def ranAbyV(Bravais,dmin,dmax,V):
'needs a doc string'
cell = [0,0,0,0,0,0]
bad = True
while bad:
bad = False
cell = rancell(Bravais,dmin,dmax)
G,g = G2lat.cell2Gmat(cell)
A = G2lat.Gmat2A(G)
if G2lat.calc_rVsq(A) < 1:
scaleAbyV(A,V)
cell = G2lat.A2cell(A)
for i in range(3):
bad |= cell[i] < dmin
return A
def ranAbyV(Bravais,dmin,dmax,V):
'needs a doc string'
cell = [0,0,0,0,0,0]
bad = True
while bad:
bad = False
cell = rancell(Bravais,dmin,dmax)
G,g = G2lat.cell2Gmat(cell)
A = G2lat.Gmat2A(G)
if G2lat.calc_rVsq(A) < 1:
scaleAbyV(A,V)
cell = G2lat.A2cell(A)
for i in range(3):
bad |= cell[i] < dmin
return A
def ReadJANAPhase(self, filename, parent=None):
'''Read a phase from a JANA2006 m50 & m40 files.
'''
self.errors = 'Error opening file'
fp = open(filename, 'Ur') #contains only cell & spcgroup
Phase = {}
Title = os.path.basename(filename)
Type = 'nuclear'
Atoms = []
Atypes = []
SuperVec = [[0, 0, .1], False, 4]
S = fp.readline()
line = 1
SGData = None
SuperSg = ''
cell = None
nqi = 0
version = '2000'
while S:
self.errors = 'Error reading at line ' + str(line)
if 'title' in S and S != 'title\n':
Title = S.split()[1]
elif 'Jana2006' in S:
self.warnings += '\nJana2006 file detected'
version = '2006'
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))
G, g = G2lat.cell2Gmat(cell)
ast = np.sqrt(np.diag(G))
Mast = np.multiply.outer(ast, ast)
elif 'spgroup' in S:
if 'X' in S:
raise self.ImportException(
"Ad hoc Supersymmetry centering " + S +
" not allowed in GSAS-II")
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 = 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 'qi' in S[:2]:
if nqi:
raise self.ImportException(
"Supersymmetry too high; GSAS-II limited to (3+1) supersymmetry"
)
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 = fp.readline()
line += 1
fp.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 = G2obj.P1SGData # 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])]
Spos = []
Sadp = []
Sfrac = []
Smag = []
XYZ = [float(S1[27:36]), float(S1[36:45]), float(S1[45:54])]
SytSym, Mult = G2spc.SytSym(XYZ, SGData)[:2]
aType = Atypes[int(S1[9:11]) - 1]
Name = S1[:8].strip()
if S1[11:15].strip() == '1':
S2 = file2.readline()
Uiso = S2[:9]
if version == '2000':
Uiso = R2pisq * float(Uiso) / 4. #Biso -> Uiso
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])
] #Uij in Jana2006!
if version == '2000':
Uij = R2pisq * G2lat.UijtoU6(
G2lat.U6toUij(Uij) / Mast
) #these things are betaij in Jana2000! need to convert to Uij
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
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 [
'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])
]
#these are betaij modulations in Jana2000! need to convert to Uij modulations
if version == '2000':
vals[:6] = R2pisq * G2lat.UijtoU6(
G2lat.U6toUij(vals[:6]) /
Mast) #convert sin bij to Uij
vals[6:] = R2pisq * G2lat.UijtoU6(
G2lat.U6toUij(vals[6:]) /
Mast) #convert cos bij to Uij
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.maxsize))
Atom.append({
'SS1': {
'Sfrac': [
waveType,
] + Sfrac,
'Spos': [
waveType,
] + Spos,
'Sadp': [
'Fourier',
] + Sadp,
'Smag': [
'Fourier',
] + 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 = G2obj.SetNewPhase(Name=Title,
SGData=SGData,
cell=cell + [
Volume,
])
Phase['General']['Type'] = Type
Phase['General']['Modulated'] = True
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