def test1():
if NeedTestData: TestData()
ibrav, A, Pwr, peaks = TestData2
print('bad cell:', G2lat.A2cell(A))
print('FitHKL')
OK, smin, A, result = FitHKL(ibrav, peaks, A, Pwr)
result = refinePeaks(peaks, ibrav, A)
N, M20, X20, A = result
print('refinePeaks:', N, M20, X20, A)
def test0():
if NeedTestData: TestData()
ibrav, cell, bestcell, Pwr, peaks = TestData
print('best cell:', bestcell)
print('old cell:', cell)
Peaks = np.array(peaks)
HKL = Peaks[4:7]
print(calc_M20(peaks, HKL))
A = G2lat.cell2A(cell)
OK, smin, A, result = FitHKL(ibrav, peaks, A, Pwr)
print('new cell:', G2lat.A2cell(A))
print('x:', result[0])
print('cov_x:', result[1])
print('infodict:')
for item in result[2]:
print(item, result[2][item])
print('msg:', result[3])
print('ier:', result[4])
result = refinePeaks(peaks, ibrav, A)
N, M20, X20, A = result
print('refinePeaks:', N, M20, X20, G2lat.A2cell(A))
print('compare bestcell:', bestcell)
def test0():
if NeedTestData: TestData()
msg = 'test FitHKL'
ibrav, cell, bestcell, Pwr, peaks = TestData
print 'best cell:', bestcell
print 'old cell:', cell
Peaks = np.array(peaks)
HKL = Peaks[4:7]
print calc_M20(peaks, HKL)
A = G2lat.cell2A(cell)
OK, smin, A, result = FitHKL(ibrav, peaks, A, Pwr)
print 'new cell:', G2lat.A2cell(A)
print 'x:', result[0]
print 'cov_x:', result[1]
print 'infodict:'
for item in result[2]:
print item, result[2][item]
print 'msg:', result[3]
print 'ier:', result[4]
result = refinePeaks(peaks, ibrav, A)
N, M20, X20, A = result
print 'refinePeaks:', N, M20, X20, G2lat.A2cell(A)
print 'compare bestcell:', bestcell
def convert_lattice(self, paramList, params):
'''
Convert between A and unit cell parameters. A is defined in GSAS-II
as A = [G11, G22, G33, 2*G12, 2*G13, 2*G23] with G as the
reciprocal metric tensor elements.
'''
latparamList = [
'0::A0', '1::A0', '2::A0', '3::A0', '4::A0', '5::A0', '6::A0',
'7::A0', '8::A0', '9::A0', '10::A0'
]
check = any(item in paramList for item in latparamList)
if check is True:
return G2latt.A2cell(params)
else:
return G2latt.cell2A(params)
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 monoCellReduce(ibrav,A):
'needs a doc string'
a,b,c,alp,bet,gam = G2lat.A2cell(A)
G,g = G2lat.A2Gmat(A)
if ibrav in [13]:
u = [0,0,-1]
v = [1,0,2]
anew = math.sqrt(np.dot(np.dot(v,g),v))
if anew < a:
cang = np.dot(np.dot(u,g),v)/(anew*c)
beta = acosd(-abs(cang))
A = G2lat.cell2A([anew,b,c,90,beta,90])
else:
u = [-1,0,0]
v = [1,0,1]
cnew = math.sqrt(np.dot(np.dot(v,g),v))
if cnew < c:
cang = np.dot(np.dot(u,g),v)/(a*cnew)
beta = acosd(-abs(cang))
A = G2lat.cell2A([a,b,cnew,90,beta,90])
return A
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 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, []