3.1. 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
drdq	Partial derivative of atomic coordinates with respect to generalized coordinates	drdq.raw	1	Nframes * Natoms * 3 * Ngen_coords

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