 | |
|---|
| 3209 | Sample = Histogram['Sample Parameters'] |
|---|
| 3210 | sampSig = SetSampleParms(pfx,Sample,parmDict,sigDict) |
|---|
| 3211 | |
|---|
| 3212 | print >>pFile,'\n Histogram: ',histogram,' histogram Id: ',hId |
|---|
| 3213 | print >>pFile,135*'=' |
|---|
| 3214 | print >>pFile,' PWDR histogram weight factor = '+'%.3f'%(Histogram['wtFactor']) |
|---|
| 3215 | print >>pFile,' Final refinement wR = %.2f%% on %d observations in this histogram'%(Histogram['Residuals']['wR'],Histogram['Residuals']['Nobs']) |
|---|
| 3216 | print >>pFile,' Other residuals: R = %.2f%%, Rb = %.2f%%, wRb = %.2f%% wRmin = %.2f%%'% \ |
|---|
| 3217 | (Histogram['Residuals']['R'],Histogram['Residuals']['Rb'],Histogram['Residuals']['wRb'],Histogram['Residuals']['wRmin']) |
|---|
| 3218 | if Print: |
|---|
| 3219 | print >>pFile,' Instrument type: ',Sample['Type'] |
|---|
| 3220 | if FFtables != None and 'N' not in Inst['Type'][0]: |
|---|
| 3221 | PrintFprime(FFtables,pfx,pFile) |
|---|
| 3222 | PrintSampleParmsSig(Sample,sampSig) |
|---|
| 3223 | PrintInstParmsSig(Inst,instSig) |
|---|
| 3224 | PrintBackgroundSig(Background,backSig) |
|---|
| 3225 | |
|---|
