| 1 | # -*- coding: utf-8 -*- |
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| 2 | ########### SVN repository information ################### |
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| 3 | # $Date: 2020-11-28 02:48:26 +0000 (Sat, 28 Nov 2020) $ |
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| 4 | # $Author: toby $ |
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| 5 | # $Revision: 4661 $ |
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| 6 | # $URL: trunk/GSASIIstrIO.py $ |
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| 7 | # $Id: GSASIIstrIO.py 4661 2020-11-28 02:48:26Z toby $ |
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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 | Contains routines for reading from GPX files and printing to the .LST file. |
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| 14 | Used for refinements and in G2scriptable. |
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| 15 | |
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| 16 | Should not contain any wxpython references as this should be able to be used |
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| 17 | in non-GUI settings. |
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| 18 | |
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| 19 | ''' |
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| 20 | from __future__ import division, print_function |
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| 21 | import platform |
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| 22 | import os |
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| 23 | import os.path as ospath |
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| 24 | import time |
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| 25 | import math |
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| 26 | import copy |
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| 27 | if '2' in platform.python_version_tuple()[0]: |
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| 28 | import cPickle |
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| 29 | else: |
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| 30 | import pickle as cPickle |
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| 31 | import numpy as np |
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| 32 | import numpy.ma as ma |
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| 33 | import GSASIIpath |
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| 34 | GSASIIpath.SetVersionNumber("$Revision: 4661 $") |
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| 35 | import GSASIIElem as G2el |
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| 36 | import GSASIIlattice as G2lat |
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| 37 | import GSASIIspc as G2spc |
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| 38 | import GSASIIobj as G2obj |
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| 39 | import GSASIImapvars as G2mv |
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| 40 | import GSASIImath as G2mth |
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| 41 | import GSASIIfiles as G2fil |
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| 42 | import GSASIIpy3 as G2py3 |
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| 43 | |
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| 44 | sind = lambda x: np.sin(x*np.pi/180.) |
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| 45 | cosd = lambda x: np.cos(x*np.pi/180.) |
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| 46 | tand = lambda x: np.tan(x*np.pi/180.) |
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| 47 | asind = lambda x: 180.*np.arcsin(x)/np.pi |
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| 48 | acosd = lambda x: 180.*np.arccos(x)/np.pi |
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| 49 | atan2d = lambda y,x: 180.*np.arctan2(y,x)/np.pi |
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| 50 | |
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| 51 | ateln2 = 8.0*math.log(2.0) |
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| 52 | |
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| 53 | #=============================================================================== |
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| 54 | # Support for GPX file reading |
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| 55 | #=============================================================================== |
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| 56 | def cPickleLoad(fp): |
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| 57 | if '2' in platform.python_version_tuple()[0]: |
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| 58 | return cPickle.load(fp) |
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| 59 | else: |
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| 60 | return cPickle.load(fp,encoding='latin-1') |
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| 61 | |
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| 62 | gpxIndex = {}; gpxNamelist = []; gpxSize = -1 |
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| 63 | '''Global variables used in :func:`IndexGPX` to see if file has changed |
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| 64 | (gpxSize) and to index where to find each 1st-level tree item in the file. |
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| 65 | ''' |
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| 66 | |
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| 67 | def GetFullGPX(GPXfile): |
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| 68 | ''' Returns complete contents of GSASII gpx file. |
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| 69 | Used in :func:`GSASIIscriptable.LoadDictFromProjFile`. |
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| 70 | |
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| 71 | :param str GPXfile: full .gpx file name |
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| 72 | :returns: Project,nameList, where |
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| 73 | |
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| 74 | * Project (dict) is a representation of gpx file following the GSAS-II |
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| 75 | tree structure for each item: key = tree name (e.g. 'Controls', |
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| 76 | 'Restraints', etc.), data is dict |
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| 77 | * nameList (list) has names of main tree entries & subentries used to reconstruct project file |
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| 78 | ''' |
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| 79 | return IndexGPX(GPXfile,read=True) |
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| 80 | |
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| 81 | def IndexGPX(GPXfile,read=False): |
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| 82 | '''Create an index to a GPX file, optionally the file into memory. |
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| 83 | The byte size of the GPX file is saved. If this routine is called |
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| 84 | again, and if this size does not change, indexing is not repeated |
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| 85 | since it is assumed the file has not changed (this can be overriden |
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| 86 | by setting read=True). |
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| 87 | |
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| 88 | :param str GPXfile: full .gpx file name |
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| 89 | :returns: Project,nameList if read=, where |
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| 90 | |
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| 91 | * Project (dict) is a representation of gpx file following the GSAS-II |
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| 92 | tree structure for each item: key = tree name (e.g. 'Controls', |
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| 93 | 'Restraints', etc.), data is dict |
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| 94 | * nameList (list) has names of main tree entries & subentries used to reconstruct project file |
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| 95 | ''' |
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| 96 | global gpxSize |
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| 97 | if gpxSize == os.path.getsize(GPXfile) and not read: |
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| 98 | return |
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| 99 | global gpxIndex |
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| 100 | gpxIndex = {} |
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| 101 | global gpxNamelist |
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| 102 | gpxNamelist = [] |
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| 103 | if GSASIIpath.GetConfigValue('debug'): print("DBG: Indexing GPX file") |
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| 104 | gpxSize = os.path.getsize(GPXfile) |
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| 105 | fp = open(GPXfile,'rb') |
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| 106 | Project = {} |
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| 107 | try: |
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| 108 | while True: |
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| 109 | pos = fp.tell() |
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| 110 | data = cPickleLoad(fp) |
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| 111 | datum = data[0] |
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| 112 | gpxIndex[datum[0]] = pos |
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| 113 | if read: Project[datum[0]] = {'data':datum[1]} |
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| 114 | gpxNamelist.append([datum[0],]) |
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| 115 | for datus in data[1:]: |
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| 116 | if read: Project[datum[0]][datus[0]] = datus[1] |
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| 117 | gpxNamelist[-1].append(datus[0]) |
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| 118 | # print('project load successful') |
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| 119 | except EOFError: |
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| 120 | pass |
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| 121 | except Exception as msg: |
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| 122 | G2fil.G2Print('Read Error:',msg) |
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| 123 | raise Exception("Error reading file "+str(GPXfile)+". This is not a GSAS-II .gpx file") |
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| 124 | finally: |
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| 125 | fp.close() |
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| 126 | if read: return Project,gpxNamelist |
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| 127 | |
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| 128 | def GetControls(GPXfile): |
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| 129 | ''' Returns dictionary of control items found in GSASII gpx file |
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| 130 | |
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| 131 | :param str GPXfile: full .gpx file name |
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| 132 | :return: dictionary of control items |
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| 133 | ''' |
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| 134 | Controls = copy.deepcopy(G2obj.DefaultControls) |
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| 135 | IndexGPX(GPXfile) |
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| 136 | pos = gpxIndex.get('Controls') |
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| 137 | if pos is None: |
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| 138 | G2fil.G2Print('Warning: Controls not found in gpx file {}'.format(GPXfile)) |
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| 139 | return Controls |
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| 140 | fp = open(GPXfile,'rb') |
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| 141 | fp.seek(pos) |
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| 142 | datum = cPickleLoad(fp)[0] |
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| 143 | fp.close() |
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| 144 | Controls.update(datum[1]) |
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| 145 | return Controls |
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| 146 | |
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| 147 | def GetConstraints(GPXfile): |
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| 148 | '''Read the constraints from the GPX file and interpret them |
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| 149 | |
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| 150 | called in :func:`ReadCheckConstraints`, :func:`GSASIIstrMain.Refine` |
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| 151 | and :func:`GSASIIstrMain.SeqRefine`. |
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| 152 | ''' |
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| 153 | IndexGPX(GPXfile) |
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| 154 | fl = open(GPXfile,'rb') |
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| 155 | pos = gpxIndex.get('Constraints') |
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| 156 | if pos is None: |
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| 157 | raise Exception("No constraints in GPX file") |
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| 158 | fl.seek(pos) |
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| 159 | datum = cPickleLoad(fl)[0] |
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| 160 | fl.close() |
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| 161 | constList = [] |
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| 162 | for item in datum[1]: |
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| 163 | if item.startswith('_'): continue |
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| 164 | constList += datum[1][item] |
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| 165 | constDict,fixedList,ignored = ProcessConstraints(constList) |
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| 166 | if ignored: |
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| 167 | G2fil.G2Print ('Warning: {} Constraints were rejected. Was a constrained phase, histogram or atom deleted?'.format(ignored)) |
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| 168 | return constDict,fixedList |
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| 169 | |
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| 170 | def ProcessConstraints(constList): |
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| 171 | """Interpret the constraints in the constList input into a dictionary, etc. |
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| 172 | All :class:`GSASIIobj.G2VarObj` objects are mapped to the appropriate |
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| 173 | phase/hist/atoms based on the object internals (random Ids). If this can't be |
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| 174 | done (if a phase has been deleted, etc.), the variable is ignored. |
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| 175 | If the constraint cannot be used due to too many dropped variables, |
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| 176 | it is counted as ignored. |
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| 177 | |
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| 178 | :param list constList: a list of lists where each item in the outer list |
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| 179 | specifies a constraint of some form, as described in the :mod:`GSASIIobj` |
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| 180 | :ref:`Constraint definition <Constraint_definitions_table>`. |
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| 181 | |
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| 182 | :returns: a tuple of (constDict,fixedList,ignored) where: |
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| 183 | |
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| 184 | * constDict (list of dicts) contains the constraint relationships |
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| 185 | * fixedList (list) contains the fixed values for each type |
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| 186 | of constraint. |
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| 187 | * ignored (int) counts the number of invalid constraint items |
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| 188 | (should always be zero!) |
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| 189 | """ |
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| 190 | constDict = [] |
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| 191 | fixedList = [] |
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| 192 | ignored = 0 |
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| 193 | for item in constList: |
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| 194 | if item[-1] == 'h': |
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| 195 | # process a hold |
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| 196 | fixedList.append('0') |
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| 197 | var = str(item[0][1]) |
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| 198 | if '?' not in var: |
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| 199 | constDict.append({var:0.0}) |
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| 200 | else: |
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| 201 | ignored += 1 |
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| 202 | elif item[-1] == 'f': |
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| 203 | # process a new variable |
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| 204 | fixedList.append(None) |
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| 205 | D = {} |
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| 206 | varyFlag = item[-2] |
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| 207 | varname = item[-3] |
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| 208 | for term in item[:-3]: |
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| 209 | var = str(term[1]) |
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| 210 | if '?' not in var: |
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| 211 | D[var] = term[0] |
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| 212 | if len(D) > 1: |
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| 213 | # add extra dict terms for input variable name and vary flag |
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| 214 | if varname is not None: |
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| 215 | varname = str(varname) # in case this is a G2VarObj |
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| 216 | if ':' in varname: |
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| 217 | D['_name'] = varname |
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| 218 | else: |
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| 219 | D['_name'] = '::' + varname |
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| 220 | D['_vary'] = varyFlag == True # force to bool |
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| 221 | constDict.append(D) |
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| 222 | else: |
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| 223 | ignored += 1 |
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| 224 | #constFlag[-1] = ['Vary'] |
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| 225 | elif item[-1] == 'c': |
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| 226 | # process a contraint relationship |
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| 227 | D = {} |
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| 228 | for term in item[:-3]: |
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| 229 | var = str(term[1]) |
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| 230 | if '?' not in var: |
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| 231 | D[var] = term[0] |
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| 232 | if len(D) >= 1: |
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| 233 | fixedList.append(str(item[-3])) |
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| 234 | constDict.append(D) |
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| 235 | else: |
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| 236 | ignored += 1 |
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| 237 | elif item[-1] == 'e': |
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| 238 | # process an equivalence |
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| 239 | firstmult = None |
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| 240 | eqlist = [] |
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| 241 | for term in item[:-3]: |
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| 242 | if term[0] == 0: term[0] = 1.0 |
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| 243 | var = str(term[1]) |
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| 244 | if '?' in var: continue |
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| 245 | if firstmult is None: |
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| 246 | firstmult = term[0] |
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| 247 | firstvar = var |
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| 248 | else: |
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| 249 | eqlist.append([var,firstmult/term[0]]) |
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| 250 | if len(eqlist) > 0: |
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| 251 | G2mv.StoreEquivalence(firstvar,eqlist,False) |
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| 252 | else: |
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| 253 | ignored += 1 |
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| 254 | else: |
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| 255 | ignored += 1 |
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| 256 | return constDict,fixedList,ignored |
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| 257 | |
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| 258 | def ReadCheckConstraints(GPXfile, seqHist=None): |
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| 259 | '''Load constraints and related info and return any error or warning messages |
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| 260 | This is done from the GPX file rather than the tree. |
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| 261 | |
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| 262 | :param dict seqHist: defines a specific histogram to be loaded for a sequential |
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| 263 | refinement, if None (default) all are loaded. |
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| 264 | ''' |
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| 265 | # init constraints |
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| 266 | G2mv.InitVars() |
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| 267 | # get variables |
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| 268 | Histograms,Phases = GetUsedHistogramsAndPhases(GPXfile) |
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| 269 | if not Phases: |
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| 270 | return 'Error: No phases or no histograms in phases!','' |
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| 271 | if not Histograms: |
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| 272 | return 'Error: no diffraction data','' |
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| 273 | constrDict,fixedList = GetConstraints(GPXfile) # load user constraints before internally generated ones |
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| 274 | if seqHist: Histograms = {seqHist:Histograms[seqHist]} # sequential fit: only need one histogram |
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| 275 | rigidbodyDict = GetRigidBodies(GPXfile) |
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| 276 | rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]}) |
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| 277 | rbVary,rbDict = GetRigidBodyModels(rigidbodyDict,Print=False) |
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| 278 | Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables,MFtables,maxSSwave = \ |
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| 279 | GetPhaseData(Phases,RestraintDict=None,rbIds=rbIds,Print=False) # generates atom symmetry constraints |
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| 280 | hapVary,hapDict,controlDict = GetHistogramPhaseData(Phases,Histograms,Print=False,resetRefList=False) |
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| 281 | histVary,histDict,controlDict = GetHistogramData(Histograms,Print=False) |
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| 282 | varyList = rbVary+phaseVary+hapVary+histVary |
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| 283 | msg = G2mv.EvaluateMultipliers(constrDict,phaseDict,hapDict,histDict) |
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| 284 | if msg: |
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| 285 | return 'Unable to interpret multiplier(s): '+msg,'' |
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| 286 | errmsg, warnmsg = G2mv.CheckConstraints(varyList,constrDict,fixedList) |
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| 287 | if errmsg: |
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| 288 | # print some diagnostic info on the constraints |
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| 289 | G2fil.G2Print('Error in constraints:\n'+errmsg+ |
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| 290 | '\nRefinement not possible due to conflict in constraints, see below:\n') |
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| 291 | G2fil.G2Print(G2mv.VarRemapShow(varyList,True),mode='error') |
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| 292 | return errmsg, warnmsg |
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| 293 | |
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| 294 | def makeTwinFrConstr(Phases,Histograms,hapVary): |
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| 295 | TwConstr = [] |
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| 296 | TwFixed = [] |
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| 297 | for Phase in Phases: |
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| 298 | pId = Phases[Phase]['pId'] |
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| 299 | for Histogram in Phases[Phase]['Histograms']: |
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| 300 | try: |
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| 301 | hId = Histograms[Histogram]['hId'] |
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| 302 | phfx = '%d:%d:'%(pId,hId) |
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| 303 | if phfx+'TwinFr:0' in hapVary: |
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| 304 | TwFixed.append('1.0') #constraint value |
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| 305 | nTwin = len(Phases[Phase]['Histograms'][Histogram]['Twins']) |
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| 306 | TwConstr.append({phfx+'TwinFr:'+str(i):'1.0' for i in range(nTwin)}) |
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| 307 | except KeyError: #unused histograms? |
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| 308 | pass |
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| 309 | return TwConstr,TwFixed |
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| 310 | |
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| 311 | def GetRestraints(GPXfile): |
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| 312 | '''Read the restraints from the GPX file. |
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| 313 | Throws an exception if not found in the .GPX file |
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| 314 | ''' |
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| 315 | IndexGPX(GPXfile) |
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| 316 | fl = open(GPXfile,'rb') |
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| 317 | pos = gpxIndex.get('Restraints') |
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| 318 | if pos is None: |
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| 319 | raise Exception("No Restraints in GPX file") |
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| 320 | fl.seek(pos) |
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| 321 | datum = cPickleLoad(fl)[0] |
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| 322 | fl.close() |
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| 323 | return datum[1] |
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| 324 | |
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| 325 | def GetRigidBodies(GPXfile): |
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| 326 | '''Read the rigid body models from the GPX file |
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| 327 | ''' |
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| 328 | IndexGPX(GPXfile) |
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| 329 | fl = open(GPXfile,'rb') |
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| 330 | pos = gpxIndex.get('Rigid bodies') |
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| 331 | if pos is None: |
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| 332 | raise Exception("No Rigid bodies in GPX file") |
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| 333 | fl.seek(pos) |
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| 334 | datum = cPickleLoad(fl)[0] |
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| 335 | fl.close() |
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| 336 | return datum[1] |
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| 337 | |
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| 338 | def GetFprime(controlDict,Histograms): |
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| 339 | 'Needs a doc string' |
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| 340 | FFtables = controlDict['FFtables'] |
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| 341 | if not FFtables: |
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| 342 | return |
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| 343 | histoList = list(Histograms.keys()) |
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| 344 | histoList.sort() |
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| 345 | for histogram in histoList: |
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| 346 | if histogram[:4] in ['PWDR','HKLF']: |
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| 347 | Histogram = Histograms[histogram] |
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| 348 | hId = Histogram['hId'] |
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| 349 | hfx = ':%d:'%(hId) |
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| 350 | if 'X' in controlDict[hfx+'histType']: |
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| 351 | keV = controlDict[hfx+'keV'] |
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| 352 | for El in FFtables: |
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| 353 | Orbs = G2el.GetXsectionCoeff(El.split('+')[0].split('-')[0]) |
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| 354 | FP,FPP,Mu = G2el.FPcalc(Orbs, keV) |
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| 355 | FFtables[El][hfx+'FP'] = FP |
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| 356 | FFtables[El][hfx+'FPP'] = FPP |
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| 357 | |
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| 358 | def PrintFprime(FFtables,pfx,pFile): |
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| 359 | pFile.write('\n Resonant form factors:(ref: D.T. Cromer & D.A. Liberman (1981), Acta Cryst. A37, 267-268.)\n') |
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| 360 | Elstr = ' Element:' |
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| 361 | FPstr = " f' :" |
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| 362 | FPPstr = ' f" :' |
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| 363 | for El in FFtables: |
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| 364 | Elstr += ' %8s'%(El) |
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| 365 | FPstr += ' %8.3f'%(FFtables[El][pfx+'FP']) |
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| 366 | FPPstr += ' %8.3f'%(FFtables[El][pfx+'FPP']) |
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| 367 | pFile.write(Elstr+'\n') |
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| 368 | pFile.write(FPstr+'\n') |
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| 369 | pFile.write(FPPstr+'\n') |
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| 370 | |
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| 371 | def PrintISOmodes(pFile,Phases,parmDict,sigDict): |
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| 372 | '''Prints the values for the ISODISTORT modes into the project's |
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| 373 | .lst file after a refinement. |
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| 374 | ''' |
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| 375 | for phase in Phases: |
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| 376 | if 'ISODISTORT' not in Phases[phase]: continue |
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| 377 | data = Phases[phase] |
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| 378 | ISO = data['ISODISTORT'] |
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| 379 | if 'G2VarList' in ISO: |
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| 380 | deltaList = [] |
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| 381 | for gv,Ilbl in zip(ISO['G2VarList'],ISO['IsoVarList']): |
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| 382 | dvar = gv.varname() |
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| 383 | var = dvar.replace('::dA','::A') |
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| 384 | albl = Ilbl[:Ilbl.rfind('_')] |
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| 385 | v = Ilbl[Ilbl.rfind('_')+1:] |
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| 386 | pval = ISO['ParentStructure'][albl][['dx','dy','dz'].index(v)] |
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| 387 | if var in parmDict: |
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| 388 | cval = parmDict[var] |
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| 389 | else: |
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| 390 | print('PrintISOmodes Error: Atom not found',"No value found for parameter "+str(var)) |
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| 391 | return |
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| 392 | deltaList.append(cval-pval) |
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| 393 | modeVals = np.inner(ISO['Var2ModeMatrix'],deltaList) |
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| 394 | |
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| 395 | if 'G2OccVarList' in ISO: |
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| 396 | deltaOccList = [] |
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| 397 | for gv,Ilbl in zip(ISO['G2OccVarList'],ISO['OccVarList']): |
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| 398 | var = gv.varname() |
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| 399 | albl = Ilbl[:Ilbl.rfind('_')] |
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| 400 | pval = ISO['BaseOcc'][albl] |
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| 401 | if var in parmDict: |
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| 402 | cval = parmDict[var] |
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| 403 | else: |
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| 404 | print('PrintISOmodes Error: Atom not found',"No value found for parameter "+str(var)) |
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| 405 | return |
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| 406 | deltaOccList.append(cval-pval) |
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| 407 | modeOccVals = np.inner(ISO['Var2OccMatrix'],deltaOccList) |
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| 408 | |
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| 409 | if 'G2VarList' in ISO: |
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| 410 | pFile.write('\n ISODISTORT Displacive Modes for phase {}\n'.format(data['General'].get('Name',''))) |
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| 411 | l = str(max([len(i) for i in ISO['IsoModeList']])+3) |
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| 412 | fmt = ' {:'+l+'}{}' |
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| 413 | for var,val,norm,G2mode in zip( |
|---|
| 414 | ISO['IsoModeList'],modeVals,ISO['NormList'],ISO['G2ModeList'] ): |
|---|
| 415 | try: |
|---|
| 416 | value = G2py3.FormatSigFigs(val/norm) |
|---|
| 417 | if str(G2mode) in sigDict: |
|---|
| 418 | value = G2mth.ValEsd(val/norm,sigDict[str(G2mode)]/norm) |
|---|
| 419 | except TypeError: |
|---|
| 420 | value = '?' |
|---|
| 421 | pFile.write(fmt.format(var,value)+'\n') |
|---|
| 422 | |
|---|
| 423 | if 'G2OccVarList' in ISO: |
|---|
| 424 | pFile.write('\n ISODISTORT Occupancy Modes for phase {}\n'.format(data['General'].get('Name',''))) |
|---|
| 425 | l = str(max([len(i) for i in ISO['OccModeList']])+3) |
|---|
| 426 | fmt = ' {:'+l+'}{}' |
|---|
| 427 | for var,val,norm,G2mode in zip( |
|---|
| 428 | ISO['OccModeList'],modeOccVals,ISO['OccNormList'],ISO['G2OccModeList'] ): |
|---|
| 429 | try: |
|---|
| 430 | value = G2py3.FormatSigFigs(val/norm) |
|---|
| 431 | if str(G2mode) in sigDict: |
|---|
| 432 | value = G2mth.ValEsd(val/norm,sigDict[str(G2mode)]/norm) |
|---|
| 433 | except TypeError: |
|---|
| 434 | value = '?' |
|---|
| 435 | pFile.write(fmt.format(var,value)+'\n') |
|---|
| 436 | |
|---|
| 437 | def GetPhaseNames(GPXfile): |
|---|
| 438 | ''' Returns a list of phase names found under 'Phases' in GSASII gpx file |
|---|
| 439 | |
|---|
| 440 | :param str GPXfile: full .gpx file name |
|---|
| 441 | :return: list of phase names |
|---|
| 442 | ''' |
|---|
| 443 | IndexGPX(GPXfile) |
|---|
| 444 | fl = open(GPXfile,'rb') |
|---|
| 445 | pos = gpxIndex.get('Phases') |
|---|
| 446 | if pos is None: |
|---|
| 447 | raise Exception("No Phases in GPX file") |
|---|
| 448 | fl.seek(pos) |
|---|
| 449 | data = cPickleLoad(fl) |
|---|
| 450 | fl.close() |
|---|
| 451 | return [datus[0] for datus in data[1:]] |
|---|
| 452 | |
|---|
| 453 | def GetAllPhaseData(GPXfile,PhaseName): |
|---|
| 454 | ''' Returns the entire dictionary for PhaseName from GSASII gpx file |
|---|
| 455 | |
|---|
| 456 | :param str GPXfile: full .gpx file name |
|---|
| 457 | :param str PhaseName: phase name |
|---|
| 458 | :return: phase dictionary or None if PhaseName is not present |
|---|
| 459 | ''' |
|---|
| 460 | IndexGPX(GPXfile) |
|---|
| 461 | fl = open(GPXfile,'rb') |
|---|
| 462 | pos = gpxIndex.get('Phases') |
|---|
| 463 | if pos is None: |
|---|
| 464 | raise Exception("No Phases in GPX file") |
|---|
| 465 | fl.seek(pos) |
|---|
| 466 | data = cPickleLoad(fl) |
|---|
| 467 | fl.close() |
|---|
| 468 | |
|---|
| 469 | for datus in data[1:]: |
|---|
| 470 | if datus[0] == PhaseName: |
|---|
| 471 | return datus[1] |
|---|
| 472 | |
|---|
| 473 | def GetHistograms(GPXfile,hNames): |
|---|
| 474 | """ Returns a dictionary of histograms found in GSASII gpx file |
|---|
| 475 | |
|---|
| 476 | :param str GPXfile: full .gpx file name |
|---|
| 477 | :param str hNames: list of histogram names |
|---|
| 478 | :return: dictionary of histograms (types = PWDR & HKLF) |
|---|
| 479 | |
|---|
| 480 | """ |
|---|
| 481 | IndexGPX(GPXfile) |
|---|
| 482 | fl = open(GPXfile,'rb') |
|---|
| 483 | Histograms = {} |
|---|
| 484 | for hist in hNames: |
|---|
| 485 | pos = gpxIndex.get(hist) |
|---|
| 486 | if pos is None: |
|---|
| 487 | raise Exception("Histogram {} not found in GPX file".format(hist)) |
|---|
| 488 | fl.seek(pos) |
|---|
| 489 | data = cPickleLoad(fl) |
|---|
| 490 | datum = data[0] |
|---|
| 491 | if 'PWDR' in hist[:4]: |
|---|
| 492 | PWDRdata = {} |
|---|
| 493 | PWDRdata.update(datum[1][0]) #weight factor |
|---|
| 494 | PWDRdata['Data'] = ma.array(ma.getdata(datum[1][1])) #masked powder data arrays/clear previous masks |
|---|
| 495 | PWDRdata[data[2][0]] = data[2][1] #Limits & excluded regions (if any) |
|---|
| 496 | PWDRdata[data[3][0]] = data[3][1] #Background |
|---|
| 497 | PWDRdata[data[4][0]] = data[4][1] #Instrument parameters |
|---|
| 498 | PWDRdata[data[5][0]] = data[5][1] #Sample parameters |
|---|
| 499 | try: |
|---|
| 500 | PWDRdata[data[9][0]] = data[9][1] #Reflection lists might be missing |
|---|
| 501 | except IndexError: |
|---|
| 502 | PWDRdata['Reflection Lists'] = {} |
|---|
| 503 | PWDRdata['Residuals'] = {} |
|---|
| 504 | Histograms[hist] = PWDRdata |
|---|
| 505 | elif 'HKLF' in hist[:4]: |
|---|
| 506 | HKLFdata = {} |
|---|
| 507 | HKLFdata.update(datum[1][0]) #weight factor |
|---|
| 508 | #patch |
|---|
| 509 | if 'list' in str(type(datum[1][1])): |
|---|
| 510 | #if isinstance(datum[1][1],list): |
|---|
| 511 | RefData = {'RefList':[],'FF':{}} |
|---|
| 512 | for ref in datum[1][1]: |
|---|
| 513 | RefData['RefList'].append(ref[:11]+[ref[13],]) |
|---|
| 514 | RefData['RefList'] = np.array(RefData['RefList']) |
|---|
| 515 | datum[1][1] = RefData |
|---|
| 516 | #end patch |
|---|
| 517 | datum[1][1]['FF'] = {} |
|---|
| 518 | HKLFdata['Data'] = datum[1][1] |
|---|
| 519 | HKLFdata[data[1][0]] = data[1][1] #Instrument parameters |
|---|
| 520 | HKLFdata['Reflection Lists'] = None |
|---|
| 521 | HKLFdata['Residuals'] = {} |
|---|
| 522 | Histograms[hist] = HKLFdata |
|---|
| 523 | fl.close() |
|---|
| 524 | return Histograms |
|---|
| 525 | |
|---|
| 526 | def GetHistogramNames(GPXfile,hTypes): |
|---|
| 527 | """ Returns a list of histogram names found in a GSAS-II .gpx file that |
|---|
| 528 | match specifed histogram types. Names are returned in the order they |
|---|
| 529 | appear in the file. |
|---|
| 530 | |
|---|
| 531 | :param str GPXfile: full .gpx file name |
|---|
| 532 | :param str hTypes: list of histogram types |
|---|
| 533 | :return: list of histogram names (types = PWDR & HKLF) |
|---|
| 534 | |
|---|
| 535 | """ |
|---|
| 536 | IndexGPX(GPXfile) |
|---|
| 537 | return [n[0] for n in gpxNamelist if n[0][:4] in hTypes] |
|---|
| 538 | |
|---|
| 539 | def GetUsedHistogramsAndPhases(GPXfile): |
|---|
| 540 | ''' Returns all histograms that are found in any phase |
|---|
| 541 | and any phase that uses a histogram. This also |
|---|
| 542 | assigns numbers to used phases and histograms by the |
|---|
| 543 | order they appear in the file. |
|---|
| 544 | |
|---|
| 545 | :param str GPXfile: full .gpx file name |
|---|
| 546 | :returns: (Histograms,Phases) |
|---|
| 547 | |
|---|
| 548 | * Histograms = dictionary of histograms as {name:data,...} |
|---|
| 549 | * Phases = dictionary of phases that use histograms |
|---|
| 550 | |
|---|
| 551 | ''' |
|---|
| 552 | phaseNames = GetPhaseNames(GPXfile) |
|---|
| 553 | histoList = GetHistogramNames(GPXfile,['PWDR','HKLF']) |
|---|
| 554 | allHistograms = GetHistograms(GPXfile,histoList) |
|---|
| 555 | phaseData = {} |
|---|
| 556 | for name in phaseNames: |
|---|
| 557 | phaseData[name] = GetAllPhaseData(GPXfile,name) |
|---|
| 558 | Histograms = {} |
|---|
| 559 | Phases = {} |
|---|
| 560 | for phase in phaseData: |
|---|
| 561 | Phase = phaseData[phase] |
|---|
| 562 | if Phase['General']['Type'] == 'faulted': continue #don't use faulted phases! |
|---|
| 563 | if Phase['Histograms']: |
|---|
| 564 | for hist in Phase['Histograms']: |
|---|
| 565 | if 'Use' not in Phase['Histograms'][hist]: #patch |
|---|
| 566 | Phase['Histograms'][hist]['Use'] = True |
|---|
| 567 | if Phase['Histograms'][hist]['Use'] and phase not in Phases: |
|---|
| 568 | pId = phaseNames.index(phase) |
|---|
| 569 | Phase['pId'] = pId |
|---|
| 570 | Phases[phase] = Phase |
|---|
| 571 | if hist not in Histograms and Phase['Histograms'][hist]['Use']: |
|---|
| 572 | try: |
|---|
| 573 | Histograms[hist] = allHistograms[hist] |
|---|
| 574 | hId = histoList.index(hist) |
|---|
| 575 | Histograms[hist]['hId'] = hId |
|---|
| 576 | except KeyError: # would happen if a referenced histogram were |
|---|
| 577 | # renamed or deleted |
|---|
| 578 | G2fil.G2Print('Warning: For phase "'+phase+ |
|---|
| 579 | '" unresolved reference to histogram "'+hist+'"') |
|---|
| 580 | # load the fix background info into the histograms |
|---|
| 581 | for hist in Histograms: |
|---|
| 582 | if 'Background' not in Histograms[hist]: continue |
|---|
| 583 | fixedBkg = Histograms[hist]['Background'][1].get('background PWDR') |
|---|
| 584 | if fixedBkg: |
|---|
| 585 | if not fixedBkg[0]: continue |
|---|
| 586 | # patch: add refinement flag, if needed |
|---|
| 587 | if len(fixedBkg) == 2: fixedBkg += [False] |
|---|
| 588 | h = Histograms[hist]['Background'][1] |
|---|
| 589 | try: |
|---|
| 590 | Limits = Histograms[hist]['Limits'][1] |
|---|
| 591 | x = Histograms[hist]['Data'][0] |
|---|
| 592 | xB = np.searchsorted(x,Limits[0]) |
|---|
| 593 | xF = np.searchsorted(x,Limits[1])+1 |
|---|
| 594 | h['_fixedValues'] = allHistograms[fixedBkg[0]]['Data'][1][xB:xF] |
|---|
| 595 | h['_fixedMult'],h['_fixedVary'] = fixedBkg[1:] |
|---|
| 596 | except KeyError: # would happen if a referenced histogram were renamed or deleted |
|---|
| 597 | G2fil.G2Print('Warning: For hist "{}" unresolved background reference to hist "{}"' |
|---|
| 598 | .format(hist,fixedBkg[0])) |
|---|
| 599 | G2obj.IndexAllIds(Histograms=Histograms,Phases=Phases) |
|---|
| 600 | return Histograms,Phases |
|---|
| 601 | |
|---|
| 602 | def getBackupName(GPXfile,makeBack): |
|---|
| 603 | ''' |
|---|
| 604 | Get the name for the backup .gpx file name |
|---|
| 605 | |
|---|
| 606 | :param str GPXfile: full .gpx file name |
|---|
| 607 | :param bool makeBack: if True the name of a new file is returned, if |
|---|
| 608 | False the name of the last file that exists is returned |
|---|
| 609 | :returns: the name of a backup file |
|---|
| 610 | |
|---|
| 611 | ''' |
|---|
| 612 | GPXpath,GPXname = ospath.split(GPXfile) |
|---|
| 613 | if GPXpath == '': GPXpath = '.' |
|---|
| 614 | Name = ospath.splitext(GPXname)[0] |
|---|
| 615 | files = os.listdir(GPXpath) |
|---|
| 616 | last = 0 |
|---|
| 617 | for name in files: |
|---|
| 618 | name = name.split('.') |
|---|
| 619 | if len(name) == 3 and name[0] == Name and 'bak' in name[1]: |
|---|
| 620 | if makeBack: |
|---|
| 621 | last = max(last,int(name[1].strip('bak'))+1) |
|---|
| 622 | else: |
|---|
| 623 | last = max(last,int(name[1].strip('bak'))) |
|---|
| 624 | GPXback = ospath.join(GPXpath,ospath.splitext(GPXname)[0]+'.bak'+str(last)+'.gpx') |
|---|
| 625 | return GPXback |
|---|
| 626 | |
|---|
| 627 | def GPXBackup(GPXfile,makeBack=True): |
|---|
| 628 | ''' |
|---|
| 629 | makes a backup of the specified .gpx file |
|---|
| 630 | |
|---|
| 631 | :param str GPXfile: full .gpx file name |
|---|
| 632 | :param bool makeBack: if True (default), the backup is written to |
|---|
| 633 | a new file; if False, the last backup is overwritten |
|---|
| 634 | :returns: the name of the backup file that was written |
|---|
| 635 | ''' |
|---|
| 636 | import distutils.file_util as dfu |
|---|
| 637 | GPXback = getBackupName(GPXfile,makeBack) |
|---|
| 638 | tries = 0 |
|---|
| 639 | while True: |
|---|
| 640 | try: |
|---|
| 641 | dfu.copy_file(GPXfile,GPXback) |
|---|
| 642 | break |
|---|
| 643 | except: |
|---|
| 644 | tries += 1 |
|---|
| 645 | if tries > 10: |
|---|
| 646 | return GPXfile #failed! |
|---|
| 647 | time.sleep(1) #just wait a second! |
|---|
| 648 | return GPXback |
|---|
| 649 | |
|---|
| 650 | def SetUsedHistogramsAndPhases(GPXfile,Histograms,Phases,RigidBodies,CovData,parmFrozenList,makeBack=True): |
|---|
| 651 | ''' Updates gpxfile from all histograms that are found in any phase |
|---|
| 652 | and any phase that used a histogram. Also updates rigid body definitions. |
|---|
| 653 | This is used for non-sequential fits, but not for sequential fitting. |
|---|
| 654 | |
|---|
| 655 | :param str GPXfile: full .gpx file name |
|---|
| 656 | :param dict Histograms: dictionary of histograms as {name:data,...} |
|---|
| 657 | :param dict Phases: dictionary of phases that use histograms |
|---|
| 658 | :param dict RigidBodies: dictionary of rigid bodies |
|---|
| 659 | :param dict CovData: dictionary of refined variables, varyList, & covariance matrix |
|---|
| 660 | :param list parmFrozenList: list of parameters (as str) that are frozen |
|---|
| 661 | due to limits; converted to :class:`GSASIIobj.G2VarObj` objects. |
|---|
| 662 | :param bool makeBack: True if new backup of .gpx file is to be made; else |
|---|
| 663 | use the last one made |
|---|
| 664 | ''' |
|---|
| 665 | |
|---|
| 666 | import distutils.file_util as dfu |
|---|
| 667 | GPXback = GPXBackup(GPXfile,makeBack) |
|---|
| 668 | G2fil.G2Print ('Read from file:'+GPXback) |
|---|
| 669 | G2fil.G2Print ('Save to file :'+GPXfile) |
|---|
| 670 | infile = open(GPXback,'rb') |
|---|
| 671 | outfile = open(GPXfile,'wb') |
|---|
| 672 | while True: |
|---|
| 673 | try: |
|---|
| 674 | data = cPickleLoad(infile) |
|---|
| 675 | except EOFError: |
|---|
| 676 | break |
|---|
| 677 | datum = data[0] |
|---|
| 678 | # print 'read: ',datum[0] |
|---|
| 679 | if datum[0] == 'Phases': |
|---|
| 680 | for iphase in range(len(data)): |
|---|
| 681 | if data[iphase][0] in Phases: |
|---|
| 682 | phaseName = data[iphase][0] |
|---|
| 683 | data[iphase][1].update(Phases[phaseName]) |
|---|
| 684 | elif datum[0] == 'Covariance': |
|---|
| 685 | data[0][1] = CovData |
|---|
| 686 | elif datum[0] == 'Rigid bodies': |
|---|
| 687 | data[0][1] = RigidBodies |
|---|
| 688 | elif datum[0] == 'Controls': |
|---|
| 689 | Controls = data[0][1] |
|---|
| 690 | if 'parmFrozen' not in Controls: |
|---|
| 691 | Controls['parmFrozen'] = {} |
|---|
| 692 | Controls['parmFrozen']['FrozenList'] = [ |
|---|
| 693 | i if type(i) is G2obj.G2VarObj |
|---|
| 694 | else G2obj.G2VarObj(i) |
|---|
| 695 | for i in parmFrozenList] |
|---|
| 696 | try: |
|---|
| 697 | histogram = Histograms[datum[0]] |
|---|
| 698 | # print 'found ',datum[0] |
|---|
| 699 | data[0][1][1] = histogram['Data'] |
|---|
| 700 | data[0][1][0].update(histogram['Residuals']) |
|---|
| 701 | for datus in data[1:]: |
|---|
| 702 | # print ' read: ',datus[0] |
|---|
| 703 | if datus[0] in ['Instrument Parameters','Sample Parameters','Reflection Lists']: |
|---|
| 704 | datus[1] = histogram[datus[0]] |
|---|
| 705 | if datus[0] == 'Background': # remove fixed background from file |
|---|
| 706 | d1 = {key:histogram['Background'][1][key] |
|---|
| 707 | for key in histogram['Background'][1] |
|---|
| 708 | if not key.startswith('_fixed')} |
|---|
| 709 | datus[1] = copy.deepcopy(histogram['Background']) |
|---|
| 710 | datus[1][1] = d1 |
|---|
| 711 | except KeyError: |
|---|
| 712 | pass |
|---|
| 713 | try: |
|---|
| 714 | cPickle.dump(data,outfile,1) |
|---|
| 715 | except AttributeError: |
|---|
| 716 | G2fil.G2Print ('ERROR - bad data in least squares result') |
|---|
| 717 | infile.close() |
|---|
| 718 | outfile.close() |
|---|
| 719 | dfu.copy_file(GPXback,GPXfile) |
|---|
| 720 | G2fil.G2Print ('GPX file save failed - old version retained',mode='error') |
|---|
| 721 | return |
|---|
| 722 | |
|---|
| 723 | infile.close() |
|---|
| 724 | outfile.close() |
|---|
| 725 | |
|---|
| 726 | G2fil.G2Print ('GPX file save successful') |
|---|
| 727 | |
|---|
| 728 | def GetSeqResult(GPXfile): |
|---|
| 729 | ''' |
|---|
| 730 | Returns the sequential results table information from a GPX file. |
|---|
| 731 | Called at the beginning of :meth:`GSASIIstrMain.SeqRefine` |
|---|
| 732 | |
|---|
| 733 | :param str GPXfile: full .gpx file name |
|---|
| 734 | :returns: a dict containing the sequential results table |
|---|
| 735 | ''' |
|---|
| 736 | IndexGPX(GPXfile) |
|---|
| 737 | pos = gpxIndex.get('Sequential results') |
|---|
| 738 | if pos is None: |
|---|
| 739 | return {} |
|---|
| 740 | fl = open(GPXfile,'rb') |
|---|
| 741 | fl.seek(pos) |
|---|
| 742 | datum = cPickleLoad(fl)[0] |
|---|
| 743 | fl.close() |
|---|
| 744 | return datum[1] |
|---|
| 745 | |
|---|
| 746 | def SetupSeqSavePhases(GPXfile): |
|---|
| 747 | '''Initialize the files used to save intermediate results from |
|---|
| 748 | sequential fits. |
|---|
| 749 | ''' |
|---|
| 750 | IndexGPX(GPXfile) |
|---|
| 751 | # load initial Phase results from GPX |
|---|
| 752 | fl = open(GPXfile,'rb') |
|---|
| 753 | pos = gpxIndex.get('Phases') |
|---|
| 754 | if pos is None: |
|---|
| 755 | raise Exception("No Phases in GPX file") |
|---|
| 756 | fl.seek(pos) |
|---|
| 757 | data = cPickleLoad(fl) |
|---|
| 758 | fl.close() |
|---|
| 759 | # create GPX-like file to store latest Phase info; init with start vals |
|---|
| 760 | GPXphase = os.path.splitext(GPXfile)[0]+'.seqPhase' |
|---|
| 761 | fp = open(GPXphase,'wb') |
|---|
| 762 | cPickle.dump(data,fp,1) |
|---|
| 763 | fp.close() |
|---|
| 764 | # create empty file for histogram info |
|---|
| 765 | GPXhist = os.path.splitext(GPXfile)[0]+'.seqHist' |
|---|
| 766 | fp = open(GPXhist,'wb') |
|---|
| 767 | fp.close() |
|---|
| 768 | |
|---|
| 769 | def SaveUpdatedHistogramsAndPhases(GPXfile,Histograms,Phases,RigidBodies,CovData,parmFrozen): |
|---|
| 770 | ''' |
|---|
| 771 | Save phase and histogram information into "pseudo-gpx" files. The phase |
|---|
| 772 | information is overwritten each time this is called, but histogram information is |
|---|
| 773 | appended after each sequential step. |
|---|
| 774 | |
|---|
| 775 | :param str GPXfile: full .gpx file name |
|---|
| 776 | :param dict Histograms: dictionary of histograms as {name:data,...} |
|---|
| 777 | :param dict Phases: dictionary of phases that use histograms |
|---|
| 778 | :param dict RigidBodies: dictionary of rigid bodies |
|---|
| 779 | :param dict CovData: dictionary of refined variables, varyList, & covariance matrix |
|---|
| 780 | :param dict parmFrozen: dict with frozen parameters for all phases |
|---|
| 781 | and histograms (specified as str values) |
|---|
| 782 | ''' |
|---|
| 783 | |
|---|
| 784 | import distutils.file_util as dfu |
|---|
| 785 | |
|---|
| 786 | GPXphase = os.path.splitext(GPXfile)[0]+'.seqPhase' |
|---|
| 787 | fp = open(GPXphase,'rb') |
|---|
| 788 | data = cPickleLoad(fp) # first block in file should be Phases |
|---|
| 789 | if data[0][0] != 'Phases': |
|---|
| 790 | raise Exception('Unexpected block in {} file. How did this happen?' |
|---|
| 791 | .format(GPXphase)) |
|---|
| 792 | fp.close() |
|---|
| 793 | # update previous phase info |
|---|
| 794 | for datum in data[1:]: |
|---|
| 795 | if datum[0] in Phases: |
|---|
| 796 | datum[1].update(Phases[datum[0]]) |
|---|
| 797 | # save latest Phase/refinement info |
|---|
| 798 | fp = open(GPXphase,'wb') |
|---|
| 799 | cPickle.dump(data,fp,1) |
|---|
| 800 | cPickle.dump([['Covariance',CovData]],fp,1) |
|---|
| 801 | cPickle.dump([['Rigid bodies',RigidBodies]],fp,1) |
|---|
| 802 | cPickle.dump([['parmFrozen',parmFrozen]],fp,1) |
|---|
| 803 | fp.close() |
|---|
| 804 | # create an entry that looks like a PWDR tree item |
|---|
| 805 | for key in Histograms: |
|---|
| 806 | if key.startswith('PWDR '): |
|---|
| 807 | break |
|---|
| 808 | else: |
|---|
| 809 | raise Exception('No PWDR entry in Histogram dict!') |
|---|
| 810 | histname = key |
|---|
| 811 | hist = copy.deepcopy(Histograms[key]) |
|---|
| 812 | xfer_dict = {'Index Peak List': [[], []], |
|---|
| 813 | 'Comments': [], |
|---|
| 814 | 'Unit Cells List': [], |
|---|
| 815 | 'Peak List': {'peaks': [], 'sigDict': {}}, |
|---|
| 816 | } |
|---|
| 817 | histData = hist['Data'] |
|---|
| 818 | del hist['Data'] |
|---|
| 819 | for key in ('Limits','Background','Instrument Parameters', |
|---|
| 820 | 'Sample Parameters','Reflection Lists'): |
|---|
| 821 | xfer_dict[key] = hist[key] |
|---|
| 822 | if key == 'Background': # remove fixed background from file |
|---|
| 823 | xfer_dict['Background'][1] = {k:hist['Background'][1][k] |
|---|
| 824 | for k in hist['Background'][1] |
|---|
| 825 | if not k.startswith('_fixed')} |
|---|
| 826 | del hist[key] |
|---|
| 827 | # xform into a gpx-type entry |
|---|
| 828 | data = [] |
|---|
| 829 | data.append([histname,[hist,histData,histname]]) |
|---|
| 830 | for key in ['Comments','Limits','Background','Instrument Parameters', |
|---|
| 831 | 'Sample Parameters','Peak List','Index Peak List', |
|---|
| 832 | 'Unit Cells List','Reflection Lists']: |
|---|
| 833 | data.append([key,xfer_dict[key]]) |
|---|
| 834 | # append histogram to histogram info |
|---|
| 835 | GPXhist = os.path.splitext(GPXfile)[0]+'.seqHist' |
|---|
| 836 | fp = open(GPXhist,'ab') |
|---|
| 837 | cPickle.dump(data,fp,1) |
|---|
| 838 | fp.close() |
|---|
| 839 | return |
|---|
| 840 | |
|---|
| 841 | def SetSeqResult(GPXfile,Histograms,SeqResult): |
|---|
| 842 | ''' |
|---|
| 843 | Places the sequential results information into a GPX file |
|---|
| 844 | after a refinement has been completed. |
|---|
| 845 | Called at the end of :meth:`GSASIIstrMain.SeqRefine` |
|---|
| 846 | |
|---|
| 847 | :param str GPXfile: full .gpx file name |
|---|
| 848 | ''' |
|---|
| 849 | GPXback = GPXBackup(GPXfile) |
|---|
| 850 | G2fil.G2Print ('Read from file:'+GPXback) |
|---|
| 851 | G2fil.G2Print ('Save to file :'+GPXfile) |
|---|
| 852 | GPXphase = os.path.splitext(GPXfile)[0]+'.seqPhase' |
|---|
| 853 | fp = open(GPXphase,'rb') |
|---|
| 854 | data = cPickleLoad(fp) # first block in file should be Phases |
|---|
| 855 | if data[0][0] != 'Phases': |
|---|
| 856 | raise Exception('Unexpected block in {} file. How did this happen?'.format(GPXphase)) |
|---|
| 857 | Phases = {} |
|---|
| 858 | for name,vals in data[1:]: |
|---|
| 859 | Phases[name] = vals |
|---|
| 860 | name,CovData = cPickleLoad(fp)[0] # 2nd block in file should be Covariance |
|---|
| 861 | name,RigidBodies = cPickleLoad(fp)[0] # 3rd block in file should be Rigid Bodies |
|---|
| 862 | name,parmFrozenDict = cPickleLoad(fp)[0] # 4th block in file should be frozen parameters |
|---|
| 863 | fp.close() |
|---|
| 864 | GPXhist = os.path.splitext(GPXfile)[0]+'.seqHist' |
|---|
| 865 | hist = open(GPXhist,'rb') |
|---|
| 866 | # build an index to the GPXhist file |
|---|
| 867 | histIndex = {} |
|---|
| 868 | while True: |
|---|
| 869 | loc = hist.tell() |
|---|
| 870 | try: |
|---|
| 871 | datum = cPickleLoad(hist)[0] |
|---|
| 872 | except EOFError: |
|---|
| 873 | break |
|---|
| 874 | histIndex[datum[0]] = loc |
|---|
| 875 | |
|---|
| 876 | infile = open(GPXback,'rb') |
|---|
| 877 | outfile = open(GPXfile,'wb') |
|---|
| 878 | while True: |
|---|
| 879 | try: |
|---|
| 880 | data = cPickleLoad(infile) |
|---|
| 881 | except EOFError: |
|---|
| 882 | break |
|---|
| 883 | datum = data[0] |
|---|
| 884 | if datum[0] == 'Sequential results': |
|---|
| 885 | data[0][1] = SeqResult |
|---|
| 886 | elif datum[0] == 'Phases': |
|---|
| 887 | for pdata in data[1:]: |
|---|
| 888 | if pdata[0] in Phases: |
|---|
| 889 | pdata[1].update(Phases[pdata[0]]) |
|---|
| 890 | elif datum[0] == 'Covariance': |
|---|
| 891 | data[0][1] = CovData |
|---|
| 892 | elif datum[0] == 'Rigid bodies': |
|---|
| 893 | data[0][1] = RigidBodies |
|---|
| 894 | elif datum[0] == 'Controls': # reset the Copy Next flag after a sequential fit |
|---|
| 895 | Controls = data[0][1] |
|---|
| 896 | Controls['Copy2Next'] = False |
|---|
| 897 | for key in parmFrozenDict: |
|---|
| 898 | Controls['parmFrozen'][key] = [ |
|---|
| 899 | i if type(i) is G2obj.G2VarObj |
|---|
| 900 | else G2obj.G2VarObj(i) |
|---|
| 901 | for i in parmFrozenDict[key]] |
|---|
| 902 | elif datum[0] in histIndex: |
|---|
| 903 | hist.seek(histIndex[datum[0]]) |
|---|
| 904 | hdata = cPickleLoad(hist) |
|---|
| 905 | if data[0][0] != hdata[0][0]: |
|---|
| 906 | G2fil.G2Print('Error! Updating {} with {}'.format(data[0][0],hdata[0][0])) |
|---|
| 907 | data[0] = hdata[0] |
|---|
| 908 | xferItems = ['Background','Instrument Parameters','Sample Parameters','Reflection Lists'] |
|---|
| 909 | hItems = {name:j+1 for j,(name,val) in enumerate(hdata[1:]) if name in xferItems} |
|---|
| 910 | for j,(name,val) in enumerate(data[1:]): |
|---|
| 911 | if name not in xferItems: continue |
|---|
| 912 | data[j+1][1] = hdata[hItems[name]][1] |
|---|
| 913 | cPickle.dump(data,outfile,1) |
|---|
| 914 | hist.close() |
|---|
| 915 | infile.close() |
|---|
| 916 | outfile.close() |
|---|
| 917 | # clean up tmp files |
|---|
| 918 | try: |
|---|
| 919 | os.remove(GPXphase) |
|---|
| 920 | except: |
|---|
| 921 | G2fil.G2Print('Warning: unable to delete {}'.format(GPXphase)) |
|---|
| 922 | try: |
|---|
| 923 | os.remove(GPXhist) |
|---|
| 924 | except: |
|---|
| 925 | G2fil.G2Print('Warning: unable to delete {}'.format(GPXhist)) |
|---|
| 926 | G2fil.G2Print ('GPX file merge completed') |
|---|
| 927 | |
|---|
| 928 | #============================================================================== |
|---|
| 929 | # Refinement routines |
|---|
| 930 | #============================================================================== |
|---|
| 931 | def ShowBanner(pFile=None): |
|---|
| 932 | 'Print authorship, copyright and citation notice' |
|---|
| 933 | pFile.write(80*'*'+'\n') |
|---|
| 934 | pFile.write(' General Structure Analysis System-II Crystal Structure Refinement\n') |
|---|
| 935 | pFile.write(' by Robert B. Von Dreele & Brian H. Toby\n') |
|---|
| 936 | pFile.write(' Argonne National Laboratory(C), 2010\n') |
|---|
| 937 | pFile.write(' This product includes software developed by the UChicago Argonne, LLC,\n') |
|---|
| 938 | pFile.write(' as Operator of Argonne National Laboratory.\n') |
|---|
| 939 | pFile.write(' Please cite:\n') |
|---|
| 940 | pFile.write(' B.H. Toby & R.B. Von Dreele, J. Appl. Cryst. 46, 544-549 (2013)\n') |
|---|
| 941 | |
|---|
| 942 | pFile.write(80*'*'+'\n') |
|---|
| 943 | |
|---|
| 944 | def ShowControls(Controls,pFile=None,SeqRef=False,preFrozenCount=0): |
|---|
| 945 | 'Print controls information' |
|---|
| 946 | pFile.write(' Least squares controls:\n') |
|---|
| 947 | pFile.write(' Refinement type: %s\n'%Controls['deriv type']) |
|---|
| 948 | if 'Hessian' in Controls['deriv type']: |
|---|
| 949 | pFile.write(' Maximum number of cycles: %d\n'%Controls['max cyc']) |
|---|
| 950 | else: |
|---|
| 951 | pFile.write(' Minimum delta-M/M for convergence: %.2g\n'%(Controls['min dM/M'])) |
|---|
| 952 | pFile.write(' Regularize hydrogens (if any): %s\n'%Controls.get('HatomFix',False)) |
|---|
| 953 | pFile.write(' Initial shift factor: %.3f\n'%(Controls['shift factor'])) |
|---|
| 954 | if SeqRef: |
|---|
| 955 | pFile.write(' Sequential refinement controls:\n') |
|---|
| 956 | pFile.write(' Copy of histogram results to next: %s\n'%(Controls['Copy2Next'])) |
|---|
| 957 | pFile.write(' Process histograms in reverse order: %s\n'%(Controls['Reverse Seq'])) |
|---|
| 958 | if preFrozenCount: |
|---|
| 959 | pFile.write('\n Starting refinement with {} Frozen variables\n\n'.format(preFrozenCount)) |
|---|
| 960 | |
|---|
| 961 | def GetPawleyConstr(SGLaue,PawleyRef,im,pawleyVary): |
|---|
| 962 | 'needs a doc string' |
|---|
| 963 | # if SGLaue in ['-1','2/m','mmm']: |
|---|
| 964 | # return #no Pawley symmetry required constraints |
|---|
| 965 | eqvDict = {} |
|---|
| 966 | for i,varyI in enumerate(pawleyVary): |
|---|
| 967 | eqvDict[varyI] = [] |
|---|
| 968 | refI = int(varyI.split(':')[-1]) |
|---|
| 969 | ih,ik,il = PawleyRef[refI][:3] |
|---|
| 970 | dspI = PawleyRef[refI][4+im] |
|---|
| 971 | for varyJ in pawleyVary[i+1:]: |
|---|
| 972 | refJ = int(varyJ.split(':')[-1]) |
|---|
| 973 | jh,jk,jl = PawleyRef[refJ][:3] |
|---|
| 974 | dspJ = PawleyRef[refJ][4+im] |
|---|
| 975 | if SGLaue in ['4/m','4/mmm']: |
|---|
| 976 | isum = ih**2+ik**2 |
|---|
| 977 | jsum = jh**2+jk**2 |
|---|
| 978 | if abs(il) == abs(jl) and isum == jsum: |
|---|
| 979 | eqvDict[varyI].append(varyJ) |
|---|
| 980 | elif SGLaue in ['3R','3mR']: |
|---|
| 981 | isum = ih**2+ik**2+il**2 |
|---|
| 982 | jsum = jh**2+jk**2+jl**2 |
|---|
| 983 | isum2 = ih*ik+ih*il+ik*il |
|---|
| 984 | jsum2 = jh*jk+jh*jl+jk*jl |
|---|
| 985 | if isum == jsum and isum2 == jsum2: |
|---|
| 986 | eqvDict[varyI].append(varyJ) |
|---|
| 987 | elif SGLaue in ['3','3m1','31m','6/m','6/mmm']: |
|---|
| 988 | isum = ih**2+ik**2+ih*ik |
|---|
| 989 | jsum = jh**2+jk**2+jh*jk |
|---|
| 990 | if abs(il) == abs(jl) and isum == jsum: |
|---|
| 991 | eqvDict[varyI].append(varyJ) |
|---|
| 992 | elif SGLaue in ['m3','m3m']: |
|---|
| 993 | isum = ih**2+ik**2+il**2 |
|---|
| 994 | jsum = jh**2+jk**2+jl**2 |
|---|
| 995 | if isum == jsum: |
|---|
| 996 | eqvDict[varyI].append(varyJ) |
|---|
| 997 | elif abs(dspI-dspJ)/dspI < 1.e-4: |
|---|
| 998 | eqvDict[varyI].append(varyJ) |
|---|
| 999 | for item in pawleyVary: |
|---|
| 1000 | if eqvDict[item]: |
|---|
| 1001 | for item2 in pawleyVary: |
|---|
| 1002 | if item2 in eqvDict[item]: |
|---|
| 1003 | eqvDict[item2] = [] |
|---|
| 1004 | G2mv.StoreEquivalence(item,eqvDict[item]) |
|---|
| 1005 | |
|---|
| 1006 | def cellVary(pfx,SGData): |
|---|
| 1007 | '''Creates equivalences for a phase based on the Laue class. |
|---|
| 1008 | Returns a list of A tensor terms that are non-zero. |
|---|
| 1009 | ''' |
|---|
| 1010 | if SGData['SGLaue'] in ['-1',]: |
|---|
| 1011 | return [pfx+'A0',pfx+'A1',pfx+'A2',pfx+'A3',pfx+'A4',pfx+'A5'] |
|---|
| 1012 | elif SGData['SGLaue'] in ['2/m',]: |
|---|
| 1013 | if SGData['SGUniq'] == 'a': |
|---|
| 1014 | return [pfx+'A0',pfx+'A1',pfx+'A2',pfx+'A5'] |
|---|
| 1015 | elif SGData['SGUniq'] == 'b': |
|---|
| 1016 | return [pfx+'A0',pfx+'A1',pfx+'A2',pfx+'A4'] |
|---|
| 1017 | else: |
|---|
| 1018 | return [pfx+'A0',pfx+'A1',pfx+'A2',pfx+'A3'] |
|---|
| 1019 | elif SGData['SGLaue'] in ['mmm',]: |
|---|
| 1020 | return [pfx+'A0',pfx+'A1',pfx+'A2'] |
|---|
| 1021 | elif SGData['SGLaue'] in ['4/m','4/mmm']: |
|---|
| 1022 | G2mv.StoreEquivalence(pfx+'A0',(pfx+'A1',)) |
|---|
| 1023 | return [pfx+'A0',pfx+'A1',pfx+'A2'] |
|---|
| 1024 | elif SGData['SGLaue'] in ['6/m','6/mmm','3m1', '31m', '3']: |
|---|
| 1025 | G2mv.StoreEquivalence(pfx+'A0',(pfx+'A1',pfx+'A3',)) |
|---|
| 1026 | return [pfx+'A0',pfx+'A1',pfx+'A2',pfx+'A3'] |
|---|
| 1027 | elif SGData['SGLaue'] in ['3R', '3mR']: |
|---|
| 1028 | G2mv.StoreEquivalence(pfx+'A0',(pfx+'A1',pfx+'A2',)) |
|---|
| 1029 | G2mv.StoreEquivalence(pfx+'A3',(pfx+'A4',pfx+'A5',)) |
|---|
| 1030 | return [pfx+'A0',pfx+'A1',pfx+'A2',pfx+'A3',pfx+'A4',pfx+'A5'] |
|---|
| 1031 | elif SGData['SGLaue'] in ['m3m','m3']: |
|---|
| 1032 | G2mv.StoreEquivalence(pfx+'A0',(pfx+'A1',pfx+'A2',)) |
|---|
| 1033 | return [pfx+'A0',pfx+'A1',pfx+'A2'] |
|---|
| 1034 | |
|---|
| 1035 | def modVary(pfx,SSGData): |
|---|
| 1036 | vary = [] |
|---|
| 1037 | for i,item in enumerate(SSGData['modSymb']): |
|---|
| 1038 | if item in ['a','b','g']: |
|---|
| 1039 | vary.append(pfx+'mV%d'%(i)) |
|---|
| 1040 | return vary |
|---|
| 1041 | |
|---|
| 1042 | ################################################################################ |
|---|
| 1043 | ##### Rigid Body Models and not General.get('doPawley') |
|---|
| 1044 | ################################################################################ |
|---|
| 1045 | |
|---|
| 1046 | def GetRigidBodyModels(rigidbodyDict,Print=True,pFile=None): |
|---|
| 1047 | 'Get Rigid body info from tree entry and print it to .LST file' |
|---|
| 1048 | |
|---|
| 1049 | def PrintResRBModel(RBModel): |
|---|
| 1050 | pFile.write('Residue RB name: %s no.atoms: %d, No. times used: %d\n'% |
|---|
| 1051 | (RBModel['RBname'],len(RBModel['rbTypes']),RBModel['useCount'])) |
|---|
| 1052 | for i in WriteResRBModel(RBModel): |
|---|
| 1053 | pFile.write(i) |
|---|
| 1054 | |
|---|
| 1055 | def PrintVecRBModel(RBModel): |
|---|
| 1056 | pFile.write('Vector RB name: %s no.atoms: %d No. times used: %d\n'% |
|---|
| 1057 | (RBModel['RBname'],len(RBModel['rbTypes']),RBModel['useCount'])) |
|---|
| 1058 | for i in WriteVecRBModel(RBModel): |
|---|
| 1059 | pFile.write(i) |
|---|
| 1060 | pFile.write('Orientation defined by: atom %s -> atom %s & atom %s -> atom %s\n'% |
|---|
| 1061 | (RBModel['rbRef'][0],RBModel['rbRef'][1],RBModel['rbRef'][0],RBModel['rbRef'][2])) |
|---|
| 1062 | |
|---|
| 1063 | rbVary = [] |
|---|
| 1064 | rbDict = {} |
|---|
| 1065 | rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]}) |
|---|
| 1066 | if len(rbIds['Vector']): |
|---|
| 1067 | for irb,item in enumerate(rbIds['Vector']): |
|---|
| 1068 | if rigidbodyDict['Vector'][item]['useCount']: |
|---|
| 1069 | RBmags = rigidbodyDict['Vector'][item]['VectMag'] |
|---|
| 1070 | RBrefs = rigidbodyDict['Vector'][item]['VectRef'] |
|---|
| 1071 | for i,[mag,ref] in enumerate(zip(RBmags,RBrefs)): |
|---|
| 1072 | pid = '::RBV;'+str(i)+':'+str(irb) |
|---|
| 1073 | rbDict[pid] = mag |
|---|
| 1074 | if ref: |
|---|
| 1075 | rbVary.append(pid) |
|---|
| 1076 | if Print: |
|---|
| 1077 | pFile.write('\nVector rigid body model:\n') |
|---|
| 1078 | PrintVecRBModel(rigidbodyDict['Vector'][item]) |
|---|
| 1079 | if len(rbIds['Residue']): |
|---|
| 1080 | for item in rbIds['Residue']: |
|---|
| 1081 | if rigidbodyDict['Residue'][item]['useCount']: |
|---|
| 1082 | if Print: |
|---|
| 1083 | pFile.write('\nResidue rigid body model:\n') |
|---|
| 1084 | PrintResRBModel(rigidbodyDict['Residue'][item]) |
|---|
| 1085 | return rbVary,rbDict |
|---|
| 1086 | |
|---|
| 1087 | def SetRigidBodyModels(parmDict,sigDict,rigidbodyDict,pFile=None): |
|---|
| 1088 | 'needs a doc string' |
|---|
| 1089 | |
|---|
| 1090 | def PrintRBVectandSig(VectRB,VectSig): |
|---|
| 1091 | pFile.write('\n Rigid body vector magnitudes for %s:\n'%VectRB['RBname']) |
|---|
| 1092 | namstr = ' names :' |
|---|
| 1093 | valstr = ' values:' |
|---|
| 1094 | sigstr = ' esds :' |
|---|
| 1095 | for i,[val,sig] in enumerate(zip(VectRB['VectMag'],VectSig)): |
|---|
| 1096 | namstr += '%12s'%('Vect '+str(i)) |
|---|
| 1097 | valstr += '%12.4f'%(val) |
|---|
| 1098 | if sig: |
|---|
| 1099 | sigstr += '%12.4f'%(sig) |
|---|
| 1100 | else: |
|---|
| 1101 | sigstr += 12*' ' |
|---|
| 1102 | pFile.write(namstr+'\n') |
|---|
| 1103 | pFile.write(valstr+'\n') |
|---|
| 1104 | pFile.write(sigstr+'\n') |
|---|
| 1105 | |
|---|
| 1106 | RBIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]}) #these are lists of rbIds |
|---|
| 1107 | if not RBIds['Vector']: |
|---|
| 1108 | return |
|---|
| 1109 | for irb,item in enumerate(RBIds['Vector']): |
|---|
| 1110 | if rigidbodyDict['Vector'][item]['useCount']: |
|---|
| 1111 | VectSig = [] |
|---|
| 1112 | RBmags = rigidbodyDict['Vector'][item]['VectMag'] |
|---|
| 1113 | for i,mag in enumerate(RBmags): |
|---|
| 1114 | name = '::RBV;'+str(i)+':'+str(irb) |
|---|
| 1115 | if name in sigDict: |
|---|
| 1116 | VectSig.append(sigDict[name]) |
|---|
| 1117 | PrintRBVectandSig(rigidbodyDict['Vector'][item],VectSig) |
|---|
| 1118 | |
|---|
| 1119 | ################################################################################ |
|---|
| 1120 | ##### Phase data |
|---|
| 1121 | ################################################################################ |
|---|
| 1122 | def GetPhaseData(PhaseData,RestraintDict={},rbIds={},Print=True,pFile=None,seqRef=False): |
|---|
| 1123 | '''Setup the phase information for a structural refinement, used for |
|---|
| 1124 | regular and sequential refinements, optionally printing information |
|---|
| 1125 | to the .lst file (if Print is True) |
|---|
| 1126 | ''' |
|---|
| 1127 | |
|---|
| 1128 | def PrintFFtable(FFtable): |
|---|
| 1129 | pFile.write('\n X-ray scattering factors:\n') |
|---|
| 1130 | pFile.write(' Symbol fa fb fc\n') |
|---|
| 1131 | pFile.write(99*'-'+'\n') |
|---|
| 1132 | for Ename in FFtable: |
|---|
| 1133 | ffdata = FFtable[Ename] |
|---|
| 1134 | fa = ffdata['fa'] |
|---|
| 1135 | fb = ffdata['fb'] |
|---|
| 1136 | pFile.write(' %8s %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f\n'% |
|---|
| 1137 | (Ename.ljust(8),fa[0],fa[1],fa[2],fa[3],fb[0],fb[1],fb[2],fb[3],ffdata['fc'])) |
|---|
| 1138 | |
|---|
| 1139 | def PrintMFtable(MFtable): |
|---|
| 1140 | pFile.write('\n <j0> Magnetic scattering factors:\n') |
|---|
| 1141 | pFile.write(' Symbol mfa mfb mfc\n') |
|---|
| 1142 | pFile.write(99*'-'+'\n') |
|---|
| 1143 | for Ename in MFtable: |
|---|
| 1144 | mfdata = MFtable[Ename] |
|---|
| 1145 | fa = mfdata['mfa'] |
|---|
| 1146 | fb = mfdata['mfb'] |
|---|
| 1147 | pFile.write(' %8s %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f\n'% |
|---|
| 1148 | (Ename.ljust(8),fa[0],fa[1],fa[2],fa[3],fb[0],fb[1],fb[2],fb[3],mfdata['mfc'])) |
|---|
| 1149 | pFile.write('\n <j2> Magnetic scattering factors:\n') |
|---|
| 1150 | pFile.write(' Symbol nfa nfb nfc\n') |
|---|
| 1151 | pFile.write(99*'-'+'\n') |
|---|
| 1152 | for Ename in MFtable: |
|---|
| 1153 | mfdata = MFtable[Ename] |
|---|
| 1154 | fa = mfdata['nfa'] |
|---|
| 1155 | fb = mfdata['nfb'] |
|---|
| 1156 | pFile.write(' %8s %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f\n'% |
|---|
| 1157 | (Ename.ljust(8),fa[0],fa[1],fa[2],fa[3],fb[0],fb[1],fb[2],fb[3],mfdata['nfc'])) |
|---|
| 1158 | |
|---|
| 1159 | def PrintBLtable(BLtable): |
|---|
| 1160 | pFile.write('\n Neutron scattering factors:\n') |
|---|
| 1161 | pFile.write(' Symbol isotope mass b resonant terms\n') |
|---|
| 1162 | pFile.write(99*'-'+'\n') |
|---|
| 1163 | for Ename in BLtable: |
|---|
| 1164 | bldata = BLtable[Ename] |
|---|
| 1165 | isotope = bldata[0] |
|---|
| 1166 | mass = bldata[1]['Mass'] |
|---|
| 1167 | if 'BW-LS' in bldata[1]: |
|---|
| 1168 | bres = bldata[1]['BW-LS'] |
|---|
| 1169 | blen = 0 |
|---|
| 1170 | else: |
|---|
| 1171 | blen = bldata[1]['SL'][0] |
|---|
| 1172 | bres = [] |
|---|
| 1173 | line = ' %8s%11s %10.3f %8.3f'%(Ename.ljust(8),isotope.center(11),mass,blen) |
|---|
| 1174 | for item in bres: |
|---|
| 1175 | line += '%10.5g'%(item) |
|---|
| 1176 | pFile.write(line+'\n') |
|---|
| 1177 | |
|---|
| 1178 | def PrintRBObjects(resRBData,vecRBData): |
|---|
| 1179 | |
|---|
| 1180 | def PrintRBThermals(): |
|---|
| 1181 | tlstr = ['11','22','33','12','13','23'] |
|---|
| 1182 | sstr = ['12','13','21','23','31','32','AA','BB'] |
|---|
| 1183 | TLS = RB['ThermalMotion'][1] |
|---|
| 1184 | TLSvar = RB['ThermalMotion'][2] |
|---|
| 1185 | if 'T' in RB['ThermalMotion'][0]: |
|---|
| 1186 | pFile.write('TLS data\n') |
|---|
| 1187 | text = '' |
|---|
| 1188 | for i in range(6): |
|---|
| 1189 | text += 'T'+tlstr[i]+' %8.4f %s '%(TLS[i],str(TLSvar[i])[0]) |
|---|
| 1190 | pFile.write(text+'\n') |
|---|
| 1191 | if 'L' in RB['ThermalMotion'][0]: |
|---|
| 1192 | text = '' |
|---|
| 1193 | for i in range(6,12): |
|---|
| 1194 | text += 'L'+tlstr[i-6]+' %8.2f %s '%(TLS[i],str(TLSvar[i])[0]) |
|---|
| 1195 | pFile.write(text+'\n') |
|---|
| 1196 | if 'S' in RB['ThermalMotion'][0]: |
|---|
| 1197 | text = '' |
|---|
| 1198 | for i in range(12,20): |
|---|
| 1199 | text += 'S'+sstr[i-12]+' %8.3f %s '%(TLS[i],str(TLSvar[i])[0]) |
|---|
| 1200 | pFile.write(text+'\n') |
|---|
| 1201 | if 'U' in RB['ThermalMotion'][0]: |
|---|
| 1202 | pFile.write('Uiso data\n') |
|---|
| 1203 | text = 'Uiso'+' %10.3f %s'%(TLS[0],str(TLSvar[0])[0]) |
|---|
| 1204 | pFile.write(text+'\n') |
|---|
| 1205 | |
|---|
| 1206 | if len(resRBData): |
|---|
| 1207 | for RB in resRBData: |
|---|
| 1208 | Oxyz = RB['Orig'][0] |
|---|
| 1209 | Qrijk = RB['Orient'][0] |
|---|
| 1210 | Angle = 2.0*acosd(Qrijk[0]) |
|---|
| 1211 | pFile.write('\nRBObject %s at %10.4f %10.4f %10.4f Refine? %s\n'% |
|---|
| 1212 | (RB['RBname'],Oxyz[0],Oxyz[1],Oxyz[2],RB['Orig'][1])) |
|---|
| 1213 | pFile.write('Orientation angle,vector: %10.3f %10.4f %10.4f %10.4f Refine? %s\n'% |
|---|
| 1214 | (Angle,Qrijk[1],Qrijk[2],Qrijk[3],RB['Orient'][1])) |
|---|
| 1215 | Torsions = RB['Torsions'] |
|---|
| 1216 | if len(Torsions): |
|---|
| 1217 | text = 'Torsions: ' |
|---|
| 1218 | for torsion in Torsions: |
|---|
| 1219 | text += '%10.4f Refine? %s'%(torsion[0],torsion[1]) |
|---|
| 1220 | pFile.write(text+'\n') |
|---|
| 1221 | PrintRBThermals() |
|---|
| 1222 | if len(vecRBData): |
|---|
| 1223 | for RB in vecRBData: |
|---|
| 1224 | Oxyz = RB['Orig'][0] |
|---|
| 1225 | Qrijk = RB['Orient'][0] |
|---|
| 1226 | Angle = 2.0*acosd(Qrijk[0]) |
|---|
| 1227 | pFile.write('\nRBObject %s at %10.4f %10.4f %10.4f Refine? %s\n'% |
|---|
| 1228 | (RB['RBname'],Oxyz[0],Oxyz[1],Oxyz[2],RB['Orig'][1])) |
|---|
| 1229 | pFile.write('Orientation angle,vector: %10.3f %10.4f %10.4f %10.4f Refine? %s\n'% |
|---|
| 1230 | (Angle,Qrijk[1],Qrijk[2],Qrijk[3],RB['Orient'][1])) |
|---|
| 1231 | PrintRBThermals() |
|---|
| 1232 | |
|---|
| 1233 | def PrintAtoms(General,Atoms): |
|---|
| 1234 | cx,ct,cs,cia = General['AtomPtrs'] |
|---|
| 1235 | pFile.write('\n Atoms:\n') |
|---|
| 1236 | line = ' name type refine? x y z '+ \ |
|---|
| 1237 | ' frac site sym mult I/A Uiso U11 U22 U33 U12 U13 U23' |
|---|
| 1238 | if General['Type'] == 'macromolecular': |
|---|
| 1239 | line = ' res no residue chain'+line |
|---|
| 1240 | pFile.write(line+'\n') |
|---|
| 1241 | if General['Type'] in ['nuclear','magnetic','faulted',]: |
|---|
| 1242 | pFile.write(135*'-'+'\n') |
|---|
| 1243 | for i,at in enumerate(Atoms): |
|---|
| 1244 | line = '%7s'%(at[ct-1])+'%7s'%(at[ct])+'%7s'%(at[ct+1])+'%10.5f'%(at[cx])+'%10.5f'%(at[cx+1])+ \ |
|---|
| 1245 | '%10.5f'%(at[cx+2])+'%8.3f'%(at[cx+3])+'%7s'%(at[cs])+'%5d'%(at[cs+1])+'%5s'%(at[cia]) |
|---|
| 1246 | if at[cia] == 'I': |
|---|
| 1247 | line += '%8.5f'%(at[cia+1])+48*' ' |
|---|
| 1248 | else: |
|---|
| 1249 | line += 8*' ' |
|---|
| 1250 | for j in range(6): |
|---|
| 1251 | line += '%8.5f'%(at[cia+2+j]) |
|---|
| 1252 | pFile.write(line+'\n') |
|---|
| 1253 | elif General['Type'] == 'macromolecular': |
|---|
| 1254 | pFile.write(135*'-'+'\n') |
|---|
| 1255 | for i,at in enumerate(Atoms): |
|---|
| 1256 | 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])+ \ |
|---|
| 1257 | '%10.5f'%(at[cx+2])+'%8.3f'%(at[cx+3])+'%7s'%(at[cs])+'%5d'%(at[cs+1])+'%5s'%(at[cia]) |
|---|
| 1258 | if at[cia] == 'I': |
|---|
| 1259 | line += '%8.4f'%(at[cia+1])+48*' ' |
|---|
| 1260 | else: |
|---|
| 1261 | line += 8*' ' |
|---|
| 1262 | for j in range(6): |
|---|
| 1263 | line += '%8.4f'%(at[cia+2+j]) |
|---|
| 1264 | pFile.write(line+'\n') |
|---|
| 1265 | |
|---|
| 1266 | def PrintMoments(General,Atoms): |
|---|
| 1267 | cx,ct,cs,cia = General['AtomPtrs'] |
|---|
| 1268 | cmx = cx+4 |
|---|
| 1269 | AtInfo = dict(zip(General['AtomTypes'],General['Lande g'])) |
|---|
| 1270 | pFile.write('\n Magnetic moments:\n') |
|---|
| 1271 | line = ' name type refine? Mx My Mz ' |
|---|
| 1272 | pFile.write(line+'\n') |
|---|
| 1273 | pFile.write(135*'-'+'\n') |
|---|
| 1274 | for i,at in enumerate(Atoms): |
|---|
| 1275 | if AtInfo[at[ct]]: |
|---|
| 1276 | line = '%7s'%(at[ct-1])+'%7s'%(at[ct])+'%7s'%(at[ct+1])+'%10.5f'%(at[cmx])+'%10.5f'%(at[cmx+1])+ \ |
|---|
| 1277 | '%10.5f'%(at[cmx+2]) |
|---|
| 1278 | pFile.write(line+'\n') |
|---|
| 1279 | |
|---|
| 1280 | |
|---|
| 1281 | def PrintWaves(General,Atoms): |
|---|
| 1282 | cx,ct,cs,cia = General['AtomPtrs'] |
|---|
| 1283 | pFile.write('\n Modulation waves\n') |
|---|
| 1284 | names = {'Sfrac':['Fsin','Fcos','Fzero','Fwid'],'Spos':['Xsin','Ysin','Zsin','Xcos','Ycos','Zcos','Tmin','Tmax','Xmax','Ymax','Zmax'], |
|---|
| 1285 | 'Sadp':['U11sin','U22sin','U33sin','U12sin','U13sin','U23sin','U11cos','U22cos', |
|---|
| 1286 | 'U33cos','U12cos','U13cos','U23cos'],'Smag':['MXsin','MYsin','MZsin','MXcos','MYcos','MZcos']} |
|---|
| 1287 | pFile.write(135*'-'+'\n') |
|---|
| 1288 | for i,at in enumerate(Atoms): |
|---|
| 1289 | AtomSS = at[-1]['SS1'] |
|---|
| 1290 | for Stype in ['Sfrac','Spos','Sadp','Smag']: |
|---|
| 1291 | Waves = AtomSS[Stype] |
|---|
| 1292 | if len(Waves): |
|---|
| 1293 | pFile.write(' atom: %s, site sym: %s, type: %s wave type: %s:\n'% |
|---|
| 1294 | (at[ct-1],at[cs],Stype,Waves[0])) |
|---|
| 1295 | else: |
|---|
| 1296 | continue |
|---|
| 1297 | for iw,wave in enumerate(Waves[1:]): |
|---|
| 1298 | line = '' |
|---|
| 1299 | if Waves[0] in ['Block','ZigZag'] and Stype == 'Spos' and not iw: |
|---|
| 1300 | for item in names[Stype][6:]: |
|---|
| 1301 | line += '%8s '%(item) |
|---|
| 1302 | else: |
|---|
| 1303 | if Stype == 'Spos': |
|---|
| 1304 | for item in names[Stype][:6]: |
|---|
| 1305 | line += '%8s '%(item) |
|---|
| 1306 | else: |
|---|
| 1307 | for item in names[Stype]: |
|---|
| 1308 | line += '%8s '%(item) |
|---|
| 1309 | pFile.write(line+'\n') |
|---|
| 1310 | line = '' |
|---|
| 1311 | for item in wave[0]: |
|---|
| 1312 | line += '%8.4f '%(item) |
|---|
| 1313 | line += ' Refine? '+str(wave[1]) |
|---|
| 1314 | pFile.write(line+'\n') |
|---|
| 1315 | |
|---|
| 1316 | def PrintTexture(textureData): |
|---|
| 1317 | topstr = '\n Spherical harmonics texture: Order:' + \ |
|---|
| 1318 | str(textureData['Order']) |
|---|
| 1319 | if textureData['Order']: |
|---|
| 1320 | pFile.write('%s Refine? %s\n'%(topstr,textureData['SH Coeff'][0])) |
|---|
| 1321 | else: |
|---|
| 1322 | pFile.write(topstr+'\n') |
|---|
| 1323 | return |
|---|
| 1324 | names = ['omega','chi','phi'] |
|---|
| 1325 | line = '\n' |
|---|
| 1326 | for name in names: |
|---|
| 1327 | line += ' SH '+name+':'+'%12.4f'%(textureData['Sample '+name][1])+' Refine? '+str(textureData['Sample '+name][0]) |
|---|
| 1328 | pFile.write(line+'\n') |
|---|
| 1329 | pFile.write('\n Texture coefficients:\n') |
|---|
| 1330 | SHcoeff = textureData['SH Coeff'][1] |
|---|
| 1331 | SHkeys = list(SHcoeff.keys()) |
|---|
| 1332 | nCoeff = len(SHcoeff) |
|---|
| 1333 | nBlock = nCoeff//10+1 |
|---|
| 1334 | iBeg = 0 |
|---|
| 1335 | iFin = min(iBeg+10,nCoeff) |
|---|
| 1336 | for block in range(nBlock): |
|---|
| 1337 | ptlbls = ' names :' |
|---|
| 1338 | ptstr = ' values:' |
|---|
| 1339 | for item in SHkeys[iBeg:iFin]: |
|---|
| 1340 | ptlbls += '%12s'%(item) |
|---|
| 1341 | ptstr += '%12.4f'%(SHcoeff[item]) |
|---|
| 1342 | pFile.write(ptlbls+'\n') |
|---|
| 1343 | pFile.write(ptstr+'\n') |
|---|
| 1344 | iBeg += 10 |
|---|
| 1345 | iFin = min(iBeg+10,nCoeff) |
|---|
| 1346 | |
|---|
| 1347 | def MakeRBParms(rbKey,phaseVary,phaseDict): |
|---|
| 1348 | rbid = str(rbids.index(RB['RBId'])) |
|---|
| 1349 | pfxRB = pfx+'RB'+rbKey+'P' |
|---|
| 1350 | pstr = ['x','y','z'] |
|---|
| 1351 | ostr = ['a','i','j','k'] |
|---|
| 1352 | for i in range(3): |
|---|
| 1353 | name = pfxRB+pstr[i]+':'+str(iRB)+':'+rbid |
|---|
| 1354 | phaseDict[name] = RB['Orig'][0][i] |
|---|
| 1355 | if RB['Orig'][1]: |
|---|
| 1356 | phaseVary += [name,] |
|---|
| 1357 | pfxRB = pfx+'RB'+rbKey+'O' |
|---|
| 1358 | for i in range(4): |
|---|
| 1359 | name = pfxRB+ostr[i]+':'+str(iRB)+':'+rbid |
|---|
| 1360 | phaseDict[name] = RB['Orient'][0][i] |
|---|
| 1361 | if RB['Orient'][1] == 'AV' and i: |
|---|
| 1362 | phaseVary += [name,] |
|---|
| 1363 | elif RB['Orient'][1] == 'A' and not i: |
|---|
| 1364 | phaseVary += [name,] |
|---|
| 1365 | |
|---|
| 1366 | def MakeRBThermals(rbKey,phaseVary,phaseDict): |
|---|
| 1367 | rbid = str(rbids.index(RB['RBId'])) |
|---|
| 1368 | tlstr = ['11','22','33','12','13','23'] |
|---|
| 1369 | sstr = ['12','13','21','23','31','32','AA','BB'] |
|---|
| 1370 | if 'T' in RB['ThermalMotion'][0]: |
|---|
| 1371 | pfxRB = pfx+'RB'+rbKey+'T' |
|---|
| 1372 | for i in range(6): |
|---|
| 1373 | name = pfxRB+tlstr[i]+':'+str(iRB)+':'+rbid |
|---|
| 1374 | phaseDict[name] = RB['ThermalMotion'][1][i] |
|---|
| 1375 | if RB['ThermalMotion'][2][i]: |
|---|
| 1376 | phaseVary += [name,] |
|---|
| 1377 | if 'L' in RB['ThermalMotion'][0]: |
|---|
| 1378 | pfxRB = pfx+'RB'+rbKey+'L' |
|---|
| 1379 | for i in range(6): |
|---|
| 1380 | name = pfxRB+tlstr[i]+':'+str(iRB)+':'+rbid |
|---|
| 1381 | phaseDict[name] = RB['ThermalMotion'][1][i+6] |
|---|
| 1382 | if RB['ThermalMotion'][2][i+6]: |
|---|
| 1383 | phaseVary += [name,] |
|---|
| 1384 | if 'S' in RB['ThermalMotion'][0]: |
|---|
| 1385 | pfxRB = pfx+'RB'+rbKey+'S' |
|---|
| 1386 | for i in range(8): |
|---|
| 1387 | name = pfxRB+sstr[i]+':'+str(iRB)+':'+rbid |
|---|
| 1388 | phaseDict[name] = RB['ThermalMotion'][1][i+12] |
|---|
| 1389 | if RB['ThermalMotion'][2][i+12]: |
|---|
| 1390 | phaseVary += [name,] |
|---|
| 1391 | if 'U' in RB['ThermalMotion'][0]: |
|---|
| 1392 | name = pfx+'RB'+rbKey+'U:'+str(iRB)+':'+rbid |
|---|
| 1393 | phaseDict[name] = RB['ThermalMotion'][1][0] |
|---|
| 1394 | if RB['ThermalMotion'][2][0]: |
|---|
| 1395 | phaseVary += [name,] |
|---|
| 1396 | |
|---|
| 1397 | def MakeRBTorsions(rbKey,phaseVary,phaseDict): |
|---|
| 1398 | rbid = str(rbids.index(RB['RBId'])) |
|---|
| 1399 | pfxRB = pfx+'RB'+rbKey+'Tr;' |
|---|
| 1400 | for i,torsion in enumerate(RB['Torsions']): |
|---|
| 1401 | name = pfxRB+str(i)+':'+str(iRB)+':'+rbid |
|---|
| 1402 | phaseDict[name] = torsion[0] |
|---|
| 1403 | if torsion[1]: |
|---|
| 1404 | phaseVary += [name,] |
|---|
| 1405 | |
|---|
| 1406 | if Print: |
|---|
| 1407 | pFile.write('\n Phases:\n') |
|---|
| 1408 | phaseVary = [] |
|---|
| 1409 | phaseDict = {} |
|---|
| 1410 | pawleyLookup = {} |
|---|
| 1411 | FFtables = {} #scattering factors - xrays |
|---|
| 1412 | MFtables = {} #Mag. form factors |
|---|
| 1413 | BLtables = {} # neutrons |
|---|
| 1414 | Natoms = {} |
|---|
| 1415 | maxSSwave = {} |
|---|
| 1416 | shModels = ['cylindrical','none','shear - 2/m','rolling - mmm'] |
|---|
| 1417 | SamSym = dict(zip(shModels,['0','-1','2/m','mmm'])) |
|---|
| 1418 | atomIndx = {} |
|---|
| 1419 | for name in PhaseData: |
|---|
| 1420 | General = PhaseData[name]['General'] |
|---|
| 1421 | pId = PhaseData[name]['pId'] |
|---|
| 1422 | pfx = str(pId)+'::' |
|---|
| 1423 | FFtable = G2el.GetFFtable(General['AtomTypes']) |
|---|
| 1424 | BLtable = G2el.GetBLtable(General) |
|---|
| 1425 | FFtables.update(FFtable) |
|---|
| 1426 | BLtables.update(BLtable) |
|---|
| 1427 | phaseDict[pfx+'isMag'] = False |
|---|
| 1428 | SGData = General['SGData'] |
|---|
| 1429 | SGtext,SGtable = G2spc.SGPrint(SGData) |
|---|
| 1430 | if General['Type'] == 'magnetic': |
|---|
| 1431 | MFtable = G2el.GetMFtable(General['AtomTypes'],General['Lande g']) |
|---|
| 1432 | MFtables.update(MFtable) |
|---|
| 1433 | phaseDict[pfx+'isMag'] = True |
|---|
| 1434 | SpnFlp = SGData['SpnFlp'] |
|---|
| 1435 | Atoms = PhaseData[name]['Atoms'] |
|---|
| 1436 | if Atoms and not General.get('doPawley'): |
|---|
| 1437 | cx,ct,cs,cia = General['AtomPtrs'] |
|---|
| 1438 | AtLookup = G2mth.FillAtomLookUp(Atoms,cia+8) |
|---|
| 1439 | PawleyRef = PhaseData[name].get('Pawley ref',[]) |
|---|
| 1440 | cell = General['Cell'] |
|---|
| 1441 | A = G2lat.cell2A(cell[1:7]) |
|---|
| 1442 | phaseDict.update({pfx+'A0':A[0],pfx+'A1':A[1],pfx+'A2':A[2], |
|---|
| 1443 | pfx+'A3':A[3],pfx+'A4':A[4],pfx+'A5':A[5],pfx+'Vol':G2lat.calc_V(A)}) |
|---|
| 1444 | if cell[0]: |
|---|
| 1445 | phaseVary += cellVary(pfx,SGData) #also fills in symmetry required constraints |
|---|
| 1446 | SSGtext = [] #no superstructure |
|---|
| 1447 | im = 0 |
|---|
| 1448 | if General.get('Modulated',False): |
|---|
| 1449 | im = 1 #refl offset |
|---|
| 1450 | Vec,vRef,maxH = General['SuperVec'] |
|---|
| 1451 | phaseDict.update({pfx+'mV0':Vec[0],pfx+'mV1':Vec[1],pfx+'mV2':Vec[2]}) |
|---|
| 1452 | SSGData = General['SSGData'] |
|---|
| 1453 | SSGtext,SSGtable = G2spc.SSGPrint(SGData,SSGData) |
|---|
| 1454 | if vRef: |
|---|
| 1455 | phaseVary += modVary(pfx,SSGData) |
|---|
| 1456 | resRBData = PhaseData[name]['RBModels'].get('Residue',[]) |
|---|
| 1457 | if resRBData: |
|---|
| 1458 | rbids = rbIds['Residue'] #NB: used in the MakeRB routines |
|---|
| 1459 | for iRB,RB in enumerate(resRBData): |
|---|
| 1460 | MakeRBParms('R',phaseVary,phaseDict) |
|---|
| 1461 | MakeRBThermals('R',phaseVary,phaseDict) |
|---|
| 1462 | MakeRBTorsions('R',phaseVary,phaseDict) |
|---|
| 1463 | |
|---|
| 1464 | vecRBData = PhaseData[name]['RBModels'].get('Vector',[]) |
|---|
| 1465 | if vecRBData: |
|---|
| 1466 | rbids = rbIds['Vector'] #NB: used in the MakeRB routines |
|---|
| 1467 | for iRB,RB in enumerate(vecRBData): |
|---|
| 1468 | MakeRBParms('V',phaseVary,phaseDict) |
|---|
| 1469 | MakeRBThermals('V',phaseVary,phaseDict) |
|---|
| 1470 | |
|---|
| 1471 | Natoms[pfx] = 0 |
|---|
| 1472 | maxSSwave[pfx] = {'Sfrac':0,'Spos':0,'Sadp':0,'Smag':0} |
|---|
| 1473 | if Atoms and not General.get('doPawley'): |
|---|
| 1474 | cx,ct,cs,cia = General['AtomPtrs'] |
|---|
| 1475 | Natoms[pfx] = len(Atoms) |
|---|
| 1476 | for i,at in enumerate(Atoms): |
|---|
| 1477 | atomIndx[at[cia+8]] = [pfx,i] #lookup table for restraints |
|---|
| 1478 | phaseDict.update({pfx+'Atype:'+str(i):at[ct],pfx+'Afrac:'+str(i):at[cx+3],pfx+'Amul:'+str(i):at[cs+1], |
|---|
| 1479 | pfx+'Ax:'+str(i):at[cx],pfx+'Ay:'+str(i):at[cx+1],pfx+'Az:'+str(i):at[cx+2], |
|---|
| 1480 | pfx+'dAx:'+str(i):0.,pfx+'dAy:'+str(i):0.,pfx+'dAz:'+str(i):0., #refined shifts for x,y,z |
|---|
| 1481 | pfx+'AI/A:'+str(i):at[cia],}) |
|---|
| 1482 | if at[cia] == 'I': |
|---|
| 1483 | phaseDict[pfx+'AUiso:'+str(i)] = at[cia+1] |
|---|
| 1484 | else: |
|---|
| 1485 | phaseDict.update({pfx+'AU11:'+str(i):at[cia+2],pfx+'AU22:'+str(i):at[cia+3],pfx+'AU33:'+str(i):at[cia+4], |
|---|
| 1486 | pfx+'AU12:'+str(i):at[cia+5],pfx+'AU13:'+str(i):at[cia+6],pfx+'AU23:'+str(i):at[cia+7]}) |
|---|
| 1487 | if General['Type'] == 'magnetic': |
|---|
| 1488 | phaseDict.update({pfx+'AMx:'+str(i):at[cx+4],pfx+'AMy:'+str(i):at[cx+5],pfx+'AMz:'+str(i):at[cx+6]}) |
|---|
| 1489 | if 'F' in at[ct+1]: |
|---|
| 1490 | phaseVary.append(pfx+'Afrac:'+str(i)) |
|---|
| 1491 | if 'X' in at[ct+1]: |
|---|
| 1492 | try: #patch for sytsym name changes |
|---|
| 1493 | xId,xCoef = G2spc.GetCSxinel(at[cs]) |
|---|
| 1494 | except KeyError: |
|---|
| 1495 | Sytsym = G2spc.SytSym(at[cx:cx+3],SGData)[0] |
|---|
| 1496 | at[cs] = Sytsym |
|---|
| 1497 | xId,xCoef = G2spc.GetCSxinel(at[cs]) |
|---|
| 1498 | names = [pfx+'dAx:'+str(i),pfx+'dAy:'+str(i),pfx+'dAz:'+str(i)] |
|---|
| 1499 | equivs = [[],[],[]] |
|---|
| 1500 | for j in range(3): |
|---|
| 1501 | if xId[j] > 0: |
|---|
| 1502 | phaseVary.append(names[j]) |
|---|
| 1503 | equivs[xId[j]-1].append([names[j],xCoef[j]]) |
|---|
| 1504 | for equiv in equivs: |
|---|
| 1505 | if len(equiv) > 1: |
|---|
| 1506 | name = equiv[0][0] |
|---|
| 1507 | coef = equiv[0][1] |
|---|
| 1508 | for eqv in equiv[1:]: |
|---|
| 1509 | eqv[1] /= coef |
|---|
| 1510 | G2mv.StoreEquivalence(name,(eqv,)) |
|---|
| 1511 | if 'U' in at[ct+1]: |
|---|
| 1512 | if at[cia] == 'I': |
|---|
| 1513 | phaseVary.append(pfx+'AUiso:'+str(i)) |
|---|
| 1514 | else: |
|---|
| 1515 | try: #patch for sytsym name changes |
|---|
| 1516 | uId,uCoef = G2spc.GetCSuinel(at[cs])[:2] |
|---|
| 1517 | except KeyError: |
|---|
| 1518 | Sytsym = G2spc.SytSym(at[cx:cx+3],SGData)[0] |
|---|
| 1519 | at[cs] = Sytsym |
|---|
| 1520 | uId,uCoef = G2spc.GetCSuinel(at[cs])[:2] |
|---|
| 1521 | names = [pfx+'AU11:'+str(i),pfx+'AU22:'+str(i),pfx+'AU33:'+str(i), |
|---|
| 1522 | pfx+'AU12:'+str(i),pfx+'AU13:'+str(i),pfx+'AU23:'+str(i)] |
|---|
| 1523 | equivs = [[],[],[],[],[],[]] |
|---|
| 1524 | for j in range(6): |
|---|
| 1525 | if uId[j] > 0: |
|---|
| 1526 | phaseVary.append(names[j]) |
|---|
| 1527 | equivs[uId[j]-1].append([names[j],uCoef[j]]) |
|---|
| 1528 | for equiv in equivs: |
|---|
| 1529 | if len(equiv) > 1: |
|---|
| 1530 | name = equiv[0][0] |
|---|
| 1531 | coef = equiv[0][1] |
|---|
| 1532 | for eqv in equiv[1:]: |
|---|
| 1533 | eqv[1] /= coef |
|---|
| 1534 | G2mv.StoreEquivalence(name,(eqv,)) |
|---|
| 1535 | if 'M' in at[ct+1]: |
|---|
| 1536 | SytSym,Mul,Nop,dupDir = G2spc.SytSym(at[cx:cx+3],SGData) |
|---|
| 1537 | mId,mCoef = G2spc.GetCSpqinel(SpnFlp,dupDir) |
|---|
| 1538 | names = [pfx+'AMx:'+str(i),pfx+'AMy:'+str(i),pfx+'AMz:'+str(i)] |
|---|
| 1539 | equivs = [[],[],[]] |
|---|
| 1540 | for j in range(3): |
|---|
| 1541 | if mId[j] > 0: |
|---|
| 1542 | phaseVary.append(names[j]) |
|---|
| 1543 | equivs[mId[j]-1].append([names[j],mCoef[j]]) |
|---|
| 1544 | for equiv in equivs: |
|---|
| 1545 | if len(equiv) > 1: |
|---|
| 1546 | name = equiv[0][0] |
|---|
| 1547 | coef = equiv[0][1] |
|---|
| 1548 | for eqv in equiv[1:]: |
|---|
| 1549 | eqv[1] /= coef |
|---|
| 1550 | G2mv.StoreEquivalence(name,(eqv,)) |
|---|
| 1551 | if General.get('Modulated',False): |
|---|
| 1552 | AtomSS = at[-1]['SS1'] |
|---|
| 1553 | for Stype in ['Sfrac','Spos','Sadp','Smag']: |
|---|
| 1554 | Waves = AtomSS[Stype] |
|---|
| 1555 | if len(Waves): |
|---|
| 1556 | waveType = Waves[0] |
|---|
| 1557 | else: |
|---|
| 1558 | continue |
|---|
| 1559 | phaseDict[pfx+Stype[1].upper()+'waveType:'+str(i)] = waveType |
|---|
| 1560 | nx = 0 |
|---|
| 1561 | for iw,wave in enumerate(Waves[1:]): |
|---|
| 1562 | if not iw: |
|---|
| 1563 | if waveType in ['ZigZag','Block']: |
|---|
| 1564 | nx = 1 |
|---|
| 1565 | CSI = G2spc.GetSSfxuinel(waveType,Stype,1,at[cx:cx+3],SGData,SSGData) |
|---|
| 1566 | else: |
|---|
| 1567 | CSI = G2spc.GetSSfxuinel('Fourier',Stype,iw+1-nx,at[cx:cx+3],SGData,SSGData) |
|---|
| 1568 | uId,uCoef = CSI[0] |
|---|
| 1569 | stiw = str(i)+':'+str(iw) |
|---|
| 1570 | if Stype == 'Spos': |
|---|
| 1571 | if waveType in ['ZigZag','Block',] and not iw: |
|---|
| 1572 | names = [pfx+'Tmin:'+stiw,pfx+'Tmax:'+stiw,pfx+'Xmax:'+stiw,pfx+'Ymax:'+stiw,pfx+'Zmax:'+stiw] |
|---|
| 1573 | equivs = [[],[], [],[],[]] |
|---|
| 1574 | else: |
|---|
| 1575 | names = [pfx+'Xsin:'+stiw,pfx+'Ysin:'+stiw,pfx+'Zsin:'+stiw, |
|---|
| 1576 | pfx+'Xcos:'+stiw,pfx+'Ycos:'+stiw,pfx+'Zcos:'+stiw] |
|---|
| 1577 | equivs = [[],[],[], [],[],[]] |
|---|
| 1578 | elif Stype == 'Sadp': |
|---|
| 1579 | names = [pfx+'U11sin:'+stiw,pfx+'U22sin:'+stiw,pfx+'U33sin:'+stiw, |
|---|
| 1580 | pfx+'U12sin:'+stiw,pfx+'U13sin:'+stiw,pfx+'U23sin:'+stiw, |
|---|
| 1581 | pfx+'U11cos:'+stiw,pfx+'U22cos:'+stiw,pfx+'U33cos:'+stiw, |
|---|
| 1582 | pfx+'U12cos:'+stiw,pfx+'U13cos:'+stiw,pfx+'U23cos:'+stiw] |
|---|
| 1583 | equivs = [[],[],[],[],[],[], [],[],[],[],[],[]] |
|---|
| 1584 | elif Stype == 'Sfrac': |
|---|
| 1585 | equivs = [[],[]] |
|---|
| 1586 | if 'Crenel' in waveType and not iw: |
|---|
| 1587 | names = [pfx+'Fzero:'+stiw,pfx+'Fwid:'+stiw] |
|---|
| 1588 | else: |
|---|
| 1589 | names = [pfx+'Fsin:'+stiw,pfx+'Fcos:'+stiw] |
|---|
| 1590 | elif Stype == 'Smag': |
|---|
| 1591 | equivs = [[],[],[], [],[],[]] |
|---|
| 1592 | names = [pfx+'MXsin:'+stiw,pfx+'MYsin:'+stiw,pfx+'MZsin:'+stiw, |
|---|
| 1593 | pfx+'MXcos:'+stiw,pfx+'MYcos:'+stiw,pfx+'MZcos:'+stiw] |
|---|
| 1594 | phaseDict.update(dict(zip(names,wave[0]))) |
|---|
| 1595 | if wave[1]: #what do we do here for multiple terms in modulation constraints? |
|---|
| 1596 | for j in range(len(equivs)): |
|---|
| 1597 | if uId[j][0] > 0: |
|---|
| 1598 | phaseVary.append(names[j]) |
|---|
| 1599 | equivs[uId[j][0]-1].append([names[j],uCoef[j][0]]) |
|---|
| 1600 | for equiv in equivs: |
|---|
| 1601 | if len(equiv) > 1: |
|---|
| 1602 | name = equiv[0][0] |
|---|
| 1603 | coef = equiv[0][1] |
|---|
| 1604 | for eqv in equiv[1:]: |
|---|
| 1605 | eqv[1] /= coef |
|---|
| 1606 | G2mv.StoreEquivalence(name,(eqv,)) |
|---|
| 1607 | maxSSwave[pfx][Stype] = max(maxSSwave[pfx][Stype],iw+1) |
|---|
| 1608 | textureData = General['SH Texture'] |
|---|
| 1609 | if textureData['Order'] and not seqRef: |
|---|
| 1610 | phaseDict[pfx+'SHorder'] = textureData['Order'] |
|---|
| 1611 | phaseDict[pfx+'SHmodel'] = SamSym[textureData['Model']] |
|---|
| 1612 | for item in ['omega','chi','phi']: |
|---|
| 1613 | phaseDict[pfx+'SH '+item] = textureData['Sample '+item][1] |
|---|
| 1614 | if textureData['Sample '+item][0]: |
|---|
| 1615 | phaseVary.append(pfx+'SH '+item) |
|---|
| 1616 | for item in textureData['SH Coeff'][1]: |
|---|
| 1617 | phaseDict[pfx+item] = textureData['SH Coeff'][1][item] |
|---|
| 1618 | if textureData['SH Coeff'][0]: |
|---|
| 1619 | phaseVary.append(pfx+item) |
|---|
| 1620 | |
|---|
| 1621 | if Print: |
|---|
| 1622 | pFile.write('\n Phase name: %s\n'%General['Name']) |
|---|
| 1623 | pFile.write(135*'='+'\n') |
|---|
| 1624 | PrintFFtable(FFtable) |
|---|
| 1625 | PrintBLtable(BLtable) |
|---|
| 1626 | if General['Type'] == 'magnetic': |
|---|
| 1627 | PrintMFtable(MFtable) |
|---|
| 1628 | pFile.write('\n') |
|---|
| 1629 | #how do we print magnetic symmetry table? TBD |
|---|
| 1630 | if len(SSGtext): #if superstructure |
|---|
| 1631 | for line in SSGtext: pFile.write(line+'\n') |
|---|
| 1632 | if len(SSGtable): |
|---|
| 1633 | for item in SSGtable: |
|---|
| 1634 | line = ' %s '%(item) |
|---|
| 1635 | pFile.write(line+'\n') |
|---|
| 1636 | else: |
|---|
| 1637 | pFile.write(' ( 1) %s\n'%(SSGtable[0])) |
|---|
| 1638 | else: |
|---|
| 1639 | for line in SGtext: pFile.write(line+'\n') |
|---|
| 1640 | if len(SGtable): |
|---|
| 1641 | for item in SGtable: |
|---|
| 1642 | line = ' %s '%(item) |
|---|
| 1643 | pFile.write(line+'\n') |
|---|
| 1644 | else: |
|---|
| 1645 | pFile.write(' ( 1) %s\n'%(SGtable[0])) |
|---|
| 1646 | PrintRBObjects(resRBData,vecRBData) |
|---|
| 1647 | PrintAtoms(General,Atoms) |
|---|
| 1648 | if General['Type'] == 'magnetic': |
|---|
| 1649 | PrintMoments(General,Atoms) |
|---|
| 1650 | if General.get('Modulated',False): |
|---|
| 1651 | PrintWaves(General,Atoms) |
|---|
| 1652 | pFile.write('\n Unit cell: a = %.5f b = %.5f c = %.5f alpha = %.3f beta = %.3f gamma = %.3f volume = %.3f Refine? %s\n'% |
|---|
| 1653 | (cell[1],cell[2],cell[3],cell[4],cell[5],cell[6],cell[7],cell[0])) |
|---|
| 1654 | if len(SSGtext): #if superstructure |
|---|
| 1655 | pFile.write('\n Modulation vector: mV0 = %.4f mV1 = %.4f mV2 = %.4f max mod. index = %d Refine? %s\n'% |
|---|
| 1656 | (Vec[0],Vec[1],Vec[2],maxH,vRef)) |
|---|
| 1657 | if not seqRef: |
|---|
| 1658 | PrintTexture(textureData) |
|---|
| 1659 | if name in RestraintDict: |
|---|
| 1660 | PrintRestraints(cell[1:7],SGData,General['AtomPtrs'],Atoms,AtLookup, |
|---|
| 1661 | textureData,RestraintDict[name],pFile) |
|---|
| 1662 | |
|---|
| 1663 | elif PawleyRef: |
|---|
| 1664 | if Print: |
|---|
| 1665 | pFile.write('\n Phase name: %s\n'%General['Name']) |
|---|
| 1666 | pFile.write(135*'='+'\n') |
|---|
| 1667 | pFile.write('\n') |
|---|
| 1668 | if len(SSGtext): #if superstructure |
|---|
| 1669 | for line in SSGtext: pFile.write(line+'\n') |
|---|
| 1670 | if len(SSGtable): |
|---|
| 1671 | for item in SSGtable: |
|---|
| 1672 | line = ' %s '%(item) |
|---|
| 1673 | pFile.write(line+'\n') |
|---|
| 1674 | else: |
|---|
| 1675 | pFile.write(' ( 1) %s\n'%SSGtable[0]) |
|---|
| 1676 | else: |
|---|
| 1677 | for line in SGtext: pFile.write(line+'\n') |
|---|
| 1678 | if len(SGtable): |
|---|
| 1679 | for item in SGtable: |
|---|
| 1680 | line = ' %s '%(item) |
|---|
| 1681 | pFile.write(line+'\n') |
|---|
| 1682 | else: |
|---|
| 1683 | pFile.write(' ( 1) %s\n'%(SGtable[0])) |
|---|
| 1684 | pFile.write('\n Unit cell: a = %.5f b = %.5f c = %.5f alpha = %.3f beta = %.3f gamma = %.3f volume = %.3f Refine? %s\n'% |
|---|
| 1685 | (cell[1],cell[2],cell[3],cell[4],cell[5],cell[6],cell[7],cell[0])) |
|---|
| 1686 | if len(SSGtext): #if superstructure |
|---|
| 1687 | pFile.write('\n Modulation vector: mV0 = %.4f mV1 = %.4f mV2 = %.4f max mod. index = %d Refine? %s\n'% |
|---|
| 1688 | (Vec[0],Vec[1],Vec[2],maxH,vRef)) |
|---|
| 1689 | pawleyVary = [] |
|---|
| 1690 | for i,refl in enumerate(PawleyRef): |
|---|
| 1691 | phaseDict[pfx+'PWLref:'+str(i)] = refl[6+im] |
|---|
| 1692 | if im: |
|---|
| 1693 | pawleyLookup[pfx+'%d,%d,%d,%d'%(refl[0],refl[1],refl[2],refl[3])] = i |
|---|
| 1694 | else: |
|---|
| 1695 | pawleyLookup[pfx+'%d,%d,%d'%(refl[0],refl[1],refl[2])] = i |
|---|
| 1696 | if refl[5+im]: |
|---|
| 1697 | pawleyVary.append(pfx+'PWLref:'+str(i)) |
|---|
| 1698 | GetPawleyConstr(SGData['SGLaue'],PawleyRef,im,pawleyVary) #does G2mv.StoreEquivalence |
|---|
| 1699 | phaseVary += pawleyVary |
|---|
| 1700 | |
|---|
| 1701 | return Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables,MFtables,maxSSwave |
|---|
| 1702 | |
|---|
| 1703 | def cellFill(pfx,SGData,parmDict,sigDict): |
|---|
| 1704 | '''Returns the filled-out reciprocal cell (A) terms and their uncertainties |
|---|
| 1705 | from the parameter and sig dictionaries. |
|---|
| 1706 | |
|---|
| 1707 | :param str pfx: parameter prefix ("n::", where n is a phase number) |
|---|
| 1708 | :param dict SGdata: a symmetry object |
|---|
| 1709 | :param dict parmDict: a dictionary of parameters |
|---|
| 1710 | :param dict sigDict: a dictionary of uncertainties on parameters |
|---|
| 1711 | |
|---|
| 1712 | :returns: A,sigA where each is a list of six terms with the A terms |
|---|
| 1713 | ''' |
|---|
| 1714 | if SGData['SGLaue'] in ['-1',]: |
|---|
| 1715 | A = [parmDict[pfx+'A0'],parmDict[pfx+'A1'],parmDict[pfx+'A2'], |
|---|
| 1716 | parmDict[pfx+'A3'],parmDict[pfx+'A4'],parmDict[pfx+'A5']] |
|---|
| 1717 | elif SGData['SGLaue'] in ['2/m',]: |
|---|
| 1718 | if SGData['SGUniq'] == 'a': |
|---|
| 1719 | A = [parmDict[pfx+'A0'],parmDict[pfx+'A1'],parmDict[pfx+'A2'], |
|---|
| 1720 | 0,0,parmDict[pfx+'A5']] |
|---|
| 1721 | elif SGData['SGUniq'] == 'b': |
|---|
| 1722 | A = [parmDict[pfx+'A0'],parmDict[pfx+'A1'],parmDict[pfx+'A2'], |
|---|
| 1723 | 0,parmDict[pfx+'A4'],0] |
|---|
| 1724 | else: |
|---|
| 1725 | A = [parmDict[pfx+'A0'],parmDict[pfx+'A1'],parmDict[pfx+'A2'], |
|---|
| 1726 | parmDict[pfx+'A3'],0,0] |
|---|
| 1727 | elif SGData['SGLaue'] in ['mmm',]: |
|---|
| 1728 | A = [parmDict[pfx+'A0'],parmDict[pfx+'A1'],parmDict[pfx+'A2'],0,0,0] |
|---|
| 1729 | elif SGData['SGLaue'] in ['4/m','4/mmm']: |
|---|
| 1730 | A = [parmDict[pfx+'A0'],parmDict[pfx+'A0'],parmDict[pfx+'A2'],0,0,0] |
|---|
| 1731 | elif SGData['SGLaue'] in ['6/m','6/mmm','3m1', '31m', '3']: |
|---|
| 1732 | A = [parmDict[pfx+'A0'],parmDict[pfx+'A0'],parmDict[pfx+'A2'], |
|---|
| 1733 | parmDict[pfx+'A0'],0,0] |
|---|
| 1734 | elif SGData['SGLaue'] in ['3R', '3mR']: |
|---|
| 1735 | A = [parmDict[pfx+'A0'],parmDict[pfx+'A0'],parmDict[pfx+'A0'], |
|---|
| 1736 | parmDict[pfx+'A3'],parmDict[pfx+'A3'],parmDict[pfx+'A3']] |
|---|
| 1737 | elif SGData['SGLaue'] in ['m3m','m3']: |
|---|
| 1738 | A = [parmDict[pfx+'A0'],parmDict[pfx+'A0'],parmDict[pfx+'A0'],0,0,0] |
|---|
| 1739 | |
|---|
| 1740 | try: |
|---|
| 1741 | if SGData['SGLaue'] in ['-1',]: |
|---|
| 1742 | sigA = [sigDict[pfx+'A0'],sigDict[pfx+'A1'],sigDict[pfx+'A2'], |
|---|
| 1743 | sigDict[pfx+'A3'],sigDict[pfx+'A4'],sigDict[pfx+'A5']] |
|---|
| 1744 | elif SGData['SGLaue'] in ['2/m',]: |
|---|
| 1745 | if SGData['SGUniq'] == 'a': |
|---|
| 1746 | sigA = [sigDict[pfx+'A0'],sigDict[pfx+'A1'],sigDict[pfx+'A2'], |
|---|
| 1747 | 0,0,sigDict[pfx+'A5']] |
|---|
| 1748 | elif SGData['SGUniq'] == 'b': |
|---|
| 1749 | sigA = [sigDict[pfx+'A0'],sigDict[pfx+'A1'],sigDict[pfx+'A2'], |
|---|
| 1750 | 0,sigDict[pfx+'A4'],0] |
|---|
| 1751 | else: |
|---|
| 1752 | sigA = [sigDict[pfx+'A0'],sigDict[pfx+'A1'],sigDict[pfx+'A2'], |
|---|
| 1753 | sigDict[pfx+'A3'],0,0] |
|---|
| 1754 | elif SGData['SGLaue'] in ['mmm',]: |
|---|
| 1755 | sigA = [sigDict[pfx+'A0'],sigDict[pfx+'A1'],sigDict[pfx+'A2'],0,0,0] |
|---|
| 1756 | elif SGData['SGLaue'] in ['4/m','4/mmm']: |
|---|
| 1757 | sigA = [sigDict[pfx+'A0'],0,sigDict[pfx+'A2'],0,0,0] |
|---|
| 1758 | elif SGData['SGLaue'] in ['6/m','6/mmm','3m1', '31m', '3']: |
|---|
| 1759 | sigA = [sigDict[pfx+'A0'],0,sigDict[pfx+'A2'],0,0,0] |
|---|
| 1760 | elif SGData['SGLaue'] in ['3R', '3mR']: |
|---|
| 1761 | sigA = [sigDict[pfx+'A0'],0,0,sigDict[pfx+'A3'],0,0] |
|---|
| 1762 | elif SGData['SGLaue'] in ['m3m','m3']: |
|---|
| 1763 | sigA = [sigDict[pfx+'A0'],0,0,0,0,0] |
|---|
| 1764 | except KeyError: |
|---|
| 1765 | sigA = [0,0,0,0,0,0] |
|---|
| 1766 | return A,sigA |
|---|
| 1767 | |
|---|
| 1768 | def PrintRestraints(cell,SGData,AtPtrs,Atoms,AtLookup,textureData,phaseRest,pFile): |
|---|
| 1769 | 'needs a doc string' |
|---|
| 1770 | if phaseRest: |
|---|
| 1771 | Amat = G2lat.cell2AB(cell)[0] |
|---|
| 1772 | cx,ct,cs = AtPtrs[:3] |
|---|
| 1773 | names = [['Bond','Bonds'],['Angle','Angles'],['Plane','Planes'], |
|---|
| 1774 | ['Chiral','Volumes'],['Torsion','Torsions'],['Rama','Ramas'], |
|---|
| 1775 | ['ChemComp','Sites'],['Texture','HKLs']] |
|---|
| 1776 | for name,rest in names: |
|---|
| 1777 | itemRest = phaseRest[name] |
|---|
| 1778 | if rest in itemRest and itemRest[rest] and itemRest['Use']: |
|---|
| 1779 | pFile.write('\n %s restraint weight factor %10.3f Use: %s\n'%(name,itemRest['wtFactor'],str(itemRest['Use']))) |
|---|
| 1780 | if name in ['Bond','Angle','Plane','Chiral']: |
|---|
| 1781 | pFile.write(' calc obs sig delt/sig atoms(symOp): \n') |
|---|
| 1782 | for indx,ops,obs,esd in itemRest[rest]: |
|---|
| 1783 | try: |
|---|
| 1784 | AtNames = G2mth.GetAtomItemsById(Atoms,AtLookup,indx,ct-1) |
|---|
| 1785 | AtName = '' |
|---|
| 1786 | for i,Aname in enumerate(AtNames): |
|---|
| 1787 | AtName += Aname |
|---|
| 1788 | if ops[i] == '1': |
|---|
| 1789 | AtName += '-' |
|---|
| 1790 | else: |
|---|
| 1791 | AtName += '+('+ops[i]+')-' |
|---|
| 1792 | XYZ = np.array(G2mth.GetAtomItemsById(Atoms,AtLookup,indx,cx,3)) |
|---|
| 1793 | XYZ = G2mth.getSyXYZ(XYZ,ops,SGData) |
|---|
| 1794 | if name == 'Bond': |
|---|
| 1795 | calc = G2mth.getRestDist(XYZ,Amat) |
|---|
| 1796 | elif name == 'Angle': |
|---|
| 1797 | calc = G2mth.getRestAngle(XYZ,Amat) |
|---|
| 1798 | elif name == 'Plane': |
|---|
| 1799 | calc = G2mth.getRestPlane(XYZ,Amat) |
|---|
| 1800 | elif name == 'Chiral': |
|---|
| 1801 | calc = G2mth.getRestChiral(XYZ,Amat) |
|---|
| 1802 | pFile.write(' %9.3f %9.3f %8.3f %8.3f %s\n'%(calc,obs,esd,(obs-calc)/esd,AtName[:-1])) |
|---|
| 1803 | except KeyError: |
|---|
| 1804 | del itemRest[rest] |
|---|
| 1805 | elif name in ['Torsion','Rama']: |
|---|
| 1806 | pFile.write(' atoms(symOp) calc obs sig delt/sig torsions: \n') |
|---|
| 1807 | coeffDict = itemRest['Coeff'] |
|---|
| 1808 | for indx,ops,cofName,esd in itemRest[rest]: |
|---|
| 1809 | AtNames = G2mth.GetAtomItemsById(Atoms,AtLookup,indx,ct-1) |
|---|
| 1810 | AtName = '' |
|---|
| 1811 | for i,Aname in enumerate(AtNames): |
|---|
| 1812 | AtName += Aname+'+('+ops[i]+')-' |
|---|
| 1813 | XYZ = np.array(G2mth.GetAtomItemsById(Atoms,AtLookup,indx,cx,3)) |
|---|
| 1814 | XYZ = G2mth.getSyXYZ(XYZ,ops,SGData) |
|---|
| 1815 | if name == 'Torsion': |
|---|
| 1816 | tor = G2mth.getRestTorsion(XYZ,Amat) |
|---|
| 1817 | restr,calc = G2mth.calcTorsionEnergy(tor,coeffDict[cofName]) |
|---|
| 1818 | pFile.write(' %8.3f %8.3f %.3f %8.3f %8.3f %s\n'%(calc,obs,esd,(obs-calc)/esd,tor,AtName[:-1])) |
|---|
| 1819 | else: |
|---|
| 1820 | phi,psi = G2mth.getRestRama(XYZ,Amat) |
|---|
| 1821 | restr,calc = G2mth.calcRamaEnergy(phi,psi,coeffDict[cofName]) |
|---|
| 1822 | pFile.write(' %8.3f %8.3f %8.3f %8.3f %8.3f %8.3f %s\n'%(calc,obs,esd,(obs-calc)/esd,phi,psi,AtName[:-1])) |
|---|
| 1823 | elif name == 'ChemComp': |
|---|
| 1824 | pFile.write(' atoms mul*frac factor prod\n') |
|---|
| 1825 | for indx,factors,obs,esd in itemRest[rest]: |
|---|
| 1826 | try: |
|---|
| 1827 | atoms = G2mth.GetAtomItemsById(Atoms,AtLookup,indx,ct-1) |
|---|
| 1828 | mul = np.array(G2mth.GetAtomItemsById(Atoms,AtLookup,indx,cs+1)) |
|---|
| 1829 | frac = np.array(G2mth.GetAtomItemsById(Atoms,AtLookup,indx,cs-1)) |
|---|
| 1830 | mulfrac = mul*frac |
|---|
| 1831 | calcs = mul*frac*factors |
|---|
| 1832 | for iatm,[atom,mf,fr,clc] in enumerate(zip(atoms,mulfrac,factors,calcs)): |
|---|
| 1833 | pFile.write(' %10s %8.3f %8.3f %8.3f\n'%(atom,mf,fr,clc)) |
|---|
| 1834 | pFile.write(' Sum: calc: %8.3f obs: %8.3f esd: %8.3f\n'%(np.sum(calcs),obs,esd)) |
|---|
| 1835 | except KeyError: |
|---|
| 1836 | del itemRest[rest] |
|---|
| 1837 | elif name == 'Texture' and textureData['Order']: |
|---|
| 1838 | Start = False |
|---|
| 1839 | SHCoef = textureData['SH Coeff'][1] |
|---|
| 1840 | shModels = ['cylindrical','none','shear - 2/m','rolling - mmm'] |
|---|
| 1841 | SamSym = dict(zip(shModels,['0','-1','2/m','mmm'])) |
|---|
| 1842 | pFile.write (' HKL grid neg esd sum neg num neg use unit? unit esd \n') |
|---|
| 1843 | for hkl,grid,esd1,ifesd2,esd2 in itemRest[rest]: |
|---|
| 1844 | phi,beta = G2lat.CrsAng(np.array(hkl),cell,SGData) |
|---|
| 1845 | ODFln = G2lat.Flnh(Start,SHCoef,phi,beta,SGData) |
|---|
| 1846 | R,P,Z = G2mth.getRestPolefig(ODFln,SamSym[textureData['Model']],grid) |
|---|
| 1847 | Z = ma.masked_greater(Z,0.0) |
|---|
| 1848 | num = ma.count(Z) |
|---|
| 1849 | sum = 0 |
|---|
| 1850 | if num: |
|---|
| 1851 | sum = np.sum(Z) |
|---|
| 1852 | pFile.write (' %d %d %d %d %8.3f %8.3f %8d %s %8.3f\n'%(hkl[0],hkl[1],hkl[2],grid,esd1,sum,num,str(ifesd2),esd2)) |
|---|
| 1853 | |
|---|
| 1854 | def getCellEsd(pfx,SGData,A,covData): |
|---|
| 1855 | 'needs a doc string' |
|---|
| 1856 | rVsq = G2lat.calc_rVsq(A) |
|---|
| 1857 | G,g = G2lat.A2Gmat(A) #get recip. & real metric tensors |
|---|
| 1858 | RMnames = [pfx+'A0',pfx+'A1',pfx+'A2',pfx+'A3',pfx+'A4',pfx+'A5'] |
|---|
| 1859 | varyList = covData['varyList'] |
|---|
| 1860 | covMatrix = covData['covMatrix'] |
|---|
| 1861 | if len(covMatrix): |
|---|
| 1862 | vcov = G2mth.getVCov(RMnames,varyList,covMatrix) |
|---|
| 1863 | if SGData['SGLaue'] in ['3', '3m1', '31m', '6/m', '6/mmm']: |
|---|
| 1864 | vcov[1,1] = vcov[3,3] = vcov[0,1] = vcov[1,0] = vcov[0,0] |
|---|
| 1865 | vcov[1,3] = vcov[3,1] = vcov[0,3] = vcov[3,0] = vcov[0,0] |
|---|
| 1866 | vcov[1,2] = vcov[2,1] = vcov[2,3] = vcov[3,2] = vcov[0,2] |
|---|
| 1867 | elif SGData['SGLaue'] in ['m3','m3m']: |
|---|
| 1868 | vcov[0:3,0:3] = vcov[0,0] |
|---|
| 1869 | elif SGData['SGLaue'] in ['4/m', '4/mmm']: |
|---|
| 1870 | vcov[0:2,0:2] = vcov[0,0] |
|---|
| 1871 | vcov[1,2] = vcov[2,1] = vcov[0,2] |
|---|
| 1872 | elif SGData['SGLaue'] in ['3R','3mR']: |
|---|
| 1873 | vcov[0:3,0:3] = vcov[0,0] |
|---|
| 1874 | # vcov[4,4] = vcov[5,5] = vcov[3,3] |
|---|
| 1875 | vcov[3:6,3:6] = vcov[3,3] |
|---|
| 1876 | vcov[0:3,3:6] = vcov[0,3] |
|---|
| 1877 | vcov[3:6,0:3] = vcov[3,0] |
|---|
| 1878 | else: |
|---|
| 1879 | vcov = np.eye(6) |
|---|
| 1880 | delt = 1.e-9 |
|---|
| 1881 | drVdA = np.zeros(6) |
|---|
| 1882 | for i in range(6): |
|---|
| 1883 | A[i] += delt |
|---|
| 1884 | drVdA[i] = G2lat.calc_rVsq(A) |
|---|
| 1885 | A[i] -= 2*delt |
|---|
| 1886 | drVdA[i] -= G2lat.calc_rVsq(A) |
|---|
| 1887 | A[i] += delt |
|---|
| 1888 | drVdA /= 2.*delt |
|---|
| 1889 | srcvlsq = np.inner(drVdA,np.inner(drVdA,vcov)) |
|---|
| 1890 | Vol = 1/np.sqrt(rVsq) |
|---|
| 1891 | sigVol = Vol**3*np.sqrt(srcvlsq)/2. #ok - checks with GSAS |
|---|
| 1892 | |
|---|
| 1893 | dcdA = np.zeros((6,6)) |
|---|
| 1894 | for i in range(6): |
|---|
| 1895 | pdcdA =np.zeros(6) |
|---|
| 1896 | A[i] += delt |
|---|
| 1897 | pdcdA += G2lat.A2cell(A) |
|---|
| 1898 | A[i] -= 2*delt |
|---|
| 1899 | pdcdA -= G2lat.A2cell(A) |
|---|
| 1900 | A[i] += delt |
|---|
| 1901 | dcdA[i] = pdcdA/(2.*delt) |
|---|
| 1902 | |
|---|
| 1903 | sigMat = np.inner(dcdA,np.inner(dcdA,vcov)) |
|---|
| 1904 | var = np.diag(sigMat) |
|---|
| 1905 | CS = np.where(var>0.,np.sqrt(var),0.) |
|---|
| 1906 | if SGData['SGLaue'] in ['3', '3m1', '31m', '6/m', '6/mmm','m3','m3m','4/m','4/mmm']: |
|---|
| 1907 | CS[3:6] = 0.0 |
|---|
| 1908 | return [CS[0],CS[1],CS[2],CS[5],CS[4],CS[3],sigVol] |
|---|
| 1909 | |
|---|
| 1910 | def SetPhaseData(parmDict,sigDict,Phases,RBIds,covData,RestraintDict=None,pFile=None): |
|---|
| 1911 | '''Called after a refinement to transfer parameters from the parameter dict to |
|---|
| 1912 | the phase(s) information read from a GPX file. Also prints values to the .lst file |
|---|
| 1913 | ''' |
|---|
| 1914 | |
|---|
| 1915 | def PrintAtomsAndSig(General,Atoms,atomsSig): |
|---|
| 1916 | pFile.write('\n Atoms:\n') |
|---|
| 1917 | line = ' name x y z frac Uiso U11 U22 U33 U12 U13 U23' |
|---|
| 1918 | if General['Type'] == 'macromolecular': |
|---|
| 1919 | line = ' res no residue chain '+line |
|---|
| 1920 | cx,ct,cs,cia = General['AtomPtrs'] |
|---|
| 1921 | pFile.write(line+'\n') |
|---|
| 1922 | pFile.write(135*'-'+'\n') |
|---|
| 1923 | fmt = {0:'%7s',ct:'%7s',cx:'%10.5f',cx+1:'%10.5f',cx+2:'%10.5f',cx+3:'%8.3f',cia+1:'%8.5f', |
|---|
| 1924 | cia+2:'%8.5f',cia+3:'%8.5f',cia+4:'%8.5f',cia+5:'%8.5f',cia+6:'%8.5f',cia+7:'%8.5f'} |
|---|
| 1925 | noFXsig = {cx:[10*' ','%10s'],cx+1:[10*' ','%10s'],cx+2:[10*' ','%10s'],cx+3:[8*' ','%8s']} |
|---|
| 1926 | for atyp in General['AtomTypes']: #zero composition |
|---|
| 1927 | General['NoAtoms'][atyp] = 0. |
|---|
| 1928 | for i,at in enumerate(Atoms): |
|---|
| 1929 | General['NoAtoms'][at[ct]] += at[cx+3]*float(at[cx+5]) #new composition |
|---|
| 1930 | if General['Type'] == 'macromolecular': |
|---|
| 1931 | name = ' %s %s %s %s:'%(at[0],at[1],at[2],at[3]) |
|---|
| 1932 | valstr = ' values: ' |
|---|
| 1933 | sigstr = ' sig : ' |
|---|
| 1934 | else: |
|---|
| 1935 | name = fmt[0]%(at[ct-1])+fmt[1]%(at[ct])+':' |
|---|
| 1936 | valstr = ' values:' |
|---|
| 1937 | sigstr = ' sig :' |
|---|
| 1938 | for ind in range(cx,cx+4): |
|---|
| 1939 | sigind = str(i)+':'+str(ind) |
|---|
| 1940 | valstr += fmt[ind]%(at[ind]) |
|---|
| 1941 | if sigind in atomsSig: |
|---|
| 1942 | sigstr += fmt[ind]%(atomsSig[sigind]) |
|---|
| 1943 | else: |
|---|
| 1944 | sigstr += noFXsig[ind][1]%(noFXsig[ind][0]) |
|---|
| 1945 | if at[cia] == 'I': |
|---|
| 1946 | valstr += fmt[cia+1]%(at[cia+1]) |
|---|
| 1947 | if '%d:%d'%(i,cia+1) in atomsSig: |
|---|
| 1948 | sigstr += fmt[cia+1]%(atomsSig['%d:%d'%(i,cia+1)]) |
|---|
| 1949 | else: |
|---|
| 1950 | sigstr += 8*' ' |
|---|
| 1951 | else: |
|---|
| 1952 | valstr += 8*' ' |
|---|
| 1953 | sigstr += 8*' ' |
|---|
| 1954 | for ind in range(cia+2,cia+8): |
|---|
| 1955 | sigind = str(i)+':'+str(ind) |
|---|
| 1956 | valstr += fmt[ind]%(at[ind]) |
|---|
| 1957 | if sigind in atomsSig: |
|---|
| 1958 | sigstr += fmt[ind]%(atomsSig[sigind]) |
|---|
| 1959 | else: |
|---|
| 1960 | sigstr += 8*' ' |
|---|
| 1961 | pFile.write(name+'\n') |
|---|
| 1962 | pFile.write(valstr+'\n') |
|---|
| 1963 | pFile.write(sigstr+'\n') |
|---|
| 1964 | |
|---|
| 1965 | def PrintMomentsAndSig(General,Atoms,atomsSig): |
|---|
| 1966 | cell = General['Cell'][1:7] |
|---|
| 1967 | G = G2lat.fillgmat(cell) |
|---|
| 1968 | ast = np.sqrt(np.diag(G)) |
|---|
| 1969 | GS = G/np.outer(ast,ast) |
|---|
| 1970 | pFile.write('\n Magnetic Moments:\n') #add magnitude & angle, etc.? TBD |
|---|
| 1971 | line = ' name Mx My Mz |Mag|' |
|---|
| 1972 | cx,ct,cs,cia = General['AtomPtrs'] |
|---|
| 1973 | cmx = cx+4 |
|---|
| 1974 | AtInfo = dict(zip(General['AtomTypes'],General['Lande g'])) |
|---|
| 1975 | pFile.write(line+'\n') |
|---|
| 1976 | pFile.write(135*'-'+'\n') |
|---|
| 1977 | fmt = {0:'%7s',ct:'%7s',cmx:'%10.3f',cmx+1:'%10.3f',cmx+2:'%10.3f'} |
|---|
| 1978 | noFXsig = {cmx:[10*' ','%10s'],cmx+1:[10*' ','%10s'],cmx+2:[10*' ','%10s']} |
|---|
| 1979 | for i,at in enumerate(Atoms): |
|---|
| 1980 | if AtInfo[at[ct]]: |
|---|
| 1981 | name = fmt[0]%(at[ct-1])+fmt[1]%(at[ct])+':' |
|---|
| 1982 | valstr = ' values:' |
|---|
| 1983 | sigstr = ' sig :' |
|---|
| 1984 | for ind in range(cmx,cmx+3): |
|---|
| 1985 | sigind = str(i)+':'+str(ind) |
|---|
| 1986 | valstr += fmt[ind]%(at[ind]) |
|---|
| 1987 | if sigind in atomsSig: |
|---|
| 1988 | sigstr += fmt[ind]%(atomsSig[sigind]) |
|---|
| 1989 | else: |
|---|
| 1990 | sigstr += noFXsig[ind][1]%(noFXsig[ind][0]) |
|---|
| 1991 | mag = np.array(at[cmx:cmx+3]) |
|---|
| 1992 | Mag = np.sqrt(np.inner(mag,np.inner(mag,GS))) |
|---|
| 1993 | valstr += '%10.3f'%Mag |
|---|
| 1994 | sigstr += 10*' ' |
|---|
| 1995 | pFile.write(name+'\n') |
|---|
| 1996 | pFile.write(valstr+'\n') |
|---|
| 1997 | pFile.write(sigstr+'\n') |
|---|
| 1998 | |
|---|
| 1999 | def PrintWavesAndSig(General,Atoms,wavesSig): |
|---|
| 2000 | cx,ct,cs,cia = General['AtomPtrs'] |
|---|
| 2001 | pFile.write('\n Modulation waves\n') |
|---|
| 2002 | names = {'Sfrac':['Fsin','Fcos','Fzero','Fwid'],'Spos':['Xsin','Ysin','Zsin','Xcos','Ycos','Zcos','Tmin','Tmax','Xmax','Ymax','Zmax'], |
|---|
| 2003 | 'Sadp':['U11sin','U22sin','U33sin','U12sin','U13sin','U23sin','U11cos','U22cos', |
|---|
| 2004 | 'U33cos','U12cos','U13cos','U23cos'],'Smag':['MXsin','MYsin','MZsin','MXcos','MYcos','MZcos']} |
|---|
| 2005 | pFile.write(135*'-'+'\n') |
|---|
| 2006 | for i,at in enumerate(Atoms): |
|---|
| 2007 | AtomSS = at[-1]['SS1'] |
|---|
| 2008 | for Stype in ['Sfrac','Spos','Sadp','Smag']: |
|---|
| 2009 | Waves = AtomSS[Stype] |
|---|
| 2010 | if len(Waves) > 1: |
|---|
| 2011 | waveType = Waves[0] |
|---|
| 2012 | else: |
|---|
| 2013 | continue |
|---|
| 2014 | if len(Waves): |
|---|
| 2015 | pFile.write(' atom: %s, site sym: %s, type: %s wave type: %s:\n'% |
|---|
| 2016 | (at[ct-1],at[cs],Stype,waveType)) |
|---|
| 2017 | for iw,wave in enumerate(Waves[1:]): |
|---|
| 2018 | stiw = ':'+str(i)+':'+str(iw) |
|---|
| 2019 | namstr = ' names :' |
|---|
| 2020 | valstr = ' values:' |
|---|
| 2021 | sigstr = ' esds :' |
|---|
| 2022 | if Stype == 'Spos': |
|---|
| 2023 | nt = 6 |
|---|
| 2024 | ot = 0 |
|---|
| 2025 | if waveType in ['ZigZag','Block',] and not iw: |
|---|
| 2026 | nt = 5 |
|---|
| 2027 | ot = 6 |
|---|
| 2028 | for j in range(nt): |
|---|
| 2029 | name = names['Spos'][j+ot] |
|---|
| 2030 | namstr += '%12s'%(name) |
|---|
| 2031 | valstr += '%12.4f'%(wave[0][j]) |
|---|
| 2032 | if name+stiw in wavesSig: |
|---|
| 2033 | sigstr += '%12.4f'%(wavesSig[name+stiw]) |
|---|
| 2034 | else: |
|---|
| 2035 | sigstr += 12*' ' |
|---|
| 2036 | elif Stype == 'Sfrac': |
|---|
| 2037 | ot = 0 |
|---|
| 2038 | if 'Crenel' in waveType and not iw: |
|---|
| 2039 | ot = 2 |
|---|
| 2040 | for j in range(2): |
|---|
| 2041 | name = names['Sfrac'][j+ot] |
|---|
| 2042 | namstr += '%12s'%(names['Sfrac'][j+ot]) |
|---|
| 2043 | valstr += '%12.4f'%(wave[0][j]) |
|---|
| 2044 | if name+stiw in wavesSig: |
|---|
| 2045 | sigstr += '%12.4f'%(wavesSig[name+stiw]) |
|---|
| 2046 | else: |
|---|
| 2047 | sigstr += 12*' ' |
|---|
| 2048 | elif Stype == 'Sadp': |
|---|
| 2049 | for j in range(12): |
|---|
| 2050 | name = names['Sadp'][j] |
|---|
| 2051 | namstr += '%10s'%(names['Sadp'][j]) |
|---|
| 2052 | valstr += '%10.6f'%(wave[0][j]) |
|---|
| 2053 | if name+stiw in wavesSig: |
|---|
| 2054 | sigstr += '%10.6f'%(wavesSig[name+stiw]) |
|---|
| 2055 | else: |
|---|
| 2056 | sigstr += 10*' ' |
|---|
| 2057 | elif Stype == 'Smag': |
|---|
| 2058 | for j in range(6): |
|---|
| 2059 | name = names['Smag'][j] |
|---|
| 2060 | namstr += '%12s'%(names['Smag'][j]) |
|---|
| 2061 | valstr += '%12.4f'%(wave[0][j]) |
|---|
| 2062 | if name+stiw in wavesSig: |
|---|
| 2063 | sigstr += '%12.4f'%(wavesSig[name+stiw]) |
|---|
| 2064 | else: |
|---|
| 2065 | sigstr += 12*' ' |
|---|
| 2066 | |
|---|
| 2067 | pFile.write(namstr+'\n') |
|---|
| 2068 | pFile.write(valstr+'\n') |
|---|
| 2069 | pFile.write(sigstr+'\n') |
|---|
| 2070 | |
|---|
| 2071 | |
|---|
| 2072 | def PrintRBObjPOAndSig(rbfx,rbsx): |
|---|
| 2073 | for i in WriteRBObjPOAndSig(pfx,rbfx,rbsx,parmDict,sigDict): |
|---|
| 2074 | pFile.write(i+'\n') |
|---|
| 2075 | |
|---|
| 2076 | def PrintRBObjTLSAndSig(rbfx,rbsx,TLS): |
|---|
| 2077 | for i in WriteRBObjTLSAndSig(pfx,rbfx,rbsx,TLS,parmDict,sigDict): |
|---|
| 2078 | pFile.write(i) |
|---|
| 2079 | |
|---|
| 2080 | def PrintRBObjTorAndSig(rbsx): |
|---|
| 2081 | nTors = len(RBObj['Torsions']) |
|---|
| 2082 | if nTors: |
|---|
| 2083 | for i in WriteRBObjTorAndSig(pfx,rbsx,parmDict,sigDict,nTors): |
|---|
| 2084 | pFile.write(i) |
|---|
| 2085 | |
|---|
| 2086 | def PrintSHtextureAndSig(textureData,SHtextureSig): |
|---|
| 2087 | Tindx = 1.0 |
|---|
| 2088 | Tvar = 0.0 |
|---|
| 2089 | pFile.write('\n Spherical harmonics texture: Order: %d\n'%textureData['Order']) |
|---|
| 2090 | names = ['omega','chi','phi'] |
|---|
| 2091 | namstr = ' names :' |
|---|
| 2092 | ptstr = ' values:' |
|---|
| 2093 | sigstr = ' esds :' |
|---|
| 2094 | for name in names: |
|---|
| 2095 | namstr += '%12s'%(name) |
|---|
| 2096 | ptstr += '%12.3f'%(textureData['Sample '+name][1]) |
|---|
| 2097 | if 'Sample '+name in SHtextureSig: |
|---|
| 2098 | sigstr += '%12.3f'%(SHtextureSig['Sample '+name]) |
|---|
| 2099 | else: |
|---|
| 2100 | sigstr += 12*' ' |
|---|
| 2101 | pFile.write(namstr+'\n') |
|---|
| 2102 | pFile.write(ptstr+'\n') |
|---|
| 2103 | pFile.write(sigstr+'\n') |
|---|
| 2104 | pFile.write('\n Texture coefficients:\n') |
|---|
| 2105 | SHcoeff = textureData['SH Coeff'][1] |
|---|
| 2106 | SHkeys = list(SHcoeff.keys()) |
|---|
| 2107 | nCoeff = len(SHcoeff) |
|---|
| 2108 | nBlock = nCoeff//10+1 |
|---|
| 2109 | iBeg = 0 |
|---|
| 2110 | iFin = min(iBeg+10,nCoeff) |
|---|
| 2111 | for block in range(nBlock): |
|---|
| 2112 | namstr = ' names :' |
|---|
| 2113 | ptstr = ' values:' |
|---|
| 2114 | sigstr = ' esds :' |
|---|
| 2115 | for name in SHkeys[iBeg:iFin]: |
|---|
| 2116 | namstr += '%12s'%(name) |
|---|
| 2117 | ptstr += '%12.3f'%(SHcoeff[name]) |
|---|
| 2118 | l = 2.0*eval(name.strip('C'))[0]+1 |
|---|
| 2119 | Tindx += SHcoeff[name]**2/l |
|---|
| 2120 | if name in SHtextureSig: |
|---|
| 2121 | Tvar += (2.*SHcoeff[name]*SHtextureSig[name]/l)**2 |
|---|
| 2122 | sigstr += '%12.3f'%(SHtextureSig[name]) |
|---|
| 2123 | else: |
|---|
| 2124 | sigstr += 12*' ' |
|---|
| 2125 | pFile.write(namstr+'\n') |
|---|
| 2126 | pFile.write(ptstr+'\n') |
|---|
| 2127 | pFile.write(sigstr+'\n') |
|---|
| 2128 | iBeg += 10 |
|---|
| 2129 | iFin = min(iBeg+10,nCoeff) |
|---|
| 2130 | pFile.write(' Texture index J = %.3f(%d)'%(Tindx,int(1000*np.sqrt(Tvar)))) |
|---|
| 2131 | |
|---|
| 2132 | ########################################################################## |
|---|
| 2133 | # SetPhaseData starts here |
|---|
| 2134 | pFile.write('\n Phases:\n') |
|---|
| 2135 | for phase in Phases: |
|---|
| 2136 | pFile.write(' Result for phase: %s\n'%phase) |
|---|
| 2137 | pFile.write(135*'='+'\n') |
|---|
| 2138 | Phase = Phases[phase] |
|---|
| 2139 | General = Phase['General'] |
|---|
| 2140 | SGData = General['SGData'] |
|---|
| 2141 | Atoms = Phase['Atoms'] |
|---|
| 2142 | AtLookup = [] |
|---|
| 2143 | if Atoms and not General.get('doPawley'): |
|---|
| 2144 | cx,ct,cs,cia = General['AtomPtrs'] |
|---|
| 2145 | AtLookup = G2mth.FillAtomLookUp(Atoms,cia+8) |
|---|
| 2146 | cell = General['Cell'] |
|---|
| 2147 | pId = Phase['pId'] |
|---|
| 2148 | pfx = str(pId)+'::' |
|---|
| 2149 | if cell[0]: |
|---|
| 2150 | A,sigA = cellFill(pfx,SGData,parmDict,sigDict) |
|---|
| 2151 | cellSig = getCellEsd(pfx,SGData,A,covData) #includes sigVol |
|---|
| 2152 | pFile.write(' Reciprocal metric tensor: \n') |
|---|
| 2153 | ptfmt = "%15.9f" |
|---|
| 2154 | names = ['A11','A22','A33','A12','A13','A23'] |
|---|
| 2155 | namstr = ' names :' |
|---|
| 2156 | ptstr = ' values:' |
|---|
| 2157 | sigstr = ' esds :' |
|---|
| 2158 | for name,a,siga in zip(names,A,sigA): |
|---|
| 2159 | namstr += '%15s'%(name) |
|---|
| 2160 | ptstr += ptfmt%(a) |
|---|
| 2161 | if siga: |
|---|
| 2162 | sigstr += ptfmt%(siga) |
|---|
| 2163 | else: |
|---|
| 2164 | sigstr += 15*' ' |
|---|
| 2165 | pFile.write(namstr+'\n') |
|---|
| 2166 | pFile.write(ptstr+'\n') |
|---|
| 2167 | pFile.write(sigstr+'\n') |
|---|
| 2168 | cell[1:7] = G2lat.A2cell(A) |
|---|
| 2169 | cell[7] = G2lat.calc_V(A) |
|---|
| 2170 | pFile.write(' New unit cell:\n') |
|---|
| 2171 | ptfmt = ["%12.6f","%12.6f","%12.6f","%12.4f","%12.4f","%12.4f","%12.3f"] |
|---|
| 2172 | names = ['a','b','c','alpha','beta','gamma','Volume'] |
|---|
| 2173 | namstr = ' names :' |
|---|
| 2174 | ptstr = ' values:' |
|---|
| 2175 | sigstr = ' esds :' |
|---|
| 2176 | for name,fmt,a,siga in zip(names,ptfmt,cell[1:8],cellSig): |
|---|
| 2177 | namstr += '%12s'%(name) |
|---|
| 2178 | ptstr += fmt%(a) |
|---|
| 2179 | if siga: |
|---|
| 2180 | sigstr += fmt%(siga) |
|---|
| 2181 | else: |
|---|
| 2182 | sigstr += 12*' ' |
|---|
| 2183 | pFile.write(namstr+'\n') |
|---|
| 2184 | pFile.write(ptstr+'\n') |
|---|
| 2185 | pFile.write(sigstr+'\n') |
|---|
| 2186 | ik = 6 #for Pawley stuff below |
|---|
| 2187 | if General.get('Modulated',False): |
|---|
| 2188 | ik = 7 |
|---|
| 2189 | Vec,vRef,maxH = General['SuperVec'] |
|---|
| 2190 | if vRef: |
|---|
| 2191 | pFile.write(' New modulation vector:\n') |
|---|
| 2192 | namstr = ' names :' |
|---|
| 2193 | ptstr = ' values:' |
|---|
| 2194 | sigstr = ' esds :' |
|---|
| 2195 | for iv,var in enumerate(['mV0','mV1','mV2']): |
|---|
| 2196 | namstr += '%12s'%(pfx+var) |
|---|
| 2197 | ptstr += '%12.6f'%(parmDict[pfx+var]) |
|---|
| 2198 | if pfx+var in sigDict: |
|---|
| 2199 | Vec[iv] = parmDict[pfx+var] |
|---|
| 2200 | sigstr += '%12.6f'%(sigDict[pfx+var]) |
|---|
| 2201 | else: |
|---|
| 2202 | sigstr += 12*' ' |
|---|
| 2203 | pFile.write(namstr+'\n') |
|---|
| 2204 | pFile.write(ptstr+'\n') |
|---|
| 2205 | pFile.write(sigstr+'\n') |
|---|
| 2206 | |
|---|
| 2207 | General['Mass'] = 0. |
|---|
| 2208 | if Phase['General'].get('doPawley'): |
|---|
| 2209 | pawleyRef = Phase['Pawley ref'] |
|---|
| 2210 | for i,refl in enumerate(pawleyRef): |
|---|
| 2211 | key = pfx+'PWLref:'+str(i) |
|---|
| 2212 | refl[ik] = parmDict[key] |
|---|
| 2213 | if key in sigDict: |
|---|
| 2214 | refl[ik+1] = sigDict[key] |
|---|
| 2215 | else: |
|---|
| 2216 | refl[ik+1] = 0 |
|---|
| 2217 | else: |
|---|
| 2218 | VRBIds = RBIds['Vector'] |
|---|
| 2219 | RRBIds = RBIds['Residue'] |
|---|
| 2220 | RBModels = Phase['RBModels'] |
|---|
| 2221 | for irb,RBObj in enumerate(RBModels.get('Vector',[])): |
|---|
| 2222 | jrb = VRBIds.index(RBObj['RBId']) |
|---|
| 2223 | rbsx = str(irb)+':'+str(jrb) |
|---|
| 2224 | pFile.write(' Vector rigid body parameters:\n') |
|---|
| 2225 | PrintRBObjPOAndSig('RBV',rbsx) |
|---|
| 2226 | PrintRBObjTLSAndSig('RBV',rbsx,RBObj['ThermalMotion'][0]) |
|---|
| 2227 | for irb,RBObj in enumerate(RBModels.get('Residue',[])): |
|---|
| 2228 | jrb = RRBIds.index(RBObj['RBId']) |
|---|
| 2229 | rbsx = str(irb)+':'+str(jrb) |
|---|
| 2230 | pFile.write(' Residue rigid body parameters:\n') |
|---|
| 2231 | PrintRBObjPOAndSig('RBR',rbsx) |
|---|
| 2232 | PrintRBObjTLSAndSig('RBR',rbsx,RBObj['ThermalMotion'][0]) |
|---|
| 2233 | PrintRBObjTorAndSig(rbsx) |
|---|
| 2234 | atomsSig = {} |
|---|
| 2235 | wavesSig = {} |
|---|
| 2236 | cx,ct,cs,cia = General['AtomPtrs'] |
|---|
| 2237 | for i,at in enumerate(Atoms): |
|---|
| 2238 | names = {cx:pfx+'Ax:'+str(i),cx+1:pfx+'Ay:'+str(i),cx+2:pfx+'Az:'+str(i),cx+3:pfx+'Afrac:'+str(i), |
|---|
| 2239 | cia+1:pfx+'AUiso:'+str(i),cia+2:pfx+'AU11:'+str(i),cia+3:pfx+'AU22:'+str(i),cia+4:pfx+'AU33:'+str(i), |
|---|
| 2240 | cia+5:pfx+'AU12:'+str(i),cia+6:pfx+'AU13:'+str(i),cia+7:pfx+'AU23:'+str(i), |
|---|
| 2241 | cx+4:pfx+'AMx:'+str(i),cx+5:pfx+'AMy:'+str(i),cx+6:pfx+'AMz:'+str(i)} |
|---|
| 2242 | for ind in range(cx,cx+4): |
|---|
| 2243 | at[ind] = parmDict[names[ind]] |
|---|
| 2244 | if ind in range(cx,cx+3): |
|---|
| 2245 | name = names[ind].replace('A','dA') |
|---|
| 2246 | else: |
|---|
| 2247 | name = names[ind] |
|---|
| 2248 | if name in sigDict: |
|---|
| 2249 | atomsSig[str(i)+':'+str(ind)] = sigDict[name] |
|---|
| 2250 | if at[cia] == 'I': |
|---|
| 2251 | at[cia+1] = parmDict[names[cia+1]] |
|---|
| 2252 | if names[cia+1] in sigDict: |
|---|
| 2253 | atomsSig['%d:%d'%(i,cia+1)] = sigDict[names[cia+1]] |
|---|
| 2254 | else: |
|---|
| 2255 | for ind in range(cia+2,cia+8): |
|---|
| 2256 | at[ind] = parmDict[names[ind]] |
|---|
| 2257 | if names[ind] in sigDict: |
|---|
| 2258 | atomsSig[str(i)+':'+str(ind)] = sigDict[names[ind]] |
|---|
| 2259 | if General['Type'] == 'magnetic': |
|---|
| 2260 | for ind in range(cx+4,cx+7): |
|---|
| 2261 | at[ind] = parmDict[names[ind]] |
|---|
| 2262 | if names[ind] in sigDict: |
|---|
| 2263 | atomsSig[str(i)+':'+str(ind)] = sigDict[names[ind]] |
|---|
| 2264 | ind = General['AtomTypes'].index(at[ct]) |
|---|
| 2265 | General['Mass'] += General['AtomMass'][ind]*at[cx+3]*at[cx+5] |
|---|
| 2266 | if General.get('Modulated',False): |
|---|
| 2267 | AtomSS = at[-1]['SS1'] |
|---|
| 2268 | for Stype in ['Sfrac','Spos','Sadp','Smag']: |
|---|
| 2269 | Waves = AtomSS[Stype] |
|---|
| 2270 | if len(Waves): |
|---|
| 2271 | waveType = Waves[0] |
|---|
| 2272 | else: |
|---|
| 2273 | continue |
|---|
| 2274 | for iw,wave in enumerate(Waves[1:]): |
|---|
| 2275 | stiw = str(i)+':'+str(iw) |
|---|
| 2276 | if Stype == 'Spos': |
|---|
| 2277 | if waveType in ['ZigZag','Block',] and not iw: |
|---|
| 2278 | names = ['Tmin:'+stiw,'Tmax:'+stiw,'Xmax:'+stiw,'Ymax:'+stiw,'Zmax:'+stiw] |
|---|
| 2279 | else: |
|---|
| 2280 | names = ['Xsin:'+stiw,'Ysin:'+stiw,'Zsin:'+stiw, |
|---|
| 2281 | 'Xcos:'+stiw,'Ycos:'+stiw,'Zcos:'+stiw] |
|---|
| 2282 | elif Stype == 'Sadp': |
|---|
| 2283 | names = ['U11sin:'+stiw,'U22sin:'+stiw,'U33sin:'+stiw, |
|---|
| 2284 | 'U12sin:'+stiw,'U13sin:'+stiw,'U23sin:'+stiw, |
|---|
| 2285 | 'U11cos:'+stiw,'U22cos:'+stiw,'U33cos:'+stiw, |
|---|
| 2286 | 'U12cos:'+stiw,'U13cos:'+stiw,'U23cos:'+stiw] |
|---|
| 2287 | elif Stype == 'Sfrac': |
|---|
| 2288 | if 'Crenel' in waveType and not iw: |
|---|
| 2289 | names = ['Fzero:'+stiw,'Fwid:'+stiw] |
|---|
| 2290 | else: |
|---|
| 2291 | names = ['Fsin:'+stiw,'Fcos:'+stiw] |
|---|
| 2292 | elif Stype == 'Smag': |
|---|
| 2293 | names = ['MXsin:'+stiw,'MYsin:'+stiw,'MZsin:'+stiw, |
|---|
| 2294 | 'MXcos:'+stiw,'MYcos:'+stiw,'MZcos:'+stiw] |
|---|
| 2295 | for iname,name in enumerate(names): |
|---|
| 2296 | AtomSS[Stype][iw+1][0][iname] = parmDict[pfx+name] |
|---|
| 2297 | if pfx+name in sigDict: |
|---|
| 2298 | wavesSig[name] = sigDict[pfx+name] |
|---|
| 2299 | |
|---|
| 2300 | PrintAtomsAndSig(General,Atoms,atomsSig) |
|---|
| 2301 | if General['Type'] == 'magnetic': |
|---|
| 2302 | PrintMomentsAndSig(General,Atoms,atomsSig) |
|---|
| 2303 | if General.get('Modulated',False): |
|---|
| 2304 | PrintWavesAndSig(General,Atoms,wavesSig) |
|---|
| 2305 | |
|---|
| 2306 | density = G2mth.getDensity(General)[0] |
|---|
| 2307 | pFile.write('\n Density: %f.4 g/cm**3\n'%density) |
|---|
| 2308 | |
|---|
| 2309 | |
|---|
| 2310 | textureData = General['SH Texture'] |
|---|
| 2311 | if textureData['Order']: |
|---|
| 2312 | SHtextureSig = {} |
|---|
| 2313 | for name in ['omega','chi','phi']: |
|---|
| 2314 | aname = pfx+'SH '+name |
|---|
| 2315 | textureData['Sample '+name][1] = parmDict[aname] |
|---|
| 2316 | if aname in sigDict: |
|---|
| 2317 | SHtextureSig['Sample '+name] = sigDict[aname] |
|---|
| 2318 | for name in textureData['SH Coeff'][1]: |
|---|
| 2319 | aname = pfx+name |
|---|
| 2320 | textureData['SH Coeff'][1][name] = parmDict[aname] |
|---|
| 2321 | if aname in sigDict: |
|---|
| 2322 | SHtextureSig[name] = sigDict[aname] |
|---|
| 2323 | PrintSHtextureAndSig(textureData,SHtextureSig) |
|---|
| 2324 | if phase in RestraintDict and not Phase['General'].get('doPawley'): |
|---|
| 2325 | PrintRestraints(cell[1:7],SGData,General['AtomPtrs'],Atoms,AtLookup, |
|---|
| 2326 | textureData,RestraintDict[phase],pFile) |
|---|
| 2327 | |
|---|
| 2328 | ################################################################################ |
|---|
| 2329 | ##### Histogram & Phase data |
|---|
| 2330 | ################################################################################ |
|---|
| 2331 | |
|---|
| 2332 | def GetHistogramPhaseData(Phases,Histograms,Print=True,pFile=None,resetRefList=True): |
|---|
| 2333 | '''Loads the HAP histogram/phase information into dicts |
|---|
| 2334 | |
|---|
| 2335 | :param dict Phases: phase information |
|---|
| 2336 | :param dict Histograms: Histogram information |
|---|
| 2337 | :param bool Print: prints information as it is read |
|---|
| 2338 | :param file pFile: file object to print to (the default, None causes printing to the console) |
|---|
| 2339 | :param bool resetRefList: Should the contents of the Reflection List be initialized |
|---|
| 2340 | on loading. The default, True, initializes the Reflection List as it is loaded. |
|---|
| 2341 | |
|---|
| 2342 | :returns: (hapVary,hapDict,controlDict) |
|---|
| 2343 | * hapVary: list of refined variables |
|---|
| 2344 | * hapDict: dict with refined variables and their values |
|---|
| 2345 | * controlDict: dict with fixed parameters |
|---|
| 2346 | ''' |
|---|
| 2347 | |
|---|
| 2348 | def PrintSize(hapData): |
|---|
| 2349 | if hapData[0] in ['isotropic','uniaxial']: |
|---|
| 2350 | line = '\n Size model : %9s'%(hapData[0]) |
|---|
| 2351 | line += ' equatorial:'+'%12.3f'%(hapData[1][0])+' Refine? '+str(hapData[2][0]) |
|---|
| 2352 | if hapData[0] == 'uniaxial': |
|---|
| 2353 | line += ' axial:'+'%12.3f'%(hapData[1][1])+' Refine? '+str(hapData[2][1]) |
|---|
| 2354 | line += '\n\t LG mixing coeff.: %12.4f'%(hapData[1][2])+' Refine? '+str(hapData[2][2]) |
|---|
| 2355 | pFile.write(line+'\n') |
|---|
| 2356 | else: |
|---|
| 2357 | pFile.write('\n Size model : %s\n\t LG mixing coeff.:%12.4f Refine? %s\n'% |
|---|
| 2358 | (hapData[0],hapData[1][2],hapData[2][2])) |
|---|
| 2359 | Snames = ['S11','S22','S33','S12','S13','S23'] |
|---|
| 2360 | ptlbls = ' names :' |
|---|
| 2361 | ptstr = ' values:' |
|---|
| 2362 | varstr = ' refine:' |
|---|
| 2363 | for i,name in enumerate(Snames): |
|---|
| 2364 | ptlbls += '%12s' % (name) |
|---|
| 2365 | ptstr += '%12.3f' % (hapData[4][i]) |
|---|
| 2366 | varstr += '%12s' % (str(hapData[5][i])) |
|---|
| 2367 | pFile.write(ptlbls+'\n') |
|---|
| 2368 | pFile.write(ptstr+'\n') |
|---|
| 2369 | pFile.write(varstr+'\n') |
|---|
| 2370 | |
|---|
| 2371 | def PrintMuStrain(hapData,SGData): |
|---|
| 2372 | if hapData[0] in ['isotropic','uniaxial']: |
|---|
| 2373 | line = '\n Mustrain model: %9s'%(hapData[0]) |
|---|
| 2374 | line += ' equatorial:'+'%12.1f'%(hapData[1][0])+' Refine? '+str(hapData[2][0]) |
|---|
| 2375 | if hapData[0] == 'uniaxial': |
|---|
| 2376 | line += ' axial:'+'%12.1f'%(hapData[1][1])+' Refine? '+str(hapData[2][1]) |
|---|
| 2377 | line +='\n\t LG mixing coeff.:%12.4f'%(hapData[1][2])+' Refine? '+str(hapData[2][2]) |
|---|
| 2378 | pFile.write(line+'\n') |
|---|
| 2379 | else: |
|---|
| 2380 | pFile.write('\n Mustrain model: %s\n\t LG mixing coeff.:%12.4f Refine? %s\n'% |
|---|
| 2381 | (hapData[0],hapData[1][2],hapData[2][2])) |
|---|
| 2382 | Snames = G2spc.MustrainNames(SGData) |
|---|
| 2383 | ptlbls = ' names :' |
|---|
| 2384 | ptstr = ' values:' |
|---|
| 2385 | varstr = ' refine:' |
|---|
| 2386 | for i,name in enumerate(Snames): |
|---|
| 2387 | ptlbls += '%12s' % (name) |
|---|
| 2388 | ptstr += '%12.1f' % (hapData[4][i]) |
|---|
| 2389 | varstr += '%12s' % (str(hapData[5][i])) |
|---|
| 2390 | pFile.write(ptlbls+'\n') |
|---|
| 2391 | pFile.write(ptstr+'\n') |
|---|
| 2392 | pFile.write(varstr+'\n') |
|---|
| 2393 | |
|---|
| 2394 | def PrintHStrain(hapData,SGData): |
|---|
| 2395 | pFile.write('\n Hydrostatic/elastic strain:\n') |
|---|
| 2396 | Hsnames = G2spc.HStrainNames(SGData) |
|---|
| 2397 | ptlbls = ' names :' |
|---|
| 2398 | ptstr = ' values:' |
|---|
| 2399 | varstr = ' refine:' |
|---|
| 2400 | for i,name in enumerate(Hsnames): |
|---|
| 2401 | ptlbls += '%12s' % (name) |
|---|
| 2402 | ptstr += '%12.4g' % (hapData[0][i]) |
|---|
| 2403 | varstr += '%12s' % (str(hapData[1][i])) |
|---|
| 2404 | pFile.write(ptlbls+'\n') |
|---|
| 2405 | pFile.write(ptstr+'\n') |
|---|
| 2406 | pFile.write(varstr+'\n') |
|---|
| 2407 | |
|---|
| 2408 | def PrintSHPO(hapData): |
|---|
| 2409 | pFile.write('\n Spherical harmonics preferred orientation: Order: %d Refine? %s\n'%(hapData[4],hapData[2])) |
|---|
| 2410 | ptlbls = ' names :' |
|---|
| 2411 | ptstr = ' values:' |
|---|
| 2412 | for item in hapData[5]: |
|---|
| 2413 | ptlbls += '%12s'%(item) |
|---|
| 2414 | ptstr += '%12.3f'%(hapData[5][item]) |
|---|
| 2415 | pFile.write(ptlbls+'\n') |
|---|
| 2416 | pFile.write(ptstr+'\n') |
|---|
| 2417 | |
|---|
| 2418 | def PrintBabinet(hapData): |
|---|
| 2419 | pFile.write('\n Babinet form factor modification:\n') |
|---|
| 2420 | ptlbls = ' names :' |
|---|
| 2421 | ptstr = ' values:' |
|---|
| 2422 | varstr = ' refine:' |
|---|
| 2423 | for name in ['BabA','BabU']: |
|---|
| 2424 | ptlbls += '%12s' % (name) |
|---|
| 2425 | ptstr += '%12.6f' % (hapData[name][0]) |
|---|
| 2426 | varstr += '%12s' % (str(hapData[name][1])) |
|---|
| 2427 | pFile.write(ptlbls+'\n') |
|---|
| 2428 | pFile.write(ptstr+'\n') |
|---|
| 2429 | pFile.write(varstr+'\n') |
|---|
| 2430 | |
|---|
| 2431 | hapDict = {} |
|---|
| 2432 | hapVary = [] |
|---|
| 2433 | controlDict = {} |
|---|
| 2434 | |
|---|
| 2435 | for phase in Phases: |
|---|
| 2436 | HistoPhase = Phases[phase]['Histograms'] |
|---|
| 2437 | SGData = Phases[phase]['General']['SGData'] |
|---|
| 2438 | cell = Phases[phase]['General']['Cell'][1:7] |
|---|
| 2439 | A = G2lat.cell2A(cell) |
|---|
| 2440 | if Phases[phase]['General'].get('Modulated',False): |
|---|
| 2441 | SSGData = Phases[phase]['General']['SSGData'] |
|---|
| 2442 | Vec,x,maxH = Phases[phase]['General']['SuperVec'] |
|---|
| 2443 | pId = Phases[phase]['pId'] |
|---|
| 2444 | for histogram in Histograms: |
|---|
| 2445 | if histogram not in HistoPhase and phase in Histograms[histogram]['Reflection Lists']: |
|---|
| 2446 | #remove previously created reflection list if histogram is removed from phase |
|---|
| 2447 | #print("removing ",phase,"from",histogram) |
|---|
| 2448 | del Histograms[histogram]['Reflection Lists'][phase] |
|---|
| 2449 | histoList = list(HistoPhase.keys()) |
|---|
| 2450 | histoList.sort() |
|---|
| 2451 | for histogram in histoList: |
|---|
| 2452 | try: |
|---|
| 2453 | Histogram = Histograms[histogram] |
|---|
| 2454 | except KeyError: |
|---|
| 2455 | #skip if histogram not included e.g. in a sequential refinement |
|---|
| 2456 | continue |
|---|
| 2457 | if not HistoPhase[histogram]['Use']: #remove previously created & now unused phase reflection list |
|---|
| 2458 | if phase in Histograms[histogram]['Reflection Lists']: |
|---|
| 2459 | del Histograms[histogram]['Reflection Lists'][phase] |
|---|
| 2460 | continue |
|---|
| 2461 | hapData = HistoPhase[histogram] |
|---|
| 2462 | hId = Histogram['hId'] |
|---|
| 2463 | if 'PWDR' in histogram: |
|---|
| 2464 | limits = Histogram['Limits'][1] |
|---|
| 2465 | inst = Histogram['Instrument Parameters'][0] #TODO - grab table here if present |
|---|
| 2466 | if 'C' in inst['Type'][1]: |
|---|
| 2467 | try: |
|---|
| 2468 | wave = inst['Lam'][1] |
|---|
| 2469 | except KeyError: |
|---|
| 2470 | wave = inst['Lam1'][1] |
|---|
| 2471 | dmin = wave/(2.0*sind(limits[1]/2.0)) |
|---|
| 2472 | elif 'T' in inst['Type'][0]: |
|---|
| 2473 | dmin = limits[0]/inst['difC'][1] |
|---|
| 2474 | else: |
|---|
| 2475 | wave = inst['Lam'][1] |
|---|
| 2476 | dmin = wave/(2.0*sind(limits[1]/2.0)) |
|---|
| 2477 | pfx = str(pId)+':'+str(hId)+':' |
|---|
| 2478 | if Phases[phase]['General']['doPawley']: |
|---|
| 2479 | hapDict[pfx+'LeBail'] = False #Pawley supercedes LeBail |
|---|
| 2480 | hapDict[pfx+'newLeBail'] = True |
|---|
| 2481 | Tmin = G2lat.Dsp2pos(inst,dmin) |
|---|
| 2482 | if 'T' in inst['Type'][1]: |
|---|
| 2483 | limits[0] = max(limits[0],Tmin) |
|---|
| 2484 | else: |
|---|
| 2485 | limits[1] = min(limits[1],Tmin) |
|---|
| 2486 | else: |
|---|
| 2487 | hapDict[pfx+'LeBail'] = hapData.get('LeBail',False) |
|---|
| 2488 | hapDict[pfx+'newLeBail'] = hapData.get('newLeBail',True) |
|---|
| 2489 | if Phases[phase]['General']['Type'] == 'magnetic': |
|---|
| 2490 | dmin = max(dmin,Phases[phase]['General'].get('MagDmin',0.)) |
|---|
| 2491 | for item in ['Scale','Extinction']: |
|---|
| 2492 | hapDict[pfx+item] = hapData[item][0] |
|---|
| 2493 | if hapData[item][1] and not hapDict[pfx+'LeBail']: |
|---|
| 2494 | hapVary.append(pfx+item) |
|---|
| 2495 | names = G2spc.HStrainNames(SGData) |
|---|
| 2496 | HSvals = [] |
|---|
| 2497 | for i,name in enumerate(names): |
|---|
| 2498 | hapDict[pfx+name] = hapData['HStrain'][0][i] |
|---|
| 2499 | HSvals.append(hapDict[pfx+name]) |
|---|
| 2500 | if hapData['HStrain'][1][i]: |
|---|
| 2501 | hapVary.append(pfx+name) |
|---|
| 2502 | if 'Layer Disp' in hapData: |
|---|
| 2503 | hapDict[pfx+'LayerDisp'] = hapData['Layer Disp'][0] |
|---|
| 2504 | if hapData['Layer Disp'][1]: |
|---|
| 2505 | hapVary.append(pfx+'LayerDisp') |
|---|
| 2506 | else: |
|---|
| 2507 | hapDict[pfx+'LayerDisp'] = 0.0 |
|---|
| 2508 | controlDict[pfx+'poType'] = hapData['Pref.Ori.'][0] |
|---|
| 2509 | if hapData['Pref.Ori.'][0] == 'MD': |
|---|
| 2510 | hapDict[pfx+'MD'] = hapData['Pref.Ori.'][1] |
|---|
| 2511 | controlDict[pfx+'MDAxis'] = hapData['Pref.Ori.'][3] |
|---|
| 2512 | if hapData['Pref.Ori.'][2] and not hapDict[pfx+'LeBail']: |
|---|
| 2513 | hapVary.append(pfx+'MD') |
|---|
| 2514 | else: #'SH' spherical harmonics |
|---|
| 2515 | controlDict[pfx+'SHord'] = hapData['Pref.Ori.'][4] |
|---|
| 2516 | controlDict[pfx+'SHncof'] = len(hapData['Pref.Ori.'][5]) |
|---|
| 2517 | controlDict[pfx+'SHnames'] = G2lat.GenSHCoeff(SGData['SGLaue'],'0',controlDict[pfx+'SHord'],False) |
|---|
| 2518 | controlDict[pfx+'SHhkl'] = [] |
|---|
| 2519 | try: #patch for old Pref.Ori. items |
|---|
| 2520 | controlDict[pfx+'SHtoler'] = 0.1 |
|---|
| 2521 | if hapData['Pref.Ori.'][6][0] != '': |
|---|
| 2522 | controlDict[pfx+'SHhkl'] = [eval(a.replace(' ',',')) for a in hapData['Pref.Ori.'][6]] |
|---|
| 2523 | controlDict[pfx+'SHtoler'] = hapData['Pref.Ori.'][7] |
|---|
| 2524 | except IndexError: |
|---|
| 2525 | pass |
|---|
| 2526 | for item in hapData['Pref.Ori.'][5]: |
|---|
| 2527 | hapDict[pfx+item] = hapData['Pref.Ori.'][5][item] |
|---|
| 2528 | if hapData['Pref.Ori.'][2] and not hapDict[pfx+'LeBail']: |
|---|
| 2529 | hapVary.append(pfx+item) |
|---|
| 2530 | for item in ['Mustrain','Size']: |
|---|
| 2531 | controlDict[pfx+item+'Type'] = hapData[item][0] |
|---|
| 2532 | hapDict[pfx+item+';mx'] = hapData[item][1][2] |
|---|
| 2533 | if hapData[item][2][2]: |
|---|
| 2534 | hapVary.append(pfx+item+';mx') |
|---|
| 2535 | if hapData[item][0] in ['isotropic','uniaxial']: |
|---|
| 2536 | hapDict[pfx+item+';i'] = hapData[item][1][0] |
|---|
| 2537 | if hapData[item][2][0]: |
|---|
| 2538 | hapVary.append(pfx+item+';i') |
|---|
| 2539 | if hapData[item][0] == 'uniaxial': |
|---|
| 2540 | controlDict[pfx+item+'Axis'] = hapData[item][3] |
|---|
| 2541 | hapDict[pfx+item+';a'] = hapData[item][1][1] |
|---|
| 2542 | if hapData[item][2][1]: |
|---|
| 2543 | hapVary.append(pfx+item+';a') |
|---|
| 2544 | else: #generalized for mustrain or ellipsoidal for size |
|---|
| 2545 | Nterms = len(hapData[item][4]) |
|---|
| 2546 | if item == 'Mustrain': |
|---|
| 2547 | names = G2spc.MustrainNames(SGData) |
|---|
| 2548 | pwrs = [] |
|---|
| 2549 | for name in names: |
|---|
| 2550 | h,k,l = name[1:] |
|---|
| 2551 | pwrs.append([int(h),int(k),int(l)]) |
|---|
| 2552 | controlDict[pfx+'MuPwrs'] = pwrs |
|---|
| 2553 | for i in range(Nterms): |
|---|
| 2554 | sfx = ';'+str(i) |
|---|
| 2555 | hapDict[pfx+item+sfx] = hapData[item][4][i] |
|---|
| 2556 | if hapData[item][5][i]: |
|---|
| 2557 | hapVary.append(pfx+item+sfx) |
|---|
| 2558 | if Phases[phase]['General']['Type'] != 'magnetic': |
|---|
| 2559 | for bab in ['BabA','BabU']: |
|---|
| 2560 | hapDict[pfx+bab] = hapData['Babinet'][bab][0] |
|---|
| 2561 | if hapData['Babinet'][bab][1] and not hapDict[pfx+'LeBail']: |
|---|
| 2562 | hapVary.append(pfx+bab) |
|---|
| 2563 | |
|---|
| 2564 | if Print: |
|---|
| 2565 | pFile.write('\n Phase: %s in histogram: %s\n'%(phase,histogram)) |
|---|
| 2566 | pFile.write(135*'='+'\n') |
|---|
| 2567 | if hapDict[pfx+'LeBail']: |
|---|
| 2568 | pFile.write(' Perform LeBail extraction\n') |
|---|
| 2569 | else: |
|---|
| 2570 | pFile.write(' Phase fraction : %10.4f Refine? %s\n'%(hapData['Scale'][0],hapData['Scale'][1])) |
|---|
| 2571 | pFile.write(' Extinction coeff: %10.4f Refine? %s\n'%(hapData['Extinction'][0],hapData['Extinction'][1])) |
|---|
| 2572 | if hapData['Pref.Ori.'][0] == 'MD': |
|---|
| 2573 | Ax = hapData['Pref.Ori.'][3] |
|---|
| 2574 | pFile.write(' March-Dollase PO: %10.4f Refine? %s Axis: %d %d %d\n'% |
|---|
| 2575 | (hapData['Pref.Ori.'][1],hapData['Pref.Ori.'][2],Ax[0],Ax[1],Ax[2])) |
|---|
| 2576 | else: #'SH' for spherical harmonics |
|---|
| 2577 | PrintSHPO(hapData['Pref.Ori.']) |
|---|
| 2578 | pFile.write(' Penalty hkl list: %s tolerance: %.2f\n'%(controlDict[pfx+'SHhkl'],controlDict[pfx+'SHtoler'])) |
|---|
| 2579 | PrintSize(hapData['Size']) |
|---|
| 2580 | PrintMuStrain(hapData['Mustrain'],SGData) |
|---|
| 2581 | PrintHStrain(hapData['HStrain'],SGData) |
|---|
| 2582 | if 'Layer Disp' in hapData: |
|---|
| 2583 | pFile.write(' Layer Displacement: %10.3f Refine? %s\n'%(hapData['Layer Disp'][0],hapData['Layer Disp'][1])) |
|---|
| 2584 | if Phases[phase]['General']['Type'] != 'magnetic': |
|---|
| 2585 | if hapData['Babinet']['BabA'][0]: |
|---|
| 2586 | PrintBabinet(hapData['Babinet']) |
|---|
| 2587 | if phase in Histogram['Reflection Lists'] and 'RefList' not in Histogram['Reflection Lists'][phase] and hapData.get('LeBail',False): |
|---|
| 2588 | hapData['newLeBail'] = True |
|---|
| 2589 | if resetRefList and (not hapDict[pfx+'LeBail'] or (hapData.get('LeBail',False) and hapData['newLeBail'])): |
|---|
| 2590 | if hapData.get('LeBail',True): #stop regeneating reflections for LeBail |
|---|
| 2591 | hapData['newLeBail'] = False |
|---|
| 2592 | refList = [] |
|---|
| 2593 | # Uniq = [] |
|---|
| 2594 | # Phi = [] |
|---|
| 2595 | useExt = 'magnetic' in Phases[phase]['General']['Type'] and 'N' in inst['Type'][0] |
|---|
| 2596 | if Phases[phase]['General'].get('Modulated',False): |
|---|
| 2597 | ifSuper = True |
|---|
| 2598 | HKLd = np.array(G2lat.GenSSHLaue(dmin,SGData,SSGData,Vec,maxH,A)) |
|---|
| 2599 | HKLd = G2mth.sortArray(HKLd,4,reverse=True) |
|---|
| 2600 | for h,k,l,m,d in HKLd: |
|---|
| 2601 | ext,mul,uniq,phi = G2spc.GenHKLf([h,k,l],SGData) |
|---|
| 2602 | mul *= 2 # for powder overlap of Friedel pairs |
|---|
| 2603 | if m or not ext or useExt: |
|---|
| 2604 | if 'C' in inst['Type'][0]: |
|---|
| 2605 | pos = G2lat.Dsp2pos(inst,d) |
|---|
| 2606 | if limits[0] < pos < limits[1]: |
|---|
| 2607 | refList.append([h,k,l,m,mul,d, pos,0.0,0.0,0.0,1., 0.0,0.0,1.0,1.0,1.0]) |
|---|
| 2608 | #... sig,gam,fotsq,fctsq, phase,icorr,prfo,abs,ext |
|---|
| 2609 | # Uniq.append(uniq) |
|---|
| 2610 | # Phi.append(phi) |
|---|
| 2611 | elif 'T' in inst['Type'][0]: |
|---|
| 2612 | pos = G2lat.Dsp2pos(inst,d) |
|---|
| 2613 | if limits[0] < pos < limits[1]: |
|---|
| 2614 | wave = inst['difC'][1]*d/(252.816*inst['fltPath'][0]) |
|---|
| 2615 | refList.append([h,k,l,m,mul,d, pos,0.0,0.0,0.0,1., 0.0,0.0,0.0,0.0,wave, 1.0,1.0,1.0]) |
|---|
| 2616 | # ... sig,gam,fotsq,fctsq, phase,icorr,alp,bet,wave, prfo,abs,ext |
|---|
| 2617 | #TODO - if tabulated put alp & bet in here |
|---|
| 2618 | # Uniq.append(uniq) |
|---|
| 2619 | # Phi.append(phi) |
|---|
| 2620 | elif 'B' in inst['Type'][0]: |
|---|
| 2621 | pos = G2lat.Dsp2pos(inst,d) |
|---|
| 2622 | if limits[0] < pos < limits[1]: |
|---|
| 2623 | refList.append([h,k,l,m,mul,d, pos,0.0,0.0,0.0,1., 0.0,0.0,0.0,0.0, 1.0,1.0,1.0]) |
|---|
| 2624 | # ... sig,gam,fotsq,fctsq, phase,icorr,alp,bet, prfo,abs,ext |
|---|
| 2625 | else: |
|---|
| 2626 | ifSuper = False |
|---|
| 2627 | HKLd = np.array(G2lat.GenHLaue(dmin,SGData,A)) |
|---|
| 2628 | HKLd = G2mth.sortArray(HKLd,3,reverse=True) |
|---|
| 2629 | for h,k,l,d in HKLd: |
|---|
| 2630 | ext,mul,uniq,phi = G2spc.GenHKLf([h,k,l],SGData) |
|---|
| 2631 | if ext and 'N' in inst['Type'][0] and 'MagSpGrp' in SGData: |
|---|
| 2632 | ext = G2spc.checkMagextc([h,k,l],SGData) |
|---|
| 2633 | mul *= 2 # for powder overlap of Friedel pairs |
|---|
| 2634 | if ext and not useExt: |
|---|
| 2635 | continue |
|---|
| 2636 | if 'C' in inst['Type'][0]: |
|---|
| 2637 | pos = G2lat.Dsp2pos(inst,d) |
|---|
| 2638 | if limits[0] < pos < limits[1]: |
|---|
| 2639 | refList.append([h,k,l,mul,d, pos,0.0,0.0,0.0,1., 0.0,0.0,1.0,1.0,1.0]) |
|---|
| 2640 | #... sig,gam,fotsq,fctsq, phase,icorr,prfo,abs,ext |
|---|
| 2641 | # Uniq.append(uniq) |
|---|
| 2642 | # Phi.append(phi) |
|---|
| 2643 | elif 'T' in inst['Type'][0]: |
|---|
| 2644 | pos = G2lat.Dsp2pos(inst,d) |
|---|
| 2645 | if limits[0] < pos < limits[1]: |
|---|
| 2646 | wave = inst['difC'][1]*d/(252.816*inst['fltPath'][0]) |
|---|
| 2647 | refList.append([h,k,l,mul,d, pos,0.0,0.0,0.0,1., 0.0,0.0,0.0,0.0,wave, 1.0,1.0,1.0]) |
|---|
| 2648 | # ... sig,gam,fotsq,fctsq, phase,icorr,alp,bet,wave, prfo,abs,ext |
|---|
| 2649 | # Uniq.append(uniq) |
|---|
| 2650 | # Phi.append(phi) |
|---|
| 2651 | elif 'B' in inst['Type'][0]: |
|---|
| 2652 | pos = G2lat.Dsp2pos(inst,d) |
|---|
| 2653 | if limits[0] < pos < limits[1]: |
|---|
| 2654 | refList.append([h,k,l,mul,d, pos,0.0,0.0,0.0,1., 0.0,0.0,0.0,0.0, 1.0,1.0,1.0]) |
|---|
| 2655 | # ... sig,gam,fotsq,fctsq, phase,icorr,alp,bet, prfo,abs,ext |
|---|
| 2656 | Histogram['Reflection Lists'][phase] = {'RefList':np.array(refList),'FF':{},'Type':inst['Type'][0],'Super':ifSuper} |
|---|
| 2657 | elif 'HKLF' in histogram: |
|---|
| 2658 | inst = Histogram['Instrument Parameters'][0] |
|---|
| 2659 | hId = Histogram['hId'] |
|---|
| 2660 | hfx = ':%d:'%(hId) |
|---|
| 2661 | for item in inst: |
|---|
| 2662 | if type(inst) is not list and item != 'Type': continue # skip over non-refined items (such as InstName) |
|---|
| 2663 | hapDict[hfx+item] = inst[item][1] |
|---|
| 2664 | pfx = str(pId)+':'+str(hId)+':' |
|---|
| 2665 | hapDict[pfx+'Scale'] = hapData['Scale'][0] |
|---|
| 2666 | if hapData['Scale'][1]: |
|---|
| 2667 | hapVary.append(pfx+'Scale') |
|---|
| 2668 | |
|---|
| 2669 | extApprox,extType,extParms = hapData['Extinction'] |
|---|
| 2670 | controlDict[pfx+'EType'] = extType |
|---|
| 2671 | controlDict[pfx+'EApprox'] = extApprox |
|---|
| 2672 | if 'C' in inst['Type'][0]: |
|---|
| 2673 | controlDict[pfx+'Tbar'] = extParms['Tbar'] |
|---|
| 2674 | controlDict[pfx+'Cos2TM'] = extParms['Cos2TM'] |
|---|
| 2675 | if 'Primary' in extType: |
|---|
| 2676 | Ekey = ['Ep',] |
|---|
| 2677 | elif 'I & II' in extType: |
|---|
| 2678 | Ekey = ['Eg','Es'] |
|---|
| 2679 | elif 'Secondary Type II' == extType: |
|---|
| 2680 | Ekey = ['Es',] |
|---|
| 2681 | elif 'Secondary Type I' == extType: |
|---|
| 2682 | Ekey = ['Eg',] |
|---|
| 2683 | else: #'None' |
|---|
| 2684 | Ekey = [] |
|---|
| 2685 | for eKey in Ekey: |
|---|
| 2686 | hapDict[pfx+eKey] = extParms[eKey][0] |
|---|
| 2687 | if extParms[eKey][1]: |
|---|
| 2688 | hapVary.append(pfx+eKey) |
|---|
| 2689 | for bab in ['BabA','BabU']: |
|---|
| 2690 | hapDict[pfx+bab] = hapData['Babinet'][bab][0] |
|---|
| 2691 | if hapData['Babinet'][bab][1]: |
|---|
| 2692 | hapVary.append(pfx+bab) |
|---|
| 2693 | Twins = hapData.get('Twins',[[np.array([[1,0,0],[0,1,0],[0,0,1]]),[1.0,False,0]],]) |
|---|
| 2694 | if len(Twins) == 1: |
|---|
| 2695 | hapDict[pfx+'Flack'] = hapData.get('Flack',[0.,False])[0] |
|---|
| 2696 | if hapData.get('Flack',[0,False])[1]: |
|---|
| 2697 | hapVary.append(pfx+'Flack') |
|---|
| 2698 | sumTwFr = 0. |
|---|
| 2699 | controlDict[pfx+'TwinLaw'] = [] |
|---|
| 2700 | controlDict[pfx+'TwinInv'] = [] |
|---|
| 2701 | NTL = 0 |
|---|
| 2702 | for it,twin in enumerate(Twins): |
|---|
| 2703 | if 'bool' in str(type(twin[0])): |
|---|
| 2704 | controlDict[pfx+'TwinInv'].append(twin[0]) |
|---|
| 2705 | controlDict[pfx+'TwinLaw'].append(np.zeros((3,3))) |
|---|
| 2706 | else: |
|---|
| 2707 | NTL += 1 |
|---|
| 2708 | controlDict[pfx+'TwinInv'].append(False) |
|---|
| 2709 | controlDict[pfx+'TwinLaw'].append(twin[0]) |
|---|
| 2710 | if it: |
|---|
| 2711 | hapDict[pfx+'TwinFr:'+str(it)] = twin[1] |
|---|
| 2712 | sumTwFr += twin[1] |
|---|
| 2713 | else: |
|---|
| 2714 | hapDict[pfx+'TwinFr:0'] = twin[1][0] |
|---|
| 2715 | controlDict[pfx+'TwinNMN'] = twin[1][1] |
|---|
| 2716 | if Twins[0][1][1]: |
|---|
| 2717 | hapVary.append(pfx+'TwinFr:'+str(it)) |
|---|
| 2718 | controlDict[pfx+'NTL'] = NTL |
|---|
| 2719 | #need to make constraint on TwinFr |
|---|
| 2720 | controlDict[pfx+'TwinLaw'] = np.array(controlDict[pfx+'TwinLaw']) |
|---|
| 2721 | if len(Twins) > 1: #force sum to unity |
|---|
| 2722 | hapDict[pfx+'TwinFr:0'] = 1.-sumTwFr |
|---|
| 2723 | if Print: |
|---|
| 2724 | pFile.write('\n Phase: %s in histogram: %s\n'%(phase,histogram)) |
|---|
| 2725 | pFile.write(135*'='+'\n') |
|---|
| 2726 | pFile.write(' Scale factor : %10.4f Refine? %s\n'%(hapData['Scale'][0],hapData['Scale'][1])) |
|---|
| 2727 | if extType != 'None': |
|---|
| 2728 | pFile.write(' Extinction Type: %15s approx: %10s\n'%(extType,extApprox)) |
|---|
| 2729 | text = ' Parameters :' |
|---|
| 2730 | for eKey in Ekey: |
|---|
| 2731 | text += ' %4s : %10.3e Refine? '%(eKey,extParms[eKey][0])+str(extParms[eKey][1]) |
|---|
| 2732 | pFile.write(text+'\n') |
|---|
| 2733 | if hapData['Babinet']['BabA'][0]: |
|---|
| 2734 | PrintBabinet(hapData['Babinet']) |
|---|
| 2735 | if not SGData['SGInv'] and len(Twins) == 1: |
|---|
| 2736 | pFile.write(' Flack parameter: %10.3f Refine? %s\n'%(hapData['Flack'][0],hapData['Flack'][1])) |
|---|
| 2737 | if len(Twins) > 1: |
|---|
| 2738 | for it,twin in enumerate(Twins): |
|---|
| 2739 | if 'bool' in str(type(twin[0])): |
|---|
| 2740 | pFile.write(' Nonmerohedral twin fr.: %5.3f Inv? %s Refine? %s\n'% |
|---|
| 2741 | (hapDict[pfx+'TwinFr:'+str(it)],str(controlDict[pfx+'TwinInv'][it]),str(Twins[0][1][1]))) |
|---|
| 2742 | else: |
|---|
| 2743 | pFile.write(' Twin law: %s Twin fr.: %5.3f Refine? %s\n'% |
|---|
| 2744 | (str(twin[0]).replace('\n',','),hapDict[pfx+'TwinFr:'+str(it)],str(Twins[0][1][1]))) |
|---|
| 2745 | |
|---|
| 2746 | Histogram['Reflection Lists'] = phase |
|---|
| 2747 | |
|---|
| 2748 | return hapVary,hapDict,controlDict |
|---|
| 2749 | |
|---|
| 2750 | def SetHistogramPhaseData(parmDict,sigDict,Phases,Histograms,FFtables,Print=True,pFile=None): |
|---|
| 2751 | 'needs a doc string' |
|---|
| 2752 | |
|---|
| 2753 | def PrintSizeAndSig(hapData,sizeSig): |
|---|
| 2754 | line = '\n Size model: %9s'%(hapData[0]) |
|---|
| 2755 | refine = False |
|---|
| 2756 | if hapData[0] in ['isotropic','uniaxial']: |
|---|
| 2757 | line += ' equatorial:%12.5f'%(hapData[1][0]) |
|---|
| 2758 | if sizeSig[0][0]: |
|---|
| 2759 | line += ', sig:%8.4f'%(sizeSig[0][0]) |
|---|
| 2760 | refine = True |
|---|
| 2761 | if hapData[0] == 'uniaxial': |
|---|
| 2762 | line += ' axial:%12.4f'%(hapData[1][1]) |
|---|
| 2763 | if sizeSig[0][1]: |
|---|
| 2764 | refine = True |
|---|
| 2765 | line += ', sig:%8.4f'%(sizeSig[0][1]) |
|---|
| 2766 | line += ' LG mix coeff.:%12.4f'%(hapData[1][2]) |
|---|
| 2767 | if sizeSig[0][2]: |
|---|
| 2768 | refine = True |
|---|
| 2769 | line += ', sig:%8.4f'%(sizeSig[0][2]) |
|---|
| 2770 | if refine: |
|---|
| 2771 | pFile.write(line+'\n') |
|---|
| 2772 | else: |
|---|
| 2773 | line += ' LG mix coeff.:%12.4f'%(hapData[1][2]) |
|---|
| 2774 | if sizeSig[0][2]: |
|---|
| 2775 | refine = True |
|---|
| 2776 | line += ', sig:%8.4f'%(sizeSig[0][2]) |
|---|
| 2777 | Snames = ['S11','S22','S33','S12','S13','S23'] |
|---|
| 2778 | ptlbls = ' name :' |
|---|
| 2779 | ptstr = ' value :' |
|---|
| 2780 | sigstr = ' sig :' |
|---|
| 2781 | for i,name in enumerate(Snames): |
|---|
| 2782 | ptlbls += '%12s' % (name) |
|---|
| 2783 | ptstr += '%12.6f' % (hapData[4][i]) |
|---|
| 2784 | if sizeSig[1][i]: |
|---|
| 2785 | refine = True |
|---|
| 2786 | sigstr += '%12.6f' % (sizeSig[1][i]) |
|---|
| 2787 | else: |
|---|
| 2788 | sigstr += 12*' ' |
|---|
| 2789 | if refine: |
|---|
| 2790 | pFile.write(line+'\n') |
|---|
| 2791 | pFile.write(ptlbls+'\n') |
|---|
| 2792 | pFile.write(ptstr+'\n') |
|---|
| 2793 | pFile.write(sigstr+'\n') |
|---|
| 2794 | |
|---|
| 2795 | def PrintMuStrainAndSig(hapData,mustrainSig,SGData): |
|---|
| 2796 | line = '\n Mustrain model: %9s\n'%(hapData[0]) |
|---|
| 2797 | refine = False |
|---|
| 2798 | if hapData[0] in ['isotropic','uniaxial']: |
|---|
| 2799 | line += ' equatorial:%12.1f'%(hapData[1][0]) |
|---|
| 2800 | if mustrainSig[0][0]: |
|---|
| 2801 | line += ', sig:%8.1f'%(mustrainSig[0][0]) |
|---|
| 2802 | refine = True |
|---|
| 2803 | if hapData[0] == 'uniaxial': |
|---|
| 2804 | line += ' axial:%12.1f'%(hapData[1][1]) |
|---|
| 2805 | if mustrainSig[0][1]: |
|---|
| 2806 | line += ', sig:%8.1f'%(mustrainSig[0][1]) |
|---|
| 2807 | line += ' LG mix coeff.:%12.4f'%(hapData[1][2]) |
|---|
| 2808 | if mustrainSig[0][2]: |
|---|
| 2809 | refine = True |
|---|
| 2810 | line += ', sig:%8.3f'%(mustrainSig[0][2]) |
|---|
| 2811 | if refine: |
|---|
| 2812 | pFile.write(line+'\n') |
|---|
| 2813 | else: |
|---|
| 2814 | line += ' LG mix coeff.:%12.4f'%(hapData[1][2]) |
|---|
| 2815 | if mustrainSig[0][2]: |
|---|
| 2816 | refine = True |
|---|
| 2817 | line += ', sig:%8.3f'%(mustrainSig[0][2]) |
|---|
| 2818 | Snames = G2spc.MustrainNames(SGData) |
|---|
| 2819 | ptlbls = ' name :' |
|---|
| 2820 | ptstr = ' value :' |
|---|
| 2821 | sigstr = ' sig :' |
|---|
| 2822 | for i,name in enumerate(Snames): |
|---|
| 2823 | ptlbls += '%12s' % (name) |
|---|
| 2824 | ptstr += '%12.1f' % (hapData[4][i]) |
|---|
| 2825 | if mustrainSig[1][i]: |
|---|
| 2826 | refine = True |
|---|
| 2827 | sigstr += '%12.1f' % (mustrainSig[1][i]) |
|---|
| 2828 | else: |
|---|
| 2829 | sigstr += 12*' ' |
|---|
| 2830 | if refine: |
|---|
| 2831 | pFile.write(line+'\n') |
|---|
| 2832 | pFile.write(ptlbls+'\n') |
|---|
| 2833 | pFile.write(ptstr+'\n') |
|---|
| 2834 | pFile.write(sigstr+'\n') |
|---|
| 2835 | |
|---|
| 2836 | def PrintHStrainAndSig(hapData,strainSig,SGData): |
|---|
| 2837 | Hsnames = G2spc.HStrainNames(SGData) |
|---|
| 2838 | ptlbls = ' name :' |
|---|
| 2839 | ptstr = ' value :' |
|---|
| 2840 | sigstr = ' sig :' |
|---|
| 2841 | refine = False |
|---|
| 2842 | for i,name in enumerate(Hsnames): |
|---|
| 2843 | ptlbls += '%12s' % (name) |
|---|
| 2844 | ptstr += '%12.4g' % (hapData[0][i]) |
|---|
| 2845 | if name in strainSig: |
|---|
| 2846 | refine = True |
|---|
| 2847 | sigstr += '%12.4g' % (strainSig[name]) |
|---|
| 2848 | else: |
|---|
| 2849 | sigstr += 12*' ' |
|---|
| 2850 | if refine: |
|---|
| 2851 | pFile.write('\n Hydrostatic/elastic strain:\n') |
|---|
| 2852 | pFile.write(ptlbls+'\n') |
|---|
| 2853 | pFile.write(ptstr+'\n') |
|---|
| 2854 | pFile.write(sigstr+'\n') |
|---|
| 2855 | |
|---|
| 2856 | def PrintSHPOAndSig(pfx,hapData,POsig): |
|---|
| 2857 | Tindx = 1.0 |
|---|
| 2858 | Tvar = 0.0 |
|---|
| 2859 | pFile.write('\n Spherical harmonics preferred orientation: Order: %d\n'%hapData[4]) |
|---|
| 2860 | ptlbls = ' names :' |
|---|
| 2861 | ptstr = ' values:' |
|---|
| 2862 | sigstr = ' sig :' |
|---|
| 2863 | for item in hapData[5]: |
|---|
| 2864 | ptlbls += '%12s'%(item) |
|---|
| 2865 | ptstr += '%12.3f'%(hapData[5][item]) |
|---|
| 2866 | l = 2.0*eval(item.strip('C'))[0]+1 |
|---|
| 2867 | Tindx += hapData[5][item]**2/l |
|---|
| 2868 | if pfx+item in POsig: |
|---|
| 2869 | Tvar += (2.*hapData[5][item]*POsig[pfx+item]/l)**2 |
|---|
| 2870 | sigstr += '%12.3f'%(POsig[pfx+item]) |
|---|
| 2871 | else: |
|---|
| 2872 | sigstr += 12*' ' |
|---|
| 2873 | pFile.write(ptlbls+'\n') |
|---|
| 2874 | pFile.write(ptstr+'\n') |
|---|
| 2875 | pFile.write(sigstr+'\n') |
|---|
| 2876 | pFile.write('\n Texture index J = %.3f(%d)\n'%(Tindx,int(1000*np.sqrt(Tvar)))) |
|---|
| 2877 | |
|---|
| 2878 | def PrintExtAndSig(pfx,hapData,ScalExtSig): |
|---|
| 2879 | pFile.write('\n Single crystal extinction: Type: %s Approx: %s\n'%(hapData[0],hapData[1])) |
|---|
| 2880 | text = '' |
|---|
| 2881 | for item in hapData[2]: |
|---|
| 2882 | if pfx+item in ScalExtSig: |
|---|
| 2883 | text += ' %s: '%(item) |
|---|
| 2884 | text += '%12.2e'%(hapData[2][item][0]) |
|---|
| 2885 | if pfx+item in ScalExtSig: |
|---|
| 2886 | text += ' sig: %12.2e'%(ScalExtSig[pfx+item]) |
|---|
| 2887 | pFile.write(text+'\n') |
|---|
| 2888 | |
|---|
| 2889 | def PrintBabinetAndSig(pfx,hapData,BabSig): |
|---|
| 2890 | pFile.write('\n Babinet form factor modification:\n') |
|---|
| 2891 | ptlbls = ' names :' |
|---|
| 2892 | ptstr = ' values:' |
|---|
| 2893 | sigstr = ' sig :' |
|---|
| 2894 | for item in hapData: |
|---|
| 2895 | ptlbls += '%12s'%(item) |
|---|
| 2896 | ptstr += '%12.3f'%(hapData[item][0]) |
|---|
| 2897 | if pfx+item in BabSig: |
|---|
| 2898 | sigstr += '%12.3f'%(BabSig[pfx+item]) |
|---|
| 2899 | else: |
|---|
| 2900 | sigstr += 12*' ' |
|---|
| 2901 | pFile.write(ptlbls+'\n') |
|---|
| 2902 | pFile.write(ptstr+'\n') |
|---|
| 2903 | pFile.write(sigstr+'\n') |
|---|
| 2904 | |
|---|
| 2905 | def PrintTwinsAndSig(pfx,twinData,TwinSig): |
|---|
| 2906 | pFile.write('\n Twin Law fractions :\n') |
|---|
| 2907 | ptlbls = ' names :' |
|---|
| 2908 | ptstr = ' values:' |
|---|
| 2909 | sigstr = ' sig :' |
|---|
| 2910 | for it,item in enumerate(twinData): |
|---|
| 2911 | ptlbls += ' twin #%d'%(it) |
|---|
| 2912 | if it: |
|---|
| 2913 | ptstr += '%12.3f'%(item[1]) |
|---|
| 2914 | else: |
|---|
| 2915 | ptstr += '%12.3f'%(item[1][0]) |
|---|
| 2916 | if pfx+'TwinFr:'+str(it) in TwinSig: |
|---|
| 2917 | sigstr += '%12.3f'%(TwinSig[pfx+'TwinFr:'+str(it)]) |
|---|
| 2918 | else: |
|---|
| 2919 | sigstr += 12*' ' |
|---|
| 2920 | pFile.write(ptlbls+'\n') |
|---|
| 2921 | pFile.write(ptstr+'\n') |
|---|
| 2922 | pFile.write(sigstr+'\n') |
|---|
| 2923 | |
|---|
| 2924 | |
|---|
| 2925 | PhFrExtPOSig = {} |
|---|
| 2926 | SizeMuStrSig = {} |
|---|
| 2927 | ScalExtSig = {} |
|---|
| 2928 | BabSig = {} |
|---|
| 2929 | TwinFrSig = {} |
|---|
| 2930 | wtFrSum = {} |
|---|
| 2931 | for phase in Phases: |
|---|
| 2932 | HistoPhase = Phases[phase]['Histograms'] |
|---|
| 2933 | General = Phases[phase]['General'] |
|---|
| 2934 | SGData = General['SGData'] |
|---|
| 2935 | pId = Phases[phase]['pId'] |
|---|
| 2936 | histoList = list(HistoPhase.keys()) |
|---|
| 2937 | histoList.sort() |
|---|
| 2938 | for histogram in histoList: |
|---|
| 2939 | try: |
|---|
| 2940 | Histogram = Histograms[histogram] |
|---|
| 2941 | except KeyError: |
|---|
| 2942 | #skip if histogram not included e.g. in a sequential refinement |
|---|
| 2943 | continue |
|---|
| 2944 | if not Phases[phase]['Histograms'][histogram]['Use']: |
|---|
| 2945 | #skip if phase absent from this histogram |
|---|
| 2946 | continue |
|---|
| 2947 | hapData = HistoPhase[histogram] |
|---|
| 2948 | hId = Histogram['hId'] |
|---|
| 2949 | pfx = str(pId)+':'+str(hId)+':' |
|---|
| 2950 | if hId not in wtFrSum: |
|---|
| 2951 | wtFrSum[hId] = 0. |
|---|
| 2952 | if 'PWDR' in histogram: |
|---|
| 2953 | for item in ['Scale','Extinction']: |
|---|
| 2954 | hapData[item][0] = parmDict[pfx+item] |
|---|
| 2955 | if pfx+item in sigDict and not parmDict[pfx+'LeBail']: |
|---|
| 2956 | PhFrExtPOSig.update({pfx+item:sigDict[pfx+item],}) |
|---|
| 2957 | wtFrSum[hId] += hapData['Scale'][0]*General['Mass'] |
|---|
| 2958 | if hapData['Pref.Ori.'][0] == 'MD': |
|---|
| 2959 | hapData['Pref.Ori.'][1] = parmDict[pfx+'MD'] |
|---|
| 2960 | if pfx+'MD' in sigDict and not parmDict[pfx+'LeBail']: |
|---|
| 2961 | PhFrExtPOSig.update({pfx+'MD':sigDict[pfx+'MD'],}) |
|---|
| 2962 | else: #'SH' spherical harmonics |
|---|
| 2963 | for item in hapData['Pref.Ori.'][5]: |
|---|
| 2964 | hapData['Pref.Ori.'][5][item] = parmDict[pfx+item] |
|---|
| 2965 | if pfx+item in sigDict and not parmDict[pfx+'LeBail']: |
|---|
| 2966 | PhFrExtPOSig.update({pfx+item:sigDict[pfx+item],}) |
|---|
| 2967 | SizeMuStrSig.update({pfx+'Mustrain':[[0,0,0],[0 for i in range(len(hapData['Mustrain'][4]))]], |
|---|
| 2968 | pfx+'Size':[[0,0,0],[0 for i in range(len(hapData['Size'][4]))]], |
|---|
| 2969 | pfx+'HStrain':{}}) |
|---|
| 2970 | for item in ['Mustrain','Size']: |
|---|
| 2971 | hapData[item][1][2] = parmDict[pfx+item+';mx'] |
|---|
| 2972 | # hapData[item][1][2] = min(1.,max(0.,hapData[item][1][2])) |
|---|
| 2973 | if pfx+item+';mx' in sigDict: |
|---|
| 2974 | SizeMuStrSig[pfx+item][0][2] = sigDict[pfx+item+';mx'] |
|---|
| 2975 | if hapData[item][0] in ['isotropic','uniaxial']: |
|---|
| 2976 | hapData[item][1][0] = parmDict[pfx+item+';i'] |
|---|
| 2977 | if item == 'Size': |
|---|
| 2978 | hapData[item][1][0] = min(10.,max(0.001,hapData[item][1][0])) |
|---|
| 2979 | if pfx+item+';i' in sigDict: |
|---|
| 2980 | SizeMuStrSig[pfx+item][0][0] = sigDict[pfx+item+';i'] |
|---|
| 2981 | if hapData[item][0] == 'uniaxial': |
|---|
| 2982 | hapData[item][1][1] = parmDict[pfx+item+';a'] |
|---|
| 2983 | if item == 'Size': |
|---|
| 2984 | hapData[item][1][1] = min(10.,max(0.001,hapData[item][1][1])) |
|---|
| 2985 | if pfx+item+';a' in sigDict: |
|---|
| 2986 | SizeMuStrSig[pfx+item][0][1] = sigDict[pfx+item+';a'] |
|---|
| 2987 | else: #generalized for mustrain or ellipsoidal for size |
|---|
| 2988 | Nterms = len(hapData[item][4]) |
|---|
| 2989 | for i in range(Nterms): |
|---|
| 2990 | sfx = ';'+str(i) |
|---|
| 2991 | hapData[item][4][i] = parmDict[pfx+item+sfx] |
|---|
| 2992 | if pfx+item+sfx in sigDict: |
|---|
| 2993 | SizeMuStrSig[pfx+item][1][i] = sigDict[pfx+item+sfx] |
|---|
| 2994 | names = G2spc.HStrainNames(SGData) |
|---|
| 2995 | for i,name in enumerate(names): |
|---|
| 2996 | hapData['HStrain'][0][i] = parmDict[pfx+name] |
|---|
| 2997 | if pfx+name in sigDict: |
|---|
| 2998 | SizeMuStrSig[pfx+'HStrain'][name] = sigDict[pfx+name] |
|---|
| 2999 | if 'Layer Disp' in hapData: |
|---|
| 3000 | hapData['Layer Disp'][0] = parmDict[pfx+'LayerDisp'] |
|---|
| 3001 | if pfx+'LayerDisp' in sigDict: |
|---|
| 3002 | SizeMuStrSig[pfx+'LayerDisp'] = sigDict[pfx+'LayerDisp'] |
|---|
| 3003 | if Phases[phase]['General']['Type'] != 'magnetic': |
|---|
| 3004 | for name in ['BabA','BabU']: |
|---|
| 3005 | hapData['Babinet'][name][0] = parmDict[pfx+name] |
|---|
| 3006 | if pfx+name in sigDict and not parmDict[pfx+'LeBail']: |
|---|
| 3007 | BabSig[pfx+name] = sigDict[pfx+name] |
|---|
| 3008 | |
|---|
| 3009 | elif 'HKLF' in histogram: |
|---|
| 3010 | for item in ['Scale','Flack']: |
|---|
| 3011 | if parmDict.get(pfx+item): |
|---|
| 3012 | hapData[item][0] = parmDict[pfx+item] |
|---|
| 3013 | if pfx+item in sigDict: |
|---|
| 3014 | ScalExtSig[pfx+item] = sigDict[pfx+item] |
|---|
| 3015 | for item in ['Ep','Eg','Es']: |
|---|
| 3016 | if parmDict.get(pfx+item): |
|---|
| 3017 | hapData['Extinction'][2][item][0] = parmDict[pfx+item] |
|---|
| 3018 | if pfx+item in sigDict: |
|---|
| 3019 | ScalExtSig[pfx+item] = sigDict[pfx+item] |
|---|
| 3020 | for item in ['BabA','BabU']: |
|---|
| 3021 | hapData['Babinet'][item][0] = parmDict[pfx+item] |
|---|
| 3022 | if pfx+item in sigDict: |
|---|
| 3023 | BabSig[pfx+item] = sigDict[pfx+item] |
|---|
| 3024 | if 'Twins' in hapData: |
|---|
| 3025 | it = 1 |
|---|
| 3026 | sumTwFr = 0. |
|---|
| 3027 | while True: |
|---|
| 3028 | try: |
|---|
| 3029 | hapData['Twins'][it][1] = parmDict[pfx+'TwinFr:'+str(it)] |
|---|
| 3030 | if pfx+'TwinFr:'+str(it) in sigDict: |
|---|
| 3031 | TwinFrSig[pfx+'TwinFr:'+str(it)] = sigDict[pfx+'TwinFr:'+str(it)] |
|---|
| 3032 | if it: |
|---|
| 3033 | sumTwFr += hapData['Twins'][it][1] |
|---|
| 3034 | it += 1 |
|---|
| 3035 | except KeyError: |
|---|
| 3036 | break |
|---|
| 3037 | hapData['Twins'][0][1][0] = 1.-sumTwFr |
|---|
| 3038 | |
|---|
| 3039 | if Print: |
|---|
| 3040 | for phase in Phases: |
|---|
| 3041 | HistoPhase = Phases[phase]['Histograms'] |
|---|
| 3042 | General = Phases[phase]['General'] |
|---|
| 3043 | SGData = General['SGData'] |
|---|
| 3044 | pId = Phases[phase]['pId'] |
|---|
| 3045 | histoList = list(HistoPhase.keys()) |
|---|
| 3046 | histoList.sort() |
|---|
| 3047 | for histogram in histoList: |
|---|
| 3048 | try: |
|---|
| 3049 | Histogram = Histograms[histogram] |
|---|
| 3050 | except KeyError: |
|---|
| 3051 | #skip if histogram not included e.g. in a sequential refinement |
|---|
| 3052 | continue |
|---|
| 3053 | hapData = HistoPhase[histogram] |
|---|
| 3054 | hId = Histogram['hId'] |
|---|
| 3055 | Histogram['Residuals'][str(pId)+'::Name'] = phase |
|---|
| 3056 | pfx = str(pId)+':'+str(hId)+':' |
|---|
| 3057 | hfx = ':%s:'%(hId) |
|---|
| 3058 | if pfx+'Nref' not in Histogram['Residuals']: #skip not used phase in histogram |
|---|
| 3059 | continue |
|---|
| 3060 | pFile.write('\n Phase: %s in histogram: %s\n'%(phase,histogram)) |
|---|
| 3061 | pFile.write(135*'='+'\n') |
|---|
| 3062 | if 'PWDR' in histogram: |
|---|
| 3063 | pFile.write(' Final refinement RF, RF^2 = %.2f%%, %.2f%% on %d reflections\n'% |
|---|
| 3064 | (Histogram['Residuals'][pfx+'Rf'],Histogram['Residuals'][pfx+'Rf^2'],Histogram['Residuals'][pfx+'Nref'])) |
|---|
| 3065 | pFile.write(' Durbin-Watson statistic = %.3f\n'%(Histogram['Residuals']['Durbin-Watson'])) |
|---|
| 3066 | pFile.write(' Bragg intensity sum = %.3g\n'%(Histogram['Residuals'][pfx+'sumInt'])) |
|---|
| 3067 | |
|---|
| 3068 | if parmDict[pfx+'LeBail']: |
|---|
| 3069 | pFile.write(' Performed LeBail extraction for phase %s in histogram %s\n'%(phase,histogram)) |
|---|
| 3070 | else: |
|---|
| 3071 | if pfx+'Scale' in PhFrExtPOSig: |
|---|
| 3072 | wtFr = hapData['Scale'][0]*General['Mass']/wtFrSum[hId] |
|---|
| 3073 | sigwtFr = PhFrExtPOSig[pfx+'Scale']*wtFr/hapData['Scale'][0] |
|---|
| 3074 | pFile.write(' Phase fraction : %10.5f, sig %10.5f Weight fraction : %8.5f, sig %10.5f\n'% |
|---|
| 3075 | (hapData['Scale'][0],PhFrExtPOSig[pfx+'Scale'],wtFr,sigwtFr)) |
|---|
| 3076 | if pfx+'Extinction' in PhFrExtPOSig: |
|---|
| 3077 | pFile.write(' Extinction coeff: %10.4f, sig %10.4f\n'%(hapData['Extinction'][0],PhFrExtPOSig[pfx+'Extinction'])) |
|---|
| 3078 | if hapData['Pref.Ori.'][0] == 'MD': |
|---|
| 3079 | if pfx+'MD' in PhFrExtPOSig: |
|---|
| 3080 | pFile.write(' March-Dollase PO: %10.4f, sig %10.4f\n'%(hapData['Pref.Ori.'][1],PhFrExtPOSig[pfx+'MD'])) |
|---|
| 3081 | else: |
|---|
| 3082 | PrintSHPOAndSig(pfx,hapData['Pref.Ori.'],PhFrExtPOSig) |
|---|
| 3083 | PrintSizeAndSig(hapData['Size'],SizeMuStrSig[pfx+'Size']) |
|---|
| 3084 | PrintMuStrainAndSig(hapData['Mustrain'],SizeMuStrSig[pfx+'Mustrain'],SGData) |
|---|
| 3085 | PrintHStrainAndSig(hapData['HStrain'],SizeMuStrSig[pfx+'HStrain'],SGData) |
|---|
| 3086 | if pfx+'LayerDisp' in SizeMuStrSig: |
|---|
| 3087 | pFile.write(' Layer displacement : %10.3f, sig %10.3f\n'%(hapData['Layer Disp'][0],SizeMuStrSig[pfx+'LayerDisp'])) |
|---|
| 3088 | if Phases[phase]['General']['Type'] != 'magnetic' and not parmDict[pfx+'LeBail']: |
|---|
| 3089 | if len(BabSig): |
|---|
| 3090 | PrintBabinetAndSig(pfx,hapData['Babinet'],BabSig) |
|---|
| 3091 | |
|---|
| 3092 | elif 'HKLF' in histogram: |
|---|
| 3093 | Inst = Histogram['Instrument Parameters'][0] |
|---|
| 3094 | pFile.write(' Final refinement RF, RF^2 = %.2f%%, %.2f%% on %d reflections (%d user rejected, %d sp.gp.extinct)\n'% |
|---|
| 3095 | (Histogram['Residuals'][pfx+'Rf'],Histogram['Residuals'][pfx+'Rf^2'],Histogram['Residuals'][pfx+'Nref'], |
|---|
| 3096 | Histogram['Residuals'][pfx+'Nrej'],Histogram['Residuals'][pfx+'Next'])) |
|---|
| 3097 | if FFtables != None and 'N' not in Inst['Type'][0]: |
|---|
| 3098 | PrintFprime(FFtables,hfx,pFile) |
|---|
| 3099 | pFile.write(' HKLF histogram weight factor = %.3f\n'%(Histogram['wtFactor'])) |
|---|
| 3100 | if pfx+'Scale' in ScalExtSig: |
|---|
| 3101 | pFile.write(' Scale factor : %10.4f, sig %10.4f\n'%(hapData['Scale'][0],ScalExtSig[pfx+'Scale'])) |
|---|
| 3102 | if hapData['Extinction'][0] != 'None': |
|---|
| 3103 | PrintExtAndSig(pfx,hapData['Extinction'],ScalExtSig) |
|---|
| 3104 | if len(BabSig): |
|---|
| 3105 | PrintBabinetAndSig(pfx,hapData['Babinet'],BabSig) |
|---|
| 3106 | if pfx+'Flack' in ScalExtSig: |
|---|
| 3107 | pFile.write(' Flack parameter : %10.3f, sig %10.3f\n'%(hapData['Flack'][0],ScalExtSig[pfx+'Flack'])) |
|---|
| 3108 | if len(TwinFrSig): |
|---|
| 3109 | PrintTwinsAndSig(pfx,hapData['Twins'],TwinFrSig) |
|---|
| 3110 | |
|---|
| 3111 | ################################################################################ |
|---|
| 3112 | ##### Histogram data |
|---|
| 3113 | ################################################################################ |
|---|
| 3114 | |
|---|
| 3115 | def GetHistogramData(Histograms,Print=True,pFile=None): |
|---|
| 3116 | 'needs a doc string' |
|---|
| 3117 | |
|---|
| 3118 | def GetBackgroundParms(hId,Background): |
|---|
| 3119 | Back = Background[0] |
|---|
| 3120 | DebyePeaks = Background[1] |
|---|
| 3121 | bakType,bakFlag = Back[:2] |
|---|
| 3122 | backVals = Back[3:] |
|---|
| 3123 | backNames = [':'+str(hId)+':Back;'+str(i) for i in range(len(backVals))] |
|---|
| 3124 | backDict = dict(zip(backNames,backVals)) |
|---|
| 3125 | backVary = [] |
|---|
| 3126 | if bakFlag: |
|---|
| 3127 | backVary = backNames |
|---|
| 3128 | backDict[':'+str(hId)+':nDebye'] = DebyePeaks['nDebye'] |
|---|
| 3129 | backDict[':'+str(hId)+':nPeaks'] = DebyePeaks['nPeaks'] |
|---|
| 3130 | debyeDict = {} |
|---|
| 3131 | debyeList = [] |
|---|
| 3132 | for i in range(DebyePeaks['nDebye']): |
|---|
| 3133 | debyeNames = [':'+str(hId)+':DebyeA;'+str(i),':'+str(hId)+':DebyeR;'+str(i),':'+str(hId)+':DebyeU;'+str(i)] |
|---|
| 3134 | debyeDict.update(dict(zip(debyeNames,DebyePeaks['debyeTerms'][i][::2]))) |
|---|
| 3135 | debyeList += zip(debyeNames,DebyePeaks['debyeTerms'][i][1::2]) |
|---|
| 3136 | debyeVary = [] |
|---|
| 3137 | for item in debyeList: |
|---|
| 3138 | if item[1]: |
|---|
| 3139 | debyeVary.append(item[0]) |
|---|
| 3140 | backDict.update(debyeDict) |
|---|
| 3141 | backVary += debyeVary |
|---|
| 3142 | peakDict = {} |
|---|
| 3143 | peakList = [] |
|---|
| 3144 | for i in range(DebyePeaks['nPeaks']): |
|---|
| 3145 | peakNames = [':'+str(hId)+':BkPkpos;'+str(i),':'+str(hId)+ \ |
|---|
| 3146 | ':BkPkint;'+str(i),':'+str(hId)+':BkPksig;'+str(i),':'+str(hId)+':BkPkgam;'+str(i)] |
|---|
| 3147 | peakDict.update(dict(zip(peakNames,DebyePeaks['peaksList'][i][::2]))) |
|---|
| 3148 | peakList += zip(peakNames,DebyePeaks['peaksList'][i][1::2]) |
|---|
| 3149 | peakVary = [] |
|---|
| 3150 | for item in peakList: |
|---|
| 3151 | if item[1]: |
|---|
| 3152 | peakVary.append(item[0]) |
|---|
| 3153 | backDict.update(peakDict) |
|---|
| 3154 | backVary += peakVary |
|---|
| 3155 | return bakType,backDict,backVary |
|---|
| 3156 | |
|---|
| 3157 | def GetInstParms(hId,Inst): |
|---|
| 3158 | #patch |
|---|
| 3159 | if 'Z' not in Inst: |
|---|
| 3160 | Inst['Z'] = [0.0,0.0,False] |
|---|
| 3161 | dataType = Inst['Type'][0] |
|---|
| 3162 | instDict = {} |
|---|
| 3163 | insVary = [] |
|---|
| 3164 | pfx = ':'+str(hId)+':' |
|---|
| 3165 | insKeys = list(Inst.keys()) |
|---|
| 3166 | insKeys.sort() |
|---|
| 3167 | for item in insKeys: |
|---|
| 3168 | if item in 'Azimuth': |
|---|
| 3169 | continue |
|---|
| 3170 | insName = pfx+item |
|---|
| 3171 | instDict[insName] = Inst[item][1] |
|---|
| 3172 | if len(Inst[item]) > 2 and Inst[item][2]: |
|---|
| 3173 | insVary.append(insName) |
|---|
| 3174 | if 'C' in dataType: |
|---|
| 3175 | instDict[pfx+'SH/L'] = max(instDict[pfx+'SH/L'],0.0005) |
|---|
| 3176 | elif 'T' in dataType: #trap zero alp, bet coeff. |
|---|
| 3177 | if not instDict[pfx+'alpha']: |
|---|
| 3178 | instDict[pfx+'alpha'] = 1.0 |
|---|
| 3179 | if not instDict[pfx+'beta-0'] and not instDict[pfx+'beta-1']: |
|---|
| 3180 | instDict[pfx+'beta-1'] = 1.0 |
|---|
| 3181 | elif 'B' in dataType: #trap zero alp, bet coeff. |
|---|
| 3182 | if not instDict[pfx+'alpha-0'] and not instDict[pfx+'alpha-1']: |
|---|
| 3183 | instDict[pfx+'alpha-1'] = 1.0 |
|---|
| 3184 | if not instDict[pfx+'beta-0'] and not instDict[pfx+'beta-1']: |
|---|
| 3185 | instDict[pfx+'beta-1'] = 1.0 |
|---|
| 3186 | return dataType,instDict,insVary |
|---|
| 3187 | |
|---|
| 3188 | def GetSampleParms(hId,Sample): |
|---|
| 3189 | sampVary = [] |
|---|
| 3190 | hfx = ':'+str(hId)+':' |
|---|
| 3191 | sampDict = {hfx+'Gonio. radius':Sample['Gonio. radius'],hfx+'Omega':Sample['Omega'], |
|---|
| 3192 | hfx+'Chi':Sample['Chi'],hfx+'Phi':Sample['Phi'],hfx+'Azimuth':Sample['Azimuth']} |
|---|
| 3193 | for key in ('Temperature','Pressure','FreePrm1','FreePrm2','FreePrm3'): |
|---|
| 3194 | if key in Sample: |
|---|
| 3195 | sampDict[hfx+key] = Sample[key] |
|---|
| 3196 | Type = Sample['Type'] |
|---|
| 3197 | if 'Bragg' in Type: #Bragg-Brentano |
|---|
| 3198 | for item in ['Scale','Shift','Transparency','SurfRoughA','SurfRoughB']: |
|---|
| 3199 | sampDict[hfx+item] = Sample[item][0] |
|---|
| 3200 | if Sample[item][1]: |
|---|
| 3201 | sampVary.append(hfx+item) |
|---|
| 3202 | elif 'Debye' in Type: #Debye-Scherrer |
|---|
| 3203 | for item in ['Scale','Absorption','DisplaceX','DisplaceY']: |
|---|
| 3204 | sampDict[hfx+item] = Sample[item][0] |
|---|
| 3205 | if Sample[item][1]: |
|---|
| 3206 | sampVary.append(hfx+item) |
|---|
| 3207 | return Type,sampDict,sampVary |
|---|
| 3208 | |
|---|
| 3209 | def PrintBackground(Background): |
|---|
| 3210 | Back = Background[0] |
|---|
| 3211 | DebyePeaks = Background[1] |
|---|
| 3212 | pFile.write('\n Background function: %s Refine? %s\n'%(Back[0],Back[1])) |
|---|
| 3213 | line = ' Coefficients: ' |
|---|
| 3214 | for i,back in enumerate(Back[3:]): |
|---|
| 3215 | line += '%10.3f'%(back) |
|---|
| 3216 | if i and not i%10: |
|---|
| 3217 | line += '\n'+15*' ' |
|---|
| 3218 | pFile.write(line+'\n') |
|---|
| 3219 | if DebyePeaks['nDebye']: |
|---|
| 3220 | pFile.write('\n Debye diffuse scattering coefficients\n') |
|---|
| 3221 | parms = ['DebyeA','DebyeR','DebyeU'] |
|---|
| 3222 | line = ' names : ' |
|---|
| 3223 | for parm in parms: |
|---|
| 3224 | line += '%8s refine?'%(parm) |
|---|
| 3225 | pFile.write(line+'\n') |
|---|
| 3226 | for j,term in enumerate(DebyePeaks['debyeTerms']): |
|---|
| 3227 | line = ' term'+'%2d'%(j)+':' |
|---|
| 3228 | for i in range(3): |
|---|
| 3229 | line += '%10.3f %5s'%(term[2*i],bool(term[2*i+1])) |
|---|
| 3230 | pFile.write(line+'\n') |
|---|
| 3231 | if DebyePeaks['nPeaks']: |
|---|
| 3232 | pFile.write('\n Single peak coefficients\n') |
|---|
| 3233 | parms = ['BkPkpos','BkPkint','BkPksig','BkPkgam'] |
|---|
| 3234 | line = ' names : ' |
|---|
| 3235 | for parm in parms: |
|---|
| 3236 | line += '%8s refine?'%(parm) |
|---|
| 3237 | pFile.write(line+'\n') |
|---|
| 3238 | for j,term in enumerate(DebyePeaks['peaksList']): |
|---|
| 3239 | line = ' peak'+'%2d'%(j)+':' |
|---|
| 3240 | for i in range(4): |
|---|
| 3241 | line += '%12.3f %5s'%(term[2*i],bool(term[2*i+1])) |
|---|
| 3242 | pFile.write(line+'\n') |
|---|
| 3243 | |
|---|
| 3244 | def PrintInstParms(Inst): |
|---|
| 3245 | pFile.write('\n Instrument Parameters:\n') |
|---|
| 3246 | insKeys = list(Inst.keys()) |
|---|
| 3247 | insKeys.sort() |
|---|
| 3248 | iBeg = 0 |
|---|
| 3249 | Ok = True |
|---|
| 3250 | while Ok: |
|---|
| 3251 | ptlbls = ' name :' |
|---|
| 3252 | ptstr = ' value :' |
|---|
| 3253 | varstr = ' refine:' |
|---|
| 3254 | iFin = min(iBeg+9,len(insKeys)) |
|---|
| 3255 | for item in insKeys[iBeg:iFin]: |
|---|
| 3256 | if item not in ['Type','Source']: |
|---|
| 3257 | ptlbls += '%12s' % (item) |
|---|
| 3258 | ptstr += '%12.6f' % (Inst[item][1]) |
|---|
| 3259 | if item in ['Lam1','Lam2','Azimuth','fltPath','2-theta',]: |
|---|
| 3260 | varstr += 12*' ' |
|---|
| 3261 | else: |
|---|
| 3262 | varstr += '%12s' % (str(bool(Inst[item][2]))) |
|---|
| 3263 | pFile.write(ptlbls+'\n') |
|---|
| 3264 | pFile.write(ptstr+'\n') |
|---|
| 3265 | pFile.write(varstr+'\n') |
|---|
| 3266 | iBeg = iFin |
|---|
| 3267 | if iBeg == len(insKeys): |
|---|
| 3268 | Ok = False |
|---|
| 3269 | else: |
|---|
| 3270 | pFile.write('\n') |
|---|
| 3271 | |
|---|
| 3272 | def PrintSampleParms(Sample): |
|---|
| 3273 | pFile.write('\n Sample Parameters:\n') |
|---|
| 3274 | pFile.write(' Goniometer omega = %.2f, chi = %.2f, phi = %.2f\n'% |
|---|
| 3275 | (Sample['Omega'],Sample['Chi'],Sample['Phi'])) |
|---|
| 3276 | ptlbls = ' name :' |
|---|
| 3277 | ptstr = ' value :' |
|---|
| 3278 | varstr = ' refine:' |
|---|
| 3279 | if 'Bragg' in Sample['Type']: |
|---|
| 3280 | for item in ['Scale','Shift','Transparency','SurfRoughA','SurfRoughB']: |
|---|
| 3281 | ptlbls += '%14s'%(item) |
|---|
| 3282 | ptstr += '%14.4f'%(Sample[item][0]) |
|---|
| 3283 | varstr += '%14s'%(str(bool(Sample[item][1]))) |
|---|
| 3284 | |
|---|
| 3285 | elif 'Debye' in Type: #Debye-Scherrer |
|---|
| 3286 | for item in ['Scale','Absorption','DisplaceX','DisplaceY']: |
|---|
| 3287 | ptlbls += '%14s'%(item) |
|---|
| 3288 | ptstr += '%14.4f'%(Sample[item][0]) |
|---|
| 3289 | varstr += '%14s'%(str(bool(Sample[item][1]))) |
|---|
| 3290 | |
|---|
| 3291 | pFile.write(ptlbls+'\n') |
|---|
| 3292 | pFile.write(ptstr+'\n') |
|---|
| 3293 | pFile.write(varstr+'\n') |
|---|
| 3294 | |
|---|
| 3295 | histDict = {} |
|---|
| 3296 | histVary = [] |
|---|
| 3297 | controlDict = {} |
|---|
| 3298 | histoList = list(Histograms.keys()) |
|---|
| 3299 | histoList.sort() |
|---|
| 3300 | for histogram in histoList: |
|---|
| 3301 | if 'PWDR' in histogram: |
|---|
| 3302 | Histogram = Histograms[histogram] |
|---|
| 3303 | hId = Histogram['hId'] |
|---|
| 3304 | pfx = ':'+str(hId)+':' |
|---|
| 3305 | controlDict[pfx+'wtFactor'] = Histogram['wtFactor'] |
|---|
| 3306 | controlDict[pfx+'Limits'] = Histogram['Limits'][1] |
|---|
| 3307 | controlDict[pfx+'Exclude'] = Histogram['Limits'][2:] |
|---|
| 3308 | for excl in controlDict[pfx+'Exclude']: |
|---|
| 3309 | Histogram['Data'][0] = ma.masked_inside(Histogram['Data'][0],excl[0],excl[1]) |
|---|
| 3310 | if controlDict[pfx+'Exclude']: |
|---|
| 3311 | ma.mask_rows(Histogram['Data']) |
|---|
| 3312 | Background = Histogram['Background'] |
|---|
| 3313 | Type,bakDict,bakVary = GetBackgroundParms(hId,Background) |
|---|
| 3314 | controlDict[pfx+'bakType'] = Type |
|---|
| 3315 | histDict.update(bakDict) |
|---|
| 3316 | histVary += bakVary |
|---|
| 3317 | |
|---|
| 3318 | Inst = Histogram['Instrument Parameters'] #TODO ? ignores tabulated alp,bet & delt for TOF |
|---|
| 3319 | if 'T' in Type and len(Inst[1]): #patch - back-to-back exponential contribution to TOF line shape is removed |
|---|
| 3320 | G2fil.G2Print ('Warning: tabulated profile coefficients are ignored') |
|---|
| 3321 | Type,instDict,insVary = GetInstParms(hId,Inst[0]) |
|---|
| 3322 | controlDict[pfx+'histType'] = Type |
|---|
| 3323 | if 'XC' in Type or 'XB' in Type: |
|---|
| 3324 | if pfx+'Lam1' in instDict: |
|---|
| 3325 | controlDict[pfx+'keV'] = 12.397639/instDict[pfx+'Lam1'] |
|---|
| 3326 | else: |
|---|
| 3327 | controlDict[pfx+'keV'] = 12.397639/instDict[pfx+'Lam'] |
|---|
| 3328 | histDict.update(instDict) |
|---|
| 3329 | histVary += insVary |
|---|
| 3330 | |
|---|
| 3331 | Sample = Histogram['Sample Parameters'] |
|---|
| 3332 | Type,sampDict,sampVary = GetSampleParms(hId,Sample) |
|---|
| 3333 | controlDict[pfx+'instType'] = Type |
|---|
| 3334 | histDict.update(sampDict) |
|---|
| 3335 | histVary += sampVary |
|---|
| 3336 | |
|---|
| 3337 | |
|---|
| 3338 | if Print: |
|---|
| 3339 | pFile.write('\n Histogram: %s histogram Id: %d\n'%(histogram,hId)) |
|---|
| 3340 | pFile.write(135*'='+'\n') |
|---|
| 3341 | Units = {'C':' deg','T':' msec','B':' deg'} |
|---|
| 3342 | units = Units[controlDict[pfx+'histType'][2]] |
|---|
| 3343 | Limits = controlDict[pfx+'Limits'] |
|---|
| 3344 | pFile.write(' Instrument type: %s\n'%Sample['Type']) |
|---|
| 3345 | pFile.write(' Histogram limits: %8.2f%s to %8.2f%s\n'%(Limits[0],units,Limits[1],units)) |
|---|
| 3346 | if len(controlDict[pfx+'Exclude']): |
|---|
| 3347 | excls = controlDict[pfx+'Exclude'] |
|---|
| 3348 | for excl in excls: |
|---|
| 3349 | pFile.write(' Excluded region: %8.2f%s to %8.2f%s\n'%(excl[0],units,excl[1],units)) |
|---|
| 3350 | PrintSampleParms(Sample) |
|---|
| 3351 | PrintInstParms(Inst[0]) |
|---|
| 3352 | PrintBackground(Background) |
|---|
| 3353 | elif 'HKLF' in histogram: |
|---|
| 3354 | Histogram = Histograms[histogram] |
|---|
| 3355 | hId = Histogram['hId'] |
|---|
| 3356 | pfx = ':'+str(hId)+':' |
|---|
| 3357 | controlDict[pfx+'wtFactor'] = Histogram['wtFactor'] |
|---|
| 3358 | Inst = Histogram['Instrument Parameters'][0] |
|---|
| 3359 | controlDict[pfx+'histType'] = Inst['Type'][0] |
|---|
| 3360 | if 'X' in Inst['Type'][0]: |
|---|
| 3361 | histDict[pfx+'Lam'] = Inst['Lam'][1] |
|---|
| 3362 | controlDict[pfx+'keV'] = 12.397639/histDict[pfx+'Lam'] |
|---|
| 3363 | elif 'NC' in Inst['Type'][0] or 'NB' in Inst['Type'][0]: |
|---|
| 3364 | histDict[pfx+'Lam'] = Inst['Lam'][1] |
|---|
| 3365 | return histVary,histDict,controlDict |
|---|
| 3366 | |
|---|
| 3367 | def SetHistogramData(parmDict,sigDict,Histograms,FFtables,Print=True,pFile=None,seq=False): |
|---|
| 3368 | 'Shows histogram data after a refinement' |
|---|
| 3369 | |
|---|
| 3370 | def SetBackgroundParms(pfx,Background,parmDict,sigDict): |
|---|
| 3371 | Back = Background[0] |
|---|
| 3372 | DebyePeaks = Background[1] |
|---|
| 3373 | lenBack = len(Back[3:]) |
|---|
| 3374 | backSig = [0 for i in range(lenBack+3*DebyePeaks['nDebye']+4*DebyePeaks['nPeaks'])] |
|---|
| 3375 | for i in range(lenBack): |
|---|
| 3376 | Back[3+i] = parmDict[pfx+'Back;'+str(i)] |
|---|
| 3377 | if pfx+'Back;'+str(i) in sigDict: |
|---|
| 3378 | backSig[i] = sigDict[pfx+'Back;'+str(i)] |
|---|
| 3379 | if DebyePeaks['nDebye']: |
|---|
| 3380 | for i in range(DebyePeaks['nDebye']): |
|---|
| 3381 | names = [pfx+'DebyeA;'+str(i),pfx+'DebyeR;'+str(i),pfx+'DebyeU;'+str(i)] |
|---|
| 3382 | for j,name in enumerate(names): |
|---|
| 3383 | DebyePeaks['debyeTerms'][i][2*j] = parmDict[name] |
|---|
| 3384 | if name in sigDict: |
|---|
| 3385 | backSig[lenBack+3*i+j] = sigDict[name] |
|---|
| 3386 | if DebyePeaks['nPeaks']: |
|---|
| 3387 | for i in range(DebyePeaks['nPeaks']): |
|---|
| 3388 | names = [pfx+'BkPkpos;'+str(i),pfx+'BkPkint;'+str(i), |
|---|
| 3389 | pfx+'BkPksig;'+str(i),pfx+'BkPkgam;'+str(i)] |
|---|
| 3390 | for j,name in enumerate(names): |
|---|
| 3391 | DebyePeaks['peaksList'][i][2*j] = parmDict[name] |
|---|
| 3392 | if name in sigDict: |
|---|
| 3393 | backSig[lenBack+3*DebyePeaks['nDebye']+4*i+j] = sigDict[name] |
|---|
| 3394 | return backSig |
|---|
| 3395 | |
|---|
| 3396 | def SetInstParms(pfx,Inst,parmDict,sigDict): |
|---|
| 3397 | instSig = {} |
|---|
| 3398 | insKeys = list(Inst.keys()) |
|---|
| 3399 | insKeys.sort() |
|---|
| 3400 | for item in insKeys: |
|---|
| 3401 | insName = pfx+item |
|---|
| 3402 | Inst[item][1] = parmDict[insName] |
|---|
| 3403 | if insName in sigDict: |
|---|
| 3404 | instSig[item] = sigDict[insName] |
|---|
| 3405 | else: |
|---|
| 3406 | instSig[item] = 0 |
|---|
| 3407 | return instSig |
|---|
| 3408 | |
|---|
| 3409 | def SetSampleParms(pfx,Sample,parmDict,sigDict): |
|---|
| 3410 | if 'Bragg' in Sample['Type']: #Bragg-Brentano |
|---|
| 3411 | sampSig = [0 for i in range(5)] |
|---|
| 3412 | for i,item in enumerate(['Scale','Shift','Transparency','SurfRoughA','SurfRoughB']): |
|---|
| 3413 | Sample[item][0] = parmDict[pfx+item] |
|---|
| 3414 | if pfx+item in sigDict: |
|---|
| 3415 | sampSig[i] = sigDict[pfx+item] |
|---|
| 3416 | elif 'Debye' in Sample['Type']: #Debye-Scherrer |
|---|
| 3417 | sampSig = [0 for i in range(4)] |
|---|
| 3418 | for i,item in enumerate(['Scale','Absorption','DisplaceX','DisplaceY']): |
|---|
| 3419 | Sample[item][0] = parmDict[pfx+item] |
|---|
| 3420 | if pfx+item in sigDict: |
|---|
| 3421 | sampSig[i] = sigDict[pfx+item] |
|---|
| 3422 | return sampSig |
|---|
| 3423 | |
|---|
| 3424 | def PrintBackgroundSig(Background,backSig): |
|---|
| 3425 | Back = Background[0] |
|---|
| 3426 | DebyePeaks = Background[1] |
|---|
| 3427 | valstr = ' value : ' |
|---|
| 3428 | sigstr = ' sig : ' |
|---|
| 3429 | refine = False |
|---|
| 3430 | for i,back in enumerate(Back[3:]): |
|---|
| 3431 | valstr += '%10.4g'%(back) |
|---|
| 3432 | if Back[1]: |
|---|
| 3433 | refine = True |
|---|
| 3434 | sigstr += '%10.4g'%(backSig[i]) |
|---|
| 3435 | else: |
|---|
| 3436 | sigstr += 10*' ' |
|---|
| 3437 | if refine: |
|---|
| 3438 | pFile.write('\n Background function: %s\n'%Back[0]) |
|---|
| 3439 | pFile.write(valstr+'\n') |
|---|
| 3440 | pFile.write(sigstr+'\n') |
|---|
| 3441 | if DebyePeaks['nDebye']: |
|---|
| 3442 | ifAny = False |
|---|
| 3443 | ptfmt = "%12.3f" |
|---|
| 3444 | names = ' names :' |
|---|
| 3445 | ptstr = ' values:' |
|---|
| 3446 | sigstr = ' esds :' |
|---|
| 3447 | for item in sigDict: |
|---|
| 3448 | if 'Debye' in item: |
|---|
| 3449 | ifAny = True |
|---|
| 3450 | names += '%12s'%(item) |
|---|
| 3451 | ptstr += ptfmt%(parmDict[item]) |
|---|
| 3452 | sigstr += ptfmt%(sigDict[item]) |
|---|
| 3453 | if ifAny: |
|---|
| 3454 | pFile.write('\n Debye diffuse scattering coefficients\n') |
|---|
| 3455 | pFile.write(names+'\n') |
|---|
| 3456 | pFile.write(ptstr+'\n') |
|---|
| 3457 | pFile.write(sigstr+'\n') |
|---|
| 3458 | if DebyePeaks['nPeaks']: |
|---|
| 3459 | pFile.write('\n Single peak coefficients:\n') |
|---|
| 3460 | parms = ['BkPkpos','BkPkint','BkPksig','BkPkgam'] |
|---|
| 3461 | line = ' peak no. ' |
|---|
| 3462 | for parm in parms: |
|---|
| 3463 | line += '%14s%12s'%(parm.center(14),'esd'.center(12)) |
|---|
| 3464 | pFile.write(line+'\n') |
|---|
| 3465 | for ip in range(DebyePeaks['nPeaks']): |
|---|
| 3466 | ptstr = ' %4d '%(ip) |
|---|
| 3467 | for parm in parms: |
|---|
| 3468 | fmt = '%14.3f' |
|---|
| 3469 | efmt = '%12.3f' |
|---|
| 3470 | if parm == 'BkPkpos': |
|---|
| 3471 | fmt = '%14.4f' |
|---|
| 3472 | efmt = '%12.4f' |
|---|
| 3473 | name = pfx+parm+';%d'%(ip) |
|---|
| 3474 | ptstr += fmt%(parmDict[name]) |
|---|
| 3475 | if name in sigDict: |
|---|
| 3476 | ptstr += efmt%(sigDict[name]) |
|---|
| 3477 | else: |
|---|
| 3478 | ptstr += 12*' ' |
|---|
| 3479 | pFile.write(ptstr+'\n') |
|---|
| 3480 | sumBk = np.array(Histogram['sumBk']) |
|---|
| 3481 | pFile.write(' Background sums: empirical %.3g, Debye %.3g, peaks %.3g, Total %.3g\n'% |
|---|
| 3482 | (sumBk[0],sumBk[1],sumBk[2],np.sum(sumBk))) |
|---|
| 3483 | |
|---|
| 3484 | def PrintInstParmsSig(Inst,instSig): |
|---|
| 3485 | refine = False |
|---|
| 3486 | insKeys = list(instSig.keys()) |
|---|
| 3487 | insKeys.sort() |
|---|
| 3488 | iBeg = 0 |
|---|
| 3489 | Ok = True |
|---|
| 3490 | while Ok: |
|---|
| 3491 | ptlbls = ' names :' |
|---|
| 3492 | ptstr = ' value :' |
|---|
| 3493 | sigstr = ' sig :' |
|---|
| 3494 | iFin = min(iBeg+9,len(insKeys)) |
|---|
| 3495 | for name in insKeys[iBeg:iFin]: |
|---|
| 3496 | if name not in ['Type','Lam1','Lam2','Azimuth','Source','fltPath']: |
|---|
| 3497 | ptlbls += '%12s' % (name) |
|---|
| 3498 | ptstr += '%12.6f' % (Inst[name][1]) |
|---|
| 3499 | if instSig[name]: |
|---|
| 3500 | refine = True |
|---|
| 3501 | sigstr += '%12.6f' % (instSig[name]) |
|---|
| 3502 | else: |
|---|
| 3503 | sigstr += 12*' ' |
|---|
| 3504 | if refine: |
|---|
| 3505 | pFile.write('\n Instrument Parameters:\n') |
|---|
| 3506 | pFile.write(ptlbls+'\n') |
|---|
| 3507 | pFile.write(ptstr+'\n') |
|---|
| 3508 | pFile.write(sigstr+'\n') |
|---|
| 3509 | iBeg = iFin |
|---|
| 3510 | if iBeg == len(insKeys): |
|---|
| 3511 | Ok = False |
|---|
| 3512 | |
|---|
| 3513 | def PrintSampleParmsSig(Sample,sampleSig): |
|---|
| 3514 | ptlbls = ' names :' |
|---|
| 3515 | ptstr = ' values:' |
|---|
| 3516 | sigstr = ' sig :' |
|---|
| 3517 | refine = False |
|---|
| 3518 | if 'Bragg' in Sample['Type']: |
|---|
| 3519 | for i,item in enumerate(['Scale','Shift','Transparency','SurfRoughA','SurfRoughB']): |
|---|
| 3520 | ptlbls += '%14s'%(item) |
|---|
| 3521 | ptstr += '%14.4f'%(Sample[item][0]) |
|---|
| 3522 | if sampleSig[i]: |
|---|
| 3523 | refine = True |
|---|
| 3524 | sigstr += '%14.4f'%(sampleSig[i]) |
|---|
| 3525 | else: |
|---|
| 3526 | sigstr += 14*' ' |
|---|
| 3527 | |
|---|
| 3528 | elif 'Debye' in Sample['Type']: #Debye-Scherrer |
|---|
| 3529 | for i,item in enumerate(['Scale','Absorption','DisplaceX','DisplaceY']): |
|---|
| 3530 | ptlbls += '%14s'%(item) |
|---|
| 3531 | ptstr += '%14.4f'%(Sample[item][0]) |
|---|
| 3532 | if sampleSig[i]: |
|---|
| 3533 | refine = True |
|---|
| 3534 | sigstr += '%14.4f'%(sampleSig[i]) |
|---|
| 3535 | else: |
|---|
| 3536 | sigstr += 14*' ' |
|---|
| 3537 | |
|---|
| 3538 | if refine: |
|---|
| 3539 | pFile.write('\n Sample Parameters:\n') |
|---|
| 3540 | pFile.write(ptlbls+'\n') |
|---|
| 3541 | pFile.write(ptstr+'\n') |
|---|
| 3542 | pFile.write(sigstr+'\n') |
|---|
| 3543 | |
|---|
| 3544 | histoList = list(Histograms.keys()) |
|---|
| 3545 | histoList.sort() |
|---|
| 3546 | for histogram in histoList: |
|---|
| 3547 | if 'PWDR' in histogram: |
|---|
| 3548 | Histogram = Histograms[histogram] |
|---|
| 3549 | hId = Histogram['hId'] |
|---|
| 3550 | pfx = ':'+str(hId)+':' |
|---|
| 3551 | Background = Histogram['Background'] |
|---|
| 3552 | backSig = SetBackgroundParms(pfx,Background,parmDict,sigDict) |
|---|
| 3553 | |
|---|
| 3554 | Inst = Histogram['Instrument Parameters'][0] |
|---|
| 3555 | instSig = SetInstParms(pfx,Inst,parmDict,sigDict) |
|---|
| 3556 | |
|---|
| 3557 | Sample = Histogram['Sample Parameters'] |
|---|
| 3558 | sampSig = SetSampleParms(pfx,Sample,parmDict,sigDict) |
|---|
| 3559 | |
|---|
| 3560 | if not seq: |
|---|
| 3561 | pFile.write('\n Histogram: %s histogram Id: %d\n'%(histogram,hId)) |
|---|
| 3562 | pFile.write(135*'='+'\n') |
|---|
| 3563 | pFile.write(' PWDR histogram weight factor = '+'%.3f\n'%(Histogram['wtFactor'])) |
|---|
| 3564 | pFile.write(' Final refinement wR = %.2f%% on %d observations in this histogram\n'% |
|---|
| 3565 | (Histogram['Residuals']['wR'],Histogram['Residuals']['Nobs'])) |
|---|
| 3566 | pFile.write(' Other residuals: R = %.2f%%, R-bkg = %.2f%%, wR-bkg = %.2f%% wRmin = %.2f%%\n'% |
|---|
| 3567 | (Histogram['Residuals']['R'],Histogram['Residuals']['Rb'],Histogram['Residuals']['wR'],Histogram['Residuals']['wRmin'])) |
|---|
| 3568 | if Print: |
|---|
| 3569 | pFile.write(' Instrument type: %s\n'%Sample['Type']) |
|---|
| 3570 | if FFtables != None and 'N' not in Inst['Type'][0]: |
|---|
| 3571 | PrintFprime(FFtables,pfx,pFile) |
|---|
| 3572 | PrintSampleParmsSig(Sample,sampSig) |
|---|
| 3573 | PrintInstParmsSig(Inst,instSig) |
|---|
| 3574 | PrintBackgroundSig(Background,backSig) |
|---|
| 3575 | |
|---|
| 3576 | def WriteRBObjPOAndSig(pfx,rbfx,rbsx,parmDict,sigDict): |
|---|
| 3577 | '''Cribbed version of PrintRBObjPOAndSig but returns lists of strings. |
|---|
| 3578 | Moved so it can be used in ExportCIF |
|---|
| 3579 | ''' |
|---|
| 3580 | namstr = ' names :' |
|---|
| 3581 | valstr = ' values:' |
|---|
| 3582 | sigstr = ' esds :' |
|---|
| 3583 | for i,px in enumerate(['Px:','Py:','Pz:']): |
|---|
| 3584 | name = pfx+rbfx+px+rbsx |
|---|
| 3585 | namstr += '%12s'%('Pos '+px[1]) |
|---|
| 3586 | valstr += '%12.5f'%(parmDict[name]) |
|---|
| 3587 | if name in sigDict: |
|---|
| 3588 | sigstr += '%12.5f'%(sigDict[name]) |
|---|
| 3589 | else: |
|---|
| 3590 | sigstr += 12*' ' |
|---|
| 3591 | for i,po in enumerate(['Oa:','Oi:','Oj:','Ok:']): |
|---|
| 3592 | name = pfx+rbfx+po+rbsx |
|---|
| 3593 | namstr += '%12s'%('Ori '+po[1]) |
|---|
| 3594 | valstr += '%12.5f'%(parmDict[name]) |
|---|
| 3595 | if name in sigDict: |
|---|
| 3596 | sigstr += '%12.5f'%(sigDict[name]) |
|---|
| 3597 | else: |
|---|
| 3598 | sigstr += 12*' ' |
|---|
| 3599 | return (namstr,valstr,sigstr) |
|---|
| 3600 | |
|---|
| 3601 | def WriteRBObjTLSAndSig(pfx,rbfx,rbsx,TLS,parmDict,sigDict): |
|---|
| 3602 | '''Cribbed version of PrintRBObjTLSAndSig but returns lists of strings. |
|---|
| 3603 | Moved so it can be used in ExportCIF |
|---|
| 3604 | ''' |
|---|
| 3605 | out = [] |
|---|
| 3606 | namstr = ' names :' |
|---|
| 3607 | valstr = ' values:' |
|---|
| 3608 | sigstr = ' esds :' |
|---|
| 3609 | if 'N' not in TLS: |
|---|
| 3610 | out.append(' Thermal motion:\n') |
|---|
| 3611 | if 'T' in TLS: |
|---|
| 3612 | for i,pt in enumerate(['T11:','T22:','T33:','T12:','T13:','T23:']): |
|---|
| 3613 | name = pfx+rbfx+pt+rbsx |
|---|
| 3614 | namstr += '%12s'%(pt[:3]) |
|---|
| 3615 | valstr += '%12.5f'%(parmDict[name]) |
|---|
| 3616 | if name in sigDict: |
|---|
| 3617 | sigstr += '%12.5f'%(sigDict[name]) |
|---|
| 3618 | else: |
|---|
| 3619 | sigstr += 12*' ' |
|---|
| 3620 | out.append(namstr+'\n') |
|---|
| 3621 | out.append(valstr+'\n') |
|---|
| 3622 | out.append(sigstr+'\n') |
|---|
| 3623 | if 'L' in TLS: |
|---|
| 3624 | namstr = ' names :' |
|---|
| 3625 | valstr = ' values:' |
|---|
| 3626 | sigstr = ' esds :' |
|---|
| 3627 | for i,pt in enumerate(['L11:','L22:','L33:','L12:','L13:','L23:']): |
|---|
| 3628 | name = pfx+rbfx+pt+rbsx |
|---|
| 3629 | namstr += '%12s'%(pt[:3]) |
|---|
| 3630 | valstr += '%12.3f'%(parmDict[name]) |
|---|
| 3631 | if name in sigDict: |
|---|
| 3632 | sigstr += '%12.3f'%(sigDict[name]) |
|---|
| 3633 | else: |
|---|
| 3634 | sigstr += 12*' ' |
|---|
| 3635 | out.append(namstr+'\n') |
|---|
| 3636 | out.append(valstr+'\n') |
|---|
| 3637 | out.append(sigstr+'\n') |
|---|
| 3638 | if 'S' in TLS: |
|---|
| 3639 | namstr = ' names :' |
|---|
| 3640 | valstr = ' values:' |
|---|
| 3641 | sigstr = ' esds :' |
|---|
| 3642 | for i,pt in enumerate(['S12:','S13:','S21:','S23:','S31:','S32:','SAA:','SBB:']): |
|---|
| 3643 | name = pfx+rbfx+pt+rbsx |
|---|
| 3644 | namstr += '%12s'%(pt[:3]) |
|---|
| 3645 | valstr += '%12.4f'%(parmDict[name]) |
|---|
| 3646 | if name in sigDict: |
|---|
| 3647 | sigstr += '%12.4f'%(sigDict[name]) |
|---|
| 3648 | else: |
|---|
| 3649 | sigstr += 12*' ' |
|---|
| 3650 | out.append(namstr+'\n') |
|---|
| 3651 | out.append(valstr+'\n') |
|---|
| 3652 | out.append(sigstr+'\n') |
|---|
| 3653 | if 'U' in TLS: |
|---|
| 3654 | name = pfx+rbfx+'U:'+rbsx |
|---|
| 3655 | namstr = ' names :'+'%12s'%('Uiso') |
|---|
| 3656 | valstr = ' values:'+'%12.5f'%(parmDict[name]) |
|---|
| 3657 | if name in sigDict: |
|---|
| 3658 | sigstr = ' esds :'+'%12.5f'%(sigDict[name]) |
|---|
| 3659 | else: |
|---|
| 3660 | sigstr = ' esds :'+12*' ' |
|---|
| 3661 | out.append(namstr+'\n') |
|---|
| 3662 | out.append(valstr+'\n') |
|---|
| 3663 | out.append(sigstr+'\n') |
|---|
| 3664 | return out |
|---|
| 3665 | |
|---|
| 3666 | def WriteRBObjTorAndSig(pfx,rbsx,parmDict,sigDict,nTors): |
|---|
| 3667 | '''Cribbed version of PrintRBObjTorAndSig but returns lists of strings. |
|---|
| 3668 | Moved so it can be used in ExportCIF |
|---|
| 3669 | ''' |
|---|
| 3670 | out = [] |
|---|
| 3671 | namstr = ' names :' |
|---|
| 3672 | valstr = ' values:' |
|---|
| 3673 | sigstr = ' esds :' |
|---|
| 3674 | out.append(' Torsions:\n') |
|---|
| 3675 | for it in range(nTors): |
|---|
| 3676 | name = pfx+'RBRTr;'+str(it)+':'+rbsx |
|---|
| 3677 | namstr += '%12s'%('Tor'+str(it)) |
|---|
| 3678 | valstr += '%12.4f'%(parmDict[name]) |
|---|
| 3679 | if name in sigDict: |
|---|
| 3680 | sigstr += '%12.4f'%(sigDict[name]) |
|---|
| 3681 | out.append(namstr+'\n') |
|---|
| 3682 | out.append(valstr+'\n') |
|---|
| 3683 | out.append(sigstr+'\n') |
|---|
| 3684 | return out |
|---|
| 3685 | |
|---|
| 3686 | def WriteResRBModel(RBModel): |
|---|
| 3687 | '''Write description of a residue rigid body. Code shifted from |
|---|
| 3688 | PrintResRBModel to make usable from G2export_CIF |
|---|
| 3689 | ''' |
|---|
| 3690 | out = [] |
|---|
| 3691 | atNames = RBModel['atNames'] |
|---|
| 3692 | rbRef = RBModel['rbRef'] |
|---|
| 3693 | rbSeq = RBModel['rbSeq'] |
|---|
| 3694 | out.append(' At name x y z\n') |
|---|
| 3695 | for name,xyz in zip(atNames,RBModel['rbXYZ']): |
|---|
| 3696 | out.append(' %8s %10.4f %10.4f %10.4f\n'%(name,xyz[0],xyz[1],xyz[2])) |
|---|
| 3697 | out.append(' Orientation defined by: %s -> %s & %s -> %s\n'% |
|---|
| 3698 | (atNames[rbRef[0]],atNames[rbRef[1]],atNames[rbRef[0]],atNames[rbRef[2]])) |
|---|
| 3699 | if rbSeq: |
|---|
| 3700 | for i,rbseq in enumerate(rbSeq): |
|---|
| 3701 | # nameLst = [atNames[i] for i in rbseq[3]] |
|---|
| 3702 | out.append(' Torsion sequence %d Bond: %s - %s riding: %s\n'% |
|---|
| 3703 | (i,atNames[rbseq[0]],atNames[rbseq[1]],str([atNames[i] for i in rbseq[3]]))) |
|---|
| 3704 | return out |
|---|
| 3705 | |
|---|
| 3706 | def WriteVecRBModel(RBModel,sigDict={},irb=None): |
|---|
| 3707 | '''Write description of a vector rigid body. Code shifted from |
|---|
| 3708 | PrintVecRBModel to make usable from G2export_CIF |
|---|
| 3709 | ''' |
|---|
| 3710 | out = [] |
|---|
| 3711 | rbRef = RBModel['rbRef'] |
|---|
| 3712 | atTypes = RBModel['rbTypes'] |
|---|
| 3713 | for i in range(len(RBModel['VectMag'])): |
|---|
| 3714 | if sigDict and irb is not None: |
|---|
| 3715 | name = '::RBV;'+str(i)+':'+str(irb) |
|---|
| 3716 | s = G2mth.ValEsd(RBModel['VectMag'][i],sigDict.get(name,-.0001)) |
|---|
| 3717 | out.append('Vector no.: %d Magnitude: %s\n'%(i,s)) |
|---|
| 3718 | else: |
|---|
| 3719 | out.append('Vector no.: %d Magnitude: %8.4f Refine? %s\n'% |
|---|
| 3720 | (i,RBModel['VectMag'][i],RBModel['VectRef'][i])) |
|---|
| 3721 | out.append(' No. Type vx vy vz\n') |
|---|
| 3722 | for j,[name,xyz] in enumerate(zip(atTypes,RBModel['rbVect'][i])): |
|---|
| 3723 | out.append(' %d %2s %10.4f %10.4f %10.4f\n'%(j,name,xyz[0],xyz[1],xyz[2])) |
|---|
| 3724 | out.append(' No. Type x y z\n') |
|---|
| 3725 | for i,[name,xyz] in enumerate(zip(atTypes,RBModel['rbXYZ'])): |
|---|
| 3726 | out.append(' %d %2s %10.4f %10.4f %10.4f\n'%(i,name,xyz[0],xyz[1],xyz[2])) |
|---|
| 3727 | return out |
|---|
