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system.md

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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 {ref}type_map <model/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 {ref}type_map <model/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 {ref}type_map <model/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