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📚 GPUMDkit Tutorials

Welcome to GPUMDkit, a command-line toolkit for GPUMD and NEP.

What it does

GPUMDkit helps you perform common tasks in computational materials science without writing custom scripts. It supports format conversion, structure analysis, property calculation, visualization, and batch workflows — all from one command-line tool.

Common Tasks

I want to... Tutorial
Install GPUMDkit and run my first command Quick Start
Convert VASP, LAMMPS, CP2K, or CIF files to extxyz Format Conversion
Check structure distances, filter datasets, or find outliers Analyzer Scripts
Calculate MSD, ionic conductivity, or descriptors Calculator Scripts
Analyze polar materials, ferroelectrics, or ABO3 systems Polar Material Analysis
Plot NEP training results or thermodynamic data Plot Scripts
Run batch DFT or MD simulations Workflow Scripts
Select representative structures from a dataset Structure Sampling
Add my own shortcuts to GPUMDkit Custom Commands

Before you start

Installation

git clone https://github.com/zhyan0603/GPUMDkit.git
cd GPUMDkit
source ./install.sh

Dependencies

conda create -n gpumdkit python=3.12
conda activate gpumdkit
pip install neptrain dpdata calorine

Interactive mode

gpumdkit.sh

This opens a menu where you can select modules by number.

CLI mode

gpumdkit.sh -<option> [args...]

For example:

gpumdkit.sh -pos2exyz POSCAR model.xyz
gpumdkit.sh -plt train
gpumdkit.sh -calc msd trajectory.xyz Li 10

Use gpumdkit.sh -h to see all available options.

Module Overview

Module Menu CLI Description
Format Conversion 1 -out2xyz, -pos2exyz File conversion
Sample Structures 2 interactive menu, -frame_range, -pynep (deprecated) Structure sampling
Workflow 3 - Batch processing
Calculators 4 -calc <type> Property calculations
Analyzer 5 -range, -min_dist Structure analysis
Visualization 6 -plt <type> Plotting tools
Utilities 7 -time, -clean Utility functions

All Tutorials

Tutorial Description
Quick Start Installation and first steps
Command Reference One-page CLI and menu reference
Format Conversion Convert between file formats
Calculator Scripts Compute material properties
Analyzer Scripts Structure analysis and validation
Plot Scripts Plotting and visualization
Workflow Scripts Batch processing and automation
Structure Sampling Structure selection methods
Custom Commands User-defined GPUMDkit shortcuts
Active Learning Workflow Batch active-learning workflow notes
Polar Material Analysis Ferroelectric and polarization tools
Contributing to GPUMDkit Development notes
  • GitHub: https://github.com/zhyan0603/GPUMDkit
  • Documentation: https://zhyan0603.github.io/GPUMDkit/