# 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.raw is provided, the system atom type should be mapped to type_map.raw in type.raw and will be mapped to the model atom type when training; otherwise, the system atom type will be always mapped to the model atom type (whether type_map is set or not)

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 XX XY XZ YX YY YZ ZX ZY ZZ

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 numb_copy (int) times

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 XX XY XZ YX YY YZ ZX ZY ZZ

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 XX XY XZ YX YY YZ ZX ZY ZZ

atomic_polarizability

Atomic polarizability

atomic_polarizability.raw

Any

Nframes * Natoms * 9

in the order XX XY XZ YX YY YZ ZX ZY ZZ

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