def from_lm_params(cls, params: lm.Parameters) -> NRGParams:
d = {}
for k1, k2 in zip(
['gamma', 'theta', 'center', 'amp', 'lin', 'const', 'lin_occ'],
['g', 'theta', 'mid', 'amp', 'lin', 'const', 'occ_lin']):
par = params.get(k2, None)
if par is not None:
v = par.value
elif k1 == 'gamma':
v = 0 # This will cause issues if not set somewhere else, but no better choice here.
else:
v = 0 if k1 != 'amp' else 1 # Most things should default to zero except for amp
d[k1] = v
return cls(**d)
class FeffPathGroup(Group):
def __init__(self,
filename=None,
label=None,
s02=None,
degen=None,
e0=None,
ei=None,
deltar=None,
sigma2=None,
third=None,
fourth=None,
_larch=None,
**kws):
kwargs = dict(name='FeffPath: %s' % filename)
kwargs.update(kws)
Group.__init__(self, **kwargs)
self.filename = filename
self.params = None
self.label = label
self.spline_coefs = None
def_degen = 1
self._feffdat = None
if filename is not None:
self._feffdat = FeffDatFile(filename=filename)
self.geom = self._feffdat.geom
def_degen = self._feffdat.degen
if self.label is None:
self.label = self.__geom2label()
self.degen = def_degen if degen is None else degen
self.s02 = 1.0 if s02 is None else s02
self.e0 = 0.0 if e0 is None else e0
self.ei = 0.0 if ei is None else ei
self.deltar = 0.0 if deltar is None else deltar
self.sigma2 = 0.0 if sigma2 is None else sigma2
self.third = 0.0 if third is None else third
self.fourth = 0.0 if fourth is None else fourth
self.k = None
self.chi = None
if self._feffdat is not None:
self.create_spline_coefs()
def __geom2label(self):
"""generate label by hashing path geometry"""
rep = []
if self.geom is not None:
for atom in self.geom:
rep.extend(atom)
if self._feffdat is not None:
rep.append(self._feffdat.degen)
rep.append(self._feffdat.reff)
for attr in ('s02', 'e0', 'ei', 'deltar', 'sigma2', 'third', 'fourth'):
rep.append(getattr(self, attr, '_'))
s = "|".join([str(i) for i in rep])
return "p%s" % (b32hash(s)[:8].lower())
def __copy__(self):
return FeffPathGroup(filename=self.filename,
s02=self.s02,
degen=self.degen,
e0=self.e0,
ei=self.ei,
deltar=self.deltar,
sigma2=self.sigma2,
third=self.third,
fourth=self.fourth)
def __deepcopy__(self, memo):
return FeffPathGroup(filename=self.filename,
s02=self.s02,
degen=self.degen,
e0=self.e0,
ei=self.ei,
deltar=self.deltar,
sigma2=self.sigma2,
third=self.third,
fourth=self.fourth)
@property
def reff(self):
return self._feffdat.reff
@reff.setter
def reff(self, val):
pass
@property
def nleg(self):
return self._feffdat.nleg
@nleg.setter
def nleg(self, val):
pass
@property
def rmass(self):
return self._feffdat.rmass
@rmass.setter
def rmass(self, val):
pass
def __repr__(self):
if self.filename is not None:
return '<FeffPath Group %s>' % self.filename
return '<FeffPath Group (empty)>'
def create_path_params(self, params=None):
"""
create Path Parameters within the current lmfit.Parameters namespace
"""
if params is not None:
self.params = params
if self.params is None:
self.params = Parameters()
if self.params._asteval.symtable.get('sigma2_debye', None) is None:
add_sigma2funcs(self.params)
if self.label is None:
self.label = self.__geom2label()
self.store_feffdat()
for pname in PATH_PARS:
val = getattr(self, pname)
attr = 'value'
if isinstance(val, str):
attr = 'expr'
kws = {'vary': False, attr: val}
parname = fix_varname(PATHPAR_FMT % (pname, self.label))
self.params.add(parname, **kws)
def create_spline_coefs(self):
"""pre-calculate spline coefficients for feff data"""
self.spline_coefs = {}
fdat = self._feffdat
self.spline_coefs['pha'] = UnivariateSpline(fdat.k, fdat.pha, s=0)
self.spline_coefs['amp'] = UnivariateSpline(fdat.k, fdat.amp, s=0)
self.spline_coefs['rep'] = UnivariateSpline(fdat.k, fdat.rep, s=0)
self.spline_coefs['lam'] = UnivariateSpline(fdat.k, fdat.lam, s=0)
def store_feffdat(self):
"""stores data about this Feff path in the Parameters
symbol table for use as `reff` and in sigma2 calcs
"""
symtab = self.params._asteval.symtable
symtab['feffpath'] = self._feffdat
symtab['reff'] = self._feffdat.reff
def __path_params(self, **kws):
"""evaluate path parameter value. Returns
(degen, s02, e0, ei, deltar, sigma2, third, fourth)
"""
# put 'reff' and '_feffdat' into the symboltable so that
# they can be used in constraint expressions
self.store_feffdat()
if self.params is None:
self.create_path_params()
out = []
for pname in PATH_PARS:
val = kws.get(pname, None)
parname = fix_varname(PATHPAR_FMT % (pname, self.label))
if val is None:
val = self.params[parname]._getval()
out.append(val)
return out
def path_paramvals(self, **kws):
(deg, s02, e0, ei, delr, ss2, c3, c4) = self.__path_params()
return dict(degen=deg,
s02=s02,
e0=e0,
ei=ei,
deltar=delr,
sigma2=ss2,
third=c3,
fourth=c4)
def report(self):
"return text report of parameters"
tmpvals = self.__path_params()
pathpars = {}
for pname in ('degen', 's02', 'e0', 'deltar', 'sigma2', 'third',
'fourth', 'ei'):
parname = fix_varname(PATHPAR_FMT % (pname, self.label))
if parname in self.params:
pathpars[pname] = (self.params[parname].value,
self.params[parname].stderr)
geomlabel = ' atom x y z ipot'
geomformat = ' %4s % .4f, % .4f, % .4f %i'
out = [' Path %s, Feff.dat file = %s' % (self.label, self.filename)]
out.append(geomlabel)
for atsym, iz, ipot, amass, x, y, z in self.geom:
s = geomformat % (atsym, x, y, z, ipot)
if ipot == 0: s = "%s (absorber)" % s
out.append(s)
stderrs = {}
out.append(' {:7s}= {:s}'.format('reff',
gformat(self._feffdat.reff)))
for pname in ('degen', 's02', 'e0', 'r', 'deltar', 'sigma2', 'third',
'fourth', 'ei'):
val = strval = getattr(self, pname, 0)
parname = fix_varname(PATHPAR_FMT % (pname, self.label))
std = None
if pname == 'r':
parname = fix_varname(PATHPAR_FMT % ('deltar', self.label))
par = self.params.get(parname, None)
val = par.value + self._feffdat.reff
strval = 'reff + ' + getattr(self, 'deltar', 0)
std = par.stderr
else:
if pname in pathpars:
val, std = pathpars[pname]
else:
par = self.params.get(parname, None)
if par is not None:
val = par.value
std = par.stderr
if std is None or std <= 0:
svalue = gformat(val)
else:
svalue = "{:s} +/-{:s}".format(gformat(val), gformat(std))
if pname == 's02':
pname = 'n*s02'
svalue = " {:7s}= {:s}".format(pname, svalue)
if isinstance(strval, str):
svalue = "{:s} '{:s}'".format(svalue, strval)
if val == 0 and pname in ('third', 'fourth', 'ei'):
continue
out.append(svalue)
return '\n'.join(out)
def _calc_chi(self,
k=None,
kmax=None,
kstep=None,
degen=None,
s02=None,
e0=None,
ei=None,
deltar=None,
sigma2=None,
third=None,
fourth=None,
debug=False,
interp='cubic',
**kws):
"""calculate chi(k) with the provided parameters"""
fdat = self._feffdat
if fdat.reff < 0.05:
print('reff is too small to calculate chi(k)')
return
# make sure we have a k array
if k is None:
if kmax is None:
kmax = 30.0
kmax = min(max(fdat.k), kmax)
if kstep is None: kstep = 0.05
k = kstep * np.arange(int(1.01 + kmax / kstep), dtype='float64')
reff = fdat.reff
# get values for all the path parameters
(degen, s02, e0, ei, deltar, sigma2, third, fourth) = \
self.__path_params(degen=degen, s02=s02, e0=e0, ei=ei,
deltar=deltar, sigma2=sigma2,
third=third, fourth=fourth)
# create e0-shifted energy and k, careful to look for |e0| ~= 0.
en = k * k - e0 * ETOK
if min(abs(en)) < SMALL:
try:
en[np.where(abs(en) < 2 * SMALL)] = SMALL
except ValueError:
pass
# q is the e0-shifted wavenumber
q = np.sign(en) * np.sqrt(abs(en))
# lookup Feff.dat values (pha, amp, rep, lam)
if interp.startswith('lin'):
pha = np.interp(q, fdat.k, fdat.pha)
amp = np.interp(q, fdat.k, fdat.amp)
rep = np.interp(q, fdat.k, fdat.rep)
lam = np.interp(q, fdat.k, fdat.lam)
else:
pha = self.spline_coefs['pha'](q)
amp = self.spline_coefs['amp'](q)
rep = self.spline_coefs['rep'](q)
lam = self.spline_coefs['lam'](q)
if debug:
self.debug_k = q
self.debug_pha = pha
self.debug_amp = amp
self.debug_rep = rep
self.debug_lam = lam
# p = complex wavenumber, and its square:
pp = (rep + 1j / lam)**2 + 1j * ei * ETOK
p = np.sqrt(pp)
# the xafs equation:
cchi = np.exp(-2 * reff * p.imag - 2 * pp *
(sigma2 - pp * fourth / 3) + 1j *
(2 * q * reff + pha + 2 * p *
(deltar - 2 * sigma2 / reff - 2 * pp * third / 3)))
cchi = degen * s02 * amp * cchi / (q * (reff + deltar)**2)
cchi[0] = 2 * cchi[1] - cchi[2]
# outputs:
self.k = k
self.p = p
self.chi = cchi.imag
self.chi_imag = -cchi.real
class FeffPathGroup(Group):
def __init__(self, filename=None, _larch=None,
label=None, s02=None, degen=None, e0=None,
ei=None, deltar=None, sigma2=None,
third=None, fourth=None, **kws):
kwargs = dict(name='FeffPath: %s' % filename)
kwargs.update(kws)
Group.__init__(self, **kwargs)
self._larch = _larch
self.filename = filename
self.params = None
self.label = label
self.spline_coefs = None
def_degen = 1
self._feffdat = None
if filename is not None:
self._feffdat = FeffDatFile(filename=filename, _larch=_larch)
self.geom = self._feffdat.geom
def_degen = self._feffdat.degen
if self.label is None:
self.label = self.__geom2label()
self.degen = def_degen if degen is None else degen
self.s02 = 1.0 if s02 is None else s02
self.e0 = 0.0 if e0 is None else e0
self.ei = 0.0 if ei is None else ei
self.deltar = 0.0 if deltar is None else deltar
self.sigma2 = 0.0 if sigma2 is None else sigma2
self.third = 0.0 if third is None else third
self.fourth = 0.0 if fourth is None else fourth
self.k = None
self.chi = None
if self._feffdat is not None:
self.create_spline_coefs()
def __geom2label(self):
"""generate label by hashing path geometry"""
rep = []
if self.geom is not None:
for atom in self.geom:
rep.extend(atom)
if self._feffdat is not None:
rep.append(self._feffdat.degen)
rep.append(self._feffdat.reff)
for attr in ('s02', 'e0', 'ei', 'deltar', 'sigma2', 'third', 'fourth'):
rep.append(getattr(self, attr, '_'))
s = "|".join([str(i) for i in rep])
return "p%s" % (b32hash(s)[:8].lower())
def __copy__(self):
return FeffPathGroup(filename=self.filename, _larch=self._larch,
s02=self.s02, degen=self.degen, e0=self.e0,
ei=self.ei, deltar=self.deltar, sigma2=self.sigma2,
third=self.third, fourth=self.fourth)
def __deepcopy__(self, memo):
return FeffPathGroup(filename=self.filename, _larch=self._larch,
s02=self.s02, degen=self.degen, e0=self.e0,
ei=self.ei, deltar=self.deltar, sigma2=self.sigma2,
third=self.third, fourth=self.fourth)
@property
def reff(self): return self._feffdat.reff
@reff.setter
def reff(self, val): pass
@property
def nleg(self): return self._feffdat.nleg
@nleg.setter
def nleg(self, val): pass
@property
def rmass(self): return self._feffdat.rmass
@rmass.setter
def rmass(self, val): pass
def __repr__(self):
if self.filename is not None:
return '<FeffPath Group %s>' % self.filename
return '<FeffPath Group (empty)>'
def create_path_params(self):
"""
create Path Parameters within the current fiteval
"""
self.params = Parameters(asteval=self._larch.symtable._sys.fiteval)
if self.label is None:
self.label = self.__geom2label()
self.store_feffdat()
for pname in PATH_PARS:
val = getattr(self, pname)
attr = 'value'
if isinstance(val, six.string_types):
attr = 'expr'
kws = {'vary': False, attr: val}
parname = fix_varname(PATHPAR_FMT % (pname, self.label))
self.params.add(parname, **kws)
def create_spline_coefs(self):
"""pre-calculate spline coefficients for feff data"""
self.spline_coefs = {}
fdat = self._feffdat
self.spline_coefs['pha'] = UnivariateSpline(fdat.k, fdat.pha, s=0)
self.spline_coefs['amp'] = UnivariateSpline(fdat.k, fdat.amp, s=0)
self.spline_coefs['rep'] = UnivariateSpline(fdat.k, fdat.rep, s=0)
self.spline_coefs['lam'] = UnivariateSpline(fdat.k, fdat.lam, s=0)
def store_feffdat(self):
"""stores data about this Feff path in the fiteval
symbol table for use as `reff` and in sigma2 calcs
"""
fiteval = self._larch.symtable._sys.fiteval
fdat = self._feffdat
fiteval.symtable['feffpath'] = fdat
fiteval.symtable['reff'] = fdat.reff
return fiteval
def __path_params(self, **kws):
"""evaluate path parameter value. Returns
(degen, s02, e0, ei, deltar, sigma2, third, fourth)
"""
# put 'reff' and '_feffdat' into the symboltable so that
# they can be used in constraint expressions, and get
# fiteval evaluator
self.store_feffdat()
if self.params is None:
self.create_path_params()
out = []
for pname in PATH_PARS:
val = kws.get(pname, None)
parname = fix_varname(PATHPAR_FMT % (pname, self.label))
if val is None:
val = self.params[parname]._getval()
out.append(val)
return out
def path_paramvals(self, **kws):
(deg, s02, e0, ei, delr, ss2, c3, c4) = self.__path_params()
return dict(degen=deg, s02=s02, e0=e0, ei=ei, deltar=delr,
sigma2=ss2, third=c3, fourth=c4)
def report(self):
"return text report of parameters"
(deg, s02, e0, ei, delr, ss2, c3, c4) = self.__path_params()
geomlabel = ' atom x y z ipot'
geomformat = ' %4s % .4f, % .4f, % .4f %i'
out = [' Path %s, Feff.dat file = %s' % (self.label, self.filename)]
out.append(geomlabel)
for atsym, iz, ipot, amass, x, y, z in self.geom:
s = geomformat % (atsym, x, y, z, ipot)
if ipot == 0: s = "%s (absorber)" % s
out.append(s)
stderrs = {}
out.append(' {:7s}= {:.5f}'.format('reff', self._feffdat.reff))
for pname in ('degen', 's02', 'e0', 'r',
'deltar', 'sigma2', 'third', 'fourth', 'ei'):
val = strval = getattr(self, pname, 0)
parname = fix_varname(PATHPAR_FMT % (pname, self.label))
std = None
if pname == 'r':
parname = fix_varname(PATHPAR_FMT % ('deltar', self.label))
par = self.params.get(parname, None)
val = par.value + self._feffdat.reff
strval = 'reff + ' + getattr(self, 'deltar', 0)
std = par.stderr
else:
par = self.params.get(parname, None)
if par is not None:
val = par.value
std = par.stderr
if std is None or std <= 0:
svalue = "{: 5f}".format(val)
else:
svalue = "{: 5f} +/- {:5f}".format(val, std)
if pname == 's02': pname = 'n*s02'
svalue = " {:7s}= {:s}".format(pname, svalue)
if isinstance(strval, six.string_types):
svalue = "{:s} '{:s}'".format(svalue, strval)
if val == 0 and pname in ('third', 'fourth', 'ei'):
continue
out.append(svalue)
return '\n'.join(out)
def _calc_chi(self, k=None, kmax=None, kstep=None, degen=None, s02=None,
e0=None, ei=None, deltar=None, sigma2=None,
third=None, fourth=None, debug=False, interp='cubic', **kws):
"""calculate chi(k) with the provided parameters"""
fdat = self._feffdat
if fdat.reff < 0.05:
self._larch.writer.write('reff is too small to calculate chi(k)')
return
# make sure we have a k array
if k is None:
if kmax is None:
kmax = 30.0
kmax = min(max(fdat.k), kmax)
if kstep is None: kstep = 0.05
k = kstep * np.arange(int(1.01 + kmax/kstep), dtype='float64')
reff = fdat.reff
# get values for all the path parameters
(degen, s02, e0, ei, deltar, sigma2, third, fourth) = \
self.__path_params(degen=degen, s02=s02, e0=e0, ei=ei,
deltar=deltar, sigma2=sigma2,
third=third, fourth=fourth)
# create e0-shifted energy and k, careful to look for |e0| ~= 0.
en = k*k - e0*ETOK
if min(abs(en)) < SMALL:
try:
en[np.where(abs(en) < 2*SMALL)] = SMALL
except ValueError:
pass
# q is the e0-shifted wavenumber
q = np.sign(en)*np.sqrt(abs(en))
# lookup Feff.dat values (pha, amp, rep, lam)
if interp.startswith('lin'):
pha = np.interp(q, fdat.k, fdat.pha)
amp = np.interp(q, fdat.k, fdat.amp)
rep = np.interp(q, fdat.k, fdat.rep)
lam = np.interp(q, fdat.k, fdat.lam)
else:
pha = self.spline_coefs['pha'](q)
amp = self.spline_coefs['amp'](q)
rep = self.spline_coefs['rep'](q)
lam = self.spline_coefs['lam'](q)
if debug:
self.debug_k = q
self.debug_pha = pha
self.debug_amp = amp
self.debug_rep = rep
self.debug_lam = lam
# p = complex wavenumber, and its square:
pp = (rep + 1j/lam)**2 + 1j * ei * ETOK
p = np.sqrt(pp)
# the xafs equation:
cchi = np.exp(-2*reff*p.imag - 2*pp*(sigma2 - pp*fourth/3) +
1j*(2*q*reff + pha +
2*p*(deltar - 2*sigma2/reff - 2*pp*third/3) ))
cchi = degen * s02 * amp * cchi / (q*(reff + deltar)**2)
cchi[0] = 2*cchi[1] - cchi[2]
# outputs:
self.k = k
self.p = p
self.chi = cchi.imag
self.chi_imag = -cchi.real
params2 = Parameters()
params2.add('alpha', value= 1, min=0)
params2.add('power', value= 1)
result2 = minimize(fcn2min, params2, args=(x, data))
# calculate final result
final1 = data + result1.residual
final2 = data + result2.residual
# write error report
report_errors(params1)
pp = pprint.PrettyPrinter(indent=4)
pp.pprint(params1)
print params1.get('alpha')
p=params1.get('alpha')
print "standard error ", p.stderr
total= np.sum(result1.residual)
print "sum of residuals: ", total
#print "xtol: ", result1.xtol
print "reduced chi-square: ", result1.redchi
#print "asteval", result1.asteval
print "message:", result1.message
print "ier:", result1.ier
print "chisqr:", result1.chisqr
print "redchi:", result1.redchi
pp.pprint(result1)