def do_fit(self, which, firstshell=False, fittest='baseline'):
if which == 'testrun':
folder = self.testrun
elif which == 'baseline':
folder = self.baseline
else:
folder = realpath(join(self.folder, fittest, which))
#endif
data = read_xdi(join(self.path, 'NiO.chik'), _larch=self._larch)
if hasattr(data, 'wavenumber'):
data.k = data.wavenumber
gds = Group(amp=Parameter(1, vary=True, _larch=self._larch),
enot=Parameter(1e-7, vary=True, _larch=self._larch),
sso=Parameter(0.003, vary=True, _larch=self._larch),
_larch=self._larch)
if firstshell:
gds.delr = Parameter(1e-7, vary=True, _larch=self._larch)
dr1param = 'delr'
else:
gds.alpha = Parameter(1e-7, vary=True, _larch=self._larch)
gds.ssni = Parameter(0.003, vary=True, _larch=self._larch)
gds.sso2 = Parameter(0.003, vary=True, _larch=self._larch)
#gds.sso3 = Parameter(0.003, vary=True, _larch=self._larch)
gds.ssni2 = Parameter(0.003, vary=True, _larch=self._larch)
#gds.ssni3 = Parameter(0.003, vary=True, _larch=self._larch)
#gds.ssni4 = Parameter(0.003, vary=True, _larch=self._larch)
dr1param = 'alpha*reff'
paths = list()
paths.append(
feffpath(
realpath(join(folder, "feff0001.dat")), # 1st shell O SS
s02='amp',
e0='enot',
sigma2='sso',
deltar=dr1param,
_larch=self._larch))
if not firstshell:
paths.append(
feffpath(
realpath(join(folder, "feff0002.dat")), # 2nd shell Ni SS
s02='amp',
e0='enot',
sigma2='ssni',
deltar='alpha*reff',
_larch=self._larch))
paths.append(
feffpath(
realpath(join(folder, "feff0003.dat")), # O-O triangle
s02='amp',
e0='enot',
sigma2='1.5*sso',
deltar='alpha*reff',
_larch=self._larch))
paths.append(
feffpath(
realpath(join(folder, "feff0004.dat")), # O-Ni triangle
s02='amp',
e0='enot',
sigma2='sso+ssni/2',
deltar='alpha*reff',
_larch=self._larch))
paths.append(
feffpath(
realpath(join(folder, "feff0005.dat")), # 3rd shell O SS
s02='amp',
e0='enot',
sigma2='sso2',
deltar='alpha*reff',
_larch=self._larch))
paths.append(
feffpath(
realpath(join(folder, "feff0006.dat")), # 4th shell Ni SS
s02='amp',
e0='enot',
sigma2='ssni2',
deltar='alpha*reff',
_larch=self._larch))
paths.append(
feffpath(
realpath(join(folder,
"feff0007.dat")), # O-O non-forward linear
s02='amp',
e0='enot',
sigma2='sso*2',
deltar='alpha*reff',
_larch=self._larch))
paths.append(
feffpath(
realpath(join(folder,
"feff0008.dat")), # O-Ni forward scattering
s02='amp',
e0='enot',
sigma2='ssni2',
deltar='alpha*reff',
_larch=self._larch))
paths.append(
feffpath(
realpath(join(folder,
"feff0009.dat")), # O-O forward through absorber
s02='amp',
e0='enot',
sigma2='sso*2',
deltar='alpha*reff',
_larch=self._larch))
paths.append(
feffpath(
realpath(join(folder,
"feff0011.dat")), # O-Ni-O double forward
s02='amp',
e0='enot',
sigma2='ssni2',
deltar='alpha*reff',
_larch=self._larch))
paths.append(
feffpath(
realpath(
join(folder, "feff0010.dat")
), # O-O rattle (the order of 10 and 11 is different in Demeter's pathfinder!)
s02='amp',
e0='enot',
sigma2='sso*4',
deltar='alpha*reff',
_larch=self._larch))
rx = 4.2
if firstshell: rx = 1.95
trans = feffit_transform(kmin=3,
kmax=15.938,
kw=(2, 1, 3),
dk=1,
window='hanning',
rmin=1.0,
rmax=rx,
_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 = 0.6 * max(dset.data.chir_mag)
_newplot(dset.data.r,
dset.data.chir_mag + offset,
xmax=8,
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',
_larch=self._larch)
_plot(dset.data.r, dset.data.chir_re, label='data', _larch=self._larch)
_plot(dset.model.r,
dset.model.chir_re,
label='fit',
_larch=self._larch)
#end if
if self.verbose:
print feffit_report(fit, _larch=self._larch)
#end if
shells = ''
if firstshell: shells = '_1st'
write_ascii(join(self.folder, fittest, "fit_" + which + shells + ".k"),
dset.data.k,
dset.data.chi,
dset.model.chi,
labels="r data_mag fit_mag data_re fit_re",
_larch=self._larch)
write_ascii(join(self.folder, fittest, "fit_" + which + shells + ".r"),
dset.data.r,
dset.data.chir_mag,
dset.model.chir_mag,
dset.data.chir_re,
dset.model.chir_re,
labels="r data_mag fit_mag data_re fit_re",
_larch=self._larch)
renderer = pystache.Renderer()
with open(join(self.folder, fittest, 'fit_' + which + shells + '.gp'),
'w') as inp:
inp.write(
renderer.render_path(
'plot.mustache', # gnuplot mustache file
{
'material': 'NiO',
'model': which,
'fittest': fittest,
'shells': shells,
'kmin': 3,
'kmax': 15.938,
'rmin': 1.0,
'rmax': rx,
'offset': 1,
}))
return fit
def do_fit(self, which, firstshell=False, fittest='baseline'):
if which == 'testrun':
folder = self.testrun
elif which == 'baseline':
folder = self.baseline
else:
folder = realpath(join(self.folder, fittest, which))
#endif
data = read_xdi(join(self.path, 'NiO.chik'), _larch=self._larch)
if hasattr(data, 'wavenumber'):
data.k = data.wavenumber
gds = Group(amp = Parameter(1, vary=True, _larch=self._larch),
enot = Parameter(1e-7, vary=True, _larch=self._larch),
sso = Parameter(0.003, vary=True, _larch=self._larch), _larch=self._larch )
if firstshell:
gds.delr = Parameter(1e-7, vary=True, _larch=self._larch)
dr1param = 'delr'
else:
gds.alpha = Parameter(1e-7, vary=True, _larch=self._larch)
gds.ssni = Parameter(0.003, vary=True, _larch=self._larch)
gds.sso2 = Parameter(0.003, vary=True, _larch=self._larch)
#gds.sso3 = Parameter(0.003, vary=True, _larch=self._larch)
gds.ssni2 = Parameter(0.003, vary=True, _larch=self._larch)
#gds.ssni3 = Parameter(0.003, vary=True, _larch=self._larch)
#gds.ssni4 = Parameter(0.003, vary=True, _larch=self._larch)
dr1param = 'alpha*reff'
paths = list()
paths.append(feffpath(realpath(join(folder, "feff0001.dat")), # 1st shell O SS
s02 = 'amp',
e0 = 'enot',
sigma2 = 'sso',
deltar = dr1param, _larch=self._larch))
if not firstshell:
paths.append(feffpath(realpath(join(folder, "feff0002.dat")), # 2nd shell Ni SS
s02 = 'amp',
e0 = 'enot',
sigma2 = 'ssni',
deltar = 'alpha*reff', _larch=self._larch))
paths.append(feffpath(realpath(join(folder, "feff0003.dat")), # O-O triangle
s02 = 'amp',
e0 = 'enot',
sigma2 = '1.5*sso',
deltar = 'alpha*reff', _larch=self._larch))
paths.append(feffpath(realpath(join(folder, "feff0004.dat")), # O-Ni triangle
s02 = 'amp',
e0 = 'enot',
sigma2 = 'sso+ssni/2',
deltar = 'alpha*reff', _larch=self._larch))
paths.append(feffpath(realpath(join(folder, "feff0005.dat")), # 3rd shell O SS
s02 = 'amp',
e0 = 'enot',
sigma2 = 'sso2',
deltar = 'alpha*reff', _larch=self._larch))
paths.append(feffpath(realpath(join(folder, "feff0006.dat")), # 4th shell Ni SS
s02 = 'amp',
e0 = 'enot',
sigma2 = 'ssni2',
deltar = 'alpha*reff', _larch=self._larch))
paths.append(feffpath(realpath(join(folder, "feff0007.dat")), # O-O non-forward linear
s02 = 'amp',
e0 = 'enot',
sigma2 = 'sso*2',
deltar = 'alpha*reff', _larch=self._larch))
paths.append(feffpath(realpath(join(folder, "feff0008.dat")), # O-Ni forward scattering
s02 = 'amp',
e0 = 'enot',
sigma2 = 'ssni2',
deltar = 'alpha*reff', _larch=self._larch))
paths.append(feffpath(realpath(join(folder, "feff0009.dat")), # O-O forward through absorber
s02 = 'amp',
e0 = 'enot',
sigma2 = 'sso*2',
deltar = 'alpha*reff', _larch=self._larch))
paths.append(feffpath(realpath(join(folder, "feff0011.dat")), # O-Ni-O double forward
s02 = 'amp',
e0 = 'enot',
sigma2 = 'ssni2',
deltar = 'alpha*reff', _larch=self._larch))
paths.append(feffpath(realpath(join(folder, "feff0010.dat")), # O-O rattle (the order of 10 and 11 is different in Demeter's pathfinder!)
s02 = 'amp',
e0 = 'enot',
sigma2 = 'sso*4',
deltar = 'alpha*reff', _larch=self._larch))
rx = 4.2
if firstshell: rx = 1.95
trans = feffit_transform(kmin=3, kmax=15.938, kw=(2,1,3), dk=1, window='hanning', rmin=1.0, rmax=rx, _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 = 0.6*max(dset.data.chir_mag)
_newplot(dset.data.r, dset.data.chir_mag+offset, xmax=8,
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', _larch=self._larch)
_plot(dset.data.r, dset.data.chir_re, label='data', _larch=self._larch)
_plot(dset.model.r, dset.model.chir_re, label='fit', _larch=self._larch)
#end if
if self.verbose:
print feffit_report(fit, _larch=self._larch)
#end if
shells = ''
if firstshell: shells='_1st'
write_ascii(join(self.folder, fittest, "fit_"+which+shells+".k"), dset.data.k, dset.data.chi, dset.model.chi,
labels="r data_mag fit_mag data_re fit_re", _larch=self._larch)
write_ascii(join(self.folder, fittest, "fit_"+which+shells+".r"), dset.data.r, dset.data.chir_mag, dset.model.chir_mag,
dset.data.chir_re, dset.model.chir_re, labels="r data_mag fit_mag data_re fit_re", _larch=self._larch)
renderer = pystache.Renderer()
with open(join(self.folder, fittest,'fit_'+which+shells+'.gp'), 'w') as inp:
inp.write(renderer.render_path( 'plot.mustache', # gnuplot mustache file
{'material': 'NiO',
'model': which,
'fittest': fittest,
'shells': shells,
'kmin': 3,
'kmax': 15.938,
'rmin': 1.0,
'rmax': rx,
'offset': 1,
} ))
return fit
def do_fit(self, which, firstshell=False, fittest='baseline'):
if which == 'testrun':
folder = self.testrun
elif which == 'baseline':
folder = self.baseline
else:
folder = realpath(join(self.folder, fittest, which))
#endif
data = read_xdi(join(self.path, 'BaZrO3.chik'), _larch=self._larch)
gds = Group(amp = Parameter(0.95, vary=True, _larch=self._larch),
enot = Parameter(1e-7, vary=True, _larch=self._larch),
sso = Parameter(0.003, vary=True, _larch=self._larch),
czr = Parameter(0., vary=False, _larch=self._larch), _larch=self._larch )
if firstshell:
gds.delr = Parameter(1e-7, vary=True, _larch=self._larch)
dr1param = 'delr'
else:
gds.alpha = Parameter(0.00001, vary=True, _larch=self._larch)
gds.ssba = Parameter(0.003, vary=True, _larch=self._larch)
gds.sszr = Parameter(0.003, vary=True, _larch=self._larch)
gds.eba = Parameter(1e-7, vary=True, _larch=self._larch)
gds.ezr = Parameter(1e-7, vary=True, _larch=self._larch)
#gds.eba = Parameter(expr='enot', _larch=self._larch)
#gdsezr = Parameter(expr='enot', _larch=self._larch)
gds.sso2 = Parameter(0.003, vary=True, _larch=self._larch)
dr1param = 'alpha*reff'
paths = list()
paths.append(feffpath(realpath(join(folder, "feff0001.dat")),
s02 = 'amp',
deltar = dr1param,
e0 = 'enot',
sigma2 = 'sso',
_larch=self._larch))
if not firstshell:
paths.append(feffpath(realpath(join(folder, "feff0002.dat")),
s02 = 'amp',
deltar = 'alpha*reff',
e0 = 'enot',
sigma2 = 'sso*1.5',
_larch=self._larch))
paths.append(feffpath(realpath(join(folder, "feff0003.dat")),
s02 = 'amp',
deltar = 'alpha*reff',
e0 = 'eba',
sigma2 = 'ssba',
_larch=self._larch))
paths.append(feffpath(realpath(join(folder, "feff0004.dat")),
s02 = 'amp',
deltar = 'alpha*reff',
e0 = 'ezr',
sigma2 = 'sszr',
third = 'czr',
_larch=self._larch))
paths.append(feffpath(realpath(join(folder, "feff0005.dat")),
s02 = 'amp',
deltar = 'alpha*reff',
e0 = 'enot',
sigma2 = 'sso*2',
_larch=self._larch))
paths.append(feffpath(realpath(join(folder, "feff0006.dat")),
s02 = 'amp',
deltar = 'alpha*reff',
e0 = '(enot+ezr)/2',
sigma2 = 'sszr',
third = 'czr',
_larch=self._larch))
paths.append(feffpath(realpath(join(folder, "feff0007.dat")),
s02 = 'amp',
deltar = 'alpha*reff',
e0 = 'enot',
sigma2 = 'sso*2',
_larch=self._larch))
paths.append(feffpath(realpath(join(folder, "feff0009.dat")),
s02 = 'amp',
deltar = 'alpha*reff',
e0 = '(2*enot+ezr)/3',
sigma2 = 'sszr',
third = 'czr',
_larch=self._larch))
paths.append(feffpath(realpath(join(folder, "feff0008.dat")),
s02 = 'amp',
deltar = 'alpha*reff',
e0 = 'enot',
sigma2 = 'sso*4',
_larch=self._larch))
paths.append(feffpath(realpath(join(folder, "feff0011.dat")),
s02 = 'amp',
deltar = 'alpha*reff',
e0 = '(enot+eba)/2',
sigma2 = 'ssba+sso',
_larch=self._larch))
paths.append(feffpath(realpath(join(folder, "feff0012.dat")),
s02 = 'amp',
deltar = 'alpha*reff',
e0 = 'enot',
sigma2 = 'sso2',
_larch=self._larch))
paths.append(feffpath(realpath(join(folder, "feff0013.dat")),
s02 = 'amp',
deltar = 'alpha*reff',
e0 = 'enot',
sigma2 = 'sso+sso2',
_larch=self._larch))
rx = 4.5
if firstshell: rx = 1.95
trans = feffit_transform(kmin=3, kmax=14.5, kw=(2,1,3), dk=1, window='hanning', rmin=1.2, rmax=rx, _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,
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', _larch=self._larch)
_plot(dset.data.r, dset.data.chir_re, label='data', _larch=self._larch)
_plot(dset.model.r, dset.model.chir_re, label='fit', _larch=self._larch)
#end if
if self.verbose:
print feffit_report(fit, _larch=self._larch)
#end if
shells = ''
if firstshell: shells='_1st'
write_ascii(join(self.folder, fittest, "fit_"+which+shells+".k"), dset.data.k, dset.data.chi, dset.model.chi,
labels="r data_mag fit_mag data_re fit_re", _larch=self._larch)
write_ascii(join(self.folder, fittest, "fit_"+which+shells+".r"), dset.data.r, dset.data.chir_mag, dset.model.chir_mag,
dset.data.chir_re, dset.model.chir_re, labels="r data_mag fit_mag data_re fit_re", _larch=self._larch)
renderer = pystache.Renderer()
with open(join(self.folder, fittest, 'fit_'+which+shells+'.gp'), 'w') as inp:
inp.write(renderer.render_path( 'plot.mustache', # gnuplot mustache file
{'material': 'BaZrO3',
'model': which,
'fittest': fittest,
'shells': shells,
'kmin': 3,
'kmax': 14.5,
'rmin': 1.2,
'rmax': rx,
'offset': 1,
} ))
return fit
def do_fit(self, which, firstshell=False, fittest='baseline'):
if which == 'testrun':
folder = self.testrun
elif which == 'baseline':
folder = self.baseline
else:
folder = realpath(join(self.folder, fittest, which))
#endif
data = read_xdi(join(self.path, 'Copper.chik'), _larch=self._larch)
gds = Group(amp = Parameter(1, vary=True, _larch=self._larch),
enot = Parameter(1e-7, vary=True, _larch=self._larch),
ss1 = Parameter(0.003, vary=True, _larch=self._larch), _larch=self._larch )
if firstshell:
gds.delr = Parameter(1e-7, vary=True, _larch=self._larch)
dr1param = 'delr'
else:
gds.thetad = Parameter(500, vary=True, _larch=self._larch)
gds.temp = Parameter(10, vary=False, _larch=self._larch)
gds.alpha = Parameter(1e-7, vary=True, _larch=self._larch)
dr1param = 'alpha*reff'
imax = 16
if firstshell: imax = 2
paths = list()
for index in range(1,imax):
nnnn = realpath(join(folder, "feff%4.4d.dat" % index))
if not exists(nnnn):
continue
#end if
if index > 1:
sigsqr = 'sigma2_debye(temp, thetad)'
else:
sigsqr = 'ss1'
#end if
paths.append(feffpath(nnnn,
s02 = 'amp',
e0 = 'enot',
sigma2 = sigsqr,
deltar = dr1param, _larch=self._larch))
#end for
rx = 5.0
if firstshell: rx = 2.8
trans = feffit_transform(kmin=3, kmax=15, kw=(2,1,3), dk=1, window='hanning', rmin=1, rmax=rx, _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,
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', _larch=self._larch)
_plot(dset.data.r, dset.data.chir_re, label='data', _larch=self._larch)
_plot(dset.model.r, dset.model.chir_re, label='fit', _larch=self._larch)
#end if
if self.verbose:
print feffit_report(fit, _larch=self._larch)
#end if
shells = ''
if firstshell: shells='_1st'
write_ascii(join(self.folder, fittest, "fit_"+which+shells+".k"), dset.data.k, dset.data.chi, dset.model.chi,
labels="r data_mag fit_mag data_re fit_re", _larch=self._larch)
write_ascii(join(self.folder, fittest, "fit_"+which+shells+".r"), dset.data.r, dset.data.chir_mag, dset.model.chir_mag,
dset.data.chir_re, dset.model.chir_re, labels="r data_mag fit_mag data_re fit_re", _larch=self._larch)
renderer = pystache.Renderer()
with open(join(self.folder, fittest, 'fit_'+which+shells+'.gp'), 'w') as inp:
inp.write(renderer.render_path( 'plot.mustache', # gnuplot mustache file
{'material': 'Copper',
'model': which,
'fittest': fittest,
'shells': shells,
'kmin': 3,
'kmax': 15,
'rmin': 1,
'rmax': rx,
'offset': 2,
} ))
return fit
def do_fit(self, which, firstshell=False, fittest='baseline'):
if which == 'testrun':
folder = self.testrun
elif which == 'baseline':
folder = self.baseline
else:
folder = realpath(join(self.folder, fittest, which))
#endif
data = read_xdi(join(self.path, 'Copper.chik'), _larch=self._larch)
gds = Group(amp=Parameter(1, vary=True, _larch=self._larch),
enot=Parameter(1e-7, vary=True, _larch=self._larch),
ss1=Parameter(0.003, vary=True, _larch=self._larch),
_larch=self._larch)
if firstshell:
gds.delr = Parameter(1e-7, vary=True, _larch=self._larch)
dr1param = 'delr'
else:
gds.thetad = Parameter(500, vary=True, _larch=self._larch)
gds.temp = Parameter(10, vary=False, _larch=self._larch)
gds.alpha = Parameter(1e-7, vary=True, _larch=self._larch)
dr1param = 'alpha*reff'
imax = 16
if firstshell: imax = 2
paths = list()
for index in range(1, imax):
nnnn = realpath(join(folder, "feff%4.4d.dat" % index))
if not exists(nnnn):
continue
#end if
if index > 1:
sigsqr = 'sigma2_debye(temp, thetad)'
else:
sigsqr = 'ss1'
#end if
paths.append(
feffpath(nnnn,
s02='amp',
e0='enot',
sigma2=sigsqr,
deltar=dr1param,
_larch=self._larch))
#end for
rx = 5.0
if firstshell: rx = 2.8
trans = feffit_transform(kmin=3,
kmax=15,
kw=(2, 1, 3),
dk=1,
window='hanning',
rmin=1,
rmax=rx,
_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,
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',
_larch=self._larch)
_plot(dset.data.r, dset.data.chir_re, label='data', _larch=self._larch)
_plot(dset.model.r,
dset.model.chir_re,
label='fit',
_larch=self._larch)
#end if
if self.verbose:
print feffit_report(fit, _larch=self._larch)
#end if
shells = ''
if firstshell: shells = '_1st'
write_ascii(join(self.folder, fittest, "fit_" + which + shells + ".k"),
dset.data.k,
dset.data.chi,
dset.model.chi,
labels="r data_mag fit_mag data_re fit_re",
_larch=self._larch)
write_ascii(join(self.folder, fittest, "fit_" + which + shells + ".r"),
dset.data.r,
dset.data.chir_mag,
dset.model.chir_mag,
dset.data.chir_re,
dset.model.chir_re,
labels="r data_mag fit_mag data_re fit_re",
_larch=self._larch)
renderer = pystache.Renderer()
with open(join(self.folder, fittest, 'fit_' + which + shells + '.gp'),
'w') as inp:
inp.write(
renderer.render_path(
'plot.mustache', # gnuplot mustache file
{
'material': 'Copper',
'model': which,
'fittest': fittest,
'shells': shells,
'kmin': 3,
'kmax': 15,
'rmin': 1,
'rmax': rx,
'offset': 2,
}))
return fit
def do_fit(self, which, firstshell=False, fittest='baseline'):
if which == 'testrun':
folder = self.testrun
elif which == 'baseline':
folder = self.baseline
else:
folder = realpath(join(self.folder, fittest, which))
#endif
data = read_xdi(join(self.path, 'FeS2.chik'), _larch=self._larch)
gds = Group(amp=Parameter(1, vary=True, _larch=self._larch),
enot=Parameter(1e-7, vary=True, _larch=self._larch),
ss=Parameter(0.003, vary=True, _larch=self._larch),
_larch=self._larch)
if firstshell:
gds.delr = Parameter(1e-7, vary=True, _larch=self._larch)
dr1param = 'delr'
else:
gds.alpha = Parameter(1e-7, vary=True, _larch=self._larch)
gds.ss2 = Parameter(0.003, vary=True, _larch=self._larch)
gds.ss3 = Parameter(expr='ss2', _larch=self._larch)
gds.ssfe = Parameter(0.003, vary=True, _larch=self._larch)
dr1param = 'alpha*reff'
paths = list()
paths.append(
feffpath(
realpath(join(folder, "feff0001.dat")), # 1st shell S SS
s02='amp',
e0='enot',
sigma2='ss',
deltar=dr1param,
_larch=self._larch))
if not firstshell:
paths.append(
feffpath(
realpath(join(folder, "feff0002.dat")), # 2nd shell S SS
s02='amp',
e0='enot',
sigma2='ss2',
deltar='alpha*reff',
_larch=self._larch))
paths.append(
feffpath(
realpath(join(folder, "feff0003.dat")), # 3rd shell S SS
s02='amp',
e0='enot',
sigma2='ss3',
deltar='alpha*reff',
_larch=self._larch))
paths.append(
feffpath(
realpath(join(folder, "feff0004.dat")), # 4th shell Fe SS
s02='amp',
e0='enot',
sigma2='ssfe',
deltar='alpha*reff',
_larch=self._larch))
paths.append(
feffpath(
realpath(join(folder, "feff0005.dat")), # S-S triangle
s02='amp',
e0='enot',
sigma2='ss*1.5',
deltar='alpha*reff',
_larch=self._larch))
paths.append(
feffpath(
realpath(join(folder, "feff0006.dat")), # S-Fe triangle
s02='amp',
e0='enot',
sigma2='ss/2+ssfe',
deltar='alpha*reff',
_larch=self._larch))
paths.append(
feffpath(
realpath(join(folder,
"feff0012.dat")), # S-S non-forward linear
s02='amp',
e0='enot',
sigma2='ss*2',
deltar='alpha*reff',
_larch=self._larch))
paths.append(
feffpath(
realpath(join(folder,
"feff0013.dat")), # S-S forward scattering
s02='amp',
e0='enot',
sigma2='ss*2',
deltar='alpha*reff',
_larch=self._larch))
paths.append(
feffpath(
realpath(join(folder, "feff0014.dat")), # S-S rattle
s02='amp',
e0='enot',
sigma2='ss*4',
deltar='alpha*reff',
_larch=self._larch))
rx = 4.2
if firstshell: rx = 2.3
trans = feffit_transform(kmin=3,
kmax=12.956,
kw=(2, 1, 3),
dk=1,
window='hanning',
rmin=1.2,
rmax=rx,
_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 = 0.6 * max(dset.data.chir_mag)
_newplot(dset.data.r,
dset.data.chir_mag + offset,
xmax=8,
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',
_larch=self._larch)
_plot(dset.data.r, dset.data.chir_re, label='data', _larch=self._larch)
_plot(dset.model.r,
dset.model.chir_re,
label='fit',
_larch=self._larch)
#end if
if self.verbose:
print feffit_report(fit, _larch=self._larch)
#end if
shells = ''
if firstshell: shells = '_1st'
write_ascii(join(self.folder, fittest, "fit_" + which + shells + ".k"),
dset.data.k,
dset.data.chi,
dset.model.chi,
labels="r data_mag fit_mag data_re fit_re",
_larch=self._larch)
write_ascii(join(self.folder, fittest, "fit_" + which + shells + ".r"),
dset.data.r,
dset.data.chir_mag,
dset.model.chir_mag,
dset.data.chir_re,
dset.model.chir_re,
labels="r data_mag fit_mag data_re fit_re",
_larch=self._larch)
renderer = pystache.Renderer()
with open(join(self.folder, fittest, 'fit_' + which + shells + '.gp'),
'w') as inp:
inp.write(
renderer.render_path(
'plot.mustache', # gnuplot mustache file
{
'material': 'FeS2',
'model': which,
'fittest': fittest,
'shells': shells,
'kmin': 3,
'kmax': 12.956,
'rmin': 1.2,
'rmax': rx,
'offset': 1,
}))
return fit
