Molecular Data Representation¶
mlcg.data defines the AtomicData class, the data structure used as input to models. It contains one or more atomic structures with associated physical properties. AtomicData instances also store the outputs of models through which they pass.
- class mlcg.data.atomic_data.AtomicData(**kwargs)[source]¶
A data object holding atomic structures. The attribute names are defined in
mlcg.data._keys- pos¶
set of atomic positions in each structures
- Type:
[n_atoms * n_structures, 3]
- atom_types¶
if atoms then it’s the atomic number, if it’s a CG bead then it’s a number defined by the CG mapping
- Type:
[n_atoms * n_structures]
- masses¶
Masses of each atom
- Type:
[n_atoms * n_structures]
- pbc¶
periodic boundary conditions
- Type:
[n_structures, 3] (Optional)
- cell¶
unit cell of the atomic structure. Lattice vectors are defined row wise
- Type:
[n_structures, 3, 3] (Optional)
- tag¶
metadata about each structure
- Type:
[n_structures] (Optional)
- energy¶
reference energy associated with each structures
- Type:
[n_structures] (Optional)
- forces¶
reference forces associated with each structures
- Type:
[n_atoms * n_structures, 3] (Optional)
- velocities¶
velocities associated with each structure
- Type:
[n_atoms * n_structures, 3] (optional)
- neighbor_list¶
contains information about the connectivity formatted according to mlcg.neighbor_list.neighbor_list.make_neighbor_list.
- Type:
Dict[str, Dict[str, Any]] (Optional)