def test_ConstrainAsSpaceGroup_args(self):
"""Test the arguments processing of constrainAsSpaceGroup function.
"""
from diffpy.srfit.structure.sgconstraints import constrainAsSpaceGroup
from diffpy.Structure.SpaceGroups import GetSpaceGroup
stru = makeLaMnO3_P1()
parset = DiffpyStructureParSet("LaMnO3", stru)
sgpars = constrainAsSpaceGroup(parset, "P b n m")
sg = GetSpaceGroup('P b n m')
parset2 = DiffpyStructureParSet("LMO", makeLaMnO3_P1())
sgpars2 = constrainAsSpaceGroup(parset2, sg)
list(sgpars)
list(sgpars2)
self.assertEqual(sgpars.names, sgpars2.names)
return
def test_ConstrainAsSpaceGroup_args(self):
"""Test the arguments processing of constrainAsSpaceGroup function.
"""
from diffpy.srfit.structure.sgconstraints import constrainAsSpaceGroup
from diffpy.Structure.SpaceGroups import GetSpaceGroup
stru = makeLaMnO3_P1()
parset = DiffpyStructureParSet("LaMnO3", stru)
sgpars = constrainAsSpaceGroup(parset, "P b n m")
sg = GetSpaceGroup('P b n m')
parset2 = DiffpyStructureParSet("LMO", makeLaMnO3_P1())
sgpars2 = constrainAsSpaceGroup(parset2, sg)
list(sgpars)
list(sgpars2)
self.assertEquals(sgpars.names, sgpars2.names)
return
def test_DiffPy_constrainAsSpaceGroup(self):
"""Test the constrainAsSpaceGroup function."""
from diffpy.srfit.structure.diffpyparset import DiffpyStructureParSet
from diffpy.srfit.structure.sgconstraints import constrainAsSpaceGroup
stru = makeLaMnO3_P1()
parset = DiffpyStructureParSet("LaMnO3", stru)
sgpars = constrainAsSpaceGroup(parset, "P b n m",
scatterers = parset.getScatterers()[::2],
constrainadps = True)
# Make sure that the new parameters were created
for par in sgpars:
self.assertNotEqual(None, par)
self.assertNotEqual(None, par.getValue() )
# Test the unconstrained atoms
for scatterer in parset.getScatterers()[1::2]:
self.assertFalse(scatterer.x.const)
self.assertFalse(scatterer.y.const)
self.assertFalse(scatterer.z.const)
self.assertFalse(scatterer.U11.const)
self.assertFalse(scatterer.U22.const)
self.assertFalse(scatterer.U33.const)
self.assertFalse(scatterer.U12.const)
self.assertFalse(scatterer.U13.const)
self.assertFalse(scatterer.U23.const)
self.assertEqual(0, len(scatterer._constraints))
proxied = [p.par for p in sgpars]
def _consttest(par):
return par.const
def _constrainedtest(par):
return par.constrained
def _proxytest(par):
return par in proxied
def _alltests(par):
return _consttest(par) or _constrainedtest(par) or _proxytest(par)
for idx, scatterer in enumerate(parset.getScatterers()[::2]):
# Under this scheme, atom 6 is free to vary
test = False
for par in [scatterer.x, scatterer.y, scatterer.z]:
test |= _alltests(par)
self.assertTrue(test)
test = False
for par in [scatterer.U11, scatterer.U22, scatterer.U33,
scatterer.U12, scatterer.U13, scatterer.U23]:
test |= _alltests(par)
self.assertTrue(test)
return
def testConstrainAsSpaceGroup(self):
"""Test the constrainAsSpaceGroup function."""
from diffpy.srfit.structure.sgconstraints import constrainAsSpaceGroup
stru = makeLaMnO3_P1()
parset = DiffpyStructureParSet("LaMnO3", stru)
sgpars = constrainAsSpaceGroup(parset, "P b n m",
scatterers = parset.getScatterers()[::2],
constrainadps = True)
# Make sure that the new parameters were created
for par in sgpars:
self.assertNotEquals(None, par)
self.assertNotEquals(None, par.getValue() )
# Test the unconstrained atoms
for scatterer in parset.getScatterers()[1::2]:
self.assertFalse(scatterer.x.const)
self.assertFalse(scatterer.y.const)
self.assertFalse(scatterer.z.const)
self.assertFalse(scatterer.U11.const)
self.assertFalse(scatterer.U22.const)
self.assertFalse(scatterer.U33.const)
self.assertFalse(scatterer.U12.const)
self.assertFalse(scatterer.U13.const)
self.assertFalse(scatterer.U23.const)
self.assertEquals(0, len(scatterer._constraints))
proxied = [p.par for p in sgpars]
def _consttest(par):
return par.const
def _constrainedtest(par):
return par.constrained
def _proxytest(par):
return par in proxied
def _alltests(par):
return _consttest(par) or _constrainedtest(par) or _proxytest(par)
for idx, scatterer in enumerate(parset.getScatterers()[::2]):
# Under this scheme, atom 6 is free to vary
test = False
for par in [scatterer.x, scatterer.y, scatterer.z]:
test |= _alltests(par)
self.assertTrue(test)
test = False
for par in [scatterer.U11, scatterer.U22, scatterer.U33,
scatterer.U12, scatterer.U13, scatterer.U23]:
test |= _alltests(par)
self.assertTrue(test)
return
def constrainAsSpaceGroup(self, generator, spacegroup, lat=True, xyz=False, adp=False, addphasename=False):
'''
constrain phase using space group
param generator: generator.phase in recipe to constrain
param spacegroup: space group in number or string "87" or "F m 3 m"
param lat: bool, constrain lattice parameters
param xyz: bool, constrain xyz of atoms
param adp: bool, constrain adp of atoms
param addphasename: bool, if add phase name to name of variable
'''
from diffpy.srfit.structure.sgconstraints import constrainAsSpaceGroup, _constrainAsSpaceGroup
from diffpy.Structure.spacegroupmod import SpaceGroup
generator = self.returnGenerator(generator)
recipe = self.recipe
phase = generator.phase
phasename = generator.name
if isinstance(phase, DiffpyStructureParSet):
if isinstance(spacegroup, SpaceGroup):
sgpars = _constrainAsSpaceGroup(phase, spacegroup)
else:
sgpars = constrainAsSpaceGroup(phase, spacegroup)
elif isinstance(phase, ObjCrystCrystalParSet):
sgpars = phase.sgpars
if lat:
for par in sgpars.latpars:
parname = par.name
parname = phasename + '_' + \
parname if addphasename else parname
self.addVar(par, parname, par.value, tags=['lat'])
if xyz:
for par in sgpars.xyzpars:
element = getElement(par.par.obj)
parname = '_'.join([element, par.name])
parname = phasename + '_' + \
parname if addphasename else parname
self.addVar(
par, parname, par.value, tags=['xyz', element + '_xyz'])
if adp:
for par in sgpars.adppars:
element = getElement(par.par.obj)
parname = '_'.join([element, par.name])
parname = phasename + '_' + \
parname if addphasename else parname
self.addVar(
par, parname, par.value, tags=['adp', element + '_adp'])
def get_sgpars(parset: Union[ObjCrystCrystalParSet, DiffpyStructureParSet],
sg: Union[int, str] = None):
"""Constrain the structure by space group and get the independent parameters."""
if isinstance(parset, ObjCrystCrystalParSet):
if sg is not None:
print(
"ObjCrystCrystalParSet does not accept explicit space group constrain. "
"Implicit space group is used.")
sgpars = parset.sgpars
elif isinstance(parset, DiffpyStructureParSet):
if sg is None:
sg = 'P1'
print("No explicit space group for DiffpyStructureParSet. "
"Use 'P1' symmetry.")
sgpars = constrainAsSpaceGroup(parset, sg, constrainadps=False)
else:
raise ValueError("{} does not allow space group constrain.".format(
type(parset)))
return sgpars
def sgconstrain(recipe: MyRecipe,
gen_name: str,
con_name: str = None,
sg: Union[int, str] = None,
dv: Dict[str, float] = None,
scatterers: List = None,
constrainxyz=False) -> None:
"""
Constrain the generator by space group. The constrained parameters are scale, delta2, lattice parameters, ADPs and
xyz coordinates. The lattice constants and xyz coordinates are constrained by space group while the ADPs are
constrained by elements. All paramters will be added as '{par.name}_{gen.name}'
The default values, ranges and tags for parameters:
scale: 0, (0, inf), scale_{gen.name}
delta2: 0, (0, 5), delta2_{gen.name}
lat: par.value, (par.value +/- 10%), lat_{gen.name}
adp: 0.006, (0.001, 0.02), adp_{gen.name}
xyz: par.value, (par.value +/- 0.1), xyz_{gen.name}
Parameters
----------
recipe
The recipe to add variables.
gen_name
The name of the PDFGenerator to constrain.
con_name
The name of the FitContribution where the PDFGenerator is in. If None, get it according to the name of the first
ConConfig in 'recipe.configs'. Default None.
sg
The space group. The expression can be the string or integer. If None, use the space group in GenConfig. Default
None.
dv
The default value of the constrained parameters. If None, the default values will be used. Default None.
scatterers
The argument scatters of the constrainAsSpaceGroup. If None, None will be used. Default None.
constrainxyz
Whether to constrain xyz coordinates.
Returns
-------
None
"""
def get_config():
if con_name is None:
return recipe.configs[0]
for config in recipe.configs:
if config.name == con_name:
return config
else:
raise ValueError(
f"No ConConfig in recipe '{recipe.name}' match the '{con_name}'."
)
def get_sg():
config = get_config()
for genconfig in config.phases:
if genconfig.name == gen_name:
return genconfig.sg
else:
raise ValueError(
f"No GenConfig in the FitContribution '{config.name}' match the '{gen_name}'."
)
# get sg
if sg is None:
sg = get_sg()
# set default of variables
dv = dv if dv else {}
con = getattr(recipe, con_name) if con_name else getattr(
recipe, recipe.configs[0].name)
gen = getattr(con, gen_name)
# add scale
name = f'scale_{gen.name}'
recipe.addVar(gen.scale, name=name,
value=dv.get(name, 0.)).boundRange(0., np.inf)
# add delta2
name = f'delta2_{gen.name}'
recipe.addVar(gen.delta2, name=name, value=dv.get(name,
0.)).boundRange(0., 5.)
# constrain by spacegroup
sgpars = constrainAsSpaceGroup(gen.phase,
sg,
constrainadps=False,
scatterers=scatterers)
print(
f"Constrain '{gen.name}' by space group '{sg}' without constraining ADPs."
)
# add latpars
for par in sgpars.latpars:
name = f'{par.name}_{gen.name}'
tag = f'lat_{gen.name}'
recipe.addVar(par, name=name, value=dv.get(name, par.value),
tag=tag).boundWindow(par.value * 0.1)
# constrain adps
atoms = gen.phase.getScatterers()
elements = Counter([atom.element for atom in atoms]).keys()
adp = {
element: recipe.newVar(f'Uiso_{element}_{gen.name}',
value=dv.get(f'Uiso_{element}_{gen.name}',
0.006),
tag=f'adp_{gen.name}').boundRange(0.001, 0.02)
for element in elements
}
for atom in atoms:
recipe.constrain(atom.Uiso, adp[atom.element])
# add xyzpars
if constrainxyz:
for par in sgpars.xyzpars:
name = f'{par.name}_{gen.name}'
tag = f'xyz_{gen.name}'
recipe.addVar(par,
name=name,
value=dv.get(name, par.value),
tag=tag).boundWindow(0.1)
return
def sgconstrain(recipe: MyRecipe,
gen: Union[PDFGenerator, DebyePDFGenerator],
sg: Union[int, str],
dv: Dict[str, float] = None,
scatterers: List = None) -> None:
"""
Constrain the generator by space group. The constrained parameters are scale, delta2, lattice parameters, ADPs and
xyz coordinates. The lattice constants and xyz coordinates are constrained by space group while the ADPs are
constrained by elements. All paramters will be added as '{par.name}_{gen.name}'
The default values, ranges and tags for parameters:
scale: 0, (0, inf), scale_{gen.name}
delta2: 0, (0, inf), delta2_{gen.name}
lat: par.value, (par.value +/- 20%), lat_{gen.name}
adp: 0.006, (0, inf), adp_{gen.name}
xyz: par.value, (par.value +/- 0.2), xyz_{gen.name}
Parameters
----------
recipe
The recipe to add variables.
gen
The generator to constrain.
sg
The space group. The expression can be the string or integer.
dv
The default value of the constrained parameters.
scatterers
The argument scatters of the constrainAsSpaceGroup.
Returns
-------
None
"""
dv = dv if dv else {}
# add scale
name = f'scale_{gen.name}'
recipe.addVar(gen.scale, name=name,
value=dv.get(name, 0.)).boundRange(0., np.inf)
# add delta2
name = f'delta2_{gen.name}'
recipe.addVar(gen.delta2, name=name,
value=dv.get(name, 0.)).boundRange(0., np.inf)
# constrain lat
sgpars = constrainAsSpaceGroup(gen.phase,
sg,
constrainadps=False,
scatterers=scatterers)
for par in sgpars.latpars:
name = f'{par.name}_{gen.name}'
tag = f'lat_{gen.name}'
recipe.addVar(par, name=name, value=dv.get(name, par.value),
tag=tag).boundWindow(par.value * 0.2)
# constrain adp
atoms = gen.phase.getScatterers()
elements = Counter([atom.element for atom in atoms]).keys()
adp = {
element: recipe.newVar(f'Uiso_{element}_{gen.name}',
value=dv.get(f'Uiso_{element}_{gen.name}',
0.006),
tag=f'adp_{gen.name}').boundRange(0., np.inf)
for element in elements
}
for atom in atoms:
recipe.constrain(atom.Uiso, adp[atom.element])
# constrain xyz
for par in sgpars.xyzpars:
name = f'{par.name}_{gen.name}'
tag = f'xyz_{gen.name}'
recipe.addVar(par, name=name, value=dv.get(name, par.value),
tag=tag).boundWindow(0.2)
return