Tutorial

Announcement

The main features of ChecMate have been integrated into ai2-kit's CLL workflow.

lf you use this workflow or the corresponding functions in ai2-kit's CLL in in your research, please cite the following paper:

Yu-Xin Guo, Yong-Bin Zhuang, Jueli Shi, Jun Cheng; ChecMatE: A workflow package to automatically generate machine learning potentials and phase diagrams for semiconductor alloys. J. Chem. Phys. 7 September 2023; 159 (9): 094801. https://doi.org/10.1063/5.0166858

Install necessary tools

It is suggested to create a virtual environment via conda for your project. After your conda environment is activated, run the following command to install necessary tools.

pip install --user poetry

Install project

cd checmate/
poetry install

There may be a connection error during this process, try a few more times.

Configure pymatgen potcar

Before you run checmate, you should configure the pymatgen with the potcar files in your laptops/hpc/etc.. if you are using the potcar files from vasp 5.4, you should set

pmg config --add PMG_DEFAULT_FUNCTIONAL PBE_54

if you are using the potcar files from vasp 5.2, you should set

pmg config --add PMG_DEFAULT_FUNCTIONAL PBE_52

Otherwise, skip the above commands.

In the next, one should generate pymatgen potcar files using

pmg config -p <original_potentials_dir> mypsp

a mypsp directory will be created in current directory. move mypsp to <somewhere>

configure the path, through which the pymatgen can find the potentials, the mypsp

pmg config --add PMG_VASP_PSP_DIR  <somewhere>/mypsp 

We refer interested readers to https://pymatgen.org/installation.html for detailed setup.

Run commands / scripts

checmate -s SETTING WORKFLOW

where the argument SETTING is the name of the parameter file in the JSON/YAML format, which should be determined by the user beforehand. And the argument WORKFLOW is the name of a specific workflow.

checmate --help