├── .flake8 ├── .gaspyrc_template.json ├── .gitignore ├── .gitmodules ├── README.md ├── dockerfile ├── Dockerfile └── bashrc_additions.sh ├── examples ├── README.md ├── populate_catalog.py └── update_collections.py ├── gaspy ├── __init__.py ├── atoms_operators.py ├── defaults.py ├── fireworks_helper_scripts.py ├── gasdb.py ├── mongo.py ├── tasks │ ├── __init__.py │ ├── atoms_generators.py │ ├── calculation_finders.py │ ├── core.py │ ├── db_managers │ │ ├── __init__.py │ │ ├── adsorption.py │ │ ├── atoms.py │ │ ├── catalog.py │ │ └── surfaces.py │ ├── make_fireworks.py │ └── metadata_calculators.py ├── tests │ ├── .gaspyrc_template.json │ ├── README.md │ ├── __init__.py │ ├── atoms_operators_test.py │ ├── fireworks_helper_scripts_test.py │ ├── gasdb_test.py │ ├── learning_tests │ │ ├── __init__.py │ │ ├── pymatgen_test.py │ │ └── pytest.ini │ ├── mongo_test.py │ ├── pytest.ini │ ├── regression_baselines │ │ ├── atoms_operators │ │ │ ├── CO_dissociate_Pt12Si5_110_fingerprint.pkl │ │ │ ├── CO_top_Cu_211_fingerprint.pkl │ │ │ ├── OH_desorb_CoSb2_110_fingerprint.pkl │ │ │ ├── OOH_dissociate_Ni4W_001_fingerprint.pkl │ │ │ ├── OOH_hollow_FeNi_001_fingerprint.pkl │ │ │ ├── O_hollow_AlAu2Cu_210_fingerprint.pkl │ │ │ ├── adsorption_vectors_list_for_AlAu2Cu_210.pkl │ │ │ ├── adsorption_vectors_list_for_CoSb2_110.pkl │ │ │ ├── adsorption_vectors_list_for_Cu_211.pkl │ │ │ ├── adsorption_vectors_list_for_FeNi_001.pkl │ │ │ ├── adsorption_vectors_list_for_Ni4W_001.pkl │ │ │ ├── adsorption_vectors_list_for_Pt12Si5_110.pkl │ │ │ ├── bulk_cn_dicts.pkl │ │ │ ├── flipped_AlAu2Cu_210.traj │ │ │ ├── flipped_CoSb2_110.traj │ │ │ ├── flipped_Cu_211.traj │ │ │ ├── flipped_FeNi_001.traj │ │ │ ├── flipped_Ni4W_001.traj │ │ │ ├── flipped_Pt12Si5_110.traj │ │ │ ├── sites_for_AlAu2Cu_210.pkl │ │ │ ├── sites_for_CoSb2_110.pkl │ │ │ ├── sites_for_Cu_211.pkl │ │ │ ├── sites_for_FeNi_001.pkl │ │ │ ├── sites_for_Ni4W_001.pkl │ │ │ ├── sites_for_Pt12Si5_110.pkl │ │ │ ├── slabs_of_mp-30_100.pkl │ │ │ ├── slabs_of_mp-30_111.pkl │ │ │ ├── slabs_of_mp-867306_111.pkl │ │ │ ├── slabs_of_mp-867306_211.pkl │ │ │ ├── surface_sites_for_AlAu2Cu_210.pkl │ │ │ ├── surface_sites_for_CoSb2_110.pkl │ │ │ ├── surface_sites_for_Cu_211.pkl │ │ │ ├── surface_sites_for_FeNi_001.pkl │ │ │ ├── surface_sites_for_Ni4W_001.pkl │ │ │ └── surface_sites_for_Pt12Si5_110.pkl │ │ ├── fireworks_helper_scripts │ │ │ ├── trajhex_for_CO_dissociate_Pt12Si5_110.pkl │ │ │ ├── trajhex_for_CO_top_Cu_211.pkl │ │ │ ├── trajhex_for_C_hollow_AlAu2Cu_210.pkl │ │ │ ├── trajhex_for_OH_desorb_CoSb2_110.pkl │ │ │ ├── trajhex_for_OOH_dissociate_Ni4W_001.pkl │ │ │ ├── trajhex_for_OOH_hollow_FeNi_001.pkl │ │ │ └── trajhex_for_O_hollow_AlAu2Cu_210.pkl │ │ ├── gasdb │ │ │ ├── aggregated_surface_documents_.pkl │ │ │ ├── aggregated_surface_documents_dates.pkl │ │ │ ├── hashed_doc_ignoring_mpid.pkl │ │ │ ├── hashed_doc_ignoring_mpid_top.pkl │ │ │ ├── hashed_doc_ignoring_nothing.pkl │ │ │ ├── unsimulated_catalog_docs_4c23d6bc1d9c3748081486751d059da04bb2cb509af065e7ed7bc7a3.pkl │ │ │ └── unsimulated_catalog_docs_e0ba80c3b932dfe2bf79a4c27ff619971c0a65729acdefaef509002d.pkl │ │ ├── learning_tests │ │ │ └── pymatgen │ │ │ │ ├── Cu_FCC_structure.pkl │ │ │ │ ├── adsorption_sites_for_AlAu2Cu_210.pkl │ │ │ │ ├── adsorption_sites_for_CoSb2_110.pkl │ │ │ │ ├── adsorption_sites_for_Cu_211.pkl │ │ │ │ ├── adsorption_sites_for_FeNi_001.pkl │ │ │ │ ├── adsorption_sites_for_Ni4W_001.pkl │ │ │ │ └── adsorption_sites_for_Pt12Si5_110.pkl │ │ ├── mongo │ │ │ ├── atoms_dict_for_Cu_FCC.pkl │ │ │ ├── atoms_dict_for_Pt_slab.pkl │ │ │ ├── calculator_dict_for_Cu_FCC.pkl │ │ │ └── results_dict_for_Cu_FCC.pkl │ │ └── tasks │ │ │ └── atoms_generators │ │ │ └── slab_docs_Cu_FCC.pkl │ ├── tasks_tests │ │ ├── __init__.py │ │ ├── atoms_generators_test.py │ │ ├── calculation_finders_test.py │ │ ├── core_test.py │ │ ├── db_managers_tests │ │ │ ├── __init__.py │ │ │ ├── adsorption_test.py │ │ │ ├── atoms_test.py │ │ │ ├── catalog_test.py │ │ │ └── surfaces_test.py │ │ ├── make_fireworks_test.py │ │ ├── metadata_calculators_test.py │ │ ├── pytest.ini │ │ └── utils.py │ ├── test_caches │ │ ├── .gitignore │ │ └── mp_stoichs │ │ │ └── .gitignore │ ├── test_cases │ │ ├── __init__.py │ │ ├── adslabs │ │ │ ├── CO_dissociate_Pt12Si5_110.traj │ │ │ ├── CO_top_Cu_211.traj │ │ │ ├── OH_desorb_CoSb2_110.traj │ │ │ ├── OOH_dissociate_Ni4W_001.traj │ │ │ ├── OOH_hollow_FeNi_001.traj │ │ │ └── O_hollow_AlAu2Cu_210.traj │ │ ├── bulk_atoms_of_slabs │ │ │ ├── AlAu2Cu.pkl │ │ │ ├── CoSb2.pkl │ │ │ ├── Cu.pkl │ │ │ ├── FeNi.pkl │ │ │ ├── Ni4W.pkl │ │ │ └── Pt12Si5.pkl │ │ ├── bulks │ │ │ └── Cu_FCC.traj │ │ ├── fireworks │ │ │ ├── 353727.pkl │ │ │ ├── 4573.pkl │ │ │ └── 74480.pkl │ │ ├── launches_backup_directory │ │ │ └── 101392.tar.gz │ │ ├── mongo_test_collections │ │ │ ├── __init__.py │ │ │ ├── mongo_utils.py │ │ │ ├── unit_testing_adsorption_docs.pkl │ │ │ ├── unit_testing_atoms_docs.pkl │ │ │ ├── unit_testing_catalog_docs.pkl │ │ │ └── unit_testing_surface_energy_docs.pkl │ │ ├── relaxed │ │ │ └── Pt_slab.traj │ │ ├── slabs │ │ │ ├── AlAu2Cu_210.traj │ │ │ ├── CoSb2_110.traj │ │ │ ├── Cu_211.traj │ │ │ ├── FeNi_001.traj │ │ │ ├── Ni4W_001.traj │ │ │ └── Pt12Si5_110.traj │ │ └── utils.py │ └── utils_test.py ├── utils.py └── vasp_functions.py ├── license.txt ├── logs └── .gitignore ├── maintenance ├── README.md └── clean_up_fw.sh ├── open_container_via_docker.sh └── open_container_via_shifter.sh /.flake8: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ulissigroup/GASpy/HEAD/.flake8 -------------------------------------------------------------------------------- /.gaspyrc_template.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ulissigroup/GASpy/HEAD/.gaspyrc_template.json 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