gpumd

Description:
Runs molecular dynamics simulations using GPUMD.

Input Parameters

Usage:

NepTrain gpumd <model_path> [options]

Tip

For simplicity in execution and to reduce input parameters, ./run.in and ./nep.txt are used as the default input files. However, these file paths must be valid.
If the filenames are incorrect, please specify them using the appropriate parameters.

Options:

  • <model_path>
    Structure path or file (supports xyz and vasp formats).

  • -dir, --directory
    Path for GPUMD calculations. Default: ./cache/gpumd.

  • -in, --in
    Path to run.in file. Default: ./run.in.

  • -nep, --nep
    Path to potential function file. Default: ./nep.txt.

  • -t, --time
    Molecular dynamics simulation time (ps). Default: 10.

  • -T, --temperature Simulation temperature(s) (K). Default: 300.

  • -o, --out Output file for trajectory. Default: ./trajectory.xyz.

Output

GPUMD will output files in the directory (default is ./cache/gpumd) along with GPUMD’s standard output files. The resulting trajectories are saved to the path specified by --out.

Example

Tip

Direct execution will run on the local machine. If you need to submit the job to a queueing system, place this command at the end of the submission script.

Minimal Execution Command

If ./run.in and ./nep.txt already exist in the directory, and your structure files are stored in the structure folder, you can run the following command directly from the directory. This will perform a 10 ps molecular dynamics (MD) simulation at 300 K for all structure files in the structure folder:

NepTrain gpumd structure

Modifying Parameters

To run MD simulations for all structures at temperatures ranging from 100 K to 600 K with a step of 100 K, you can use either of the following commands:

NepTrain gpumd structure -T 100 200 300 400 500 600

Or use a shell shortcut to create an array:

NepTrain gpumd structure -T {100...600...100}