def refinePeaks(peaks,ibrav,A,ifX20=True):
'needs a doc string'
dmin = getDmin(peaks)
smin = 1.0e10
pwr = 8
maxTries = 10
OK = False
tries = 0
sgtype = G2lat.make_sgtype(ibrav)
HKL = G2lat.GenHBravais(dmin,ibrav,A, sg_type=sgtype)
while len(HKL) > 2 and IndexPeaks(peaks,HKL)[0]:
Pwr = pwr - (tries % 2)
HKL = []
tries += 1
osmin = smin
oldA = A[:]
Vold = G2lat.calc_V(oldA)
OK,smin,A,result = FitHKL(ibrav,peaks,A,Pwr)
Vnew = G2lat.calc_V(A)
if Vnew > 2.0*Vold or Vnew < 2.:
A = ranAbyR(ibrav,oldA,tries+1,maxTries,ran2axis)
OK = False
continue
try:
HKL = G2lat.GenHBravais(dmin,ibrav,A, sgtype)
except FloatingPointError:
A = oldA
OK = False
break
if len(HKL) == 0: break #absurd cell obtained!
rat = (osmin-smin)/smin
if abs(rat) < 1.0e-5 or not OK: break
if tries > maxTries: break
if OK:
OK,smin,A,result = FitHKL(ibrav,peaks,A,2)
Peaks = np.array(peaks).T
H = Peaks[4:7]
try:
Peaks[8] = 1./np.sqrt(G2lat.calc_rDsq(H,A))
peaks = Peaks.T
except FloatingPointError:
A = oldA
M20,X20 = calc_M20(peaks,HKL,ifX20)
return len(HKL),M20,X20,A
def refinePeaks(peaks,ibrav,A,ifX20=True):
'needs a doc string'
dmin = getDmin(peaks)
smin = 1.0e10
pwr = 8
maxTries = 10
OK = False
tries = 0
HKL = G2lat.GenHBravais(dmin,ibrav,A)
while len(HKL) > 2 and IndexPeaks(peaks,HKL)[0]:
Pwr = pwr - (tries % 2)
HKL = []
tries += 1
osmin = smin
oldA = A[:]
Vold = G2lat.calc_V(oldA)
OK,smin,A,result = FitHKL(ibrav,peaks,A,Pwr)
Vnew = G2lat.calc_V(A)
if Vnew > 2.0*Vold or Vnew < 2.:
A = ranAbyR(ibrav,oldA,tries+1,maxTries,ran2axis)
OK = False
continue
try:
HKL = G2lat.GenHBravais(dmin,ibrav,A)
except FloatingPointError:
A = oldA
OK = False
break
if len(HKL) == 0: break #absurd cell obtained!
rat = (osmin-smin)/smin
if abs(rat) < 1.0e-5 or not OK: break
if tries > maxTries: break
if OK:
OK,smin,A,result = FitHKL(ibrav,peaks,A,2)
Peaks = np.array(peaks).T
H = Peaks[4:7]
try:
Peaks[8] = 1./np.sqrt(G2lat.calc_rDsq(H,A))
peaks = Peaks.T
except FloatingPointError:
A = oldA
M20,X20 = calc_M20(peaks,HKL,ifX20)
return len(HKL),M20,X20,A
def ReadEXPPhase(self, G2frame, filepointer):
'''Read a phase from a GSAS .EXP file.
'''
shModels = ['cylindrical', 'none', 'shear - 2/m', 'rolling - mmm']
textureData = {
'Order': 0,
'Model': 'cylindrical',
'Sample omega': [False, 0.0],
'Sample chi': [False, 0.0],
'Sample phi': [False, 0.0],
'SH Coeff': [False, {}],
'SHShow': False,
'PFhkl': [0, 0, 1],
'PFxyz': [0, 0, 1],
'PlotType': 'Pole figure'
}
shNcof = 0
S = 1
NPhas = []
Expr = [{}, {}, {}, {}, {}, {}, {}, {},
{}] # GSAS can have at most 9 phases
for line, S in enumerate(filepointer):
self.errors = 'Error reading at line ' + str(line + 1)
if 'EXPR NPHAS' in S[:12]:
Num = S[12:-1].count('0')
NPhas = S[12:-1].split()
if 'CRS' in S[:3]:
N = int(S[3:4]) - 1
Expr[N][S[:12]] = S[12:-1]
PNames = []
if not NPhas:
raise self.ImportException("No EXPR NPHAS record found")
self.errors = 'Error interpreting file'
for n, N in enumerate(NPhas):
if N != '0':
result = n
key = 'CRS' + str(n + 1) + ' PNAM'
PNames.append(Expr[n][key])
if len(PNames) == 0:
raise self.ImportException("No phases found")
elif len(PNames) > 1:
dlg = wx.SingleChoiceDialog(G2frame, 'Which phase to read?',
'Read phase data', PNames,
wx.CHOICEDLG_STYLE)
try:
if dlg.ShowModal() == wx.ID_OK:
result = dlg.GetSelection(
) # I think this breaks is there are skipped phases. Cant this happen?
finally:
dlg.Destroy()
EXPphase = Expr[result]
keyList = EXPphase.keys()
keyList.sort()
SGData = {}
if NPhas[result] == '1':
Ptype = 'nuclear'
elif NPhas[result] in ['2', '3']:
Ptype = 'magnetic'
elif NPhas[result] == '4':
Ptype = 'macromolecular'
elif NPhas[result] == '10':
Ptype = 'Pawley'
else:
raise self.ImportException("Phase type not recognized")
for key in keyList:
if 'PNAM' in key:
PhaseName = EXPphase[key].strip()
elif 'ABC ' in key:
abc = [
float(EXPphase[key][:10]),
float(EXPphase[key][10:20]),
float(EXPphase[key][20:30])
]
elif 'ANGLES' in key:
angles = [
float(EXPphase[key][:10]),
float(EXPphase[key][10:20]),
float(EXPphase[key][20:30])
]
elif 'SG SYM' in key:
SpGrp = EXPphase[key][:15].strip()
E, SGData = G2spc.SpcGroup(SpGrp)
if E:
SGData = G2IO.SGData # P 1 -- unlikely to need this!
self.warnings += '\nThe GSAS space group was not interpreted(!) and has been set to "P 1".'
self.warnings += "Change this in phase's General tab."
elif 'OD ' in key:
SHdata = EXPphase[key].split() # may not have all 9 values
SHvals = 9 * [0]
for i in range(9):
try:
float(SHdata[i])
SHvals[i] = SHdata[i]
except:
pass
textureData['Order'] = int(SHvals[0])
textureData['Model'] = shModels[int(SHvals[2])]
textureData['Sample omega'] = [False, float(SHvals[6])]
textureData['Sample chi'] = [False, float(SHvals[7])]
textureData['Sample phi'] = [False, float(SHvals[8])]
shNcof = int(SHvals[1])
Atoms = []
if Ptype == 'nuclear':
for key in keyList:
if 'AT' in key:
if key[11:] == 'A':
S = EXPphase[key]
elif key[11:] == 'B':
S += EXPphase[key]
Atom = [
S[50:58].strip(), S[:10].strip().capitalize(), '',
float(S[10:20]),
float(S[20:30]),
float(S[30:40]),
float(S[40:50]), '',
int(S[60:62]), S[130:131]
]
if Atom[9] == 'I':
Atom += [float(S[68:78]), 0., 0., 0., 0., 0., 0.]
elif Atom[9] == 'A':
Atom += [
0.0,
float(S[68:78]),
float(S[78:88]),
float(S[88:98]),
float(S[98:108]),
float(S[108:118]),
float(S[118:128])
]
XYZ = Atom[3:6]
Atom[7], Atom[8] = G2spc.SytSym(XYZ, SGData)
Atom.append(ran.randint(0, sys.maxint))
Atoms.append(Atom)
elif Ptype == 'macromolecular':
for key in keyList:
if 'AT' in key[6:8]:
S = EXPphase[key]
Atom = [
S[56:60], S[50:54].strip().upper(), S[54:56],
S[46:51].strip(), S[:8].strip().capitalize(), '',
float(S[16:24]),
float(S[24:32]),
float(S[32:40]),
float(S[8:16]), '1', 1, 'I',
float(S[40:46]), 0, 0, 0, 0, 0, 0
]
XYZ = Atom[6:9]
Atom[10], Atom[11] = G2spc.SytSym(XYZ, SGData)
Atom.append(ran.randint(0, sys.maxint))
Atoms.append(Atom)
Volume = G2lat.calc_V(G2lat.cell2A(abc + angles))
if shNcof:
shCoef = {}
nRec = [i + 1 for i in range((shNcof - 1) / 6 + 1)]
for irec in nRec:
ODkey = keyList[0][:6] + 'OD' + '%3dA' % (irec)
indx = EXPphase[ODkey].split()
ODkey = ODkey[:-1] + 'B'
vals = EXPphase[ODkey].split()
for i, val in enumerate(vals):
key = 'C(%s,%s,%s)' % (indx[3 * i], indx[3 * i + 1],
indx[3 * i + 2])
shCoef[key] = float(val)
textureData['SH Coeff'] = [False, shCoef]
if not SGData:
raise self.ImportException("No space group found in phase")
if not abc:
raise self.ImportException("No cell lengths found in phase")
if not angles:
raise self.ImportException("No cell angles found in phase")
if not Atoms:
raise self.ImportException("No atoms found in phase")
Phase = G2IO.SetNewPhase(Name=PhaseName,
SGData=SGData,
cell=abc + angles + [
Volume,
])
general = Phase['General']
general['Type'] = Ptype
if general['Type'] == 'macromolecular':
general['AtomPtrs'] = [6, 4, 10, 12]
else:
general['AtomPtrs'] = [3, 1, 7, 9]
general['SH Texture'] = textureData
Phase['Atoms'] = Atoms
return Phase
def ReadPDFPhase(self, G2frame, fp):
'''Read a phase from a ICDD .str file.
'''
EightPiSq = 8. * math.pi**2
self.errors = 'Error opening file'
Phase = {}
Atoms = []
S = fp.readline()
line = 1
SGData = None
cell = []
cellkey = []
while S:
if 'space_group' in S:
break
S = fp.readline()
while S:
self.errors = 'Error reading at line ' + str(line)
if 'phase_name' in S:
Title = S.split('"')[1]
elif 'Space group (HMS)' in S:
SpGrp = S.split()[-1]
SpGrpNorm = G2spc.StandardizeSpcName(SpGrp)
E, SGData = G2spc.SpcGroup(SpGrpNorm)
# space group processing failed, try to look up name in table
while E:
print(G2spc.SGErrors(E))
dlg = wx.TextEntryDialog(
G2frame,
SpGrp[:-1] +
' is invalid \nN.B.: make sure spaces separate axial fields in symbol',
'ERROR in space group symbol',
'',
style=wx.OK)
if dlg.ShowModal() == wx.ID_OK:
SpGrp = dlg.GetValue()
E, SGData = G2spc.SpcGroup(SpGrp)
else:
SGData = G2obj.P1SGData # P 1
self.warnings += '\nThe space group was not interpreted and has been set to "P 1".'
self.warnings += "Change this in phase's General tab."
dlg.Destroy()
G2spc.SGPrint(SGData) #silent check of space group symbol
elif 'a a_' in S[:7]:
data = S.split()
cell.append(float(data[2]))
cellkey.append(data[1])
elif 'b b_' in S[:7]:
data = S.split()
cell.append(float(data[2]))
cellkey.append(data[1])
elif 'b =' in S[:6]:
data = S.split('=')
indx = cellkey.index(data[1].split(';')[0])
cell.append(cell[indx])
elif 'c c_' in S[:7]:
data = S.split()
cell.append(float(data[2]))
elif 'c =' in S[:6]:
data = S.split('=')
indx = cellkey.index(data[1].split(';')[0])
cell.append(cell[indx])
elif 'al' in S[:5]:
cell.append(float(S.split()[1]))
elif 'be' in S[:5]:
cell.append(float(S.split()[1]))
elif 'ga' in S[:5]:
cell.append(float(S.split()[1]))
Volume = G2lat.calc_V(G2lat.cell2A(cell))
break
S = fp.readline()
S = fp.readline()
while S:
if '/*' in S[:5]:
break
if 'site' in S[:7]:
atom = []
xyzkey = []
data = S.split()
atom.append(data[1]) #name
pos = data.index('occ') + 1
atom.append(data[pos]) #type
atom.append('') #refine
for xid in ['x =', 'y =', 'z =']:
if xid in S:
xpos = S.index(xid) + 3
xend = xpos + S[xpos:].index(';')
if S[xpos:xend] in xyzkey:
atom.append(atom[3 + xyzkey.index(S[xpos:xend])])
else:
atom.append(eval(S[xpos:xend] + '.'))
else:
xpos = data.index(xid[0]) + 2
xyzkey.append(data[xpos - 1][1:])
atom.append(float(data[xpos]))
atom.append(float(data[pos + 2]))
SytSym, Mult = G2spc.SytSym(np.array(atom[3:6]), SGData)[:2]
atom.append(SytSym)
atom.append(Mult)
if 'beq' in S:
atom.append('I')
upos = data.index('beq')
atom.append(float(data[upos + 2]) / EightPiSq)
atom += [
0.,
0.,
0.,
0.,
0.,
0.,
]
elif 'ADPs' in S:
upos = data.index('ADPs')
atom.append('A')
atom.append(0.0)
for uid in [
'Bani11', 'Bani22', 'Bani33', 'Bani12', 'Bani13',
'Bani23'
]:
upos = data.index(uid) + 1
atom.append(float(data[upos]) / EightPiSq)
else:
atom.append('I')
atom += [
0.02,
0.,
0.,
0.,
0.,
0.,
0.,
]
atom.append(ran.randint(0, sys.maxsize))
Atoms.append(atom)
S = fp.readline()
fp.close()
self.errors = 'Error after read complete'
if not SGData:
raise self.ImportException("No space group (spcgroup entry) found")
if not cell:
raise self.ImportException("No cell found")
Phase = G2obj.SetNewPhase(Name=Title,
SGData=SGData,
cell=cell + [
Volume,
])
Phase['General']['Type'] = 'nuclear'
Phase['General']['AtomPtrs'] = [3, 1, 7, 9]
Phase['Atoms'] = Atoms
return Phase
def ReadEXPPhase(self, G2frame, filepointer):
'''Read a phase from a GSAS .EXP file.
'''
shModels = ['cylindrical', 'none', 'shear - 2/m', 'rolling - mmm']
textureData = {
'Order': 0,
'Model': 'cylindrical',
'Sample omega': [False, 0.0],
'Sample chi': [False, 0.0],
'Sample phi': [False, 0.0],
'SH Coeff': [False, {}],
'SHShow': False,
'PFhkl': [0, 0, 1],
'PFxyz': [0, 0, 1],
'PlotType': 'Pole figure'
}
shNcof = 0
S = 1
NPhas = []
Expr = [{}, {}, {}, {}, {}, {}, {}, {},
{}] # GSAS can have at most 9 phases
for line, S in enumerate(filepointer):
self.errors = 'Error reading at line ' + str(line + 1)
if 'EXPR NPHAS' in S[:12]:
NPhas = S[12:-1].split()
if 'CRS' in S[:3]:
N = int(S[3:4]) - 1
Expr[N][S[:12]] = S[12:-1]
PNames = []
if not NPhas:
raise self.ImportException("No EXPR NPHAS record found")
self.errors = 'Error interpreting file'
for n, N in enumerate(NPhas):
if N != '0':
result = n
key = 'CRS' + str(n + 1) + ' PNAM'
PNames.append(Expr[n][key])
if len(PNames) == 0:
raise self.ImportException("No phases found")
elif len(PNames) > 1:
dlg = wx.SingleChoiceDialog(G2frame, 'Which phase to read?',
'Read phase data', PNames,
wx.CHOICEDLG_STYLE)
try:
if dlg.ShowModal() == wx.ID_OK:
result = dlg.GetSelection(
) # I think this breaks is there are skipped phases. Cant this happen?
finally:
dlg.Destroy()
EXPphase = Expr[result]
keyList = list(EXPphase.keys())
keyList.sort()
SGData = {}
MPtype = ''
if NPhas[result] == '1':
Ptype = 'nuclear'
elif NPhas[result] == '2':
Ptype = 'nuclear'
MPtype = 'magnetic'
MagDmin = 1.0
elif NPhas[result] == '3':
Ptype = 'magnetic'
MagDmin = 1.0
elif NPhas[result] == '4':
Ptype = 'macromolecular'
elif NPhas[result] == '10':
Ptype = 'Pawley'
else:
raise self.ImportException("Phase type not recognized")
for key in keyList:
if 'PNAM' in key:
PhaseName = EXPphase[key].strip()
elif 'ABC ' in key:
abc = [
float(EXPphase[key][:10]),
float(EXPphase[key][10:20]),
float(EXPphase[key][20:30])
]
elif 'ANGLES' in key:
angles = [
float(EXPphase[key][:10]),
float(EXPphase[key][10:20]),
float(EXPphase[key][20:30])
]
elif 'SG SYM' in key:
SpGrp = EXPphase[key][:15].strip()
E, SGData = G2spc.SpcGroup(SpGrp)
if E:
SGData = G2obj.P1SGData # P 1 -- unlikely to need this!
self.warnings += '\nThe GSAS space group was not interpreted(!) and has been set to "P 1".'
self.warnings += "Change this in phase's General tab."
elif 'SPNFLP' in key:
SpnFlp = np.array(
[int(float(s)) for s in EXPphase[key].split()])
SpnFlp = np.where(SpnFlp == 0, 1, SpnFlp)
SpnFlp = [
1,
] + list(SpnFlp)
if SGData['SpGrp'][0] in ['A', 'B', 'C', 'I', 'R', 'F']:
SpnFlp = list(SpnFlp) + [1, 1, 1, 1]
elif 'MXDSTR' in key:
MagDmin = float(EXPphase[key][:10])
elif 'OD ' in key:
SHdata = EXPphase[key].split() # may not have all 9 values
SHvals = 9 * [0]
for i in range(9):
try:
float(SHdata[i])
SHvals[i] = SHdata[i]
except:
pass
textureData['Order'] = int(SHvals[0])
textureData['Model'] = shModels[int(SHvals[2])]
textureData['Sample omega'] = [False, float(SHvals[6])]
textureData['Sample chi'] = [False, float(SHvals[7])]
textureData['Sample phi'] = [False, float(SHvals[8])]
shNcof = int(SHvals[1])
Volume = G2lat.calc_V(G2lat.cell2A(abc + angles))
Atoms = []
MAtoms = []
Bmat = G2lat.cell2AB(abc + angles)[1]
if Ptype == 'macromolecular':
for key in keyList:
if 'AT' in key[6:8]:
S = EXPphase[key]
Atom = [
S[56:60].strip(), S[50:54].strip().upper(), S[54:56],
S[46:51].strip(), S[:8].strip().capitalize(), '',
float(S[16:24]),
float(S[24:32]),
float(S[32:40]),
float(S[8:16]), '1', 1, 'I',
float(S[40:46]), 0, 0, 0, 0, 0, 0
]
XYZ = Atom[6:9]
Atom[10], Atom[11] = G2spc.SytSym(XYZ, SGData)[:2]
Atom.append(ran.randint(0, sys.maxsize))
Atoms.append(Atom)
else:
for key in keyList:
if 'AT' in key:
if key[11:] == 'A':
S = EXPphase[key]
elif key[11:] == 'B':
S1 = EXPphase[key]
Atom = [
S[50:58].strip(), S[:10].strip().capitalize(), '',
float(S[10:20]),
float(S[20:30]),
float(S[30:40]),
float(S[40:50]), '',
int(S[60:62]), S1[62:63]
]
#float(S[40:50]),'',int(S[60:62]),S1[130:131]]
if Atom[9] == 'I':
Atom += [float(S1[0:10]), 0., 0., 0., 0., 0., 0.]
elif Atom[9] == 'A':
Atom += [
0.0,
float(S1[0:10]),
float(S1[10:20]),
float(S1[20:30]),
float(S1[30:40]),
float(S1[40:50]),
float(S1[50:60])
]
else:
print('Error in line with key: ' + key)
Atom += [0., 0., 0., 0., 0., 0., 0.]
XYZ = Atom[3:6]
Atom[7], Atom[8] = G2spc.SytSym(XYZ, SGData)[:2]
Atom.append(ran.randint(0, sys.maxsize))
Atoms.append(Atom)
elif key[11:] == 'M' and key[6:8] == 'AT':
S = EXPphase[key]
mom = np.array(
[float(S[:10]),
float(S[10:20]),
float(S[20:30])])
mag = np.sqrt(np.sum(mom**2))
mom = np.inner(Bmat, mom) * mag
MAtoms.append(Atom)
MAtoms[-1] = Atom[:7] + list(mom) + Atom[7:]
if shNcof:
shCoef = {}
nRec = [i + 1 for i in range((shNcof - 1) // 6 + 1)]
for irec in nRec:
ODkey = keyList[0][:6] + 'OD' + '%3dA' % (irec)
indx = EXPphase[ODkey].split()
ODkey = ODkey[:-1] + 'B'
vals = EXPphase[ODkey].split()
for i, val in enumerate(vals):
key = 'C(%s,%s,%s)' % (indx[3 * i], indx[3 * i + 1],
indx[3 * i + 2])
shCoef[key] = float(val)
textureData['SH Coeff'] = [False, shCoef]
if not SGData:
raise self.ImportException("No space group found in phase")
if not abc:
raise self.ImportException("No cell lengths found in phase")
if not angles:
raise self.ImportException("No cell angles found in phase")
if not Atoms:
raise self.ImportException("No atoms found in phase")
self.Phase['General'].update({
'Type':
Ptype,
'Name':
PhaseName,
'Cell': [
False,
] + abc + angles + [
Volume,
],
'SGData':
SGData
})
if MPtype == 'magnetic':
self.MPhase['General'].update({
'Type':
'magnetic',
'Name':
PhaseName + ' mag',
'Cell': [
False,
] + abc + angles + [
Volume,
],
'SGData':
SGData
})
else:
self.MPhase = None
if Ptype == 'macromolecular':
self.Phase['General']['AtomPtrs'] = [6, 4, 10, 12]
self.Phase['Atoms'] = Atoms
elif Ptype == 'magnetic':
self.Phase['General']['AtomPtrs'] = [3, 1, 10, 12]
self.Phase['General']['SGData']['SGSpin'] = SpnFlp
self.Phase['General']['MagDmin'] = MagDmin
self.Phase['Atoms'] = MAtoms
else: #nuclear
self.Phase['General']['AtomPtrs'] = [3, 1, 7, 9]
self.Phase['General']['SH Texture'] = textureData
self.Phase['Atoms'] = Atoms
if MPtype == 'magnetic':
self.MPhase['General']['AtomPtrs'] = [3, 1, 10, 12]
self.MPhase['General']['SGData']['SGSpin'] = SpnFlp
self.MPhase['General']['MagDmin'] = MagDmin
self.MPhase['Atoms'] = MAtoms
def ReadPDBPhase(self,filename,parent=None):
'''Read a phase from a PDB file.
'''
EightPiSq = 8.*math.pi**2
self.errors = 'Error opening file'
file = open(filename, 'Ur')
Phase = {}
Title = ''
Compnd = ''
Atoms = []
A = np.zeros(shape=(3,3))
S = file.readline()
line = 1
SGData = None
cell = None
while S:
self.errors = 'Error reading at line '+str(line)
Atom = []
if 'TITLE' in S[:5]:
Title = S[10:72].strip()
elif 'COMPND ' in S[:10]:
Compnd = S[10:72].strip()
elif 'CRYST' in S[:5]:
abc = S[7:34].split()
angles = S[34:55].split()
cell=[float(abc[0]),float(abc[1]),float(abc[2]),
float(angles[0]),float(angles[1]),float(angles[2])]
Volume = G2lat.calc_V(G2lat.cell2A(cell))
AA,AB = G2lat.cell2AB(cell)
SpGrp = S[55:65]
E,SGData = G2spc.SpcGroup(SpGrp)
# space group processing failed, try to look up name in table
if E:
SpGrpNorm = G2spc.StandardizeSpcName(SpGrp)
if SpGrpNorm:
E,SGData = G2spc.SpcGroup(SpGrpNorm)
while E:
print G2spc.SGErrors(E)
dlg = wx.TextEntryDialog(parent,
SpGrp[:-1]+' is invalid \nN.B.: make sure spaces separate axial fields in symbol',
'ERROR in space group symbol','',style=wx.OK)
if dlg.ShowModal() == wx.ID_OK:
SpGrp = dlg.GetValue()
E,SGData = G2spc.SpcGroup(SpGrp)
else:
SGData = G2IO.SGData # P 1
self.warnings += '\nThe space group was not interpreted and has been set to "P 1".'
self.warnings += "Change this in phase's General tab."
dlg.Destroy()
SGlines = G2spc.SGPrint(SGData)
for l in SGlines: print l
elif 'SCALE' in S[:5]:
V = S[10:41].split()
A[int(S[5])-1] = [float(V[0]),float(V[1]),float(V[2])]
elif 'ATOM' in S[:4] or 'HETATM' in S[:6]:
if not SGData:
self.warnings += '\nThe space group was not read before atoms and has been set to "P 1". '
self.warnings += "Change this in phase's General tab."
SGData = G2IO.SGData # P 1
XYZ = [float(S[31:39]),float(S[39:47]),float(S[47:55])]
XYZ = np.inner(AB,XYZ)
XYZ = np.where(abs(XYZ)<0.00001,0,XYZ)
SytSym,Mult = G2spc.SytSym(XYZ,SGData)
Uiso = float(S[61:67])/EightPiSq
Type = S[12:14].lower()
if Type[0] in '123456789':
Type = Type[1:]
Atom = [S[22:27].strip(),S[17:20].upper(),S[20:22],
S[12:17].strip(),Type.strip().capitalize(),'',XYZ[0],XYZ[1],XYZ[2],
float(S[55:61]),SytSym,Mult,'I',Uiso,0,0,0,0,0,0]
S = file.readline()
line += 1
if 'ANISOU' in S[:6]:
Uij = S[30:72].split()
Uij = [float(Uij[0])/10000.,float(Uij[1])/10000.,float(Uij[2])/10000.,
float(Uij[3])/10000.,float(Uij[4])/10000.,float(Uij[5])/10000.]
Atom = Atom[:14]+Uij
Atom[12] = 'A'
Atom.append(ran.randint(0,sys.maxint))
Atoms.append(Atom)
S = file.readline()
line += 1
file.close()
self.errors = 'Error after read complete'
if Title:
PhaseName = Title
elif Compnd:
PhaseName = Compnd
else:
PhaseName = 'None'
if not SGData:
raise self.ImportException("No space group (CRYST entry) found")
if not cell:
raise self.ImportException("No cell (CRYST entry) found")
Phase = G2IO.SetNewPhase(Name=PhaseName,SGData=SGData,cell=cell+[Volume,])
Phase['General']['Type'] = 'macromolecular'
Phase['General']['AtomPtrs'] = [6,4,10,12]
Phase['Atoms'] = Atoms
return Phase
def ReadJANAPhase(self,filename,parent=None):
'''Read a phase from a JANA2006 m50 & m40 files.
'''
self.errors = 'Error opening file'
file = open(filename, 'Ur') #contains only cell & spcgroup
Phase = {}
Title = os.path.basename(filename)
Compnd = ''
Type = 'nuclear'
Atoms = []
Atypes = []
SuperVec = [[0,0,.1],False,4]
S = file.readline()
line = 1
SGData = None
SuperSg = ''
cell = None
nqi = 0
while S:
self.errors = 'Error reading at line '+str(line)
if 'title' in S and S != 'title\n':
Title = S.split()[1]
elif 'cell' in S[:4]:
cell = S[5:].split()
cell=[float(cell[0]),float(cell[1]),float(cell[2]),
float(cell[3]),float(cell[4]),float(cell[5])]
Volume = G2lat.calc_V(G2lat.cell2A(cell))
elif 'spgroup' in S:
if 'X' in S:
raise self.ImportException("Supersymmetry "+S+" too high; GSAS-II limited to (3+1) supersymmetry")
SpGrp = S.split()[1]
SuperSg = ''
if '(' in SpGrp: #supercell symmetry - split in 2
SuperStr = SpGrp.split('(')
SpGrp = SuperStr[0]
SuperSg = '('+SuperStr[1]
SpGrpNorm = G2spc.StandardizeSpcName(SpGrp)
E,SGData = G2spc.SpcGroup(SpGrpNorm)
# space group processing failed, try to look up name in table
while E:
print G2spc.SGErrors(E)
dlg = wx.TextEntryDialog(parent,
SpGrp[:-1]+' is invalid \nN.B.: make sure spaces separate axial fields in symbol',
'ERROR in space group symbol','',style=wx.OK)
if dlg.ShowModal() == wx.ID_OK:
SpGrp = dlg.GetValue()
E,SGData = G2spc.SpcGroup(SpGrp)
else:
SGData = G2IO.SGData # P 1
self.warnings += '\nThe space group was not interpreted and has been set to "P 1".'
self.warnings += "Change this in phase's General tab."
dlg.Destroy()
SGlines = G2spc.SGPrint(SGData)
elif 'qi' in S[:2]:
if nqi:
raise self.ImportException("Supersymmetry too high; GSAS-II limited to (3+1) supersymmetry")
Type = 'modulated'
vec = S.split()[1:]
SuperVec = [[float(vec[i]) for i in range(3)],False,4]
nqi += 1
elif 'atom' in S[:4]:
Atypes.append(S.split()[1])
S = file.readline()
line += 1
file.close()
#read atoms from m40 file
if not SGData:
self.warnings += '\nThe space group was not read before atoms and has been set to "P 1". '
self.warnings += "Change this in phase's General tab."
SGData = G2IO.SGData # P 1
waveTypes = ['Fourier','Sawtooth','ZigZag',]
filename2 = os.path.splitext(filename)[0]+'.m40'
file2 = open(filename2,'Ur')
S = file2.readline()
line = 1
self.errors = 'Error reading at line '+str(line)
nAtoms = int(S.split()[0])
for i in range(4):
S = file2.readline()
for i in range(nAtoms):
S1 = file2.readline()
S1N = S1.split()[-3:] # no. occ, no. pos waves, no. ADP waves
S1N = [int(i) for i in S1N]
S1T = list(S1[60:63])
waveType = waveTypes[int(S1T[1])]
crenelType = ''
Spos = []
Sadp = []
Sfrac = []
Smag = []
XYZ = [float(S1[27:36]),float(S1[36:45]),float(S1[45:54])]
SytSym,Mult = G2spc.SytSym(XYZ,SGData)
aType = Atypes[int(S1[9:11])-1]
Name = S1[:8].strip()
if S1[11:15].strip() == '1':
S2 = file2.readline()
Uiso = float(S2[:9])
Uij = [0,0,0,0,0,0]
IA = 'I'
elif S1[11:15].strip() == '2':
S2 = file2.readline()
IA = 'A'
Uiso = 0.
Uij = [float(S2[:9]),float(S2[9:18]),float(S2[18:27]),
float(S2[27:36]),float(S2[36:45]),float(S2[45:54])]
for i in range(S1N[0]):
if not i:
FS = file2.readline()
Sfrac.append(FS[:9]) #'O' or 'delta' = 'length' for crenel
if int(S1T[0]): #"", "Legendre" or "Xharm" in 18:27 for "crenel"!
waveType = 'Crenel/Fourier' #all waves 'Fourier' no other choice
crenelType = FS[18:27]
Sfrac.append(file2.readline()[:18]) #if not crenel = Osin & Ocos
# else Osin & Ocos except last one is X40 = 'Center'
for i in range(S1N[1]):
Spos.append(file2.readline()[:54])
for i in range(S1N[2]):
Sadp.append(file2.readline()[:54]+file2.readline())
if sum(S1N): #if any waves: skip mystery line?
file2.readline()
for i,it in enumerate(Sfrac):
print i,it
if not i:
if 'Crenel' in waveType:
vals = [float(it),float(Sfrac[-1][:9])]
else:
vals = [float(it),]
else:
vals = [float(it[:9]),float(it[9:18])]
if 'Crenel' in waveType and i == len(Sfrac)-1:
del Sfrac[-1]
break
Sfrac[i] = [vals,False]
print Sfrac[i]
for i,it in enumerate(Spos):
if waveType in ['ZigZag','Sawtooth'] and not i:
vals = [float(it[:9]),float(it[9:18]),float(it[18:27]),float(it[27:36])]
else:
vals = [float(it[:9]),float(it[9:18]),float(it[18:27]),float(it[27:36]),float(it[36:45]),float(it[45:54])]
Spos[i] = [vals,False]
for i,it in enumerate(Sadp):
vals = [float(it[:9]),float(it[9:18]),float(it[18:27]),float(it[27:36]),float(it[36:45]),float(it[45:54]),
float(it[54:63]),float(it[63:72]),float(it[72:81]),float(it[81:90]),float(it[90:99]),float(it[99:108])]
Sadp[i] = [vals,False]
Atom = [Name,aType,'',XYZ[0],XYZ[1],XYZ[2],1.0,SytSym,Mult,IA,Uiso]
Atom += Uij
Atom.append(ran.randint(0,sys.maxint))
Atom.append([])
Atom.append([])
Atom.append({'SS1':{'waveType':waveType,'crenelType':crenelType,'Sfrac':Sfrac,'Spos':Spos,'Sadp':Sadp,'Smag':Smag}}) #SS2 is for (3+2), etc.
Atoms.append(Atom)
file2.close()
self.errors = 'Error after read complete'
if not SGData:
raise self.ImportException("No space group (spcgroup entry) found")
if not cell:
raise self.ImportException("No cell found")
Phase = G2IO.SetNewPhase(Name=Title,SGData=SGData,cell=cell+[Volume,])
Phase['General']['Type'] = Type
Phase['General']['Super'] = nqi
Phase['General']['SuperVec'] = SuperVec
Phase['General']['SuperSg'] = SuperSg
if SuperSg:
Phase['General']['SSGData'] = G2spc.SSpcGroup(SGData,SuperSg)[1]
Phase['General']['AtomPtrs'] = [3,1,7,9]
Phase['Atoms'] = Atoms
return Phase
def ReadEXPPhase(self, G2frame,filepointer):
'''Read a phase from a GSAS .EXP file.
'''
shModels = ['cylindrical','none','shear - 2/m','rolling - mmm']
textureData = {'Order':0,'Model':'cylindrical','Sample omega':[False,0.0],
'Sample chi':[False,0.0],'Sample phi':[False,0.0],'SH Coeff':[False,{}],
'SHShow':False,'PFhkl':[0,0,1],'PFxyz':[0,0,1],'PlotType':'Pole figure'}
shNcof = 0
S = 1
NPhas = []
Expr = [{},{},{},{},{},{},{},{},{}] # GSAS can have at most 9 phases
for line,S in enumerate(filepointer):
self.errors = 'Error reading at line '+str(line+1)
if 'EXPR NPHAS' in S[:12]:
Num = S[12:-1].count('0')
NPhas = S[12:-1].split()
if 'CRS' in S[:3]:
N = int(S[3:4])-1
Expr[N][S[:12]] = S[12:-1]
PNames = []
if not NPhas:
raise self.ImportException("No EXPR NPHAS record found")
self.errors = 'Error interpreting file'
for n,N in enumerate(NPhas):
if N != '0':
result = n
key = 'CRS'+str(n+1)+' PNAM'
PNames.append(Expr[n][key])
if len(PNames) == 0:
raise self.ImportException("No phases found")
elif len(PNames) > 1:
dlg = wx.SingleChoiceDialog(G2frame, 'Which phase to read?', 'Read phase data', PNames, wx.CHOICEDLG_STYLE)
try:
if dlg.ShowModal() == wx.ID_OK:
result = dlg.GetSelection() # I think this breaks is there are skipped phases. Cant this happen?
finally:
dlg.Destroy()
EXPphase = Expr[result]
keyList = EXPphase.keys()
keyList.sort()
SGData = {}
if NPhas[result] == '1':
Ptype = 'nuclear'
elif NPhas[result] in ['2','3']:
Ptype = 'magnetic'
elif NPhas[result] == '4':
Ptype = 'macromolecular'
elif NPhas[result] == '10':
Ptype = 'Pawley'
else:
raise self.ImportException("Phase type not recognized")
for key in keyList:
if 'PNAM' in key:
PhaseName = EXPphase[key].strip()
elif 'ABC ' in key:
abc = [float(EXPphase[key][:10]),float(EXPphase[key][10:20]),float(EXPphase[key][20:30])]
elif 'ANGLES' in key:
angles = [float(EXPphase[key][:10]),float(EXPphase[key][10:20]),float(EXPphase[key][20:30])]
elif 'SG SYM' in key:
SpGrp = EXPphase[key][:15].strip()
E,SGData = G2spc.SpcGroup(SpGrp)
if E:
SGData = G2IO.SGData # P 1 -- unlikely to need this!
self.warnings += '\nThe GSAS space group was not interpreted(!) and has been set to "P 1".'
self.warnings += "Change this in phase's General tab."
elif 'OD ' in key:
SHdata = EXPphase[key].split() # may not have all 9 values
SHvals = 9*[0]
for i in range(9):
try:
float(SHdata[i])
SHvals[i] = SHdata[i]
except:
pass
textureData['Order'] = int(SHvals[0])
textureData['Model'] = shModels[int(SHvals[2])]
textureData['Sample omega'] = [False,float(SHvals[6])]
textureData['Sample chi'] = [False,float(SHvals[7])]
textureData['Sample phi'] = [False,float(SHvals[8])]
shNcof = int(SHvals[1])
Atoms = []
if Ptype == 'nuclear':
for key in keyList:
if 'AT' in key:
if key[11:] == 'A':
S = EXPphase[key]
elif key[11:] == 'B':
S += EXPphase[key]
Atom = [S[50:58].strip(),S[:10].strip().capitalize(),'',
float(S[10:20]),float(S[20:30]),float(S[30:40]),
float(S[40:50]),'',int(S[60:62]),S[130:131]]
if Atom[9] == 'I':
Atom += [float(S[68:78]),0.,0.,0.,0.,0.,0.]
elif Atom[9] == 'A':
Atom += [0.0,float(S[68:78]),float(S[78:88]),
float(S[88:98]),float(S[98:108]),
float(S[108:118]),float(S[118:128])]
XYZ = Atom[3:6]
Atom[7],Atom[8] = G2spc.SytSym(XYZ,SGData)
Atom.append(ran.randint(0,sys.maxint))
Atoms.append(Atom)
elif Ptype == 'macromolecular':
for key in keyList:
if 'AT' in key[6:8]:
S = EXPphase[key]
Atom = [S[56:60],S[50:54].strip().upper(),S[54:56],
S[46:51].strip(),S[:8].strip().capitalize(),'',
float(S[16:24]),float(S[24:32]),float(S[32:40]),
float(S[8:16]),'1',1,'I',float(S[40:46]),0,0,0,0,0,0]
XYZ = Atom[6:9]
Atom[10],Atom[11] = G2spc.SytSym(XYZ,SGData)
Atom.append(ran.randint(0,sys.maxint))
Atoms.append(Atom)
Volume = G2lat.calc_V(G2lat.cell2A(abc+angles))
if shNcof:
shCoef = {}
nRec = [i+1 for i in range((shNcof-1)/6+1)]
for irec in nRec:
ODkey = keyList[0][:6]+'OD'+'%3dA'%(irec)
indx = EXPphase[ODkey].split()
ODkey = ODkey[:-1]+'B'
vals = EXPphase[ODkey].split()
for i,val in enumerate(vals):
key = 'C(%s,%s,%s)'%(indx[3*i],indx[3*i+1],indx[3*i+2])
shCoef[key] = float(val)
textureData['SH Coeff'] = [False,shCoef]
if not SGData:
raise self.ImportException("No space group found in phase")
if not abc:
raise self.ImportException("No cell lengths found in phase")
if not angles:
raise self.ImportException("No cell angles found in phase")
if not Atoms:
raise self.ImportException("No atoms found in phase")
Phase = G2IO.SetNewPhase(Name=PhaseName,SGData=SGData,cell=abc+angles+[Volume,])
general = Phase['General']
general['Type'] = Ptype
if general['Type'] =='macromolecular':
general['AtomPtrs'] = [6,4,10,12]
else:
general['AtomPtrs'] = [3,1,7,9]
general['SH Texture'] = textureData
Phase['Atoms'] = Atoms
return Phase
def scaleAbyV(A,V):
'needs a doc string'
v = G2lat.calc_V(A)
scale = math.exp(math.log(v/V)/3.)**2
for i in range(6):
A[i] *= scale
def scaleAbyV(A,V):
'needs a doc string'
v = G2lat.calc_V(A)
scale = math.exp(math.log(v/V)/3.)**2
for i in range(6):
A[i] *= scale
def ReadINSPhase(self, filename, parent=None):
'''Read a phase from a INS file.
'''
Shelx = [
'TITL', 'CELL', 'ZERR', 'LATT', 'SYMM', 'SFAC', 'DISP', 'UNIT',
'LAUE', 'EADP', 'MORE', 'TIME', 'HKLF', 'OMIT', 'SHEL', 'BASF',
'TWIN', 'EXTI', 'SWAT', 'HOPE', 'MERG', 'SPEC', 'RESI', 'RTAB',
'MPLA', 'HFIX', 'MOVE', 'ANIS', 'AFIX', 'FRAG', 'FEND', 'EXYZ',
'EDAP', 'EQIV', 'CONN', 'PART', 'BIND', 'FREE', 'DFIX', 'DANG',
'BUMP', 'SAME', 'SADI', 'CHIV', 'FLAT', 'DELU', 'SIMU', 'DEFS',
'ISOR', 'NCSY', 'SUMP', 'L.S.', 'CGLS', 'BLOC', 'DAMP', 'STIR',
'WGHT', 'FVAR', 'BOND', 'CONF', 'MPLA', 'HTAB', 'LIST', 'ACTA',
'SIZE', 'TEMP', 'WPDB', 'FMAP', 'GRID', 'PLAN', 'MOLE'
]
self.errors = 'Error opening file'
fp = open(filename, 'Ur')
Phase = {}
Title = ''
Atoms = []
aTypes = []
S = fp.readline()
line = 1
SGData = None
cell = None
while S:
if '!' in S:
S = S.split('!')[0]
self.errors = 'Error reading at line ' + str(line)
Atom = []
if 'TITL' in S[:4].upper():
Title = S[4:72].strip()
elif not S.strip():
pass
elif 'CELL' in S[:4].upper():
cellRec = S.split()
abc = cellRec[2:5]
angles = cellRec[5:8]
cell = [
float(abc[0]),
float(abc[1]),
float(abc[2]),
float(angles[0]),
float(angles[1]),
float(angles[2])
]
Volume = G2lat.calc_V(G2lat.cell2A(cell))
AA, AB = G2lat.cell2AB(cell)
SGData = G2obj.P1SGData # P 1
self.warnings += '\nThe space group is not given in an ins file and has been set to "P 1".'
self.warnings += "\nChange this in phase's General tab; NB: it might be in the Phase name."
elif S[:4].upper() in 'SFAC':
aTypes = S[4:].split()
if 'H' in aTypes:
self.warnings += '\n\nHydrogen atoms found; consider replacing them with stereochemically tied ones'
self.warnings += '\nas Shelx constraints & HFIX commands are ignored.'
self.warnings += "\nDo 'Edit/Insert H atoms' in this phase's Atoms tab after deleting the old ones."
elif S[0] == 'Q':
pass
elif '\x1a' in S[:4]:
pass
elif S[:3].upper() == 'REM':
pass
elif S[:3].upper() == 'END':
pass
elif S[:4].strip().upper(
) not in Shelx: #this will find an atom record!
AtRec = S.split()
Atype = aTypes[int(AtRec[1]) - 1]
Aname = AtRec[0]
Afrac = abs(float(AtRec[5])) % 10.
x, y, z = AtRec[2:5]
XYZ = np.array([float(x), float(y), float(z)])
XYZ = np.where(np.abs(XYZ) < 0.00001, 0, XYZ)
SytSym, Mult = G2spc.SytSym(XYZ, SGData)[:2]
if '=' not in S:
IA = 'I'
Uiso = float(AtRec[6])
if Uiso < 0. or Uiso > 1.0:
Uiso = 0.025
Uij = [0. for i in range(6)]
else:
IA = 'A'
Uiso = 0.
Ustr = AtRec[6:8]
S = fp.readline()
if '!' in S:
S = S.split('!')[0]
AtRec = S.split()
line += 1
Ustr += AtRec
Uij = [float(Ustr[i]) for i in range(6)]
Uij = Uij[0:3] + [Uij[5], Uij[4], Uij[3]]
Atom = [
Aname, Atype, '', XYZ[0], XYZ[1], XYZ[2], Afrac, SytSym,
Mult, IA, Uiso
]
Atom += Uij
Atom.append(ran.randint(0, sys.maxsize))
Atoms.append(Atom)
S = fp.readline()
line += 1
fp.close()
self.errors = 'Error after read complete'
Phase = G2obj.SetNewPhase(Name='ShelX phase',
SGData=SGData,
cell=cell + [
Volume,
])
Phase['General']['Name'] = Title
Phase['General']['Type'] = 'nuclear'
Phase['General']['AtomPtrs'] = [3, 1, 7, 9]
Phase['Atoms'] = Atoms
return Phase
def Reader(self,filename,filepointer, ParentFrame=None, usedRanIdList=[], **unused):
self.isodistort_warnings = ''
self.Phase = G2IO.SetNewPhase(Name='new phase',SGData=G2IO.P1SGData) # create a new empty phase dict
# make sure the ranId is really unique!
while self.Phase['ranId'] in usedRanIdList:
self.Phase['ranId'] = ran.randint(0,sys.maxint)
returnstat = False
cellitems = (
'_cell_length_a','_cell_length_b','_cell_length_c',
'_cell_angle_alpha','_cell_angle_beta','_cell_angle_gamma',)
cellwaveitems = (
'_cell_wave_vector_seq_id',
'_cell_wave_vector_x','_cell_wave_vector_y','_cell_wave_vector_z')
reqitems = (
'_atom_site_fract_x',
'_atom_site_fract_y',
'_atom_site_fract_z',
)
phasenamefields = (
'_chemical_name_common',
'_pd_phase_name',
'_chemical_formula_sum'
)
try:
self.ShowBusy() # this can take a while
try:
cf = G2IO.ReadCIF(filename)
except Exception as detail:
self.errors = "Parse or reading of file failed in pyCifRW; check syntax of file in enCIFer or CheckCIF"
return False
finally:
self.DoneBusy()
# scan blocks for structural info
self.errors = 'Error during scan of blocks for datasets'
str_blklist = []
for blk in cf.keys():
for r in reqitems+cellitems:
if r not in cf[blk].keys():
break
else:
str_blklist.append(blk)
if not str_blklist:
selblk = None # no block to choose
elif len(str_blklist) == 1: # only one choice
selblk = 0
else: # choose from options
choice = []
for blknm in str_blklist:
choice.append('')
# accumumlate some info about this phase
choice[-1] += blknm + ': '
for i in phasenamefields: # get a name for the phase
name = cf[blknm].get(i).strip()
if name is None or name == '?' or name == '.':
continue
else:
choice[-1] += name.strip()[:20] + ', '
break
na = len(cf[blknm].get("_atom_site_fract_x"))
if na == 1:
choice[-1] += '1 atom'
else:
choice[-1] += ('%d' % nd) + ' atoms'
choice[-1] += ', cell: '
fmt = "%.2f,"
for i,key in enumerate(cellitems):
if i == 3: fmt = "%.f,"
if i == 5: fmt = "%.f"
choice[-1] += fmt % cif.get_number_with_esd(
cf[blknm].get(key))[0]
sg = cf[blknm].get("_symmetry_space_group_name_H-M",'')
if not sg: sg = cf[blknm].get("_space_group_name_H-M_alt",'')
if sg: choice[-1] += ', (' + sg.strip() + ')'
selblk = self.PhaseSelector(
choice,
ParentFrame=ParentFrame,
title= 'Select a phase from one the CIF data_ blocks below',
size=(600,100)
)
self.errors = 'Error during reading of selected block'
if selblk is None:
returnstat = False # no block selected or available
else:
blknm = str_blklist[selblk]
blk = cf[str_blklist[selblk]]
E = True
Super = False
SpGrp = blk.get("_symmetry_space_group_name_H-M",'')
if not SpGrp:
SpGrp = blk.get("_space_group_name_H-M_alt",'')
if not SpGrp:
sspgrp = blk.get("_space_group_ssg_name",'').split('(')
SpGrp = sspgrp[0]
SuperSg = '('+sspgrp[1].replace('\\','')
Super = True
SuperVec = [[0,0,.1],False,4]
# try normalizing the space group, to see if we can pick the space group out of a table
SpGrpNorm = G2spc.StandardizeSpcName(SpGrp)
if SpGrpNorm:
E,SGData = G2spc.SpcGroup(SpGrpNorm)
# nope, try the space group "out of the Box"
if E and SpGrp:
E,SGData = G2spc.SpcGroup(SpGrp)
if E:
if not SpGrp:
self.warnings += 'No space group name was found in the CIF.'
self.warnings += '\nThe space group has been set to "P 1". '
self.warnings += "Change this in phase's General tab."
else:
self.warnings += 'ERROR in space group symbol '+SpGrp
self.warnings += '\nThe space group has been set to "P 1". '
self.warnings += "Change this in phase's General tab."
self.warnings += '\nAre there spaces separating axial fields?\n\nError msg: '
self.warnings += G2spc.SGErrors(E)
SGData = G2IO.SGData # P 1
self.Phase['General']['SGData'] = SGData
# cell parameters
cell = []
for lbl in cellitems:
cell.append(cif.get_number_with_esd(blk[lbl])[0])
Volume = G2lat.calc_V(G2lat.cell2A(cell))
self.Phase['General']['Cell'] = [False,]+cell+[Volume,]
# read in atoms
self.errors = 'Error during reading of atoms'
atomlbllist = [] # table to look up atom IDs
atomloop = blk.GetLoop('_atom_site_label')
atomkeys = [i.lower() for i in atomloop.keys()]
if not blk.get('_atom_site_type_symbol'):
self.isodistort_warnings += '\nlack of atom types prevents ISODISTORT processing'
if blk.get('_atom_site_aniso_label'):
anisoloop = blk.GetLoop('_atom_site_aniso_label')
anisokeys = [i.lower() for i in anisoloop.keys()]
else:
anisoloop = None
anisokeys = []
self.Phase['Atoms'] = []
G2AtomDict = { '_atom_site_type_symbol' : 1,
'_atom_site_label' : 0,
'_atom_site_fract_x' : 3,
'_atom_site_fract_y' : 4,
'_atom_site_fract_z' : 5,
'_atom_site_occupancy' : 6,
'_atom_site_aniso_u_11' : 11,
'_atom_site_aniso_u_22' : 12,
'_atom_site_aniso_u_33' : 13,
'_atom_site_aniso_u_12' : 14,
'_atom_site_aniso_u_13' : 15,
'_atom_site_aniso_u_23' : 16, }
ranIdlookup = {}
for aitem in atomloop:
atomlist = ['','','',0,0,0,1.0,'',0,'I',0.01,0,0,0,0,0,0,0]
atomlist[-1] = ran.randint(0,sys.maxint) # add a random Id
while atomlist[-1] in ranIdlookup:
atomlist[-1] = ran.randint(0,sys.maxint) # make it unique
for val,key in zip(aitem,atomkeys):
col = G2AtomDict.get(key)
if col >= 3:
atomlist[col] = cif.get_number_with_esd(val)[0]
elif col is not None:
atomlist[col] = val
elif key in ('_atom_site_thermal_displace_type',
'_atom_site_adp_type'): #Iso or Aniso?
if val.lower() == 'uani':
atomlist[9] = 'A'
elif key == '_atom_site_u_iso_or_equiv':
atomlist[10] =cif.get_number_with_esd(val)[0]
if not atomlist[1] and atomlist[0]:
for i in range(2,0,-1):
typ = atomlist[0].strip()[:i]
if G2elem.CheckElement(typ):
atomlist[1] = typ
if not atomlist[1]: atomlist[1] = 'Xe'
ulbl = '_atom_site_aniso_label'
if atomlist[9] == 'A' and atomlist[0] in blk.get(ulbl):
for val,key in zip(anisoloop.GetKeyedPacket(ulbl,atomlist[0]),
anisokeys):
col = G2AtomDict.get(key)
if col:
atomlist[col] = cif.get_number_with_esd(val)[0]
atomlist[7],atomlist[8] = G2spc.SytSym(atomlist[3:6],SGData)
atomlist[1] = G2elem.FixValence(atomlist[1])
self.Phase['Atoms'].append(atomlist)
ranIdlookup[atomlist[0]] = atomlist[-1]
if atomlist[0] in atomlbllist:
self.warnings += ' ERROR: repeated atom label: '+atomlist[0]
else:
atomlbllist.append(atomlist[0])
if len(atomlbllist) != len(self.Phase['Atoms']):
self.isodistort_warnings += '\nRepeated atom labels prevents ISODISTORT decode'
for lbl in phasenamefields: # get a name for the phase
name = blk.get(lbl)
if name is None:
continue
name = name.strip()
if name == '?' or name == '.':
continue
else:
break
else: # no name found, use block name for lack of a better choice
name = blknm
self.Phase['General']['Name'] = name.strip()[:20]
self.Phase['General']['Super'] = Super
if Super:
self.Phase['General']['Type'] = 'modulated'
self.Phase['General']['SuperVec'] = SuperVec
self.Phase['General']['SuperSg'] = SuperSg
self.Phase['General']['SSGData'] = G2spc.SSpcGroup(SGData,SuperSg)[1]
if not self.isodistort_warnings:
if blk.get('_iso_displacivemode_label') or blk.get('_iso_occupancymode_label'):
self.errors = "Error while processing ISODISTORT constraints"
self.ISODISTORT_proc(blk,atomlbllist,ranIdlookup)
else:
self.warnings += self.isodistort_warnings
returnstat = True
except Exception as detail:
self.errors += '\n '+str(detail)
print 'CIF error:',detail # for testing
print sys.exc_info()[0] # for testing
import traceback
print traceback.format_exc()
returnstat = False
return returnstat
def DoIndexPeaks(peaks, controls, bravais, ifX20=True):
'needs a doc string'
delt = 0.005 #lowest d-spacing cushion - can be fixed?
amin = 2.5
amax = 5.0 * getDmax(peaks)
dmin = getDmin(peaks) - delt
bravaisNames = [
'Cubic-F', 'Cubic-I', 'Cubic-P', 'Trigonal-R', 'Trigonal/Hexagonal-P',
'Tetragonal-I', 'Tetragonal-P', 'Orthorhombic-F', 'Orthorhombic-I',
'Orthorhombic-C', 'Orthorhombic-P', 'Monoclinic-C', 'Monoclinic-P',
'Triclinic'
]
tries = [
'1st', '2nd', '3rd', '4th', '5th', '6th', '7th', '8th', '9th', '10th'
]
N1s = [1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 200]
N2s = [1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4]
Nm = [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4]
Nobs = len(peaks)
zero, ncno = controls[1:3]
ncMax = Nobs * ncno
print "%s %8.3f %8.3f" % ('lattice parameter range = ', amin, amax)
print "%s %.4f %s %d %s %d" % ('Zero =', zero, 'Nc/No max =', ncno,
' Max Nc =', ncno * Nobs)
cells = []
for ibrav in range(14):
begin = time.time()
if bravais[ibrav]:
print 'cell search for ', bravaisNames[ibrav]
print ' M20 X20 Nc a b c alpha beta gamma volume V-test'
V1 = controls[3]
bestM20 = 0
topM20 = 0
cycle = 0
while cycle < 5:
dlg = wx.ProgressDialog(
"Generated reflections",
tries[cycle] + " cell search for " + bravaisNames[ibrav],
ncMax,
style=wx.PD_ELAPSED_TIME | wx.PD_AUTO_HIDE
| wx.PD_REMAINING_TIME | wx.PD_CAN_ABORT)
screenSize = wx.ClientDisplayRect()
Size = dlg.GetSize()
dlg.SetPosition(
wx.Point(screenSize[2] - Size[0] - 305, screenSize[1] + 5))
try:
GoOn = True
while GoOn: #Loop over increment of volume
N2 = 0
while N2 < N2s[ibrav]: #Table 2 step (iii)
if ibrav > 2:
if not N2:
A = []
GoOn, Nc, M20, X20, A = findBestCell(
dlg, ncMax, A, Nm[ibrav] * N1s[ibrav],
ibrav, peaks, V1, ifX20)
if A:
GoOn, Nc, M20, X20, A = findBestCell(
dlg, ncMax, A[:], N1s[ibrav], ibrav,
peaks, 0, ifX20)
else:
GoOn, Nc, M20, X20, A = findBestCell(
dlg, ncMax, 0, Nm[ibrav] * N1s[ibrav],
ibrav, peaks, V1, ifX20)
if Nc >= ncMax:
GoOn = False
break
elif 3 * Nc < Nobs:
N2 = 10
break
else:
if not GoOn:
break
if M20 > 1.0:
bestM20 = max(bestM20, M20)
A = halfCell(ibrav, A[:], peaks)
if ibrav in [12]:
A = monoCellReduce(ibrav, A[:])
HKL = G2lat.GenHBravais(dmin, ibrav, A)
peaks = IndexPeaks(peaks, HKL)[1]
a, b, c, alp, bet, gam = G2lat.A2cell(A)
V = G2lat.calc_V(A)
if M20 >= 2.0:
print "%10.3f %3d %3d %10.5f %10.5f %10.5f %10.3f %10.3f %10.3f %10.2f %10.2f" % (
M20, X20, Nc, a, b, c, alp, bet,
gam, V, V1)
cells.append([
M20, X20, ibrav, a, b, c, alp, bet,
gam, V, False, False
])
if not GoOn:
break
N2 += 1
if ibrav < 11:
V1 *= 1.1
elif ibrav in range(11, 14):
V1 *= 1.05
if not GoOn:
if bestM20 > topM20:
topM20 = bestM20
if cells:
V1 = cells[0][9]
else:
V1 = 25
ncMax += Nobs
cycle += 1
print 'Restart search, new Max Nc = ', ncMax
else:
cycle = 10
finally:
dlg.Destroy()
print '%s%s%s%s'%('finished cell search for ',bravaisNames[ibrav], \
', elapsed time = ',G2lat.sec2HMS(time.time()-begin))
if cells:
return True, dmin, cells
else:
return False, 0, []
def DoIndexPeaks(peaks,controls,bravais,ifX20=True):
'needs a doc string'
delt = 0.005 #lowest d-spacing cushion - can be fixed?
amin = 2.5
amax = 5.0*getDmax(peaks)
dmin = getDmin(peaks)-delt
bravaisNames = ['Cubic-F','Cubic-I','Cubic-P','Trigonal-R','Trigonal/Hexagonal-P',
'Tetragonal-I','Tetragonal-P','Orthorhombic-F','Orthorhombic-I','Orthorhombic-C',
'Orthorhombic-P','Monoclinic-C','Monoclinic-P','Triclinic']
tries = ['1st','2nd','3rd','4th','5th','6th','7th','8th','9th','10th']
N1s = [1,1,1, 5,5, 5,5, 50,50,50,50, 50,50, 200]
N2s = [1,1,1, 2,2, 2,2, 2,2,2,2, 2,2, 4]
Nm = [1,1,1, 1,1, 1,1, 1,1,1,1, 2,2, 4]
Nobs = len(peaks)
zero,ncno = controls[1:3]
ncMax = Nobs*ncno
print "%s %8.3f %8.3f" % ('lattice parameter range = ',amin,amax)
print "%s %.4f %s %d %s %d" % ('Zero =',zero,'Nc/No max =',ncno,' Max Nc =',ncno*Nobs)
cells = []
for ibrav in range(14):
begin = time.time()
if bravais[ibrav]:
print 'cell search for ',bravaisNames[ibrav]
print ' M20 X20 Nc a b c alpha beta gamma volume V-test'
V1 = controls[3]
bestM20 = 0
topM20 = 0
cycle = 0
while cycle < 5:
dlg = wx.ProgressDialog("Generated reflections",tries[cycle]+" cell search for "+bravaisNames[ibrav],ncMax,
style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE|wx.PD_REMAINING_TIME|wx.PD_CAN_ABORT)
screenSize = wx.ClientDisplayRect()
Size = dlg.GetSize()
dlg.SetPosition(wx.Point(screenSize[2]-Size[0]-305,screenSize[1]+5))
try:
GoOn = True
while GoOn: #Loop over increment of volume
N2 = 0
while N2 < N2s[ibrav]: #Table 2 step (iii)
if ibrav > 2:
if not N2:
A = []
GoOn,Nc,M20,X20,A = findBestCell(dlg,ncMax,A,Nm[ibrav]*N1s[ibrav],ibrav,peaks,V1,ifX20)
if A:
GoOn,Nc,M20,X20,A = findBestCell(dlg,ncMax,A[:],N1s[ibrav],ibrav,peaks,0,ifX20)
else:
GoOn,Nc,M20,X20,A = findBestCell(dlg,ncMax,0,Nm[ibrav]*N1s[ibrav],ibrav,peaks,V1,ifX20)
if Nc >= ncMax:
GoOn = False
break
elif 3*Nc < Nobs:
N2 = 10
break
else:
if not GoOn:
break
if M20 > 1.0:
bestM20 = max(bestM20,M20)
A = halfCell(ibrav,A[:],peaks)
if ibrav in [12]:
A = monoCellReduce(ibrav,A[:])
HKL = G2lat.GenHBravais(dmin,ibrav,A)
peaks = IndexPeaks(peaks,HKL)[1]
a,b,c,alp,bet,gam = G2lat.A2cell(A)
V = G2lat.calc_V(A)
if M20 >= 2.0:
print "%10.3f %3d %3d %10.5f %10.5f %10.5f %10.3f %10.3f %10.3f %10.2f %10.2f" % (M20,X20,Nc,a,b,c,alp,bet,gam,V,V1)
cells.append([M20,X20,ibrav,a,b,c,alp,bet,gam,V,False,False])
if not GoOn:
break
N2 += 1
if ibrav < 11:
V1 *= 1.1
elif ibrav in range(11,14):
V1 *= 1.05
if not GoOn:
if bestM20 > topM20:
topM20 = bestM20
if cells:
V1 = cells[0][9]
else:
V1 = 25
ncMax += Nobs
cycle += 1
print 'Restart search, new Max Nc = ',ncMax
else:
cycle = 10
finally:
dlg.Destroy()
print '%s%s%s%s'%('finished cell search for ',bravaisNames[ibrav], \
', elapsed time = ',G2lat.sec2HMS(time.time()-begin))
if cells:
return True,dmin,cells
else:
return False,0,[]
def ReadJANAPhase(self, filename, parent=None):
'''Read a phase from a JANA2006 m50 & m40 files.
'''
self.errors = 'Error opening file'
file = open(filename, 'Ur') #contains only cell & spcgroup
Phase = {}
Title = os.path.basename(filename)
Compnd = ''
Type = 'nuclear'
Atoms = []
Atypes = []
SuperVec = [[0, 0, .1], False, 4]
S = file.readline()
line = 1
SGData = None
SuperSg = ''
cell = None
nqi = 0
while S:
self.errors = 'Error reading at line ' + str(line)
if 'title' in S and S != 'title\n':
Title = S.split()[1]
elif 'cell' in S[:4]:
cell = S[5:].split()
cell = [
float(cell[0]),
float(cell[1]),
float(cell[2]),
float(cell[3]),
float(cell[4]),
float(cell[5])
]
Volume = G2lat.calc_V(G2lat.cell2A(cell))
elif 'spgroup' in S:
if 'X' in S:
raise self.ImportException(
"Supersymmetry " + S +
" too high; GSAS-II limited to (3+1) supersymmetry")
SpGrp = S.split()[1]
SuperSg = ''
if '(' in SpGrp: #supercell symmetry - split in 2
SuperStr = SpGrp.split('(')
SpGrp = SuperStr[0]
SuperSg = '(' + SuperStr[1]
SpGrpNorm = G2spc.StandardizeSpcName(SpGrp)
E, SGData = G2spc.SpcGroup(SpGrpNorm)
# space group processing failed, try to look up name in table
while E:
print G2spc.SGErrors(E)
dlg = wx.TextEntryDialog(
parent,
SpGrp[:-1] +
' is invalid \nN.B.: make sure spaces separate axial fields in symbol',
'ERROR in space group symbol',
'',
style=wx.OK)
if dlg.ShowModal() == wx.ID_OK:
SpGrp = dlg.GetValue()
E, SGData = G2spc.SpcGroup(SpGrp)
else:
SGData = G2IO.SGData # P 1
self.warnings += '\nThe space group was not interpreted and has been set to "P 1".'
self.warnings += "Change this in phase's General tab."
dlg.Destroy()
SGlines = G2spc.SGPrint(SGData)
elif 'qi' in S[:2]:
if nqi:
raise self.ImportException(
"Supersymmetry too high; GSAS-II limited to (3+1) supersymmetry"
)
Type = 'modulated'
vec = S.split()[1:]
SuperVec = [[float(vec[i]) for i in range(3)], False, 4]
nqi += 1
elif 'atom' in S[:4]:
Atypes.append(S.split()[1])
S = file.readline()
line += 1
file.close()
#read atoms from m40 file
if not SGData:
self.warnings += '\nThe space group was not read before atoms and has been set to "P 1". '
self.warnings += "Change this in phase's General tab."
SGData = G2IO.SGData # P 1
waveTypes = [
'Fourier',
'Sawtooth',
'ZigZag',
]
filename2 = os.path.splitext(filename)[0] + '.m40'
file2 = open(filename2, 'Ur')
S = file2.readline()
line = 1
self.errors = 'Error reading at line ' + str(line)
nAtoms = int(S.split()[0])
for i in range(4):
S = file2.readline()
for i in range(nAtoms):
S1 = file2.readline()
S1N = S1.split()[-3:] # no. occ, no. pos waves, no. ADP waves
S1N = [int(i) for i in S1N]
S1T = list(S1[60:63])
waveType = waveTypes[int(S1T[1])]
crenelType = ''
Spos = []
Sadp = []
Sfrac = []
Smag = []
XYZ = [float(S1[27:36]), float(S1[36:45]), float(S1[45:54])]
SytSym, Mult = G2spc.SytSym(XYZ, SGData)
aType = Atypes[int(S1[9:11]) - 1]
Name = S1[:8].strip()
if S1[11:15].strip() == '1':
S2 = file2.readline()
Uiso = float(S2[:9])
Uij = [0, 0, 0, 0, 0, 0]
IA = 'I'
elif S1[11:15].strip() == '2':
S2 = file2.readline()
IA = 'A'
Uiso = 0.
Uij = [
float(S2[:9]),
float(S2[9:18]),
float(S2[18:27]),
float(S2[27:36]),
float(S2[36:45]),
float(S2[45:54])
]
for i in range(S1N[0]):
if not i:
FS = file2.readline()
Sfrac.append(FS[:9]) #'O' or 'delta' = 'length' for crenel
if int(
S1T[0]
): #"", "Legendre" or "Xharm" in 18:27 for "crenel"!
waveType = 'Crenel/Fourier' #all waves 'Fourier' no other choice
crenelType = FS[18:27]
Sfrac.append(
file2.readline()[:18]) #if not crenel = Osin & Ocos
# else Osin & Ocos except last one is X40 = 'Center'
for i in range(S1N[1]):
Spos.append(file2.readline()[:54])
for i in range(S1N[2]):
Sadp.append(file2.readline()[:54] + file2.readline())
if sum(S1N): #if any waves: skip mystery line?
file2.readline()
for i, it in enumerate(Sfrac):
print i, it
if not i:
if 'Crenel' in waveType:
vals = [float(it), float(Sfrac[-1][:9])]
else:
vals = [
float(it),
]
else:
vals = [float(it[:9]), float(it[9:18])]
if 'Crenel' in waveType and i == len(Sfrac) - 1:
del Sfrac[-1]
break
Sfrac[i] = [vals, False]
print Sfrac[i]
for i, it in enumerate(Spos):
if waveType in ['ZigZag', 'Sawtooth'] and not i:
vals = [
float(it[:9]),
float(it[9:18]),
float(it[18:27]),
float(it[27:36])
]
else:
vals = [
float(it[:9]),
float(it[9:18]),
float(it[18:27]),
float(it[27:36]),
float(it[36:45]),
float(it[45:54])
]
Spos[i] = [vals, False]
for i, it in enumerate(Sadp):
vals = [
float(it[:9]),
float(it[9:18]),
float(it[18:27]),
float(it[27:36]),
float(it[36:45]),
float(it[45:54]),
float(it[54:63]),
float(it[63:72]),
float(it[72:81]),
float(it[81:90]),
float(it[90:99]),
float(it[99:108])
]
Sadp[i] = [vals, False]
Atom = [
Name, aType, '', XYZ[0], XYZ[1], XYZ[2], 1.0, SytSym, Mult, IA,
Uiso
]
Atom += Uij
Atom.append(ran.randint(0, sys.maxint))
Atom.append([])
Atom.append([])
Atom.append({
'SS1': {
'waveType': waveType,
'crenelType': crenelType,
'Sfrac': Sfrac,
'Spos': Spos,
'Sadp': Sadp,
'Smag': Smag
}
}) #SS2 is for (3+2), etc.
Atoms.append(Atom)
file2.close()
self.errors = 'Error after read complete'
if not SGData:
raise self.ImportException("No space group (spcgroup entry) found")
if not cell:
raise self.ImportException("No cell found")
Phase = G2IO.SetNewPhase(Name=Title,
SGData=SGData,
cell=cell + [
Volume,
])
Phase['General']['Type'] = Type
Phase['General']['Super'] = nqi
Phase['General']['SuperVec'] = SuperVec
Phase['General']['SuperSg'] = SuperSg
if SuperSg:
Phase['General']['SSGData'] = G2spc.SSpcGroup(SGData, SuperSg)[1]
Phase['General']['AtomPtrs'] = [3, 1, 7, 9]
Phase['Atoms'] = Atoms
return Phase
def DoIndexPeaks(peaks,controls,bravais,dlg,ifX20=True,timeout=None):
'needs a doc string'
delt = 0.005 #lowest d-spacing cushion - can be fixed?
amin = 2.5
amax = 5.0*getDmax(peaks)
dmin = getDmin(peaks)-delt
bravaisNames = ['Cubic-F','Cubic-I','Cubic-P','Trigonal-R','Trigonal/Hexagonal-P',
'Tetragonal-I','Tetragonal-P','Orthorhombic-F','Orthorhombic-I','Orthorhombic-A',
'Orthorhombic-B','Orthorhombic-C',
'Orthorhombic-P','Monoclinic-I','Monoclinic-C','Monoclinic-P','Triclinic']
tries = ['1st','2nd','3rd','4th','5th','6th','7th','8th','9th','10th']
N1s = [1,1,1, 5,5, 5,5, 50,50,50,50,50,50, 100,100,100, 200]
N2s = [1,1,1, 2,2, 2,2, 2,2,2,2,2,2, 2,2,2, 4]
Nm = [1,1,1, 1,1, 1,1, 1,1,1,1,1,1, 2,2,2, 4]
notUse = 0
for peak in peaks:
if not peak[2]:
notUse += 1
Nobs = len(peaks)-notUse
zero,ncno = controls[1:3]
ncMax = Nobs*ncno
print ("%s %8.3f %8.3f" % ('lattice parameter range = ',amin,amax))
print ("%s %.4f %s %d %s %d" % ('Zero =',zero,'Nc/No max =',ncno,' Max Nc =',ncno*Nobs))
cells = []
lastcell = np.zeros(7)
for ibrav in range(17):
begin = time.time()
if bravais[ibrav]:
print ('cell search for ',bravaisNames[ibrav])
print (' M20 X20 Nc a b c alpha beta gamma volume V-test')
V1 = controls[3]
bestM20 = 0
topM20 = 0
cycle = 0
while cycle < 5:
if dlg:
dlg.Raise()
dlg.Update(0,newmsg=tries[cycle]+" cell search for "+bravaisNames[ibrav])
try:
GoOn = True
while GoOn: #Loop over increment of volume
N2 = 0
while N2 < N2s[ibrav]: #Table 2 step (iii)
if time.time() - begin > timeout:
GoOn = False
break
if ibrav > 2:
if not N2:
A = []
GoOn,Skip,Nc,M20,X20,A = findBestCell(dlg,ncMax,A,Nm[ibrav]*N1s[ibrav],ibrav,peaks,V1,ifX20)
if Skip:
break
if A:
GoOn,Skip,Nc,M20,X20,A = findBestCell(dlg,ncMax,A[:],N1s[ibrav],ibrav,peaks,0,ifX20)
else:
GoOn,Skip,Nc,M20,X20,A = findBestCell(dlg,ncMax,0,Nm[ibrav]*N1s[ibrav],ibrav,peaks,V1,ifX20)
if Skip:
break
elif Nc >= ncMax:
GoOn = False
break
elif 3*Nc < Nobs:
N2 = 10
break
else:
if not GoOn:
break
if 1.e6 > M20 > 1.0: #exclude nonsense
bestM20 = max(bestM20,M20)
A = halfCell(ibrav,A[:],peaks)
if ibrav in [14,]:
A = monoCellReduce(ibrav,A[:])
HKL = G2lat.GenHBravais(dmin,ibrav,A)
peaks = IndexPeaks(peaks,HKL)[1]
a,b,c,alp,bet,gam = G2lat.A2cell(A)
V = G2lat.calc_V(A)
if M20 >= 10.0 and X20 <= 2:
cell = [M20,X20,ibrav,a,b,c,alp,bet,gam,V,False,False, Nc]
newcell = np.array(cell[3:10])
if not np.allclose(newcell,lastcell):
print ("%10.3f %3d %3d %10.5f %10.5f %10.5f %10.3f %10.3f %10.3f %10.2f %10.2f %s" \
%(M20,X20,Nc,a,b,c,alp,bet,gam,V,V1,bravaisNames[ibrav]))
cells.append(cell)
lastcell = np.array(cell[3:10])
if not GoOn:
break
N2 += 1
if Skip:
cycle = 10
GoOn = False
break
if ibrav < 13:
V1 *= 1.1
elif ibrav in range(13,17):
V1 *= 1.025
if not GoOn:
if bestM20 > topM20:
topM20 = bestM20
if cells:
V1 = cells[0][9]
else:
V1 = controls[3]
ncMax += Nobs
cycle += 1
print ('Restart search, new Max Nc = %d'%ncMax)
else:
cycle = 10
finally:
pass
# dlg.Destroy()
print ('%s%s%s%s%s%d'%('finished cell search for ',bravaisNames[ibrav], \
', elapsed time = ',G2lat.sec2HMS(time.time()-begin),' Vfinal ',V1))
if cells:
return True,dmin,cells
else:
return False,0,[]
def ReadPDBPhase(self, filename, parent=None):
'''Read a phase from a PDB file.
'''
EightPiSq = 8. * math.pi**2
self.errors = 'Error opening file'
file = open(filename, 'Ur')
Phase = {}
Title = ''
Compnd = ''
Atoms = []
A = np.zeros(shape=(3, 3))
S = file.readline()
line = 1
SGData = None
cell = None
while S:
self.errors = 'Error reading at line ' + str(line)
Atom = []
if 'TITLE' in S[:5]:
Title = S[10:72].strip()
elif 'COMPND ' in S[:10]:
Compnd = S[10:72].strip()
elif 'CRYST' in S[:5]:
abc = S[7:34].split()
angles = S[34:55].split()
cell = [
float(abc[0]),
float(abc[1]),
float(abc[2]),
float(angles[0]),
float(angles[1]),
float(angles[2])
]
Volume = G2lat.calc_V(G2lat.cell2A(cell))
AA, AB = G2lat.cell2AB(cell)
SpGrp = S[55:65]
E, SGData = G2spc.SpcGroup(SpGrp)
# space group processing failed, try to look up name in table
if E:
SpGrpNorm = G2spc.StandardizeSpcName(SpGrp)
if SpGrpNorm:
E, SGData = G2spc.SpcGroup(SpGrpNorm)
while E:
print G2spc.SGErrors(E)
dlg = wx.TextEntryDialog(
parent,
SpGrp[:-1] +
' is invalid \nN.B.: make sure spaces separate axial fields in symbol',
'ERROR in space group symbol',
'',
style=wx.OK)
if dlg.ShowModal() == wx.ID_OK:
SpGrp = dlg.GetValue()
E, SGData = G2spc.SpcGroup(SpGrp)
else:
SGData = G2IO.SGData # P 1
self.warnings += '\nThe space group was not interpreted and has been set to "P 1".'
self.warnings += "Change this in phase's General tab."
dlg.Destroy()
SGlines = G2spc.SGPrint(SGData)
for l in SGlines:
print l
elif 'SCALE' in S[:5]:
V = S[10:41].split()
A[int(S[5]) - 1] = [float(V[0]), float(V[1]), float(V[2])]
elif 'ATOM' in S[:4] or 'HETATM' in S[:6]:
if not SGData:
self.warnings += '\nThe space group was not read before atoms and has been set to "P 1". '
self.warnings += "Change this in phase's General tab."
SGData = G2IO.SGData # P 1
XYZ = [float(S[31:39]), float(S[39:47]), float(S[47:55])]
XYZ = np.inner(AB, XYZ)
XYZ = np.where(abs(XYZ) < 0.00001, 0, XYZ)
SytSym, Mult = G2spc.SytSym(XYZ, SGData)
Uiso = float(S[61:67]) / EightPiSq
Type = S[12:14].lower()
if Type[0] in '123456789':
Type = Type[1:]
Atom = [
S[22:27].strip(), S[17:20].upper(), S[20:22],
S[12:17].strip(),
Type.strip().capitalize(), '', XYZ[0], XYZ[1], XYZ[2],
float(S[55:61]), SytSym, Mult, 'I', Uiso, 0, 0, 0, 0, 0, 0
]
S = file.readline()
line += 1
if 'ANISOU' in S[:6]:
Uij = S[30:72].split()
Uij = [
float(Uij[0]) / 10000.,
float(Uij[1]) / 10000.,
float(Uij[2]) / 10000.,
float(Uij[3]) / 10000.,
float(Uij[4]) / 10000.,
float(Uij[5]) / 10000.
]
Atom = Atom[:14] + Uij
Atom[12] = 'A'
Atom.append(ran.randint(0, sys.maxint))
Atoms.append(Atom)
S = file.readline()
line += 1
file.close()
self.errors = 'Error after read complete'
if Title:
PhaseName = Title
elif Compnd:
PhaseName = Compnd
else:
PhaseName = 'None'
if not SGData:
raise self.ImportException("No space group (CRYST entry) found")
if not cell:
raise self.ImportException("No cell (CRYST entry) found")
Phase = G2IO.SetNewPhase(Name=PhaseName,
SGData=SGData,
cell=cell + [
Volume,
])
Phase['General']['Type'] = 'macromolecular'
Phase['General']['AtomPtrs'] = [6, 4, 10, 12]
Phase['Atoms'] = Atoms
return Phase
def Readrmc6fPhase(self, filename, parent=None):
'''Read a phase from a rmc6f file.
'''
self.errors = 'Error opening file'
fp = open(filename, 'Ur')
Phase = {}
Title = os.path.split(filename)
G2G.SaveGPXdirectory(Title[0])
Title = os.path.splitext(Title[1])[0]
Atoms = []
S = fp.readline()
line = 1
SGData = None
cell = None
IA = 'I'
Uiso = 0.01
Uij = [0. for i in range(6)]
while S:
self.errors = 'Error reading at line ' + str(line)
Atom = []
if 'Cell' in S[:4]:
cellRec = S.split(':')[1].split()
abc = cellRec[:3]
angles = cellRec[3:]
cell = [
float(abc[0]),
float(abc[1]),
float(abc[2]),
float(angles[0]),
float(angles[1]),
float(angles[2])
]
Volume = G2lat.calc_V(G2lat.cell2A(cell))
AA, AB = G2lat.cell2AB(cell)
SGData = G2obj.P1SGData # P 1
elif 'Atoms' in S[:5]:
S = fp.readline()[:-1]
AtRec = S.split()
for ix, s in enumerate(AtRec):
if '.' in s:
break #is points at x
while S:
AtRec = S.split()
Atype = AtRec[1]
Aname = Atype + AtRec[0]
Afrac = 1.0
x, y, z = AtRec[ix:ix + 3]
XYZ = np.array([float(x), float(y), float(z)])
SytSym, Mult = '1', 1
Atom = [
Aname, Atype, '', XYZ[0], XYZ[1], XYZ[2], Afrac,
SytSym, Mult, IA, Uiso
]
Atom += Uij
Atom.append(ran.randint(0, sys.maxsize))
Atoms.append(Atom)
S = fp.readline()[:-1]
S = fp.readline()
line += 1
fp.close()
self.errors = 'Error after read complete'
Phase = G2obj.SetNewPhase(Name='RMCProfile phase',
SGData=SGData,
cell=cell + [
Volume,
])
Phase['General']['Name'] = Title
Phase['General']['Type'] = 'nuclear'
Phase['General']['AtomPtrs'] = [3, 1, 7, 9]
Phase['Atoms'] = Atoms
return Phase