The input file

Jump to navigation Jump to search


  • The file contains all the training data for the NEP potential.
  • The file contains all the testing data for the NEP potential.
  • These two files have the same format. Therefore, we only refer to the file below for simplicity.

Data format

The data format in this file is fixed:

N_1  has_virial
N_2  has_virial
N_Nc has_virial
Data for configuration 1
Data for configuration 2
Data for configuration Nc


  • Nc is the total number of configurations (systems, or structures).
  • N_i is the number of atoms in configuration i.
  • The has_virial flag (can only be 0 or 1) dictates whether or not there is virial information for the current configuration.
  • Data for one configuration occupy N_i + 2 lines:
    • The first line should have 1 or 7 numbers. If has_virial for the current configuration is 0, this line only has one number, which is the total energy of the current configuration. If has_virial for the current configuration is 1, this line has 7 numbers, which are the total energy of the current configuration followed by 6 virial components (in the order of xx, yy, zz, xy, yz, and zx) of the current configuration.
    • The second line should have nine numbers defining the cell vectors ([math]\vec{a}[/math], [math]\vec{b}[/math], [math]\vec{c}[/math]): ax ay az bx by bz cx cy cz.
    • In the remaining N_i lines, each line contains 7 numbers, corresponding to the atom type, position components (x, y, z), and force components (fx, fy, fz): type x y z fx fy fz.
      • In GPUMD-v2.6, the atom type is the atomic number (that is, number of protons).
      • In GPUMD-v2.7, the atom type is a non-negative integer defined by the user. In an [math]n[/math]-element system, these numbers should be integers from 0 to [math]n-1[/math]. For example, in PbTe, one can assign type 0 to Te and type 1 to Pb.


In this file:

  • Length and position are in units of Angstrom.
  • Energy is in units of eV.
  • Force is in units of eV/Angstrom.
  • Virial is in units of eV (so virial divided by volume gives pressure).


  • Periodic boundary conditions are always assumed for all directions in each configuration. When the box thickness in a direction is smaller than twice of the radial cutoff distance, the code will replicate the box in that direction. The user should be aware that this can increase the computation time.
  • The minimal number of atoms in a configuration is 1. The user is responsible for choosing a good referene energy when preparing the energy data.
  • The energy and virial data refer to the total energy and virial for the system. They are not per-atom but per-box quantities.