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 refinePeaksT(peaks, difC, ibrav, A, Zero, ZeroRef):
'needs a doc string'
dmin = getDmin(peaks)
OK, smin, Aref, Z, result = FitHKLT(difC, ibrav, peaks, A, Zero, ZeroRef)
Peaks = np.array(peaks).T
H = Peaks[4:7]
Peaks[8] = 1. / np.sqrt(G2lat.calc_rDsqT(H, Aref, Z, Peaks[0], difC))
peaks = Peaks.T
HKL = G2lat.GenHBravais(dmin, ibrav, A)
M20, X20 = calc_M20(peaks, HKL)
return len(HKL), M20, X20, Aref, Z
def refinePeaksTSS(peaks, difC, Inst, SGData, SSGData, maxH, ibrav, A, vec,
vecRef, Zero, ZeroRef):
'needs a doc string'
dmin = getDmin(peaks)
OK, smin, Aref, Vref, Z, result = FitHKLTSS(difC, ibrav, peaks, A, vec,
vecRef, Zero, ZeroRef)
Peaks = np.array(peaks).T
H = Peaks[4:8]
Peaks[9] = 1. / np.sqrt(
G2lat.calc_rDsqTSS(H, Aref, Vref, Z, Peaks[0], difC))
peaks = Peaks.T
HKL = G2pwd.getHKLMpeak(dmin, Inst, SGData, SSGData, Vref, maxH, Aref)
HKL = G2lat.GenHBravais(dmin, ibrav, A)
M20, X20 = calc_M20SS(peaks, HKL)
return len(HKL), M20, X20, Aref, Vref, Z
def findBestCell(dlg,ncMax,A,Ntries,ibrav,peaks,V1,ifX20=True):
'needs a doc string'
# dlg & ncMax are used for wx progress bar
# A != 0 find the best A near input A,
# A = 0 for random cell, volume normalized to V1;
# returns number of generated hkls, M20, X20 & A for best found
mHKL = [3,3,3, 5,5, 5,5, 7,7,7,7,7,7, 9,9,9, 10]
dmin = getDmin(peaks)-0.05
amin = 2.5
amax = 5.*getDmax(peaks)
Asave = []
GoOn = True
Skip = False
if A:
HKL = G2lat.GenHBravais(dmin,ibrav,A[:])
if len(HKL) > mHKL[ibrav]:
peaks = IndexPeaks(peaks,HKL)[1]
Asave.append([calc_M20(peaks,HKL,ifX20),A[:]])
tries = 0
while tries < Ntries and GoOn:
if A:
Abeg = ranAbyR(ibrav,A,tries+1,Ntries,ran2axis)
if ibrav > 12: #monoclinic & triclinic
Abeg = ranAbyR(ibrav,A,tries/10+1,Ntries,ran2axis)
else:
Abeg = ranAbyV(ibrav,amin,amax,V1)
HKL = G2lat.GenHBravais(dmin,ibrav,Abeg)
Nc = len(HKL)
if Nc >= ncMax:
GoOn = False
else:
if dlg:
dlg.Raise()
GoOn = dlg.Update(100*Nc/ncMax)[0]
if Skip or not GoOn:
GoOn = False
break
if IndexPeaks(peaks,HKL)[0] and len(HKL) > mHKL[ibrav]:
Lhkl,M20,X20,Aref = refinePeaks(peaks,ibrav,Abeg,ifX20)
Asave.append([calc_M20(peaks,HKL,ifX20),Aref[:]])
if ibrav in [9,10,11]: #C-centered orthorhombic
for i in range(2):
Abeg = rotOrthoA(Abeg[:])
Lhkl,M20,X20,Aref = refinePeaks(peaks,ibrav,Abeg,ifX20)
HKL = G2lat.GenHBravais(dmin,ibrav,Aref)
peaks = IndexPeaks(peaks,HKL)[1]
Asave.append([calc_M20(peaks,HKL,ifX20),Aref[:]])
elif ibrav == 13: #C-centered monoclinic
Abeg = swapMonoA(Abeg[:])
Lhkl,M20,X20,Aref = refinePeaks(peaks,ibrav,Abeg,ifX20)
HKL = G2lat.GenHBravais(dmin,ibrav,Aref)
peaks = IndexPeaks(peaks,HKL)[1]
Asave.append([calc_M20(peaks,HKL,ifX20),Aref[:]])
else:
break
Nc = len(HKL)
tries += 1
X = sortM20(Asave)
if X:
Lhkl,M20,X20,A = refinePeaks(peaks,ibrav,X[0][1],ifX20)
return GoOn,Skip,Lhkl,M20,X20,A
else:
return GoOn,Skip,0,0,0,0
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, []