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improve: ase try to get virials from different sources #660

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Merged
njzjz merged 3 commits into from
Jul 16, 2025
Merged

improve: ase try to get virials from different sources #660

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6655453
read virial from ase
link89 Jul 16, 2025
d6906f6
fix broken doc
link89 Jul 16, 2025
457de06
revert m2r fix
link89 Jul 16, 2025
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23 changes: 15 additions & 8 deletions dpdata/plugins/ase.py
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Original file line number Diff line number Diff line change
Expand Up @@ -63,6 +63,8 @@ def from_labeled_system(self, atoms: ase.Atoms, **kwargs) -> dict:
"""Convert ase.Atoms to a LabeledSystem. Energies and forces
are calculated by the calculator.

Note that this method will try to load virials from either virial field or converted from stress tensor.

Parameters
----------
atoms : ase.Atoms
Expand Down Expand Up @@ -94,13 +96,19 @@ def from_labeled_system(self, atoms: ase.Atoms, **kwargs) -> dict:
"energies": np.array([energies]),
"forces": np.array([forces]),
}
try:
stress = atoms.get_stress(voigt=False)
except PropertyNotImplementedError:
pass
else:
virials = np.array([-atoms.get_volume() * stress])
info_dict["virials"] = virials

# try to get virials from different sources
virials = atoms.info.get("virial")
if virials is None:
try:
stress = atoms.get_stress(voigt=False)
except PropertyNotImplementedError:
pass
else:
virials = -atoms.get_volume() * stress
if virials is not None:
info_dict["virials"] = np.array([virials])

return info_dict

def from_multi_systems(
Expand Down Expand Up @@ -166,7 +174,6 @@ def to_labeled_system(self, data, *args, **kwargs) -> list[ase.Atoms]:

structures = []
species = [data["atom_names"][tt] for tt in data["atom_types"]]

for ii in range(data["coords"].shape[0]):
structure = Atoms(
symbols=species,
Expand Down