def make(self, crystal, r, g, dg=None, meta=None):
"""
Construct new srfit recipe from CIF structure and PDF data
Parameters
----------
crystal : pyobjcryst.Crystal
The CIF structure to be fitted to the PDF data in-place.
r : array_like
The r-grid of the fitted PDF dataset in Angstroms.
g : array_like
The fitted PDF values per each `r` point.
dg : array_like, optional
The estimated standard deviations at each of `g` values.
When unspecified, *dg* is assumed 1 leading to underestimated
standard errors of the refined variables.
meta : dict, optional
A dictionary of extra metadata to be used when constructing
`PDFContribution` in the srfit recipe. The common recognized
keys are ``stype`` for radiation type ("X" or "N"), ``qmax``
for the Q-range used in the experiment, ``delta1``, ``delta2``,
``qbroad`` for peak sharpening and broadening factors and
``qdamp`` for the Q-resolution related signal dampening.
Returns
-------
recipe : FitRecipe
The new FitRecipe for in-place fitting of `crystal` to PDF data.
"""
if not isinstance(crystal, Crystal):
emsg = "crystal must be of the pyobjcryst.Crystal type."
raise TypeError(emsg)
cpdf = PDFContribution('cpdf')
cpdf.profile.setObservedProfile(r, g, dg)
m = {} if meta is None else dict(meta)
cpdf.profile.meta.update(m)
cpdf.addStructure('cif', crystal)
cpdf.setCalculationRange(self.rmin, self.rmax)
if self.nyquist:
if not 'qmax' in m:
emsg = "Nyquist spacing requires 'qmax' metadata."
raise ValueError(emsg)
assert m['qmax'] == cpdf.cif.getQmax()
cpdf.setCalculationRange(dx=numpy.pi / m['qmax'])
# create FitRecipe
recipe = FitRecipe()
recipe.clearFitHooks()
recipe.addContribution(cpdf)
recipe.addVar(cpdf.scale)
# get symmetry allowed structure parameters
sgpars = cpdf.cif.phase.sgpars
# constrain available lattice parameters
for p in sgpars.latpars:
recipe.addVar(p, tags=['phase', 'lattice'])
# constrain free atom positions
for p in sgpars.xyzpars:
recipe.addVar(p, tags=['phase', 'positions'])
# constrain adps
isosymbol = sgpars.isosymbol
fbbiso = self.fbbiso
# make a dummy diffpy.structure.Atom with isotropic Biso = fbbiso
afbiso = _dummyAtomWithBiso(crystal, self.fbbiso)
tags = ['phase', 'adps']
for p in sgpars.adppars:
if p.name.startswith(isosymbol):
recipe.addVar(p, value=p.value or fbbiso, tags=tags)
continue
# we have anisotropic site here, but constrain as isotropic
# if so requested
if self.isotropy:
# extract site index for this sg parameter. Use it to get
# the parameter for its Biso value.
idx = int(p.name.split('_')[-1])
psite = cpdf.cif.phase.scatterers[idx]
pbiso = psite.Biso
n = isosymbol + '_{}'.format(idx)
v = pbiso.value or fbbiso
# avoid applying duplicate constrain to pbiso
if recipe.get(n) is None:
recipe.addVar(pbiso, name=n, value=v, tags=tags)
continue
# here we constrain an anisotropic site.
# make sure its ADPs are nonzero.
spa = p.par.obj
if not all((spa.B11, spa.B22, spa.B33)):
spa.B11 = afbiso.B11
spa.B22 = afbiso.B22
spa.B33 = afbiso.B33
spa.B12 = afbiso.B12
spa.B13 = afbiso.B13
spa.B23 = afbiso.B23
recipe.addVar(p, tags=tags)
# constrain delta2, qdamp and qbroad
p = cpdf.cif.delta2
v = p.value or self.fbdelta2
recipe.addVar(p, value=v, tag='phase')
p = cpdf.qdamp
v = p.value or self.fbqdamp
recipe.addVar(p, value=v, tag='experiment')
p = cpdf.qbroad
v = p.value or self.fbqbroad
recipe.addVar(p, value=v, tag='experiment')
return recipe
