deepmd.pt.utils.preprocess
Module Contents
Classes
Functions
| Move outer atoms into region by mirror. |
| Tell the sequential cell ID in its 3D space. |
| Tell shift count to move the atom into region. |
| Build cell list on atoms inside region. |
| Make ghost atoms who are valid neighbors. |
| For each atom inside region, build its neighbor list. |
| Compute smooth weight for descriptor elements. |
| Based on atom coordinates, return environment matrix. |
Attributes
- deepmd.pt.utils.preprocess.normalize_coord(coord, region: Region3D, nloc: int)[source]
Move outer atoms into region by mirror.
Args: - coord: shape is [nloc*3]
- deepmd.pt.utils.preprocess.compute_serial_cid(cell_offset, ncell)[source]
Tell the sequential cell ID in its 3D space.
Args: - cell_offset: shape is [3] - ncell: shape is [3]
- deepmd.pt.utils.preprocess.compute_pbc_shift(cell_offset, ncell)[source]
Tell shift count to move the atom into region.
- deepmd.pt.utils.preprocess.build_inside_clist(coord, region: Region3D, ncell)[source]
Build cell list on atoms inside region.
Args: - coord: shape is [nloc*3] - ncell: shape is [3]
- deepmd.pt.utils.preprocess.append_neighbors(coord, region: Region3D, atype, rcut: float)[source]
Make ghost atoms who are valid neighbors.
Args: - coord: shape is [nloc*3] - atype: shape is [nloc]
- deepmd.pt.utils.preprocess.build_neighbor_list(nloc: int, coord, atype, rcut: float, sec, mapping, type_split=True, min_check=False)[source]
For each atom inside region, build its neighbor list.
Args: - coord: shape is [nall*3] - atype: shape is [nall]
- deepmd.pt.utils.preprocess.compute_smooth_weight(distance, rmin: float, rmax: float)[source]
Compute smooth weight for descriptor elements.
- deepmd.pt.utils.preprocess.make_env_mat(coord, atype, region, rcut: float | list, sec, pbc=True, type_split=True, min_check=False)[source]
Based on atom coordinates, return environment matrix.
- Returns:
- nlist:
nlist
, [nloc
,nnei
] - merged_coord_shift:
shift
on
nall
atoms
, [nall
, 3] - merged_mapping:
mapping
from
nall
index
to
nloc
index
, [nall
]
- nlist: