├── .github └── workflows │ └── CI.yml ├── .gitignore ├── LICENSE ├── README.md ├── examples ├── data │ ├── ala15_folded.xyz │ ├── ethanol.npz │ └── sapt10k.zip ├── evaluate_so3lr_on_dataset.ipynb ├── npt_jaxmd.ipynb ├── nvt_jaxmd.ipynb ├── production_run.ipynb └── so3lr_colab_example.ipynb ├── logo.png ├── pyproject.toml ├── so3lr ├── __init__.py ├── ase_utils.py ├── base_calculator.py ├── cli │ ├── md_settings.yaml │ ├── so3lr_cli.py │ ├── so3lr_eval.py │ ├── so3lr_finetune.py │ ├── so3lr_md.py │ └── tune_ewald.py ├── config │ └── finetune.yaml ├── graph.py ├── jaxmd_utils.py ├── jraph_utils.py ├── params │ ├── checkpoints │ │ └── ckpt_5150000 │ │ │ ├── metrics │ │ │ └── metrics │ │ │ └── params │ │ │ ├── _METADATA │ │ │ ├── checkpoint │ │ │ ├── d │ │ │ └── 5edd6d991f93f778ac042c854686f92f │ │ │ ├── manifest.ocdbt │ │ │ └── ocdbt.process_0 │ │ │ ├── d │ │ │ ├── 459c4747977e7ee679aaae25ca79408a │ │ │ ├── 9cbd7d40bf68ed0e4db5da9ba8f7a329 │ │ │ └── e2924edc5eb2af94e5c1bda27081fbb9 │ │ │ └── manifest.ocdbt │ ├── hyperparameters.json │ ├── hyperparameters.yaml │ └── params.pkl ├── potential.py └── prepare_dimer_xyz.py └── tests ├── test_ase.py ├── test_data ├── atat.xyz ├── atat_ase.npz ├── atat_jaxmd.npz ├── bb.xyz ├── bb_ase.npz ├── bb_jaxmd.npz ├── dha.xyz ├── dha_ase.npz ├── dha_jaxmd.npz ├── water_64.xyz ├── water_ase.npz └── water_jaxmd.npz ├── test_jaxmd.py ├── test_potential.py └── test_readme.py /.github/workflows/CI.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/general-molecular-simulations/so3lr/HEAD/.github/workflows/CI.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/general-molecular-simulations/so3lr/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/general-molecular-simulations/so3lr/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/general-molecular-simulations/so3lr/HEAD/README.md -------------------------------------------------------------------------------- /examples/data/ala15_folded.xyz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/general-molecular-simulations/so3lr/HEAD/examples/data/ala15_folded.xyz -------------------------------------------------------------------------------- /examples/data/ethanol.npz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/general-molecular-simulations/so3lr/HEAD/examples/data/ethanol.npz -------------------------------------------------------------------------------- /examples/data/sapt10k.zip: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/general-molecular-simulations/so3lr/HEAD/examples/data/sapt10k.zip -------------------------------------------------------------------------------- /examples/evaluate_so3lr_on_dataset.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/general-molecular-simulations/so3lr/HEAD/examples/evaluate_so3lr_on_dataset.ipynb -------------------------------------------------------------------------------- /examples/npt_jaxmd.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/general-molecular-simulations/so3lr/HEAD/examples/npt_jaxmd.ipynb -------------------------------------------------------------------------------- /examples/nvt_jaxmd.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/general-molecular-simulations/so3lr/HEAD/examples/nvt_jaxmd.ipynb -------------------------------------------------------------------------------- /examples/production_run.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/general-molecular-simulations/so3lr/HEAD/examples/production_run.ipynb -------------------------------------------------------------------------------- /examples/so3lr_colab_example.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/general-molecular-simulations/so3lr/HEAD/examples/so3lr_colab_example.ipynb -------------------------------------------------------------------------------- /logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/general-molecular-simulations/so3lr/HEAD/logo.png -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/general-molecular-simulations/so3lr/HEAD/pyproject.toml -------------------------------------------------------------------------------- /so3lr/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/general-molecular-simulations/so3lr/HEAD/so3lr/__init__.py -------------------------------------------------------------------------------- /so3lr/ase_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/general-molecular-simulations/so3lr/HEAD/so3lr/ase_utils.py -------------------------------------------------------------------------------- /so3lr/base_calculator.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/general-molecular-simulations/so3lr/HEAD/so3lr/base_calculator.py -------------------------------------------------------------------------------- /so3lr/cli/md_settings.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/general-molecular-simulations/so3lr/HEAD/so3lr/cli/md_settings.yaml -------------------------------------------------------------------------------- /so3lr/cli/so3lr_cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/general-molecular-simulations/so3lr/HEAD/so3lr/cli/so3lr_cli.py -------------------------------------------------------------------------------- /so3lr/cli/so3lr_eval.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/general-molecular-simulations/so3lr/HEAD/so3lr/cli/so3lr_eval.py -------------------------------------------------------------------------------- /so3lr/cli/so3lr_finetune.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/general-molecular-simulations/so3lr/HEAD/so3lr/cli/so3lr_finetune.py -------------------------------------------------------------------------------- /so3lr/cli/so3lr_md.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/general-molecular-simulations/so3lr/HEAD/so3lr/cli/so3lr_md.py -------------------------------------------------------------------------------- /so3lr/cli/tune_ewald.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/general-molecular-simulations/so3lr/HEAD/so3lr/cli/tune_ewald.py -------------------------------------------------------------------------------- /so3lr/config/finetune.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/general-molecular-simulations/so3lr/HEAD/so3lr/config/finetune.yaml -------------------------------------------------------------------------------- /so3lr/graph.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/general-molecular-simulations/so3lr/HEAD/so3lr/graph.py -------------------------------------------------------------------------------- /so3lr/jaxmd_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/general-molecular-simulations/so3lr/HEAD/so3lr/jaxmd_utils.py -------------------------------------------------------------------------------- /so3lr/jraph_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/general-molecular-simulations/so3lr/HEAD/so3lr/jraph_utils.py -------------------------------------------------------------------------------- /so3lr/params/checkpoints/ckpt_5150000/metrics/metrics: -------------------------------------------------------------------------------- 1 | {"loss": 0.06745345890522003} -------------------------------------------------------------------------------- /so3lr/params/checkpoints/ckpt_5150000/params/_METADATA: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/general-molecular-simulations/so3lr/HEAD/so3lr/params/checkpoints/ckpt_5150000/params/_METADATA -------------------------------------------------------------------------------- /so3lr/params/checkpoints/ckpt_5150000/params/checkpoint: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/general-molecular-simulations/so3lr/HEAD/so3lr/params/checkpoints/ckpt_5150000/params/checkpoint -------------------------------------------------------------------------------- /so3lr/params/checkpoints/ckpt_5150000/params/d/5edd6d991f93f778ac042c854686f92f: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/general-molecular-simulations/so3lr/HEAD/so3lr/params/checkpoints/ckpt_5150000/params/d/5edd6d991f93f778ac042c854686f92f -------------------------------------------------------------------------------- /so3lr/params/checkpoints/ckpt_5150000/params/manifest.ocdbt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/general-molecular-simulations/so3lr/HEAD/so3lr/params/checkpoints/ckpt_5150000/params/manifest.ocdbt -------------------------------------------------------------------------------- /so3lr/params/checkpoints/ckpt_5150000/params/ocdbt.process_0/d/459c4747977e7ee679aaae25ca79408a: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/general-molecular-simulations/so3lr/HEAD/so3lr/params/checkpoints/ckpt_5150000/params/ocdbt.process_0/d/459c4747977e7ee679aaae25ca79408a -------------------------------------------------------------------------------- /so3lr/params/checkpoints/ckpt_5150000/params/ocdbt.process_0/d/9cbd7d40bf68ed0e4db5da9ba8f7a329: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/general-molecular-simulations/so3lr/HEAD/so3lr/params/checkpoints/ckpt_5150000/params/ocdbt.process_0/d/9cbd7d40bf68ed0e4db5da9ba8f7a329 -------------------------------------------------------------------------------- /so3lr/params/checkpoints/ckpt_5150000/params/ocdbt.process_0/d/e2924edc5eb2af94e5c1bda27081fbb9: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/general-molecular-simulations/so3lr/HEAD/so3lr/params/checkpoints/ckpt_5150000/params/ocdbt.process_0/d/e2924edc5eb2af94e5c1bda27081fbb9 -------------------------------------------------------------------------------- /so3lr/params/checkpoints/ckpt_5150000/params/ocdbt.process_0/manifest.ocdbt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/general-molecular-simulations/so3lr/HEAD/so3lr/params/checkpoints/ckpt_5150000/params/ocdbt.process_0/manifest.ocdbt -------------------------------------------------------------------------------- /so3lr/params/hyperparameters.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/general-molecular-simulations/so3lr/HEAD/so3lr/params/hyperparameters.json -------------------------------------------------------------------------------- /so3lr/params/hyperparameters.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/general-molecular-simulations/so3lr/HEAD/so3lr/params/hyperparameters.yaml -------------------------------------------------------------------------------- /so3lr/params/params.pkl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/general-molecular-simulations/so3lr/HEAD/so3lr/params/params.pkl -------------------------------------------------------------------------------- /so3lr/potential.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/general-molecular-simulations/so3lr/HEAD/so3lr/potential.py -------------------------------------------------------------------------------- /so3lr/prepare_dimer_xyz.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/general-molecular-simulations/so3lr/HEAD/so3lr/prepare_dimer_xyz.py -------------------------------------------------------------------------------- /tests/test_ase.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/general-molecular-simulations/so3lr/HEAD/tests/test_ase.py -------------------------------------------------------------------------------- /tests/test_data/atat.xyz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/general-molecular-simulations/so3lr/HEAD/tests/test_data/atat.xyz -------------------------------------------------------------------------------- /tests/test_data/atat_ase.npz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/general-molecular-simulations/so3lr/HEAD/tests/test_data/atat_ase.npz -------------------------------------------------------------------------------- /tests/test_data/atat_jaxmd.npz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/general-molecular-simulations/so3lr/HEAD/tests/test_data/atat_jaxmd.npz -------------------------------------------------------------------------------- /tests/test_data/bb.xyz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/general-molecular-simulations/so3lr/HEAD/tests/test_data/bb.xyz -------------------------------------------------------------------------------- /tests/test_data/bb_ase.npz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/general-molecular-simulations/so3lr/HEAD/tests/test_data/bb_ase.npz -------------------------------------------------------------------------------- /tests/test_data/bb_jaxmd.npz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/general-molecular-simulations/so3lr/HEAD/tests/test_data/bb_jaxmd.npz -------------------------------------------------------------------------------- /tests/test_data/dha.xyz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/general-molecular-simulations/so3lr/HEAD/tests/test_data/dha.xyz -------------------------------------------------------------------------------- /tests/test_data/dha_ase.npz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/general-molecular-simulations/so3lr/HEAD/tests/test_data/dha_ase.npz -------------------------------------------------------------------------------- /tests/test_data/dha_jaxmd.npz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/general-molecular-simulations/so3lr/HEAD/tests/test_data/dha_jaxmd.npz -------------------------------------------------------------------------------- /tests/test_data/water_64.xyz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/general-molecular-simulations/so3lr/HEAD/tests/test_data/water_64.xyz -------------------------------------------------------------------------------- /tests/test_data/water_ase.npz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/general-molecular-simulations/so3lr/HEAD/tests/test_data/water_ase.npz -------------------------------------------------------------------------------- /tests/test_data/water_jaxmd.npz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/general-molecular-simulations/so3lr/HEAD/tests/test_data/water_jaxmd.npz -------------------------------------------------------------------------------- /tests/test_jaxmd.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/general-molecular-simulations/so3lr/HEAD/tests/test_jaxmd.py -------------------------------------------------------------------------------- /tests/test_potential.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/general-molecular-simulations/so3lr/HEAD/tests/test_potential.py -------------------------------------------------------------------------------- /tests/test_readme.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/general-molecular-simulations/so3lr/HEAD/tests/test_readme.py --------------------------------------------------------------------------------