2.1. System
DeePMD-kit takes a system as the data structure. A snapshot of a system is called a frame. A system may contain multiple frames with the same atom types and numbers, i.e. the same formula (like H2O
). To contains data with different formulas, one usually needs to divide data into multiple systems, which may sometimes result in sparse-frame systems. See a new system format to further combine different systems with the same atom numbers, when training with descriptor se_atten
.
A system should contain system properties, input frame properties, and labeled frame properties. The system property contains the following property:
ID | Property | Raw file | Required/Optional | Shape | Description |
---|---|---|---|---|---|
type | Atom type indexes | type.raw | Required | Natoms | Integers that start with 0. If both the training parameter type_map is set and |
type_map | Atom type names | type_map.raw | Optional | Ntypes | Atom names that map to atom type, which is unnecessary to be contained in the periodic table. Only works when the training parameter type_map is set |
nopbc | Non-periodic system | nopbc | Optional | 1 | If True, this system is non-periodic; otherwise it’s periodic |
The input frame properties contain the following property, the first axis of which is the number of frames:
ID | Property | Raw file | Unit | Required/Optional | Shape | Description |
---|---|---|---|---|---|---|
coord | Atomic coordinates | coord.raw | Å | Required | Nframes * Natoms * 3 | |
box | Boxes | box.raw | Å | Required if periodic | Nframes * 3 * 3 | in the order |
fparam | Extra frame parameters | fparam.raw | Any | Optional | Nframes * Any | |
aparam | Extra atomic parameters | aparam.raw | Any | Optional | Nframes * aparam * Any | |
numb_copy | Each frame is copied by the | prob.raw | 1 | Optional | Nframes | Integer; Default is 1 for all frames |
The labeled frame properties are listed as follows, all of which will be used for training if and only if the loss function contains such property:
ID | Property | Raw file | Unit | Shape | Description |
---|---|---|---|---|---|
energy | Frame energies | energy.raw | eV | Nframes | |
force | Atomic forces | force.raw | eV/Å | Nframes * Natoms * 3 | |
virial | Frame virial | virial.raw | eV | Nframes * 9 | in the order |
atom_ener | Atomic energies | atom_ener.raw | eV | Nframes * Natoms | |
atom_pref | Weights of atomic forces | atom_pref.raw | 1 | Nframes * Natoms | |
dipole | Frame dipole | dipole.raw | Any | Nframes * 3 | |
atomic_dipole | Atomic dipole | atomic_dipole.raw | Any | Nframes * Natoms * 3 | |
polarizability | Frame polarizability | polarizability.raw | Any | Nframes * 9 | in the order |
atomic_polarizability | Atomic polarizability | atomic_polarizability.raw | Any | Nframes * Natoms * 9 | in the order |
In general, we always use the following convention of units:
Property | Unit |
---|---|
Time | ps |
Length | Å |
Energy | eV |
Force | eV/Å |
Virial | eV |
Pressure | Bar |