def lattice_to_dict(lattice: SrRealParSet, angunits="rad") -> dict:
"""Convert lattice parameter set to dictionary. If angle is in radian, convert it to degree."""
dct = dict(zip(lattice.getNames(), lattice.getValues()))
if angunits == "rad":
for angle in ('alpha', 'beta', 'gamma'):
dct[angle] = math.degrees(dct[angle])
return dct
def __init__(self, name, stru):
"""Initialize
name -- A name for the structure
stru -- A diffpy.structure.Structure instance
"""
SrRealParSet.__init__(self, name)
self.stru = stru
self.addParameterSet(DiffpyLatticeParSet(stru.lattice))
self.atoms = []
cdict = {}
for a in stru:
el = a.element.title()
# Try to sanitize the name.
el = el.replace("+","p")
el = el.replace("-","m")
i = cdict.get(el, 0)
aname = "%s%i"%(el,i)
cdict[el] = i+1
atom = DiffpyAtomParSet(aname, a)
self.addParameterSet(atom)
self.atoms.append(atom)
return
def __init__(self, name, stru):
"""Initialize
name -- A name for the structure
stru -- A diffpy.Structure.Structure instance
"""
SrRealParSet.__init__(self, name)
self.stru = stru
self.addParameterSet(DiffpyLatticeParSet(stru.lattice))
self.atoms = []
cdict = {}
for a in stru:
el = a.element.title()
# Try to sanitize the name.
el = el.replace("+", "p")
el = el.replace("-", "m")
i = cdict.get(el, 0)
aname = "%s%i" % (el, i)
cdict[el] = i + 1
atom = DiffpyAtomParSet(aname, a)
self.addParameterSet(atom)
self.atoms.append(atom)
return
def phase_to_dict(phase: SrRealParSet) -> dict:
"""Convert structure parameter set to dictionary."""
return {
'lattice':
lattice_to_dict(phase.getLattice(),
angunits=getattr(phase, 'angunits', 'deg')),
'atoms': [atom_to_dict(atom) for atom in phase.getScatterers()],
'space_group':
get_space_group_number(phase)
}
def get_space_group_number(phase: SrRealParSet) -> int:
"""Get the space group number of the structure parameter."""
# if symmetry is not used or the structure object is from diffpy.structure
if not phase.usingSymmetry() or isinstance(phase.stru, Structure):
return 1
stru: Crystal = phase.stru
# noinspection PyArgumentList
space_group: SpaceGroup = stru.GetSpaceGroup()
# noinspection PyArgumentList
return space_group.GetSpaceGroupNumber()
def _getSrRealStructure(self):
"""Get the structure object for use with SrReal calculators.
If this is periodic, then return the structure, otherwise, pass it
inside of a nosymmetry wrapper. This takes the extra step of wrapping
the structure in a nometa wrapper.
"""
stru = SrRealParSet._getSrRealStructure(self)
return nometa(stru)
def _getSrRealStructure(self):
"""Get the structure object for use with SrReal calculators.
If this is periodic, then return the structure, otherwise, pass it
inside of a nosymmetry wrapper. This takes the extra step of wrapping
the structure in a nometa wrapper.
"""
from diffpy.srreal.structureadapter import nometa
stru = SrRealParSet._getSrRealStructure(self)
return nometa(stru)
def __init__(self, name, stru):
SrRealParSet.__init__(self, name)
self.stru = stru
self.lat = stru.lat
stru = self.stru
occ = ParameterAdapterExt("occ", stru, getter=_getValue, setter=self._updateOcc, attr="occ")
self.addParameter(occ)
self.addParameter(ParameterProxy("occupancy", occ))
uij = ParameterAdapterExt('uij', stru, getter=_getValue, setter=self._updateUij, attr='uij_c')
self.addParameter(uij)
self.addParameter(ParameterProxy('U', uij))
xyz = ParameterAdapterExt('xyz', stru, getter=_getValue, setter=self._updateXYZ, attr='xyz_c')
self.addParameter(xyz)
uiso = ParameterAdapterExt('uiso', stru, getter=_getValue, setter=self._updateUiso, attr='uiso')
self.addParameter(uiso)
self._zoomscale = 1.0
self.addParameter(ParameterAdapter('zoomscale', self, getter=_getValue, setter=self._updateZoomscale, attr='_zoomscale'))
self._initSrRealStructure()
return
def atom_to_dict(atom: SrRealParSet) -> dict:
"""Convert atom parameter set to dictionary."""
dct = dict(zip(atom.getNames(), atom.getValues()))
dct.update({'name': atom.name, 'element': atom.element})
return dct
