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Tools related to GPUMD and NEP

  • Below is a list of the tools related to GPUMD and NEP (only the initial creator is listed).
  • Hope you find them helpful, but you should use them with caution.
  • If you have questions on a tool, you can try to contact the creator.
Folder Creator Email Brief Description
abacus2xyz Benrui Tang [email protected] Get train.xyz from ABACUS outputs.
add_groups Yuwen Zhang [email protected] Generate grouping method(s) for model.xyz.
castep2exyz Yanzhou Wang [email protected] Get train.xyz from CASTEP outputs.
cp2k2xyz Zherui Chen [email protected] Get train.xyz from CP2K outputs or vice versa.
deep2nep Ke Xu [email protected] Oudated?
doc_3.3.1 Zheyong Fan [email protected] Documentation for some parts of GPUMD-v3.3.1.
dp2xyz Ke Xu [email protected] Convert DP training data to xyz format.
exyz2pdb Zherui Chem [email protected] Convert exyz to pdb.
for_coding Zheyong Fan [email protected] Something useful for Zheyong Fan only.
get_max_rmse_xyz Ke Xu [email protected] Identify structures with the largest errors.
gmx2exyz Zherui Chen [email protected] Convert the trr trajectory of gmx to the exyz trajectory.
gpumdkit Zihan Yan [email protected] A shell toolkit for GPUMD.
md_tersoff Zheyong Fan [email protected] Already in MD book; can be removed later.
mtp2nep Who? Outdated?
mtp2xyz Ke Xu [email protected] Convert MTP training data to xyz format.
nep2xyz Ke Xu [email protected] Outdated?
pca_sampling Penghua Ying [email protected] Farthest-point sampling based on calorine.
perturbed2poscar Who? What?
rdf_adf Ke Xu [email protected] Calculate RDF and ADF using OVITO.
runner2xyz Ke Xu [email protected] Convert RUNNER training data to xyz format.
select_xyz_frames Zherui Chen [email protected] Select frames from the exyz file.
shift_energy_to_zero Nan Xu [email protected] Shift the average energy of each species to zero for a dataset.
split_xyz Yong Wang [email protected] Some functionalities for training/test data.
vasp2xyz Yanzhou Wang [email protected] Get train.xyz from VASP outputs.
vim Ke Xu [email protected] Highlight GPUMD grammar in vim.
xyz2gro Who? Convert xyz file to gro file.

Python packages related to GPUMD and/or NEP:

Package link comment
calorine https://gitlab.com/materials-modeling/calorine calorine is a Python package for running and analyzing molecular dynamics (MD) simulations via GPUMD. It also provides functionality for constructing and sampling neuroevolution potential (NEP) models via GPUMD.
GPUMD-Wizard https://github.com/Jonsnow-willow/GPUMD-Wizard GPUMD-Wizard is a material structure processing software based on ASE (Atomic Simulation Environment) providing automation capabilities for calculating various properties of metals. Additionally, it aims to run and analyze molecular dynamics (MD) simulations using GPUMD.
gpyumd https://github.com/AlexGabourie/gpyumd gpyumd is a Python3 interface for GPUMD. It helps users generate input and process output files based on the details provided by the GPUMD documentation. It currently supports up to GPUMD-v3.3.1 and only the gpumd executable.
mdapy https://github.com/mushroomfire/mdapy The mdapy python library provides an array of powerful, flexible, and straightforward tools to analyze atomic trajectories generated from Molecular Dynamics (MD) simulations.
pynep https://github.com/bigd4/PyNEP PyNEP is a python interface of the machine learning potential NEP used in GPUMD.
somd https://github.com/initqp/somd SOMD is an ab-initio molecular dynamics (AIMD) package designed for the SIESTA DFT code. The SOMD code provides some common functionalities to perform standard Born-Oppenheimer molecular dynamics (BOMD) simulations, and contains a simple wrapper to the Neuroevolution Potential (NEP) package. The SOMD code may be used to automatically build NEPs by the mean of the active-learning methodology.
NepTrainKit https://github.com/aboys-cb/NepTrainKit NepTrainKit is a Python package for visualizing and manipulating training datasets for NEP.