| 1 | # -*- coding: utf-8 -*- |
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| 2 | ########### SVN repository information ################### |
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| 3 | # $Date: 2020-12-30 16:43:56 +0000 (Wed, 30 Dec 2020) $ |
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| 4 | # $Author: toby $ |
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| 5 | # $Revision: 4686 $ |
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| 6 | # $URL: trunk/GSASIIstrIO.py $ |
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| 7 | # $Id: GSASIIstrIO.py 4686 2020-12-30 16:43:56Z 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: 4686 $") |
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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 PrintBlength(BLtables,wave,pFile): |
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| 372 | pFile.write('\n Resonant neutron scattering lengths:\n') |
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| 373 | Elstr = ' Element:' |
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| 374 | FPstr = " b' :" |
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| 375 | FPPstr = ' b" :' |
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| 376 | for El in BLtables: |
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| 377 | BP,BPP = G2el.BlenResCW([El,],BLtables,wave) |
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| 378 | Elstr += ' %8s'%(El) |
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| 379 | FPstr += ' %8.3f'%(BP) |
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| 380 | FPPstr += ' %8.3f'%(BPP) |
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| 381 | pFile.write(Elstr+'\n') |
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| 382 | pFile.write(FPstr+'\n') |
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| 383 | pFile.write(FPPstr+'\n') |
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| 384 | |
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| 385 | def PrintISOmodes(pFile,Phases,parmDict,sigDict): |
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| 386 | '''Prints the values for the ISODISTORT modes into the project's |
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| 387 | .lst file after a refinement. |
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| 388 | ''' |
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| 389 | for phase in Phases: |
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| 390 | if 'ISODISTORT' not in Phases[phase]: continue |
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| 391 | data = Phases[phase] |
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| 392 | ISO = data['ISODISTORT'] |
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| 393 | if 'G2VarList' in ISO: |
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| 394 | deltaList = [] |
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| 395 | for gv,Ilbl in zip(ISO['G2VarList'],ISO['IsoVarList']): |
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| 396 | dvar = gv.varname() |
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| 397 | var = dvar.replace('::dA','::A') |
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| 398 | albl = Ilbl[:Ilbl.rfind('_')] |
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| 399 | v = Ilbl[Ilbl.rfind('_')+1:] |
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| 400 | pval = ISO['ParentStructure'][albl][['dx','dy','dz'].index(v)] |
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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 | deltaList.append(cval-pval) |
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| 407 | modeVals = np.inner(ISO['Var2ModeMatrix'],deltaList) |
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| 408 | |
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| 409 | if 'G2OccVarList' in ISO: |
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| 410 | deltaOccList = [] |
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| 411 | for gv,Ilbl in zip(ISO['G2OccVarList'],ISO['OccVarList']): |
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| 412 | var = gv.varname() |
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| 413 | albl = Ilbl[:Ilbl.rfind('_')] |
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| 414 | pval = ISO['BaseOcc'][albl] |
|---|
| 415 | if var in parmDict: |
|---|
| 416 | cval = parmDict[var] |
|---|
| 417 | else: |
|---|
| 418 | print('PrintISOmodes Error: Atom not found',"No value found for parameter "+str(var)) |
|---|
| 419 | return |
|---|
| 420 | deltaOccList.append(cval-pval) |
|---|
| 421 | modeOccVals = np.inner(ISO['Var2OccMatrix'],deltaOccList) |
|---|
| 422 | |
|---|
| 423 | if 'G2VarList' in ISO: |
|---|
| 424 | pFile.write('\n ISODISTORT Displacive Modes for phase {}\n'.format(data['General'].get('Name',''))) |
|---|
| 425 | l = str(max([len(i) for i in ISO['IsoModeList']])+3) |
|---|
| 426 | fmt = ' {:'+l+'}{}' |
|---|
| 427 | for var,val,norm,G2mode in zip( |
|---|
| 428 | ISO['IsoModeList'],modeVals,ISO['NormList'],ISO['G2ModeList'] ): |
|---|
| 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 | if 'G2OccVarList' in ISO: |
|---|
| 438 | pFile.write('\n ISODISTORT Occupancy Modes for phase {}\n'.format(data['General'].get('Name',''))) |
|---|
| 439 | l = str(max([len(i) for i in ISO['OccModeList']])+3) |
|---|
| 440 | fmt = ' {:'+l+'}{}' |
|---|
| 441 | for var,val,norm,G2mode in zip( |
|---|
| 442 | ISO['OccModeList'],modeOccVals,ISO['OccNormList'],ISO['G2OccModeList'] ): |
|---|
| 443 | try: |
|---|
| 444 | value = G2py3.FormatSigFigs(val/norm) |
|---|
| 445 | if str(G2mode) in sigDict: |
|---|
| 446 | value = G2mth.ValEsd(val/norm,sigDict[str(G2mode)]/norm) |
|---|
| 447 | except TypeError: |
|---|
| 448 | value = '?' |
|---|
| 449 | pFile.write(fmt.format(var,value)+'\n') |
|---|
| 450 | |
|---|
| 451 | def GetPhaseNames(GPXfile): |
|---|
| 452 | ''' Returns a list of phase names found under 'Phases' in GSASII gpx file |
|---|
| 453 | |
|---|
| 454 | :param str GPXfile: full .gpx file name |
|---|
| 455 | :return: list of phase names |
|---|
| 456 | ''' |
|---|
| 457 | IndexGPX(GPXfile) |
|---|
| 458 | fl = open(GPXfile,'rb') |
|---|
| 459 | pos = gpxIndex.get('Phases') |
|---|
| 460 | if pos is None: |
|---|
| 461 | raise Exception("No Phases in GPX file") |
|---|
| 462 | fl.seek(pos) |
|---|
| 463 | data = cPickleLoad(fl) |
|---|
| 464 | fl.close() |
|---|
| 465 | return [datus[0] for datus in data[1:]] |
|---|
| 466 | |
|---|
| 467 | def GetAllPhaseData(GPXfile,PhaseName): |
|---|
| 468 | ''' Returns the entire dictionary for PhaseName from GSASII gpx file |
|---|
| 469 | |
|---|
| 470 | :param str GPXfile: full .gpx file name |
|---|
| 471 | :param str PhaseName: phase name |
|---|
| 472 | :return: phase dictionary or None if PhaseName is not present |
|---|
| 473 | ''' |
|---|
| 474 | IndexGPX(GPXfile) |
|---|
| 475 | fl = open(GPXfile,'rb') |
|---|
| 476 | pos = gpxIndex.get('Phases') |
|---|
| 477 | if pos is None: |
|---|
| 478 | raise Exception("No Phases in GPX file") |
|---|
| 479 | fl.seek(pos) |
|---|
| 480 | data = cPickleLoad(fl) |
|---|
| 481 | fl.close() |
|---|
| 482 | |
|---|
| 483 | for datus in data[1:]: |
|---|
| 484 | if datus[0] == PhaseName: |
|---|
| 485 | return datus[1] |
|---|
| 486 | |
|---|
| 487 | def GetHistograms(GPXfile,hNames): |
|---|
| 488 | """ Returns a dictionary of histograms found in GSASII gpx file |
|---|
| 489 | |
|---|
| 490 | :param str GPXfile: full .gpx file name |
|---|
| 491 | :param str hNames: list of histogram names |
|---|
| 492 | :return: dictionary of histograms (types = PWDR & HKLF) |
|---|
| 493 | |
|---|
| 494 | """ |
|---|
| 495 | IndexGPX(GPXfile) |
|---|
| 496 | fl = open(GPXfile,'rb') |
|---|
| 497 | Histograms = {} |
|---|
| 498 | for hist in hNames: |
|---|
| 499 | pos = gpxIndex.get(hist) |
|---|
| 500 | if pos is None: |
|---|
| 501 | raise Exception("Histogram {} not found in GPX file".format(hist)) |
|---|
| 502 | fl.seek(pos) |
|---|
| 503 | data = cPickleLoad(fl) |
|---|
| 504 | datum = data[0] |
|---|
| 505 | if 'PWDR' in hist[:4]: |
|---|
| 506 | PWDRdata = {} |
|---|
| 507 | PWDRdata.update(datum[1][0]) #weight factor |
|---|
| 508 | PWDRdata['Data'] = ma.array(ma.getdata(datum[1][1])) #masked powder data arrays/clear previous masks |
|---|
| 509 | PWDRdata[data[2][0]] = data[2][1] #Limits & excluded regions (if any) |
|---|
| 510 | PWDRdata[data[3][0]] = data[3][1] #Background |
|---|
| 511 | PWDRdata[data[4][0]] = data[4][1] #Instrument parameters |
|---|
| 512 | PWDRdata[data[5][0]] = data[5][1] #Sample parameters |
|---|
| 513 | try: |
|---|
| 514 | PWDRdata[data[9][0]] = data[9][1] #Reflection lists might be missing |
|---|
| 515 | except IndexError: |
|---|
| 516 | PWDRdata['Reflection Lists'] = {} |
|---|
| 517 | PWDRdata['Residuals'] = {} |
|---|
| 518 | Histograms[hist] = PWDRdata |
|---|
| 519 | elif 'HKLF' in hist[:4]: |
|---|
| 520 | HKLFdata = {} |
|---|
| 521 | HKLFdata.update(datum[1][0]) #weight factor |
|---|
| 522 | #patch |
|---|
| 523 | if 'list' in str(type(datum[1][1])): |
|---|
| 524 | #if isinstance(datum[1][1],list): |
|---|
| 525 | RefData = {'RefList':[],'FF':{}} |
|---|
| 526 | for ref in datum[1][1]: |
|---|
| 527 | RefData['RefList'].append(ref[:11]+[ref[13],]) |
|---|
| 528 | RefData['RefList'] = np.array(RefData['RefList']) |
|---|
| 529 | datum[1][1] = RefData |
|---|
| 530 | #end patch |
|---|
| 531 | datum[1][1]['FF'] = {} |
|---|
| 532 | HKLFdata['Data'] = datum[1][1] |
|---|
| 533 | HKLFdata[data[1][0]] = data[1][1] #Instrument parameters |
|---|
| 534 | HKLFdata['Reflection Lists'] = None |
|---|
| 535 | HKLFdata['Residuals'] = {} |
|---|
| 536 | Histograms[hist] = HKLFdata |
|---|
| 537 | fl.close() |
|---|
| 538 | return Histograms |
|---|
| 539 | |
|---|
| 540 | def GetHistogramNames(GPXfile,hTypes): |
|---|
| 541 | """ Returns a list of histogram names found in a GSAS-II .gpx file that |
|---|
| 542 | match specifed histogram types. Names are returned in the order they |
|---|
| 543 | appear in the file. |
|---|
| 544 | |
|---|
| 545 | :param str GPXfile: full .gpx file name |
|---|
| 546 | :param str hTypes: list of histogram types |
|---|
| 547 | :return: list of histogram names (types = PWDR & HKLF) |
|---|
| 548 | |
|---|
| 549 | """ |
|---|
| 550 | IndexGPX(GPXfile) |
|---|
| 551 | return [n[0] for n in gpxNamelist if n[0][:4] in hTypes] |
|---|
| 552 | |
|---|
| 553 | def GetUsedHistogramsAndPhases(GPXfile): |
|---|
| 554 | ''' Returns all histograms that are found in any phase |
|---|
| 555 | and any phase that uses a histogram. This also |
|---|
| 556 | assigns numbers to used phases and histograms by the |
|---|
| 557 | order they appear in the file. |
|---|
| 558 | |
|---|
| 559 | :param str GPXfile: full .gpx file name |
|---|
| 560 | :returns: (Histograms,Phases) |
|---|
| 561 | |
|---|
| 562 | * Histograms = dictionary of histograms as {name:data,...} |
|---|
| 563 | * Phases = dictionary of phases that use histograms |
|---|
| 564 | |
|---|
| 565 | ''' |
|---|
| 566 | phaseNames = GetPhaseNames(GPXfile) |
|---|
| 567 | histoList = GetHistogramNames(GPXfile,['PWDR','HKLF']) |
|---|
| 568 | allHistograms = GetHistograms(GPXfile,histoList) |
|---|
| 569 | phaseData = {} |
|---|
| 570 | for name in phaseNames: |
|---|
| 571 | phaseData[name] = GetAllPhaseData(GPXfile,name) |
|---|
| 572 | Histograms = {} |
|---|
| 573 | Phases = {} |
|---|
| 574 | for phase in phaseData: |
|---|
| 575 | Phase = phaseData[phase] |
|---|
| 576 | if Phase['General']['Type'] == 'faulted': continue #don't use faulted phases! |
|---|
| 577 | if Phase['Histograms']: |
|---|
| 578 | for hist in Phase['Histograms']: |
|---|
| 579 | if 'Use' not in Phase['Histograms'][hist]: #patch |
|---|
| 580 | Phase['Histograms'][hist]['Use'] = True |
|---|
| 581 | if Phase['Histograms'][hist]['Use'] and phase not in Phases: |
|---|
| 582 | pId = phaseNames.index(phase) |
|---|
| 583 | Phase['pId'] = pId |
|---|
| 584 | Phases[phase] = Phase |
|---|
| 585 | if hist not in Histograms and Phase['Histograms'][hist]['Use']: |
|---|
| 586 | try: |
|---|
| 587 | Histograms[hist] = allHistograms[hist] |
|---|
| 588 | hId = histoList.index(hist) |
|---|
| 589 | Histograms[hist]['hId'] = hId |
|---|
| 590 | except KeyError: # would happen if a referenced histogram were |
|---|
| 591 | # renamed or deleted |
|---|
| 592 | G2fil.G2Print('Warning: For phase "'+phase+ |
|---|
| 593 | '" unresolved reference to histogram "'+hist+'"') |
|---|
| 594 | # load the fix background info into the histograms |
|---|
| 595 | for hist in Histograms: |
|---|
| 596 | if 'Background' not in Histograms[hist]: continue |
|---|
| 597 | fixedBkg = Histograms[hist]['Background'][1].get('background PWDR') |
|---|
| 598 | if fixedBkg: |
|---|
| 599 | if not fixedBkg[0]: continue |
|---|
| 600 | # patch: add refinement flag, if needed |
|---|
| 601 | if len(fixedBkg) == 2: fixedBkg += [False] |
|---|
| 602 | h = Histograms[hist]['Background'][1] |
|---|
| 603 | try: |
|---|
| 604 | Limits = Histograms[hist]['Limits'][1] |
|---|
| 605 | x = Histograms[hist]['Data'][0] |
|---|
| 606 | xB = np.searchsorted(x,Limits[0]) |
|---|
| 607 | xF = np.searchsorted(x,Limits[1])+1 |
|---|
| 608 | h['fixback'] = allHistograms[fixedBkg[0]]['Data'][1][xB:xF] |
|---|
| 609 | except KeyError: # would happen if a referenced histogram were renamed or deleted |
|---|
| 610 | G2fil.G2Print('Warning: For hist "{}" unresolved background reference to hist "{}"' |
|---|
| 611 | .format(hist,fixedBkg[0])) |
|---|
| 612 | G2obj.IndexAllIds(Histograms=Histograms,Phases=Phases) |
|---|
| 613 | return Histograms,Phases |
|---|
| 614 | |
|---|
| 615 | def getBackupName(GPXfile,makeBack): |
|---|
| 616 | ''' |
|---|
| 617 | Get the name for the backup .gpx file name |
|---|
| 618 | |
|---|
| 619 | :param str GPXfile: full .gpx file name |
|---|
| 620 | :param bool makeBack: if True the name of a new file is returned, if |
|---|
| 621 | False the name of the last file that exists is returned |
|---|
| 622 | :returns: the name of a backup file |
|---|
| 623 | |
|---|
| 624 | ''' |
|---|
| 625 | GPXpath,GPXname = ospath.split(GPXfile) |
|---|
| 626 | if GPXpath == '': GPXpath = '.' |
|---|
| 627 | Name = ospath.splitext(GPXname)[0] |
|---|
| 628 | files = os.listdir(GPXpath) |
|---|
| 629 | last = 0 |
|---|
| 630 | for name in files: |
|---|
| 631 | name = name.split('.') |
|---|
| 632 | if len(name) == 3 and name[0] == Name and 'bak' in name[1]: |
|---|
| 633 | if makeBack: |
|---|
| 634 | last = max(last,int(name[1].strip('bak'))+1) |
|---|
| 635 | else: |
|---|
| 636 | last = max(last,int(name[1].strip('bak'))) |
|---|
| 637 | GPXback = ospath.join(GPXpath,ospath.splitext(GPXname)[0]+'.bak'+str(last)+'.gpx') |
|---|
| 638 | return GPXback |
|---|
| 639 | |
|---|
| 640 | def GPXBackup(GPXfile,makeBack=True): |
|---|
| 641 | ''' |
|---|
| 642 | makes a backup of the specified .gpx file |
|---|
| 643 | |
|---|
| 644 | :param str GPXfile: full .gpx file name |
|---|
| 645 | :param bool makeBack: if True (default), the backup is written to |
|---|
| 646 | a new file; if False, the last backup is overwritten |
|---|
| 647 | :returns: the name of the backup file that was written |
|---|
| 648 | ''' |
|---|
| 649 | import distutils.file_util as dfu |
|---|
| 650 | GPXback = getBackupName(GPXfile,makeBack) |
|---|
| 651 | tries = 0 |
|---|
| 652 | while True: |
|---|
| 653 | try: |
|---|
| 654 | dfu.copy_file(GPXfile,GPXback) |
|---|
| 655 | break |
|---|
| 656 | except: |
|---|
| 657 | tries += 1 |
|---|
| 658 | if tries > 10: |
|---|
| 659 | return GPXfile #failed! |
|---|
| 660 | time.sleep(1) #just wait a second! |
|---|
| 661 | return GPXback |
|---|
| 662 | |
|---|
| 663 | def SetUsedHistogramsAndPhases(GPXfile,Histograms,Phases,RigidBodies,CovData,parmFrozenList,makeBack=True): |
|---|
| 664 | ''' Updates gpxfile from all histograms that are found in any phase |
|---|
| 665 | and any phase that used a histogram. Also updates rigid body definitions. |
|---|
| 666 | This is used for non-sequential fits, but not for sequential fitting. |
|---|
| 667 | |
|---|
| 668 | :param str GPXfile: full .gpx file name |
|---|
| 669 | :param dict Histograms: dictionary of histograms as {name:data,...} |
|---|
| 670 | :param dict Phases: dictionary of phases that use histograms |
|---|
| 671 | :param dict RigidBodies: dictionary of rigid bodies |
|---|
| 672 | :param dict CovData: dictionary of refined variables, varyList, & covariance matrix |
|---|
| 673 | :param list parmFrozenList: list of parameters (as str) that are frozen |
|---|
| 674 | due to limits; converted to :class:`GSASIIobj.G2VarObj` objects. |
|---|
| 675 | :param bool makeBack: True if new backup of .gpx file is to be made; else |
|---|
| 676 | use the last one made |
|---|
| 677 | ''' |
|---|
| 678 | |
|---|
| 679 | import distutils.file_util as dfu |
|---|
| 680 | GPXback = GPXBackup(GPXfile,makeBack) |
|---|
| 681 | G2fil.G2Print ('Read from file:'+GPXback) |
|---|
| 682 | G2fil.G2Print ('Save to file :'+GPXfile) |
|---|
| 683 | infile = open(GPXback,'rb') |
|---|
| 684 | outfile = open(GPXfile,'wb') |
|---|
| 685 | while True: |
|---|
| 686 | try: |
|---|
| 687 | data = cPickleLoad(infile) |
|---|
| 688 | except EOFError: |
|---|
| 689 | break |
|---|
| 690 | datum = data[0] |
|---|
| 691 | # print 'read: ',datum[0] |
|---|
| 692 | if datum[0] == 'Phases': |
|---|
| 693 | for iphase in range(len(data)): |
|---|
| 694 | if data[iphase][0] in Phases: |
|---|
| 695 | phaseName = data[iphase][0] |
|---|
| 696 | data[iphase][1].update(Phases[phaseName]) |
|---|
| 697 | elif datum[0] == 'Covariance': |
|---|
| 698 | data[0][1] = CovData |
|---|
| 699 | elif datum[0] == 'Rigid bodies': |
|---|
| 700 | data[0][1] = RigidBodies |
|---|
| 701 | elif datum[0] == 'Controls': |
|---|
| 702 | Controls = data[0][1] |
|---|
| 703 | if 'parmFrozen' not in Controls: |
|---|
| 704 | Controls['parmFrozen'] = {} |
|---|
| 705 | Controls['parmFrozen']['FrozenList'] = [ |
|---|
| 706 | i if type(i) is G2obj.G2VarObj |
|---|
| 707 | else G2obj.G2VarObj(i) |
|---|
| 708 | for i in parmFrozenList] |
|---|
| 709 | try: |
|---|
| 710 | histogram = Histograms[datum[0]] |
|---|
| 711 | # print 'found ',datum[0] |
|---|
| 712 | data[0][1][1] = histogram['Data'] |
|---|
| 713 | data[0][1][0].update(histogram['Residuals']) |
|---|
| 714 | for datus in data[1:]: |
|---|
| 715 | # print ' read: ',datus[0] |
|---|
| 716 | if datus[0] in ['Instrument Parameters','Sample Parameters','Reflection Lists']: |
|---|
| 717 | datus[1] = histogram[datus[0]] |
|---|
| 718 | if datus[0] == 'Background': # remove fixed background from file |
|---|
| 719 | d1 = {key:histogram['Background'][1][key] |
|---|
| 720 | for key in histogram['Background'][1] |
|---|
| 721 | if not key.startswith('_fixed')} |
|---|
| 722 | datus[1] = copy.deepcopy(histogram['Background']) |
|---|
| 723 | datus[1][1] = d1 |
|---|
| 724 | except KeyError: |
|---|
| 725 | pass |
|---|
| 726 | try: |
|---|
| 727 | cPickle.dump(data,outfile,1) |
|---|
| 728 | except AttributeError: |
|---|
| 729 | G2fil.G2Print ('ERROR - bad data in least squares result') |
|---|
| 730 | infile.close() |
|---|
| 731 | outfile.close() |
|---|
| 732 | dfu.copy_file(GPXback,GPXfile) |
|---|
| 733 | G2fil.G2Print ('GPX file save failed - old version retained',mode='error') |
|---|
| 734 | return |
|---|
| 735 | |
|---|
| 736 | infile.close() |
|---|
| 737 | outfile.close() |
|---|
| 738 | |
|---|
| 739 | G2fil.G2Print ('GPX file save successful') |
|---|
| 740 | |
|---|
| 741 | def GetSeqResult(GPXfile): |
|---|
| 742 | ''' |
|---|
| 743 | Returns the sequential results table information from a GPX file. |
|---|
| 744 | Called at the beginning of :meth:`GSASIIstrMain.SeqRefine` |
|---|
| 745 | |
|---|
| 746 | :param str GPXfile: full .gpx file name |
|---|
| 747 | :returns: a dict containing the sequential results table |
|---|
| 748 | ''' |
|---|
| 749 | IndexGPX(GPXfile) |
|---|
| 750 | pos = gpxIndex.get('Sequential results') |
|---|
| 751 | if pos is None: |
|---|
| 752 | return {} |
|---|
| 753 | fl = open(GPXfile,'rb') |
|---|
| 754 | fl.seek(pos) |
|---|
| 755 | datum = cPickleLoad(fl)[0] |
|---|
| 756 | fl.close() |
|---|
| 757 | return datum[1] |
|---|
| 758 | |
|---|
| 759 | def SetupSeqSavePhases(GPXfile): |
|---|
| 760 | '''Initialize the files used to save intermediate results from |
|---|
| 761 | sequential fits. |
|---|
| 762 | ''' |
|---|
| 763 | IndexGPX(GPXfile) |
|---|
| 764 | # load initial Phase results from GPX |
|---|
| 765 | fl = open(GPXfile,'rb') |
|---|
| 766 | pos = gpxIndex.get('Phases') |
|---|
| 767 | if pos is None: |
|---|
| 768 | raise Exception("No Phases in GPX file") |
|---|
| 769 | fl.seek(pos) |
|---|
| 770 | data = cPickleLoad(fl) |
|---|
| 771 | fl.close() |
|---|
| 772 | # create GPX-like file to store latest Phase info; init with start vals |
|---|
| 773 | GPXphase = os.path.splitext(GPXfile)[0]+'.seqPhase' |
|---|
| 774 | fp = open(GPXphase,'wb') |
|---|
| 775 | cPickle.dump(data,fp,1) |
|---|
| 776 | fp.close() |
|---|
| 777 | # create empty file for histogram info |
|---|
| 778 | GPXhist = os.path.splitext(GPXfile)[0]+'.seqHist' |
|---|
| 779 | fp = open(GPXhist,'wb') |
|---|
| 780 | fp.close() |
|---|
| 781 | |
|---|
| 782 | def SaveUpdatedHistogramsAndPhases(GPXfile,Histograms,Phases,RigidBodies,CovData,parmFrozen): |
|---|
| 783 | ''' |
|---|
| 784 | Save phase and histogram information into "pseudo-gpx" files. The phase |
|---|
| 785 | information is overwritten each time this is called, but histogram information is |
|---|
| 786 | appended after each sequential step. |
|---|
| 787 | |
|---|
| 788 | :param str GPXfile: full .gpx file name |
|---|
| 789 | :param dict Histograms: dictionary of histograms as {name:data,...} |
|---|
| 790 | :param dict Phases: dictionary of phases that use histograms |
|---|
| 791 | :param dict RigidBodies: dictionary of rigid bodies |
|---|
| 792 | :param dict CovData: dictionary of refined variables, varyList, & covariance matrix |
|---|
| 793 | :param dict parmFrozen: dict with frozen parameters for all phases |
|---|
| 794 | and histograms (specified as str values) |
|---|
| 795 | ''' |
|---|
| 796 | |
|---|
| 797 | import distutils.file_util as dfu |
|---|
| 798 | |
|---|
| 799 | GPXphase = os.path.splitext(GPXfile)[0]+'.seqPhase' |
|---|
| 800 | fp = open(GPXphase,'rb') |
|---|
| 801 | data = cPickleLoad(fp) # first block in file should be Phases |
|---|
| 802 | if data[0][0] != 'Phases': |
|---|
| 803 | raise Exception('Unexpected block in {} file. How did this happen?' |
|---|
| 804 | .format(GPXphase)) |
|---|
| 805 | fp.close() |
|---|
| 806 | # update previous phase info |
|---|
| 807 | for datum in data[1:]: |
|---|
| 808 | if datum[0] in Phases: |
|---|
| 809 | datum[1].update(Phases[datum[0]]) |
|---|
| 810 | # save latest Phase/refinement info |
|---|
| 811 | fp = open(GPXphase,'wb') |
|---|
| 812 | cPickle.dump(data,fp,1) |
|---|
| 813 | cPickle.dump([['Covariance',CovData]],fp,1) |
|---|
| 814 | cPickle.dump([['Rigid bodies',RigidBodies]],fp,1) |
|---|
| 815 | cPickle.dump([['parmFrozen',parmFrozen]],fp,1) |
|---|
| 816 | fp.close() |
|---|
| 817 | # create an entry that looks like a PWDR tree item |
|---|
| 818 | for key in Histograms: |
|---|
| 819 | if key.startswith('PWDR '): |
|---|
| 820 | break |
|---|
| 821 | else: |
|---|
| 822 | raise Exception('No PWDR entry in Histogram dict!') |
|---|
| 823 | histname = key |
|---|
| 824 | hist = copy.deepcopy(Histograms[key]) |
|---|
| 825 | xfer_dict = {'Index Peak List': [[], []], |
|---|
| 826 | 'Comments': [], |
|---|
| 827 | 'Unit Cells List': [], |
|---|
| 828 | 'Peak List': {'peaks': [], 'sigDict': {}}, |
|---|
| 829 | } |
|---|
| 830 | histData = hist['Data'] |
|---|
| 831 | del hist['Data'] |
|---|
| 832 | for key in ('Limits','Background','Instrument Parameters', |
|---|
| 833 | 'Sample Parameters','Reflection Lists'): |
|---|
| 834 | xfer_dict[key] = hist[key] |
|---|
| 835 | if key == 'Background': # remove fixed background from file |
|---|
| 836 | xfer_dict['Background'][1] = {k:hist['Background'][1][k] |
|---|
| 837 | for k in hist['Background'][1] |
|---|
| 838 | if not k.startswith('_fixed')} |
|---|
| 839 | del hist[key] |
|---|
| 840 | # xform into a gpx-type entry |
|---|
| 841 | data = [] |
|---|
| 842 | data.append([histname,[hist,histData,histname]]) |
|---|
| 843 | for key in ['Comments','Limits','Background','Instrument Parameters', |
|---|
| 844 | 'Sample Parameters','Peak List','Index Peak List', |
|---|
| 845 | 'Unit Cells List','Reflection Lists']: |
|---|
| 846 | data.append([key,xfer_dict[key]]) |
|---|
| 847 | # append histogram to histogram info |
|---|
| 848 | GPXhist = os.path.splitext(GPXfile)[0]+'.seqHist' |
|---|
| 849 | fp = open(GPXhist,'ab') |
|---|
| 850 | cPickle.dump(data,fp,1) |
|---|
| 851 | fp.close() |
|---|
| 852 | return |
|---|
| 853 | |
|---|
| 854 | def SetSeqResult(GPXfile,Histograms,SeqResult): |
|---|
| 855 | ''' |
|---|
| 856 | Places the sequential results information into a GPX file |
|---|
| 857 | after a refinement has been completed. |
|---|
| 858 | Called at the end of :meth:`GSASIIstrMain.SeqRefine` |
|---|
| 859 | |
|---|
| 860 | :param str GPXfile: full .gpx file name |
|---|
| 861 | ''' |
|---|
| 862 | GPXback = GPXBackup(GPXfile) |
|---|
| 863 | G2fil.G2Print ('Read from file:'+GPXback) |
|---|
| 864 | G2fil.G2Print ('Save to file :'+GPXfile) |
|---|
| 865 | GPXphase = os.path.splitext(GPXfile)[0]+'.seqPhase' |
|---|
| 866 | fp = open(GPXphase,'rb') |
|---|
| 867 | data = cPickleLoad(fp) # first block in file should be Phases |
|---|
| 868 | if data[0][0] != 'Phases': |
|---|
| 869 | raise Exception('Unexpected block in {} file. How did this happen?'.format(GPXphase)) |
|---|
| 870 | Phases = {} |
|---|
| 871 | for name,vals in data[1:]: |
|---|
| 872 | Phases[name] = vals |
|---|
| 873 | name,CovData = cPickleLoad(fp)[0] # 2nd block in file should be Covariance |
|---|
| 874 | name,RigidBodies = cPickleLoad(fp)[0] # 3rd block in file should be Rigid Bodies |
|---|
| 875 | name,parmFrozenDict = cPickleLoad(fp)[0] # 4th block in file should be frozen parameters |
|---|
| 876 | fp.close() |
|---|
| 877 | GPXhist = os.path.splitext(GPXfile)[0]+'.seqHist' |
|---|
| 878 | hist = open(GPXhist,'rb') |
|---|
| 879 | # build an index to the GPXhist file |
|---|
| 880 | histIndex = {} |
|---|
| 881 | while True: |
|---|
| 882 | loc = hist.tell() |
|---|
| 883 | try: |
|---|
| 884 | datum = cPickleLoad(hist)[0] |
|---|
| 885 | except EOFError: |
|---|
| 886 | break |
|---|
| 887 | histIndex[datum[0]] = loc |
|---|
| 888 | |
|---|
| 889 | infile = open(GPXback,'rb') |
|---|
| 890 | outfile = open(GPXfile,'wb') |
|---|
| 891 | while True: |
|---|
| 892 | try: |
|---|
| 893 | data = cPickleLoad(infile) |
|---|
| 894 | except EOFError: |
|---|
| 895 | break |
|---|
| 896 | datum = data[0] |
|---|
| 897 | if datum[0] == 'Sequential results': |
|---|
| 898 | data[0][1] = SeqResult |
|---|
| 899 | elif datum[0] == 'Phases': |
|---|
| 900 | for pdata in data[1:]: |
|---|
| 901 | if pdata[0] in Phases: |
|---|
| 902 | pdata[1].update(Phases[pdata[0]]) |
|---|
| 903 | elif datum[0] == 'Covariance': |
|---|
| 904 | data[0][1] = CovData |
|---|
| 905 | elif datum[0] == 'Rigid bodies': |
|---|
| 906 | data[0][1] = RigidBodies |
|---|
| 907 | elif datum[0] == 'Controls': # reset the Copy Next flag after a sequential fit |
|---|
| 908 | Controls = data[0][1] |
|---|
| 909 | Controls['Copy2Next'] = False |
|---|
| 910 | for key in parmFrozenDict: |
|---|
| 911 | Controls['parmFrozen'][key] = [ |
|---|
| 912 | i if type(i) is G2obj.G2VarObj |
|---|
| 913 | else G2obj.G2VarObj(i) |
|---|
| 914 | for i in parmFrozenDict[key]] |
|---|
| 915 | elif datum[0] in histIndex: |
|---|
| 916 | hist.seek(histIndex[datum[0]]) |
|---|
| 917 | hdata = cPickleLoad(hist) |
|---|
| 918 | if data[0][0] != hdata[0][0]: |
|---|
| 919 | G2fil.G2Print('Error! Updating {} with {}'.format(data[0][0],hdata[0][0])) |
|---|
| 920 | data[0] = hdata[0] |
|---|
| 921 | xferItems = ['Background','Instrument Parameters','Sample Parameters','Reflection Lists'] |
|---|
| 922 | hItems = {name:j+1 for j,(name,val) in enumerate(hdata[1:]) if name in xferItems} |
|---|
| 923 | for j,(name,val) in enumerate(data[1:]): |
|---|
| 924 | if name not in xferItems: continue |
|---|
| 925 | data[j+1][1] = hdata[hItems[name]][1] |
|---|
| 926 | cPickle.dump(data,outfile,1) |
|---|
| 927 | hist.close() |
|---|
| 928 | infile.close() |
|---|
| 929 | outfile.close() |
|---|
| 930 | # clean up tmp files |
|---|
| 931 | try: |
|---|
| 932 | os.remove(GPXphase) |
|---|
| 933 | except: |
|---|
| 934 | G2fil.G2Print('Warning: unable to delete {}'.format(GPXphase)) |
|---|
| 935 | try: |
|---|
| 936 | os.remove(GPXhist) |
|---|
| 937 | except: |
|---|
| 938 | G2fil.G2Print('Warning: unable to delete {}'.format(GPXhist)) |
|---|
| 939 | G2fil.G2Print ('GPX file merge completed') |
|---|
| 940 | |
|---|
| 941 | #============================================================================== |
|---|
| 942 | # Refinement routines |
|---|
| 943 | #============================================================================== |
|---|
| 944 | def ShowBanner(pFile=None): |
|---|
| 945 | 'Print authorship, copyright and citation notice' |
|---|
| 946 | pFile.write(80*'*'+'\n') |
|---|
| 947 | pFile.write(' General Structure Analysis System-II Crystal Structure Refinement\n') |
|---|
| 948 | pFile.write(' by Robert B. Von Dreele & Brian H. Toby\n') |
|---|
| 949 | pFile.write(' Argonne National Laboratory(C), 2010\n') |
|---|
| 950 | pFile.write(' This product includes software developed by the UChicago Argonne, LLC,\n') |
|---|
| 951 | pFile.write(' as Operator of Argonne National Laboratory.\n') |
|---|
| 952 | pFile.write(' Please cite:\n') |
|---|
| 953 | pFile.write(' B.H. Toby & R.B. Von Dreele, J. Appl. Cryst. 46, 544-549 (2013)\n') |
|---|
| 954 | |
|---|
| 955 | pFile.write(80*'*'+'\n') |
|---|
| 956 | |
|---|
| 957 | def ShowControls(Controls,pFile=None,SeqRef=False,preFrozenCount=0): |
|---|
| 958 | 'Print controls information' |
|---|
| 959 | pFile.write(' Least squares controls:\n') |
|---|
| 960 | pFile.write(' Refinement type: %s\n'%Controls['deriv type']) |
|---|
| 961 | if 'Hessian' in Controls['deriv type']: |
|---|
| 962 | pFile.write(' Maximum number of cycles: %d\n'%Controls['max cyc']) |
|---|
| 963 | else: |
|---|
| 964 | pFile.write(' Minimum delta-M/M for convergence: %.2g\n'%(Controls['min dM/M'])) |
|---|
| 965 | pFile.write(' Regularize hydrogens (if any): %s\n'%Controls.get('HatomFix',False)) |
|---|
| 966 | pFile.write(' Initial shift factor: %.3f\n'%(Controls['shift factor'])) |
|---|
| 967 | if SeqRef: |
|---|
| 968 | pFile.write(' Sequential refinement controls:\n') |
|---|
| 969 | pFile.write(' Copy of histogram results to next: %s\n'%(Controls['Copy2Next'])) |
|---|
| 970 | pFile.write(' Process histograms in reverse order: %s\n'%(Controls['Reverse Seq'])) |
|---|
| 971 | if preFrozenCount: |
|---|
| 972 | pFile.write('\n Starting refinement with {} Frozen variables\n\n'.format(preFrozenCount)) |
|---|
| 973 | |
|---|
| 974 | def GetPawleyConstr(SGLaue,PawleyRef,im,pawleyVary): |
|---|
| 975 | 'needs a doc string' |
|---|
| 976 | # if SGLaue in ['-1','2/m','mmm']: |
|---|
| 977 | # return #no Pawley symmetry required constraints |
|---|
| 978 | eqvDict = {} |
|---|
| 979 | for i,varyI in enumerate(pawleyVary): |
|---|
| 980 | eqvDict[varyI] = [] |
|---|
| 981 | refI = int(varyI.split(':')[-1]) |
|---|
| 982 | ih,ik,il = PawleyRef[refI][:3] |
|---|
| 983 | dspI = PawleyRef[refI][4+im] |
|---|
| 984 | for varyJ in pawleyVary[i+1:]: |
|---|
| 985 | refJ = int(varyJ.split(':')[-1]) |
|---|
| 986 | jh,jk,jl = PawleyRef[refJ][:3] |
|---|
| 987 | dspJ = PawleyRef[refJ][4+im] |
|---|
| 988 | if SGLaue in ['4/m','4/mmm']: |
|---|
| 989 | isum = ih**2+ik**2 |
|---|
| 990 | jsum = jh**2+jk**2 |
|---|
| 991 | if abs(il) == abs(jl) and isum == jsum: |
|---|
| 992 | eqvDict[varyI].append(varyJ) |
|---|
| 993 | elif SGLaue in ['3R','3mR']: |
|---|
| 994 | isum = ih**2+ik**2+il**2 |
|---|
| 995 | jsum = jh**2+jk**2+jl**2 |
|---|
| 996 | isum2 = ih*ik+ih*il+ik*il |
|---|
| 997 | jsum2 = jh*jk+jh*jl+jk*jl |
|---|
| 998 | if isum == jsum and isum2 == jsum2: |
|---|
| 999 | eqvDict[varyI].append(varyJ) |
|---|
| 1000 | elif SGLaue in ['3','3m1','31m','6/m','6/mmm']: |
|---|
| 1001 | isum = ih**2+ik**2+ih*ik |
|---|
| 1002 | jsum = jh**2+jk**2+jh*jk |
|---|
| 1003 | if abs(il) == abs(jl) and isum == jsum: |
|---|
| 1004 | eqvDict[varyI].append(varyJ) |
|---|
| 1005 | elif SGLaue in ['m3','m3m']: |
|---|
| 1006 | isum = ih**2+ik**2+il**2 |
|---|
| 1007 | jsum = jh**2+jk**2+jl**2 |
|---|
| 1008 | if isum == jsum: |
|---|
| 1009 | eqvDict[varyI].append(varyJ) |
|---|
| 1010 | elif abs(dspI-dspJ)/dspI < 1.e-4: |
|---|
| 1011 | eqvDict[varyI].append(varyJ) |
|---|
| 1012 | for item in pawleyVary: |
|---|
| 1013 | if eqvDict[item]: |
|---|
| 1014 | for item2 in pawleyVary: |
|---|
| 1015 | if item2 in eqvDict[item]: |
|---|
| 1016 | eqvDict[item2] = [] |
|---|
| 1017 | G2mv.StoreEquivalence(item,eqvDict[item]) |
|---|
| 1018 | |
|---|
| 1019 | def cellVary(pfx,SGData): |
|---|
| 1020 | '''Creates equivalences for a phase based on the Laue class. |
|---|
| 1021 | Returns a list of A tensor terms that are non-zero. |
|---|
| 1022 | ''' |
|---|
| 1023 | if SGData['SGLaue'] in ['-1',]: |
|---|
| 1024 | return [pfx+'A0',pfx+'A1',pfx+'A2',pfx+'A3',pfx+'A4',pfx+'A5'] |
|---|
| 1025 | elif SGData['SGLaue'] in ['2/m',]: |
|---|
| 1026 | if SGData['SGUniq'] == 'a': |
|---|
| 1027 | return [pfx+'A0',pfx+'A1',pfx+'A2',pfx+'A5'] |
|---|
| 1028 | elif SGData['SGUniq'] == 'b': |
|---|
| 1029 | return [pfx+'A0',pfx+'A1',pfx+'A2',pfx+'A4'] |
|---|
| 1030 | else: |
|---|
| 1031 | return [pfx+'A0',pfx+'A1',pfx+'A2',pfx+'A3'] |
|---|
| 1032 | elif SGData['SGLaue'] in ['mmm',]: |
|---|
| 1033 | return [pfx+'A0',pfx+'A1',pfx+'A2'] |
|---|
| 1034 | elif SGData['SGLaue'] in ['4/m','4/mmm']: |
|---|
| 1035 | G2mv.StoreEquivalence(pfx+'A0',(pfx+'A1',)) |
|---|
| 1036 | return [pfx+'A0',pfx+'A1',pfx+'A2'] |
|---|
| 1037 | elif SGData['SGLaue'] in ['6/m','6/mmm','3m1', '31m', '3']: |
|---|
| 1038 | G2mv.StoreEquivalence(pfx+'A0',(pfx+'A1',pfx+'A3',)) |
|---|
| 1039 | return [pfx+'A0',pfx+'A1',pfx+'A2',pfx+'A3'] |
|---|
| 1040 | elif SGData['SGLaue'] in ['3R', '3mR']: |
|---|
| 1041 | G2mv.StoreEquivalence(pfx+'A0',(pfx+'A1',pfx+'A2',)) |
|---|
| 1042 | G2mv.StoreEquivalence(pfx+'A3',(pfx+'A4',pfx+'A5',)) |
|---|
| 1043 | return [pfx+'A0',pfx+'A1',pfx+'A2',pfx+'A3',pfx+'A4',pfx+'A5'] |
|---|
| 1044 | elif SGData['SGLaue'] in ['m3m','m3']: |
|---|
| 1045 | G2mv.StoreEquivalence(pfx+'A0',(pfx+'A1',pfx+'A2',)) |
|---|
| 1046 | return [pfx+'A0',pfx+'A1',pfx+'A2'] |
|---|
| 1047 | |
|---|
| 1048 | def modVary(pfx,SSGData): |
|---|
| 1049 | vary = [] |
|---|
| 1050 | for i,item in enumerate(SSGData['modSymb']): |
|---|
| 1051 | if item in ['a','b','g']: |
|---|
| 1052 | vary.append(pfx+'mV%d'%(i)) |
|---|
| 1053 | return vary |
|---|
| 1054 | |
|---|
| 1055 | ################################################################################ |
|---|
| 1056 | ##### Rigid Body Models and not General.get('doPawley') |
|---|
| 1057 | ################################################################################ |
|---|
| 1058 | |
|---|
| 1059 | def GetRigidBodyModels(rigidbodyDict,Print=True,pFile=None): |
|---|
| 1060 | 'Get Rigid body info from tree entry and print it to .LST file' |
|---|
| 1061 | |
|---|
| 1062 | def PrintResRBModel(RBModel): |
|---|
| 1063 | pFile.write('Residue RB name: %s no.atoms: %d, No. times used: %d\n'% |
|---|
| 1064 | (RBModel['RBname'],len(RBModel['rbTypes']),RBModel['useCount'])) |
|---|
| 1065 | for i in WriteResRBModel(RBModel): |
|---|
| 1066 | pFile.write(i) |
|---|
| 1067 | |
|---|
| 1068 | def PrintVecRBModel(RBModel): |
|---|
| 1069 | pFile.write('Vector RB name: %s no.atoms: %d No. times used: %d\n'% |
|---|
| 1070 | (RBModel['RBname'],len(RBModel['rbTypes']),RBModel['useCount'])) |
|---|
| 1071 | for i in WriteVecRBModel(RBModel): |
|---|
| 1072 | pFile.write(i) |
|---|
| 1073 | pFile.write('Orientation defined by: atom %s -> atom %s & atom %s -> atom %s\n'% |
|---|
| 1074 | (RBModel['rbRef'][0],RBModel['rbRef'][1],RBModel['rbRef'][0],RBModel['rbRef'][2])) |
|---|
| 1075 | |
|---|
| 1076 | rbVary = [] |
|---|
| 1077 | rbDict = {} |
|---|
| 1078 | rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]}) |
|---|
| 1079 | if len(rbIds['Vector']): |
|---|
| 1080 | for irb,item in enumerate(rbIds['Vector']): |
|---|
| 1081 | if rigidbodyDict['Vector'][item]['useCount']: |
|---|
| 1082 | RBmags = rigidbodyDict['Vector'][item]['VectMag'] |
|---|
| 1083 | RBrefs = rigidbodyDict['Vector'][item]['VectRef'] |
|---|
| 1084 | for i,[mag,ref] in enumerate(zip(RBmags,RBrefs)): |
|---|
| 1085 | pid = '::RBV;'+str(i)+':'+str(irb) |
|---|
| 1086 | rbDict[pid] = mag |
|---|
| 1087 | if ref: |
|---|
| 1088 | rbVary.append(pid) |
|---|
| 1089 | if Print: |
|---|
| 1090 | pFile.write('\nVector rigid body model:\n') |
|---|
| 1091 | PrintVecRBModel(rigidbodyDict['Vector'][item]) |
|---|
| 1092 | if len(rbIds['Residue']): |
|---|
| 1093 | for item in rbIds['Residue']: |
|---|
| 1094 | if rigidbodyDict['Residue'][item]['useCount']: |
|---|
| 1095 | if Print: |
|---|
| 1096 | pFile.write('\nResidue rigid body model:\n') |
|---|
| 1097 | PrintResRBModel(rigidbodyDict['Residue'][item]) |
|---|
| 1098 | return rbVary,rbDict |
|---|
| 1099 | |
|---|
| 1100 | def SetRigidBodyModels(parmDict,sigDict,rigidbodyDict,pFile=None): |
|---|
| 1101 | 'needs a doc string' |
|---|
| 1102 | |
|---|
| 1103 | def PrintRBVectandSig(VectRB,VectSig): |
|---|
| 1104 | pFile.write('\n Rigid body vector magnitudes for %s:\n'%VectRB['RBname']) |
|---|
| 1105 | namstr = ' names :' |
|---|
| 1106 | valstr = ' values:' |
|---|
| 1107 | sigstr = ' esds :' |
|---|
| 1108 | for i,[val,sig] in enumerate(zip(VectRB['VectMag'],VectSig)): |
|---|
| 1109 | namstr += '%12s'%('Vect '+str(i)) |
|---|
| 1110 | valstr += '%12.4f'%(val) |
|---|
| 1111 | if sig: |
|---|
| 1112 | sigstr += '%12.4f'%(sig) |
|---|
| 1113 | else: |
|---|
| 1114 | sigstr += 12*' ' |
|---|
| 1115 | pFile.write(namstr+'\n') |
|---|
| 1116 | pFile.write(valstr+'\n') |
|---|
| 1117 | pFile.write(sigstr+'\n') |
|---|
| 1118 | |
|---|
| 1119 | RBIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]}) #these are lists of rbIds |
|---|
| 1120 | if not RBIds['Vector']: |
|---|
| 1121 | return |
|---|
| 1122 | for irb,item in enumerate(RBIds['Vector']): |
|---|
| 1123 | if rigidbodyDict['Vector'][item]['useCount']: |
|---|
| 1124 | VectSig = [] |
|---|
| 1125 | RBmags = rigidbodyDict['Vector'][item]['VectMag'] |
|---|
| 1126 | for i,mag in enumerate(RBmags): |
|---|
| 1127 | name = '::RBV;'+str(i)+':'+str(irb) |
|---|
| 1128 | if name in sigDict: |
|---|
| 1129 | VectSig.append(sigDict[name]) |
|---|
| 1130 | PrintRBVectandSig(rigidbodyDict['Vector'][item],VectSig) |
|---|
| 1131 | |
|---|
| 1132 | ################################################################################ |
|---|
| 1133 | ##### Phase data |
|---|
| 1134 | ################################################################################ |
|---|
| 1135 | def GetPhaseData(PhaseData,RestraintDict={},rbIds={},Print=True,pFile=None,seqRef=False): |
|---|
| 1136 | '''Setup the phase information for a structural refinement, used for |
|---|
| 1137 | regular and sequential refinements, optionally printing information |
|---|
| 1138 | to the .lst file (if Print is True) |
|---|
| 1139 | ''' |
|---|
| 1140 | |
|---|
| 1141 | def PrintFFtable(FFtable): |
|---|
| 1142 | pFile.write('\n X-ray scattering factors:\n') |
|---|
| 1143 | pFile.write(' Symbol fa fb fc\n') |
|---|
| 1144 | pFile.write(99*'-'+'\n') |
|---|
| 1145 | for Ename in FFtable: |
|---|
| 1146 | ffdata = FFtable[Ename] |
|---|
| 1147 | fa = ffdata['fa'] |
|---|
| 1148 | fb = ffdata['fb'] |
|---|
| 1149 | pFile.write(' %8s %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f\n'% |
|---|
| 1150 | (Ename.ljust(8),fa[0],fa[1],fa[2],fa[3],fb[0],fb[1],fb[2],fb[3],ffdata['fc'])) |
|---|
| 1151 | |
|---|
| 1152 | def PrintMFtable(MFtable): |
|---|
| 1153 | pFile.write('\n <j0> Magnetic scattering factors:\n') |
|---|
| 1154 | pFile.write(' Symbol mfa mfb mfc\n') |
|---|
| 1155 | pFile.write(99*'-'+'\n') |
|---|
| 1156 | for Ename in MFtable: |
|---|
| 1157 | mfdata = MFtable[Ename] |
|---|
| 1158 | fa = mfdata['mfa'] |
|---|
| 1159 | fb = mfdata['mfb'] |
|---|
| 1160 | pFile.write(' %8s %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f\n'% |
|---|
| 1161 | (Ename.ljust(8),fa[0],fa[1],fa[2],fa[3],fb[0],fb[1],fb[2],fb[3],mfdata['mfc'])) |
|---|
| 1162 | pFile.write('\n <j2> Magnetic scattering factors:\n') |
|---|
| 1163 | pFile.write(' Symbol nfa nfb nfc\n') |
|---|
| 1164 | pFile.write(99*'-'+'\n') |
|---|
| 1165 | for Ename in MFtable: |
|---|
| 1166 | mfdata = MFtable[Ename] |
|---|
| 1167 | fa = mfdata['nfa'] |
|---|
| 1168 | fb = mfdata['nfb'] |
|---|
| 1169 | pFile.write(' %8s %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f\n'% |
|---|
| 1170 | (Ename.ljust(8),fa[0],fa[1],fa[2],fa[3],fb[0],fb[1],fb[2],fb[3],mfdata['nfc'])) |
|---|
| 1171 | |
|---|
| 1172 | def PrintBLtable(BLtable): |
|---|
| 1173 | pFile.write('\n Neutron scattering factors:\n') |
|---|
| 1174 | pFile.write(' Symbol isotope mass b resonant terms\n') |
|---|
| 1175 | pFile.write(99*'-'+'\n') |
|---|
| 1176 | for Ename in BLtable: |
|---|
| 1177 | bldata = BLtable[Ename] |
|---|
| 1178 | isotope = bldata[0] |
|---|
| 1179 | mass = bldata[1]['Mass'] |
|---|
| 1180 | if 'BW-LS' in bldata[1]: |
|---|
| 1181 | bres = bldata[1]['BW-LS'] |
|---|
| 1182 | blen = 0 |
|---|
| 1183 | else: |
|---|
| 1184 | blen = bldata[1]['SL'][0] |
|---|
| 1185 | bres = [] |
|---|
| 1186 | line = ' %8s%11s %10.3f %8.3f'%(Ename.ljust(8),isotope.center(11),mass,blen) |
|---|
| 1187 | for item in bres: |
|---|
| 1188 | line += '%10.5g'%(item) |
|---|
| 1189 | pFile.write(line+'\n') |
|---|
| 1190 | |
|---|
| 1191 | def PrintRBObjects(resRBData,vecRBData): |
|---|
| 1192 | |
|---|
| 1193 | def PrintRBThermals(): |
|---|
| 1194 | tlstr = ['11','22','33','12','13','23'] |
|---|
| 1195 | sstr = ['12','13','21','23','31','32','AA','BB'] |
|---|
| 1196 | TLS = RB['ThermalMotion'][1] |
|---|
| 1197 | TLSvar = RB['ThermalMotion'][2] |
|---|
| 1198 | if 'T' in RB['ThermalMotion'][0]: |
|---|
| 1199 | pFile.write('TLS data\n') |
|---|
| 1200 | text = '' |
|---|
| 1201 | for i in range(6): |
|---|
| 1202 | text += 'T'+tlstr[i]+' %8.4f %s '%(TLS[i],str(TLSvar[i])[0]) |
|---|
| 1203 | pFile.write(text+'\n') |
|---|
| 1204 | if 'L' in RB['ThermalMotion'][0]: |
|---|
| 1205 | text = '' |
|---|
| 1206 | for i in range(6,12): |
|---|
| 1207 | text += 'L'+tlstr[i-6]+' %8.2f %s '%(TLS[i],str(TLSvar[i])[0]) |
|---|
| 1208 | pFile.write(text+'\n') |
|---|
| 1209 | if 'S' in RB['ThermalMotion'][0]: |
|---|
| 1210 | text = '' |
|---|
| 1211 | for i in range(12,20): |
|---|
| 1212 | text += 'S'+sstr[i-12]+' %8.3f %s '%(TLS[i],str(TLSvar[i])[0]) |
|---|
| 1213 | pFile.write(text+'\n') |
|---|
| 1214 | if 'U' in RB['ThermalMotion'][0]: |
|---|
| 1215 | pFile.write('Uiso data\n') |
|---|
| 1216 | text = 'Uiso'+' %10.3f %s'%(TLS[0],str(TLSvar[0])[0]) |
|---|
| 1217 | pFile.write(text+'\n') |
|---|
| 1218 | |
|---|
| 1219 | if len(resRBData): |
|---|
| 1220 | for RB in resRBData: |
|---|
| 1221 | Oxyz = RB['Orig'][0] |
|---|
| 1222 | Qrijk = RB['Orient'][0] |
|---|
| 1223 | Angle = 2.0*acosd(Qrijk[0]) |
|---|
| 1224 | pFile.write('\nRBObject %s at %10.4f %10.4f %10.4f Refine? %s\n'% |
|---|
| 1225 | (RB['RBname'],Oxyz[0],Oxyz[1],Oxyz[2],RB['Orig'][1])) |
|---|
| 1226 | pFile.write('Orientation angle,vector: %10.3f %10.4f %10.4f %10.4f Refine? %s\n'% |
|---|
| 1227 | (Angle,Qrijk[1],Qrijk[2],Qrijk[3],RB['Orient'][1])) |
|---|
| 1228 | Torsions = RB['Torsions'] |
|---|
| 1229 | if len(Torsions): |
|---|
| 1230 | text = 'Torsions: ' |
|---|
| 1231 | for torsion in Torsions: |
|---|
| 1232 | text += '%10.4f Refine? %s'%(torsion[0],torsion[1]) |
|---|
| 1233 | pFile.write(text+'\n') |
|---|
| 1234 | PrintRBThermals() |
|---|
| 1235 | if len(vecRBData): |
|---|
| 1236 | for RB in vecRBData: |
|---|
| 1237 | Oxyz = RB['Orig'][0] |
|---|
| 1238 | Qrijk = RB['Orient'][0] |
|---|
| 1239 | Angle = 2.0*acosd(Qrijk[0]) |
|---|
| 1240 | pFile.write('\nRBObject %s at %10.4f %10.4f %10.4f Refine? %s\n'% |
|---|
| 1241 | (RB['RBname'],Oxyz[0],Oxyz[1],Oxyz[2],RB['Orig'][1])) |
|---|
| 1242 | pFile.write('Orientation angle,vector: %10.3f %10.4f %10.4f %10.4f Refine? %s\n'% |
|---|
| 1243 | (Angle,Qrijk[1],Qrijk[2],Qrijk[3],RB['Orient'][1])) |
|---|
| 1244 | PrintRBThermals() |
|---|
| 1245 | |
|---|
| 1246 | def PrintAtoms(General,Atoms): |
|---|
| 1247 | cx,ct,cs,cia = General['AtomPtrs'] |
|---|
| 1248 | pFile.write('\n Atoms:\n') |
|---|
| 1249 | line = ' name type refine? x y z '+ \ |
|---|
| 1250 | ' frac site sym mult I/A Uiso U11 U22 U33 U12 U13 U23' |
|---|
| 1251 | if General['Type'] == 'macromolecular': |
|---|
| 1252 | line = ' res no residue chain'+line |
|---|
| 1253 | pFile.write(line+'\n') |
|---|
| 1254 | if General['Type'] in ['nuclear','magnetic','faulted',]: |
|---|
| 1255 | pFile.write(135*'-'+'\n') |
|---|
| 1256 | for i,at in enumerate(Atoms): |
|---|
| 1257 | line = '%7s'%(at[ct-1])+'%7s'%(at[ct])+'%7s'%(at[ct+1])+'%10.5f'%(at[cx])+'%10.5f'%(at[cx+1])+ \ |
|---|
| 1258 | '%10.5f'%(at[cx+2])+'%8.3f'%(at[cx+3])+'%7s'%(at[cs])+'%5d'%(at[cs+1])+'%5s'%(at[cia]) |
|---|
| 1259 | if at[cia] == 'I': |
|---|
| 1260 | line += '%8.5f'%(at[cia+1])+48*' ' |
|---|
| 1261 | else: |
|---|
| 1262 | line += 8*' ' |
|---|
| 1263 | for j in range(6): |
|---|
| 1264 | line += '%8.5f'%(at[cia+2+j]) |
|---|
| 1265 | pFile.write(line+'\n') |
|---|
| 1266 | elif General['Type'] == 'macromolecular': |
|---|
| 1267 | pFile.write(135*'-'+'\n') |
|---|
| 1268 | for i,at in enumerate(Atoms): |
|---|
| 1269 | 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])+ \ |
|---|
| 1270 | '%10.5f'%(at[cx+2])+'%8.3f'%(at[cx+3])+'%7s'%(at[cs])+'%5d'%(at[cs+1])+'%5s'%(at[cia]) |
|---|
| 1271 | if at[cia] == 'I': |
|---|
| 1272 | line += '%8.4f'%(at[cia+1])+48*' ' |
|---|
| 1273 | else: |
|---|
| 1274 | line += 8*' ' |
|---|
| 1275 | for j in range(6): |
|---|
| 1276 | line += '%8.4f'%(at[cia+2+j]) |
|---|
| 1277 | pFile.write(line+'\n') |
|---|
| 1278 | |
|---|
| 1279 | def PrintMoments(General,Atoms): |
|---|
| 1280 | cx,ct,cs,cia = General['AtomPtrs'] |
|---|
| 1281 | cmx = cx+4 |
|---|
| 1282 | AtInfo = dict(zip(General['AtomTypes'],General['Lande g'])) |
|---|
| 1283 | pFile.write('\n Magnetic moments:\n') |
|---|
| 1284 | line = ' name type refine? Mx My Mz ' |
|---|
| 1285 | pFile.write(line+'\n') |
|---|
| 1286 | pFile.write(135*'-'+'\n') |
|---|
| 1287 | for i,at in enumerate(Atoms): |
|---|
| 1288 | if AtInfo[at[ct]]: |
|---|
| 1289 | line = '%7s'%(at[ct-1])+'%7s'%(at[ct])+'%7s'%(at[ct+1])+'%10.5f'%(at[cmx])+'%10.5f'%(at[cmx+1])+ \ |
|---|
| 1290 | '%10.5f'%(at[cmx+2]) |
|---|
| 1291 | pFile.write(line+'\n') |
|---|
| 1292 | |
|---|
| 1293 | |
|---|
| 1294 | def PrintWaves(General,Atoms): |
|---|
| 1295 | cx,ct,cs,cia = General['AtomPtrs'] |
|---|
| 1296 | pFile.write('\n Modulation waves\n') |
|---|
| 1297 | names = {'Sfrac':['Fsin','Fcos','Fzero','Fwid'],'Spos':['Xsin','Ysin','Zsin','Xcos','Ycos','Zcos','Tmin','Tmax','Xmax','Ymax','Zmax'], |
|---|
| 1298 | 'Sadp':['U11sin','U22sin','U33sin','U12sin','U13sin','U23sin','U11cos','U22cos', |
|---|
| 1299 | 'U33cos','U12cos','U13cos','U23cos'],'Smag':['MXsin','MYsin','MZsin','MXcos','MYcos','MZcos']} |
|---|
| 1300 | pFile.write(135*'-'+'\n') |
|---|
| 1301 | for i,at in enumerate(Atoms): |
|---|
| 1302 | AtomSS = at[-1]['SS1'] |
|---|
| 1303 | for Stype in ['Sfrac','Spos','Sadp','Smag']: |
|---|
| 1304 | Waves = AtomSS[Stype] |
|---|
| 1305 | if len(Waves): |
|---|
| 1306 | pFile.write(' atom: %s, site sym: %s, type: %s wave type: %s:\n'% |
|---|
| 1307 | (at[ct-1],at[cs],Stype,Waves[0])) |
|---|
| 1308 | else: |
|---|
| 1309 | continue |
|---|
| 1310 | for iw,wave in enumerate(Waves[1:]): |
|---|
| 1311 | line = '' |
|---|
| 1312 | if Waves[0] in ['Block','ZigZag'] and Stype == 'Spos' and not iw: |
|---|
| 1313 | for item in names[Stype][6:]: |
|---|
| 1314 | line += '%8s '%(item) |
|---|
| 1315 | else: |
|---|
| 1316 | if Stype == 'Spos': |
|---|
| 1317 | for item in names[Stype][:6]: |
|---|
| 1318 | line += '%8s '%(item) |
|---|
| 1319 | else: |
|---|
| 1320 | for item in names[Stype]: |
|---|
| 1321 | line += '%8s '%(item) |
|---|
| 1322 | pFile.write(line+'\n') |
|---|
| 1323 | line = '' |
|---|
| 1324 | for item in wave[0]: |
|---|
| 1325 | line += '%8.4f '%(item) |
|---|
| 1326 | line += ' Refine? '+str(wave[1]) |
|---|
| 1327 | pFile.write(line+'\n') |
|---|
| 1328 | |
|---|
| 1329 | def PrintTexture(textureData): |
|---|
| 1330 | topstr = '\n Spherical harmonics texture: Order:' + \ |
|---|
| 1331 | str(textureData['Order']) |
|---|
| 1332 | if textureData['Order']: |
|---|
| 1333 | pFile.write('%s Refine? %s\n'%(topstr,textureData['SH Coeff'][0])) |
|---|
| 1334 | else: |
|---|
| 1335 | pFile.write(topstr+'\n') |
|---|
| 1336 | return |
|---|
| 1337 | names = ['omega','chi','phi'] |
|---|
| 1338 | line = '\n' |
|---|
| 1339 | for name in names: |
|---|
| 1340 | line += ' SH '+name+':'+'%12.4f'%(textureData['Sample '+name][1])+' Refine? '+str(textureData['Sample '+name][0]) |
|---|
| 1341 | pFile.write(line+'\n') |
|---|
| 1342 | pFile.write('\n Texture coefficients:\n') |
|---|
| 1343 | SHcoeff = textureData['SH Coeff'][1] |
|---|
| 1344 | SHkeys = list(SHcoeff.keys()) |
|---|
| 1345 | nCoeff = len(SHcoeff) |
|---|
| 1346 | nBlock = nCoeff//10+1 |
|---|
| 1347 | iBeg = 0 |
|---|
| 1348 | iFin = min(iBeg+10,nCoeff) |
|---|
| 1349 | for block in range(nBlock): |
|---|
| 1350 | ptlbls = ' names :' |
|---|
| 1351 | ptstr = ' values:' |
|---|
| 1352 | for item in SHkeys[iBeg:iFin]: |
|---|
| 1353 | ptlbls += '%12s'%(item) |
|---|
| 1354 | ptstr += '%12.4f'%(SHcoeff[item]) |
|---|
| 1355 | pFile.write(ptlbls+'\n') |
|---|
| 1356 | pFile.write(ptstr+'\n') |
|---|
| 1357 | iBeg += 10 |
|---|
| 1358 | iFin = min(iBeg+10,nCoeff) |
|---|
| 1359 | |
|---|
| 1360 | def MakeRBParms(rbKey,phaseVary,phaseDict): |
|---|
| 1361 | rbid = str(rbids.index(RB['RBId'])) |
|---|
| 1362 | pfxRB = pfx+'RB'+rbKey+'P' |
|---|
| 1363 | pstr = ['x','y','z'] |
|---|
| 1364 | ostr = ['a','i','j','k'] |
|---|
| 1365 | for i in range(3): |
|---|
| 1366 | name = pfxRB+pstr[i]+':'+str(iRB)+':'+rbid |
|---|
| 1367 | phaseDict[name] = RB['Orig'][0][i] |
|---|
| 1368 | if RB['Orig'][1]: |
|---|
| 1369 | phaseVary += [name,] |
|---|
| 1370 | pfxRB = pfx+'RB'+rbKey+'O' |
|---|
| 1371 | for i in range(4): |
|---|
| 1372 | name = pfxRB+ostr[i]+':'+str(iRB)+':'+rbid |
|---|
| 1373 | phaseDict[name] = RB['Orient'][0][i] |
|---|
| 1374 | if RB['Orient'][1] == 'AV' and i: |
|---|
| 1375 | phaseVary += [name,] |
|---|
| 1376 | elif RB['Orient'][1] == 'A' and not i: |
|---|
| 1377 | phaseVary += [name,] |
|---|
| 1378 | |
|---|
| 1379 | def MakeRBThermals(rbKey,phaseVary,phaseDict): |
|---|
| 1380 | rbid = str(rbids.index(RB['RBId'])) |
|---|
| 1381 | tlstr = ['11','22','33','12','13','23'] |
|---|
| 1382 | sstr = ['12','13','21','23','31','32','AA','BB'] |
|---|
| 1383 | if 'T' in RB['ThermalMotion'][0]: |
|---|
| 1384 | pfxRB = pfx+'RB'+rbKey+'T' |
|---|
| 1385 | for i in range(6): |
|---|
| 1386 | name = pfxRB+tlstr[i]+':'+str(iRB)+':'+rbid |
|---|
| 1387 | phaseDict[name] = RB['ThermalMotion'][1][i] |
|---|
| 1388 | if RB['ThermalMotion'][2][i]: |
|---|
| 1389 | phaseVary += [name,] |
|---|
| 1390 | if 'L' in RB['ThermalMotion'][0]: |
|---|
| 1391 | pfxRB = pfx+'RB'+rbKey+'L' |
|---|
| 1392 | for i in range(6): |
|---|
| 1393 | name = pfxRB+tlstr[i]+':'+str(iRB)+':'+rbid |
|---|
| 1394 | phaseDict[name] = RB['ThermalMotion'][1][i+6] |
|---|
| 1395 | if RB['ThermalMotion'][2][i+6]: |
|---|
| 1396 | phaseVary += [name,] |
|---|
| 1397 | if 'S' in RB['ThermalMotion'][0]: |
|---|
| 1398 | pfxRB = pfx+'RB'+rbKey+'S' |
|---|
| 1399 | for i in range(8): |
|---|
| 1400 | name = pfxRB+sstr[i]+':'+str(iRB)+':'+rbid |
|---|
| 1401 | phaseDict[name] = RB['ThermalMotion'][1][i+12] |
|---|
| 1402 | if RB['ThermalMotion'][2][i+12]: |
|---|
| 1403 | phaseVary += [name,] |
|---|
| 1404 | if 'U' in RB['ThermalMotion'][0]: |
|---|
| 1405 | name = pfx+'RB'+rbKey+'U:'+str(iRB)+':'+rbid |
|---|
| 1406 | phaseDict[name] = RB['ThermalMotion'][1][0] |
|---|
| 1407 | if RB['ThermalMotion'][2][0]: |
|---|
| 1408 | phaseVary += [name,] |
|---|
| 1409 | |
|---|
| 1410 | def MakeRBTorsions(rbKey,phaseVary,phaseDict): |
|---|
| 1411 | rbid = str(rbids.index(RB['RBId'])) |
|---|
| 1412 | pfxRB = pfx+'RB'+rbKey+'Tr;' |
|---|
| 1413 | for i,torsion in enumerate(RB['Torsions']): |
|---|
| 1414 | name = pfxRB+str(i)+':'+str(iRB)+':'+rbid |
|---|
| 1415 | phaseDict[name] = torsion[0] |
|---|
| 1416 | if torsion[1]: |
|---|
| 1417 | phaseVary += [name,] |
|---|
| 1418 | |
|---|
| 1419 | if Print: |
|---|
| 1420 | pFile.write('\n Phases:\n') |
|---|
| 1421 | phaseVary = [] |
|---|
| 1422 | phaseDict = {} |
|---|
| 1423 | pawleyLookup = {} |
|---|
| 1424 | FFtables = {} #scattering factors - xrays |
|---|
| 1425 | MFtables = {} #Mag. form factors |
|---|
| 1426 | BLtables = {} # neutrons |
|---|
| 1427 | Natoms = {} |
|---|
| 1428 | maxSSwave = {} |
|---|
| 1429 | shModels = ['cylindrical','none','shear - 2/m','rolling - mmm'] |
|---|
| 1430 | SamSym = dict(zip(shModels,['0','-1','2/m','mmm'])) |
|---|
| 1431 | atomIndx = {} |
|---|
| 1432 | for name in PhaseData: |
|---|
| 1433 | General = PhaseData[name]['General'] |
|---|
| 1434 | pId = PhaseData[name]['pId'] |
|---|
| 1435 | pfx = str(pId)+'::' |
|---|
| 1436 | FFtable = G2el.GetFFtable(General['AtomTypes']) |
|---|
| 1437 | BLtable = G2el.GetBLtable(General) |
|---|
| 1438 | FFtables.update(FFtable) |
|---|
| 1439 | BLtables.update(BLtable) |
|---|
| 1440 | phaseDict[pfx+'isMag'] = False |
|---|
| 1441 | SGData = General['SGData'] |
|---|
| 1442 | SGtext,SGtable = G2spc.SGPrint(SGData) |
|---|
| 1443 | if General['Type'] == 'magnetic': |
|---|
| 1444 | MFtable = G2el.GetMFtable(General['AtomTypes'],General['Lande g']) |
|---|
| 1445 | MFtables.update(MFtable) |
|---|
| 1446 | phaseDict[pfx+'isMag'] = True |
|---|
| 1447 | SpnFlp = SGData['SpnFlp'] |
|---|
| 1448 | Atoms = PhaseData[name]['Atoms'] |
|---|
| 1449 | if Atoms and not General.get('doPawley'): |
|---|
| 1450 | cx,ct,cs,cia = General['AtomPtrs'] |
|---|
| 1451 | AtLookup = G2mth.FillAtomLookUp(Atoms,cia+8) |
|---|
| 1452 | PawleyRef = PhaseData[name].get('Pawley ref',[]) |
|---|
| 1453 | cell = General['Cell'] |
|---|
| 1454 | A = G2lat.cell2A(cell[1:7]) |
|---|
| 1455 | phaseDict.update({pfx+'A0':A[0],pfx+'A1':A[1],pfx+'A2':A[2], |
|---|
| 1456 | pfx+'A3':A[3],pfx+'A4':A[4],pfx+'A5':A[5],pfx+'Vol':G2lat.calc_V(A)}) |
|---|
| 1457 | if cell[0]: |
|---|
| 1458 | phaseVary += cellVary(pfx,SGData) #also fills in symmetry required constraints |
|---|
| 1459 | SSGtext = [] #no superstructure |
|---|
| 1460 | im = 0 |
|---|
| 1461 | if General.get('Modulated',False): |
|---|
| 1462 | im = 1 #refl offset |
|---|
| 1463 | Vec,vRef,maxH = General['SuperVec'] |
|---|
| 1464 | phaseDict.update({pfx+'mV0':Vec[0],pfx+'mV1':Vec[1],pfx+'mV2':Vec[2]}) |
|---|
| 1465 | SSGData = General['SSGData'] |
|---|
| 1466 | SSGtext,SSGtable = G2spc.SSGPrint(SGData,SSGData) |
|---|
| 1467 | if vRef: |
|---|
| 1468 | phaseVary += modVary(pfx,SSGData) |
|---|
| 1469 | resRBData = PhaseData[name]['RBModels'].get('Residue',[]) |
|---|
| 1470 | if resRBData: |
|---|
| 1471 | rbids = rbIds['Residue'] #NB: used in the MakeRB routines |
|---|
| 1472 | for iRB,RB in enumerate(resRBData): |
|---|
| 1473 | MakeRBParms('R',phaseVary,phaseDict) |
|---|
| 1474 | MakeRBThermals('R',phaseVary,phaseDict) |
|---|
| 1475 | MakeRBTorsions('R',phaseVary,phaseDict) |
|---|
| 1476 | |
|---|
| 1477 | vecRBData = PhaseData[name]['RBModels'].get('Vector',[]) |
|---|
| 1478 | if vecRBData: |
|---|
| 1479 | rbids = rbIds['Vector'] #NB: used in the MakeRB routines |
|---|
| 1480 | for iRB,RB in enumerate(vecRBData): |
|---|
| 1481 | MakeRBParms('V',phaseVary,phaseDict) |
|---|
| 1482 | MakeRBThermals('V',phaseVary,phaseDict) |
|---|
| 1483 | |
|---|
| 1484 | Natoms[pfx] = 0 |
|---|
| 1485 | maxSSwave[pfx] = {'Sfrac':0,'Spos':0,'Sadp':0,'Smag':0} |
|---|
| 1486 | if Atoms and not General.get('doPawley'): |
|---|
| 1487 | cx,ct,cs,cia = General['AtomPtrs'] |
|---|
| 1488 | Natoms[pfx] = len(Atoms) |
|---|
| 1489 | for i,at in enumerate(Atoms): |
|---|
| 1490 | atomIndx[at[cia+8]] = [pfx,i] #lookup table for restraints |
|---|
| 1491 | phaseDict.update({pfx+'Atype:'+str(i):at[ct],pfx+'Afrac:'+str(i):at[cx+3],pfx+'Amul:'+str(i):at[cs+1], |
|---|
| 1492 | pfx+'Ax:'+str(i):at[cx],pfx+'Ay:'+str(i):at[cx+1],pfx+'Az:'+str(i):at[cx+2], |
|---|
| 1493 | pfx+'dAx:'+str(i):0.,pfx+'dAy:'+str(i):0.,pfx+'dAz:'+str(i):0., #refined shifts for x,y,z |
|---|
| 1494 | pfx+'AI/A:'+str(i):at[cia],}) |
|---|
| 1495 | if at[cia] == 'I': |
|---|
| 1496 | phaseDict[pfx+'AUiso:'+str(i)] = at[cia+1] |
|---|
| 1497 | else: |
|---|
| 1498 | phaseDict.update({pfx+'AU11:'+str(i):at[cia+2],pfx+'AU22:'+str(i):at[cia+3],pfx+'AU33:'+str(i):at[cia+4], |
|---|
| 1499 | pfx+'AU12:'+str(i):at[cia+5],pfx+'AU13:'+str(i):at[cia+6],pfx+'AU23:'+str(i):at[cia+7]}) |
|---|
| 1500 | if General['Type'] == 'magnetic': |
|---|
| 1501 | phaseDict.update({pfx+'AMx:'+str(i):at[cx+4],pfx+'AMy:'+str(i):at[cx+5],pfx+'AMz:'+str(i):at[cx+6]}) |
|---|
| 1502 | if 'F' in at[ct+1]: |
|---|
| 1503 | phaseVary.append(pfx+'Afrac:'+str(i)) |
|---|
| 1504 | if 'X' in at[ct+1]: |
|---|
| 1505 | try: #patch for sytsym name changes |
|---|
| 1506 | xId,xCoef = G2spc.GetCSxinel(at[cs]) |
|---|
| 1507 | except KeyError: |
|---|
| 1508 | Sytsym = G2spc.SytSym(at[cx:cx+3],SGData)[0] |
|---|
| 1509 | at[cs] = Sytsym |
|---|
| 1510 | xId,xCoef = G2spc.GetCSxinel(at[cs]) |
|---|
| 1511 | names = [pfx+'dAx:'+str(i),pfx+'dAy:'+str(i),pfx+'dAz:'+str(i)] |
|---|
| 1512 | equivs = [[],[],[]] |
|---|
| 1513 | for j in range(3): |
|---|
| 1514 | if xId[j] > 0: |
|---|
| 1515 | phaseVary.append(names[j]) |
|---|
| 1516 | equivs[xId[j]-1].append([names[j],xCoef[j]]) |
|---|
| 1517 | for equiv in equivs: |
|---|
| 1518 | if len(equiv) > 1: |
|---|
| 1519 | name = equiv[0][0] |
|---|
| 1520 | coef = equiv[0][1] |
|---|
| 1521 | for eqv in equiv[1:]: |
|---|
| 1522 | eqv[1] /= coef |
|---|
| 1523 | G2mv.StoreEquivalence(name,(eqv,)) |
|---|
| 1524 | if 'U' in at[ct+1]: |
|---|
| 1525 | if at[cia] == 'I': |
|---|
| 1526 | phaseVary.append(pfx+'AUiso:'+str(i)) |
|---|
| 1527 | else: |
|---|
| 1528 | try: #patch for sytsym name changes |
|---|
| 1529 | uId,uCoef = G2spc.GetCSuinel(at[cs])[:2] |
|---|
| 1530 | except KeyError: |
|---|
| 1531 | Sytsym = G2spc.SytSym(at[cx:cx+3],SGData)[0] |
|---|
| 1532 | at[cs] = Sytsym |
|---|
| 1533 | uId,uCoef = G2spc.GetCSuinel(at[cs])[:2] |
|---|
| 1534 | names = [pfx+'AU11:'+str(i),pfx+'AU22:'+str(i),pfx+'AU33:'+str(i), |
|---|
| 1535 | pfx+'AU12:'+str(i),pfx+'AU13:'+str(i),pfx+'AU23:'+str(i)] |
|---|
| 1536 | equivs = [[],[],[],[],[],[]] |
|---|
| 1537 | for j in range(6): |
|---|
| 1538 | if uId[j] > 0: |
|---|
| 1539 | phaseVary.append(names[j]) |
|---|
| 1540 | equivs[uId[j]-1].append([names[j],uCoef[j]]) |
|---|
| 1541 | for equiv in equivs: |
|---|
| 1542 | if len(equiv) > 1: |
|---|
| 1543 | name = equiv[0][0] |
|---|
| 1544 | coef = equiv[0][1] |
|---|
| 1545 | for eqv in equiv[1:]: |
|---|
| 1546 | eqv[1] /= coef |
|---|
| 1547 | G2mv.StoreEquivalence(name,(eqv,)) |
|---|
| 1548 | if 'M' in at[ct+1]: |
|---|
| 1549 | SytSym,Mul,Nop,dupDir = G2spc.SytSym(at[cx:cx+3],SGData) |
|---|
| 1550 | mId,mCoef = G2spc.GetCSpqinel(SpnFlp,dupDir) |
|---|
| 1551 | names = [pfx+'AMx:'+str(i),pfx+'AMy:'+str(i),pfx+'AMz:'+str(i)] |
|---|
| 1552 | equivs = [[],[],[]] |
|---|
| 1553 | for j in range(3): |
|---|
| 1554 | if mId[j] > 0: |
|---|
| 1555 | phaseVary.append(names[j]) |
|---|
| 1556 | equivs[mId[j]-1].append([names[j],mCoef[j]]) |
|---|
| 1557 | for equiv in equivs: |
|---|
| 1558 | if len(equiv) > 1: |
|---|
| 1559 | name = equiv[0][0] |
|---|
| 1560 | coef = equiv[0][1] |
|---|
| 1561 | for eqv in equiv[1:]: |
|---|
| 1562 | eqv[1] /= coef |
|---|
| 1563 | G2mv.StoreEquivalence(name,(eqv,)) |
|---|
| 1564 | if General.get('Modulated',False): |
|---|
| 1565 | AtomSS = at[-1]['SS1'] |
|---|
| 1566 | for Stype in ['Sfrac','Spos','Sadp','Smag']: |
|---|
| 1567 | Waves = AtomSS[Stype] |
|---|
| 1568 | if len(Waves): |
|---|
| 1569 | waveType = Waves[0] |
|---|
| 1570 | else: |
|---|
| 1571 | continue |
|---|
| 1572 | phaseDict[pfx+Stype[1].upper()+'waveType:'+str(i)] = waveType |
|---|
| 1573 | nx = 0 |
|---|
| 1574 | for iw,wave in enumerate(Waves[1:]): |
|---|
| 1575 | if not iw: |
|---|
| 1576 | if waveType in ['ZigZag','Block']: |
|---|
| 1577 | nx = 1 |
|---|
| 1578 | CSI = G2spc.GetSSfxuinel(waveType,Stype,1,at[cx:cx+3],SGData,SSGData) |
|---|
| 1579 | else: |
|---|
| 1580 | CSI = G2spc.GetSSfxuinel('Fourier',Stype,iw+1-nx,at[cx:cx+3],SGData,SSGData) |
|---|
| 1581 | uId,uCoef = CSI[0] |
|---|
| 1582 | stiw = str(i)+':'+str(iw) |
|---|
| 1583 | if Stype == 'Spos': |
|---|
| 1584 | if waveType in ['ZigZag','Block',] and not iw: |
|---|
| 1585 | names = [pfx+'Tmin:'+stiw,pfx+'Tmax:'+stiw,pfx+'Xmax:'+stiw,pfx+'Ymax:'+stiw,pfx+'Zmax:'+stiw] |
|---|
| 1586 | equivs = [[],[], [],[],[]] |
|---|
| 1587 | else: |
|---|
| 1588 | names = [pfx+'Xsin:'+stiw,pfx+'Ysin:'+stiw,pfx+'Zsin:'+stiw, |
|---|
| 1589 | pfx+'Xcos:'+stiw,pfx+'Ycos:'+stiw,pfx+'Zcos:'+stiw] |
|---|
| 1590 | equivs = [[],[],[], [],[],[]] |
|---|
| 1591 | elif Stype == 'Sadp': |
|---|
| 1592 | names = [pfx+'U11sin:'+stiw,pfx+'U22sin:'+stiw,pfx+'U33sin:'+stiw, |
|---|
| 1593 | pfx+'U12sin:'+stiw,pfx+'U13sin:'+stiw,pfx+'U23sin:'+stiw, |
|---|
| 1594 | pfx+'U11cos:'+stiw,pfx+'U22cos:'+stiw,pfx+'U33cos:'+stiw, |
|---|
| 1595 | pfx+'U12cos:'+stiw,pfx+'U13cos:'+stiw,pfx+'U23cos:'+stiw] |
|---|
| 1596 | equivs = [[],[],[],[],[],[], [],[],[],[],[],[]] |
|---|
| 1597 | elif Stype == 'Sfrac': |
|---|
| 1598 | equivs = [[],[]] |
|---|
| 1599 | if 'Crenel' in waveType and not iw: |
|---|
| 1600 | names = [pfx+'Fzero:'+stiw,pfx+'Fwid:'+stiw] |
|---|
| 1601 | else: |
|---|
| 1602 | names = [pfx+'Fsin:'+stiw,pfx+'Fcos:'+stiw] |
|---|
| 1603 | elif Stype == 'Smag': |
|---|
| 1604 | equivs = [[],[],[], [],[],[]] |
|---|
| 1605 | names = [pfx+'MXsin:'+stiw,pfx+'MYsin:'+stiw,pfx+'MZsin:'+stiw, |
|---|
| 1606 | pfx+'MXcos:'+stiw,pfx+'MYcos:'+stiw,pfx+'MZcos:'+stiw] |
|---|
| 1607 | phaseDict.update(dict(zip(names,wave[0]))) |
|---|
| 1608 | if wave[1]: #what do we do here for multiple terms in modulation constraints? |
|---|
| 1609 | for j in range(len(equivs)): |
|---|
| 1610 | if uId[j][0] > 0: |
|---|
| 1611 | phaseVary.append(names[j]) |
|---|
| 1612 | equivs[uId[j][0]-1].append([names[j],uCoef[j][0]]) |
|---|
| 1613 | for equiv in equivs: |
|---|
| 1614 | if len(equiv) > 1: |
|---|
| 1615 | name = equiv[0][0] |
|---|
| 1616 | coef = equiv[0][1] |
|---|
| 1617 | for eqv in equiv[1:]: |
|---|
| 1618 | eqv[1] /= coef |
|---|
| 1619 | G2mv.StoreEquivalence(name,(eqv,)) |
|---|
| 1620 | maxSSwave[pfx][Stype] = max(maxSSwave[pfx][Stype],iw+1) |
|---|
| 1621 | textureData = General['SH Texture'] |
|---|
| 1622 | if textureData['Order'] and not seqRef: |
|---|
| 1623 | phaseDict[pfx+'SHorder'] = textureData['Order'] |
|---|
| 1624 | phaseDict[pfx+'SHmodel'] = SamSym[textureData['Model']] |
|---|
| 1625 | for item in ['omega','chi','phi']: |
|---|
| 1626 | phaseDict[pfx+'SH '+item] = textureData['Sample '+item][1] |
|---|
| 1627 | if textureData['Sample '+item][0]: |
|---|
| 1628 | phaseVary.append(pfx+'SH '+item) |
|---|
| 1629 | for item in textureData['SH Coeff'][1]: |
|---|
| 1630 | phaseDict[pfx+item] = textureData['SH Coeff'][1][item] |
|---|
| 1631 | if textureData['SH Coeff'][0]: |
|---|
| 1632 | phaseVary.append(pfx+item) |
|---|
| 1633 | |
|---|
| 1634 | if Print: |
|---|
| 1635 | pFile.write('\n Phase name: %s\n'%General['Name']) |
|---|
| 1636 | pFile.write(135*'='+'\n') |
|---|
| 1637 | PrintFFtable(FFtable) |
|---|
| 1638 | PrintBLtable(BLtable) |
|---|
| 1639 | if General['Type'] == 'magnetic': |
|---|
| 1640 | PrintMFtable(MFtable) |
|---|
| 1641 | pFile.write('\n') |
|---|
| 1642 | #how do we print magnetic symmetry table? TBD |
|---|
| 1643 | if len(SSGtext): #if superstructure |
|---|
| 1644 | for line in SSGtext: pFile.write(line+'\n') |
|---|
| 1645 | if len(SSGtable): |
|---|
| 1646 | for item in SSGtable: |
|---|
| 1647 | line = ' %s '%(item) |
|---|
| 1648 | pFile.write(line+'\n') |
|---|
| 1649 | else: |
|---|
| 1650 | pFile.write(' ( 1) %s\n'%(SSGtable[0])) |
|---|
| 1651 | else: |
|---|
| 1652 | for line in SGtext: pFile.write(line+'\n') |
|---|
| 1653 | if len(SGtable): |
|---|
| 1654 | for item in SGtable: |
|---|
| 1655 | line = ' %s '%(item) |
|---|
| 1656 | pFile.write(line+'\n') |
|---|
| 1657 | else: |
|---|
| 1658 | pFile.write(' ( 1) %s\n'%(SGtable[0])) |
|---|
| 1659 | PrintRBObjects(resRBData,vecRBData) |
|---|
| 1660 | PrintAtoms(General,Atoms) |
|---|
| 1661 | if General['Type'] == 'magnetic': |
|---|
| 1662 | PrintMoments(General,Atoms) |
|---|
| 1663 | if General.get('Modulated',False): |
|---|
| 1664 | PrintWaves(General,Atoms) |
|---|
| 1665 | pFile.write('\n Unit cell: a = %.5f b = %.5f c = %.5f alpha = %.3f beta = %.3f gamma = %.3f volume = %.3f Refine? %s\n'% |
|---|
| 1666 | (cell[1],cell[2],cell[3],cell[4],cell[5],cell[6],cell[7],cell[0])) |
|---|
| 1667 | if len(SSGtext): #if superstructure |
|---|
| 1668 | pFile.write('\n Modulation vector: mV0 = %.4f mV1 = %.4f mV2 = %.4f max mod. index = %d Refine? %s\n'% |
|---|
| 1669 | (Vec[0],Vec[1],Vec[2],maxH,vRef)) |
|---|
| 1670 | if not seqRef: |
|---|
| 1671 | PrintTexture(textureData) |
|---|
| 1672 | if name in RestraintDict: |
|---|
| 1673 | PrintRestraints(cell[1:7],SGData,General['AtomPtrs'],Atoms,AtLookup, |
|---|
| 1674 | textureData,RestraintDict[name],pFile) |
|---|
| 1675 | |
|---|
| 1676 | elif PawleyRef: |
|---|
| 1677 | if Print: |
|---|
| 1678 | pFile.write('\n Phase name: %s\n'%General['Name']) |
|---|
| 1679 | pFile.write(135*'='+'\n') |
|---|
| 1680 | pFile.write('\n') |
|---|
| 1681 | if len(SSGtext): #if superstructure |
|---|
| 1682 | for line in SSGtext: pFile.write(line+'\n') |
|---|
| 1683 | if len(SSGtable): |
|---|
| 1684 | for item in SSGtable: |
|---|
| 1685 | line = ' %s '%(item) |
|---|
| 1686 | pFile.write(line+'\n') |
|---|
| 1687 | else: |
|---|
| 1688 | pFile.write(' ( 1) %s\n'%SSGtable[0]) |
|---|
| 1689 | else: |
|---|
| 1690 | for line in SGtext: pFile.write(line+'\n') |
|---|
| 1691 | if len(SGtable): |
|---|
| 1692 | for item in SGtable: |
|---|
| 1693 | line = ' %s '%(item) |
|---|
| 1694 | pFile.write(line+'\n') |
|---|
| 1695 | else: |
|---|
| 1696 | pFile.write(' ( 1) %s\n'%(SGtable[0])) |
|---|
| 1697 | pFile.write('\n Unit cell: a = %.5f b = %.5f c = %.5f alpha = %.3f beta = %.3f gamma = %.3f volume = %.3f Refine? %s\n'% |
|---|
| 1698 | (cell[1],cell[2],cell[3],cell[4],cell[5],cell[6],cell[7],cell[0])) |
|---|
| 1699 | if len(SSGtext): #if superstructure |
|---|
| 1700 | pFile.write('\n Modulation vector: mV0 = %.4f mV1 = %.4f mV2 = %.4f max mod. index = %d Refine? %s\n'% |
|---|
| 1701 | (Vec[0],Vec[1],Vec[2],maxH,vRef)) |
|---|
| 1702 | pawleyVary = [] |
|---|
| 1703 | for i,refl in enumerate(PawleyRef): |
|---|
| 1704 | phaseDict[pfx+'PWLref:'+str(i)] = refl[6+im] |
|---|
| 1705 | if im: |
|---|
| 1706 | pawleyLookup[pfx+'%d,%d,%d,%d'%(refl[0],refl[1],refl[2],refl[3])] = i |
|---|
| 1707 | else: |
|---|
| 1708 | pawleyLookup[pfx+'%d,%d,%d'%(refl[0],refl[1],refl[2])] = i |
|---|
| 1709 | if refl[5+im]: |
|---|
| 1710 | pawleyVary.append(pfx+'PWLref:'+str(i)) |
|---|
| 1711 | GetPawleyConstr(SGData['SGLaue'],PawleyRef,im,pawleyVary) #does G2mv.StoreEquivalence |
|---|
| 1712 | phaseVary += pawleyVary |
|---|
| 1713 | |
|---|
| 1714 | return Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables,MFtables,maxSSwave |
|---|
| 1715 | |
|---|
| 1716 | def cellFill(pfx,SGData,parmDict,sigDict): |
|---|
| 1717 | '''Returns the filled-out reciprocal cell (A) terms and their uncertainties |
|---|
| 1718 | from the parameter and sig dictionaries. |
|---|
| 1719 | |
|---|
| 1720 | :param str pfx: parameter prefix ("n::", where n is a phase number) |
|---|
| 1721 | :param dict SGdata: a symmetry object |
|---|
| 1722 | :param dict parmDict: a dictionary of parameters |
|---|
| 1723 | :param dict sigDict: a dictionary of uncertainties on parameters |
|---|
| 1724 | |
|---|
| 1725 | :returns: A,sigA where each is a list of six terms with the A terms |
|---|
| 1726 | ''' |
|---|
| 1727 | if SGData['SGLaue'] in ['-1',]: |
|---|
| 1728 | A = [parmDict[pfx+'A0'],parmDict[pfx+'A1'],parmDict[pfx+'A2'], |
|---|
| 1729 | parmDict[pfx+'A3'],parmDict[pfx+'A4'],parmDict[pfx+'A5']] |
|---|
| 1730 | elif SGData['SGLaue'] in ['2/m',]: |
|---|
| 1731 | if SGData['SGUniq'] == 'a': |
|---|
| 1732 | A = [parmDict[pfx+'A0'],parmDict[pfx+'A1'],parmDict[pfx+'A2'], |
|---|
| 1733 | 0,0,parmDict[pfx+'A5']] |
|---|
| 1734 | elif SGData['SGUniq'] == 'b': |
|---|
| 1735 | A = [parmDict[pfx+'A0'],parmDict[pfx+'A1'],parmDict[pfx+'A2'], |
|---|
| 1736 | 0,parmDict[pfx+'A4'],0] |
|---|
| 1737 | else: |
|---|
| 1738 | A = [parmDict[pfx+'A0'],parmDict[pfx+'A1'],parmDict[pfx+'A2'], |
|---|
| 1739 | parmDict[pfx+'A3'],0,0] |
|---|
| 1740 | elif SGData['SGLaue'] in ['mmm',]: |
|---|
| 1741 | A = [parmDict[pfx+'A0'],parmDict[pfx+'A1'],parmDict[pfx+'A2'],0,0,0] |
|---|
| 1742 | elif SGData['SGLaue'] in ['4/m','4/mmm']: |
|---|
| 1743 | A = [parmDict[pfx+'A0'],parmDict[pfx+'A0'],parmDict[pfx+'A2'],0,0,0] |
|---|
| 1744 | elif SGData['SGLaue'] in ['6/m','6/mmm','3m1', '31m', '3']: |
|---|
| 1745 | A = [parmDict[pfx+'A0'],parmDict[pfx+'A0'],parmDict[pfx+'A2'], |
|---|
| 1746 | parmDict[pfx+'A0'],0,0] |
|---|
| 1747 | elif SGData['SGLaue'] in ['3R', '3mR']: |
|---|
| 1748 | A = [parmDict[pfx+'A0'],parmDict[pfx+'A0'],parmDict[pfx+'A0'], |
|---|
| 1749 | parmDict[pfx+'A3'],parmDict[pfx+'A3'],parmDict[pfx+'A3']] |
|---|
| 1750 | elif SGData['SGLaue'] in ['m3m','m3']: |
|---|
| 1751 | A = [parmDict[pfx+'A0'],parmDict[pfx+'A0'],parmDict[pfx+'A0'],0,0,0] |
|---|
| 1752 | |
|---|
| 1753 | try: |
|---|
| 1754 | if SGData['SGLaue'] in ['-1',]: |
|---|
| 1755 | sigA = [sigDict[pfx+'A0'],sigDict[pfx+'A1'],sigDict[pfx+'A2'], |
|---|
| 1756 | sigDict[pfx+'A3'],sigDict[pfx+'A4'],sigDict[pfx+'A5']] |
|---|
| 1757 | elif SGData['SGLaue'] in ['2/m',]: |
|---|
| 1758 | if SGData['SGUniq'] == 'a': |
|---|
| 1759 | sigA = [sigDict[pfx+'A0'],sigDict[pfx+'A1'],sigDict[pfx+'A2'], |
|---|
| 1760 | 0,0,sigDict[pfx+'A5']] |
|---|
| 1761 | elif SGData['SGUniq'] == 'b': |
|---|
| 1762 | sigA = [sigDict[pfx+'A0'],sigDict[pfx+'A1'],sigDict[pfx+'A2'], |
|---|
| 1763 | 0,sigDict[pfx+'A4'],0] |
|---|
| 1764 | else: |
|---|
| 1765 | sigA = [sigDict[pfx+'A0'],sigDict[pfx+'A1'],sigDict[pfx+'A2'], |
|---|
| 1766 | sigDict[pfx+'A3'],0,0] |
|---|
| 1767 | elif SGData['SGLaue'] in ['mmm',]: |
|---|
| 1768 | sigA = [sigDict[pfx+'A0'],sigDict[pfx+'A1'],sigDict[pfx+'A2'],0,0,0] |
|---|
| 1769 | elif SGData['SGLaue'] in ['4/m','4/mmm']: |
|---|
| 1770 | sigA = [sigDict[pfx+'A0'],0,sigDict[pfx+'A2'],0,0,0] |
|---|
| 1771 | elif SGData['SGLaue'] in ['6/m','6/mmm','3m1', '31m', '3']: |
|---|
| 1772 | sigA = [sigDict[pfx+'A0'],0,sigDict[pfx+'A2'],0,0,0] |
|---|
| 1773 | elif SGData['SGLaue'] in ['3R', '3mR']: |
|---|
| 1774 | sigA = [sigDict[pfx+'A0'],0,0,sigDict[pfx+'A3'],0,0] |
|---|
| 1775 | elif SGData['SGLaue'] in ['m3m','m3']: |
|---|
| 1776 | sigA = [sigDict[pfx+'A0'],0,0,0,0,0] |
|---|
| 1777 | except KeyError: |
|---|
| 1778 | sigA = [0,0,0,0,0,0] |
|---|
| 1779 | return A,sigA |
|---|
| 1780 | |
|---|
| 1781 | def PrintRestraints(cell,SGData,AtPtrs,Atoms,AtLookup,textureData,phaseRest,pFile): |
|---|
| 1782 | 'needs a doc string' |
|---|
| 1783 | if phaseRest: |
|---|
| 1784 | Amat = G2lat.cell2AB(cell)[0] |
|---|
| 1785 | cx,ct,cs = AtPtrs[:3] |
|---|
| 1786 | names = [['Bond','Bonds'],['Angle','Angles'],['Plane','Planes'], |
|---|
| 1787 | ['Chiral','Volumes'],['Torsion','Torsions'],['Rama','Ramas'], |
|---|
| 1788 | ['ChemComp','Sites'],['Texture','HKLs']] |
|---|
| 1789 | for name,rest in names: |
|---|
| 1790 | itemRest = phaseRest[name] |
|---|
| 1791 | if rest in itemRest and itemRest[rest] and itemRest['Use']: |
|---|
| 1792 | pFile.write('\n %s restraint weight factor %10.3f Use: %s\n'%(name,itemRest['wtFactor'],str(itemRest['Use']))) |
|---|
| 1793 | if name in ['Bond','Angle','Plane','Chiral']: |
|---|
| 1794 | pFile.write(' calc obs sig delt/sig atoms(symOp): \n') |
|---|
| 1795 | for indx,ops,obs,esd in itemRest[rest]: |
|---|
| 1796 | try: |
|---|
| 1797 | AtNames = G2mth.GetAtomItemsById(Atoms,AtLookup,indx,ct-1) |
|---|
| 1798 | AtName = '' |
|---|
| 1799 | for i,Aname in enumerate(AtNames): |
|---|
| 1800 | AtName += Aname |
|---|
| 1801 | if ops[i] == '1': |
|---|
| 1802 | AtName += '-' |
|---|
| 1803 | else: |
|---|
| 1804 | AtName += '+('+ops[i]+')-' |
|---|
| 1805 | XYZ = np.array(G2mth.GetAtomItemsById(Atoms,AtLookup,indx,cx,3)) |
|---|
| 1806 | XYZ = G2mth.getSyXYZ(XYZ,ops,SGData) |
|---|
| 1807 | if name == 'Bond': |
|---|
| 1808 | calc = G2mth.getRestDist(XYZ,Amat) |
|---|
| 1809 | elif name == 'Angle': |
|---|
| 1810 | calc = G2mth.getRestAngle(XYZ,Amat) |
|---|
| 1811 | elif name == 'Plane': |
|---|
| 1812 | calc = G2mth.getRestPlane(XYZ,Amat) |
|---|
| 1813 | elif name == 'Chiral': |
|---|
| 1814 | calc = G2mth.getRestChiral(XYZ,Amat) |
|---|
| 1815 | pFile.write(' %9.3f %9.3f %8.3f %8.3f %s\n'%(calc,obs,esd,(obs-calc)/esd,AtName[:-1])) |
|---|
| 1816 | except KeyError: |
|---|
| 1817 | del itemRest[rest] |
|---|
| 1818 | elif name in ['Torsion','Rama']: |
|---|
| 1819 | pFile.write(' atoms(symOp) calc obs sig delt/sig torsions: \n') |
|---|
| 1820 | coeffDict = itemRest['Coeff'] |
|---|
| 1821 | for indx,ops,cofName,esd in itemRest[rest]: |
|---|
| 1822 | AtNames = G2mth.GetAtomItemsById(Atoms,AtLookup,indx,ct-1) |
|---|
| 1823 | AtName = '' |
|---|
| 1824 | for i,Aname in enumerate(AtNames): |
|---|
| 1825 | AtName += Aname+'+('+ops[i]+')-' |
|---|
| 1826 | XYZ = np.array(G2mth.GetAtomItemsById(Atoms,AtLookup,indx,cx,3)) |
|---|
| 1827 | XYZ = G2mth.getSyXYZ(XYZ,ops,SGData) |
|---|
| 1828 | if name == 'Torsion': |
|---|
| 1829 | tor = G2mth.getRestTorsion(XYZ,Amat) |
|---|
| 1830 | restr,calc = G2mth.calcTorsionEnergy(tor,coeffDict[cofName]) |
|---|
| 1831 | pFile.write(' %8.3f %8.3f %.3f %8.3f %8.3f %s\n'%(calc,obs,esd,(obs-calc)/esd,tor,AtName[:-1])) |
|---|
| 1832 | else: |
|---|
| 1833 | phi,psi = G2mth.getRestRama(XYZ,Amat) |
|---|
| 1834 | restr,calc = G2mth.calcRamaEnergy(phi,psi,coeffDict[cofName]) |
|---|
| 1835 | 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])) |
|---|
| 1836 | elif name == 'ChemComp': |
|---|
| 1837 | pFile.write(' atoms mul*frac factor prod\n') |
|---|
| 1838 | for indx,factors,obs,esd in itemRest[rest]: |
|---|
| 1839 | try: |
|---|
| 1840 | atoms = G2mth.GetAtomItemsById(Atoms,AtLookup,indx,ct-1) |
|---|
| 1841 | mul = np.array(G2mth.GetAtomItemsById(Atoms,AtLookup,indx,cs+1)) |
|---|
| 1842 | frac = np.array(G2mth.GetAtomItemsById(Atoms,AtLookup,indx,cs-1)) |
|---|
| 1843 | mulfrac = mul*frac |
|---|
| 1844 | calcs = mul*frac*factors |
|---|
| 1845 | for iatm,[atom,mf,fr,clc] in enumerate(zip(atoms,mulfrac,factors,calcs)): |
|---|
| 1846 | pFile.write(' %10s %8.3f %8.3f %8.3f\n'%(atom,mf,fr,clc)) |
|---|
| 1847 | pFile.write(' Sum: calc: %8.3f obs: %8.3f esd: %8.3f\n'%(np.sum(calcs),obs,esd)) |
|---|
| 1848 | except KeyError: |
|---|
| 1849 | del itemRest[rest] |
|---|
| 1850 | elif name == 'Texture' and textureData['Order']: |
|---|
| 1851 | Start = False |
|---|
| 1852 | SHCoef = textureData['SH Coeff'][1] |
|---|
| 1853 | shModels = ['cylindrical','none','shear - 2/m','rolling - mmm'] |
|---|
| 1854 | SamSym = dict(zip(shModels,['0','-1','2/m','mmm'])) |
|---|
| 1855 | pFile.write (' HKL grid neg esd sum neg num neg use unit? unit esd \n') |
|---|
| 1856 | for hkl,grid,esd1,ifesd2,esd2 in itemRest[rest]: |
|---|
| 1857 | phi,beta = G2lat.CrsAng(np.array(hkl),cell,SGData) |
|---|
| 1858 | ODFln = G2lat.Flnh(Start,SHCoef,phi,beta,SGData) |
|---|
| 1859 | R,P,Z = G2mth.getRestPolefig(ODFln,SamSym[textureData['Model']],grid) |
|---|
| 1860 | Z = ma.masked_greater(Z,0.0) |
|---|
| 1861 | num = ma.count(Z) |
|---|
| 1862 | sum = 0 |
|---|
| 1863 | if num: |
|---|
| 1864 | sum = np.sum(Z) |
|---|
| 1865 | 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)) |
|---|
| 1866 | |
|---|
| 1867 | def getCellEsd(pfx,SGData,A,covData): |
|---|
| 1868 | 'needs a doc string' |
|---|
| 1869 | rVsq = G2lat.calc_rVsq(A) |
|---|
| 1870 | G,g = G2lat.A2Gmat(A) #get recip. & real metric tensors |
|---|
| 1871 | RMnames = [pfx+'A0',pfx+'A1',pfx+'A2',pfx+'A3',pfx+'A4',pfx+'A5'] |
|---|
| 1872 | varyList = covData['varyList'] |
|---|
| 1873 | covMatrix = covData['covMatrix'] |
|---|
| 1874 | if len(covMatrix): |
|---|
| 1875 | vcov = G2mth.getVCov(RMnames,varyList,covMatrix) |
|---|
| 1876 | if SGData['SGLaue'] in ['3', '3m1', '31m', '6/m', '6/mmm']: |
|---|
| 1877 | vcov[1,1] = vcov[3,3] = vcov[0,1] = vcov[1,0] = vcov[0,0] |
|---|
| 1878 | vcov[1,3] = vcov[3,1] = vcov[0,3] = vcov[3,0] = vcov[0,0] |
|---|
| 1879 | vcov[1,2] = vcov[2,1] = vcov[2,3] = vcov[3,2] = vcov[0,2] |
|---|
| 1880 | elif SGData['SGLaue'] in ['m3','m3m']: |
|---|
| 1881 | vcov[0:3,0:3] = vcov[0,0] |
|---|
| 1882 | elif SGData['SGLaue'] in ['4/m', '4/mmm']: |
|---|
| 1883 | vcov[0:2,0:2] = vcov[0,0] |
|---|
| 1884 | vcov[1,2] = vcov[2,1] = vcov[0,2] |
|---|
| 1885 | elif SGData['SGLaue'] in ['3R','3mR']: |
|---|
| 1886 | vcov[0:3,0:3] = vcov[0,0] |
|---|
| 1887 | # vcov[4,4] = vcov[5,5] = vcov[3,3] |
|---|
| 1888 | vcov[3:6,3:6] = vcov[3,3] |
|---|
| 1889 | vcov[0:3,3:6] = vcov[0,3] |
|---|
| 1890 | vcov[3:6,0:3] = vcov[3,0] |
|---|
| 1891 | else: |
|---|
| 1892 | vcov = np.eye(6) |
|---|
| 1893 | delt = 1.e-9 |
|---|
| 1894 | drVdA = np.zeros(6) |
|---|
| 1895 | for i in range(6): |
|---|
| 1896 | A[i] += delt |
|---|
| 1897 | drVdA[i] = G2lat.calc_rVsq(A) |
|---|
| 1898 | A[i] -= 2*delt |
|---|
| 1899 | drVdA[i] -= G2lat.calc_rVsq(A) |
|---|
| 1900 | A[i] += delt |
|---|
| 1901 | drVdA /= 2.*delt |
|---|
| 1902 | srcvlsq = np.inner(drVdA,np.inner(drVdA,vcov)) |
|---|
| 1903 | Vol = 1/np.sqrt(rVsq) |
|---|
| 1904 | sigVol = Vol**3*np.sqrt(srcvlsq)/2. #ok - checks with GSAS |
|---|
| 1905 | |
|---|
| 1906 | dcdA = np.zeros((6,6)) |
|---|
| 1907 | for i in range(6): |
|---|
| 1908 | pdcdA =np.zeros(6) |
|---|
| 1909 | A[i] += delt |
|---|
| 1910 | pdcdA += G2lat.A2cell(A) |
|---|
| 1911 | A[i] -= 2*delt |
|---|
| 1912 | pdcdA -= G2lat.A2cell(A) |
|---|
| 1913 | A[i] += delt |
|---|
| 1914 | dcdA[i] = pdcdA/(2.*delt) |
|---|
| 1915 | |
|---|
| 1916 | sigMat = np.inner(dcdA,np.inner(dcdA,vcov)) |
|---|
| 1917 | var = np.diag(sigMat) |
|---|
| 1918 | CS = np.where(var>0.,np.sqrt(var),0.) |
|---|
| 1919 | if SGData['SGLaue'] in ['3', '3m1', '31m', '6/m', '6/mmm','m3','m3m','4/m','4/mmm']: |
|---|
| 1920 | CS[3:6] = 0.0 |
|---|
| 1921 | return [CS[0],CS[1],CS[2],CS[5],CS[4],CS[3],sigVol] |
|---|
| 1922 | |
|---|
| 1923 | def SetPhaseData(parmDict,sigDict,Phases,RBIds,covData,RestraintDict=None,pFile=None): |
|---|
| 1924 | '''Called after a refinement to transfer parameters from the parameter dict to |
|---|
| 1925 | the phase(s) information read from a GPX file. Also prints values to the .lst file |
|---|
| 1926 | ''' |
|---|
| 1927 | |
|---|
| 1928 | def PrintAtomsAndSig(General,Atoms,atomsSig): |
|---|
| 1929 | pFile.write('\n Atoms:\n') |
|---|
| 1930 | line = ' name x y z frac Uiso U11 U22 U33 U12 U13 U23' |
|---|
| 1931 | if General['Type'] == 'macromolecular': |
|---|
| 1932 | line = ' res no residue chain '+line |
|---|
| 1933 | cx,ct,cs,cia = General['AtomPtrs'] |
|---|
| 1934 | pFile.write(line+'\n') |
|---|
| 1935 | pFile.write(135*'-'+'\n') |
|---|
| 1936 | fmt = {0:'%7s',ct:'%7s',cx:'%10.5f',cx+1:'%10.5f',cx+2:'%10.5f',cx+3:'%8.3f',cia+1:'%8.5f', |
|---|
| 1937 | cia+2:'%8.5f',cia+3:'%8.5f',cia+4:'%8.5f',cia+5:'%8.5f',cia+6:'%8.5f',cia+7:'%8.5f'} |
|---|
| 1938 | noFXsig = {cx:[10*' ','%10s'],cx+1:[10*' ','%10s'],cx+2:[10*' ','%10s'],cx+3:[8*' ','%8s']} |
|---|
| 1939 | for atyp in General['AtomTypes']: #zero composition |
|---|
| 1940 | General['NoAtoms'][atyp] = 0. |
|---|
| 1941 | for i,at in enumerate(Atoms): |
|---|
| 1942 | General['NoAtoms'][at[ct]] += at[cx+3]*float(at[cx+5]) #new composition |
|---|
| 1943 | if General['Type'] == 'macromolecular': |
|---|
| 1944 | name = ' %s %s %s %s:'%(at[0],at[1],at[2],at[3]) |
|---|
| 1945 | valstr = ' values: ' |
|---|
| 1946 | sigstr = ' sig : ' |
|---|
| 1947 | else: |
|---|
| 1948 | name = fmt[0]%(at[ct-1])+fmt[1]%(at[ct])+':' |
|---|
| 1949 | valstr = ' values:' |
|---|
| 1950 | sigstr = ' sig :' |
|---|
| 1951 | for ind in range(cx,cx+4): |
|---|
| 1952 | sigind = str(i)+':'+str(ind) |
|---|
| 1953 | valstr += fmt[ind]%(at[ind]) |
|---|
| 1954 | if sigind in atomsSig: |
|---|
| 1955 | sigstr += fmt[ind]%(atomsSig[sigind]) |
|---|
| 1956 | else: |
|---|
| 1957 | sigstr += noFXsig[ind][1]%(noFXsig[ind][0]) |
|---|
| 1958 | if at[cia] == 'I': |
|---|
| 1959 | valstr += fmt[cia+1]%(at[cia+1]) |
|---|
| 1960 | if '%d:%d'%(i,cia+1) in atomsSig: |
|---|
| 1961 | sigstr += fmt[cia+1]%(atomsSig['%d:%d'%(i,cia+1)]) |
|---|
| 1962 | else: |
|---|
| 1963 | sigstr += 8*' ' |
|---|
| 1964 | else: |
|---|
| 1965 | valstr += 8*' ' |
|---|
| 1966 | sigstr += 8*' ' |
|---|
| 1967 | for ind in range(cia+2,cia+8): |
|---|
| 1968 | sigind = str(i)+':'+str(ind) |
|---|
| 1969 | valstr += fmt[ind]%(at[ind]) |
|---|
| 1970 | if sigind in atomsSig: |
|---|
| 1971 | sigstr += fmt[ind]%(atomsSig[sigind]) |
|---|
| 1972 | else: |
|---|
| 1973 | sigstr += 8*' ' |
|---|
| 1974 | pFile.write(name+'\n') |
|---|
| 1975 | pFile.write(valstr+'\n') |
|---|
| 1976 | pFile.write(sigstr+'\n') |
|---|
| 1977 | |
|---|
| 1978 | def PrintMomentsAndSig(General,Atoms,atomsSig): |
|---|
| 1979 | cell = General['Cell'][1:7] |
|---|
| 1980 | G = G2lat.fillgmat(cell) |
|---|
| 1981 | ast = np.sqrt(np.diag(G)) |
|---|
| 1982 | GS = G/np.outer(ast,ast) |
|---|
| 1983 | pFile.write('\n Magnetic Moments:\n') #add magnitude & angle, etc.? TBD |
|---|
| 1984 | line = ' name Mx My Mz |Mag|' |
|---|
| 1985 | cx,ct,cs,cia = General['AtomPtrs'] |
|---|
| 1986 | cmx = cx+4 |
|---|
| 1987 | AtInfo = dict(zip(General['AtomTypes'],General['Lande g'])) |
|---|
| 1988 | pFile.write(line+'\n') |
|---|
| 1989 | pFile.write(135*'-'+'\n') |
|---|
| 1990 | fmt = {0:'%7s',ct:'%7s',cmx:'%10.3f',cmx+1:'%10.3f',cmx+2:'%10.3f'} |
|---|
| 1991 | noFXsig = {cmx:[10*' ','%10s'],cmx+1:[10*' ','%10s'],cmx+2:[10*' ','%10s']} |
|---|
| 1992 | for i,at in enumerate(Atoms): |
|---|
| 1993 | if AtInfo[at[ct]]: |
|---|
| 1994 | name = fmt[0]%(at[ct-1])+fmt[1]%(at[ct])+':' |
|---|
| 1995 | valstr = ' values:' |
|---|
| 1996 | sigstr = ' sig :' |
|---|
| 1997 | for ind in range(cmx,cmx+3): |
|---|
| 1998 | sigind = str(i)+':'+str(ind) |
|---|
| 1999 | valstr += fmt[ind]%(at[ind]) |
|---|
| 2000 | if sigind in atomsSig: |
|---|
| 2001 | sigstr += fmt[ind]%(atomsSig[sigind]) |
|---|
| 2002 | else: |
|---|
| 2003 | sigstr += noFXsig[ind][1]%(noFXsig[ind][0]) |
|---|
| 2004 | mag = np.array(at[cmx:cmx+3]) |
|---|
| 2005 | Mag = np.sqrt(np.inner(mag,np.inner(mag,GS))) |
|---|
| 2006 | valstr += '%10.3f'%Mag |
|---|
| 2007 | sigstr += 10*' ' |
|---|
| 2008 | pFile.write(name+'\n') |
|---|
| 2009 | pFile.write(valstr+'\n') |
|---|
| 2010 | pFile.write(sigstr+'\n') |
|---|
| 2011 | |
|---|
| 2012 | def PrintWavesAndSig(General,Atoms,wavesSig): |
|---|
| 2013 | cx,ct,cs,cia = General['AtomPtrs'] |
|---|
| 2014 | pFile.write('\n Modulation waves\n') |
|---|
| 2015 | names = {'Sfrac':['Fsin','Fcos','Fzero','Fwid'],'Spos':['Xsin','Ysin','Zsin','Xcos','Ycos','Zcos','Tmin','Tmax','Xmax','Ymax','Zmax'], |
|---|
| 2016 | 'Sadp':['U11sin','U22sin','U33sin','U12sin','U13sin','U23sin','U11cos','U22cos', |
|---|
| 2017 | 'U33cos','U12cos','U13cos','U23cos'],'Smag':['MXsin','MYsin','MZsin','MXcos','MYcos','MZcos']} |
|---|
| 2018 | pFile.write(135*'-'+'\n') |
|---|
| 2019 | for i,at in enumerate(Atoms): |
|---|
| 2020 | AtomSS = at[-1]['SS1'] |
|---|
| 2021 | for Stype in ['Sfrac','Spos','Sadp','Smag']: |
|---|
| 2022 | Waves = AtomSS[Stype] |
|---|
| 2023 | if len(Waves) > 1: |
|---|
| 2024 | waveType = Waves[0] |
|---|
| 2025 | else: |
|---|
| 2026 | continue |
|---|
| 2027 | if len(Waves): |
|---|
| 2028 | pFile.write(' atom: %s, site sym: %s, type: %s wave type: %s:\n'% |
|---|
| 2029 | (at[ct-1],at[cs],Stype,waveType)) |
|---|
| 2030 | for iw,wave in enumerate(Waves[1:]): |
|---|
| 2031 | stiw = ':'+str(i)+':'+str(iw) |
|---|
| 2032 | namstr = ' names :' |
|---|
| 2033 | valstr = ' values:' |
|---|
| 2034 | sigstr = ' esds :' |
|---|
| 2035 | if Stype == 'Spos': |
|---|
| 2036 | nt = 6 |
|---|
| 2037 | ot = 0 |
|---|
| 2038 | if waveType in ['ZigZag','Block',] and not iw: |
|---|
| 2039 | nt = 5 |
|---|
| 2040 | ot = 6 |
|---|
| 2041 | for j in range(nt): |
|---|
| 2042 | name = names['Spos'][j+ot] |
|---|
| 2043 | namstr += '%12s'%(name) |
|---|
| 2044 | valstr += '%12.4f'%(wave[0][j]) |
|---|
| 2045 | if name+stiw in wavesSig: |
|---|
| 2046 | sigstr += '%12.4f'%(wavesSig[name+stiw]) |
|---|
| 2047 | else: |
|---|
| 2048 | sigstr += 12*' ' |
|---|
| 2049 | elif Stype == 'Sfrac': |
|---|
| 2050 | ot = 0 |
|---|
| 2051 | if 'Crenel' in waveType and not iw: |
|---|
| 2052 | ot = 2 |
|---|
| 2053 | for j in range(2): |
|---|
| 2054 | name = names['Sfrac'][j+ot] |
|---|
| 2055 | namstr += '%12s'%(names['Sfrac'][j+ot]) |
|---|
| 2056 | valstr += '%12.4f'%(wave[0][j]) |
|---|
| 2057 | if name+stiw in wavesSig: |
|---|
| 2058 | sigstr += '%12.4f'%(wavesSig[name+stiw]) |
|---|
| 2059 | else: |
|---|
| 2060 | sigstr += 12*' ' |
|---|
| 2061 | elif Stype == 'Sadp': |
|---|
| 2062 | for j in range(12): |
|---|
| 2063 | name = names['Sadp'][j] |
|---|
| 2064 | namstr += '%10s'%(names['Sadp'][j]) |
|---|
| 2065 | valstr += '%10.6f'%(wave[0][j]) |
|---|
| 2066 | if name+stiw in wavesSig: |
|---|
| 2067 | sigstr += '%10.6f'%(wavesSig[name+stiw]) |
|---|
| 2068 | else: |
|---|
| 2069 | sigstr += 10*' ' |
|---|
| 2070 | elif Stype == 'Smag': |
|---|
| 2071 | for j in range(6): |
|---|
| 2072 | name = names['Smag'][j] |
|---|
| 2073 | namstr += '%12s'%(names['Smag'][j]) |
|---|
| 2074 | valstr += '%12.4f'%(wave[0][j]) |
|---|
| 2075 | if name+stiw in wavesSig: |
|---|
| 2076 | sigstr += '%12.4f'%(wavesSig[name+stiw]) |
|---|
| 2077 | else: |
|---|
| 2078 | sigstr += 12*' ' |
|---|
| 2079 | |
|---|
| 2080 | pFile.write(namstr+'\n') |
|---|
| 2081 | pFile.write(valstr+'\n') |
|---|
| 2082 | pFile.write(sigstr+'\n') |
|---|
| 2083 | |
|---|
| 2084 | |
|---|
| 2085 | def PrintRBObjPOAndSig(rbfx,rbsx): |
|---|
| 2086 | for i in WriteRBObjPOAndSig(pfx,rbfx,rbsx,parmDict,sigDict): |
|---|
| 2087 | pFile.write(i+'\n') |
|---|
| 2088 | |
|---|
| 2089 | def PrintRBObjTLSAndSig(rbfx,rbsx,TLS): |
|---|
| 2090 | for i in WriteRBObjTLSAndSig(pfx,rbfx,rbsx,TLS,parmDict,sigDict): |
|---|
| 2091 | pFile.write(i) |
|---|
| 2092 | |
|---|
| 2093 | def PrintRBObjTorAndSig(rbsx): |
|---|
| 2094 | nTors = len(RBObj['Torsions']) |
|---|
| 2095 | if nTors: |
|---|
| 2096 | for i in WriteRBObjTorAndSig(pfx,rbsx,parmDict,sigDict,nTors): |
|---|
| 2097 | pFile.write(i) |
|---|
| 2098 | |
|---|
| 2099 | def PrintSHtextureAndSig(textureData,SHtextureSig): |
|---|
| 2100 | Tindx = 1.0 |
|---|
| 2101 | Tvar = 0.0 |
|---|
| 2102 | pFile.write('\n Spherical harmonics texture: Order: %d\n'%textureData['Order']) |
|---|
| 2103 | names = ['omega','chi','phi'] |
|---|
| 2104 | namstr = ' names :' |
|---|
| 2105 | ptstr = ' values:' |
|---|
| 2106 | sigstr = ' esds :' |
|---|
| 2107 | for name in names: |
|---|
| 2108 | namstr += '%12s'%(name) |
|---|
| 2109 | ptstr += '%12.3f'%(textureData['Sample '+name][1]) |
|---|
| 2110 | if 'Sample '+name in SHtextureSig: |
|---|
| 2111 | sigstr += '%12.3f'%(SHtextureSig['Sample '+name]) |
|---|
| 2112 | else: |
|---|
| 2113 | sigstr += 12*' ' |
|---|
| 2114 | pFile.write(namstr+'\n') |
|---|
| 2115 | pFile.write(ptstr+'\n') |
|---|
| 2116 | pFile.write(sigstr+'\n') |
|---|
| 2117 | pFile.write('\n Texture coefficients:\n') |
|---|
| 2118 | SHcoeff = textureData['SH Coeff'][1] |
|---|
| 2119 | SHkeys = list(SHcoeff.keys()) |
|---|
| 2120 | nCoeff = len(SHcoeff) |
|---|
| 2121 | nBlock = nCoeff//10+1 |
|---|
| 2122 | iBeg = 0 |
|---|
| 2123 | iFin = min(iBeg+10,nCoeff) |
|---|
| 2124 | for block in range(nBlock): |
|---|
| 2125 | namstr = ' names :' |
|---|
| 2126 | ptstr = ' values:' |
|---|
| 2127 | sigstr = ' esds :' |
|---|
| 2128 | for name in SHkeys[iBeg:iFin]: |
|---|
| 2129 | namstr += '%12s'%(name) |
|---|
| 2130 | ptstr += '%12.3f'%(SHcoeff[name]) |
|---|
| 2131 | l = 2.0*eval(name.strip('C'))[0]+1 |
|---|
| 2132 | Tindx += SHcoeff[name]**2/l |
|---|
| 2133 | if name in SHtextureSig: |
|---|
| 2134 | Tvar += (2.*SHcoeff[name]*SHtextureSig[name]/l)**2 |
|---|
| 2135 | sigstr += '%12.3f'%(SHtextureSig[name]) |
|---|
| 2136 | else: |
|---|
| 2137 | sigstr += 12*' ' |
|---|
| 2138 | pFile.write(namstr+'\n') |
|---|
| 2139 | pFile.write(ptstr+'\n') |
|---|
| 2140 | pFile.write(sigstr+'\n') |
|---|
| 2141 | iBeg += 10 |
|---|
| 2142 | iFin = min(iBeg+10,nCoeff) |
|---|
| 2143 | pFile.write(' Texture index J = %.3f(%d)'%(Tindx,int(1000*np.sqrt(Tvar)))) |
|---|
| 2144 | |
|---|
| 2145 | ########################################################################## |
|---|
| 2146 | # SetPhaseData starts here |
|---|
| 2147 | pFile.write('\n Phases:\n') |
|---|
| 2148 | for phase in Phases: |
|---|
| 2149 | pFile.write(' Result for phase: %s\n'%phase) |
|---|
| 2150 | pFile.write(135*'='+'\n') |
|---|
| 2151 | Phase = Phases[phase] |
|---|
| 2152 | General = Phase['General'] |
|---|
| 2153 | SGData = General['SGData'] |
|---|
| 2154 | Atoms = Phase['Atoms'] |
|---|
| 2155 | AtLookup = [] |
|---|
| 2156 | if Atoms and not General.get('doPawley'): |
|---|
| 2157 | cx,ct,cs,cia = General['AtomPtrs'] |
|---|
| 2158 | AtLookup = G2mth.FillAtomLookUp(Atoms,cia+8) |
|---|
| 2159 | cell = General['Cell'] |
|---|
| 2160 | pId = Phase['pId'] |
|---|
| 2161 | pfx = str(pId)+'::' |
|---|
| 2162 | if cell[0]: |
|---|
| 2163 | A,sigA = cellFill(pfx,SGData,parmDict,sigDict) |
|---|
| 2164 | cellSig = getCellEsd(pfx,SGData,A,covData) #includes sigVol |
|---|
| 2165 | pFile.write(' Reciprocal metric tensor: \n') |
|---|
| 2166 | ptfmt = "%15.9f" |
|---|
| 2167 | names = ['A11','A22','A33','A12','A13','A23'] |
|---|
| 2168 | namstr = ' names :' |
|---|
| 2169 | ptstr = ' values:' |
|---|
| 2170 | sigstr = ' esds :' |
|---|
| 2171 | for name,a,siga in zip(names,A,sigA): |
|---|
| 2172 | namstr += '%15s'%(name) |
|---|
| 2173 | ptstr += ptfmt%(a) |
|---|
| 2174 | if siga: |
|---|
| 2175 | sigstr += ptfmt%(siga) |
|---|
| 2176 | else: |
|---|
| 2177 | sigstr += 15*' ' |
|---|
| 2178 | pFile.write(namstr+'\n') |
|---|
| 2179 | pFile.write(ptstr+'\n') |
|---|
| 2180 | pFile.write(sigstr+'\n') |
|---|
| 2181 | cell[1:7] = G2lat.A2cell(A) |
|---|
| 2182 | cell[7] = G2lat.calc_V(A) |
|---|
| 2183 | pFile.write(' New unit cell:\n') |
|---|
| 2184 | ptfmt = ["%12.6f","%12.6f","%12.6f","%12.4f","%12.4f","%12.4f","%12.3f"] |
|---|
| 2185 | names = ['a','b','c','alpha','beta','gamma','Volume'] |
|---|
| 2186 | namstr = ' names :' |
|---|
| 2187 | ptstr = ' values:' |
|---|
| 2188 | sigstr = ' esds :' |
|---|
| 2189 | for name,fmt,a,siga in zip(names,ptfmt,cell[1:8],cellSig): |
|---|
| 2190 | namstr += '%12s'%(name) |
|---|
| 2191 | ptstr += fmt%(a) |
|---|
| 2192 | if siga: |
|---|
| 2193 | sigstr += fmt%(siga) |
|---|
| 2194 | else: |
|---|
| 2195 | sigstr += 12*' ' |
|---|
| 2196 | pFile.write(namstr+'\n') |
|---|
| 2197 | pFile.write(ptstr+'\n') |
|---|
| 2198 | pFile.write(sigstr+'\n') |
|---|
| 2199 | ik = 6 #for Pawley stuff below |
|---|
| 2200 | if General.get('Modulated',False): |
|---|
| 2201 | ik = 7 |
|---|
| 2202 | Vec,vRef,maxH = General['SuperVec'] |
|---|
| 2203 | if vRef: |
|---|
| 2204 | pFile.write(' New modulation vector:\n') |
|---|
| 2205 | namstr = ' names :' |
|---|
| 2206 | ptstr = ' values:' |
|---|
| 2207 | sigstr = ' esds :' |
|---|
| 2208 | for iv,var in enumerate(['mV0','mV1','mV2']): |
|---|
| 2209 | namstr += '%12s'%(pfx+var) |
|---|
| 2210 | ptstr += '%12.6f'%(parmDict[pfx+var]) |
|---|
| 2211 | if pfx+var in sigDict: |
|---|
| 2212 | Vec[iv] = parmDict[pfx+var] |
|---|
| 2213 | sigstr += '%12.6f'%(sigDict[pfx+var]) |
|---|
| 2214 | else: |
|---|
| 2215 | sigstr += 12*' ' |
|---|
| 2216 | pFile.write(namstr+'\n') |
|---|
| 2217 | pFile.write(ptstr+'\n') |
|---|
| 2218 | pFile.write(sigstr+'\n') |
|---|
| 2219 | |
|---|
| 2220 | General['Mass'] = 0. |
|---|
| 2221 | if Phase['General'].get('doPawley'): |
|---|
| 2222 | pawleyRef = Phase['Pawley ref'] |
|---|
| 2223 | for i,refl in enumerate(pawleyRef): |
|---|
| 2224 | key = pfx+'PWLref:'+str(i) |
|---|
| 2225 | refl[ik] = parmDict[key] |
|---|
| 2226 | if key in sigDict: |
|---|
| 2227 | refl[ik+1] = sigDict[key] |
|---|
| 2228 | else: |
|---|
| 2229 | refl[ik+1] = 0 |
|---|
| 2230 | else: |
|---|
| 2231 | VRBIds = RBIds['Vector'] |
|---|
| 2232 | RRBIds = RBIds['Residue'] |
|---|
| 2233 | RBModels = Phase['RBModels'] |
|---|
| 2234 | for irb,RBObj in enumerate(RBModels.get('Vector',[])): |
|---|
| 2235 | jrb = VRBIds.index(RBObj['RBId']) |
|---|
| 2236 | rbsx = str(irb)+':'+str(jrb) |
|---|
| 2237 | pFile.write(' Vector rigid body parameters:\n') |
|---|
| 2238 | PrintRBObjPOAndSig('RBV',rbsx) |
|---|
| 2239 | PrintRBObjTLSAndSig('RBV',rbsx,RBObj['ThermalMotion'][0]) |
|---|
| 2240 | for irb,RBObj in enumerate(RBModels.get('Residue',[])): |
|---|
| 2241 | jrb = RRBIds.index(RBObj['RBId']) |
|---|
| 2242 | rbsx = str(irb)+':'+str(jrb) |
|---|
| 2243 | pFile.write(' Residue rigid body parameters:\n') |
|---|
| 2244 | PrintRBObjPOAndSig('RBR',rbsx) |
|---|
| 2245 | PrintRBObjTLSAndSig('RBR',rbsx,RBObj['ThermalMotion'][0]) |
|---|
| 2246 | PrintRBObjTorAndSig(rbsx) |
|---|
| 2247 | atomsSig = {} |
|---|
| 2248 | wavesSig = {} |
|---|
| 2249 | cx,ct,cs,cia = General['AtomPtrs'] |
|---|
| 2250 | for i,at in enumerate(Atoms): |
|---|
| 2251 | names = {cx:pfx+'Ax:'+str(i),cx+1:pfx+'Ay:'+str(i),cx+2:pfx+'Az:'+str(i),cx+3:pfx+'Afrac:'+str(i), |
|---|
| 2252 | cia+1:pfx+'AUiso:'+str(i),cia+2:pfx+'AU11:'+str(i),cia+3:pfx+'AU22:'+str(i),cia+4:pfx+'AU33:'+str(i), |
|---|
| 2253 | cia+5:pfx+'AU12:'+str(i),cia+6:pfx+'AU13:'+str(i),cia+7:pfx+'AU23:'+str(i), |
|---|
| 2254 | cx+4:pfx+'AMx:'+str(i),cx+5:pfx+'AMy:'+str(i),cx+6:pfx+'AMz:'+str(i)} |
|---|
| 2255 | for ind in range(cx,cx+4): |
|---|
| 2256 | at[ind] = parmDict[names[ind]] |
|---|
| 2257 | if ind in range(cx,cx+3): |
|---|
| 2258 | name = names[ind].replace('A','dA') |
|---|
| 2259 | else: |
|---|
| 2260 | name = names[ind] |
|---|
| 2261 | if name in sigDict: |
|---|
| 2262 | atomsSig[str(i)+':'+str(ind)] = sigDict[name] |
|---|
| 2263 | if at[cia] == 'I': |
|---|
| 2264 | at[cia+1] = parmDict[names[cia+1]] |
|---|
| 2265 | if names[cia+1] in sigDict: |
|---|
| 2266 | atomsSig['%d:%d'%(i,cia+1)] = sigDict[names[cia+1]] |
|---|
| 2267 | else: |
|---|
| 2268 | for ind in range(cia+2,cia+8): |
|---|
| 2269 | at[ind] = parmDict[names[ind]] |
|---|
| 2270 | if names[ind] in sigDict: |
|---|
| 2271 | atomsSig[str(i)+':'+str(ind)] = sigDict[names[ind]] |
|---|
| 2272 | if General['Type'] == 'magnetic': |
|---|
| 2273 | for ind in range(cx+4,cx+7): |
|---|
| 2274 | at[ind] = parmDict[names[ind]] |
|---|
| 2275 | if names[ind] in sigDict: |
|---|
| 2276 | atomsSig[str(i)+':'+str(ind)] = sigDict[names[ind]] |
|---|
| 2277 | ind = General['AtomTypes'].index(at[ct]) |
|---|
| 2278 | General['Mass'] += General['AtomMass'][ind]*at[cx+3]*at[cx+5] |
|---|
| 2279 | if General.get('Modulated',False): |
|---|
| 2280 | AtomSS = at[-1]['SS1'] |
|---|
| 2281 | for Stype in ['Sfrac','Spos','Sadp','Smag']: |
|---|
| 2282 | Waves = AtomSS[Stype] |
|---|
| 2283 | if len(Waves): |
|---|
| 2284 | waveType = Waves[0] |
|---|
| 2285 | else: |
|---|
| 2286 | continue |
|---|
| 2287 | for iw,wave in enumerate(Waves[1:]): |
|---|
| 2288 | stiw = str(i)+':'+str(iw) |
|---|
| 2289 | if Stype == 'Spos': |
|---|
| 2290 | if waveType in ['ZigZag','Block',] and not iw: |
|---|
| 2291 | names = ['Tmin:'+stiw,'Tmax:'+stiw,'Xmax:'+stiw,'Ymax:'+stiw,'Zmax:'+stiw] |
|---|
| 2292 | else: |
|---|
| 2293 | names = ['Xsin:'+stiw,'Ysin:'+stiw,'Zsin:'+stiw, |
|---|
| 2294 | 'Xcos:'+stiw,'Ycos:'+stiw,'Zcos:'+stiw] |
|---|
| 2295 | elif Stype == 'Sadp': |
|---|
| 2296 | names = ['U11sin:'+stiw,'U22sin:'+stiw,'U33sin:'+stiw, |
|---|
| 2297 | 'U12sin:'+stiw,'U13sin:'+stiw,'U23sin:'+stiw, |
|---|
| 2298 | 'U11cos:'+stiw,'U22cos:'+stiw,'U33cos:'+stiw, |
|---|
| 2299 | 'U12cos:'+stiw,'U13cos:'+stiw,'U23cos:'+stiw] |
|---|
| 2300 | elif Stype == 'Sfrac': |
|---|
| 2301 | if 'Crenel' in waveType and not iw: |
|---|
| 2302 | names = ['Fzero:'+stiw,'Fwid:'+stiw] |
|---|
| 2303 | else: |
|---|
| 2304 | names = ['Fsin:'+stiw,'Fcos:'+stiw] |
|---|
| 2305 | elif Stype == 'Smag': |
|---|
| 2306 | names = ['MXsin:'+stiw,'MYsin:'+stiw,'MZsin:'+stiw, |
|---|
| 2307 | 'MXcos:'+stiw,'MYcos:'+stiw,'MZcos:'+stiw] |
|---|
| 2308 | for iname,name in enumerate(names): |
|---|
| 2309 | AtomSS[Stype][iw+1][0][iname] = parmDict[pfx+name] |
|---|
| 2310 | if pfx+name in sigDict: |
|---|
| 2311 | wavesSig[name] = sigDict[pfx+name] |
|---|
| 2312 | |
|---|
| 2313 | PrintAtomsAndSig(General,Atoms,atomsSig) |
|---|
| 2314 | if General['Type'] == 'magnetic': |
|---|
| 2315 | PrintMomentsAndSig(General,Atoms,atomsSig) |
|---|
| 2316 | if General.get('Modulated',False): |
|---|
| 2317 | PrintWavesAndSig(General,Atoms,wavesSig) |
|---|
| 2318 | |
|---|
| 2319 | density = G2mth.getDensity(General)[0] |
|---|
| 2320 | pFile.write('\n Density: {:.4f} g/cm**3\n'.format(density)) |
|---|
| 2321 | |
|---|
| 2322 | |
|---|
| 2323 | textureData = General['SH Texture'] |
|---|
| 2324 | if textureData['Order']: |
|---|
| 2325 | SHtextureSig = {} |
|---|
| 2326 | for name in ['omega','chi','phi']: |
|---|
| 2327 | aname = pfx+'SH '+name |
|---|
| 2328 | textureData['Sample '+name][1] = parmDict[aname] |
|---|
| 2329 | if aname in sigDict: |
|---|
| 2330 | SHtextureSig['Sample '+name] = sigDict[aname] |
|---|
| 2331 | for name in textureData['SH Coeff'][1]: |
|---|
| 2332 | aname = pfx+name |
|---|
| 2333 | textureData['SH Coeff'][1][name] = parmDict[aname] |
|---|
| 2334 | if aname in sigDict: |
|---|
| 2335 | SHtextureSig[name] = sigDict[aname] |
|---|
| 2336 | PrintSHtextureAndSig(textureData,SHtextureSig) |
|---|
| 2337 | if phase in RestraintDict and not Phase['General'].get('doPawley'): |
|---|
| 2338 | PrintRestraints(cell[1:7],SGData,General['AtomPtrs'],Atoms,AtLookup, |
|---|
| 2339 | textureData,RestraintDict[phase],pFile) |
|---|
| 2340 | |
|---|
| 2341 | ################################################################################ |
|---|
| 2342 | ##### Histogram & Phase data |
|---|
| 2343 | ################################################################################ |
|---|
| 2344 | |
|---|
| 2345 | def GetHistogramPhaseData(Phases,Histograms,Print=True,pFile=None,resetRefList=True): |
|---|
| 2346 | '''Loads the HAP histogram/phase information into dicts |
|---|
| 2347 | |
|---|
| 2348 | :param dict Phases: phase information |
|---|
| 2349 | :param dict Histograms: Histogram information |
|---|
| 2350 | :param bool Print: prints information as it is read |
|---|
| 2351 | :param file pFile: file object to print to (the default, None causes printing to the console) |
|---|
| 2352 | :param bool resetRefList: Should the contents of the Reflection List be initialized |
|---|
| 2353 | on loading. The default, True, initializes the Reflection List as it is loaded. |
|---|
| 2354 | |
|---|
| 2355 | :returns: (hapVary,hapDict,controlDict) |
|---|
| 2356 | * hapVary: list of refined variables |
|---|
| 2357 | * hapDict: dict with refined variables and their values |
|---|
| 2358 | * controlDict: dict with fixed parameters |
|---|
| 2359 | ''' |
|---|
| 2360 | |
|---|
| 2361 | def PrintSize(hapData): |
|---|
| 2362 | if hapData[0] in ['isotropic','uniaxial']: |
|---|
| 2363 | line = '\n Size model : %9s'%(hapData[0]) |
|---|
| 2364 | line += ' equatorial:'+'%12.3f'%(hapData[1][0])+' Refine? '+str(hapData[2][0]) |
|---|
| 2365 | if hapData[0] == 'uniaxial': |
|---|
| 2366 | line += ' axial:'+'%12.3f'%(hapData[1][1])+' Refine? '+str(hapData[2][1]) |
|---|
| 2367 | line += '\n\t LG mixing coeff.: %12.4f'%(hapData[1][2])+' Refine? '+str(hapData[2][2]) |
|---|
| 2368 | pFile.write(line+'\n') |
|---|
| 2369 | else: |
|---|
| 2370 | pFile.write('\n Size model : %s\n\t LG mixing coeff.:%12.4f Refine? %s\n'% |
|---|
| 2371 | (hapData[0],hapData[1][2],hapData[2][2])) |
|---|
| 2372 | Snames = ['S11','S22','S33','S12','S13','S23'] |
|---|
| 2373 | ptlbls = ' names :' |
|---|
| 2374 | ptstr = ' values:' |
|---|
| 2375 | varstr = ' refine:' |
|---|
| 2376 | for i,name in enumerate(Snames): |
|---|
| 2377 | ptlbls += '%12s' % (name) |
|---|
| 2378 | ptstr += '%12.3f' % (hapData[4][i]) |
|---|
| 2379 | varstr += '%12s' % (str(hapData[5][i])) |
|---|
| 2380 | pFile.write(ptlbls+'\n') |
|---|
| 2381 | pFile.write(ptstr+'\n') |
|---|
| 2382 | pFile.write(varstr+'\n') |
|---|
| 2383 | |
|---|
| 2384 | def PrintMuStrain(hapData,SGData): |
|---|
| 2385 | if hapData[0] in ['isotropic','uniaxial']: |
|---|
| 2386 | line = '\n Mustrain model: %9s'%(hapData[0]) |
|---|
| 2387 | line += ' equatorial:'+'%12.1f'%(hapData[1][0])+' Refine? '+str(hapData[2][0]) |
|---|
| 2388 | if hapData[0] == 'uniaxial': |
|---|
| 2389 | line += ' axial:'+'%12.1f'%(hapData[1][1])+' Refine? '+str(hapData[2][1]) |
|---|
| 2390 | line +='\n\t LG mixing coeff.:%12.4f'%(hapData[1][2])+' Refine? '+str(hapData[2][2]) |
|---|
| 2391 | pFile.write(line+'\n') |
|---|
| 2392 | else: |
|---|
| 2393 | pFile.write('\n Mustrain model: %s\n\t LG mixing coeff.:%12.4f Refine? %s\n'% |
|---|
| 2394 | (hapData[0],hapData[1][2],hapData[2][2])) |
|---|
| 2395 | Snames = G2spc.MustrainNames(SGData) |
|---|
| 2396 | ptlbls = ' names :' |
|---|
| 2397 | ptstr = ' values:' |
|---|
| 2398 | varstr = ' refine:' |
|---|
| 2399 | for i,name in enumerate(Snames): |
|---|
| 2400 | ptlbls += '%12s' % (name) |
|---|
| 2401 | ptstr += '%12.1f' % (hapData[4][i]) |
|---|
| 2402 | varstr += '%12s' % (str(hapData[5][i])) |
|---|
| 2403 | pFile.write(ptlbls+'\n') |
|---|
| 2404 | pFile.write(ptstr+'\n') |
|---|
| 2405 | pFile.write(varstr+'\n') |
|---|
| 2406 | |
|---|
| 2407 | def PrintHStrain(hapData,SGData): |
|---|
| 2408 | pFile.write('\n Hydrostatic/elastic strain:\n') |
|---|
| 2409 | Hsnames = G2spc.HStrainNames(SGData) |
|---|
| 2410 | ptlbls = ' names :' |
|---|
| 2411 | ptstr = ' values:' |
|---|
| 2412 | varstr = ' refine:' |
|---|
| 2413 | for i,name in enumerate(Hsnames): |
|---|
| 2414 | ptlbls += '%12s' % (name) |
|---|
| 2415 | ptstr += '%12.4g' % (hapData[0][i]) |
|---|
| 2416 | varstr += '%12s' % (str(hapData[1][i])) |
|---|
| 2417 | pFile.write(ptlbls+'\n') |
|---|
| 2418 | pFile.write(ptstr+'\n') |
|---|
| 2419 | pFile.write(varstr+'\n') |
|---|
| 2420 | |
|---|
| 2421 | def PrintSHPO(hapData): |
|---|
| 2422 | pFile.write('\n Spherical harmonics preferred orientation: Order: %d Refine? %s\n'%(hapData[4],hapData[2])) |
|---|
| 2423 | ptlbls = ' names :' |
|---|
| 2424 | ptstr = ' values:' |
|---|
| 2425 | for item in hapData[5]: |
|---|
| 2426 | ptlbls += '%12s'%(item) |
|---|
| 2427 | ptstr += '%12.3f'%(hapData[5][item]) |
|---|
| 2428 | pFile.write(ptlbls+'\n') |
|---|
| 2429 | pFile.write(ptstr+'\n') |
|---|
| 2430 | |
|---|
| 2431 | def PrintBabinet(hapData): |
|---|
| 2432 | pFile.write('\n Babinet form factor modification:\n') |
|---|
| 2433 | ptlbls = ' names :' |
|---|
| 2434 | ptstr = ' values:' |
|---|
| 2435 | varstr = ' refine:' |
|---|
| 2436 | for name in ['BabA','BabU']: |
|---|
| 2437 | ptlbls += '%12s' % (name) |
|---|
| 2438 | ptstr += '%12.6f' % (hapData[name][0]) |
|---|
| 2439 | varstr += '%12s' % (str(hapData[name][1])) |
|---|
| 2440 | pFile.write(ptlbls+'\n') |
|---|
| 2441 | pFile.write(ptstr+'\n') |
|---|
| 2442 | pFile.write(varstr+'\n') |
|---|
| 2443 | |
|---|
| 2444 | hapDict = {} |
|---|
| 2445 | hapVary = [] |
|---|
| 2446 | controlDict = {} |
|---|
| 2447 | |
|---|
| 2448 | for phase in Phases: |
|---|
| 2449 | HistoPhase = Phases[phase]['Histograms'] |
|---|
| 2450 | SGData = Phases[phase]['General']['SGData'] |
|---|
| 2451 | cell = Phases[phase]['General']['Cell'][1:7] |
|---|
| 2452 | A = G2lat.cell2A(cell) |
|---|
| 2453 | if Phases[phase]['General'].get('Modulated',False): |
|---|
| 2454 | SSGData = Phases[phase]['General']['SSGData'] |
|---|
| 2455 | Vec,x,maxH = Phases[phase]['General']['SuperVec'] |
|---|
| 2456 | pId = Phases[phase]['pId'] |
|---|
| 2457 | for histogram in Histograms: |
|---|
| 2458 | if histogram not in HistoPhase and phase in Histograms[histogram]['Reflection Lists']: |
|---|
| 2459 | #remove previously created reflection list if histogram is removed from phase |
|---|
| 2460 | #print("removing ",phase,"from",histogram) |
|---|
| 2461 | del Histograms[histogram]['Reflection Lists'][phase] |
|---|
| 2462 | histoList = list(HistoPhase.keys()) |
|---|
| 2463 | histoList.sort() |
|---|
| 2464 | for histogram in histoList: |
|---|
| 2465 | try: |
|---|
| 2466 | Histogram = Histograms[histogram] |
|---|
| 2467 | except KeyError: |
|---|
| 2468 | #skip if histogram not included e.g. in a sequential refinement |
|---|
| 2469 | continue |
|---|
| 2470 | if not HistoPhase[histogram]['Use']: #remove previously created & now unused phase reflection list |
|---|
| 2471 | if phase in Histograms[histogram]['Reflection Lists']: |
|---|
| 2472 | del Histograms[histogram]['Reflection Lists'][phase] |
|---|
| 2473 | continue |
|---|
| 2474 | hapData = HistoPhase[histogram] |
|---|
| 2475 | hId = Histogram['hId'] |
|---|
| 2476 | if 'PWDR' in histogram: |
|---|
| 2477 | limits = Histogram['Limits'][1] |
|---|
| 2478 | inst = Histogram['Instrument Parameters'][0] #TODO - grab table here if present |
|---|
| 2479 | if 'C' in inst['Type'][1]: |
|---|
| 2480 | try: |
|---|
| 2481 | wave = inst['Lam'][1] |
|---|
| 2482 | except KeyError: |
|---|
| 2483 | wave = inst['Lam1'][1] |
|---|
| 2484 | dmin = wave/(2.0*sind(limits[1]/2.0)) |
|---|
| 2485 | elif 'T' in inst['Type'][0]: |
|---|
| 2486 | dmin = limits[0]/inst['difC'][1] |
|---|
| 2487 | else: |
|---|
| 2488 | wave = inst['Lam'][1] |
|---|
| 2489 | dmin = wave/(2.0*sind(limits[1]/2.0)) |
|---|
| 2490 | pfx = str(pId)+':'+str(hId)+':' |
|---|
| 2491 | if Phases[phase]['General']['doPawley']: |
|---|
| 2492 | hapDict[pfx+'LeBail'] = False #Pawley supercedes LeBail |
|---|
| 2493 | hapDict[pfx+'newLeBail'] = True |
|---|
| 2494 | Tmin = G2lat.Dsp2pos(inst,dmin) |
|---|
| 2495 | if 'T' in inst['Type'][1]: |
|---|
| 2496 | limits[0] = max(limits[0],Tmin) |
|---|
| 2497 | else: |
|---|
| 2498 | limits[1] = min(limits[1],Tmin) |
|---|
| 2499 | else: |
|---|
| 2500 | hapDict[pfx+'LeBail'] = hapData.get('LeBail',False) |
|---|
| 2501 | hapDict[pfx+'newLeBail'] = hapData.get('newLeBail',True) |
|---|
| 2502 | if Phases[phase]['General']['Type'] == 'magnetic': |
|---|
| 2503 | dmin = max(dmin,Phases[phase]['General'].get('MagDmin',0.)) |
|---|
| 2504 | for item in ['Scale','Extinction']: |
|---|
| 2505 | hapDict[pfx+item] = hapData[item][0] |
|---|
| 2506 | if hapData[item][1] and not hapDict[pfx+'LeBail']: |
|---|
| 2507 | hapVary.append(pfx+item) |
|---|
| 2508 | names = G2spc.HStrainNames(SGData) |
|---|
| 2509 | HSvals = [] |
|---|
| 2510 | for i,name in enumerate(names): |
|---|
| 2511 | hapDict[pfx+name] = hapData['HStrain'][0][i] |
|---|
| 2512 | HSvals.append(hapDict[pfx+name]) |
|---|
| 2513 | if hapData['HStrain'][1][i]: |
|---|
| 2514 | hapVary.append(pfx+name) |
|---|
| 2515 | if 'Layer Disp' in hapData: |
|---|
| 2516 | hapDict[pfx+'LayerDisp'] = hapData['Layer Disp'][0] |
|---|
| 2517 | if hapData['Layer Disp'][1]: |
|---|
| 2518 | hapVary.append(pfx+'LayerDisp') |
|---|
| 2519 | else: |
|---|
| 2520 | hapDict[pfx+'LayerDisp'] = 0.0 |
|---|
| 2521 | controlDict[pfx+'poType'] = hapData['Pref.Ori.'][0] |
|---|
| 2522 | if hapData['Pref.Ori.'][0] == 'MD': |
|---|
| 2523 | hapDict[pfx+'MD'] = hapData['Pref.Ori.'][1] |
|---|
| 2524 | controlDict[pfx+'MDAxis'] = hapData['Pref.Ori.'][3] |
|---|
| 2525 | if hapData['Pref.Ori.'][2] and not hapDict[pfx+'LeBail']: |
|---|
| 2526 | hapVary.append(pfx+'MD') |
|---|
| 2527 | else: #'SH' spherical harmonics |
|---|
| 2528 | controlDict[pfx+'SHord'] = hapData['Pref.Ori.'][4] |
|---|
| 2529 | controlDict[pfx+'SHncof'] = len(hapData['Pref.Ori.'][5]) |
|---|
| 2530 | controlDict[pfx+'SHnames'] = G2lat.GenSHCoeff(SGData['SGLaue'],'0',controlDict[pfx+'SHord'],False) |
|---|
| 2531 | controlDict[pfx+'SHhkl'] = [] |
|---|
| 2532 | try: #patch for old Pref.Ori. items |
|---|
| 2533 | controlDict[pfx+'SHtoler'] = 0.1 |
|---|
| 2534 | if hapData['Pref.Ori.'][6][0] != '': |
|---|
| 2535 | controlDict[pfx+'SHhkl'] = [eval(a.replace(' ',',')) for a in hapData['Pref.Ori.'][6]] |
|---|
| 2536 | controlDict[pfx+'SHtoler'] = hapData['Pref.Ori.'][7] |
|---|
| 2537 | except IndexError: |
|---|
| 2538 | pass |
|---|
| 2539 | for item in hapData['Pref.Ori.'][5]: |
|---|
| 2540 | hapDict[pfx+item] = hapData['Pref.Ori.'][5][item] |
|---|
| 2541 | if hapData['Pref.Ori.'][2] and not hapDict[pfx+'LeBail']: |
|---|
| 2542 | hapVary.append(pfx+item) |
|---|
| 2543 | for item in ['Mustrain','Size']: |
|---|
| 2544 | controlDict[pfx+item+'Type'] = hapData[item][0] |
|---|
| 2545 | hapDict[pfx+item+';mx'] = hapData[item][1][2] |
|---|
| 2546 | if hapData[item][2][2]: |
|---|
| 2547 | hapVary.append(pfx+item+';mx') |
|---|
| 2548 | if hapData[item][0] in ['isotropic','uniaxial']: |
|---|
| 2549 | hapDict[pfx+item+';i'] = hapData[item][1][0] |
|---|
| 2550 | if hapData[item][2][0]: |
|---|
| 2551 | hapVary.append(pfx+item+';i') |
|---|
| 2552 | if hapData[item][0] == 'uniaxial': |
|---|
| 2553 | controlDict[pfx+item+'Axis'] = hapData[item][3] |
|---|
| 2554 | hapDict[pfx+item+';a'] = hapData[item][1][1] |
|---|
| 2555 | if hapData[item][2][1]: |
|---|
| 2556 | hapVary.append(pfx+item+';a') |
|---|
| 2557 | else: #generalized for mustrain or ellipsoidal for size |
|---|
| 2558 | Nterms = len(hapData[item][4]) |
|---|
| 2559 | if item == 'Mustrain': |
|---|
| 2560 | names = G2spc.MustrainNames(SGData) |
|---|
| 2561 | pwrs = [] |
|---|
| 2562 | for name in names: |
|---|
| 2563 | h,k,l = name[1:] |
|---|
| 2564 | pwrs.append([int(h),int(k),int(l)]) |
|---|
| 2565 | controlDict[pfx+'MuPwrs'] = pwrs |
|---|
| 2566 | for i in range(Nterms): |
|---|
| 2567 | sfx = ';'+str(i) |
|---|
| 2568 | hapDict[pfx+item+sfx] = hapData[item][4][i] |
|---|
| 2569 | if hapData[item][5][i]: |
|---|
| 2570 | hapVary.append(pfx+item+sfx) |
|---|
| 2571 | if Phases[phase]['General']['Type'] != 'magnetic': |
|---|
| 2572 | for bab in ['BabA','BabU']: |
|---|
| 2573 | hapDict[pfx+bab] = hapData['Babinet'][bab][0] |
|---|
| 2574 | if hapData['Babinet'][bab][1] and not hapDict[pfx+'LeBail']: |
|---|
| 2575 | hapVary.append(pfx+bab) |
|---|
| 2576 | |
|---|
| 2577 | if Print: |
|---|
| 2578 | pFile.write('\n Phase: %s in histogram: %s\n'%(phase,histogram)) |
|---|
| 2579 | pFile.write(135*'='+'\n') |
|---|
| 2580 | if hapDict[pfx+'LeBail']: |
|---|
| 2581 | pFile.write(' Perform LeBail extraction\n') |
|---|
| 2582 | else: |
|---|
| 2583 | pFile.write(' Phase fraction : %10.4f Refine? %s\n'%(hapData['Scale'][0],hapData['Scale'][1])) |
|---|
| 2584 | pFile.write(' Extinction coeff: %10.4f Refine? %s\n'%(hapData['Extinction'][0],hapData['Extinction'][1])) |
|---|
| 2585 | if hapData['Pref.Ori.'][0] == 'MD': |
|---|
| 2586 | Ax = hapData['Pref.Ori.'][3] |
|---|
| 2587 | pFile.write(' March-Dollase PO: %10.4f Refine? %s Axis: %d %d %d\n'% |
|---|
| 2588 | (hapData['Pref.Ori.'][1],hapData['Pref.Ori.'][2],Ax[0],Ax[1],Ax[2])) |
|---|
| 2589 | else: #'SH' for spherical harmonics |
|---|
| 2590 | PrintSHPO(hapData['Pref.Ori.']) |
|---|
| 2591 | pFile.write(' Penalty hkl list: %s tolerance: %.2f\n'%(controlDict[pfx+'SHhkl'],controlDict[pfx+'SHtoler'])) |
|---|
| 2592 | PrintSize(hapData['Size']) |
|---|
| 2593 | PrintMuStrain(hapData['Mustrain'],SGData) |
|---|
| 2594 | PrintHStrain(hapData['HStrain'],SGData) |
|---|
| 2595 | if 'Layer Disp' in hapData: |
|---|
| 2596 | pFile.write(' Layer Displacement: %10.3f Refine? %s\n'%(hapData['Layer Disp'][0],hapData['Layer Disp'][1])) |
|---|
| 2597 | if Phases[phase]['General']['Type'] != 'magnetic': |
|---|
| 2598 | if hapData['Babinet']['BabA'][0]: |
|---|
| 2599 | PrintBabinet(hapData['Babinet']) |
|---|
| 2600 | if phase in Histogram['Reflection Lists'] and 'RefList' not in Histogram['Reflection Lists'][phase] and hapData.get('LeBail',False): |
|---|
| 2601 | hapData['newLeBail'] = True |
|---|
| 2602 | if resetRefList and (not hapDict[pfx+'LeBail'] or (hapData.get('LeBail',False) and hapData['newLeBail'])): |
|---|
| 2603 | if hapData.get('LeBail',True): #stop regeneating reflections for LeBail |
|---|
| 2604 | hapData['newLeBail'] = False |
|---|
| 2605 | refList = [] |
|---|
| 2606 | # Uniq = [] |
|---|
| 2607 | # Phi = [] |
|---|
| 2608 | useExt = 'magnetic' in Phases[phase]['General']['Type'] and 'N' in inst['Type'][0] |
|---|
| 2609 | if Phases[phase]['General'].get('Modulated',False): |
|---|
| 2610 | ifSuper = True |
|---|
| 2611 | HKLd = np.array(G2lat.GenSSHLaue(dmin,SGData,SSGData,Vec,maxH,A)) |
|---|
| 2612 | HKLd = G2mth.sortArray(HKLd,4,reverse=True) |
|---|
| 2613 | for h,k,l,m,d in HKLd: |
|---|
| 2614 | ext,mul,uniq,phi = G2spc.GenHKLf([h,k,l],SGData) |
|---|
| 2615 | mul *= 2 # for powder overlap of Friedel pairs |
|---|
| 2616 | if m or not ext or useExt: |
|---|
| 2617 | if 'C' in inst['Type'][0]: |
|---|
| 2618 | pos = G2lat.Dsp2pos(inst,d) |
|---|
| 2619 | if limits[0] < pos < limits[1]: |
|---|
| 2620 | 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]) |
|---|
| 2621 | #... sig,gam,fotsq,fctsq, phase,icorr,prfo,abs,ext |
|---|
| 2622 | # Uniq.append(uniq) |
|---|
| 2623 | # Phi.append(phi) |
|---|
| 2624 | elif 'T' in inst['Type'][0]: |
|---|
| 2625 | pos = G2lat.Dsp2pos(inst,d) |
|---|
| 2626 | if limits[0] < pos < limits[1]: |
|---|
| 2627 | wave = inst['difC'][1]*d/(252.816*inst['fltPath'][0]) |
|---|
| 2628 | 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]) |
|---|
| 2629 | # ... sig,gam,fotsq,fctsq, phase,icorr,alp,bet,wave, prfo,abs,ext |
|---|
| 2630 | #TODO - if tabulated put alp & bet in here |
|---|
| 2631 | # Uniq.append(uniq) |
|---|
| 2632 | # Phi.append(phi) |
|---|
| 2633 | elif 'B' in inst['Type'][0]: |
|---|
| 2634 | pos = G2lat.Dsp2pos(inst,d) |
|---|
| 2635 | if limits[0] < pos < limits[1]: |
|---|
| 2636 | 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]) |
|---|
| 2637 | # ... sig,gam,fotsq,fctsq, phase,icorr,alp,bet, prfo,abs,ext |
|---|
| 2638 | else: |
|---|
| 2639 | ifSuper = False |
|---|
| 2640 | HKLd = np.array(G2lat.GenHLaue(dmin,SGData,A)) |
|---|
| 2641 | HKLd = G2mth.sortArray(HKLd,3,reverse=True) |
|---|
| 2642 | for h,k,l,d in HKLd: |
|---|
| 2643 | ext,mul,uniq,phi = G2spc.GenHKLf([h,k,l],SGData) |
|---|
| 2644 | if ext and 'N' in inst['Type'][0] and 'MagSpGrp' in SGData: |
|---|
| 2645 | ext = G2spc.checkMagextc([h,k,l],SGData) |
|---|
| 2646 | mul *= 2 # for powder overlap of Friedel pairs |
|---|
| 2647 | if ext and not useExt: |
|---|
| 2648 | continue |
|---|
| 2649 | if 'C' in inst['Type'][0]: |
|---|
| 2650 | pos = G2lat.Dsp2pos(inst,d) |
|---|
| 2651 | if limits[0] < pos < limits[1]: |
|---|
| 2652 | 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]) |
|---|
| 2653 | #... sig,gam,fotsq,fctsq, phase,icorr,prfo,abs,ext |
|---|
| 2654 | # Uniq.append(uniq) |
|---|
| 2655 | # Phi.append(phi) |
|---|
| 2656 | elif 'T' in inst['Type'][0]: |
|---|
| 2657 | pos = G2lat.Dsp2pos(inst,d) |
|---|
| 2658 | if limits[0] < pos < limits[1]: |
|---|
| 2659 | wave = inst['difC'][1]*d/(252.816*inst['fltPath'][0]) |
|---|
| 2660 | 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]) |
|---|
| 2661 | # ... sig,gam,fotsq,fctsq, phase,icorr,alp,bet,wave, prfo,abs,ext |
|---|
| 2662 | # Uniq.append(uniq) |
|---|
| 2663 | # Phi.append(phi) |
|---|
| 2664 | elif 'B' in inst['Type'][0]: |
|---|
| 2665 | pos = G2lat.Dsp2pos(inst,d) |
|---|
| 2666 | if limits[0] < pos < limits[1]: |
|---|
| 2667 | 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]) |
|---|
| 2668 | # ... sig,gam,fotsq,fctsq, phase,icorr,alp,bet, prfo,abs,ext |
|---|
| 2669 | Histogram['Reflection Lists'][phase] = {'RefList':np.array(refList),'FF':{},'Type':inst['Type'][0],'Super':ifSuper} |
|---|
| 2670 | elif 'HKLF' in histogram: |
|---|
| 2671 | inst = Histogram['Instrument Parameters'][0] |
|---|
| 2672 | hId = Histogram['hId'] |
|---|
| 2673 | hfx = ':%d:'%(hId) |
|---|
| 2674 | for item in inst: |
|---|
| 2675 | if type(inst) is not list and item != 'Type': continue # skip over non-refined items (such as InstName) |
|---|
| 2676 | hapDict[hfx+item] = inst[item][1] |
|---|
| 2677 | pfx = str(pId)+':'+str(hId)+':' |
|---|
| 2678 | hapDict[pfx+'Scale'] = hapData['Scale'][0] |
|---|
| 2679 | if hapData['Scale'][1]: |
|---|
| 2680 | hapVary.append(pfx+'Scale') |
|---|
| 2681 | |
|---|
| 2682 | extApprox,extType,extParms = hapData['Extinction'] |
|---|
| 2683 | controlDict[pfx+'EType'] = extType |
|---|
| 2684 | controlDict[pfx+'EApprox'] = extApprox |
|---|
| 2685 | if 'C' in inst['Type'][0]: |
|---|
| 2686 | controlDict[pfx+'Tbar'] = extParms['Tbar'] |
|---|
| 2687 | controlDict[pfx+'Cos2TM'] = extParms['Cos2TM'] |
|---|
| 2688 | if 'Primary' in extType: |
|---|
| 2689 | Ekey = ['Ep',] |
|---|
| 2690 | elif 'I & II' in extType: |
|---|
| 2691 | Ekey = ['Eg','Es'] |
|---|
| 2692 | elif 'Secondary Type II' == extType: |
|---|
| 2693 | Ekey = ['Es',] |
|---|
| 2694 | elif 'Secondary Type I' == extType: |
|---|
| 2695 | Ekey = ['Eg',] |
|---|
| 2696 | else: #'None' |
|---|
| 2697 | Ekey = [] |
|---|
| 2698 | for eKey in Ekey: |
|---|
| 2699 | hapDict[pfx+eKey] = extParms[eKey][0] |
|---|
| 2700 | if extParms[eKey][1]: |
|---|
| 2701 | hapVary.append(pfx+eKey) |
|---|
| 2702 | for bab in ['BabA','BabU']: |
|---|
| 2703 | hapDict[pfx+bab] = hapData['Babinet'][bab][0] |
|---|
| 2704 | if hapData['Babinet'][bab][1]: |
|---|
| 2705 | hapVary.append(pfx+bab) |
|---|
| 2706 | Twins = hapData.get('Twins',[[np.array([[1,0,0],[0,1,0],[0,0,1]]),[1.0,False,0]],]) |
|---|
| 2707 | if len(Twins) == 1: |
|---|
| 2708 | hapDict[pfx+'Flack'] = hapData.get('Flack',[0.,False])[0] |
|---|
| 2709 | if hapData.get('Flack',[0,False])[1]: |
|---|
| 2710 | hapVary.append(pfx+'Flack') |
|---|
| 2711 | sumTwFr = 0. |
|---|
| 2712 | controlDict[pfx+'TwinLaw'] = [] |
|---|
| 2713 | controlDict[pfx+'TwinInv'] = [] |
|---|
| 2714 | NTL = 0 |
|---|
| 2715 | for it,twin in enumerate(Twins): |
|---|
| 2716 | if 'bool' in str(type(twin[0])): |
|---|
| 2717 | controlDict[pfx+'TwinInv'].append(twin[0]) |
|---|
| 2718 | controlDict[pfx+'TwinLaw'].append(np.zeros((3,3))) |
|---|
| 2719 | else: |
|---|
| 2720 | NTL += 1 |
|---|
| 2721 | controlDict[pfx+'TwinInv'].append(False) |
|---|
| 2722 | controlDict[pfx+'TwinLaw'].append(twin[0]) |
|---|
| 2723 | if it: |
|---|
| 2724 | hapDict[pfx+'TwinFr:'+str(it)] = twin[1] |
|---|
| 2725 | sumTwFr += twin[1] |
|---|
| 2726 | else: |
|---|
| 2727 | hapDict[pfx+'TwinFr:0'] = twin[1][0] |
|---|
| 2728 | controlDict[pfx+'TwinNMN'] = twin[1][1] |
|---|
| 2729 | if Twins[0][1][1]: |
|---|
| 2730 | hapVary.append(pfx+'TwinFr:'+str(it)) |
|---|
| 2731 | controlDict[pfx+'NTL'] = NTL |
|---|
| 2732 | #need to make constraint on TwinFr |
|---|
| 2733 | controlDict[pfx+'TwinLaw'] = np.array(controlDict[pfx+'TwinLaw']) |
|---|
| 2734 | if len(Twins) > 1: #force sum to unity |
|---|
| 2735 | hapDict[pfx+'TwinFr:0'] = 1.-sumTwFr |
|---|
| 2736 | if Print: |
|---|
| 2737 | pFile.write('\n Phase: %s in histogram: %s\n'%(phase,histogram)) |
|---|
| 2738 | pFile.write(135*'='+'\n') |
|---|
| 2739 | pFile.write(' Scale factor : %10.4f Refine? %s\n'%(hapData['Scale'][0],hapData['Scale'][1])) |
|---|
| 2740 | if extType != 'None': |
|---|
| 2741 | pFile.write(' Extinction Type: %15s approx: %10s\n'%(extType,extApprox)) |
|---|
| 2742 | text = ' Parameters :' |
|---|
| 2743 | for eKey in Ekey: |
|---|
| 2744 | text += ' %4s : %10.3e Refine? '%(eKey,extParms[eKey][0])+str(extParms[eKey][1]) |
|---|
| 2745 | pFile.write(text+'\n') |
|---|
| 2746 | if hapData['Babinet']['BabA'][0]: |
|---|
| 2747 | PrintBabinet(hapData['Babinet']) |
|---|
| 2748 | if not SGData['SGInv'] and len(Twins) == 1: |
|---|
| 2749 | pFile.write(' Flack parameter: %10.3f Refine? %s\n'%(hapData['Flack'][0],hapData['Flack'][1])) |
|---|
| 2750 | if len(Twins) > 1: |
|---|
| 2751 | for it,twin in enumerate(Twins): |
|---|
| 2752 | if 'bool' in str(type(twin[0])): |
|---|
| 2753 | pFile.write(' Nonmerohedral twin fr.: %5.3f Inv? %s Refine? %s\n'% |
|---|
| 2754 | (hapDict[pfx+'TwinFr:'+str(it)],str(controlDict[pfx+'TwinInv'][it]),str(Twins[0][1][1]))) |
|---|
| 2755 | else: |
|---|
| 2756 | pFile.write(' Twin law: %s Twin fr.: %5.3f Refine? %s\n'% |
|---|
| 2757 | (str(twin[0]).replace('\n',','),hapDict[pfx+'TwinFr:'+str(it)],str(Twins[0][1][1]))) |
|---|
| 2758 | |
|---|
| 2759 | Histogram['Reflection Lists'] = phase |
|---|
| 2760 | |
|---|
| 2761 | return hapVary,hapDict,controlDict |
|---|
| 2762 | |
|---|
| 2763 | def SetHistogramPhaseData(parmDict,sigDict,Phases,Histograms,calcControls,Print=True,pFile=None): |
|---|
| 2764 | 'needs a doc string' |
|---|
| 2765 | |
|---|
| 2766 | def PrintSizeAndSig(hapData,sizeSig): |
|---|
| 2767 | line = '\n Size model: %9s'%(hapData[0]) |
|---|
| 2768 | refine = False |
|---|
| 2769 | if hapData[0] in ['isotropic','uniaxial']: |
|---|
| 2770 | line += ' equatorial:%12.5f'%(hapData[1][0]) |
|---|
| 2771 | if sizeSig[0][0]: |
|---|
| 2772 | line += ', sig:%8.4f'%(sizeSig[0][0]) |
|---|
| 2773 | refine = True |
|---|
| 2774 | if hapData[0] == 'uniaxial': |
|---|
| 2775 | line += ' axial:%12.4f'%(hapData[1][1]) |
|---|
| 2776 | if sizeSig[0][1]: |
|---|
| 2777 | refine = True |
|---|
| 2778 | line += ', sig:%8.4f'%(sizeSig[0][1]) |
|---|
| 2779 | line += ' LG mix coeff.:%12.4f'%(hapData[1][2]) |
|---|
| 2780 | if sizeSig[0][2]: |
|---|
| 2781 | refine = True |
|---|
| 2782 | line += ', sig:%8.4f'%(sizeSig[0][2]) |
|---|
| 2783 | if refine: |
|---|
| 2784 | pFile.write(line+'\n') |
|---|
| 2785 | else: |
|---|
| 2786 | line += ' LG mix coeff.:%12.4f'%(hapData[1][2]) |
|---|
| 2787 | if sizeSig[0][2]: |
|---|
| 2788 | refine = True |
|---|
| 2789 | line += ', sig:%8.4f'%(sizeSig[0][2]) |
|---|
| 2790 | Snames = ['S11','S22','S33','S12','S13','S23'] |
|---|
| 2791 | ptlbls = ' name :' |
|---|
| 2792 | ptstr = ' value :' |
|---|
| 2793 | sigstr = ' sig :' |
|---|
| 2794 | for i,name in enumerate(Snames): |
|---|
| 2795 | ptlbls += '%12s' % (name) |
|---|
| 2796 | ptstr += '%12.6f' % (hapData[4][i]) |
|---|
| 2797 | if sizeSig[1][i]: |
|---|
| 2798 | refine = True |
|---|
| 2799 | sigstr += '%12.6f' % (sizeSig[1][i]) |
|---|
| 2800 | else: |
|---|
| 2801 | sigstr += 12*' ' |
|---|
| 2802 | if refine: |
|---|
| 2803 | pFile.write(line+'\n') |
|---|
| 2804 | pFile.write(ptlbls+'\n') |
|---|
| 2805 | pFile.write(ptstr+'\n') |
|---|
| 2806 | pFile.write(sigstr+'\n') |
|---|
| 2807 | |
|---|
| 2808 | def PrintMuStrainAndSig(hapData,mustrainSig,SGData): |
|---|
| 2809 | line = '\n Mustrain model: %9s\n'%(hapData[0]) |
|---|
| 2810 | refine = False |
|---|
| 2811 | if hapData[0] in ['isotropic','uniaxial']: |
|---|
| 2812 | line += ' equatorial:%12.1f'%(hapData[1][0]) |
|---|
| 2813 | if mustrainSig[0][0]: |
|---|
| 2814 | line += ', sig:%8.1f'%(mustrainSig[0][0]) |
|---|
| 2815 | refine = True |
|---|
| 2816 | if hapData[0] == 'uniaxial': |
|---|
| 2817 | line += ' axial:%12.1f'%(hapData[1][1]) |
|---|
| 2818 | if mustrainSig[0][1]: |
|---|
| 2819 | line += ', sig:%8.1f'%(mustrainSig[0][1]) |
|---|
| 2820 | line += ' LG mix coeff.:%12.4f'%(hapData[1][2]) |
|---|
| 2821 | if mustrainSig[0][2]: |
|---|
| 2822 | refine = True |
|---|
| 2823 | line += ', sig:%8.3f'%(mustrainSig[0][2]) |
|---|
| 2824 | if refine: |
|---|
| 2825 | pFile.write(line+'\n') |
|---|
| 2826 | else: |
|---|
| 2827 | line += ' LG mix coeff.:%12.4f'%(hapData[1][2]) |
|---|
| 2828 | if mustrainSig[0][2]: |
|---|
| 2829 | refine = True |
|---|
| 2830 | line += ', sig:%8.3f'%(mustrainSig[0][2]) |
|---|
| 2831 | Snames = G2spc.MustrainNames(SGData) |
|---|
| 2832 | ptlbls = ' name :' |
|---|
| 2833 | ptstr = ' value :' |
|---|
| 2834 | sigstr = ' sig :' |
|---|
| 2835 | for i,name in enumerate(Snames): |
|---|
| 2836 | ptlbls += '%12s' % (name) |
|---|
| 2837 | ptstr += '%12.1f' % (hapData[4][i]) |
|---|
| 2838 | if mustrainSig[1][i]: |
|---|
| 2839 | refine = True |
|---|
| 2840 | sigstr += '%12.1f' % (mustrainSig[1][i]) |
|---|
| 2841 | else: |
|---|
| 2842 | sigstr += 12*' ' |
|---|
| 2843 | if refine: |
|---|
| 2844 | pFile.write(line+'\n') |
|---|
| 2845 | pFile.write(ptlbls+'\n') |
|---|
| 2846 | pFile.write(ptstr+'\n') |
|---|
| 2847 | pFile.write(sigstr+'\n') |
|---|
| 2848 | |
|---|
| 2849 | def PrintHStrainAndSig(hapData,strainSig,SGData): |
|---|
| 2850 | Hsnames = G2spc.HStrainNames(SGData) |
|---|
| 2851 | ptlbls = ' name :' |
|---|
| 2852 | ptstr = ' value :' |
|---|
| 2853 | sigstr = ' sig :' |
|---|
| 2854 | refine = False |
|---|
| 2855 | for i,name in enumerate(Hsnames): |
|---|
| 2856 | ptlbls += '%12s' % (name) |
|---|
| 2857 | ptstr += '%12.4g' % (hapData[0][i]) |
|---|
| 2858 | if name in strainSig: |
|---|
| 2859 | refine = True |
|---|
| 2860 | sigstr += '%12.4g' % (strainSig[name]) |
|---|
| 2861 | else: |
|---|
| 2862 | sigstr += 12*' ' |
|---|
| 2863 | if refine: |
|---|
| 2864 | pFile.write('\n Hydrostatic/elastic strain:\n') |
|---|
| 2865 | pFile.write(ptlbls+'\n') |
|---|
| 2866 | pFile.write(ptstr+'\n') |
|---|
| 2867 | pFile.write(sigstr+'\n') |
|---|
| 2868 | |
|---|
| 2869 | def PrintSHPOAndSig(pfx,hapData,POsig): |
|---|
| 2870 | Tindx = 1.0 |
|---|
| 2871 | Tvar = 0.0 |
|---|
| 2872 | pFile.write('\n Spherical harmonics preferred orientation: Order: %d\n'%hapData[4]) |
|---|
| 2873 | ptlbls = ' names :' |
|---|
| 2874 | ptstr = ' values:' |
|---|
| 2875 | sigstr = ' sig :' |
|---|
| 2876 | for item in hapData[5]: |
|---|
| 2877 | ptlbls += '%12s'%(item) |
|---|
| 2878 | ptstr += '%12.3f'%(hapData[5][item]) |
|---|
| 2879 | l = 2.0*eval(item.strip('C'))[0]+1 |
|---|
| 2880 | Tindx += hapData[5][item]**2/l |
|---|
| 2881 | if pfx+item in POsig: |
|---|
| 2882 | Tvar += (2.*hapData[5][item]*POsig[pfx+item]/l)**2 |
|---|
| 2883 | sigstr += '%12.3f'%(POsig[pfx+item]) |
|---|
| 2884 | else: |
|---|
| 2885 | sigstr += 12*' ' |
|---|
| 2886 | pFile.write(ptlbls+'\n') |
|---|
| 2887 | pFile.write(ptstr+'\n') |
|---|
| 2888 | pFile.write(sigstr+'\n') |
|---|
| 2889 | pFile.write('\n Texture index J = %.3f(%d)\n'%(Tindx,int(1000*np.sqrt(Tvar)))) |
|---|
| 2890 | |
|---|
| 2891 | def PrintExtAndSig(pfx,hapData,ScalExtSig): |
|---|
| 2892 | pFile.write('\n Single crystal extinction: Type: %s Approx: %s\n'%(hapData[0],hapData[1])) |
|---|
| 2893 | text = '' |
|---|
| 2894 | for item in hapData[2]: |
|---|
| 2895 | if pfx+item in ScalExtSig: |
|---|
| 2896 | text += ' %s: '%(item) |
|---|
| 2897 | text += '%12.2e'%(hapData[2][item][0]) |
|---|
| 2898 | if pfx+item in ScalExtSig: |
|---|
| 2899 | text += ' sig: %12.2e'%(ScalExtSig[pfx+item]) |
|---|
| 2900 | pFile.write(text+'\n') |
|---|
| 2901 | |
|---|
| 2902 | def PrintBabinetAndSig(pfx,hapData,BabSig): |
|---|
| 2903 | pFile.write('\n Babinet form factor modification:\n') |
|---|
| 2904 | ptlbls = ' names :' |
|---|
| 2905 | ptstr = ' values:' |
|---|
| 2906 | sigstr = ' sig :' |
|---|
| 2907 | for item in hapData: |
|---|
| 2908 | ptlbls += '%12s'%(item) |
|---|
| 2909 | ptstr += '%12.3f'%(hapData[item][0]) |
|---|
| 2910 | if pfx+item in BabSig: |
|---|
| 2911 | sigstr += '%12.3f'%(BabSig[pfx+item]) |
|---|
| 2912 | else: |
|---|
| 2913 | sigstr += 12*' ' |
|---|
| 2914 | pFile.write(ptlbls+'\n') |
|---|
| 2915 | pFile.write(ptstr+'\n') |
|---|
| 2916 | pFile.write(sigstr+'\n') |
|---|
| 2917 | |
|---|
| 2918 | def PrintTwinsAndSig(pfx,twinData,TwinSig): |
|---|
| 2919 | pFile.write('\n Twin Law fractions :\n') |
|---|
| 2920 | ptlbls = ' names :' |
|---|
| 2921 | ptstr = ' values:' |
|---|
| 2922 | sigstr = ' sig :' |
|---|
| 2923 | for it,item in enumerate(twinData): |
|---|
| 2924 | ptlbls += ' twin #%d'%(it) |
|---|
| 2925 | if it: |
|---|
| 2926 | ptstr += '%12.3f'%(item[1]) |
|---|
| 2927 | else: |
|---|
| 2928 | ptstr += '%12.3f'%(item[1][0]) |
|---|
| 2929 | if pfx+'TwinFr:'+str(it) in TwinSig: |
|---|
| 2930 | sigstr += '%12.3f'%(TwinSig[pfx+'TwinFr:'+str(it)]) |
|---|
| 2931 | else: |
|---|
| 2932 | sigstr += 12*' ' |
|---|
| 2933 | pFile.write(ptlbls+'\n') |
|---|
| 2934 | pFile.write(ptstr+'\n') |
|---|
| 2935 | pFile.write(sigstr+'\n') |
|---|
| 2936 | |
|---|
| 2937 | |
|---|
| 2938 | PhFrExtPOSig = {} |
|---|
| 2939 | SizeMuStrSig = {} |
|---|
| 2940 | ScalExtSig = {} |
|---|
| 2941 | BabSig = {} |
|---|
| 2942 | TwinFrSig = {} |
|---|
| 2943 | wtFrSum = {} |
|---|
| 2944 | for phase in Phases: |
|---|
| 2945 | HistoPhase = Phases[phase]['Histograms'] |
|---|
| 2946 | General = Phases[phase]['General'] |
|---|
| 2947 | SGData = General['SGData'] |
|---|
| 2948 | pId = Phases[phase]['pId'] |
|---|
| 2949 | histoList = list(HistoPhase.keys()) |
|---|
| 2950 | histoList.sort() |
|---|
| 2951 | for histogram in histoList: |
|---|
| 2952 | try: |
|---|
| 2953 | Histogram = Histograms[histogram] |
|---|
| 2954 | except KeyError: |
|---|
| 2955 | #skip if histogram not included e.g. in a sequential refinement |
|---|
| 2956 | continue |
|---|
| 2957 | if not Phases[phase]['Histograms'][histogram]['Use']: |
|---|
| 2958 | #skip if phase absent from this histogram |
|---|
| 2959 | continue |
|---|
| 2960 | hapData = HistoPhase[histogram] |
|---|
| 2961 | hId = Histogram['hId'] |
|---|
| 2962 | pfx = str(pId)+':'+str(hId)+':' |
|---|
| 2963 | if hId not in wtFrSum: |
|---|
| 2964 | wtFrSum[hId] = 0. |
|---|
| 2965 | if 'PWDR' in histogram: |
|---|
| 2966 | for item in ['Scale','Extinction']: |
|---|
| 2967 | hapData[item][0] = parmDict[pfx+item] |
|---|
| 2968 | if pfx+item in sigDict and not parmDict[pfx+'LeBail']: |
|---|
| 2969 | PhFrExtPOSig.update({pfx+item:sigDict[pfx+item],}) |
|---|
| 2970 | wtFrSum[hId] += hapData['Scale'][0]*General['Mass'] |
|---|
| 2971 | if hapData['Pref.Ori.'][0] == 'MD': |
|---|
| 2972 | hapData['Pref.Ori.'][1] = parmDict[pfx+'MD'] |
|---|
| 2973 | if pfx+'MD' in sigDict and not parmDict[pfx+'LeBail']: |
|---|
| 2974 | PhFrExtPOSig.update({pfx+'MD':sigDict[pfx+'MD'],}) |
|---|
| 2975 | else: #'SH' spherical harmonics |
|---|
| 2976 | for item in hapData['Pref.Ori.'][5]: |
|---|
| 2977 | hapData['Pref.Ori.'][5][item] = parmDict[pfx+item] |
|---|
| 2978 | if pfx+item in sigDict and not parmDict[pfx+'LeBail']: |
|---|
| 2979 | PhFrExtPOSig.update({pfx+item:sigDict[pfx+item],}) |
|---|
| 2980 | SizeMuStrSig.update({pfx+'Mustrain':[[0,0,0],[0 for i in range(len(hapData['Mustrain'][4]))]], |
|---|
| 2981 | pfx+'Size':[[0,0,0],[0 for i in range(len(hapData['Size'][4]))]], |
|---|
| 2982 | pfx+'HStrain':{}}) |
|---|
| 2983 | for item in ['Mustrain','Size']: |
|---|
| 2984 | hapData[item][1][2] = parmDict[pfx+item+';mx'] |
|---|
| 2985 | # hapData[item][1][2] = min(1.,max(0.,hapData[item][1][2])) |
|---|
| 2986 | if pfx+item+';mx' in sigDict: |
|---|
| 2987 | SizeMuStrSig[pfx+item][0][2] = sigDict[pfx+item+';mx'] |
|---|
| 2988 | if hapData[item][0] in ['isotropic','uniaxial']: |
|---|
| 2989 | hapData[item][1][0] = parmDict[pfx+item+';i'] |
|---|
| 2990 | if item == 'Size': |
|---|
| 2991 | hapData[item][1][0] = min(10.,max(0.001,hapData[item][1][0])) |
|---|
| 2992 | if pfx+item+';i' in sigDict: |
|---|
| 2993 | SizeMuStrSig[pfx+item][0][0] = sigDict[pfx+item+';i'] |
|---|
| 2994 | if hapData[item][0] == 'uniaxial': |
|---|
| 2995 | hapData[item][1][1] = parmDict[pfx+item+';a'] |
|---|
| 2996 | if item == 'Size': |
|---|
| 2997 | hapData[item][1][1] = min(10.,max(0.001,hapData[item][1][1])) |
|---|
| 2998 | if pfx+item+';a' in sigDict: |
|---|
| 2999 | SizeMuStrSig[pfx+item][0][1] = sigDict[pfx+item+';a'] |
|---|
| 3000 | else: #generalized for mustrain or ellipsoidal for size |
|---|
| 3001 | Nterms = len(hapData[item][4]) |
|---|
| 3002 | for i in range(Nterms): |
|---|
| 3003 | sfx = ';'+str(i) |
|---|
| 3004 | hapData[item][4][i] = parmDict[pfx+item+sfx] |
|---|
| 3005 | if pfx+item+sfx in sigDict: |
|---|
| 3006 | SizeMuStrSig[pfx+item][1][i] = sigDict[pfx+item+sfx] |
|---|
| 3007 | names = G2spc.HStrainNames(SGData) |
|---|
| 3008 | for i,name in enumerate(names): |
|---|
| 3009 | hapData['HStrain'][0][i] = parmDict[pfx+name] |
|---|
| 3010 | if pfx+name in sigDict: |
|---|
| 3011 | SizeMuStrSig[pfx+'HStrain'][name] = sigDict[pfx+name] |
|---|
| 3012 | if 'Layer Disp' in hapData: |
|---|
| 3013 | hapData['Layer Disp'][0] = parmDict[pfx+'LayerDisp'] |
|---|
| 3014 | if pfx+'LayerDisp' in sigDict: |
|---|
| 3015 | SizeMuStrSig[pfx+'LayerDisp'] = sigDict[pfx+'LayerDisp'] |
|---|
| 3016 | if Phases[phase]['General']['Type'] != 'magnetic': |
|---|
| 3017 | for name in ['BabA','BabU']: |
|---|
| 3018 | hapData['Babinet'][name][0] = parmDict[pfx+name] |
|---|
| 3019 | if pfx+name in sigDict and not parmDict[pfx+'LeBail']: |
|---|
| 3020 | BabSig[pfx+name] = sigDict[pfx+name] |
|---|
| 3021 | |
|---|
| 3022 | elif 'HKLF' in histogram: |
|---|
| 3023 | for item in ['Scale','Flack']: |
|---|
| 3024 | if parmDict.get(pfx+item): |
|---|
| 3025 | hapData[item][0] = parmDict[pfx+item] |
|---|
| 3026 | if pfx+item in sigDict: |
|---|
| 3027 | ScalExtSig[pfx+item] = sigDict[pfx+item] |
|---|
| 3028 | for item in ['Ep','Eg','Es']: |
|---|
| 3029 | if parmDict.get(pfx+item): |
|---|
| 3030 | hapData['Extinction'][2][item][0] = parmDict[pfx+item] |
|---|
| 3031 | if pfx+item in sigDict: |
|---|
| 3032 | ScalExtSig[pfx+item] = sigDict[pfx+item] |
|---|
| 3033 | for item in ['BabA','BabU']: |
|---|
| 3034 | hapData['Babinet'][item][0] = parmDict[pfx+item] |
|---|
| 3035 | if pfx+item in sigDict: |
|---|
| 3036 | BabSig[pfx+item] = sigDict[pfx+item] |
|---|
| 3037 | if 'Twins' in hapData: |
|---|
| 3038 | it = 1 |
|---|
| 3039 | sumTwFr = 0. |
|---|
| 3040 | while True: |
|---|
| 3041 | try: |
|---|
| 3042 | hapData['Twins'][it][1] = parmDict[pfx+'TwinFr:'+str(it)] |
|---|
| 3043 | if pfx+'TwinFr:'+str(it) in sigDict: |
|---|
| 3044 | TwinFrSig[pfx+'TwinFr:'+str(it)] = sigDict[pfx+'TwinFr:'+str(it)] |
|---|
| 3045 | if it: |
|---|
| 3046 | sumTwFr += hapData['Twins'][it][1] |
|---|
| 3047 | it += 1 |
|---|
| 3048 | except KeyError: |
|---|
| 3049 | break |
|---|
| 3050 | hapData['Twins'][0][1][0] = 1.-sumTwFr |
|---|
| 3051 | |
|---|
| 3052 | if Print: |
|---|
| 3053 | for phase in Phases: |
|---|
| 3054 | HistoPhase = Phases[phase]['Histograms'] |
|---|
| 3055 | General = Phases[phase]['General'] |
|---|
| 3056 | SGData = General['SGData'] |
|---|
| 3057 | pId = Phases[phase]['pId'] |
|---|
| 3058 | histoList = list(HistoPhase.keys()) |
|---|
| 3059 | histoList.sort() |
|---|
| 3060 | for histogram in histoList: |
|---|
| 3061 | try: |
|---|
| 3062 | Histogram = Histograms[histogram] |
|---|
| 3063 | except KeyError: |
|---|
| 3064 | #skip if histogram not included e.g. in a sequential refinement |
|---|
| 3065 | continue |
|---|
| 3066 | hapData = HistoPhase[histogram] |
|---|
| 3067 | hId = Histogram['hId'] |
|---|
| 3068 | Histogram['Residuals'][str(pId)+'::Name'] = phase |
|---|
| 3069 | pfx = str(pId)+':'+str(hId)+':' |
|---|
| 3070 | hfx = ':%s:'%(hId) |
|---|
| 3071 | if pfx+'Nref' not in Histogram['Residuals']: #skip not used phase in histogram |
|---|
| 3072 | continue |
|---|
| 3073 | pFile.write('\n Phase: %s in histogram: %s\n'%(phase,histogram)) |
|---|
| 3074 | pFile.write(135*'='+'\n') |
|---|
| 3075 | Inst = Histogram['Instrument Parameters'][0] |
|---|
| 3076 | if 'PWDR' in histogram: |
|---|
| 3077 | pFile.write(' Final refinement RF, RF^2 = %.2f%%, %.2f%% on %d reflections\n'% |
|---|
| 3078 | (Histogram['Residuals'][pfx+'Rf'],Histogram['Residuals'][pfx+'Rf^2'],Histogram['Residuals'][pfx+'Nref'])) |
|---|
| 3079 | pFile.write(' Durbin-Watson statistic = %.3f\n'%(Histogram['Residuals']['Durbin-Watson'])) |
|---|
| 3080 | pFile.write(' Bragg intensity sum = %.3g\n'%(Histogram['Residuals'][pfx+'sumInt'])) |
|---|
| 3081 | |
|---|
| 3082 | if parmDict[pfx+'LeBail']: |
|---|
| 3083 | pFile.write(' Performed LeBail extraction for phase %s in histogram %s\n'%(phase,histogram)) |
|---|
| 3084 | else: |
|---|
| 3085 | # if calcControls != None: #skipped in seqRefine |
|---|
| 3086 | # if 'X'in Inst['Type'][0]: |
|---|
| 3087 | # PrintFprime(calcControls['FFtables'],hfx,pFile) |
|---|
| 3088 | # elif 'NC' in Inst['Type'][0]: |
|---|
| 3089 | # PrintBlength(calcControls['BLtables'],Inst['Lam'][1],pFile) |
|---|
| 3090 | if pfx+'Scale' in PhFrExtPOSig: |
|---|
| 3091 | wtFr = hapData['Scale'][0]*General['Mass']/wtFrSum[hId] |
|---|
| 3092 | sigwtFr = PhFrExtPOSig[pfx+'Scale']*wtFr/hapData['Scale'][0] |
|---|
| 3093 | pFile.write(' Phase fraction : %10.5f, sig %10.5f Weight fraction : %8.5f, sig %10.5f\n'% |
|---|
| 3094 | (hapData['Scale'][0],PhFrExtPOSig[pfx+'Scale'],wtFr,sigwtFr)) |
|---|
| 3095 | if pfx+'Extinction' in PhFrExtPOSig: |
|---|
| 3096 | pFile.write(' Extinction coeff: %10.4f, sig %10.4f\n'%(hapData['Extinction'][0],PhFrExtPOSig[pfx+'Extinction'])) |
|---|
| 3097 | if hapData['Pref.Ori.'][0] == 'MD': |
|---|
| 3098 | if pfx+'MD' in PhFrExtPOSig: |
|---|
| 3099 | pFile.write(' March-Dollase PO: %10.4f, sig %10.4f\n'%(hapData['Pref.Ori.'][1],PhFrExtPOSig[pfx+'MD'])) |
|---|
| 3100 | else: |
|---|
| 3101 | PrintSHPOAndSig(pfx,hapData['Pref.Ori.'],PhFrExtPOSig) |
|---|
| 3102 | PrintSizeAndSig(hapData['Size'],SizeMuStrSig[pfx+'Size']) |
|---|
| 3103 | PrintMuStrainAndSig(hapData['Mustrain'],SizeMuStrSig[pfx+'Mustrain'],SGData) |
|---|
| 3104 | PrintHStrainAndSig(hapData['HStrain'],SizeMuStrSig[pfx+'HStrain'],SGData) |
|---|
| 3105 | if pfx+'LayerDisp' in SizeMuStrSig: |
|---|
| 3106 | pFile.write(' Layer displacement : %10.3f, sig %10.3f\n'%(hapData['Layer Disp'][0],SizeMuStrSig[pfx+'LayerDisp'])) |
|---|
| 3107 | if Phases[phase]['General']['Type'] != 'magnetic' and not parmDict[pfx+'LeBail']: |
|---|
| 3108 | if len(BabSig): |
|---|
| 3109 | PrintBabinetAndSig(pfx,hapData['Babinet'],BabSig) |
|---|
| 3110 | |
|---|
| 3111 | elif 'HKLF' in histogram: |
|---|
| 3112 | pFile.write(' Final refinement RF, RF^2 = %.2f%%, %.2f%% on %d reflections (%d user rejected, %d sp.gp.extinct)\n'% |
|---|
| 3113 | (Histogram['Residuals'][pfx+'Rf'],Histogram['Residuals'][pfx+'Rf^2'],Histogram['Residuals'][pfx+'Nref'], |
|---|
| 3114 | Histogram['Residuals'][pfx+'Nrej'],Histogram['Residuals'][pfx+'Next'])) |
|---|
| 3115 | if calcControls != None: #skipped in seqRefine |
|---|
| 3116 | if 'X'in Inst['Type'][0]: |
|---|
| 3117 | PrintFprime(calcControls['FFtables'],hfx,pFile) |
|---|
| 3118 | elif 'NC' in Inst['Type'][0]: |
|---|
| 3119 | PrintBlength(calcControls['BLtables'],Inst['Lam'][1],pFile) |
|---|
| 3120 | pFile.write(' HKLF histogram weight factor = %.3f\n'%(Histogram['wtFactor'])) |
|---|
| 3121 | if pfx+'Scale' in ScalExtSig: |
|---|
| 3122 | pFile.write(' Scale factor : %10.4f, sig %10.4f\n'%(hapData['Scale'][0],ScalExtSig[pfx+'Scale'])) |
|---|
| 3123 | if hapData['Extinction'][0] != 'None': |
|---|
| 3124 | PrintExtAndSig(pfx,hapData['Extinction'],ScalExtSig) |
|---|
| 3125 | if len(BabSig): |
|---|
| 3126 | PrintBabinetAndSig(pfx,hapData['Babinet'],BabSig) |
|---|
| 3127 | if pfx+'Flack' in ScalExtSig: |
|---|
| 3128 | pFile.write(' Flack parameter : %10.3f, sig %10.3f\n'%(hapData['Flack'][0],ScalExtSig[pfx+'Flack'])) |
|---|
| 3129 | if len(TwinFrSig): |
|---|
| 3130 | PrintTwinsAndSig(pfx,hapData['Twins'],TwinFrSig) |
|---|
| 3131 | |
|---|
| 3132 | ################################################################################ |
|---|
| 3133 | ##### Histogram data |
|---|
| 3134 | ################################################################################ |
|---|
| 3135 | |
|---|
| 3136 | def GetHistogramData(Histograms,Print=True,pFile=None): |
|---|
| 3137 | 'needs a doc string' |
|---|
| 3138 | |
|---|
| 3139 | def GetBackgroundParms(hId,Background): |
|---|
| 3140 | Back = Background[0] |
|---|
| 3141 | DebyePeaks = Background[1] |
|---|
| 3142 | bakType,bakFlag = Back[:2] |
|---|
| 3143 | backVals = Back[3:] |
|---|
| 3144 | backNames = [':'+str(hId)+':Back;'+str(i) for i in range(len(backVals))] |
|---|
| 3145 | backDict = dict(zip(backNames,backVals)) |
|---|
| 3146 | backVary = [] |
|---|
| 3147 | if bakFlag: |
|---|
| 3148 | backVary = backNames |
|---|
| 3149 | backDict[':'+str(hId)+':nDebye'] = DebyePeaks['nDebye'] |
|---|
| 3150 | backDict[':'+str(hId)+':nPeaks'] = DebyePeaks['nPeaks'] |
|---|
| 3151 | debyeDict = {} |
|---|
| 3152 | debyeList = [] |
|---|
| 3153 | for i in range(DebyePeaks['nDebye']): |
|---|
| 3154 | debyeNames = [':'+str(hId)+':DebyeA;'+str(i),':'+str(hId)+':DebyeR;'+str(i),':'+str(hId)+':DebyeU;'+str(i)] |
|---|
| 3155 | debyeDict.update(dict(zip(debyeNames,DebyePeaks['debyeTerms'][i][::2]))) |
|---|
| 3156 | debyeList += zip(debyeNames,DebyePeaks['debyeTerms'][i][1::2]) |
|---|
| 3157 | debyeVary = [] |
|---|
| 3158 | for item in debyeList: |
|---|
| 3159 | if item[1]: |
|---|
| 3160 | debyeVary.append(item[0]) |
|---|
| 3161 | backDict.update(debyeDict) |
|---|
| 3162 | backVary += debyeVary |
|---|
| 3163 | peakDict = {} |
|---|
| 3164 | peakList = [] |
|---|
| 3165 | for i in range(DebyePeaks['nPeaks']): |
|---|
| 3166 | peakNames = [':'+str(hId)+':BkPkpos;'+str(i),':'+str(hId)+ \ |
|---|
| 3167 | ':BkPkint;'+str(i),':'+str(hId)+':BkPksig;'+str(i),':'+str(hId)+':BkPkgam;'+str(i)] |
|---|
| 3168 | peakDict.update(dict(zip(peakNames,DebyePeaks['peaksList'][i][::2]))) |
|---|
| 3169 | peakList += zip(peakNames,DebyePeaks['peaksList'][i][1::2]) |
|---|
| 3170 | peakVary = [] |
|---|
| 3171 | for item in peakList: |
|---|
| 3172 | if item[1]: |
|---|
| 3173 | peakVary.append(item[0]) |
|---|
| 3174 | backDict.update(peakDict) |
|---|
| 3175 | backVary += peakVary |
|---|
| 3176 | if 'background PWDR' in Background[1]: |
|---|
| 3177 | backDict[':'+str(hId)+':Back File'] = Background[1]['background PWDR'][0] |
|---|
| 3178 | backDict[':'+str(hId)+':BF mult'] = Background[1]['background PWDR'][1] |
|---|
| 3179 | try: |
|---|
| 3180 | if Background[1]['background PWDR'][0] and Background[1]['background PWDR'][2]: |
|---|
| 3181 | backVary.append(':'+str(hId)+':BF mult') |
|---|
| 3182 | except IndexError: # old version without refine flag |
|---|
| 3183 | pass |
|---|
| 3184 | return bakType,backDict,backVary |
|---|
| 3185 | |
|---|
| 3186 | def GetInstParms(hId,Inst): |
|---|
| 3187 | #patch |
|---|
| 3188 | if 'Z' not in Inst: |
|---|
| 3189 | Inst['Z'] = [0.0,0.0,False] |
|---|
| 3190 | dataType = Inst['Type'][0] |
|---|
| 3191 | instDict = {} |
|---|
| 3192 | insVary = [] |
|---|
| 3193 | pfx = ':'+str(hId)+':' |
|---|
| 3194 | insKeys = list(Inst.keys()) |
|---|
| 3195 | insKeys.sort() |
|---|
| 3196 | for item in insKeys: |
|---|
| 3197 | if item in 'Azimuth': |
|---|
| 3198 | continue |
|---|
| 3199 | insName = pfx+item |
|---|
| 3200 | instDict[insName] = Inst[item][1] |
|---|
| 3201 | if len(Inst[item]) > 2 and Inst[item][2]: |
|---|
| 3202 | insVary.append(insName) |
|---|
| 3203 | if 'C' in dataType: |
|---|
| 3204 | instDict[pfx+'SH/L'] = max(instDict[pfx+'SH/L'],0.0005) |
|---|
| 3205 | elif 'T' in dataType: #trap zero alp, bet coeff. |
|---|
| 3206 | if not instDict[pfx+'alpha']: |
|---|
| 3207 | instDict[pfx+'alpha'] = 1.0 |
|---|
| 3208 | if not instDict[pfx+'beta-0'] and not instDict[pfx+'beta-1']: |
|---|
| 3209 | instDict[pfx+'beta-1'] = 1.0 |
|---|
| 3210 | elif 'B' in dataType: #trap zero alp, bet coeff. |
|---|
| 3211 | if not instDict[pfx+'alpha-0'] and not instDict[pfx+'alpha-1']: |
|---|
| 3212 | instDict[pfx+'alpha-1'] = 1.0 |
|---|
| 3213 | if not instDict[pfx+'beta-0'] and not instDict[pfx+'beta-1']: |
|---|
| 3214 | instDict[pfx+'beta-1'] = 1.0 |
|---|
| 3215 | return dataType,instDict,insVary |
|---|
| 3216 | |
|---|
| 3217 | def GetSampleParms(hId,Sample): |
|---|
| 3218 | sampVary = [] |
|---|
| 3219 | hfx = ':'+str(hId)+':' |
|---|
| 3220 | sampDict = {hfx+'Gonio. radius':Sample['Gonio. radius'],hfx+'Omega':Sample['Omega'], |
|---|
| 3221 | hfx+'Chi':Sample['Chi'],hfx+'Phi':Sample['Phi'],hfx+'Azimuth':Sample['Azimuth']} |
|---|
| 3222 | for key in ('Temperature','Pressure','FreePrm1','FreePrm2','FreePrm3'): |
|---|
| 3223 | if key in Sample: |
|---|
| 3224 | sampDict[hfx+key] = Sample[key] |
|---|
| 3225 | Type = Sample['Type'] |
|---|
| 3226 | if 'Bragg' in Type: #Bragg-Brentano |
|---|
| 3227 | for item in ['Scale','Shift','Transparency','SurfRoughA','SurfRoughB']: |
|---|
| 3228 | sampDict[hfx+item] = Sample[item][0] |
|---|
| 3229 | if Sample[item][1]: |
|---|
| 3230 | sampVary.append(hfx+item) |
|---|
| 3231 | elif 'Debye' in Type: #Debye-Scherrer |
|---|
| 3232 | for item in ['Scale','Absorption','DisplaceX','DisplaceY']: |
|---|
| 3233 | sampDict[hfx+item] = Sample[item][0] |
|---|
| 3234 | if Sample[item][1]: |
|---|
| 3235 | sampVary.append(hfx+item) |
|---|
| 3236 | return Type,sampDict,sampVary |
|---|
| 3237 | |
|---|
| 3238 | def PrintBackground(Background): |
|---|
| 3239 | Back = Background[0] |
|---|
| 3240 | DebyePeaks = Background[1] |
|---|
| 3241 | pFile.write('\n Background function: %s Refine? %s\n'%(Back[0],Back[1])) |
|---|
| 3242 | line = ' Coefficients: ' |
|---|
| 3243 | for i,back in enumerate(Back[3:]): |
|---|
| 3244 | line += '%10.3f'%(back) |
|---|
| 3245 | if i and not i%10: |
|---|
| 3246 | line += '\n'+15*' ' |
|---|
| 3247 | pFile.write(line+'\n') |
|---|
| 3248 | if DebyePeaks['nDebye']: |
|---|
| 3249 | pFile.write('\n Debye diffuse scattering coefficients\n') |
|---|
| 3250 | parms = ['DebyeA','DebyeR','DebyeU'] |
|---|
| 3251 | line = ' names : ' |
|---|
| 3252 | for parm in parms: |
|---|
| 3253 | line += '%8s refine?'%(parm) |
|---|
| 3254 | pFile.write(line+'\n') |
|---|
| 3255 | for j,term in enumerate(DebyePeaks['debyeTerms']): |
|---|
| 3256 | line = ' term'+'%2d'%(j)+':' |
|---|
| 3257 | for i in range(3): |
|---|
| 3258 | line += '%10.3f %5s'%(term[2*i],bool(term[2*i+1])) |
|---|
| 3259 | pFile.write(line+'\n') |
|---|
| 3260 | if DebyePeaks['nPeaks']: |
|---|
| 3261 | pFile.write('\n Single peak coefficients\n') |
|---|
| 3262 | parms = ['BkPkpos','BkPkint','BkPksig','BkPkgam'] |
|---|
| 3263 | line = ' names : ' |
|---|
| 3264 | for parm in parms: |
|---|
| 3265 | line += '%8s refine?'%(parm) |
|---|
| 3266 | pFile.write(line+'\n') |
|---|
| 3267 | for j,term in enumerate(DebyePeaks['peaksList']): |
|---|
| 3268 | line = ' peak'+'%2d'%(j)+':' |
|---|
| 3269 | for i in range(4): |
|---|
| 3270 | line += '%12.3f %5s'%(term[2*i],bool(term[2*i+1])) |
|---|
| 3271 | pFile.write(line+'\n') |
|---|
| 3272 | if 'background PWDR' in DebyePeaks: |
|---|
| 3273 | try: |
|---|
| 3274 | pFile.write(' Fixed background file: %s; mult: %.3f Refine? %s\n'%(DebyePeaks['background PWDR'][0], |
|---|
| 3275 | DebyePeaks['background PWDR'][1],DebyePeaks['background PWDR'][2])) |
|---|
| 3276 | except IndexError: #old version without refine flag |
|---|
| 3277 | pass |
|---|
| 3278 | |
|---|
| 3279 | def PrintInstParms(Inst): |
|---|
| 3280 | pFile.write('\n Instrument Parameters:\n') |
|---|
| 3281 | insKeys = list(Inst.keys()) |
|---|
| 3282 | insKeys.sort() |
|---|
| 3283 | iBeg = 0 |
|---|
| 3284 | Ok = True |
|---|
| 3285 | while Ok: |
|---|
| 3286 | ptlbls = ' name :' |
|---|
| 3287 | ptstr = ' value :' |
|---|
| 3288 | varstr = ' refine:' |
|---|
| 3289 | iFin = min(iBeg+9,len(insKeys)) |
|---|
| 3290 | for item in insKeys[iBeg:iFin]: |
|---|
| 3291 | if item not in ['Type','Source']: |
|---|
| 3292 | ptlbls += '%12s' % (item) |
|---|
| 3293 | ptstr += '%12.6f' % (Inst[item][1]) |
|---|
| 3294 | if item in ['Lam1','Lam2','Azimuth','fltPath','2-theta',]: |
|---|
| 3295 | varstr += 12*' ' |
|---|
| 3296 | else: |
|---|
| 3297 | varstr += '%12s' % (str(bool(Inst[item][2]))) |
|---|
| 3298 | pFile.write(ptlbls+'\n') |
|---|
| 3299 | pFile.write(ptstr+'\n') |
|---|
| 3300 | pFile.write(varstr+'\n') |
|---|
| 3301 | iBeg = iFin |
|---|
| 3302 | if iBeg == len(insKeys): |
|---|
| 3303 | Ok = False |
|---|
| 3304 | else: |
|---|
| 3305 | pFile.write('\n') |
|---|
| 3306 | |
|---|
| 3307 | def PrintSampleParms(Sample): |
|---|
| 3308 | pFile.write('\n Sample Parameters:\n') |
|---|
| 3309 | pFile.write(' Goniometer omega = %.2f, chi = %.2f, phi = %.2f\n'% |
|---|
| 3310 | (Sample['Omega'],Sample['Chi'],Sample['Phi'])) |
|---|
| 3311 | ptlbls = ' name :' |
|---|
| 3312 | ptstr = ' value :' |
|---|
| 3313 | varstr = ' refine:' |
|---|
| 3314 | if 'Bragg' in Sample['Type']: |
|---|
| 3315 | for item in ['Scale','Shift','Transparency','SurfRoughA','SurfRoughB']: |
|---|
| 3316 | ptlbls += '%14s'%(item) |
|---|
| 3317 | ptstr += '%14.4f'%(Sample[item][0]) |
|---|
| 3318 | varstr += '%14s'%(str(bool(Sample[item][1]))) |
|---|
| 3319 | |
|---|
| 3320 | elif 'Debye' in Type: #Debye-Scherrer |
|---|
| 3321 | for item in ['Scale','Absorption','DisplaceX','DisplaceY']: |
|---|
| 3322 | ptlbls += '%14s'%(item) |
|---|
| 3323 | ptstr += '%14.4f'%(Sample[item][0]) |
|---|
| 3324 | varstr += '%14s'%(str(bool(Sample[item][1]))) |
|---|
| 3325 | |
|---|
| 3326 | pFile.write(ptlbls+'\n') |
|---|
| 3327 | pFile.write(ptstr+'\n') |
|---|
| 3328 | pFile.write(varstr+'\n') |
|---|
| 3329 | |
|---|
| 3330 | histDict = {} |
|---|
| 3331 | histVary = [] |
|---|
| 3332 | controlDict = {} |
|---|
| 3333 | histoList = list(Histograms.keys()) |
|---|
| 3334 | histoList.sort() |
|---|
| 3335 | for histogram in histoList: |
|---|
| 3336 | if 'PWDR' in histogram: |
|---|
| 3337 | Histogram = Histograms[histogram] |
|---|
| 3338 | hId = Histogram['hId'] |
|---|
| 3339 | pfx = ':'+str(hId)+':' |
|---|
| 3340 | controlDict[pfx+'wtFactor'] = Histogram['wtFactor'] |
|---|
| 3341 | controlDict[pfx+'Limits'] = Histogram['Limits'][1] |
|---|
| 3342 | controlDict[pfx+'Exclude'] = Histogram['Limits'][2:] |
|---|
| 3343 | for excl in controlDict[pfx+'Exclude']: |
|---|
| 3344 | Histogram['Data'][0] = ma.masked_inside(Histogram['Data'][0],excl[0],excl[1]) |
|---|
| 3345 | if controlDict[pfx+'Exclude']: |
|---|
| 3346 | ma.mask_rows(Histogram['Data']) |
|---|
| 3347 | Background = Histogram['Background'] |
|---|
| 3348 | Type,bakDict,bakVary = GetBackgroundParms(hId,Background) |
|---|
| 3349 | controlDict[pfx+'bakType'] = Type |
|---|
| 3350 | histDict.update(bakDict) |
|---|
| 3351 | histVary += bakVary |
|---|
| 3352 | |
|---|
| 3353 | Inst = Histogram['Instrument Parameters'] #TODO ? ignores tabulated alp,bet & delt for TOF |
|---|
| 3354 | if 'T' in Type and len(Inst[1]): #patch - back-to-back exponential contribution to TOF line shape is removed |
|---|
| 3355 | G2fil.G2Print ('Warning: tabulated profile coefficients are ignored') |
|---|
| 3356 | Type,instDict,insVary = GetInstParms(hId,Inst[0]) |
|---|
| 3357 | controlDict[pfx+'histType'] = Type |
|---|
| 3358 | if 'XC' in Type or 'XB' in Type: |
|---|
| 3359 | if pfx+'Lam1' in instDict: |
|---|
| 3360 | controlDict[pfx+'keV'] = 12.397639/instDict[pfx+'Lam1'] |
|---|
| 3361 | else: |
|---|
| 3362 | controlDict[pfx+'keV'] = 12.397639/instDict[pfx+'Lam'] |
|---|
| 3363 | histDict.update(instDict) |
|---|
| 3364 | histVary += insVary |
|---|
| 3365 | |
|---|
| 3366 | Sample = Histogram['Sample Parameters'] |
|---|
| 3367 | Type,sampDict,sampVary = GetSampleParms(hId,Sample) |
|---|
| 3368 | controlDict[pfx+'instType'] = Type |
|---|
| 3369 | histDict.update(sampDict) |
|---|
| 3370 | histVary += sampVary |
|---|
| 3371 | |
|---|
| 3372 | |
|---|
| 3373 | if Print: |
|---|
| 3374 | pFile.write('\n Histogram: %s histogram Id: %d\n'%(histogram,hId)) |
|---|
| 3375 | pFile.write(135*'='+'\n') |
|---|
| 3376 | Units = {'C':' deg','T':' msec','B':' deg'} |
|---|
| 3377 | units = Units[controlDict[pfx+'histType'][2]] |
|---|
| 3378 | Limits = controlDict[pfx+'Limits'] |
|---|
| 3379 | pFile.write(' Instrument type: %s\n'%Sample['Type']) |
|---|
| 3380 | pFile.write(' Histogram limits: %8.2f%s to %8.2f%s\n'%(Limits[0],units,Limits[1],units)) |
|---|
| 3381 | if len(controlDict[pfx+'Exclude']): |
|---|
| 3382 | excls = controlDict[pfx+'Exclude'] |
|---|
| 3383 | for excl in excls: |
|---|
| 3384 | pFile.write(' Excluded region: %8.2f%s to %8.2f%s\n'%(excl[0],units,excl[1],units)) |
|---|
| 3385 | PrintSampleParms(Sample) |
|---|
| 3386 | PrintInstParms(Inst[0]) |
|---|
| 3387 | PrintBackground(Background) |
|---|
| 3388 | elif 'HKLF' in histogram: |
|---|
| 3389 | Histogram = Histograms[histogram] |
|---|
| 3390 | hId = Histogram['hId'] |
|---|
| 3391 | pfx = ':'+str(hId)+':' |
|---|
| 3392 | controlDict[pfx+'wtFactor'] = Histogram['wtFactor'] |
|---|
| 3393 | Inst = Histogram['Instrument Parameters'][0] |
|---|
| 3394 | controlDict[pfx+'histType'] = Inst['Type'][0] |
|---|
| 3395 | if 'X' in Inst['Type'][0]: |
|---|
| 3396 | histDict[pfx+'Lam'] = Inst['Lam'][1] |
|---|
| 3397 | controlDict[pfx+'keV'] = 12.397639/histDict[pfx+'Lam'] |
|---|
| 3398 | elif 'NC' in Inst['Type'][0] or 'NB' in Inst['Type'][0]: |
|---|
| 3399 | histDict[pfx+'Lam'] = Inst['Lam'][1] |
|---|
| 3400 | return histVary,histDict,controlDict |
|---|
| 3401 | |
|---|
| 3402 | def SetHistogramData(parmDict,sigDict,Histograms,calcControls,Print=True,pFile=None,seq=False): |
|---|
| 3403 | 'Shows histogram data after a refinement' |
|---|
| 3404 | |
|---|
| 3405 | def SetBackgroundParms(pfx,Background,parmDict,sigDict): |
|---|
| 3406 | Back = Background[0] |
|---|
| 3407 | DebyePeaks = Background[1] |
|---|
| 3408 | lenBack = len(Back[3:]) |
|---|
| 3409 | backSig = [0 for i in range(lenBack+3*DebyePeaks['nDebye']+4*DebyePeaks['nPeaks'])] |
|---|
| 3410 | for i in range(lenBack): |
|---|
| 3411 | Back[3+i] = parmDict[pfx+'Back;'+str(i)] |
|---|
| 3412 | if pfx+'Back;'+str(i) in sigDict: |
|---|
| 3413 | backSig[i] = sigDict[pfx+'Back;'+str(i)] |
|---|
| 3414 | if DebyePeaks['nDebye']: |
|---|
| 3415 | for i in range(DebyePeaks['nDebye']): |
|---|
| 3416 | names = [pfx+'DebyeA;'+str(i),pfx+'DebyeR;'+str(i),pfx+'DebyeU;'+str(i)] |
|---|
| 3417 | for j,name in enumerate(names): |
|---|
| 3418 | DebyePeaks['debyeTerms'][i][2*j] = parmDict[name] |
|---|
| 3419 | if name in sigDict: |
|---|
| 3420 | backSig[lenBack+3*i+j] = sigDict[name] |
|---|
| 3421 | if DebyePeaks['nPeaks']: |
|---|
| 3422 | for i in range(DebyePeaks['nPeaks']): |
|---|
| 3423 | names = [pfx+'BkPkpos;'+str(i),pfx+'BkPkint;'+str(i), |
|---|
| 3424 | pfx+'BkPksig;'+str(i),pfx+'BkPkgam;'+str(i)] |
|---|
| 3425 | for j,name in enumerate(names): |
|---|
| 3426 | DebyePeaks['peaksList'][i][2*j] = parmDict[name] |
|---|
| 3427 | if name in sigDict: |
|---|
| 3428 | backSig[lenBack+3*DebyePeaks['nDebye']+4*i+j] = sigDict[name] |
|---|
| 3429 | if pfx+'BF mult' in sigDict: |
|---|
| 3430 | DebyePeaks['background PWDR'][1] = parmDict[pfx+'BF mult'] |
|---|
| 3431 | backSig.append(sigDict[pfx+'BF mult']) |
|---|
| 3432 | |
|---|
| 3433 | return backSig |
|---|
| 3434 | |
|---|
| 3435 | def SetInstParms(pfx,Inst,parmDict,sigDict): |
|---|
| 3436 | instSig = {} |
|---|
| 3437 | insKeys = list(Inst.keys()) |
|---|
| 3438 | insKeys.sort() |
|---|
| 3439 | for item in insKeys: |
|---|
| 3440 | insName = pfx+item |
|---|
| 3441 | Inst[item][1] = parmDict[insName] |
|---|
| 3442 | if insName in sigDict: |
|---|
| 3443 | instSig[item] = sigDict[insName] |
|---|
| 3444 | else: |
|---|
| 3445 | instSig[item] = 0 |
|---|
| 3446 | return instSig |
|---|
| 3447 | |
|---|
| 3448 | def SetSampleParms(pfx,Sample,parmDict,sigDict): |
|---|
| 3449 | if 'Bragg' in Sample['Type']: #Bragg-Brentano |
|---|
| 3450 | sampSig = [0 for i in range(5)] |
|---|
| 3451 | for i,item in enumerate(['Scale','Shift','Transparency','SurfRoughA','SurfRoughB']): |
|---|
| 3452 | Sample[item][0] = parmDict[pfx+item] |
|---|
| 3453 | if pfx+item in sigDict: |
|---|
| 3454 | sampSig[i] = sigDict[pfx+item] |
|---|
| 3455 | elif 'Debye' in Sample['Type']: #Debye-Scherrer |
|---|
| 3456 | sampSig = [0 for i in range(4)] |
|---|
| 3457 | for i,item in enumerate(['Scale','Absorption','DisplaceX','DisplaceY']): |
|---|
| 3458 | Sample[item][0] = parmDict[pfx+item] |
|---|
| 3459 | if pfx+item in sigDict: |
|---|
| 3460 | sampSig[i] = sigDict[pfx+item] |
|---|
| 3461 | return sampSig |
|---|
| 3462 | |
|---|
| 3463 | def PrintBackgroundSig(Background,backSig): |
|---|
| 3464 | Back = Background[0] |
|---|
| 3465 | DebyePeaks = Background[1] |
|---|
| 3466 | valstr = ' value : ' |
|---|
| 3467 | sigstr = ' sig : ' |
|---|
| 3468 | refine = False |
|---|
| 3469 | for i,back in enumerate(Back[3:]): |
|---|
| 3470 | valstr += '%10.4g'%(back) |
|---|
| 3471 | if Back[1]: |
|---|
| 3472 | refine = True |
|---|
| 3473 | sigstr += '%10.4g'%(backSig[i]) |
|---|
| 3474 | else: |
|---|
| 3475 | sigstr += 10*' ' |
|---|
| 3476 | if refine: |
|---|
| 3477 | pFile.write('\n Background function: %s\n'%Back[0]) |
|---|
| 3478 | pFile.write(valstr+'\n') |
|---|
| 3479 | pFile.write(sigstr+'\n') |
|---|
| 3480 | if DebyePeaks['nDebye']: |
|---|
| 3481 | ifAny = False |
|---|
| 3482 | ptfmt = "%12.3f" |
|---|
| 3483 | names = ' names :' |
|---|
| 3484 | ptstr = ' values:' |
|---|
| 3485 | sigstr = ' esds :' |
|---|
| 3486 | for item in sigDict: |
|---|
| 3487 | if 'Debye' in item: |
|---|
| 3488 | ifAny = True |
|---|
| 3489 | names += '%12s'%(item) |
|---|
| 3490 | ptstr += ptfmt%(parmDict[item]) |
|---|
| 3491 | sigstr += ptfmt%(sigDict[item]) |
|---|
| 3492 | if ifAny: |
|---|
| 3493 | pFile.write('\n Debye diffuse scattering coefficients\n') |
|---|
| 3494 | pFile.write(names+'\n') |
|---|
| 3495 | pFile.write(ptstr+'\n') |
|---|
| 3496 | pFile.write(sigstr+'\n') |
|---|
| 3497 | if DebyePeaks['nPeaks']: |
|---|
| 3498 | pFile.write('\n Single peak coefficients:\n') |
|---|
| 3499 | parms = ['BkPkpos','BkPkint','BkPksig','BkPkgam'] |
|---|
| 3500 | line = ' peak no. ' |
|---|
| 3501 | for parm in parms: |
|---|
| 3502 | line += '%14s%12s'%(parm.center(14),'esd'.center(12)) |
|---|
| 3503 | pFile.write(line+'\n') |
|---|
| 3504 | for ip in range(DebyePeaks['nPeaks']): |
|---|
| 3505 | ptstr = ' %4d '%(ip) |
|---|
| 3506 | for parm in parms: |
|---|
| 3507 | fmt = '%14.3f' |
|---|
| 3508 | efmt = '%12.3f' |
|---|
| 3509 | if parm == 'BkPkpos': |
|---|
| 3510 | fmt = '%14.4f' |
|---|
| 3511 | efmt = '%12.4f' |
|---|
| 3512 | name = pfx+parm+';%d'%(ip) |
|---|
| 3513 | ptstr += fmt%(parmDict[name]) |
|---|
| 3514 | if name in sigDict: |
|---|
| 3515 | ptstr += efmt%(sigDict[name]) |
|---|
| 3516 | else: |
|---|
| 3517 | ptstr += 12*' ' |
|---|
| 3518 | pFile.write(ptstr+'\n') |
|---|
| 3519 | if 'background PWDR' in DebyePeaks and DebyePeaks['background PWDR'][2]: |
|---|
| 3520 | pFile.write(' Fixed background scale: %.3f(%d)\n'%(DebyePeaks['background PWDR'][1],int(1000*backSig[-1]))) |
|---|
| 3521 | sumBk = np.array(Histogram['sumBk']) |
|---|
| 3522 | pFile.write(' Background sums: empirical %.3g, Debye %.3g, peaks %.3g, Total %.3g\n'% |
|---|
| 3523 | (sumBk[0],sumBk[1],sumBk[2],np.sum(sumBk))) |
|---|
| 3524 | |
|---|
| 3525 | def PrintInstParmsSig(Inst,instSig): |
|---|
| 3526 | refine = False |
|---|
| 3527 | insKeys = list(instSig.keys()) |
|---|
| 3528 | insKeys.sort() |
|---|
| 3529 | iBeg = 0 |
|---|
| 3530 | Ok = True |
|---|
| 3531 | while Ok: |
|---|
| 3532 | ptlbls = ' names :' |
|---|
| 3533 | ptstr = ' value :' |
|---|
| 3534 | sigstr = ' sig :' |
|---|
| 3535 | iFin = min(iBeg+9,len(insKeys)) |
|---|
| 3536 | for name in insKeys[iBeg:iFin]: |
|---|
| 3537 | if name not in ['Type','Lam1','Lam2','Azimuth','Source','fltPath']: |
|---|
| 3538 | ptlbls += '%12s' % (name) |
|---|
| 3539 | ptstr += '%12.6f' % (Inst[name][1]) |
|---|
| 3540 | if instSig[name]: |
|---|
| 3541 | refine = True |
|---|
| 3542 | sigstr += '%12.6f' % (instSig[name]) |
|---|
| 3543 | else: |
|---|
| 3544 | sigstr += 12*' ' |
|---|
| 3545 | if refine: |
|---|
| 3546 | pFile.write('\n Instrument Parameters:\n') |
|---|
| 3547 | pFile.write(ptlbls+'\n') |
|---|
| 3548 | pFile.write(ptstr+'\n') |
|---|
| 3549 | pFile.write(sigstr+'\n') |
|---|
| 3550 | iBeg = iFin |
|---|
| 3551 | if iBeg == len(insKeys): |
|---|
| 3552 | Ok = False |
|---|
| 3553 | |
|---|
| 3554 | def PrintSampleParmsSig(Sample,sampleSig): |
|---|
| 3555 | ptlbls = ' names :' |
|---|
| 3556 | ptstr = ' values:' |
|---|
| 3557 | sigstr = ' sig :' |
|---|
| 3558 | refine = False |
|---|
| 3559 | if 'Bragg' in Sample['Type']: |
|---|
| 3560 | for i,item in enumerate(['Scale','Shift','Transparency','SurfRoughA','SurfRoughB']): |
|---|
| 3561 | ptlbls += '%14s'%(item) |
|---|
| 3562 | ptstr += '%14.4f'%(Sample[item][0]) |
|---|
| 3563 | if sampleSig[i]: |
|---|
| 3564 | refine = True |
|---|
| 3565 | sigstr += '%14.4f'%(sampleSig[i]) |
|---|
| 3566 | else: |
|---|
| 3567 | sigstr += 14*' ' |
|---|
| 3568 | |
|---|
| 3569 | elif 'Debye' in Sample['Type']: #Debye-Scherrer |
|---|
| 3570 | for i,item in enumerate(['Scale','Absorption','DisplaceX','DisplaceY']): |
|---|
| 3571 | ptlbls += '%14s'%(item) |
|---|
| 3572 | ptstr += '%14.4f'%(Sample[item][0]) |
|---|
| 3573 | if sampleSig[i]: |
|---|
| 3574 | refine = True |
|---|
| 3575 | sigstr += '%14.4f'%(sampleSig[i]) |
|---|
| 3576 | else: |
|---|
| 3577 | sigstr += 14*' ' |
|---|
| 3578 | |
|---|
| 3579 | if refine: |
|---|
| 3580 | pFile.write('\n Sample Parameters:\n') |
|---|
| 3581 | pFile.write(ptlbls+'\n') |
|---|
| 3582 | pFile.write(ptstr+'\n') |
|---|
| 3583 | pFile.write(sigstr+'\n') |
|---|
| 3584 | |
|---|
| 3585 | histoList = list(Histograms.keys()) |
|---|
| 3586 | histoList.sort() |
|---|
| 3587 | for histogram in histoList: |
|---|
| 3588 | if 'PWDR' in histogram: |
|---|
| 3589 | Histogram = Histograms[histogram] |
|---|
| 3590 | hId = Histogram['hId'] |
|---|
| 3591 | pfx = ':'+str(hId)+':' |
|---|
| 3592 | Background = Histogram['Background'] |
|---|
| 3593 | backSig = SetBackgroundParms(pfx,Background,parmDict,sigDict) |
|---|
| 3594 | |
|---|
| 3595 | Inst = Histogram['Instrument Parameters'][0] |
|---|
| 3596 | instSig = SetInstParms(pfx,Inst,parmDict,sigDict) |
|---|
| 3597 | |
|---|
| 3598 | Sample = Histogram['Sample Parameters'] |
|---|
| 3599 | sampSig = SetSampleParms(pfx,Sample,parmDict,sigDict) |
|---|
| 3600 | |
|---|
| 3601 | if not seq: |
|---|
| 3602 | pFile.write('\n Histogram: %s histogram Id: %d\n'%(histogram,hId)) |
|---|
| 3603 | pFile.write(135*'='+'\n') |
|---|
| 3604 | pFile.write(' PWDR histogram weight factor = '+'%.3f\n'%(Histogram['wtFactor'])) |
|---|
| 3605 | pFile.write(' Final refinement wR = %.2f%% on %d observations in this histogram\n'% |
|---|
| 3606 | (Histogram['Residuals']['wR'],Histogram['Residuals']['Nobs'])) |
|---|
| 3607 | pFile.write(' Other residuals: R = %.2f%%, R-bkg = %.2f%%, wR-bkg = %.2f%% wRmin = %.2f%%\n'% |
|---|
| 3608 | (Histogram['Residuals']['R'],Histogram['Residuals']['Rb'],Histogram['Residuals']['wR'],Histogram['Residuals']['wRmin'])) |
|---|
| 3609 | if Print: |
|---|
| 3610 | pFile.write(' Instrument type: %s\n'%Sample['Type']) |
|---|
| 3611 | if calcControls != None: #skipped in seqRefine |
|---|
| 3612 | if 'X' in Inst['Type'][0]: |
|---|
| 3613 | PrintFprime(calcControls['FFtables'],pfx,pFile) |
|---|
| 3614 | elif 'NC' in Inst['Type'][0]: |
|---|
| 3615 | PrintBlength(calcControls['BLtables'],Inst['Lam'][1],pFile) |
|---|
| 3616 | PrintSampleParmsSig(Sample,sampSig) |
|---|
| 3617 | PrintInstParmsSig(Inst,instSig) |
|---|
| 3618 | PrintBackgroundSig(Background,backSig) |
|---|
| 3619 | |
|---|
| 3620 | def WriteRBObjPOAndSig(pfx,rbfx,rbsx,parmDict,sigDict): |
|---|
| 3621 | '''Cribbed version of PrintRBObjPOAndSig but returns lists of strings. |
|---|
| 3622 | Moved so it can be used in ExportCIF |
|---|
| 3623 | ''' |
|---|
| 3624 | namstr = ' names :' |
|---|
| 3625 | valstr = ' values:' |
|---|
| 3626 | sigstr = ' esds :' |
|---|
| 3627 | for i,px in enumerate(['Px:','Py:','Pz:']): |
|---|
| 3628 | name = pfx+rbfx+px+rbsx |
|---|
| 3629 | namstr += '%12s'%('Pos '+px[1]) |
|---|
| 3630 | valstr += '%12.5f'%(parmDict[name]) |
|---|
| 3631 | if name in sigDict: |
|---|
| 3632 | sigstr += '%12.5f'%(sigDict[name]) |
|---|
| 3633 | else: |
|---|
| 3634 | sigstr += 12*' ' |
|---|
| 3635 | for i,po in enumerate(['Oa:','Oi:','Oj:','Ok:']): |
|---|
| 3636 | name = pfx+rbfx+po+rbsx |
|---|
| 3637 | namstr += '%12s'%('Ori '+po[1]) |
|---|
| 3638 | valstr += '%12.5f'%(parmDict[name]) |
|---|
| 3639 | if name in sigDict: |
|---|
| 3640 | sigstr += '%12.5f'%(sigDict[name]) |
|---|
| 3641 | else: |
|---|
| 3642 | sigstr += 12*' ' |
|---|
| 3643 | return (namstr,valstr,sigstr) |
|---|
| 3644 | |
|---|
| 3645 | def WriteRBObjTLSAndSig(pfx,rbfx,rbsx,TLS,parmDict,sigDict): |
|---|
| 3646 | '''Cribbed version of PrintRBObjTLSAndSig but returns lists of strings. |
|---|
| 3647 | Moved so it can be used in ExportCIF |
|---|
| 3648 | ''' |
|---|
| 3649 | out = [] |
|---|
| 3650 | namstr = ' names :' |
|---|
| 3651 | valstr = ' values:' |
|---|
| 3652 | sigstr = ' esds :' |
|---|
| 3653 | if 'N' not in TLS: |
|---|
| 3654 | out.append(' Thermal motion:\n') |
|---|
| 3655 | if 'T' in TLS: |
|---|
| 3656 | for i,pt in enumerate(['T11:','T22:','T33:','T12:','T13:','T23:']): |
|---|
| 3657 | name = pfx+rbfx+pt+rbsx |
|---|
| 3658 | namstr += '%12s'%(pt[:3]) |
|---|
| 3659 | valstr += '%12.5f'%(parmDict[name]) |
|---|
| 3660 | if name in sigDict: |
|---|
| 3661 | sigstr += '%12.5f'%(sigDict[name]) |
|---|
| 3662 | else: |
|---|
| 3663 | sigstr += 12*' ' |
|---|
| 3664 | out.append(namstr+'\n') |
|---|
| 3665 | out.append(valstr+'\n') |
|---|
| 3666 | out.append(sigstr+'\n') |
|---|
| 3667 | if 'L' in TLS: |
|---|
| 3668 | namstr = ' names :' |
|---|
| 3669 | valstr = ' values:' |
|---|
| 3670 | sigstr = ' esds :' |
|---|
| 3671 | for i,pt in enumerate(['L11:','L22:','L33:','L12:','L13:','L23:']): |
|---|
| 3672 | name = pfx+rbfx+pt+rbsx |
|---|
| 3673 | namstr += '%12s'%(pt[:3]) |
|---|
| 3674 | valstr += '%12.3f'%(parmDict[name]) |
|---|
| 3675 | if name in sigDict: |
|---|
| 3676 | sigstr += '%12.3f'%(sigDict[name]) |
|---|
| 3677 | else: |
|---|
| 3678 | sigstr += 12*' ' |
|---|
| 3679 | out.append(namstr+'\n') |
|---|
| 3680 | out.append(valstr+'\n') |
|---|
| 3681 | out.append(sigstr+'\n') |
|---|
| 3682 | if 'S' in TLS: |
|---|
| 3683 | namstr = ' names :' |
|---|
| 3684 | valstr = ' values:' |
|---|
| 3685 | sigstr = ' esds :' |
|---|
| 3686 | for i,pt in enumerate(['S12:','S13:','S21:','S23:','S31:','S32:','SAA:','SBB:']): |
|---|
| 3687 | name = pfx+rbfx+pt+rbsx |
|---|
| 3688 | namstr += '%12s'%(pt[:3]) |
|---|
| 3689 | valstr += '%12.4f'%(parmDict[name]) |
|---|
| 3690 | if name in sigDict: |
|---|
| 3691 | sigstr += '%12.4f'%(sigDict[name]) |
|---|
| 3692 | else: |
|---|
| 3693 | sigstr += 12*' ' |
|---|
| 3694 | out.append(namstr+'\n') |
|---|
| 3695 | out.append(valstr+'\n') |
|---|
| 3696 | out.append(sigstr+'\n') |
|---|
| 3697 | if 'U' in TLS: |
|---|
| 3698 | name = pfx+rbfx+'U:'+rbsx |
|---|
| 3699 | namstr = ' names :'+'%12s'%('Uiso') |
|---|
| 3700 | valstr = ' values:'+'%12.5f'%(parmDict[name]) |
|---|
| 3701 | if name in sigDict: |
|---|
| 3702 | sigstr = ' esds :'+'%12.5f'%(sigDict[name]) |
|---|
| 3703 | else: |
|---|
| 3704 | sigstr = ' esds :'+12*' ' |
|---|
| 3705 | out.append(namstr+'\n') |
|---|
| 3706 | out.append(valstr+'\n') |
|---|
| 3707 | out.append(sigstr+'\n') |
|---|
| 3708 | return out |
|---|
| 3709 | |
|---|
| 3710 | def WriteRBObjTorAndSig(pfx,rbsx,parmDict,sigDict,nTors): |
|---|
| 3711 | '''Cribbed version of PrintRBObjTorAndSig but returns lists of strings. |
|---|
| 3712 | Moved so it can be used in ExportCIF |
|---|
| 3713 | ''' |
|---|
| 3714 | out = [] |
|---|
| 3715 | namstr = ' names :' |
|---|
| 3716 | valstr = ' values:' |
|---|
| 3717 | sigstr = ' esds :' |
|---|
| 3718 | out.append(' Torsions:\n') |
|---|
| 3719 | for it in range(nTors): |
|---|
| 3720 | name = pfx+'RBRTr;'+str(it)+':'+rbsx |
|---|
| 3721 | namstr += '%12s'%('Tor'+str(it)) |
|---|
| 3722 | valstr += '%12.4f'%(parmDict[name]) |
|---|
| 3723 | if name in sigDict: |
|---|
| 3724 | sigstr += '%12.4f'%(sigDict[name]) |
|---|
| 3725 | out.append(namstr+'\n') |
|---|
| 3726 | out.append(valstr+'\n') |
|---|
| 3727 | out.append(sigstr+'\n') |
|---|
| 3728 | return out |
|---|
| 3729 | |
|---|
| 3730 | def WriteResRBModel(RBModel): |
|---|
| 3731 | '''Write description of a residue rigid body. Code shifted from |
|---|
| 3732 | PrintResRBModel to make usable from G2export_CIF |
|---|
| 3733 | ''' |
|---|
| 3734 | out = [] |
|---|
| 3735 | atNames = RBModel['atNames'] |
|---|
| 3736 | rbRef = RBModel['rbRef'] |
|---|
| 3737 | rbSeq = RBModel['rbSeq'] |
|---|
| 3738 | out.append(' At name x y z\n') |
|---|
| 3739 | for name,xyz in zip(atNames,RBModel['rbXYZ']): |
|---|
| 3740 | out.append(' %8s %10.4f %10.4f %10.4f\n'%(name,xyz[0],xyz[1],xyz[2])) |
|---|
| 3741 | out.append(' Orientation defined by: %s -> %s & %s -> %s\n'% |
|---|
| 3742 | (atNames[rbRef[0]],atNames[rbRef[1]],atNames[rbRef[0]],atNames[rbRef[2]])) |
|---|
| 3743 | if rbSeq: |
|---|
| 3744 | for i,rbseq in enumerate(rbSeq): |
|---|
| 3745 | # nameLst = [atNames[i] for i in rbseq[3]] |
|---|
| 3746 | out.append(' Torsion sequence %d Bond: %s - %s riding: %s\n'% |
|---|
| 3747 | (i,atNames[rbseq[0]],atNames[rbseq[1]],str([atNames[i] for i in rbseq[3]]))) |
|---|
| 3748 | return out |
|---|
| 3749 | |
|---|
| 3750 | def WriteVecRBModel(RBModel,sigDict={},irb=None): |
|---|
| 3751 | '''Write description of a vector rigid body. Code shifted from |
|---|
| 3752 | PrintVecRBModel to make usable from G2export_CIF |
|---|
| 3753 | ''' |
|---|
| 3754 | out = [] |
|---|
| 3755 | rbRef = RBModel['rbRef'] |
|---|
| 3756 | atTypes = RBModel['rbTypes'] |
|---|
| 3757 | for i in range(len(RBModel['VectMag'])): |
|---|
| 3758 | if sigDict and irb is not None: |
|---|
| 3759 | name = '::RBV;'+str(i)+':'+str(irb) |
|---|
| 3760 | s = G2mth.ValEsd(RBModel['VectMag'][i],sigDict.get(name,-.0001)) |
|---|
| 3761 | out.append('Vector no.: %d Magnitude: %s\n'%(i,s)) |
|---|
| 3762 | else: |
|---|
| 3763 | out.append('Vector no.: %d Magnitude: %8.4f Refine? %s\n'% |
|---|
| 3764 | (i,RBModel['VectMag'][i],RBModel['VectRef'][i])) |
|---|
| 3765 | out.append(' No. Type vx vy vz\n') |
|---|
| 3766 | for j,[name,xyz] in enumerate(zip(atTypes,RBModel['rbVect'][i])): |
|---|
| 3767 | out.append(' %d %2s %10.4f %10.4f %10.4f\n'%(j,name,xyz[0],xyz[1],xyz[2])) |
|---|
| 3768 | out.append(' No. Type x y z\n') |
|---|
| 3769 | for i,[name,xyz] in enumerate(zip(atTypes,RBModel['rbXYZ'])): |
|---|
| 3770 | out.append(' %d %2s %10.4f %10.4f %10.4f\n'%(i,name,xyz[0],xyz[1],xyz[2])) |
|---|
| 3771 | return out |
|---|
