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from os.path import realpath, exists, join
from larch import (Group, Parameter, isParameter, param_value, use_plugin_path, isNamedClass)
use_plugin_path('io')
from xdi import read_xdi
use_plugin_path('xafs')
from feffit import feffit_dataset, feffit_transform, feffit, feffit_report
from feffdat import feffpath
use_plugin_path('wx')
from plotter import (_newplot, _plot)
def do_fit(self, which):
if which == 'testrun':
folder = self.testrun
else:
folder = self.baseline
data = read_xdi(join(self.path, 'UO2.chik'), _larch=self._larch)
gds = Group(amp = Parameter(1, vary=True, _larch=self._larch),
enot = Parameter(0.01, vary=True, _larch=self._larch),
sso = Parameter(0.003, vary=True, _larch=self._larch),
ssu = Parameter(0.003, vary=True, _larch=self._larch),
sso2 = Parameter(0.003, vary=True, _larch=self._larch),
dro = Parameter(0.0001, vary=True, _larch=self._larch),
dru = Parameter(0.0001, vary=True, _larch=self._larch),
dro2 = Parameter(0.0001, vary=True, _larch=self._larch),
nu = Parameter(12, vary=True, _larch=self._larch),
no2 = Parameter(expr='2*nu', _larch=self._larch),
_larch=self._larch )
paths = list()
paths.append(feffpath(realpath(join(folder, "feff0001.dat")), # 1st shell O SS
s02 = 'amp',
e0 = 'enot',
sigma2 = 'sso',
deltar = 'dro', _larch=self._larch))
# paths.append(feffpath(realpath(join(folder, "feff0002.dat")), # triangle in first shell
# s02 = 'amp',
# e0 = 'enot',
# sigma2 = 'sso*1.5',
# deltar = 'dro*(1+sqrt(2))/2', _larch=self._larch))
paths.append(feffpath(realpath(join(folder, "feff0003.dat")), # 2nd shell U SS
degen = 1,
s02 = 'amp*nu',
e0 = 'enot',
sigma2 = 'ssu',
deltar = 'dru', _larch=self._larch))
# paths.append(feffpath(realpath(join(folder, "feff0004.dat")), # 1st shell, longer triangle
# s02 = 'amp',
# e0 = 'enot',
# sigma2 = '2*sso',
# deltar = '2*dro', _larch=self._larch))
paths.append(feffpath(realpath(join(folder, "feff0006.dat")), # 3rd shell O SS
degen = 1,
s02 = 'amp*no2',
#s02 = 'amp*nu*2',
e0 = 'enot',
sigma2 = 'sso2',
deltar = 'dro2', _larch=self._larch))
paths.append(feffpath(realpath(join(folder, "feff0007.dat")), # 1st shell, non-forward linear through absorber
s02 = 'amp',
e0 = 'enot',
sigma2 = 'sso2',
deltar = 'dro2', _larch=self._larch))
paths.append(feffpath(realpath(join(folder, "feff0008.dat")), # 1st shell forward through absorber
s02 = 'amp',
e0 = 'enot',
sigma2 = '2*sso',
deltar = '2*dro', _larch=self._larch))
paths.append(feffpath(realpath(join(folder, "feff0009.dat")), # rattle in 1st shell
s02 = 'amp',
e0 = 'enot',
sigma2 = '2*sso',
deltar = '2*dro', _larch=self._larch))
trans = feffit_transform(kmin=3, kmax=11, kw=(2,1,3), dk=1, window='hanning', rmin=1.25, rmax=4.3, _larch=self._larch)
dset = feffit_dataset(data=data, pathlist=paths, transform=trans, _larch=self._larch)
fit = feffit(gds, dset, _larch=self._larch)
if self.doplot:
offset = max(dset.data.chir_mag)
_newplot(dset.data.r, dset.data.chir_mag+offset, xmax=8, win=2,
xlabel=r'$R \rm\,(\AA)$', label='data',
ylabel=r'$|\chi(R)| \rm\,(\AA^{-3})$',
title='Fit to '+self.folder, show_legend=True, _larch=self._larch)
_plot(dset.model.r, dset.model.chir_mag+offset, label='fit', win=2, _larch=self._larch)
_plot(dset.data.r, dset.data.chir_re, label='data', win=2, _larch=self._larch)
_plot(dset.model.r, dset.model.chir_re, label='fit', win=2, _larch=self._larch)
#end if
if self.verbose:
print feffit_report(fit, _larch=self._larch)
#end if
return fit
#end def
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