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Move model deviation and ase calculator to
deepmd_utils
..., so they can benifit from multiple-backend DeepPot. Update docs. Signed-off-by: Jinzhe Zeng <[email protected]>
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,144 +1,8 @@ | ||
| # SPDX-License-Identifier: LGPL-3.0-or-later | ||
| """ASE calculator interface module.""" | ||
|
|
||
| from pathlib import ( | ||
| Path, | ||
| ) | ||
| from typing import ( | ||
| TYPE_CHECKING, | ||
| ClassVar, | ||
| Dict, | ||
| List, | ||
| Optional, | ||
| Union, | ||
| ) | ||
|
|
||
| from ase.calculators.calculator import ( | ||
| Calculator, | ||
| PropertyNotImplementedError, | ||
| all_changes, | ||
| ) | ||
|
|
||
| from deepmd import ( | ||
| DeepPotential, | ||
| from deepmd_utils.calculator import ( | ||
| DP, | ||
| ) | ||
|
|
||
| if TYPE_CHECKING: | ||
| from ase import ( | ||
| Atoms, | ||
| ) | ||
|
|
||
| __all__ = ["DP"] | ||
|
|
||
|
|
||
| class DP(Calculator): | ||
| """Implementation of ASE deepmd calculator. | ||
| Implemented propertie are `energy`, `forces` and `stress` | ||
| Parameters | ||
| ---------- | ||
| model : Union[str, Path] | ||
| path to the model | ||
| label : str, optional | ||
| calculator label, by default "DP" | ||
| type_dict : Dict[str, int], optional | ||
| mapping of element types and their numbers, best left None and the calculator | ||
| will infer this information from model, by default None | ||
| neighbor_list : ase.neighborlist.NeighborList, optional | ||
| The neighbor list object. If None, then build the native neighbor list. | ||
| Examples | ||
| -------- | ||
| Compute potential energy | ||
| >>> from ase import Atoms | ||
| >>> from deepmd.calculator import DP | ||
| >>> water = Atoms('H2O', | ||
| >>> positions=[(0.7601, 1.9270, 1), | ||
| >>> (1.9575, 1, 1), | ||
| >>> (1., 1., 1.)], | ||
| >>> cell=[100, 100, 100], | ||
| >>> calculator=DP(model="frozen_model.pb")) | ||
| >>> print(water.get_potential_energy()) | ||
| >>> print(water.get_forces()) | ||
| Run BFGS structure optimization | ||
| >>> from ase.optimize import BFGS | ||
| >>> dyn = BFGS(water) | ||
| >>> dyn.run(fmax=1e-6) | ||
| >>> print(water.get_positions()) | ||
| """ | ||
|
|
||
| name = "DP" | ||
| implemented_properties: ClassVar[List[str]] = [ | ||
| "energy", | ||
| "free_energy", | ||
| "forces", | ||
| "virial", | ||
| "stress", | ||
| ] | ||
|
|
||
| def __init__( | ||
| self, | ||
| model: Union[str, "Path"], | ||
| label: str = "DP", | ||
| type_dict: Optional[Dict[str, int]] = None, | ||
| neighbor_list=None, | ||
| **kwargs, | ||
| ) -> None: | ||
| Calculator.__init__(self, label=label, **kwargs) | ||
| self.dp = DeepPotential(str(Path(model).resolve()), neighbor_list=neighbor_list) | ||
| if type_dict: | ||
| self.type_dict = type_dict | ||
| else: | ||
| self.type_dict = dict( | ||
| zip(self.dp.get_type_map(), range(self.dp.get_ntypes())) | ||
| ) | ||
|
|
||
| def calculate( | ||
| self, | ||
| atoms: Optional["Atoms"] = None, | ||
| properties: List[str] = ["energy", "forces", "virial"], | ||
| system_changes: List[str] = all_changes, | ||
| ): | ||
| """Run calculation with deepmd model. | ||
| Parameters | ||
| ---------- | ||
| atoms : Optional[Atoms], optional | ||
| atoms object to run the calculation on, by default None | ||
| properties : List[str], optional | ||
| unused, only for function signature compatibility, | ||
| by default ["energy", "forces", "stress"] | ||
| system_changes : List[str], optional | ||
| unused, only for function signature compatibility, by default all_changes | ||
| """ | ||
| if atoms is not None: | ||
| self.atoms = atoms.copy() | ||
|
|
||
| coord = self.atoms.get_positions().reshape([1, -1]) | ||
| if sum(self.atoms.get_pbc()) > 0: | ||
| cell = self.atoms.get_cell().reshape([1, -1]) | ||
| else: | ||
| cell = None | ||
| symbols = self.atoms.get_chemical_symbols() | ||
| atype = [self.type_dict[k] for k in symbols] | ||
| e, f, v = self.dp.eval(coords=coord, cells=cell, atom_types=atype) | ||
| self.results["energy"] = e[0][0] | ||
| # see https://gitlab.com/ase/ase/-/merge_requests/2485 | ||
| self.results["free_energy"] = e[0][0] | ||
| self.results["forces"] = f[0] | ||
| self.results["virial"] = v[0].reshape(3, 3) | ||
|
|
||
| # convert virial into stress for lattice relaxation | ||
| if "stress" in properties: | ||
| if sum(atoms.get_pbc()) > 0: | ||
| # the usual convention (tensile stress is positive) | ||
| # stress = -virial / volume | ||
| stress = -0.5 * (v[0].copy() + v[0].copy().T) / atoms.get_volume() | ||
| # Voigt notation | ||
| self.results["stress"] = stress.flat[[0, 4, 8, 5, 2, 1]] | ||
| else: | ||
| raise PropertyNotImplementedError | ||
| __all__ = [ | ||
| "DP", | ||
| ] |
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