├── .gitignore ├── LICENSE ├── README.md ├── cov.xml ├── docs ├── Makefile ├── build │ ├── .buildinfo │ ├── .doctrees │ │ ├── api │ │ │ ├── index.doctree │ │ │ ├── loaders.doctree │ │ │ ├── maths.doctree │ │ │ ├── models │ │ │ │ ├── ace.doctree │ │ │ │ ├── gap.doctree │ │ │ │ ├── index.doctree │ │ │ │ └── snap.doctree │ │ │ └── optimisers.doctree │ │ ├── environment.pickle │ │ ├── examples.doctree │ │ ├── faq.doctree │ │ ├── index.doctree │ │ ├── nbsphinx │ │ │ └── notebooks │ │ │ │ └── ace_optimise.ipynb │ │ ├── notebooks │ │ │ └── ace_optimise.doctree │ │ └── quickstart.doctree │ ├── _sources │ │ ├── api │ │ │ ├── index.rst.txt │ │ │ ├── loaders.rst.txt │ │ │ ├── maths.rst.txt │ │ │ ├── models │ │ │ │ ├── ace.rst.txt │ │ │ │ ├── gap.rst.txt │ │ │ │ ├── index.rst.txt │ │ │ │ └── snap.rst.txt │ │ │ └── optimisers.rst.txt │ │ ├── examples.rst.txt │ │ ├── faq.rst.txt │ │ ├── index.rst.txt │ │ ├── notebooks │ │ │ └── ace_optimise.ipynb.txt │ │ └── quickstart.rst.txt │ ├── _static │ │ ├── basic.css │ │ ├── debug.css │ │ ├── doctools.js │ │ ├── documentation_options.js │ │ ├── file.png │ │ ├── language_data.js │ │ ├── minus.png │ │ ├── nbsphinx-broken-thumbnail.svg │ │ ├── nbsphinx-code-cells.css │ │ ├── nbsphinx-gallery.css │ │ ├── nbsphinx-no-thumbnail.svg │ │ ├── plus.png │ │ ├── pygments.css │ │ ├── scripts │ │ │ ├── furo-extensions.js │ │ │ ├── furo.js │ │ │ ├── furo.js.LICENSE.txt │ │ │ └── furo.js.map │ │ ├── searchtools.js │ │ ├── skeleton.css │ │ ├── sphinx_highlight.js │ │ └── styles │ │ │ ├── furo-extensions.css │ │ │ ├── furo-extensions.css.map │ │ │ ├── furo.css │ │ │ └── furo.css.map │ ├── api │ │ ├── index.html │ │ ├── loaders.html │ │ ├── maths.html │ │ ├── models │ │ │ ├── ace.html │ │ │ ├── gap.html │ │ │ ├── index.html │ │ │ └── snap.html │ │ └── optimisers.html │ ├── examples.html │ ├── faq.html │ ├── genindex.html │ ├── html │ │ ├── .buildinfo │ │ ├── .doctrees │ │ │ ├── api │ │ │ │ ├── index.doctree │ │ │ │ ├── loaders.doctree │ │ │ │ ├── maths.doctree │ │ │ │ ├── models │ │ │ │ │ ├── ace.doctree │ │ │ │ │ ├── gap.doctree │ │ │ │ │ ├── index.doctree │ │ │ │ │ └── snap.doctree │ │ │ │ └── optimisers.doctree │ │ │ ├── environment.pickle │ │ │ ├── examples.doctree │ │ │ ├── faq.doctree │ │ │ ├── index.doctree │ │ │ ├── nbsphinx │ │ │ │ └── notebooks │ │ │ │ │ └── ace_optimise.ipynb │ │ │ ├── notebooks │ │ │ │ └── ace_optimise.doctree │ │ │ └── quickstart.doctree │ │ ├── _sources │ │ │ ├── api │ │ │ │ ├── index.rst.txt │ │ │ │ ├── loaders.rst.txt │ │ │ │ ├── maths.rst.txt │ │ │ │ ├── models │ │ │ │ │ ├── ace.rst.txt │ │ │ │ │ ├── gap.rst.txt │ │ │ │ │ ├── index.rst.txt │ │ │ │ │ └── snap.rst.txt │ │ │ │ └── optimisers.rst.txt │ │ │ ├── examples.rst.txt │ │ │ ├── faq.rst.txt │ │ │ ├── index.rst.txt │ │ │ ├── notebooks │ │ │ │ └── ace_optimise.ipynb.txt │ │ │ └── quickstart.rst.txt │ │ ├── _static │ │ │ ├── basic.css │ │ │ ├── debug.css │ │ │ ├── doctools.js │ │ │ ├── documentation_options.js │ │ │ ├── file.png │ │ │ ├── language_data.js │ │ │ ├── minus.png │ │ │ ├── nbsphinx-broken-thumbnail.svg │ │ │ ├── nbsphinx-code-cells.css │ │ │ ├── nbsphinx-gallery.css │ │ │ ├── nbsphinx-no-thumbnail.svg │ │ │ ├── plus.png │ │ │ ├── pygments.css │ │ │ ├── scripts │ │ │ │ ├── furo-extensions.js │ │ │ │ ├── furo.js │ │ │ │ ├── furo.js.LICENSE.txt │ │ │ │ └── furo.js.map │ │ │ ├── searchtools.js │ │ │ ├── skeleton.css │ │ │ ├── sphinx_highlight.js │ │ │ ├── styles │ │ │ │ ├── furo-extensions.css │ │ │ │ ├── furo-extensions.css.map │ │ │ │ ├── furo.css │ │ │ │ └── furo.css.map │ │ │ └── xpot-logo.png │ │ ├── api │ │ │ ├── index.html │ │ │ ├── loaders.html │ │ │ ├── maths.html │ │ │ ├── models │ │ │ │ ├── ace.html │ │ │ │ ├── gap.html │ │ │ │ ├── index.html │ │ │ │ └── snap.html │ │ │ └── optimisers.html │ │ ├── examples.html │ │ ├── faq.html │ │ ├── genindex.html │ │ ├── index.html │ │ ├── notebooks │ │ │ ├── ace_optimise.html │ │ │ └── ace_optimise.ipynb │ │ ├── objects.inv │ │ ├── py-modindex.html │ │ ├── quickstart.html │ │ ├── search.html │ │ └── searchindex.js │ ├── index.html │ ├── notebooks │ │ ├── ace_optimise.html │ │ └── ace_optimise.ipynb │ ├── objects.inv │ ├── py-modindex.html │ ├── quickstart.html │ ├── search.html │ └── searchindex.js ├── make.bat └── source │ ├── api │ ├── index.rst │ ├── loaders.rst │ ├── maths.rst │ ├── models │ │ ├── ace.rst │ │ ├── gap.rst │ │ ├── index.rst │ │ └── snap.rst │ └── optimisers.rst │ ├── conf.py │ ├── examples.rst │ ├── faq.rst │ ├── index.rst │ ├── notebooks │ └── ace_optimise.ipynb │ └── quickstart.rst ├── examples ├── ace_input.hjson ├── ace_optimise.ipynb ├── ace_optimise.py ├── gap_C_XYZ │ ├── bulk_cryst_train.xyz │ ├── bulk_cryst_train.xyz.idx │ └── suft_amo_test.xyz ├── gap_input.hjson ├── gap_optimise.ipynb ├── opt_ACE │ └── test_ace │ │ ├── 1 │ │ ├── cycle_metrics.txt │ │ ├── fitting_data_info.pckl.gzip │ │ ├── log.txt │ │ ├── metrics.txt │ │ ├── target_potential.yaml │ │ ├── test_cycle_metrics.txt │ │ ├── test_data_info.pckl.gzip │ │ ├── test_ef-distributions.png │ │ ├── test_ladder_metrics.txt │ │ ├── test_metrics.txt │ │ ├── train_ef-distributions.png │ │ └── xpot-ace.yaml │ │ ├── atomistic_errors.csv │ │ ├── loss_function_errors.csv │ │ └── parameters.csv ├── opt_GAP │ └── test_GAP │ │ ├── 1 │ │ ├── gap.xml │ │ └── gap.xml.sparseX.GAP_2024_2_15_0_11_51_35_3621 │ │ ├── 2 │ │ ├── gap.xml │ │ └── gap.xml.sparseX.GAP_2024_2_15_0_11_52_25_5321 │ │ ├── 3 │ │ ├── gap.xml │ │ └── gap.xml.sparseX.GAP_2024_2_15_0_11_52_53_5031 │ │ ├── 4 │ │ ├── gap.xml │ │ └── gap.xml.sparseX.GAP_2024_2_15_0_11_53_49_1601 │ │ ├── 5 │ │ ├── gap.xml │ │ └── gap.xml.sparseX.GAP_2024_2_15_0_11_54_36_3531 │ │ ├── 6 │ │ ├── gap.xml │ │ └── gap.xml.sparseX.GAP_2024_2_15_0_11_55_17_2831 │ │ ├── 7 │ │ ├── gap.xml │ │ └── gap.xml.sparseX.GAP_2024_2_15_0_11_55_42_1511 │ │ ├── 8 │ │ ├── gap.xml │ │ └── gap.xml.sparseX.GAP_2024_2_15_0_11_56_8_4181 │ │ ├── 9 │ │ ├── gap.xml │ │ └── gap.xml.sparseX.GAP_2024_2_15_0_11_56_36_5271 │ │ ├── 10 │ │ ├── gap.xml │ │ └── gap.xml.sparseX.GAP_2024_2_15_0_11_57_6_4491 │ │ ├── atomistic_errors.csv │ │ ├── atomistic_errors_final │ │ ├── loss_function_errors.csv │ │ ├── loss_function_errors_final │ │ ├── parameters.csv │ │ └── parameters_final ├── snap-optimization │ ├── py-xpot.py │ └── snap_input_updated.hjson ├── snap_input.hjson ├── snap_optimise.ipynb ├── snap_optimise.py └── xpot-v1.2 │ ├── ace_input.hjson │ ├── ace_optimise.ipynb │ ├── gap_input.hjson │ ├── gap_optimise.ipynb │ ├── snap_input.hjson │ ├── snap_optimise.ipynb │ └── snap_optimise.py ├── images └── xpot-logo.png ├── paper-data ├── JCP-2023 │ ├── C-GAP-17 │ │ ├── SNAP │ │ │ ├── j3_l_gap17.hjson │ │ │ ├── j4_l_gap17.hjson │ │ │ ├── j5_l_gap17.hjson │ │ │ └── j6_l_gap17.hjson │ │ ├── qSNAP │ │ │ ├── j3_q_gap17.hjson │ │ │ ├── j4_q_gap17.hjson │ │ │ ├── j5_q_gap17.hjson │ │ │ └── j6_q_gap17_var_cut.hjson │ │ └── test-set-opt │ │ │ ├── best_j5_md.in │ │ │ ├── best_j5_orig.in │ │ │ ├── best_j5_rand.in │ │ │ ├── in_C_q_j5_md.hjson │ │ │ ├── in_C_q_j5_orig_test.hjson │ │ │ ├── in_C_q_j5_random.hjson │ │ │ └── test_sets │ │ │ ├── high_t_md_test.xyz │ │ │ └── test_random_spheres.xyz │ └── Zuo_2020 │ │ ├── cu │ │ └── in_cu_q_j6.hjson │ │ ├── ge │ │ └── in_ge_q_j6.hjson │ │ ├── li │ │ └── in_li_q_j6.hjson │ │ ├── mo │ │ └── in_mo_q_j6.hjson │ │ ├── ni │ │ └── in_ni_q_j6.hjson │ │ ├── py-xpot.py │ │ └── si │ │ └── in_si_q_j8.hjson └── JCTC-2024 │ ├── Sb2Te3 │ ├── Sb2Te3-900.hjson │ └── XPOT-Sb2Te3.yace │ └── Si │ ├── XPOT-ACE-1.hjson │ ├── XPOT-ACE-2.hjson │ ├── XPOT-ACE-3.hjson │ ├── XPOT-ACE-4.hjson │ └── XPOT-Si.yace ├── pyproject.toml ├── src ├── .DS_Store ├── README.md └── xpot │ ├── __init__.py │ ├── convert.py │ ├── graphing.py │ ├── loaders.py │ ├── maths.py │ ├── models │ ├── __init__.py │ ├── ace.py │ ├── defaults │ │ ├── ace_defaults.json │ │ ├── gap_defaults.json │ │ ├── grace_defaults.json │ │ ├── mace_defaults.json │ │ ├── nequip_defaults.json │ │ └── snap_defaults.json │ ├── gap.py │ ├── model.py │ └── snap.py │ ├── optimiser.py │ ├── testing.ipynb │ └── workflows.py └── tests ├── inputs ├── defaults.json ├── hypers.hjson ├── mace-test.xyz ├── mace-train.xyz ├── nequip-train.xyz ├── nequip-train.xyz.idx ├── test-test.xyz ├── test-test.xyz.idx ├── test-test.xyz.pkl.gzip ├── test.xyz ├── test.xyz.pkl.gzip ├── test.xyz.pkl.gzip.xyz ├── train-test.xyz ├── train-test.xyz.idx └── train-test.xyz.pkl.gzip ├── mock_runs ├── atomistic_errors.csv ├── loss_function_errors.csv ├── parameters.csv └── test_models │ ├── ace-input.hjson │ ├── gap-input.hjson │ ├── mace-input.hjson │ ├── nequip-input.hjson │ └── snap-input.hjson ├── test_convert.py ├── test_loaders.py ├── test_maths.py ├── test_models.py ├── test_optimiser.py └── test_workflows.py /.gitignore: -------------------------------------------------------------------------------- 1 | **/__pycache__/ 2 | -------------------------------------------------------------------------------- /LICENSE: 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