def OnSpaceGroup(event):
Flds = SGTxt.GetValue().split()
#get rid of extra spaces between fields first
for fld in Flds:
fld = fld.strip()
SpcGp = ' '.join(Flds)
# try a lookup on the user-supplied name
SpGrpNorm = G2spc.StandardizeSpcName(SpcGp)
if SpGrpNorm:
SGErr, SGData = G2spc.SpcGroup(SpGrpNorm)
else:
SGErr, SGData = G2spc.SpcGroup(SpcGp)
if SGErr:
text = [
G2spc.SGErrors(SGErr) + '\nSpace Group set to previous'
]
SGTxt.SetValue(Data['SGData']['SpGrp'])
msg = 'Space Group Error'
Style = wx.ICON_EXCLAMATION
Text = '\n'.join(text)
wx.MessageBox(Text, caption=msg, style=Style)
else:
text, table = G2spc.SGPrint(SGData)
Data['SGData'] = SGData
SGTxt.SetValue(Data['SGData']['SpGrp'])
msg = 'Space Group Information'
G2G.SGMessageBox(self, msg, text, table).Show()
SSChoice = G2spc.SSChoice(Data['SGData'])
Data['SuperSg'] = SSChoice[0]
self.UpdateData(Data)
def GenSGdat(spc):
(E, D) = GSASIIspc.SpcGroup(spc)
if E:
print >> sys.stderr, "error on: ", spc
else:
sgdat[spc] = D
sglist[spc] = GSASIIspc.SGPrint(D)
def __init__(self, parent):
self._init_ctrls(parent)
self.Bind(wx.EVT_CLOSE, self.ExitMain)
self.dataFrame = None
Data = {
'SGData': G2spc.SpcGroup('P 1')[1],
'SuperSg': '(abg)',
}
self.UpdateData(Data)
def test():
SGData = G2spc.SpcGroup('p -3 m 1')[1]
results,baseList = GetNonStdSubgroupsmag(SGData,('1/3','1/3','1/2',' ',' ',' ',' ',' ',' ',' '))
if results:
for [spgp,mv,bns,gid,altList,supList] in results:
if gid in baseList:
print('Space group:',spgp, 'BNS:',bns)
print('MV')
print(mv)
results,baseList = GetNonStdSubgroups(SGData,('1/3','1/3','1/2',' ',' ',' ',' ',' ',' ',' '))
if results:
for [spgp,mv,gid,altList,supList] in results:
if gid in baseList:
print('Space group:',spgp)
print('MV')
print(mv)
def test():
SGData = G2spc.SpcGroup('f d -3 m')[1]
print('test SUBGROUPSMAG')
results,baseList = GetNonStdSubgroupsmag(SGData,('0','0','0',' ',' ',' ',' ',' ',' ',' '))
if results:
for [spgp,bns,mv,gid,altList,supList] in results:
if gid in baseList:
print('Space group: %d %s BNS: %s'%(gid,spgp,bns))
print('MV',mv)
print('altList:',altList)
print('superList: ',supList)
print('test SUBGROUPS')
results,baseList = GetNonStdSubgroups(SGData,('1/3','1/3','1/2',' ',' ',' ',' ',' ',' ',' '))
if results:
for [spgp,mv,gid,altList,supList] in results:
if gid in baseList:
print('Space group: %d %s'%(gid,spgp))
print('MV',mv)
print('altList:',altList)
print('superList: ',supList)
def ImageCalibrate(self, data):
'Needs a doc string'
import copy
import ImageCalibrants as calFile
print 'Image calibration:'
time0 = time.time()
ring = data['ring']
pixelSize = data['pixelSize']
scalex = 1000. / pixelSize[0]
scaley = 1000. / pixelSize[1]
pixLimit = data['pixLimit']
cutoff = data['cutoff']
varyDict = data['varyList']
if varyDict['dist'] and varyDict['wave']:
print 'ERROR - you can not simultaneously calibrate distance and wavelength'
return False
if len(ring) < 5:
print 'ERROR - not enough inner ring points for ellipse'
return False
#fit start points on inner ring
data['ellipses'] = []
data['rings'] = []
outE = FitEllipse(ring)
fmt = '%s X: %.3f, Y: %.3f, phi: %.3f, R1: %.3f, R2: %.3f'
fmt2 = '%s X: %.3f, Y: %.3f, phi: %.3f, R1: %.3f, R2: %.3f, chi**2: %.3f, Np: %d'
if outE:
print fmt % ('start ellipse: ', outE[0][0], outE[0][1], outE[1],
outE[2][0], outE[2][1])
ellipse = outE
else:
return False
#setup 360 points on that ring for "good" fit
data['ellipses'].append(ellipse[:] + ('g', ))
Ring = makeRing(1.0, ellipse, pixLimit, cutoff, scalex, scaley,
self.ImageZ)
if Ring:
ellipse = FitEllipse(Ring)
Ring = makeRing(1.0, ellipse, pixLimit, cutoff, scalex, scaley,
self.ImageZ) #do again
ellipse = FitEllipse(Ring)
else:
print '1st ring not sufficiently complete to proceed'
return False
if debug:
print fmt2 % ('inner ring: ', ellipse[0][0], ellipse[0][1],
ellipse[1], ellipse[2][0], ellipse[2][1], 0., len(Ring)
) #cent,phi,radii
data['ellipses'].append(ellipse[:] + ('r', ))
data['rings'].append(np.array(Ring))
G2plt.PlotImage(self, newImage=True)
#setup for calibration
data['rings'] = []
if not data['calibrant']:
print 'no calibration material selected'
return True
skip = data['calibskip']
dmin = data['calibdmin']
#generate reflection set
Bravais, SGs, Cells = calFile.Calibrants[data['calibrant']][:3]
HKL = []
for bravais, sg, cell in zip(Bravais, SGs, Cells):
A = G2lat.cell2A(cell)
if sg:
SGData = G2spc.SpcGroup(sg)[1]
hkl = G2pwd.getHKLpeak(dmin, SGData, A)
HKL += hkl
else:
hkl = G2lat.GenHBravais(dmin, bravais, A)
HKL += hkl
HKL = G2lat.sortHKLd(HKL, True, False)[skip:]
#set up 1st ring
elcent, phi, radii = ellipse #from fit of 1st ring
dsp = HKL[0][3]
print '1st ring: try %.4f' % (dsp)
if varyDict['dist']:
wave = data['wavelength']
tth = 2.0 * asind(wave / (2. * dsp))
else: #varyDict['wave']!
dist = data['distance']
tth = npatan2d(radii[0], dist)
data['wavelength'] = wave = 2.0 * dsp * sind(tth / 2.0)
Ring0 = makeRing(dsp, ellipse, 3, cutoff, scalex, scaley, self.ImageZ)
ttth = nptand(tth)
stth = npsind(tth)
ctth = npcosd(tth)
#1st estimate of tilt; assume ellipse - don't know sign though
if varyDict['tilt']:
tilt = npasind(np.sqrt(max(0., 1. - (radii[0] / radii[1])**2)) * ctth)
if not tilt:
print 'WARNING - selected ring was fitted as a circle'
print ' - if detector was tilted we suggest you skip this ring - WARNING'
else:
tilt = data['tilt']
#1st estimate of dist: sample to detector normal to plane
if varyDict['dist']:
data['distance'] = dist = radii[0]**2 / (ttth * radii[1])
else:
dist = data['distance']
if varyDict['tilt']:
#ellipse to cone axis (x-ray beam); 2 choices depending on sign of tilt
zdisp = radii[1] * ttth * tand(tilt)
zdism = radii[1] * ttth * tand(-tilt)
#cone axis position; 2 choices. Which is right?
#NB: zdisp is || to major axis & phi is rotation of minor axis
#thus shift from beam to ellipse center is [Z*sin(phi),-Z*cos(phi)]
centp = [elcent[0] + zdisp * sind(phi), elcent[1] - zdisp * cosd(phi)]
centm = [elcent[0] + zdism * sind(phi), elcent[1] - zdism * cosd(phi)]
#check get same ellipse parms either way
#now do next ring; estimate either way & do a FitDetector each way; best fit is correct one
fail = True
i2 = 1
while fail:
dsp = HKL[i2][3]
print '2nd ring: try %.4f' % (dsp)
tth = 2.0 * asind(wave / (2. * dsp))
ellipsep = GetEllipse2(tth, 0., dist, centp, tilt, phi)
print fmt % ('plus ellipse :', ellipsep[0][0], ellipsep[0][1],
ellipsep[1], ellipsep[2][0], ellipsep[2][1])
Ringp = makeRing(dsp, ellipsep, 3, cutoff, scalex, scaley,
self.ImageZ)
parmDict = {
'dist': dist,
'det-X': centp[0],
'det-Y': centp[1],
'tilt': tilt,
'phi': phi,
'wave': wave,
'dep': 0.0
}
varyList = [item for item in varyDict if varyDict[item]]
if len(Ringp) > 10:
chip = FitDetector(np.array(Ring0 + Ringp), varyList, parmDict,
True)
tiltp = parmDict['tilt']
phip = parmDict['phi']
centp = [parmDict['det-X'], parmDict['det-Y']]
fail = False
else:
chip = 1e6
ellipsem = GetEllipse2(tth, 0., dist, centm, -tilt, phi)
print fmt % ('minus ellipse:', ellipsem[0][0], ellipsem[0][1],
ellipsem[1], ellipsem[2][0], ellipsem[2][1])
Ringm = makeRing(dsp, ellipsem, 3, cutoff, scalex, scaley,
self.ImageZ)
if len(Ringm) > 10:
parmDict['tilt'] *= -1
chim = FitDetector(np.array(Ring0 + Ringm), varyList, parmDict,
True)
tiltm = parmDict['tilt']
phim = parmDict['phi']
centm = [parmDict['det-X'], parmDict['det-Y']]
fail = False
else:
chim = 1e6
if fail:
i2 += 1
if chip < chim:
data['tilt'] = tiltp
data['center'] = centp
data['rotation'] = phip
else:
data['tilt'] = tiltm
data['center'] = centm
data['rotation'] = phim
data['ellipses'].append(ellipsep[:] + ('b', ))
data['rings'].append(np.array(Ringp))
data['ellipses'].append(ellipsem[:] + ('r', ))
data['rings'].append(np.array(Ringm))
G2plt.PlotImage(self, newImage=True)
parmDict = {
'dist': data['distance'],
'det-X': data['center'][0],
'det-Y': data['center'][1],
'tilt': data['tilt'],
'phi': data['rotation'],
'wave': data['wavelength'],
'dep': data['DetDepth']
}
varyList = [item for item in varyDict if varyDict[item]]
data['rings'] = []
data['ellipses'] = []
for i, H in enumerate(HKL):
dsp = H[3]
tth = 2.0 * asind(wave / (2. * dsp))
if tth + abs(data['tilt']) > 90.:
print 'next line is a hyperbola - search stopped'
break
if debug: print 'HKLD:', H[:4], '2-theta: %.4f' % (tth)
elcent, phi, radii = ellipse = GetEllipse(dsp, data)
data['ellipses'].append(copy.deepcopy(ellipse + ('g', )))
if debug:
print fmt % ('predicted ellipse:', elcent[0], elcent[1], phi,
radii[0], radii[1])
Ring = makeRing(dsp, ellipse, pixLimit, cutoff, scalex, scaley,
self.ImageZ)
if Ring:
data['rings'].append(np.array(Ring))
rings = np.concatenate((data['rings']), axis=0)
if i:
chisq = FitDetector(rings, varyList, parmDict, False)
data['distance'] = parmDict['dist']
data['center'] = [parmDict['det-X'], parmDict['det-Y']]
data['rotation'] = parmDict['phi']
data['tilt'] = parmDict['tilt']
data['DetDepth'] = parmDict['dep']
data['chisq'] = chisq
elcent, phi, radii = ellipse = GetEllipse(dsp, data)
if debug:
print fmt2 % ('fitted ellipse: ', elcent[0], elcent[1],
phi, radii[0], radii[1], chisq, len(rings))
data['ellipses'].append(copy.deepcopy(ellipse + ('r', )))
# G2plt.PlotImage(self,newImage=True)
else:
if debug:
print 'insufficient number of points in this ellipse to fit'
# break
G2plt.PlotImage(self, newImage=True)
fullSize = len(self.ImageZ) / scalex
if 2 * radii[1] < .9 * fullSize:
print 'Are all usable rings (>25% visible) used? Try reducing Min ring I/Ib'
N = len(data['ellipses'])
if N > 2:
FitDetector(rings, varyList, parmDict)
data['wavelength'] = parmDict['wave']
data['distance'] = parmDict['dist']
data['center'] = [parmDict['det-X'], parmDict['det-Y']]
data['rotation'] = parmDict['phi']
data['tilt'] = parmDict['tilt']
data['DetDepth'] = parmDict['dep']
for H in HKL[:N]:
ellipse = GetEllipse(H[3], data)
data['ellipses'].append(copy.deepcopy(ellipse + ('b', )))
print 'calibration time = ', time.time() - time0
G2plt.PlotImage(self, newImage=True)
return True
def ImageRecalibrate(self, data, masks):
'Needs a doc string'
import ImageCalibrants as calFile
print 'Image recalibration:'
time0 = time.time()
pixelSize = data['pixelSize']
scalex = 1000. / pixelSize[0]
scaley = 1000. / pixelSize[1]
pixLimit = data['pixLimit']
cutoff = data['cutoff']
data['rings'] = []
data['ellipses'] = []
if not data['calibrant']:
print 'no calibration material selected'
return True
skip = data['calibskip']
dmin = data['calibdmin']
Bravais, SGs, Cells = calFile.Calibrants[data['calibrant']][:3]
HKL = []
for bravais, sg, cell in zip(Bravais, SGs, Cells):
A = G2lat.cell2A(cell)
if sg:
SGData = G2spc.SpcGroup(sg)[1]
hkl = G2pwd.getHKLpeak(dmin, SGData, A)
HKL += hkl
else:
hkl = G2lat.GenHBravais(dmin, bravais, A)
HKL += hkl
HKL = G2lat.sortHKLd(HKL, True, False)
varyList = [item for item in data['varyList'] if data['varyList'][item]]
parmDict = {
'dist': data['distance'],
'det-X': data['center'][0],
'det-Y': data['center'][1],
'tilt': data['tilt'],
'phi': data['rotation'],
'wave': data['wavelength'],
'dep': data['DetDepth']
}
Found = False
wave = data['wavelength']
frame = masks['Frames']
tam = ma.make_mask_none(self.ImageZ.shape)
if frame:
tam = ma.mask_or(tam, MakeFrameMask(data, frame))
for iH, H in enumerate(HKL):
if debug: print H
dsp = H[3]
tth = 2.0 * asind(wave / (2. * dsp))
if tth + abs(data['tilt']) > 90.:
print 'next line is a hyperbola - search stopped'
break
ellipse = GetEllipse(dsp, data)
Ring = makeRing(dsp, ellipse, pixLimit, cutoff, scalex, scaley,
ma.array(self.ImageZ, mask=tam))
if Ring:
if iH >= skip:
data['rings'].append(np.array(Ring))
data['ellipses'].append(copy.deepcopy(ellipse + ('r', )))
Found = True
elif not Found: #skipping inner rings, keep looking until ring found
continue
else: #no more rings beyond edge of detector
data['ellipses'].append([])
continue
# break
rings = np.concatenate((data['rings']), axis=0)
chisq = FitDetector(rings, varyList, parmDict)
data['wavelength'] = parmDict['wave']
data['distance'] = parmDict['dist']
data['center'] = [parmDict['det-X'], parmDict['det-Y']]
data['rotation'] = np.mod(parmDict['phi'], 360.0)
data['tilt'] = parmDict['tilt']
data['DetDepth'] = parmDict['dep']
data['chisq'] = chisq
N = len(data['ellipses'])
data['ellipses'] = [] #clear away individual ellipse fits
for H in HKL[:N]:
ellipse = GetEllipse(H[3], data)
data['ellipses'].append(copy.deepcopy(ellipse + ('b', )))
print 'calibration time = ', time.time() - time0
G2plt.PlotImage(self, newImage=True)
return True
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 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 UpdateData(self, Data):
def OnExhaustive(event):
SSList = G2spc.SSChoice(Data['SGData'])
print(SSList)
def OnSpaceGroup(event):
Flds = SGTxt.GetValue().split()
#get rid of extra spaces between fields first
for fld in Flds:
fld = fld.strip()
SpcGp = ' '.join(Flds)
# try a lookup on the user-supplied name
SpGrpNorm = G2spc.StandardizeSpcName(SpcGp)
if SpGrpNorm:
SGErr, SGData = G2spc.SpcGroup(SpGrpNorm)
else:
SGErr, SGData = G2spc.SpcGroup(SpcGp)
if SGErr:
text = [
G2spc.SGErrors(SGErr) + '\nSpace Group set to previous'
]
SGTxt.SetValue(Data['SGData']['SpGrp'])
msg = 'Space Group Error'
Style = wx.ICON_EXCLAMATION
Text = '\n'.join(text)
wx.MessageBox(Text, caption=msg, style=Style)
else:
text, table = G2spc.SGPrint(SGData)
Data['SGData'] = SGData
SGTxt.SetValue(Data['SGData']['SpGrp'])
msg = 'Space Group Information'
G2G.SGMessageBox(self, msg, text, table).Show()
SSChoice = G2spc.SSChoice(Data['SGData'])
Data['SuperSg'] = SSChoice[0]
self.UpdateData(Data)
def OnSuperGp(event):
SSymbol = superGp.GetValue()
SpGrp = Data['SGData']['SpGrp']
if Data['SGData']['SGGray']: SpGrp += " 1'"
print('Try: %s%s' % (Data['SGData']['SpGrp'], SSymbol))
E, SSGData = G2spc.SSpcGroup(Data['SGData'], SSymbol)
if SSGData:
text, table = G2spc.SSGPrint(Data['SGData'], SSGData)
Data['SSGData'] = SSGData
Data['SuperSg'] = SSymbol
msg = 'Superspace Group Information'
G2G.SGMessageBox(self, msg, text, table).Show()
print('Super spacegroup operators for ' + SSGData['SSpGrp'])
for Op in SSGData['SSGOps']:
print(G2spc.SSMT2text(Op).replace(' ', ''))
if SGData['SGInv']:
for Op in SSGData['SSGOps']:
Op = [-Op[0], -Op[1] % 1.]
print(G2spc.SSMT2text(Op).replace(' ', ''))
else:
text = [E + '\nSuperspace Group set to previous']
superGp.SetValue(Data['SuperSg'])
msg = 'Superspace Group Error'
Style = wx.ICON_EXCLAMATION
Text = '\n'.join(text)
wx.MessageBox(Text, caption=msg, style=Style)
wx.CallAfter(self.UpdateData, Data)
SGData = G2spc.SpcGroup(Data['SGData']['SpGrp'])[1]
self.testSSPanel.DestroyChildren()
mainSizer = wx.FlexGridSizer(0, 2, 5, 5)
mainSizer.Add(wx.StaticText(self.testSSPanel, -1, ' Space group: '),
0, WACV)
SpGrp = Data['SGData']['SpGrp']
if Data['SGData']['SGGray']: SpGrp += " 1'"
SGTxt = wx.TextCtrl(self.testSSPanel,
-1,
value=SpGrp,
style=wx.TE_PROCESS_ENTER)
SGTxt.Bind(wx.EVT_TEXT_ENTER, OnSpaceGroup)
mainSizer.Add(SGTxt, 0, WACV)
mainSizer.Add(
wx.StaticText(self.testSSPanel,
label=' Superspace group: ' + SpGrp), 0, WACV)
ssChoice = G2spc.SSChoice(Data['SGData'])
ssSym = Data['SuperSg']
if ssChoice:
superGp = wx.ComboBox(self.testSSPanel,
value=ssSym,
choices=ssChoice,
style=wx.CB_DROPDOWN) #wx.CB_READONLY|
superGp.Bind(wx.EVT_COMBOBOX, OnSuperGp)
superGp.Bind(wx.EVT_TEXT_ENTER, OnSuperGp)
else: #nonstandard space group symbol not in my dictionary
superGp = wx.TextCtrl(self.testSSPanel,
value=ssSym,
style=wx.TE_PROCESS_ENTER)
superGp.Bind(wx.EVT_TEXT_ENTER, OnSuperGp)
mainSizer.Add(superGp, 0, WACV)
mainSizer.Add(wx.StaticText(self.testSSPanel, -1, ' Exhaustive try: '),
0, WACV)
ESStry = wx.Button(self.testSSPanel, -1, 'OK')
ESStry.Bind(wx.EVT_BUTTON, OnExhaustive)
mainSizer.Add(ESStry, 0, WACV)
self.testSSPanel.SetSizer(mainSizer)
Size = mainSizer.Fit(self.testSSPanel)
Size[0] = 800
Size[1] = max(Size[1], 350)
self.testSSPanel.SetSize(Size)
def findMV(peaks, controls, ssopt, Inst, dlg):
def Val2Vec(vec, Vref, values):
Vec = []
i = 0
for j, r in enumerate(Vref):
if r:
if values.size > 1:
Vec.append(max(-1., min(1.0, values[i])))
else:
Vec.append(max(0.0, min(1.0, values)))
i += 1
else:
Vec.append(vec[j])
return np.array(Vec)
def ZSSfunc(values,
peaks,
dmin,
Inst,
SGData,
SSGData,
vec,
Vref,
maxH,
A,
wave,
Z,
dlg=None):
Vec = Val2Vec(vec, Vref, values)
HKL = G2pwd.getHKLMpeak(dmin, Inst, SGData, SSGData, Vec, maxH, A)
Peaks = np.array(IndexSSPeaks(peaks, HKL)[1]).T
Qo = 1. / Peaks[-2]**2
Qc = G2lat.calc_rDsqZSS(Peaks[4:8], A, Vec, Z, Peaks[0], wave)
chi = np.sum((Qo - Qc)**2)
if dlg:
dlg.Pulse()
return chi
def TSSfunc(values,
peaks,
dmin,
Inst,
SGData,
SSGData,
vec,
Vref,
maxH,
A,
difC,
Z,
dlg=None):
Vec = Val2Vec(vec, Vref, values)
HKL = G2pwd.getHKLMpeak(dmin, Inst, SGData, SSGData, Vec, maxH, A)
Peaks = np.array(IndexSSPeaks(peaks, HKL)[1]).T
Qo = 1. / Peaks[-2]**2
Qc = G2lat.calc_rDsqTSS(Peaks[4:8], A, Vec, Z, Peaks[0], difC)
chi = np.sum((Qo - Qc)**2)
if dlg:
dlg.Pulse()
return chi
if 'T' in Inst['Type'][0]:
difC = Inst['difC'][1]
else:
wave = G2mth.getWave(Inst)
SGData = G2spc.SpcGroup(controls[13])[1]
SSGData = G2spc.SSpcGroup(SGData, ssopt['ssSymb'])[1]
A = G2lat.cell2A(controls[6:12])
Z = controls[1]
Vref = [True if x in ssopt['ssSymb'] else False for x in ['a', 'b', 'g']]
values = []
ranges = []
dT = 0.01 #seems to be a good choice
for v, r in zip(ssopt['ModVec'], Vref):
if r:
ranges += [
slice(dT, 1. - dT, dT),
] #NB: unique part for (00g) & (a0g); (abg)?
values += [
v,
]
dmin = getDmin(peaks) - 0.005
if 'T' in Inst['Type'][0]:
result = so.brute(TSSfunc,
ranges,
finish=so.fmin_cg,
full_output=True,
args=(peaks, dmin, Inst, SGData, SSGData,
ssopt['ModVec'], Vref, 1, A, difC, Z, dlg))
else:
result = so.brute(ZSSfunc,
ranges,
finish=so.fmin_cg,
full_output=True,
args=(peaks, dmin, Inst, SGData, SSGData,
ssopt['ModVec'], Vref, 1, A, wave, Z, dlg))
return Val2Vec(ssopt['ModVec'], Vref, result[0]), result
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 findMV(peaks, controls, ssopt, Inst, dlg):
def Val2Vec(vec, Vref, values):
Vec = []
i = 0
for j, r in enumerate(Vref):
if r:
if values.size > 1:
Vec.append(max(0.0, min(1.0, values[i])))
else:
Vec.append(max(0.0, min(1.0, values)))
i += 1
else:
Vec.append(vec[j])
return np.array(Vec)
def ZSSfunc(values,
peaks,
dmin,
Inst,
SGData,
SSGData,
vec,
Vref,
maxH,
A,
wave,
Z,
dlg=None):
Vec = Val2Vec(vec, Vref, values)
HKL = G2pwd.getHKLMpeak(dmin, Inst, SGData, SSGData, Vec, maxH, A)
Peaks = np.array(IndexSSPeaks(peaks, HKL)[1]).T
Qo = 1. / Peaks[-2]**2
Qc = G2lat.calc_rDsqZSS(Peaks[4:8], A, Vec, Z, Peaks[0], wave)
chi = np.sum((Qo - Qc)**2)
if dlg:
dlg.Pulse()
return chi
if 'C' in Inst['Type'][0]:
wave = G2mth.getWave(Inst)
else:
difC = Inst['difC'][1]
SGData = G2spc.SpcGroup(controls[13])[1]
SSGData = G2spc.SSpcGroup(SGData, ssopt['ssSymb'])[1]
A = G2lat.cell2A(controls[6:12])
Z = controls[1]
Vref = [True if x in ssopt['ssSymb'] else False for x in ['a', 'b', 'g']]
values = []
ranges = []
for v, r in zip(ssopt['ModVec'], Vref):
if r:
ranges += [
slice(.02, .98, .05),
]
values += [
v,
]
dmin = getDmin(peaks) - 0.005
Peaks = np.copy(np.array(peaks).T)
result = so.brute(ZSSfunc,
ranges,
finish=so.fmin_cg,
args=(peaks, dmin, Inst, SGData, SSGData,
ssopt['ModVec'], Vref, ssopt['maxH'], A, wave, Z,
dlg))
return Val2Vec(ssopt['ModVec'], Vref, result)