deepmd.jax.atomic_model.pairtab_atomic_model

Classes

PairTabAtomicModel

Pairwise tabulation energy model.

Module Contents

class deepmd.jax.atomic_model.pairtab_atomic_model.PairTabAtomicModel(tab_file: str, rcut: float, sel: int | list[int], type_map: list[str], rcond: float | None = None, atom_ener: list[float] | None = None, **kwargs)

Bases: deepmd.dpmodel.atomic_model.pairtab_atomic_model.PairTabAtomicModel

Pairwise tabulation energy model.

This model can be used to tabulate the pairwise energy between atoms for either short-range or long-range interactions, such as D3, LJ, ZBL, etc. It should not be used alone, but rather as one submodel of a linear (sum) model, such as DP+D3.

Do not put the model on the first model of a linear model, since the linear model fetches the type map from the first model.

At this moment, the model does not smooth the energy at the cutoff radius, so one needs to make sure the energy has been smoothed to zero.

Parameters:

tab_filestr

The path to the tabulation file.

rcutfloat

The cutoff radius.

selint or list[int]

The maxmum number of atoms in the cut-off radius.

type_maplist[str]

Mapping atom type to the name (str) of the type. For example type_map[1] gives the name of the type 1.

__setattr__(name: str, value: Any) → None

forward_common_atomic(extended_coord: deepmd.jax.env.jnp.ndarray, extended_atype: deepmd.jax.env.jnp.ndarray, nlist: deepmd.jax.env.jnp.ndarray, mapping: deepmd.jax.env.jnp.ndarray | None = None, fparam: deepmd.jax.env.jnp.ndarray | None = None, aparam: deepmd.jax.env.jnp.ndarray | None = None) → dict[str, deepmd.jax.env.jnp.ndarray]

Common interface for atomic inference.

This method accept extended coordinates, extended atom typs, neighbor list, and predict the atomic contribution of the fit property.

Parameters:

extended_coord

extended coordinates, shape: nf x (nall x 3)

extended_atype

extended atom typs, shape: nf x nall for a type < 0 indicating the atomic is virtual.

nlist

neighbor list, shape: nf x nloc x nsel

mapping

extended to local index mapping, shape: nf x nall

fparam

frame parameters, shape: nf x dim_fparam

aparam

atomic parameter, shape: nf x nloc x dim_aparam

Returns:

ret_dict

dict of output atomic properties. should implement the definition of fitting_output_def. ret_dict[“mask”] of shape nf x nloc will be provided. ret_dict[“mask”][ff,ii] == 1 indicating the ii-th atom of the ff-th frame is real. ret_dict[“mask”][ff,ii] == 0 indicating the ii-th atom of the ff-th frame is virtual.