| 1 | # -*- coding: utf-8 -*- |
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| 2 | ########### SVN repository information ################### |
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| 3 | # $Date: 2015-04-27 13:22:06 -0500 (Mon, 27 Apr 2015) $ |
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| 4 | # $Author: vondreele $ |
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| 5 | # $Revision: 1812 $ |
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| 6 | # $URL: https://subversion.xray.aps.anl.gov/pyGSAS/trunk/imports/G2phase_GPX.py $ |
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| 7 | # $Id: G2phase_GPX.py 1812 2015-04-27 18:22:06Z vondreele $ |
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| 8 | ########### SVN repository information ################### |
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| 9 | ''' |
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| 10 | *Module G2phase_INS: Import phase from SHELX INS file* |
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| 11 | -------------------------------------------------------- |
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| 12 | |
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| 13 | Copies a phase from SHELX ins file into the |
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| 14 | current project. |
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| 15 | |
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| 16 | ''' |
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| 17 | import sys |
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| 18 | import traceback |
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| 19 | import math |
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| 20 | import numpy as np |
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| 21 | import random as ran |
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| 22 | import GSASIIIO as G2IO |
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| 23 | import GSASIIspc as G2spc |
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| 24 | import GSASIIlattice as G2lat |
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| 25 | import GSASIIpath |
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| 26 | GSASIIpath.SetVersionNumber("$Revision: 1812 $") |
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| 27 | |
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| 28 | class PhaseReaderClass(G2IO.ImportPhase): |
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| 29 | 'Opens a .INS file and pulls out a selected phase' |
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| 30 | def __init__(self): |
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| 31 | super(self.__class__,self).__init__( # fancy way to say ImportPhase.__init__ |
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| 32 | extensionlist=('.ins','.INS','.res','.RES'), |
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| 33 | strictExtension=True, |
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| 34 | formatName = 'SHELX ins, res', |
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| 35 | longFormatName = 'SHELX input (*.ins, *.res) file import' |
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| 36 | ) |
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| 37 | |
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| 38 | def ContentsValidator(self, filepointer): |
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| 39 | "Test if the ins file has a CELL record" |
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| 40 | for i,l in enumerate(filepointer): |
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| 41 | if l.startswith('CELL'): |
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| 42 | break |
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| 43 | else: |
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| 44 | self.errors = 'no CELL record found' |
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| 45 | self.errors = 'This is not a valid .ins file.' |
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| 46 | return False |
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| 47 | return True |
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| 48 | |
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| 49 | def Reader(self,filename,filepointer, ParentFrame=None, **unused): |
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| 50 | 'Read a ins file using :meth:`ReadINSPhase`' |
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| 51 | #try: |
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| 52 | self.Phase = self.ReadINSPhase(filename, ParentFrame) |
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| 53 | return True |
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| 54 | #except Exception as detail: |
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| 55 | # self.errors += '\n '+str(detail) |
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| 56 | # print 'INS read error:',detail # for testing |
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| 57 | # traceback.print_exc(file=sys.stdout) |
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| 58 | # return False |
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| 59 | |
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| 60 | def ReadINSPhase(self,filename,parent=None): |
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| 61 | '''Read a phase from a INS file. |
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| 62 | ''' |
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| 63 | Shelx = ['TITL','CELL','ZERR','LATT','SYMM','SFAC','DISP','UNIT','LAUE','EADP', |
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| 64 | 'MORE','TIME','HKLF','OMIT','SHEL','BASF','TWIN','EXTI','SWAT', |
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| 65 | 'HOPE','MERG','SPEC','RESI','RTAB','MPLA','HFIX','MOVE','ANIS','AFIX', |
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| 66 | 'FRAG','FEND','EXYZ','EDAP','EQIV','CONN','PART','BIND','FREE','DFIX','DANG', |
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| 67 | 'BUMP','SAME','SADI','CHIV','FLAT','DELU','SIMU','DEFS','ISOR','NCSY', |
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| 68 | 'SUMP','L.S.','CGLS','BLOC','DAMP','STIR','WGHT','FVAR','BOND','CONF','MPLA', |
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| 69 | 'HTAB','LIST','ACTA','SIZE','TEMP','WPDB','FMAP','GRID','PLAN','MOLE'] |
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| 70 | EightPiSq = 8.*math.pi**2 |
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| 71 | self.errors = 'Error opening file' |
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| 72 | file = open(filename, 'Ur') |
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| 73 | Phase = {} |
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| 74 | Title = '' |
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| 75 | Compnd = '' |
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| 76 | Atoms = [] |
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| 77 | aTypes = [] |
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| 78 | A = np.zeros(shape=(3,3)) |
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| 79 | S = file.readline() |
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| 80 | line = 1 |
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| 81 | SGData = None |
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| 82 | cell = None |
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| 83 | numbs = [str(i) for i in range(10)] |
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| 84 | while S: |
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| 85 | if '!' in S: |
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| 86 | S = S.split('!')[0] |
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| 87 | self.errors = 'Error reading at line '+str(line) |
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| 88 | Atom = [] |
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| 89 | Aindx = [ch in numbs for ch in S[:4]] #False for all letters |
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| 90 | if 'TITL' in S[:4].upper(): |
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| 91 | Title = S[4:72].strip() |
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| 92 | elif not S.strip(): |
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| 93 | pass |
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| 94 | elif 'CELL' in S[:4].upper(): |
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| 95 | cellRec = S.split() |
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| 96 | abc = cellRec[2:5] |
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| 97 | angles = cellRec[5:8] |
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| 98 | cell=[float(abc[0]),float(abc[1]),float(abc[2]), |
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| 99 | float(angles[0]),float(angles[1]),float(angles[2])] |
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| 100 | Volume = G2lat.calc_V(G2lat.cell2A(cell)) |
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| 101 | AA,AB = G2lat.cell2AB(cell) |
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| 102 | SpGrp = 'P 1' |
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| 103 | SGData = G2IO.SGData # P 1 |
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| 104 | self.warnings += '\nThe space group is not given in an ins file and has been set to "P 1".' |
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| 105 | self.warnings += "\nChange this in phase's General tab; NB: it might be in the Phase name." |
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| 106 | elif S[:4].upper() in 'SFAC': |
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| 107 | aTypes = S[4:].split() |
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| 108 | if 'H' in aTypes: |
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| 109 | self.warnings += '\n\nHydrogen atoms found; consider replacing them with stereochemically tied ones' |
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| 110 | self.warnings += '\nas Shelx constraints & HFIX commands are ignored.' |
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| 111 | self.warnings += "\nDo 'Edit/Insert H atoms' in this phase's Atoms tab after deleting the old ones." |
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| 112 | elif S[0] == 'Q': |
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| 113 | pass |
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| 114 | elif '\x1a' in S[:4]: |
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| 115 | pass |
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| 116 | elif S[:3].upper() == 'REM': |
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| 117 | pass |
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| 118 | elif S[:3].upper() == 'END': |
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| 119 | pass |
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| 120 | elif S[:4].strip().upper() not in Shelx: #this will find an atom record! |
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| 121 | AtRec = S.split() |
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| 122 | Atype = aTypes[int(AtRec[1])-1] |
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| 123 | Aname = AtRec[0] |
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| 124 | Afrac = abs(float(AtRec[5]))%10. |
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| 125 | x,y,z = AtRec[2:5] |
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| 126 | XYZ = np.array([float(x),float(y),float(z)]) |
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| 127 | XYZ = np.where(np.abs(XYZ)<0.00001,0,XYZ) |
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| 128 | SytSym,Mult = G2spc.SytSym(XYZ,SGData)[:2] |
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| 129 | if '=' not in S: |
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| 130 | IA = 'I' |
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| 131 | Uiso = float(AtRec[6]) |
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| 132 | if Uiso < 0. or Uiso > 1.0: |
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| 133 | Uiso = 0.025 |
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| 134 | Uij = [0. for i in range(6)] |
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| 135 | else: |
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| 136 | IA = 'A' |
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| 137 | Uiso = 0. |
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| 138 | Ustr = AtRec[6:8] |
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| 139 | S = file.readline() |
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| 140 | if '!' in S: |
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| 141 | S = S.split('!')[0] |
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| 142 | AtRec = S.split() |
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| 143 | line += 1 |
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| 144 | Ustr += AtRec |
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| 145 | Uij = [float(Ustr[i]) for i in range(6)] |
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| 146 | Uij = Uij[0:3]+[Uij[5],Uij[4],Uij[3]] |
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| 147 | Atom = [Aname,Atype,'',XYZ[0],XYZ[1],XYZ[2],Afrac,SytSym,Mult,IA,Uiso] |
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| 148 | Atom += Uij |
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| 149 | Atom.append(ran.randint(0,sys.maxint)) |
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| 150 | Atoms.append(Atom) |
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| 151 | S = file.readline() |
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| 152 | line += 1 |
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| 153 | file.close() |
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| 154 | self.errors = 'Error after read complete' |
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| 155 | Phase = G2IO.SetNewPhase(Name='ShelX phase',SGData=SGData,cell=cell+[Volume,]) |
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| 156 | Phase['General']['Name'] = Title |
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| 157 | Phase['General']['Type'] = 'nuclear' |
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| 158 | Phase['General']['AtomPtrs'] = [3,1,7,9] |
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| 159 | Phase['Atoms'] = Atoms |
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| 160 | return Phase |
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