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new importer for RRUFF database entries
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‎GSASII/imports/G2phase_RRUFF.py‎

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# -*- coding: utf-8 -*-
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'''Reads structure files downloaded from the RRUFF database either as ASCII
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text files or .rtf files that somehow are generated
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'''
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from __future__ import division, print_function
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import sys
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import numpy as np
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import random as ran
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from .. import GSASIIobj as G2obj
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from .. import GSASIIspc as G2spc
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from .. import GSASIIlattice as G2lat
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class PhaseReaderClass(G2obj.ImportPhase):
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'''A quickly-written importer to open a .txt file from the RRUFF database
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https://rruff.info
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and pull out the phase info
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'''
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def __init__(self):
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super(self.__class__,self).__init__( # fancy way to say ImportPhase.__init__
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extensionlist=('.txt'),
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strictExtension=True,
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formatName = 'RRUFF DIF file',
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longFormatName = 'RRUFF database DIF file download (*.txt)'
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)
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def ContentsValidator(self, filename):
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"Test if the file has CELL PARAMETERS: and SPACE GROUP: entries"
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with open(filename,'r') as fp:
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txt = fp.read()
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status = True
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for s in ('CELL PARAMETERS:','SPACE GROUP:'):
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if not s in txt:
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print(s,'not found')
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if self.errors is None: self.errors = ''
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self.errors += f'no {s} record found; not valid. '
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status = False
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if not ' ATOM ' in txt:
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print('ATOM line not found')
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if self.errors is None: self.errors = ''
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self.errors += 'no ATOM record found; no structure. '
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status = False
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fp.close()
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return status
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def Reader(self,filename,ParentFrame=None, **unused):
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'Read a DIF file from RRUFF'
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#self.errors = 'Error opening file'
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Title = ''
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atomsmode = False
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fp = open(filename, 'r')
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SGData = None
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Atoms = []
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cell = None
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for line in fp.readlines():
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if len(line) == 0: continue
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line = line.strip()
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if atomsmode:
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# all DIF files appear to have atoms as element, X, Y, Z, OCCUPANCY, ISO(B)
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if r'\par' in line: # some files seem to have some formatting
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line = line.split('\\par')[0]
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try:
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Atype = line.split()[0]
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x,y,z,Afrac,B = [float(i) for i in line.split()[1:]]
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Uiso = B/(8*np.pi**2)
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XYZ = np.array([float(x),float(y),float(z)])
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XYZ = np.where(np.abs(XYZ)<0.00001,0,XYZ)
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SytSym,Mult = G2spc.SytSym(XYZ,SGData)[:2]
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IA = 'I'
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i = 1
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while f"{Atype}{i}" in [i[0] for i in Atoms]:
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i += 1
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if i > 999:
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Aname = f"{Atype}?"
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break
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else:
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Aname = f"{Atype}{i}"
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if Atype.upper() in ['WA','OH','OW','OA','OB','OC','OD','OE','OL','OP','OO']:
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Atype = 'O'
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Atom = [Aname,Atype,'',x,y,z,Afrac,SytSym,Mult,IA,Uiso]
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Atom += 6*[0]
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Atom.append(ran.randint(0,sys.maxsize))
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Atoms.append(Atom)
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except:
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atomsmode = False
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break
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if Title == '':
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if '\\rtf' in line: continue
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Title = line
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if r'\par' in line: # some files seem to have some formatting
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Title = line.split()[-1].split('\\')[0]
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if 'CELL PARAMETERS:' in line:
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L = line.split(':')[1]
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if r'\par' in line: # some files seem to have some formatting
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L = L.split('\\par')[0]
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cellRec = L.split()
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abc = cellRec[0:3]
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angles = cellRec[3:]
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cell=[float(abc[0]),float(abc[1]),float(abc[2]),
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float(angles[0]),float(angles[1]),float(angles[2])]
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Volume = float(G2lat.calc_V(G2lat.cell2A(cell)))
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elif 'SPACE GROUP:' in line:
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SGData = G2obj.P1SGData # P 1
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S = line.split(':')[1].strip()
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if r'\par' in S: # some files seem to have some formatting
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S = S.split()[0]
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Sinit = S
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E,SGData = G2spc.SpcGroup(S)
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if E:
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SpGrpNorm = G2spc.StandardizeSpcName(S)
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if SpGrpNorm:
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E,SGData = G2spc.SpcGroup(SpGrpNorm)
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if E and '_' in S:
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S = S.replace('_','')
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if E:
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E,SGData = G2spc.SpcGroup(S[0]+' '+S[1:])
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# some space group names that show up in RRUFF
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SGfixDict = {'B2/b': 'B 2/b 1 1', 'Bb21m':'B b 21 m',
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'P21/b': 'P 21/b 1 1', 'P21212': 'P 21 21 2',
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'P21ca': 'P 21 c a', 'P21cn': 'P 21 c n',
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'P21nb': 'P21 n b', 'P21nm': 'P21 n m',
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'P63cm': 'P63 c m', 'P63mc': 'P63 m c',
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'Pn21a': 'P n 21 a', 'Pn21m': 'P n 21 m'}
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if E and S in SGfixDict:
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E,SGData = G2spc.SpcGroup(SGfixDict[S])
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if E:
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self.warnings += f'ERROR in space group symbol {Sinit!r}'
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self.warnings += '\nThe space group has been set to "P 1". '
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self.warnings += "Change this in phase's General tab."
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self.warnings += " Error msg="+G2spc.SGErrors(E)
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print(self.warnings)
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#import GSASII.GSASIIpath
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#GSASII.GSASIIpath.IPyBreak_base()
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elif SGData['SpGrp'] in G2spc.spg2origins:
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self.warnings += f"WARNING space group {SGData['SpGrp']} has two Origins"
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#import GSASII.GSASIIpath
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#GSASII.GSASIIpath.IPyBreak_base()
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elif 'ATOM ' in line:
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atomsmode = True
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if SGData is None:
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if self.errors is None: self.errors = ''
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self.errors += 'no Space Group record found; not valid. '
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return False
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if cell is None:
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if self.errors is None: self.errors = ''
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self.errors += 'no CELL record found; not valid. '
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return False
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if len(Atoms) == 0:
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if self.errors is None: self.errors = ''
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self.errors += 'no Atoms found; not valid. '
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return False
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if cell[3] == cell[4] == cell[5] and cell[3] != 90:
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self.warnings += f'Note: {filename!r} has rhombohedral cell, changing space group'
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E,SGData = G2spc.SpcGroup(SGData['SpGrp'] + ' R')
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print(self.warnings)
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#import GSASII.GSASIIpath
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#GSASII.GSASIIpath.IPyBreak_base()
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#breakpoint()
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self.MPhase = None
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self.Phase = G2obj.SetNewPhase(Name=Title,SGData=SGData,cell=cell+[Volume,])
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self.Phase['General']['Name'] = Title
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self.Phase['General']['Type'] = 'nuclear'
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self.Phase['General']['AtomPtrs'] = [3,1,7,9]
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self.Phase['Atoms'] = Atoms
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fp.close()
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return True

‎GSASII/imports/__init__.py‎

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from . import G2phase_GPX
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from . import G2phase_INS
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from . import G2phase_rmc6f
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from . import G2phase_RRUFF
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from . import G2phase_xyz
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from . import G2pwd_BrukerBRML
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from . import G2pwd_BrukerRAW
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"G2phase_GPX",
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"G2phase_INS",
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"G2phase_rmc6f",
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"G2phase_RRUFF",
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"G2phase_xyz",
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"G2pwd_BrukerBRML",
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"G2pwd_BrukerRAW",

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