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():
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 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 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():
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 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())