def fit():
# PYTHONPATH=. bumps Al2O3.py --fit=dream --store=M1 --burn=100 --steps=500
cell = Mod.makeCell(crystalCell, spaceGroup.xtalSystem())
cell.a.pm(0.5)
cell.b.pm(0.5)
cell.c.pm(0.5)
m = Mod.Model(tt, observed, backg, 0, 0, 1, wavelength, spaceGroup, cell,
atoms, exclusions, base=min(observed), zero=-0.09459)
m.u.range(0,2)
m.zero.pm(0.1)
m.v.range(-2,0)
m.w.range(0,2)
m.eta.range(0,1)
m.scale.range(0,10)
m.base.pm(10)
for atomModel in m.atomListModel.atomModels:
atomModel.x.pm(0.1)
atomModel.z.pm(0.1)
if (atomModel.atom.multip == atomModel.sgmultip):
# atom lies on a general position
atomModel.x.pm(0.1)
atomModel.y.pm(0.1)
atomModel.z.pm(0.1)
#m.atomListModel["Al1"].z.pm(0.1)
#m.atomListModel["O1"].x.pm(0.1)
m.atomListModel["O3"].y.pm(0.1)
m.atomListModel["Pb"].B.range(0,10)
M = bumps.FitProblem(m)
M.model_update()
return M
def makeModelCell(cell, real_sgs, phases):
print(real_sgs[0].number)
cell_hkl = Mod.makeCell(cell, real_sgs[0].xtalSystem)
try:
cell_hkl.a.pm(float(phases[1]['a']['pm']))
except:
print "no a"
try:
cell_hkl.b.pm(float(phases[1]['b']['pm']))
except:
print "no b"
try:
cell_hkl.c.pm(float(phases[1]['c']['pm']))
except:
print "no c"
try:
cell_hkl.alpha.pm(float(phases[1]['alpha']['pm']))
except:
print "no alpha"
try:
cell_hkl.beta.pm(float(phases[1]['beta']['pm']))
except:
print "no beta"
try:
cell_hkl.gamma.pm(float(phases[1]['gamma']['pm']))
except:
print "no gamma"
return cell_hkl
def makeModelCell(cell, real_sgs, phases):
print(real_sgs[0].number)
cell_hkl = Mod.makeCell(cell, real_sgs[0].xtalSystem)
try:
cell_hkl.a.pm(float(phases[1]['a']['pm']))
except:
print "no a"
try:
cell_hkl.b.pm(float(phases[1]['b']['pm']))
except:
print "no b"
try:
cell_hkl.c.pm(float(phases[1]['c']['pm']))
except:
print "no c"
try:
cell_hkl.alpha.pm(float(phases[1]['alpha']['pm']))
except:
print "no alpha"
try:
cell_hkl.beta.pm(float(phases[1]['beta']['pm']))
except:
print "no beta"
try:
cell_hkl.gamma.pm(float(phases[1]['gamma']['pm']))
except:
print "no gamma"
return cell_hkl
def fit():
# PYTHONPATH=. bumps Al2O3.py --fit=dream --store=M1 --burn=100 --steps=500
cell = Mod.makeCell(crystalCell, spaceGroup.xtalSystem())
cell.a.pm(0.5)
cell.b.pm(0.5)
cell.c.pm(0.5)
m = Mod.Model(tt, observed, backg, 0, 0, 1, wavelength, spaceGroup, cell,
atoms, exclusions, base=min(observed), zero=0.00029)
m.u.range(0,2)
m.zero.pm(0.1)
m.v.range(-2,0)
m.w.range(0,2)
m.eta.range(0,1)
m.scale.range(0,10)
m.base.pm(250)
for atomModel in m.atomListModel.atomModels:
atomModel.B.range(0,10)
if H.getAtom_chemsymb(atomModel.atom).lower() != "mn":
atomModel.x.pm(1.0)
atomModel.y.pm(1.0)
if (atomModel.atom.multip == atomModel.sgmultip):
# atom lies on a general position
atomModel.x.pm(0.1)
atomModel.y.pm(0.1)
atomModel.z.pm(0.1)
m.atomListModel["O2"].z.pm(1.0)
#m.atomListModel["O1"].x.pm(0.1)
#m.atomListModel["O3"].y.pm(0.1)
#m.atomListModel["Pb"].B.range(0,10)
M = bumps.FitProblem(m)
M.model_update()
return M
def fit():
# PYTHONPATH=. bumps Al2O3.py --fit=dream --store=M1 --burn=100 --steps=500
cell = Mod.makeCell(crystalCell, spaceGroup.xtalSystem)
cell.a.pm(0.5)
cell.c.pm(0.5)
m = Mod.Model(tt, observed, backg, 0.151066141044763, -0.0914698313404034,
0.0693509296318546, wavelength, spaceGroup, cell, atoms,
exclusions)
m.u.range(0, 2)
m.v.range(-2, 0)
m.w.range(0, 2)
m.eta.range(0, 1)
m.scale.range(0, 10)
for atomModel in m.atomListModel.atomModels:
atomModel.B.range(0, 10)
if (atomModel.atom.multip == atomModel.sgmultip):
# atom lies on a general position
atomModel.x.pm(0.1)
atomModel.y.pm(0.1)
atomModel.z.pm(0.1)
m.atomListModel["Al1"].z.pm(0.1)
m.atomListModel["O1"].x.pm(0.1)
M = bumps.FitProblem(m)
M.model_update()
return M
def fit():
cell = Mod.makeCell(crystalCell, spaceGroup.xtalSystem)
cell.a.pm(5.0)
cell.b.pm(5.0)
cell.c.pm(5.0)
m = Mod.Model(tt, observed, backg, 1.548048,-0.988016,0.338780, wavelength, spaceGroup, cell,
(atomList, magAtomList), exclusions, magnetic=True,
symmetry=symmetry, newSymmetry=basisSymmetry, base=6512, scale=59.08, sxtal=True, eta=0.0382, zero=0.08416, error=error)
m.u.range(0,10)
m.v.range(-10,0)
m.w.range(0,10)
m.scale.range(0,100)
m.zero.pm(0.5)
m.eta.range(0,1)
m.base.pm(1000)
for atomModel in m.atomListModel.atomModels:
atomModel.x.range(0,1)
atomModel.y.range(0,1)
atomModel.z.range(0,1)
atomModel.B.range(0,10)
if atomModel.magnetic:
for coeff in atomModel.coeffs:
#coeff.range(-10, 10)
coeff.range(-20,20)
M = bumps.FitProblem(m)
M.model_update()
return M
def graphError():
cell = Mod.makeCell(crystalCell, spaceGroup.xtalSystem)
m = S.Model(tt, sfs2, backg, wavelength, spaceGroup, cell,
[atomList], exclusions,
scale=0.06298,hkls=refList, error=error, extinction=[0.0001054])
m.atomListModel.atomModels[0].z.range(0,0.5)
z = 0
xval = []
y = []
while (z < 0.5):
#Set a range on the x value of the first atom in the model
m.atomListModel.atomModels[0].z.value = z
m.atomListModel.atomModels[0].z.range(0, 0.5)
problem = bumps.FitProblem(m)
# monitor = fitter.StepMonitor(problem, open("sxtalFitMonitor.txt","w"))
fitted = fitter.LevenbergMarquardtFit(problem)
x, dx = fitted.solve()
xval.append(x[0])
y.append(problem.chisq())
print(x, problem.chisq())
z += 0.005
fig = plt.figure()#
mpl.pyplot.scatter(xval, yval)
mpl.pyplot.xlabel("Pr z coordinate")
mpl.pyplot.ylabel("X2 value")
fig.savefig('/mnt/storage/prnio_chisq_vals_optcfl_lm.png')
def fit():
cell = Mod.makeCell(crystalCell, spaceGroup.xtalSystem)
#cell.a.pm(5.0)
#cell.c.pm(5.0)
m = S.Model(tt,
sfs2,
backg,
wavelength,
spaceGroup,
cell, (atomList, magAtomList),
exclusions,
magnetic=True,
symmetry=symmetry,
newSymmetry=basisSymmetry,
scale=1.00,
error=error,
hkls=refList,
extinction=[0, 0, 0, 0])
m.scale.range(0, 2000)
#m.base.pm(1000)
for ext in m.extinctions:
ext.range(0, 100.0)
for atomModel in m.atomListModel.atomModels:
#atomModel.x.range(0,1)
#atomModel.y.range(0,1)
#atomModel.z.range(0,1)
#atomModel.B.range(0,10)
if atomModel.magnetic:
for coeff in atomModel.coeffs:
coeff.range(-20, 20)
#coeff.range(0,5)
M = bumps.FitProblem(m)
M.model_update()
return M
def fit():
# PYTHONPATH=. bumps Al2O3.py --fit=dream --store=M1 --burn=100 --steps=500
cell = Mod.makeCell(crystalCell, spaceGroup.xtalSystem)
cell.a.pm(0.5)
cell.b.pm(0.5)
cell.c.pm(0.5)
m = Mod.Model(tt, observed, backg, 0, 0, 1, wavelength, spaceGroup, cell,
atoms, exclusions, base=min(observed), zero=-0.09459, error=error, eta=0)
m.u.range(0,1)
m.zero.pm(0.5)
m.v.range(-1,0)
m.w.range(0,1)
m.eta.range(0,1)
m.scale.range(0,100)
m.base.pm(500)
for atomModel in m.atomListModel.atomModels:
#atomModel.x.pm(0.1)
#atomModel.z.pm(0.1)
atomModel.x.range(0,1)
atomModel.z.range(0,1)
if (atomModel.atom.multip == atomModel.sgmultip):
# atom lies on a general position
#atomModel.x.pm(0.1)
#atomModel.y.pm(0.1)
#atomModel.z.pm(0.1)
atomModel.y.range(0,1)
#m.atomListModel["Al1"].z.pm(0.1)
#m.atomListModel["O1"].x.pm(0.1)
#m.atomListModel["O3"].y.pm(0.1)
m.atomListModel["Pb"].B.range(0,10)
M = bumps.FitProblem(m)
M.model_update()
return M
def fit():
cell = Mod.makeCell(crystalCell, xtalsys(spaceGroup))
cell.a.pm(0.5)
# cell.b.pm(0.5)
cell.c.pm(0.5)
m = Mod.Model(tt, observed, backg, 1.814691, -1.482098, 0.447632 , wavelength, spaceGroup, cell,
(atomList, magAtomList), exclusions, magnetic=True,
symmetry=symmetry, newSymmetry=basisSymmetry, base=base_line, scale=94.508, eta=0.0, zero=0.04101, error=error, muR=1.280)
m.u.range(0,10)
m.v.range(-10,0)
m.w.range(0,10)
m.scale.range(0,200)
m.eta.range(0,1)
m.base.pm(1000)
m.zero.pm(0.25)
for atomModel in m.atomListModel.atomModels:
if atomModel.magnetic:
for coeff in atomModel.coeffs:
#coeff.range(-10, 10)
coeff.range(-20,20)
#pass
#atomModel.phase.range(-np.pi*2, np.pi*2)
#m.atomListModel["Mn1"].phase.range(0, np.pi*2)
#m.atomListModel["Mn2"].phase.range(-2*np.pi, 0)
M = bumps.FitProblem(m)
M.model_update()
return M
def reset(self):
#Make a cell
cell = Mod.makeCell(self.crystalCell, self.spaceGroup.xtalSystem)
#Define a model
self.model = S.Model([], [],
self.backg,
self.wavelength,
self.spaceGroup,
cell, [self.atomList],
self.exclusions,
scale=0.06298,
error=[],
extinction=[0.0001054])
#Set a range on the x value of the first atom in the model
self.model.atomListModel.atomModels[0].z.value = 0.25
self.model.atomListModel.atomModels[0].z.range(0, 0.5)
self.visited = []
self.observed = []
self.remainingActions = []
for i in range(len(self.refList)):
self.remainingActions.append(i)
self.totReward = 0
self.prevChisq = None
self.steps = 0
self.state = np.zeros(len(self.refList))
self.stateList = []
return self.state
def fit():
# makeBasis(basisSymmetry, basisIndex)
cell = Mod.makeCell(crystalCell, xtalsys(spaceGroup))
cell.a.pm(0.5)
cell.b.pm(0.5)
cell.c.pm(0.5)
# print len(H.satelliteGen(cell.cell, symmetry, float(H.getS(ttMax, wavelength))))
m = Mod.Model(
tt,
observed,
backg,
0,
0,
1,
wavelength,
spaceGroup,
cell,
(atomList, magAtomList),
exclusions,
magnetic=True,
symmetry=symmetry,
newSymmetry=basisSymmetry,
base=6512,
scale=59.143,
)
m.u.range(0, 10)
m.v.range(-10, 0)
m.w.range(0, 10)
m.scale.range(59, 60)
m.base.range(6510, 6514)
for atomModel in m.atomListModel.atomModels:
# atomModel.B.range(0, 10)
# if (atomModel.atom.multip == atomModel.sgmultip):
# # atom lies on a general position
# atomModel.x.pm(0.1)
# atomModel.y.pm(0.1)
# atomModel.z.pm(0.1)
if atomModel.magnetic:
for coeff in atomModel.coeffs:
# coeff.range(-10, 10)
coeff.range(-20, 20)
# atomModel.phase.range(0,1)
# vary Fe/Mn atom positions but keep them on the special site x,0,z
# m.atomListModel["Fe1"].x.pm(0.1)
# m.atomListModel["Fe1"].z.pm(0.1)
# m.atomListModel["Mn1"].x = m.atomListModel["Fe1"].x
# m.atomListModel["Mn1"].z = m.atomListModel["Fe1"].z
# for i in xrange(len(m.atomListModel["Fe1"].coeffs)):
# m.atomListModel["Mn1"].coeffs[i] = m.atomListModel["Fe1"].coeffs[i]
# m.atomListModel["Mn1"].phase = m.atomListModel["Fe1"].phase
# Occupancy:
# m.atomListModel["Fe1"].occ.range(0, 1)
# m.atomListModel["Mn1"].occ.range(0, 1)
# m.atomListModel["Mn1"].occ = 1 - m.atomListModel["Fe1"].occ
M = bumps.FitProblem(m)
M.model_update()
return M
def fit():
makeBasis(basisSymmetry, basisIndex)
cell = Mod.makeCell(crystalCell, xtalsys(spaceGroup))
cell.a.pm(0.2)
cell.c.pm(0.2)
m = Mod.Model(tt,
observed,
backg,
0.2979,
-0.1684,
0.03975,
wavelength,
spaceGroup,
cell, (atomList, magAtomList),
exclusions,
magnetic=True,
symmetry=symmetry,
newSymmetry=basisSymmetry)
m.u.pm(0.2)
m.v.range(-1, 0)
m.w.range(0, 1)
m.scale.range(0, 10)
for atomModel in m.atomListModel.atomModels:
# atomModel.B.range(0, 10)
# if (atomModel.atom.multip == atomModel.sgmultip):
# # atom lies on a general position
# atomModel.x.pm(0.1)
# atomModel.y.pm(0.1)
# atomModel.z.pm(0.1)
if atomModel.magnetic:
for coeff in atomModel.coeffs:
coeff.range(0, 10)
# atomModel.phase.range(0,1)
# vary Fe/Mn atom positions but keep them on the special site x,0,z
# m.atomListModel["Fe1"].x.pm(0.1)
# m.atomListModel["Fe1"].z.pm(0.1)
# m.atomListModel["Mn1"].x = m.atomListModel["Fe1"].x
# m.atomListModel["Mn1"].z = m.atomListModel["Fe1"].z
for i in xrange(len(m.atomListModel["Fe1"].coeffs)):
m.atomListModel["Mn1"].coeffs[i] = m.atomListModel["Fe1"].coeffs[i]
#m.atomListModel["Mn1"].phase = m.atomListModel["Fe1"].phase
# Occupancy:
# m.atomListModel["Fe1"].occ.range(0, 1)
# m.atomListModel["Mn1"].occ.range(0, 1)
# m.atomListModel["Mn1"].occ = 1 - m.atomListModel["Fe1"].occ
M = bumps.FitProblem(m)
M.model_update()
return M
def fit():
# PYTHONPATH=. bumps Al2O3.py --fit=dream --store=M1 --burn=100 --steps=500
cell = Mod.makeCell(crystalCell, spaceGroup.xtalSystem())
cell.a.pm(0.000001)
cell.b.pm(0.000001)
cell.c.pm(0.000001)
cell.a.set([5.536482, 5.747128, 7.692561][0])
cell.b.set([5.536482, 5.747128, 7.692561][1])
cell.c.set([5.536482, 5.747128, 7.692561][2])
m = Mod.Model(tt,
observed,
backg,
0.176001,
-0.197806,
0.091452,
wavelength,
spaceGroup,
cell,
atoms,
exclusions,
base=min(observed),
zero=0.00029)
m.u.pm(0.00001)
m.v.pm(0.00001)
m.w.pm(0.00001)
m.u.set([0.176001, -0.197806, 0.091452][0])
m.v.set([0.176001, -0.197806, 0.091452][1])
m.w.set([0.176001, -0.197806, 0.091452][2])
#m.u.range(0,2)
m.zero.pm(0.1)
#m.v.range(-2,0)
#m.w.range(0,2)
m.eta.range(0, 1)
m.scale.range(0, 10)
m.base.pm(250)
for atomModel in m.atomListModel.atomModels:
atomModel.B.range(0, 10)
if H.getAtom_chemsymb(atomModel.atom).lower() != "mn":
atomModel.x.range(0, 1)
atomModel.y.range(0, 1)
if (atomModel.atom.multip == atomModel.sgmultip):
# atom lies on a general position
atomModel.x.pm(0.1)
atomModel.y.pm(0.1)
atomModel.z.pm(0.1)
m.atomListModel["O2"].z.range(0, 1)
#m.atomListModel["O1"].x.pm(0.1)
#m.atomListModel["O3"].y.pm(0.1)
#m.atomListModel["Pb"].B.range(0,10)
M = bumps.FitProblem(m)
M.model_update()
return M
def plotSfs2():
cell = Mod.makeCell(crystalCell, spaceGroup.xtalSystem)
m = S.Model(tt, sfs2, backg, wavelength, spaceGroup, cell,
[atomList], exclusions,
scale=0.06298,hkls=refList, error=error, extinction=[0.0001054])
m.atomListModel.atomModels[0].z.range(0,0.5)
x = sfs2
y = m.theory()
plt.scatter(x, y)
plt.savefig('sfs2s.png')
def setInitParams():
#Make a cell
cell = Mod.makeCell(crystalCell, spaceGroup.xtalSystem)
#Define a model
m = S.Model([], [], backg, wavelength, spaceGroup, cell,
[atomList], exclusions,
scale=0.06298, error=[], extinction=[0.0001054])
#Set a range on the x value of the first atom in the model
#Replace this code with references to the parameters you would like to fit the model to
m.atomListModel.atomModels[0].z.value = 0.3
m.atomListModel.atomModels[0].z.range(0,0.5)
return m
def setInitParams():
#Make a cell
cell = Mod.makeCell(crystalCell, spaceGroup.xtalSystem)
#Define a model
m = S.Model([], [], backg, wavelength, spaceGroup, cell,
[atomList], exclusions,
scale=0.2163, error=[], extinction=[0.000105])
#Set a range on the x value of the first atom in the model
#Setting initial values and ranges of parameters to look at
m.atomListModel.atomModels[0].z.value = 0.5
# m.atomListModel.atomModels[0].z.value = random.random()/2
m.atomListModel.atomModels[0].z.range(0,1)
#Oxygen d z coordinate
# m.atomListModel.atomModels[5].z.value = 0.2
# m.atomListModel.atomModels[5].z.range(0,0.5)
return m
def fit():
#makeBasis(basisSymmetry, basisIndex)
cell = Mod.makeCell(crystalCell, xtalsys(spaceGroup))
cell.a.pm(0.5)
cell.b.pm(0.5)
cell.c.pm(0.5)
#print len(H.satelliteGen(cell.cell, symmetry, float(H.getS(ttMax, wavelength))))
m = Mod.Model(tt, observed, backg, 0, 0, 1, wavelength, spaceGroup, cell,
(atomList, magAtomList), exclusions, magnetic=True,
symmetry=symmetry, newSymmetry=basisSymmetry, base=6512, scale=59.143)
m.u.range(0,10)
m.v.range(-10,0)
m.w.range(0,10)
m.scale.range(59,60)
m.base.range(6510,6514)
for atomModel in m.atomListModel.atomModels:
# atomModel.B.range(0, 10)
# if (atomModel.atom.multip == atomModel.sgmultip):
# # atom lies on a general position
# atomModel.x.pm(0.1)
# atomModel.y.pm(0.1)
# atomModel.z.pm(0.1)
if atomModel.magnetic:
for coeff in atomModel.coeffs:
#coeff.range(-10, 10)
coeff.range(-20,20)
# atomModel.phase.range(0,1)
# vary Fe/Mn atom positions but keep them on the special site x,0,z
# m.atomListModel["Fe1"].x.pm(0.1)
# m.atomListModel["Fe1"].z.pm(0.1)
# m.atomListModel["Mn1"].x = m.atomListModel["Fe1"].x
# m.atomListModel["Mn1"].z = m.atomListModel["Fe1"].z
#for i in xrange(len(m.atomListModel["Fe1"].coeffs)):
#m.atomListModel["Mn1"].coeffs[i] = m.atomListModel["Fe1"].coeffs[i]
# m.atomListModel["Mn1"].phase = m.atomListModel["Fe1"].phase
# Occupancy:
# m.atomListModel["Fe1"].occ.range(0, 1)
# m.atomListModel["Mn1"].occ.range(0, 1)
# m.atomListModel["Mn1"].occ = 1 - m.atomListModel["Fe1"].occ
M = bumps.FitProblem(m)
M.model_update()
return M
def fit():
makeBasis(basisSymmetry, basisIndex)
cell = Mod.makeCell(crystalCell, xtalsys(spaceGroup))
cell.a.pm(0.2)
cell.c.pm(0.2)
m = Mod.Model(tt, observed, backg, 0.2979, -0.1684, 0.03975, wavelength, spaceGroup, cell,
(atomList, magAtomList), exclusions, magnetic=True,
symmetry=symmetry, newSymmetry=basisSymmetry)
m.u.pm(0.2)
m.v.range(-1,0)
m.w.range(0,1)
m.scale.range(0,10)
for atomModel in m.atomListModel.atomModels:
# atomModel.B.range(0, 10)
# if (atomModel.atom.multip == atomModel.sgmultip):
# # atom lies on a general position
# atomModel.x.pm(0.1)
# atomModel.y.pm(0.1)
# atomModel.z.pm(0.1)
if atomModel.magnetic:
for coeff in atomModel.coeffs:
coeff.range(0,10)
# atomModel.phase.range(0,1)
# vary Fe/Mn atom positions but keep them on the special site x,0,z
# m.atomListModel["Fe1"].x.pm(0.1)
# m.atomListModel["Fe1"].z.pm(0.1)
# m.atomListModel["Mn1"].x = m.atomListModel["Fe1"].x
# m.atomListModel["Mn1"].z = m.atomListModel["Fe1"].z
for i in xrange(len(m.atomListModel["Fe1"].coeffs)):
m.atomListModel["Mn1"].coeffs[i] = m.atomListModel["Fe1"].coeffs[i]
#m.atomListModel["Mn1"].phase = m.atomListModel["Fe1"].phase
# Occupancy:
# m.atomListModel["Fe1"].occ.range(0, 1)
# m.atomListModel["Mn1"].occ.range(0, 1)
# m.atomListModel["Mn1"].occ = 1 - m.atomListModel["Fe1"].occ
M = bumps.FitProblem(m)
M.model_update()
return M
def fit():
cell = Mod.makeCell(crystalCell, xtalsys(spaceGroup))
cell.a.pm(0.5)
cell.b.pm(0.5)
cell.c.pm(0.5)
m = Mod.Model(
tt,
observed,
backg,
0.1060,
-0.3270,
0.3360,
wavelength,
spaceGroup,
cell,
(atomList, magAtomList),
exclusions,
magnetic=True,
symmetry=symmetry,
newSymmetry=basisSymmetry,
base=base_line,
scale=27.765 / 2,
eta=0.0,
zero=-0.12671,
sxtal=True,
error=error,
)
m.u.range(0, 10)
m.v.range(-10, 0)
m.w.range(0, 10)
m.scale.range(0, 100)
m.eta.range(0, 1)
m.base.pm(500)
m.zero.pm(0.25)
for atomModel in m.atomListModel.atomModels:
if atomModel.magnetic:
for coeff in atomModel.coeffs:
# coeff.range(-10, 10)
coeff.range(-20, 20)
M = bumps.FitProblem(m)
M.model_update()
return M
def fit():
cell = Mod.makeCell(crystalCell, spaceGroup.xtalSystem)
cell.a.pm(0.5)
cell.c.pm(0.5)
m = Mod.Model(
tt,
observed,
backg,
0.226335,
-0.220125,
0.117269,
wavelength,
spaceGroup,
cell,
(atomList, magAtomList),
exclusions,
magnetic=True,
symmetry=symmetry,
newSymmetry=basisSymmetry,
eta=0.11935,
scale=0.37163,
base=base_value,
)
m.u.range(0, 10)
m.v.range(-10, 0)
m.w.range(0, 10)
m.scale.range(0, 10)
m.base.pm(500)
m.eta.range(0, 1)
for atomModel in m.atomListModel.atomModels:
# atomModel.B.range(0, 10)
# if (atomModel.atom.multip == atomModel.sgmultip):
# # atom lies on a general position
# atomModel.x.pm(0.1)
# atomModel.y.pm(0.1)
# atomModel.z.pm(0.1)
if atomModel.magnetic:
for coeff in atomModel.coeffs:
coeff.range(-10, 10)
M = bumps.FitProblem(m)
M.model_update()
return M
def fit():
cell = Mod.makeCell(crystalCell, spaceGroup.xtalSystem)
#cell.a.pm(5.0)
#cell.c.pm(5.0)
m = S.Model(tt, sfs2, backg, wavelength, spaceGroup, cell,
[atomList], exclusions,
scale=0.06298, error=error, hkls=refList, extinction=[0.0001054])
m.scale.range(0,100)
#m.base.pm(1000)
for atomModel in m.atomListModel.atomModels:
#atomModel.x.range(0,1)
#atomModel.y.range(0,1)
#atomModel.z.range(0,1)
#atomModel.B.range(0,10)
if atomModel.magnetic:
for coeff in atomModel.coeffs:
coeff.range(-20, 20)
#coeff.range(0,5)
M = bumps.FitProblem(m)
M.model_update()
return M
def fit():
# PYTHONPATH=. bumps Al2O3.py --fit=dream --store=M1 --burn=100 --steps=500
cell = Mod.makeCell(crystalCell, spaceGroup.xtalSystem())
cell.a.pm(0.0000001)
cell.b.pm(0.0000001)
cell.c.pm(0.0000001)
cell.a.set([3.815149, 3.880053, 11.664815][0])
cell.b.set([3.815149, 3.880053, 11.664815][1])
cell.c.set([3.815149, 3.880053, 11.664815][2])
m = Mod.Model(tt, observed, backg, 0.198607,-0.322513,0.338442, wavelength, spaceGroup, cell,
atoms, exclusions, base=min(observed), zero=0.19089)
m.u.pm(0.000001)
m.v.pm(0.000001)
m.w.pm(0.000001)
m.u.set(([0.198607,-0.322513,0.338442])[0])
m.v.set(([0.198607,-0.322513,0.338442])[1])
m.w.set(([0.198607,-0.322513,0.338442])[2])
m.zero.pm(0.00000001)
m.eta.range(0,1)
m.scale.range(0,10)
m.base.pm(0.0001)
for atomModel in m.atomListModel.atomModels:
atomModel.B.range(0,10)
#if (atomModel.atom.multip == atomModel.sgmultip):
## atom lies on a general position
#atomModel.x.pm(0.1)
#atomModel.y.pm(0.1)
#atomModel.z.pm(0.1)
m.atomListModel["Ba"].z.range(0,1)
m.atomListModel["CaB"].z.range(0,1)
m.atomListModel["Cu2"].z.range(0,1)
m.atomListModel["O1"].z.range(0,1)
m.atomListModel["O2"].z.range(0,1)
m.atomListModel["O3"].z.range(0,1)
#m.atomListModel["O1"].x.pm(0.1)
#m.atomListModel["O3"].y.pm(0.1)
#m.atomListModel["Pb"].B.range(0,10)
M = bumps.FitProblem(m)
M.model_update()
return M
def setInitParams():
print("Setting parameters...")
#Make a cell
cell = Mod.makeCell(crystalCell, spaceGroup.xtalSystem)
#Define a model
m = Mod.Model(tt,
observedByAlg,
backg,
1.548048,
-0.988016,
0.338780,
wavelength,
spaceGroup,
cell, (atomList, magAtomList),
exclusions,
magnetic=True,
symmetry=symmetry,
newSymmetry=basisSymmetry,
base=6512,
scale=59.08,
eta=0.0382,
zero=0.08416,
error=error)
#Set a range on the x value of the first atom in the model
m.atomListModel.atomModels[0].x.range(0, 1)
#Generate list of hkls
hkls = []
for r in m.reflections:
hkls.append(r.hkl)
# m.observed.append(m.reflections[0])
# m.observed.append(m.reflections[1])
# m.observed.append(m.reflections[2])
return m, hkls
def fit():
cell = Mod.makeCell(crystalCell, spaceGroup.xtalSystem)
#cell.a.pm(5.0)
#cell.c.pm(5.0)
m = S.Model(tt, sfs2, backg, wavelength, spaceGroup, cell,
[atomList], exclusions,
scale=0.06298, error=error, hkls=refList, extinction=0.0001054)
m.scale.range(0,100)
#m.base.pm(1000)
m.extinction.range(0,10.0)
for atomModel in m.atomListModel.atomModels:
#atomModel.x.range(0,1)
#atomModel.y.range(0,1)
#atomModel.z.range(0,1)
#atomModel.B.range(0,10)
if atomModel.magnetic:
for coeff in atomModel.coeffs:
coeff.range(-20, 20)
#coeff.range(0,5)
M = bumps.FitProblem(m)
M.model_update()
return M
def fit():
cell = Mod.makeCell(crystalCell, xtalsys(spaceGroup))
cell.a.pm(0.5)
cell.b.pm(0.5)
cell.c.pm(0.5)
m = Mod.Model(tt,
observed,
backg,
0.1060,
-0.3270,
0.3360,
wavelength,
spaceGroup,
cell, (atomList, magAtomList),
exclusions,
magnetic=True,
symmetry=symmetry,
newSymmetry=basisSymmetry,
base=base_line,
scale=27.765 / 2,
eta=0.0,
zero=-0.12671,
sxtal=True,
error=error)
m.u.range(0, 10)
m.v.range(-10, 0)
m.w.range(0, 10)
m.scale.range(0, 100)
m.eta.range(0, 1)
m.base.pm(500)
m.zero.pm(0.25)
for atomModel in m.atomListModel.atomModels:
if atomModel.magnetic:
for coeff in atomModel.coeffs:
#coeff.range(-10, 10)
coeff.range(-20, 20)
M = bumps.FitProblem(m)
M.model_update()
return M
def fit():
cell = Mod.makeCell(crystalCell, spaceGroup.xtalSystem)
#cell.a.pm(5.0)
#cell.c.pm(5.0)
m = S.Model(tt, sfs2, backg, wavelength, spaceGroup, cell,
(atomList, magAtomList), exclusions, magnetic=True,
symmetry=symmetry, newSymmetry=basisSymmetry, scale=1.557, error=error, hkls=refList)
m.scale.range(0,100)
#m.base.pm(1000)
m.extinction.range(0,10.0)
for atomModel in m.atomListModel.atomModels:
#atomModel.x.range(0,1)
#atomModel.y.range(0,1)
#atomModel.z.range(0,1)
#atomModel.B.range(0,10)
if atomModel.magnetic:
for coeff in atomModel.coeffs:
coeff.range(-20, 20)
#coeff.range(0,5)
M = bumps.FitProblem(m)
M.model_update()
return M
def fit():
#makeBasis(basisSymmetry, basisIndex)
cell = Mod.makeCell(crystalCell, xtalsys(spaceGroup))
cell.a.pm(0.5)
cell.b.pm(0.5)
cell.c.pm(0.5)
m = Mod.Model(tt, observed, backg, 1.809863, -1.476814, 0.446315, wavelength, spaceGroup, cell,
(atomList, magAtomList), exclusions, magnetic=True,
symmetry=symmetry, newSymmetry=basisSymmetry, base=6512, scale=94.064, sxtal=True, error=error)
m.u.range(0,10)
m.v.range(-10,0)
m.w.range(0,10)
m.scale.range(11,60)
m.base.range(6510,6514)
for atomModel in m.atomListModel.atomModels:
if atomModel.magnetic:
for coeff in atomModel.coeffs:
#coeff.range(-10, 10)
coeff.range(-20,20)
M = bumps.FitProblem(m)
M.model_update()
return M
def fit():
cell = Mod.makeCell(crystalCell, spaceGroup.xtalSystem)
cell.a.pm(0.5)
cell.c.pm(0.5)
m = Mod.Model(tt,
observed,
backg,
0.226335,
-0.220125,
0.117269,
wavelength,
spaceGroup,
cell, (atomList, magAtomList),
exclusions,
magnetic=True,
symmetry=symmetry,
newSymmetry=basisSymmetry,
eta=0.11935,
scale=0.37163,
base=base_value)
m.u.range(0, 10)
m.v.range(-10, 0)
m.w.range(0, 10)
m.scale.range(0, 10)
m.base.pm(500)
m.eta.range(0, 1)
for atomModel in m.atomListModel.atomModels:
# atomModel.B.range(0, 10)
# if (atomModel.atom.multip == atomModel.sgmultip):
# # atom lies on a general position
# atomModel.x.pm(0.1)
# atomModel.y.pm(0.1)
# atomModel.z.pm(0.1)
if atomModel.magnetic:
for coeff in atomModel.coeffs:
coeff.range(-10, 10)
M = bumps.FitProblem(m)
M.model_update()
return M
def fit():
# PYTHONPATH=. bumps Al2O3.py --fit=dream --store=M1 --burn=100 --steps=500
cell = Mod.makeCell(crystalCell, getSpaceGroup_crystalsys(spaceGroup))
cell.a.pm(0.5)
cell.c.pm(0.5)
m = Mod.Model(tt, observed, backg, 0, 0, 1, wavelength, spaceGroup, cell,
atoms, exclusions)
m.u.range(0, 2)
m.v.range(-2, 0)
m.w.range(0, 2)
m.scale.range(0, 10)
for atomModel in m.atomListModel.atomModels:
atomModel.B.range(0, 10)
if (atomModel.atom.multip == atomModel.sgmultip):
# atom lies on a general position
atomModel.x.pm(0.1)
atomModel.y.pm(0.1)
atomModel.z.pm(0.1)
m.atomListModel["Al1"].z.pm(0.1)
m.atomListModel["O1"].x.pm(0.1)
M = bumps.FitProblem(m)
M.model_update()
return M
def fit():
# PYTHONPATH=. bumps Al2O3.py --fit=dream --store=M1 --burn=100 --steps=500
cell = Mod.makeCell(crystalCell, getSpaceGroup_crystalsys(spaceGroup))
cell.a.pm(0.5)
cell.c.pm(0.5)
m = Mod.Model(tt, observed, backg, 0, 0, 1, wavelength, spaceGroup, cell,
atoms, exclusions)
m.u.range(0,2)
m.v.range(-2,0)
m.w.range(0,2)
m.scale.range(0,10)
for atomModel in m.atomListModel.atomModels:
atomModel.B.range(0, 10)
if (atomModel.atom.multip == atomModel.sgmultip):
# atom lies on a general position
atomModel.x.pm(0.1)
atomModel.y.pm(0.1)
atomModel.z.pm(0.1)
m.atomListModel["Al1"].z.pm(0.1)
m.atomListModel["O1"].x.pm(0.1)
M = bumps.FitProblem(m)
M.model_update()
return M
def fit():
cell = Mod.makeCell(crystalCell, xtalsys(spaceGroup))
cell.a.pm(0.5)
cell.b.pm(0.5)
cell.c.pm(0.5)
m = Mod.Model(tt, observed, backg, 1.161020, -0.658240, 0.29176, wavelength, spaceGroup, cell,
(atomList, magAtomList), exclusions, magnetic=True,
symmetry=symmetry, newSymmetry=basisSymmetry, base=base_line, scale=9.6286/np.sqrt(2.0), eta=0.1031, zero=0.0197, sxtal=True, error=error)
m.u.range(0,10)
m.v.range(-10,0)
m.w.range(0,10)
m.scale.range(0,60)
m.eta.range(0,1)
m.base.pm(500)
m.zero.pm(0.25)
for atomModel in m.atomListModel.atomModels:
if atomModel.magnetic:
for coeff in atomModel.coeffs:
#coeff.range(-10, 10)
coeff.range(-20,20)
M = bumps.FitProblem(m)
M.model_update()
return M
def fit():
# PYTHONPATH=. bumps Al2O3.py --fit=dream --store=M1 --burn=100 --steps=500
cell = Mod.makeCell(crystalCell, spaceGroup.xtalSystem)
cell.a.pm(0.5)
cell.c.pm(0.5)
m = Mod.Model(tt, observed, backg, 0.151066141044763,-0.0914698313404034,0.0693509296318546, wavelength, spaceGroup, cell,
atoms, exclusions)
m.u.range(0,2)
m.v.range(-2,0)
m.w.range(0,2)
m.eta.range(0,1)
m.scale.range(0,10)
for atomModel in m.atomListModel.atomModels:
atomModel.B.range(0, 10)
if (atomModel.atom.multip == atomModel.sgmultip):
# atom lies on a general position
atomModel.x.pm(0.1)
atomModel.y.pm(0.1)
atomModel.z.pm(0.1)
m.atomListModel["Al1"].z.pm(0.1)
m.atomListModel["O1"].x.pm(0.1)
M = bumps.FitProblem(m)
M.model_update()
return M
def fitFullModel():
cell = Mod.makeCell(crystalCell, spaceGroup.xtalSystem)
#Define a model
m = S.Model(tt, sfs2, backg, wavelength, spaceGroup, cell,
[atomList], exclusions,
scale=0.06298,hkls=refList, error=error, extinction=[0.0001054])
m.u.range(0,2)
m.zero.pm(0.1)
m.v.range(-2,0)
m.w.range(0,2)
m.eta.range(0,1)
m.scale.range(0,10)
m.base.pm(250)
for atomModel in m.atomListModel.atomModels:
atomModel.x.pm(0.1)
atomModel.z.pm(0.1)
if (atomModel.atom.multip == atomModel.sgmultip):
# atom lies on a general position
atomModel.x.pm(0.1)
atomModel.y.pm(0.1)
atomModel.z.pm(0.1)
m.atomListModel.atomModels[0].z.value = 0.3
m.atomListModel.atomModels[0].z.range(0,0.5)
problem = bumps.FitProblem(m)
fitted = fitter.SimplexFit(problem)
x, dx = fitted.solve(steps=50)
problem.model_update()
print(problem.summarize())
print(x, dx, problem.chisq())
def fit():
#makeBasis(basisSymmetry, basisIndex)
cell = Mod.makeCell(crystalCell, xtalsys(spaceGroup))
cell.a.pm(0.5)
cell.b.pm(0.5)
cell.c.pm(0.5)
m = Mod.Model(tt,
observed,
backg,
1.809863,
-1.476814,
0.446315,
wavelength,
spaceGroup,
cell, (atomList, magAtomList),
exclusions,
magnetic=True,
symmetry=symmetry,
newSymmetry=basisSymmetry,
base=6512,
scale=94.064,
sxtal=True,
error=error)
m.u.range(0, 10)
m.v.range(-10, 0)
m.w.range(0, 10)
m.scale.range(11, 60)
m.base.range(6510, 6514)
for atomModel in m.atomListModel.atomModels:
if atomModel.magnetic:
for coeff in atomModel.coeffs:
#coeff.range(-10, 10)
coeff.range(-20, 20)
M = bumps.FitProblem(m)
M.model_update()
return M
