{"id":38335410,"url":"https://github.com/cedergrouphub/multifil","last_synced_at":"2026-01-17T02:55:55.776Z","repository":{"id":95061403,"uuid":"113913751","full_name":"CederGroupHub/MultiFil","owner":"CederGroupHub","description":"High Throughput PathFinder and ApproxNEB repo","archived":false,"fork":false,"pushed_at":"2017-12-11T22:34:28.000Z","size":33,"stargazers_count":5,"open_issues_count":0,"forks_count":0,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-09-09T23:38:54.468Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"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/CederGroupHub.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,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2017-12-11T22:07:26.000Z","updated_at":"2025-08-16T11:35:44.000Z","dependencies_parsed_at":"2023-03-10T22:46:09.782Z","dependency_job_id":null,"html_url":"https://github.com/CederGroupHub/MultiFil","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/CederGroupHub/MultiFil","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CederGroupHub%2FMultiFil","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CederGroupHub%2FMultiFil/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CederGroupHub%2FMultiFil/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CederGroupHub%2FMultiFil/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/CederGroupHub","download_url":"https://codeload.github.com/CederGroupHub/MultiFil/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CederGroupHub%2FMultiFil/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28492591,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-17T02:39:23.645Z","status":"ssl_error","status_checked_at":"2026-01-17T02:34:19.649Z","response_time":85,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":[],"created_at":"2026-01-17T02:55:55.153Z","updated_at":"2026-01-17T02:55:55.771Z","avatar_url":"https://github.com/CederGroupHub.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# How to use high-throughput migration calculation machine\n\n\n\n### Citation\n\nIf you are using the codes in this repo, please consider citing the following work:\n\nRong, Z., et al., *An efficient algorithm for finding the minimum energy path for cation migration in ionic materials.* The Journal of Chemical Physics, 2016. 145(7): p. 074112.\n\n---\n\n### Setup external computational environment\n\n1. Setup a personal MongoDB database. Update access confidentiality in `settings/db_config.yaml`\n2. Install Materials Project [MPWorks](https://github.com/materialsproject/MPWorks) \nin the computation clusters to be deployed for the HT calculations.\n3. Install the following dependency packages locally and familiarize yourself with them:\n    * [pymatgen](https://github.com/materialsproject/pymatgen)\n    * [custodian](https://github.com/materialsproject/custodian)\n    * [fireworks](https://github.com/materialsproject/fireworks)\n4. Go through the files under settings and overwrite the variables where necessary\n \n\n### Deploy PathFinder HT calculations\n1. Prepare an input file in the format like `production/Mg_PF_example.txt`\n2. Run script `production/pf_production.py`\n3. Set up a crontab job to run script like `production/crontab.qlaunch.sh` regularly at the \ndesired frequency at the calculation clusters.\n\n## Deploy ApproxNEB HT calculations\n1. Prepare an input file in the format like `production/Mg_approx_neb_example.txt`, first column being the **mp-id**, \nsecond column being the **pair_index** defined in the database.\n2. Set parameters and run script `production/approx_neb_production.py`, be noted, it is supposed to run a two-phase calculations, with\nthe first phase calculating just 2 images (image 0 and image 4, the middle image), and arrive at a lower bound for the migration\n energy, if the migration energy lower bound is smaller than a threshold, then those paths are filtered out for further full MEP\n calculations. These 2 phases can be switched the adjusting the **calculated_images** parameter in `production/approx_neb_production.py`\n script. \n3. Set up a crontab job to run script like `production/crontab.qlaunch.sh` regularly at the \ndesired frequency at the calculation clusters.\n\n### Post calculation\nAfter the HT ApproxNEB calculation is finished, do the following steps:\n1. Backup the calculation files. (I do it in Vega)\n2. Update the calculation file path in the database after files migrations with script like `post_production/db_scripts/update_file_path_vega.py`\n3. Update the CONTCARs of each calculated image with script like `post_production/db_scripts/update_contcar.py`\n\n## Results Analysis\n* After the first-phase HT ApproxNEB calculation, please run `post_production/first_tier_filter.py` to print out the results.\n* After the second-phase HT ApproxNEB calculation, please run `post_production/full_mep_results.py` to print out the results.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcedergrouphub%2Fmultifil","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcedergrouphub%2Fmultifil","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcedergrouphub%2Fmultifil/lists"}