GPUMDkit

GPUMDkit is a toolkit for the GPUMD (Graphics Processing Units Molecular Dynamics) program. It provides a set of tools to streamline the use of common scripts in GPUMD and NEP (neuroevolution potential), simplifying workflows and enhancing efficiency.

Features

• Simplified Script Invocation: Easily run scripts for GPUMD and NEP.
• Workflow Automation: Automate common tasks to save time and reduce manual intervention.
• User-Friendly Interface: Intuitive shell commands designed to enhance user experience.

Installation

To install GPUMDkit, follow these steps:

1. Clone the repository or download the whole project.

2. Set the GPUMD_path and GPUMDkit_path variables in your ~/.bashrc file, for example:

   vi ~/.bashrc
   

   add these two variables

   export GPUMD_path=/your_dir_of_GPUMD
   export GPUMDkit_path=/your_dir_of_GPUMDkit

   add GPUMDkit_path to the PATH

   export PATH=/your_dir_of_GPUMDkit:${PATH}

   or move the gpumdkit.sh file to a directory in your PATH, for example:

   mv gpumdkit.sh ~/bin/

   then

   source ~/.bashrc

3. Add executable permissions to the gpumdkit.sh file:

   chmod +x gpumdkit.sh

Update

To update your local copy of GPUMDkit, simply run this command:

chmod -x gpumdkit.sh; git pull; chmod +x gpumdkit.sh

Usage

There are two options, interactive mode and command-line mode

Interactive Mode

---

1. Open your terminal.

2. Execute the gpumdkit.sh script:

   gpumdkit.sh
   

3. Follow the on-screen prompts to interactively select and run the desired script.

           ____ ____  _   _ __  __ ____  _    _ _
          / ___|  _ \| | | |  \/  |  _ \| | _(_) |_
         | |  _| |_) | | | | |\/| | | | | |/ / | __|
         | |_| |  __/| |_| | |  | | |_| |   <| | |_
          \____|_|    \___/|_|  |_|____/|_|\_\_|\__|
   
         GPUMDkit Version 1.0.6 (dev) (2025-02-26)
         Developer: Zihan YAN (yanzihan@westlake.edu.cn)
   
   ----------------------- GPUMD -----------------------
   1) Format Conversion          2) Sample Structures
   2) Workflow (dev)             4) Calculators         
   5) Developing ...             6) Developing ...      
   0) Quit!
   ------------>>
   Input the function number:
   

Command-Line Mode

---

For users familiar with the GPUMDkit , the command-line mode allows for faster execution by directly passing arguments to gpumdkit.sh. Here are some examples:

Example 1: View help information

gpumdkit.sh -h

the help information:

+==================================================================================================+
|                              GPUMDkit 1.0.6 (dev) (2025-02-26) Usage                             |
|                                                                 --- by Zihan YAN                 |
+======================================== Conversions =============================================+
| -outcar2exyz   Convert OUTCAR to extxyz       | -pos2exyz     Convert POSCAR to extxyz           |
| -castep2exyz   Convert castep to extxyz       | -pos2lmp      Convert POSCAR to LAMMPS           |
| -cp2k2exyz     Convert cp2k output to extxyz  | -lmp2exyz     Convert LAMMPS-dump to extxyz      |
| -addgroup      Add group label                | -addweight    Add weight to the struct in extxyz |
| Developing...                                 | Developing...                                    |
+========================================= Analysis ===============================================+
| -range         Print range of energy etc.     | -max_rmse     Get max RMSE from XYZ              |
| -min_dist      Get min_dist between atoms     | -min_dist_pbc Get min_dist considering PBC       |
| -filter_box    Filter struct by box limits    | -filter_value Filter struct by value (efs)       |
| -filter_dist   Filter struct by min_dist      | Developing...                                    |
+=========================================    Misc  ==============+================================+
| -plt           Plot scripts                   | -get_frame     Extract the specified frame       |
| -calc          Calculators                    | -clear_xyz     Clear extra info in XYZ file      |
| -clean         Clear files for work_dir       | -time          Time consuming Analyzer           |
| Developing...                                 | Developing...                                    |
+==================================================================================================+
| For detailed usage and examples, use: gpumdkit.sh -<option> -h                                   |
+==================================================================================================+

Example 2: Convert VASP OUTCARs to extxyz

To convert a VASP OUTCARs to an extended XYZ format (extxyz) file, use the following command:

gpumdkit.sh -out2xyz <dir_of_OUTCARs>

Example: gpumdkit.sh -out2xyz .

Example 3: Plot thermo evolution

To visualize thermo evolution from thermo.out :

gpumdkit.sh -plt thermo

You can also save images as PNG if your device doesn't support visualization:

gpumdkit.sh -plt thermo save

Refer to the Usage Instructions for more detailed examples and command options.

Join Us

We’d love your help to improve GPUMDkit! Contribute by:

• Adding Python/Shell scripts via Pull Requests.
• Contacting me at yanzihan@westlake.edu.cn.

Let’s build something useful together! 🌟

Citation

As of now, GPUMDkit is a toy model, free for anyone to use and experiment with. If you like it, please ⭐ star us on GitHub. Thanks for your support!