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implementation of central and neighbour mask for spherical expansions #420

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implementation of central and neighbour mask for spherical expansions #420

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24 changes: 24 additions & 0 deletions bindings/rascal/representations/spherical_expansion.py
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Original file line number Diff line number Diff line change
Expand Up @@ -136,6 +136,12 @@ class SphericalExpansion(BaseIO):
should contain all the species present in the structure for which
invariants will be computed

central_species : list
list of central atom species that are only computed

neighbour_species : list
list of neighbour atom species that are only computed

compute_gradients : bool
control the computation of the representation's gradients w.r.t. atomic
positions.
Expand Down Expand Up @@ -178,6 +184,8 @@ def __init__(
optimization_args=None,
expansion_by_species_method="environment wise",
global_species=None,
central_species=None,
neighbour_species=None,
compute_gradients=False,
cutoff_function_parameters=dict(),
):
Expand All @@ -195,11 +203,23 @@ class documentation
elif not isinstance(global_species, list):
global_species = list(global_species)

if neighbour_species is None:
neighbour_species = []
elif not isinstance(neighbour_species, list):
neighbour_species = list(neighbour_species)

if central_species is None:
central_species = []
elif not isinstance(central_species, list):
central_species = list(central_species)

self.update_hyperparameters(
max_radial=max_radial,
max_angular=max_angular,
expansion_by_species_method=expansion_by_species_method,
global_species=global_species,
central_species=central_species,
neighbour_species=neighbour_species,
compute_gradients=compute_gradients,
)
self.cutoff_function_parameters = deepcopy(cutoff_function_parameters)
Expand Down Expand Up @@ -258,6 +278,8 @@ def update_hyperparameters(self, **hypers):
"cutoff_function_parameters",
"expansion_by_species_method",
"global_species",
"central_species",
"neighbour_species",
}
hypers_clean = {key: hypers[key] for key in hypers if key in allowed_keys}
self.hypers.update(hypers_clean)
Expand Down Expand Up @@ -310,6 +332,8 @@ def _get_init_params(self):
max_angular=self.hypers["max_angular"],
expansion_by_species_method=self.hypers["expansion_by_species_method"],
global_species=self.hypers["global_species"],
central_species=self.hypers["central_species"],
neighbour_species=self.hypers["neighbour_species"],
compute_gradients=self.hypers["compute_gradients"],
gaussian_sigma_type=gaussian_density["type"],
gaussian_sigma_constant=gaussian_density["gaussian_sigma"]["value"],
Expand Down
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