https://github.com/chazeon/dpgen-snakemake

A lightweight Snakemake-based workflow that implements the DP-GEN scheme.
https://github.com/chazeon/dpgen-snakemake

ab-initio deep-learning machine-learning-potential snakemake-workflow workflow

Last synced: 8 months ago
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A lightweight Snakemake-based workflow that implements the DP-GEN scheme.

• Host: GitHub
• URL: https://github.com/chazeon/dpgen-snakemake
• Owner: chazeon
• Created: 2021-07-01T22:33:22.000Z (almost 5 years ago)
• Default Branch: v2
• Last Pushed: 2023-02-08T17:16:52.000Z (over 3 years ago)
• Last Synced: 2025-04-04T01:06:05.290Z (about 1 year ago)
• Topics: ab-initio, deep-learning, machine-learning-potential, snakemake-workflow, workflow
• Language: Python
• Homepage:
• Size: 13 MB
• Stars: 5
• Watchers: 3
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

          
# dpgen-snakemake

[![Test workflow scripts](https://github.com/chazeon/dpgen-snakemake/actions/workflows/main.yml/badge.svg)](https://github.com/chazeon/dpgen-snakemake/actions/workflows/main.yml)

[![codecov](https://codecov.io/gh/chazeon/dpgen-snakemake/branch/v2/graph/badge.svg?token=Q6GQAIPTNI)](https://codecov.io/gh/chazeon/dpgen-snakemake)

A lightweight [Snakemake][1]-based workflow that implements the [DP-GEN][2] scheme.

[1]: https://snakemake.readthedocs.io/en/stable/

[2]: https://arxiv.org/abs/1910.12690

## Project structure

- [**`project`**](project): Actual project files.

  - [**`workflows`**](project/workflows): Snakemake workflow files.

  - [**`scripts`**](project/scripts): Scripts for transforming input / output.

  - [**`templates`**](project/templates): Templates for generating files.

  - [**`tests`**](project/tests): Tests for the Python scripts.

- [**`project_sidecar`**](project_sidecar): Project files on the CPU machine

- [**`envs`**](envs): conda environments for workflow orchestration and DeePMD-kit training / evaluation.

## Usage

### DP-GEN Iteration

In each iteration, specify the environment variable `DPGEN_ITER_ID` then execute one one of the following rules to generate the corresponding files.

| Machine | Name of the rule           | Description                                                  |

| ------- | -------------------------- | ------------------------------------------------------------ |

| GPU     | `dp_run_train_target`      | Prepare files for the training step.                         |

| GPU     | `dp_run_model_devi_target` | Collect the newly generated potential files, then prepare the input files for the LAMMPS model deviation step. |

| GPU     | `dp_run_fp_target`         | Prepare the structures for the VASP calculation and prepare a tarball for transfer. |

| CPU     | `dp_run_fp_input`          | Collect the tarball of structures from the GPU machine.      |

| CPU     | `dp_run_fp_target`         | Collect the structures from the GPU machine, then prepare the input files for the VASP calculation. |

| CPU     | `dp_run_fp_done_target`    | Collect the VASP results and prepare for transfer.           |

| GPU     | `dp_run_fp_collect2`       | Collect VASP results from the CPU machine, then prepare the training data for the next iteration. |