In this example we will convert the DFT labeled data stored in VASP
OUTCAR format into the data format used by DeePMD-kit. The example
OUTCAR can be found in the directory.
The DeePMD-kit organize data in
system is composed by a number of
frames. One may roughly view a
frame as a snap short on an MD trajectory, but it does not necessary come from an MD simulation. A
frame records the coordinates and types of atoms, cell vectors if the periodic boundary condition is assumed, energy, atomic forces and virial. It is noted that the
frames in one
system share the same number of atoms with the same type.
It is conveninent to use dpdata to convert data generated by DFT packages to the data format used by DeePMD-kit.
To install one can execute
pip install dpdata
An example of converting data VASP data in
OUTCAR format to DeePMD-kit data can be found at
Switch to that directory, then one can convert data by using the following python script
import dpdata dsys = dpdata.LabeledSystem('OUTCAR') dsys.to('deepmd/npy', 'deepmd_data', set_size = dsys.get_nframes())
get_nframes() method gets the number of frames in the
OUTCAR, and the argument
set_size enforces that the set size is equal to the number of frames in the system, viz. only one
set is created in the
The data in DeePMD-kit format is stored in the folder