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try adding to meson.build
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‎GSASII/imports/G2phase_RRUFF.py‎

Lines changed: 147 additions & 148 deletions
Original file line numberDiff line numberDiff line change
@@ -1,155 +1,154 @@
11
'''Reads structure files downloaded from the RRUFF database either as ASCII
22
text files or .rtf files that somehow are generated
33
'''
4-
# import sys
5-
# import numpy as np
6-
# import random as ran
7-
# #from .. import GSASIIobj as G2obj
4+
import sys
5+
import numpy as np
6+
import random as ran
7+
from .. import GSASIIobj as G2obj
8+
from .. import GSASIIspc as G2spc
9+
from .. import GSASIIlattice as G2lat
810

9-
# class RRUFFReader(G2obj.ImportPhase):
10-
# '''A fairly quickly-written importer to pull out the phase info from a
11-
# RRUFF database (https://rruff.info) text file.
12-
# '''
13-
# pass
14-
# def __init__(self):
15-
# super(self.__class__,self).__init__( # fancy way to say ImportPhase.__init__
16-
# extensionlist=('.txt'),
17-
# strictExtension=True,
18-
# formatName = 'RRUFF DIF file',
19-
# longFormatName = 'RRUFF database DIF file download (*.txt)'
20-
# )
11+
class RRUFFReader(G2obj.ImportPhase):
12+
'''A fairly quickly-written importer to pull out the phase info from a
13+
RRUFF database (https://rruff.info) text file.
14+
'''
15+
def __init__(self):
16+
super(self.__class__,self).__init__( # fancy way to say ImportPhase.__init__
17+
extensionlist=('.txt'),
18+
strictExtension=True,
19+
formatName = 'RRUFF DIF file',
20+
longFormatName = 'RRUFF database DIF file download (*.txt)'
21+
)
2122

22-
# def ContentsValidator(self, filename):
23-
# "Test if the file has CELL PARAMETERS: and SPACE GROUP: entries"
24-
# with open(filename,'r') as fp:
25-
# txt = fp.read()
26-
# status = True
27-
# for s in ('CELL PARAMETERS:','SPACE GROUP:'):
28-
# if not s in txt:
29-
# print(s,'not found')
30-
# if self.errors is None: self.errors = ''
31-
# self.errors += f'no {s} record found; not valid. '
32-
# status = False
33-
# if not ' ATOM ' in txt:
34-
# print('ATOM line not found')
35-
# if self.errors is None: self.errors = ''
36-
# self.errors += 'no ATOM record found; no structure. '
37-
# status = False
38-
# fp.close()
39-
# return status
23+
def ContentsValidator(self, filename):
24+
"Test if the file has CELL PARAMETERS: and SPACE GROUP: entries"
25+
with open(filename,'r') as fp:
26+
txt = fp.read()
27+
status = True
28+
for s in ('CELL PARAMETERS:','SPACE GROUP:'):
29+
if not s in txt:
30+
print(s,'not found')
31+
if self.errors is None: self.errors = ''
32+
self.errors += f'no {s} record found; not valid. '
33+
status = False
34+
if not ' ATOM ' in txt:
35+
print('ATOM line not found')
36+
if self.errors is None: self.errors = ''
37+
self.errors += 'no ATOM record found; no structure. '
38+
status = False
39+
fp.close()
40+
return status
4041

41-
# def Reader(self,filename,ParentFrame=None, **unused):
42-
# 'Read a DIF file from RRUFF'
43-
# #self.errors = 'Error opening file'
44-
# from .. import GSASIIspc as G2spc
45-
# from .. import GSASIIlattice as G2lat
46-
# Title = ''
47-
# atomsmode = False
48-
# fp = open(filename, 'r')
49-
# SGData = None
50-
# Atoms = []
51-
# cell = None
52-
# for line in fp.readlines():
53-
# if len(line) == 0: continue
54-
# line = line.strip()
55-
# if atomsmode:
56-
# # all DIF files appear to have atoms as element, X, Y, Z, OCCUPANCY, ISO(B)
57-
# if r'\par' in line: # some files seem to have some formatting
58-
# line = line.split('\\par')[0]
59-
# try:
60-
# Atype = line.split()[0]
61-
# x,y,z,Afrac,B = [float(i) for i in line.split()[1:]]
62-
# Uiso = B/(8*np.pi**2)
63-
# XYZ = np.array([float(x),float(y),float(z)])
64-
# XYZ = np.where(np.abs(XYZ)<0.00001,0,XYZ)
65-
# SytSym,Mult = G2spc.SytSym(XYZ,SGData)[:2]
66-
# IA = 'I'
67-
# i = 1
68-
# while f"{Atype}{i}" in [i[0] for i in Atoms]:
69-
# i += 1
70-
# if i > 999:
71-
# Aname = f"{Atype}?"
72-
# break
73-
# else:
74-
# Aname = f"{Atype}{i}"
75-
# if Atype.upper() in ['WA','OH','OW','OA','OB','OC','OD','OE','OL','OP','OO']:
76-
# Atype = 'O'
77-
# Atom = [Aname,Atype,'',x,y,z,Afrac,SytSym,Mult,IA,Uiso]
78-
# Atom += 6*[0]
79-
# Atom.append(ran.randint(0,sys.maxsize))
80-
# Atoms.append(Atom)
81-
# except:
82-
# atomsmode = False
83-
# break
84-
# if Title == '':
85-
# if '\\rtf' in line: continue
86-
# Title = line
87-
# if r'\par' in line: # some files seem to have some formatting
88-
# Title = line.split()[-1].split('\\')[0]
89-
# if 'CELL PARAMETERS:' in line:
90-
# L = line.split(':')[1]
91-
# if r'\par' in line: # some files seem to have some formatting
92-
# L = L.split('\\par')[0]
93-
# cellRec = L.split()
94-
# abc = cellRec[0:3]
95-
# angles = cellRec[3:]
96-
# cell=[float(abc[0]),float(abc[1]),float(abc[2]),
97-
# float(angles[0]),float(angles[1]),float(angles[2])]
98-
# Volume = float(G2lat.calc_V(G2lat.cell2A(cell)))
99-
# elif 'SPACE GROUP:' in line:
100-
# SGData = G2obj.P1SGData # P 1
101-
# S = line.split(':')[1].strip()
102-
# if r'\par' in S: # some files seem to have some formatting
103-
# S = S.split()[0]
104-
# Sinit = S
105-
# E,SGData = G2spc.SpcGroup(S)
106-
# if E:
107-
# SpGrpNorm = G2spc.StandardizeSpcName(S)
108-
# if SpGrpNorm:
109-
# E,SGData = G2spc.SpcGroup(SpGrpNorm)
110-
# if E and '_' in S:
111-
# S = S.replace('_','')
112-
# if E:
113-
# E,SGData = G2spc.SpcGroup(S[0]+' '+S[1:])
114-
# # some space group names that show up in RRUFF
115-
# SGfixDict = {'B2/b': 'B 2/b 1 1', 'Bb21m':'B b 21 m',
116-
# 'P21/b': 'P 21/b 1 1', 'P21212': 'P 21 21 2',
117-
# 'P21ca': 'P 21 c a', 'P21cn': 'P 21 c n',
118-
# 'P21nb': 'P21 n b', 'P21nm': 'P21 n m',
119-
# 'P63cm': 'P63 c m', 'P63mc': 'P63 m c',
120-
# 'Pn21a': 'P n 21 a', 'Pn21m': 'P n 21 m'}
42+
def Reader(self,filename,ParentFrame=None, **unused):
43+
'Read a DIF file from RRUFF'
44+
#self.errors = 'Error opening file'
45+
Title = ''
46+
atomsmode = False
47+
fp = open(filename, 'r')
48+
SGData = None
49+
Atoms = []
50+
cell = None
51+
for line in fp.readlines():
52+
if len(line) == 0: continue
53+
line = line.strip()
54+
if atomsmode:
55+
# all DIF files appear to have atoms as element, X, Y, Z, OCCUPANCY, ISO(B)
56+
if r'\par' in line: # some files seem to have some formatting
57+
line = line.split('\\par')[0]
58+
try:
59+
Atype = line.split()[0]
60+
x,y,z,Afrac,B = [float(i) for i in line.split()[1:]]
61+
Uiso = B/(8*np.pi**2)
62+
XYZ = np.array([float(x),float(y),float(z)])
63+
XYZ = np.where(np.abs(XYZ)<0.00001,0,XYZ)
64+
SytSym,Mult = G2spc.SytSym(XYZ,SGData)[:2]
65+
IA = 'I'
66+
i = 1
67+
while f"{Atype}{i}" in [i[0] for i in Atoms]:
68+
i += 1
69+
if i > 999:
70+
Aname = f"{Atype}?"
71+
break
72+
else:
73+
Aname = f"{Atype}{i}"
74+
if Atype.upper() in ['WA','OH','OW','OA','OB','OC','OD','OE','OL','OP','OO']:
75+
Atype = 'O'
76+
Atom = [Aname,Atype,'',x,y,z,Afrac,SytSym,Mult,IA,Uiso]
77+
Atom += 6*[0]
78+
Atom.append(ran.randint(0,sys.maxsize))
79+
Atoms.append(Atom)
80+
except:
81+
atomsmode = False
82+
break
83+
if Title == '':
84+
if '\\rtf' in line: continue
85+
Title = line
86+
if r'\par' in line: # some files seem to have some formatting
87+
Title = line.split()[-1].split('\\')[0]
88+
if 'CELL PARAMETERS:' in line:
89+
L = line.split(':')[1]
90+
if r'\par' in line: # some files seem to have some formatting
91+
L = L.split('\\par')[0]
92+
cellRec = L.split()
93+
abc = cellRec[0:3]
94+
angles = cellRec[3:]
95+
cell=[float(abc[0]),float(abc[1]),float(abc[2]),
96+
float(angles[0]),float(angles[1]),float(angles[2])]
97+
Volume = float(G2lat.calc_V(G2lat.cell2A(cell)))
98+
elif 'SPACE GROUP:' in line:
99+
SGData = G2obj.P1SGData # P 1
100+
S = line.split(':')[1].strip()
101+
if r'\par' in S: # some files seem to have some formatting
102+
S = S.split()[0]
103+
Sinit = S
104+
E,SGData = G2spc.SpcGroup(S)
105+
if E:
106+
SpGrpNorm = G2spc.StandardizeSpcName(S)
107+
if SpGrpNorm:
108+
E,SGData = G2spc.SpcGroup(SpGrpNorm)
109+
if E and '_' in S:
110+
S = S.replace('_','')
111+
if E:
112+
E,SGData = G2spc.SpcGroup(S[0]+' '+S[1:])
113+
# some space group names that show up in RRUFF
114+
SGfixDict = {'B2/b': 'B 2/b 1 1', 'Bb21m':'B b 21 m',
115+
'P21/b': 'P 21/b 1 1', 'P21212': 'P 21 21 2',
116+
'P21ca': 'P 21 c a', 'P21cn': 'P 21 c n',
117+
'P21nb': 'P21 n b', 'P21nm': 'P21 n m',
118+
'P63cm': 'P63 c m', 'P63mc': 'P63 m c',
119+
'Pn21a': 'P n 21 a', 'Pn21m': 'P n 21 m'}
121120

122-
# if E and S in SGfixDict:
123-
# E,SGData = G2spc.SpcGroup(SGfixDict[S])
124-
# if E:
125-
# self.warnings += f'ERROR in space group symbol {Sinit!r}'
126-
# self.warnings += '\nThe space group has been set to "P 1". '
127-
# self.warnings += "Change this in phase's General tab."
128-
# self.warnings += " Error msg="+G2spc.SGErrors(E)
129-
# elif SGData['SpGrp'] in G2spc.spg2origins:
130-
# self.warnings += f"WARNING space group {SGData['SpGrp']} has two Origins"
131-
# elif 'ATOM ' in line:
132-
# atomsmode = True
133-
# if SGData is None:
134-
# if self.errors is None: self.errors = ''
135-
# self.errors += 'no Space Group record found; not valid. '
136-
# return False
137-
# if cell is None:
138-
# if self.errors is None: self.errors = ''
139-
# self.errors += 'no CELL record found; not valid. '
140-
# return False
141-
# if len(Atoms) == 0:
142-
# if self.errors is None: self.errors = ''
143-
# self.errors += 'no Atoms found; not valid. '
144-
# return False
145-
# if cell[3] == cell[4] == cell[5] and cell[3] != 90:
146-
# self.warnings += f'Note: {filename!r} has rhombohedral cell, changing space group'
147-
# E,SGData = G2spc.SpcGroup(SGData['SpGrp'] + ' R')
148-
# self.MPhase = None
149-
# self.Phase = G2obj.SetNewPhase(Name=Title,SGData=SGData,cell=cell+[Volume,])
150-
# self.Phase['General']['Name'] = Title
151-
# self.Phase['General']['Type'] = 'nuclear'
152-
# self.Phase['General']['AtomPtrs'] = [3,1,7,9]
153-
# self.Phase['Atoms'] = Atoms
154-
# fp.close()
155-
# return True
121+
if E and S in SGfixDict:
122+
E,SGData = G2spc.SpcGroup(SGfixDict[S])
123+
if E:
124+
self.warnings += f'ERROR in space group symbol {Sinit!r}'
125+
self.warnings += '\nThe space group has been set to "P 1". '
126+
self.warnings += "Change this in phase's General tab."
127+
self.warnings += " Error msg="+G2spc.SGErrors(E)
128+
elif SGData['SpGrp'] in G2spc.spg2origins:
129+
self.warnings += f"WARNING space group {SGData['SpGrp']} has two Origins"
130+
elif 'ATOM ' in line:
131+
atomsmode = True
132+
if SGData is None:
133+
if self.errors is None: self.errors = ''
134+
self.errors += 'no Space Group record found; not valid. '
135+
return False
136+
if cell is None:
137+
if self.errors is None: self.errors = ''
138+
self.errors += 'no CELL record found; not valid. '
139+
return False
140+
if len(Atoms) == 0:
141+
if self.errors is None: self.errors = ''
142+
self.errors += 'no Atoms found; not valid. '
143+
return False
144+
if cell[3] == cell[4] == cell[5] and cell[3] != 90:
145+
self.warnings += f'Note: {filename!r} has rhombohedral cell, changing space group'
146+
E,SGData = G2spc.SpcGroup(SGData['SpGrp'] + ' R')
147+
self.MPhase = None
148+
self.Phase = G2obj.SetNewPhase(Name=Title,SGData=SGData,cell=cell+[Volume,])
149+
self.Phase['General']['Name'] = Title
150+
self.Phase['General']['Type'] = 'nuclear'
151+
self.Phase['General']['AtomPtrs'] = [3,1,7,9]
152+
self.Phase['Atoms'] = Atoms
153+
fp.close()
154+
return True

‎GSASII/imports/meson.build‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -19,6 +19,7 @@ py.install_sources([
1919
'G2phase_GPX.py',
2020
'G2phase_INS.py',
2121
'G2phase_rmc6f.py',
22+
'G2phase_RRUFF.py',
2223
'G2phase_xyz.py',
2324
'G2pwd_BrukerBRML.py',
2425
'G2pwd_BrukerRAW.py',

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