{"id":21984084,"url":"https://github.com/chazeon/dpgen-snakemake","last_synced_at":"2025-10-10T16:31:13.498Z","repository":{"id":72453798,"uuid":"382171236","full_name":"chazeon/dpgen-snakemake","owner":"chazeon","description":"A lightweight Snakemake-based workflow that implements the DP-GEN scheme.","archived":false,"fork":false,"pushed_at":"2023-02-08T17:16:52.000Z","size":13583,"stargazers_count":5,"open_issues_count":0,"forks_count":0,"subscribers_count":3,"default_branch":"v2","last_synced_at":"2025-04-04T01:06:05.290Z","etag":null,"topics":["ab-initio","deep-learning","machine-learning-potential","snakemake-workflow","workflow"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/chazeon.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2021-07-01T22:33:22.000Z","updated_at":"2024-10-27T06:47:19.000Z","dependencies_parsed_at":"2023-03-16T14:15:31.908Z","dependency_job_id":null,"html_url":"https://github.com/chazeon/dpgen-snakemake","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/chazeon/dpgen-snakemake","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/chazeon%2Fdpgen-snakemake","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/chazeon%2Fdpgen-snakemake/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/chazeon%2Fdpgen-snakemake/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/chazeon%2Fdpgen-snakemake/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/chazeon","download_url":"https://codeload.github.com/chazeon/dpgen-snakemake/tar.gz/refs/heads/v2","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/chazeon%2Fdpgen-snakemake/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":279004706,"owners_count":26083750,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-10-10T02:00:06.843Z","response_time":62,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["ab-initio","deep-learning","machine-learning-potential","snakemake-workflow","workflow"],"created_at":"2024-11-29T18:07:24.784Z","updated_at":"2025-10-10T16:31:09.901Z","avatar_url":"https://github.com/chazeon.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# dpgen-snakemake\n\n[![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)\n[![codecov](https://codecov.io/gh/chazeon/dpgen-snakemake/branch/v2/graph/badge.svg?token=Q6GQAIPTNI)](https://codecov.io/gh/chazeon/dpgen-snakemake)\n\n\nA lightweight [Snakemake][1]-based workflow that implements the [DP-GEN][2] scheme.\n\n[1]: https://snakemake.readthedocs.io/en/stable/\n[2]: https://arxiv.org/abs/1910.12690\n\n## Project structure\n\n- [**`project`**](project): Actual project files.\n  - [**`workflows`**](project/workflows): Snakemake workflow files.\n  - [**`scripts`**](project/scripts): Scripts for transforming input / output.\n  - [**`templates`**](project/templates): Templates for generating files.\n  - [**`tests`**](project/tests): Tests for the Python scripts.\n- [**`project_sidecar`**](project_sidecar): Project files on the CPU machine\n- [**`envs`**](envs): conda environments for workflow orchestration and DeePMD-kit training / evaluation.\n\n## Usage\n\n### DP-GEN Iteration\n\nIn each iteration, specify the environment variable `DPGEN_ITER_ID` then execute one one of the following rules to generate the corresponding files.\n\n| Machine | Name of the rule           | Description                                                  |\n| ------- | -------------------------- | ------------------------------------------------------------ |\n| GPU     | `dp_run_train_target`      | Prepare files for the training step.                         |\n| GPU     | `dp_run_model_devi_target` | Collect the newly generated potential files, then prepare the input files for the LAMMPS model deviation step. |\n| GPU     | `dp_run_fp_target`         | Prepare the structures for the VASP calculation and prepare a tarball for transfer. |\n| CPU     | `dp_run_fp_input`          | Collect the tarball of structures from the GPU machine.      |\n| CPU     | `dp_run_fp_target`         | Collect the structures from the GPU machine, then prepare the input files for the VASP calculation. |\n| CPU     | `dp_run_fp_done_target`    | Collect the VASP results and prepare for transfer.           |\n| GPU     | `dp_run_fp_collect2`       | Collect VASP results from the CPU machine, then prepare the training data for the next iteration. |\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fchazeon%2Fdpgen-snakemake","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fchazeon%2Fdpgen-snakemake","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fchazeon%2Fdpgen-snakemake/lists"}