def add_scale(recipe: MyRecipe, gen: G, scale: bool = True) -> None:
"""Add the scale of the generator."""
if not scale:
return
recipe.addVar(gen.scale,
value=0.,
name="{}_scale".format(gen.name),
tags=["{}_scale".format(gen.name), "scale",
gen.name]).boundRange(lb=0.)
return
def add_lat(recipe: MyRecipe, gen: G, lat: tp.Union[str, None]) -> None:
"""Add the lattice parameters of the phase."""
if not lat:
return
if lat == "s":
pars = gen.phase.sgpars.latpars
elif lat == "a":
pars = gen.phase.getLattice()
else:
raise ValueError("Unknown lat: {}. Allowed: sg, all.".format(lat))
for par in pars:
recipe.addVar(par,
name="{}_{}".format(gen.name, par.name),
tags=["lat", gen.name,
"{}_lat".format(gen.name)]).boundRange(lb=0.)
return
def add_delta(recipe: MyRecipe, gen: G, delta: tp.Union[str, None]) -> None:
"""Add the delta parameter of the generator."""
if not delta:
return
if delta == "1":
par = gen.delta1
elif delta == "2":
par = gen.delta2
else:
raise ValueError(
"Unknown delta: {}. Allowed: delta1, delta2.".format(delta))
recipe.addVar(par,
value=0.,
name="{}_{}".format(gen.name, par.name),
tags=["{}_delta".format(gen.name), "delta",
gen.name]).boundRange(lb=0.)
return
def add_params(recipe: MyRecipe, con: MyContribution,
params: tp.Union[None, str, tp.List[str]]) -> None:
"""Add contribution-level parameters in the contribution."""
if not params:
return
args = {
arg.name: arg
for eq in con.eqfactory.equations if eq.name == "eq" for arg in eq.args
if arg.name != con.xname
}
if params == "a":
pars = args.values()
else:
pars = [args[p] for p in params]
for par in pars:
recipe.addVar(par, tag=par.name.split("_")[0])
return
def add_adp(
recipe: MyRecipe,
gen: G,
adp: tp.Union[str, None],
symbols: tp.Tuple[str] = ("Biso", "B11", "B22", "B33")
) -> None:
"""Add the atomic displacement parameter of the phase."""
if not adp:
return
atoms = gen.phase.getScatterers()
if adp == "e":
elements = set((atom.element for atom in atoms))
dct = dict()
for element in elements:
dct[element] = recipe.newVar(
"{}_{}_Biso".format(gen.name, bleach(element)),
value=0.05,
tags=["adp", gen.name, "{}_adp".format(gen.name)])
for atom in atoms:
recipe.constrain(atom.Biso, dct[atom.element])
return
if adp == "a":
pars = [atom.Biso for atom in atoms]
names = ["{}_Biso".format(bleach(atom.name)) for atom in atoms]
elif adp == "s":
pars = gen.phase.sgpars.adppars
names = [
rename_by_atom(par.name, atoms) for par in pars
if par.name.split("_")[0] in symbols
]
else:
raise ValueError(
"Unknown adp: {}. Allowed: element, sg, all.".format(adp))
for par, name in zip(pars, names):
recipe.addVar(par,
name="{}_{}".format(gen.name, name),
value=par.value if par.value != 0. else 0.05,
tags=["adp", gen.name,
"{}_adp".format(gen.name)]).boundRange(lb=0.)
return
def add_xyz(recipe: MyRecipe, gen: G, xyz: tp.Union[str, None]) -> None:
"""Add the coordinates of the atoms in the phase."""
if not xyz:
return
atoms = gen.phase.getScatterers()
if xyz == "s":
pars = gen.phase.sgpars.xyzpars
names = [rename_by_atom(par.name, atoms) for par in pars]
elif xyz == "a":
pars, names = list(), list()
for atom in atoms:
pars.append(atom.x)
names.append("{}_x".format(atom.name))
pars.append(atom.y)
names.append("{}_y".format(atom.name))
pars.append(atom.z)
names.append("{}_z".format(atom.name))
else:
raise ValueError("Unknown xyz: {}. Allowed: s, a.".format(xyz))
for par, name in zip(pars, names):
recipe.addVar(par,
name="{}_{}".format(gen.name, name),
tags=["xyz", gen.name, "{}_xyz".format(gen.name)])
return