def do_fit(self, which):
if which == 'testrun':
folder = self.testrun
elif which == 'baseline':
folder = self.baseline
else:
folder = realpath(join(self.folder, 'baseline', which))
#endif
print '>>>>>> %s' % folder
data = read_xdi(join(self.path, 'Copper.chik'), _larch=self._larch)
gds = Group(amp = Parameter(1, vary=True),
enot = Parameter(1e-7, vary=True),
thetad = Parameter(500, vary=True),
temp = Parameter(10, vary=False),
alpha = Parameter(1e-7, vary=True),
ss1 = Parameter(0.003, vary=True),
_larch=self._larch )
paths = list()
for index in range(1,14):
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 = 'alpha*reff', _larch=self._larch))
#end for
trans = feffit_transform(kmin=3, kmax=16, kw=(2,1,3), dk=1, window='hanning', rmin=1.7, rmax=5.1, _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
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
def do_fit(self, which):
if which == 'testrun':
folder = self.testrun
else:
folder = self.baseline
#end if
data = read_xdi(join(self.path, 'bromoadamantane.chik'), _larch=self._larch)
gds = Group(amp = Parameter(1.021, vary=False, _larch=self._larch),
enot = Parameter(4.01, vary=True, _larch=self._larch),
delr = Parameter(-0.007, vary=True, _larch=self._larch),
brc = Parameter(expr = '1.9521+delr', _larch=self._larch),
ss = Parameter(0.003, vary=True, _larch=self._larch),
phir = Parameter(109.29960 * 3.141592653589793 / 180, vary=False, _larch=self._larch),
cc = Parameter(1.53780, vary=False, _larch=self._larch),
tanbeta = Parameter(expr = '(brc+cc)*tan(phir/2) / (brc-cc)', _larch=self._larch),
beta = Parameter(expr = 'atan(tanbeta)', _larch=self._larch),
brc2 = Parameter(expr = '(brc-cc)*cos(phir/2)/cos(beta)', _larch=self._larch),
drh = Parameter(0.04, vary=True, _larch=self._larch),
ssh = Parameter(0.005, vary=True, _larch=self._larch),
ss2 = Parameter(expr = 'ss*(brc2/brc)**2', _larch=self._larch),
c3 = Parameter(-0.0007, vary=True, _larch=self._larch),
_larch=self._larch )
paths = list()
paths.append(feffpath(realpath(join(folder, "feff0001.dat")),
s02 = 'amp',
e0 = 'enot',
sigma2 = 'ss',
deltar = 'delr',
third = 'c3', _larch=self._larch))
paths.append(feffpath(realpath(join(folder, "feff0002.dat")),
s02 = 'amp',
e0 = 'enot',
sigma2 = 'ss2',
deltar = 'brc2-2.8565', _larch=self._larch))
paths.append(feffpath(realpath(join(folder, "feff0003.dat")),
s02 = 'amp',
e0 = 'enot',
sigma2 = 'ssh',
deltar = 'drh', _larch=self._larch))
paths.append(feffpath(realpath(join(folder, "feff0004.dat")),
s02 = 'amp',
e0 = 'enot',
sigma2 = '(ss+ss2)/2',
deltar = '(brc+brc2+cc)/2 - 3.173', _larch=self._larch))
paths.append(feffpath(realpath(join(folder, "feff0005.dat")),
s02 = 'amp',
e0 = 'enot',
sigma2 = '(ss+ss2)/2',
deltar = '(brc+brc2+cc)/2 - 3.173', _larch=self._larch))
trans = feffit_transform(kmin=3, kmax=13, kw=(2,1,3), dk=1, window='hanning', rmin=1.25, rmax=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
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
dmt = read_xdi(join(self.path, 'dmt.chik'), _larch=self._larch)
mmt = read_xdi(join(self.path, 'mmt.chik'), _larch=self._larch)
gds = Group(amp=Parameter(0.9, vary=True, _larch=self._larch),
enot=Parameter(1e-7, vary=True, _larch=self._larch),
delr_c=Parameter(1e-7, vary=True, _larch=self._larch),
ss_c=Parameter(0.003, vary=True, _larch=self._larch),
delr_cl=Parameter(1e-7, vary=True, _larch=self._larch),
ss_cl=Parameter(0.003, vary=True, _larch=self._larch),
_larch=self._larch)
paths_dmt = list()
paths_dmt.append(
feffpath(realpath(join(folder, "feff0001.dat")),
degen=2,
s02='amp',
e0='enot',
sigma2='ss_c',
deltar='delr_c',
_larch=self._larch))
paths_dmt.append(
feffpath(realpath(join(folder, "feff0002.dat")),
degen=2,
s02='amp',
e0='enot',
sigma2='ss_cl',
deltar='delr_cl',
_larch=self._larch))
paths_mmt = list()
paths_mmt.append(
feffpath(realpath(join(folder, "feff0001.dat")),
degen=1,
s02='amp',
e0='enot',
sigma2='ss_c',
deltar='delr_c',
_larch=self._larch))
paths_mmt.append(
feffpath(realpath(join(folder, "feff0002.dat")),
degen=3,
s02='amp',
e0='enot',
sigma2='ss_cl',
deltar='delr_cl',
_larch=self._larch))
trans = feffit_transform(kmin=3,
kmax=13,
kw=(2, 1, 3),
dk=1,
window='hanning',
rmin=1.25,
rmax=3,
_larch=self._larch)
dset = [
feffit_dataset(data=dmt,
pathlist=paths_dmt,
transform=trans,
_larch=self._larch),
feffit_dataset(data=mmt,
pathlist=paths_mmt,
transform=trans,
_larch=self._larch)
]
fit = feffit(gds, dset, _larch=self._larch)
if self.doplot:
offset = max(dset[0].data.chir_mag) / 2
_newplot(dset[0].data.r,
dset[0].data.chir_mag + offset,
xmax=5,
win=1,
xlabel=r'$R \rm\,(\AA)$',
label='dimethyltin',
ylabel=r'$|\chi(R)| \rm\,(\AA^{-3})$',
title='Fit to ' + self.folder,
show_legend=True,
_larch=self._larch)
_plot(dset[0].model.r,
dset[0].model.chir_mag + offset,
label='fit',
win=1,
_larch=self._larch)
_plot(dset[0].data.r,
dset[0].data.chir_re,
label='dimethyltin',
win=1,
_larch=self._larch)
_plot(dset[0].model.r,
dset[0].model.chir_re,
label='fit',
win=1,
_larch=self._larch)
_plot(dset[1].data.r,
dset[1].data.chir_mag + 7 * offset,
label='monomethyltin',
win=1,
_larch=self._larch)
_plot(dset[1].model.r,
dset[1].model.chir_mag + 7 * offset,
label='fit',
win=1,
_larch=self._larch)
_plot(dset[1].data.r,
dset[1].data.chir_re + 6 * offset,
label='monomethyltin',
win=1,
_larch=self._larch)
_plot(dset[1].model.r,
dset[1].model.chir_re + 6 * offset,
label='fit',
win=1,
_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 + ".k"),
dset.data[0].k,
dset.data[0].chi,
dset.model[0].chi,
labels="r data_mag fit_mag data_re fit_re",
_larch=self._larch)
write_ascii(join(self.folder, fittest, "fit_" + which + ".r"),
dset.data[0].r,
dset.data[0].chir_mag,
dset.model[0].chir_mag,
dset.data[0].chir_re,
dset.model[0].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 + '.gp'), 'w') as inp:
inp.write(
renderer.render_path(
'plot.mustache', # gnuplot mustache file
{
'material': 'methyltin',
'model': which,
'fittest': fittest,
'shells': shells,
'kmin': 3,
'kmax': 13,
'rmin': 1.25,
'rmax': 3,
'offset': 1,
}))
return fit
def do_fit(self, which):
if which == 'testrun':
folder = self.testrun
else:
folder = self.baseline
#end if
data = read_xdi(join(self.path, 'bromoadamantane.chik'),
_larch=self._larch)
gds = Group(amp=Parameter(1.021, vary=True, _larch=self._larch),
enot=Parameter(4.01, vary=True, _larch=self._larch),
delr=Parameter(-0.007, vary=True, _larch=self._larch),
brc=Parameter(expr='1.9521+delr', _larch=self._larch),
ss=Parameter(0.003, vary=True, _larch=self._larch),
phir=Parameter(109.29960 * 3.141592653589793 / 180,
vary=False,
_larch=self._larch),
cc=Parameter(1.53780, vary=False, _larch=self._larch),
tanbeta=Parameter(expr='(brc+cc)*tan(phir/2) / (brc-cc)',
_larch=self._larch),
beta=Parameter(expr='atan(tanbeta)', _larch=self._larch),
brc2=Parameter(expr='(brc-cc)*cos(phir/2)/cos(beta)',
_larch=self._larch),
drh=Parameter(0.04, vary=True, _larch=self._larch),
ssh=Parameter(0.005, vary=True, _larch=self._larch),
ss2=Parameter(expr='ss*(brc2/brc)**2', _larch=self._larch),
c3=Parameter(-0.0007, vary=True, _larch=self._larch),
_larch=self._larch)
paths = list()
paths.append(
feffpath(realpath(join(folder, "feff0001.dat")),
s02='amp',
e0='enot',
sigma2='ss',
deltar='delr',
third='c3',
_larch=self._larch))
paths.append(
feffpath(realpath(join(folder, "feff0002.dat")),
s02='amp',
e0='enot',
sigma2='ss2',
deltar='brc2-2.8565',
_larch=self._larch))
paths.append(
feffpath(realpath(join(folder, "feff0003.dat")),
s02='amp',
e0='enot',
sigma2='ssh',
deltar='drh',
_larch=self._larch))
paths.append(
feffpath(realpath(join(folder, "feff0004.dat")),
s02='amp',
e0='enot',
sigma2='(ss+ss2)/2',
deltar='(brc+brc2+cc)/2 - 3.173',
_larch=self._larch))
paths.append(
feffpath(realpath(join(folder, "feff0005.dat")),
s02='amp',
e0='enot',
sigma2='(ss+ss2)/2',
deltar='(brc+brc2+cc)/2 - 3.173',
_larch=self._larch))
trans = feffit_transform(kmin=2.5,
kmax=13,
kw=(2, 1, 3),
dk=1,
window='hanning',
rmin=1.25,
rmax=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
def do_fit(self, which):
if which == 'testrun':
folder = self.testrun
else:
folder = self.baseline
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(0.01, vary=True, _larch=self._larch),
alpha=Parameter(0.0001, vary=True, _larch=self._larch),
sso=Parameter(0.003, vary=True, _larch=self._larch),
ssni=Parameter(0.003, vary=True, _larch=self._larch),
sso2=Parameter(0.003, vary=True, _larch=self._larch),
#sso3 = Parameter(0.003, vary=True, _larch=self._larch),
ssni2=Parameter(0.003, vary=True, _larch=self._larch),
#ssni3 = Parameter(0.003, vary=True, _larch=self._larch),
#ssni4 = Parameter(0.003, vary=True, _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='alpha*reff',
_larch=self._larch))
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',
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, "feff0010.dat")), # O-Ni-O double forward
s02='amp',
e0='enot',
sigma2='ssni2',
deltar='alpha*reff',
_larch=self._larch))
trans = feffit_transform(kmin=3,
kmax=15.938,
kw=(2, 1, 3),
dk=1,
window='hanning',
rmin=1.5,
rmax=4.2,
_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,
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
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, 'UO2.chik'), _larch=self._larch)
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),
dro = Parameter(1e-7, vary=True, _larch=self._larch), _larch=self._larch )
if not firstshell:
gds.ssu = Parameter(0.003, vary=True, _larch=self._larch)
gds.sso2 = Parameter(0.003, vary=True, _larch=self._larch)
gds.dru = Parameter(1e-7, vary=True, _larch=self._larch)
gds.dro2 = Parameter(1e-7, vary=True, _larch=self._larch)
gds.nu = Parameter(12, vary=True, _larch=self._larch)
gds.no2 = Parameter(expr='2*nu', _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))
if not firstshell:
# paths.append(feffpath(realpath(join(folder, "feff0002.dat")), # triangle in first shell
# s02 = 'amp',
# e0 = 'enot',
# sigma2 = 'sso*(1+sqrt(3))**2',
# deltar = 'dro*(1+sqrt(3))/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 = 'sso*(1+sqrt(2/3))**2',
# deltar = '(1+sqrt(2/3))*dro', _larch=self._larch))
# paths.append(feffpath(realpath(join(folder, "feff0005.dat")), # 1st shell, longer U-O-U triangle
# degen = 1,
# s02 = 'amp*nu',
# e0 = 'enot',
# sigma2 = 'sso*ssu/2',
# deltar = '(1+sqrt(2/3))*dro', _larch=self._larch))
paths.append(feffpath(realpath(join(folder, "feff0006.dat")), # 3rd shell O SS
degen = 1,
s02 = 'amp*no2',
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 = '2*sso2',
deltar = '2*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))
rx = 4.3
if firstshell: rx = 2.5
trans = feffit_transform(kmin=3, kmax=11, kw=(2,1,3), dk=1, window='hanning', rmin=1.25, 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': 'UO2',
'model': which,
'fittest': fittest,
'shells': shells,
'kmin': 3,
'kmax': 11,
'rmin': 1.25,
'rmax': rx,
'offset': 0.75,
} ))
return fit
def do_fit(self, which, firstshell=False, fittest='baseline'):
firstshell = False # no 1st shell fit for this material
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, 'uranyl.chik'), _larch=self._larch)
gds = Group(amp = Parameter(1, vary=True, _larch=self._larch),
enot = Parameter(1e-7, vary=True, _larch=self._larch),
#enot = Parameter(1e-7, vary=True, _larch=self._larch, min=0, max=13),
enoteq = Parameter(expr= 'enot', _larch=self._larch),
deloax = Parameter(1e-7, vary=True, _larch=self._larch),
deloeq = Parameter(1e-7, vary=True, _larch=self._larch),
sigoax = Parameter(0.003, vary=True, _larch=self._larch),
sigoeq = Parameter(0.003, vary=True, _larch=self._larch),
nax = Parameter(2.0, vary=False, _larch=self._larch),
neq = Parameter(6, vary=False, _larch=self._larch), #, min=0, max=12),
_larch=self._larch )
paths = list()
paths.append(feffpath(realpath(join(folder, "feff0001.dat")), # axial oxygen
degen = 1,
s02 = 'amp*nax',
e0 = 'enot',
sigma2 = 'sigoax',
deltar = 'deloax', _larch=self._larch))
paths.append(feffpath(realpath(join(folder, "feff0003.dat")), # equatorial oxygen
degen = 1,
s02 = 'amp*neq',
e0 = 'enoteq',
sigma2 = 'sigoeq',
deltar = 'deloeq', _larch=self._larch))
paths.append(feffpath(realpath(join(folder, "feff0008.dat")), # axial oxygen, rattle
degen = 1,
s02 = 'amp*nax',
e0 = 'enot',
sigma2 = 'sigoax*4',
deltar = 'deloax*2', _larch=self._larch))
paths.append(feffpath(realpath(join(folder, "feff0009.dat")), # axial oxygen, non-forward
degen = 1,
s02 = 'amp*nax',
e0 = 'enot',
sigma2 = 'sigoax',
deltar = 'deloax*2', _larch=self._larch))
paths.append(feffpath(realpath(join(folder, "feff0010.dat")), # axial oxygen, forward
degen = 1,
s02 = 'amp*nax',
e0 = 'enot',
sigma2 = 'sigoax',
deltar = 'deloax*2', _larch=self._larch))
trans = feffit_transform(kmin=3, kmax=11, kw=(2,1,3), dk=1, window='hanning', rmin=1.0, rmax=3.2, _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
shells = ''
if firstshell: shells='_1st'
write_ascii(join(self.folder, fittest, "fit_"+which+".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+".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+'.gp'), 'w') as inp:
inp.write(renderer.render_path( 'plot.mustache', # gnuplot mustache file
{'material': 'uranyl',
'model': which,
'fittest': fittest,
'shells': shells,
'kmin': 3,
'kmax': 11,
'rmin': 1.0,
'rmax': 3.2,
'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
dmt = read_xdi(join(self.path, 'dmt.chik'), _larch=self._larch)
mmt = read_xdi(join(self.path, 'mmt.chik'), _larch=self._larch)
gds = Group(amp = Parameter(0.9, vary=True, _larch=self._larch),
enot = Parameter(1e-7, vary=True, _larch=self._larch),
delr_c = Parameter(1e-7, vary=True, _larch=self._larch),
ss_c = Parameter(0.003, vary=True, _larch=self._larch),
delr_cl = Parameter(1e-7, vary=True, _larch=self._larch),
ss_cl = Parameter(0.003, vary=True, _larch=self._larch),
_larch=self._larch )
paths_dmt = list()
paths_dmt.append(feffpath(realpath(join(folder, "feff0001.dat")),
degen = 2,
s02 = 'amp',
e0 = 'enot',
sigma2 = 'ss_c',
deltar = 'delr_c', _larch=self._larch))
paths_dmt.append(feffpath(realpath(join(folder, "feff0002.dat")),
degen = 2,
s02 = 'amp',
e0 = 'enot',
sigma2 = 'ss_cl',
deltar = 'delr_cl', _larch=self._larch))
paths_mmt = list()
paths_mmt.append(feffpath(realpath(join(folder, "feff0001.dat")),
degen = 1,
s02 = 'amp',
e0 = 'enot',
sigma2 = 'ss_c',
deltar = 'delr_c', _larch=self._larch))
paths_mmt.append(feffpath(realpath(join(folder, "feff0002.dat")),
degen = 3,
s02 = 'amp',
e0 = 'enot',
sigma2 = 'ss_cl',
deltar = 'delr_cl', _larch=self._larch))
trans = feffit_transform(kmin=3, kmax=13, kw=(2,1,3), dk=1, window='hanning', rmin=1.25, rmax=3, _larch=self._larch)
dset = [feffit_dataset(data=dmt, pathlist=paths_dmt, transform=trans, _larch=self._larch),
feffit_dataset(data=mmt, pathlist=paths_mmt, transform=trans, _larch=self._larch)]
fit = feffit(gds, dset, _larch=self._larch)
if self.doplot:
offset = max(dset[0].data.chir_mag)/2
_newplot(dset[0].data.r, dset[0].data.chir_mag+offset, xmax=5, win=1,
xlabel=r'$R \rm\,(\AA)$', label='dimethyltin',
ylabel=r'$|\chi(R)| \rm\,(\AA^{-3})$',
title='Fit to '+self.folder, show_legend=True, _larch=self._larch)
_plot(dset[0].model.r, dset[0].model.chir_mag+offset, label='fit', win=1, _larch=self._larch)
_plot(dset[0].data.r, dset[0].data.chir_re, label='dimethyltin', win=1, _larch=self._larch)
_plot(dset[0].model.r, dset[0].model.chir_re, label='fit', win=1, _larch=self._larch)
_plot(dset[1].data.r, dset[1].data.chir_mag+7*offset, label='monomethyltin', win=1, _larch=self._larch)
_plot(dset[1].model.r, dset[1].model.chir_mag+7*offset, label='fit', win=1, _larch=self._larch)
_plot(dset[1].data.r, dset[1].data.chir_re+6*offset, label='monomethyltin', win=1, _larch=self._larch)
_plot(dset[1].model.r, dset[1].model.chir_re+6*offset, label='fit', win=1, _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+".k"), dset.data[0].k, dset.data[0].chi, dset.model[0].chi,
labels="r data_mag fit_mag data_re fit_re", _larch=self._larch)
write_ascii(join(self.folder, fittest, "fit_"+which+".r"), dset.data[0].r, dset.data[0].chir_mag, dset.model[0].chir_mag,
dset.data[0].chir_re, dset.model[0].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+'.gp'), 'w') as inp:
inp.write(renderer.render_path( 'plot.mustache', # gnuplot mustache file
{'material': 'methyltin',
'model': which,
'fittest': fittest,
'shells': shells,
'kmin': 3,
'kmax': 13,
'rmin': 1.25,
'rmax': 3,
'offset': 1,
} ))
return fit
def do_fit(self, which):
if which == 'testrun':
folder = self.testrun
else:
folder = self.baseline
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(0.01, vary=True, _larch=self._larch),
alpha = Parameter(0.0001, vary=True, _larch=self._larch),
sso = Parameter(0.003, vary=True, _larch=self._larch),
ssni = Parameter(0.003, vary=True, _larch=self._larch),
sso2 = Parameter(0.003, vary=True, _larch=self._larch),
#sso3 = Parameter(0.003, vary=True, _larch=self._larch),
ssni2 = Parameter(0.003, vary=True, _larch=self._larch),
#ssni3 = Parameter(0.003, vary=True, _larch=self._larch),
#ssni4 = Parameter(0.003, vary=True, _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 = 'alpha*reff', _larch=self._larch))
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',
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, "feff0010.dat")), # O-Ni-O double forward
s02 = 'amp',
e0 = 'enot',
sigma2 = 'ssni2',
deltar = 'alpha*reff', _larch=self._larch))
trans = feffit_transform(kmin=3, kmax=15.938, kw=(2,1,3), dk=1, window='hanning', rmin=1.5, rmax=4.2, _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, 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
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
def do_fit(self, which, firstshell=False, fittest='baseline'):
firstshell = False # no 1st shell fit for this material
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, 'uranyl.chik'), _larch=self._larch)
gds = Group(
amp=Parameter(1, vary=True, _larch=self._larch),
enot=Parameter(1e-7, vary=True, _larch=self._larch),
#enot = Parameter(1e-7, vary=True, _larch=self._larch, min=0, max=13),
enoteq=Parameter(expr='enot', _larch=self._larch),
deloax=Parameter(1e-7, vary=True, _larch=self._larch),
deloeq=Parameter(1e-7, vary=True, _larch=self._larch),
sigoax=Parameter(0.003, vary=True, _larch=self._larch),
sigoeq=Parameter(0.003, vary=True, _larch=self._larch),
nax=Parameter(2.0, vary=False, _larch=self._larch),
neq=Parameter(6, vary=False, _larch=self._larch), #, min=0, max=12),
_larch=self._larch)
paths = list()
paths.append(
feffpath(
realpath(join(folder, "feff0001.dat")), # axial oxygen
degen=1,
s02='amp*nax',
e0='enot',
sigma2='sigoax',
deltar='deloax',
_larch=self._larch))
paths.append(
feffpath(
realpath(join(folder, "feff0003.dat")), # equatorial oxygen
degen=1,
s02='amp*neq',
e0='enoteq',
sigma2='sigoeq',
deltar='deloeq',
_larch=self._larch))
paths.append(
feffpath(
realpath(join(folder, "feff0008.dat")), # axial oxygen, rattle
degen=1,
s02='amp*nax',
e0='enot',
sigma2='sigoax*4',
deltar='deloax*2',
_larch=self._larch))
paths.append(
feffpath(
realpath(join(folder,
"feff0009.dat")), # axial oxygen, non-forward
degen=1,
s02='amp*nax',
e0='enot',
sigma2='sigoax',
deltar='deloax*2',
_larch=self._larch))
paths.append(
feffpath(
realpath(join(folder, "feff0010.dat")), # axial oxygen, forward
degen=1,
s02='amp*nax',
e0='enot',
sigma2='sigoax',
deltar='deloax*2',
_larch=self._larch))
trans = feffit_transform(kmin=3,
kmax=11,
kw=(2, 1, 3),
dk=1,
window='hanning',
rmin=1.0,
rmax=3.2,
_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
shells = ''
if firstshell: shells = '_1st'
write_ascii(join(self.folder, fittest, "fit_" + which + ".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 + ".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 + '.gp'), 'w') as inp:
inp.write(
renderer.render_path(
'plot.mustache', # gnuplot mustache file
{
'material': 'uranyl',
'model': which,
'fittest': fittest,
'shells': shells,
'kmin': 3,
'kmax': 11,
'rmin': 1.0,
'rmax': 3.2,
'offset': 1,
}))
return fit
def do_fit(self, which):
if which == 'testrun':
folder = self.testrun
elif which == 'baseline':
folder = self.baseline
else:
folder = realpath(join(self.folder, 'baseline', which))
#endif
print '>>>>>> %s' % folder
data = read_xdi(join(self.path, 'Copper.chik'), _larch=self._larch)
gds = Group(amp=Parameter(1, vary=True),
enot=Parameter(1e-7, vary=True),
thetad=Parameter(500, vary=True),
temp=Parameter(10, vary=False),
alpha=Parameter(1e-7, vary=True),
ss1=Parameter(0.003, vary=True),
_larch=self._larch)
paths = list()
for index in range(1, 14):
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='alpha*reff',
_larch=self._larch))
#end for
trans = feffit_transform(kmin=3,
kmax=16,
kw=(2, 1, 3),
dk=1,
window='hanning',
rmin=1.7,
rmax=5.1,
_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
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, 'bromoadamantane.chik'), _larch=self._larch)
gds = Group(amp = Parameter(0.9, vary=True, _larch=self._larch),
enot = Parameter(4.01, vary=True, _larch=self._larch),
delr = Parameter(1e-7 , vary=True, units='AA', decimals=3, _larch=self._larch),
ss = Parameter(0.003, vary=True, units='AA^2', _larch=self._larch),
c3 = Parameter(1e-7, vary=False, _larch=self._larch),
_larch=self._larch )
if not firstshell:
gds.brc = Parameter(expr = '1.9521+delr', units='AA', _larch=self._larch)
#gds.phir = Parameter(109.29960 * 3.141592653589793 / 180, vary=False, _larch=self._larch)
gds.cc = Parameter(1.53780, vary=False, _larch=self._larch)
#gds.tanbeta = Parameter(expr = '(brc+cc)*tan(phir/2) / (brc-cc)', _larch=self._larch)
#gds.beta = Parameter(expr = 'atan(tanbeta)', _larch=self._larch)
#gds.brc2 = Parameter(expr = '(brc-cc)*cos(phir/2)/cos(beta)', units='AA', _larch=self._larch)
gds.drh = Parameter(0.04, vary=True, units='AA', decimals=3, _larch=self._larch)
gds.ssh = Parameter(0.005, vary=True, units='AA^2', _larch=self._larch)
gds.ss2 = Parameter(expr = 'ss*(brc2/brc)**2', units ='AA^2', _larch=self._larch)
gds.drc = Parameter(0.04, vary=True, units='AA', decimals=3, _larch=self._larch)
gds.brc2 = Parameter(expr = '2.8565+drc', units='AA', decimals=3, _larch=self._larch)
paths = list()
paths.append(feffpath(realpath(join(folder, "feff0001.dat")),
s02 = 'amp',
e0 = 'enot',
sigma2 = 'ss',
deltar = 'delr',
third = 'c3', _larch=self._larch))
if not firstshell:
paths.append(feffpath(realpath(join(folder, "feff0002.dat")),
s02 = 'amp',
e0 = 'enot',
sigma2 = 'ss2',
#deltar = 'brc2-2.8565',
deltar = 'drc',_larch=self._larch))
paths.append(feffpath(realpath(join(folder, "feff0003.dat")),
s02 = 'amp',
e0 = 'enot',
sigma2 = 'ssh',
deltar = 'drh', _larch=self._larch))
paths.append(feffpath(realpath(join(folder, "feff0004.dat")),
s02 = 'amp',
e0 = 'enot',
sigma2 = '(ss+ss2)/2',
deltar = '(brc+brc2+cc)/2 - 3.173', _larch=self._larch))
paths.append(feffpath(realpath(join(folder, "feff0005.dat")),
s02 = 'amp',
e0 = 'enot',
sigma2 = '(ss+ss2)/2',
deltar = '(brc+brc2+cc)/2 - 3.173', _larch=self._larch))
rx = 3
if firstshell: rx = 1.83
trans = feffit_transform(kmin=3, kmax=11, kw=(2,1,3), dk=1, window='hanning', rmin=1, rmax=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,
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': 'bromoadamantane',
'model': which,
'fittest': fittest,
'shells': shells,
'kmin': 3,
'kmax': 13,
'rmin': 1,
'rmax': rx,
'offset': 0.2,
} ))
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, '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, '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, '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