├── .gitignore ├── LICENSE ├── Pipfile ├── Pipfile.lock ├── README.ja.md ├── README.md ├── condaenv.yaml ├── docs ├── Makefile ├── make.bat └── source │ ├── _templates │ └── autosummary │ │ └── class.rst │ ├── conf.py │ ├── description.rst │ ├── example.rst │ ├── extend.rst │ ├── index.rst │ ├── install.rst │ ├── modules │ ├── dataset.rst │ ├── format.rst │ ├── index.rst │ ├── model.rst │ ├── preprocess.rst │ ├── training.rst │ └── utils.rst │ └── usage.rst ├── examples ├── prediction_config.py └── training_config.py ├── hdnnpy ├── __init__.py ├── __main__.py ├── _version.py ├── cli │ ├── __init__.py │ ├── configurables.py │ ├── conversion_application.py │ ├── main.py │ ├── prediction_application.py │ └── training_application.py ├── dataset │ ├── __init__.py │ ├── atomic_structure.py │ ├── dataset_generator.py │ ├── descriptor │ │ ├── __init__.py │ │ ├── descriptor_dataset_base.py │ │ ├── symmetry_function_dataset.py │ │ └── weighted_symmetry_function_dataset.py │ ├── hdnnp_dataset.py │ └── property │ │ ├── __init__.py │ │ ├── interatomic_potential_dataset.py │ │ └── property_dataset_base.py ├── format │ ├── __init__.py │ └── xyz.py ├── model │ ├── __init__.py │ └── models.py ├── preprocess │ ├── __init__.py │ ├── pca.py │ ├── preprocess_base.py │ ├── scaling.py │ └── standardization.py ├── training │ ├── __init__.py │ ├── extensions.py │ ├── loss_function │ │ ├── __init__.py │ │ ├── first.py │ │ ├── loss_functions_base.py │ │ ├── potential.py │ │ └── zeroth.py │ ├── manager.py │ └── updater.py └── utils.py ├── readthedocs.yml ├── requirements.txt ├── scripts ├── merge_xyz ├── outcar2xyz └── poscars2xyz └── setup.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/LICENSE -------------------------------------------------------------------------------- /Pipfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/Pipfile -------------------------------------------------------------------------------- /Pipfile.lock: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/Pipfile.lock -------------------------------------------------------------------------------- /README.ja.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/README.ja.md -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/README.md -------------------------------------------------------------------------------- /condaenv.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/condaenv.yaml -------------------------------------------------------------------------------- /docs/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/docs/Makefile -------------------------------------------------------------------------------- /docs/make.bat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/docs/make.bat -------------------------------------------------------------------------------- /docs/source/_templates/autosummary/class.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/docs/source/_templates/autosummary/class.rst -------------------------------------------------------------------------------- /docs/source/conf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/docs/source/conf.py -------------------------------------------------------------------------------- /docs/source/description.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/docs/source/description.rst -------------------------------------------------------------------------------- /docs/source/example.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/docs/source/example.rst -------------------------------------------------------------------------------- /docs/source/extend.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/docs/source/extend.rst -------------------------------------------------------------------------------- /docs/source/index.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/docs/source/index.rst -------------------------------------------------------------------------------- /docs/source/install.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/docs/source/install.rst -------------------------------------------------------------------------------- /docs/source/modules/dataset.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/docs/source/modules/dataset.rst -------------------------------------------------------------------------------- /docs/source/modules/format.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/docs/source/modules/format.rst -------------------------------------------------------------------------------- /docs/source/modules/index.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/docs/source/modules/index.rst -------------------------------------------------------------------------------- /docs/source/modules/model.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/docs/source/modules/model.rst -------------------------------------------------------------------------------- /docs/source/modules/preprocess.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/docs/source/modules/preprocess.rst -------------------------------------------------------------------------------- /docs/source/modules/training.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/docs/source/modules/training.rst -------------------------------------------------------------------------------- /docs/source/modules/utils.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/docs/source/modules/utils.rst -------------------------------------------------------------------------------- /docs/source/usage.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/docs/source/usage.rst -------------------------------------------------------------------------------- /examples/prediction_config.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/examples/prediction_config.py -------------------------------------------------------------------------------- /examples/training_config.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/examples/training_config.py -------------------------------------------------------------------------------- /hdnnpy/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/hdnnpy/__init__.py -------------------------------------------------------------------------------- /hdnnpy/__main__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/hdnnpy/__main__.py -------------------------------------------------------------------------------- /hdnnpy/_version.py: -------------------------------------------------------------------------------- 1 | # coding=utf-8 2 | 3 | __version__ = '0.5.1.dev' 4 | -------------------------------------------------------------------------------- /hdnnpy/cli/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/hdnnpy/cli/__init__.py -------------------------------------------------------------------------------- /hdnnpy/cli/configurables.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/hdnnpy/cli/configurables.py -------------------------------------------------------------------------------- /hdnnpy/cli/conversion_application.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/hdnnpy/cli/conversion_application.py -------------------------------------------------------------------------------- /hdnnpy/cli/main.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/hdnnpy/cli/main.py -------------------------------------------------------------------------------- /hdnnpy/cli/prediction_application.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/hdnnpy/cli/prediction_application.py -------------------------------------------------------------------------------- /hdnnpy/cli/training_application.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/hdnnpy/cli/training_application.py -------------------------------------------------------------------------------- /hdnnpy/dataset/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/hdnnpy/dataset/__init__.py -------------------------------------------------------------------------------- /hdnnpy/dataset/atomic_structure.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/hdnnpy/dataset/atomic_structure.py -------------------------------------------------------------------------------- /hdnnpy/dataset/dataset_generator.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/hdnnpy/dataset/dataset_generator.py -------------------------------------------------------------------------------- /hdnnpy/dataset/descriptor/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/hdnnpy/dataset/descriptor/__init__.py -------------------------------------------------------------------------------- /hdnnpy/dataset/descriptor/descriptor_dataset_base.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/hdnnpy/dataset/descriptor/descriptor_dataset_base.py -------------------------------------------------------------------------------- /hdnnpy/dataset/descriptor/symmetry_function_dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/hdnnpy/dataset/descriptor/symmetry_function_dataset.py -------------------------------------------------------------------------------- /hdnnpy/dataset/descriptor/weighted_symmetry_function_dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/hdnnpy/dataset/descriptor/weighted_symmetry_function_dataset.py -------------------------------------------------------------------------------- /hdnnpy/dataset/hdnnp_dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/hdnnpy/dataset/hdnnp_dataset.py -------------------------------------------------------------------------------- /hdnnpy/dataset/property/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/hdnnpy/dataset/property/__init__.py -------------------------------------------------------------------------------- /hdnnpy/dataset/property/interatomic_potential_dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/hdnnpy/dataset/property/interatomic_potential_dataset.py -------------------------------------------------------------------------------- /hdnnpy/dataset/property/property_dataset_base.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/hdnnpy/dataset/property/property_dataset_base.py -------------------------------------------------------------------------------- /hdnnpy/format/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/hdnnpy/format/__init__.py -------------------------------------------------------------------------------- /hdnnpy/format/xyz.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/hdnnpy/format/xyz.py -------------------------------------------------------------------------------- /hdnnpy/model/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/hdnnpy/model/__init__.py -------------------------------------------------------------------------------- /hdnnpy/model/models.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/hdnnpy/model/models.py -------------------------------------------------------------------------------- /hdnnpy/preprocess/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/hdnnpy/preprocess/__init__.py -------------------------------------------------------------------------------- /hdnnpy/preprocess/pca.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/hdnnpy/preprocess/pca.py -------------------------------------------------------------------------------- /hdnnpy/preprocess/preprocess_base.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/hdnnpy/preprocess/preprocess_base.py -------------------------------------------------------------------------------- /hdnnpy/preprocess/scaling.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/hdnnpy/preprocess/scaling.py -------------------------------------------------------------------------------- /hdnnpy/preprocess/standardization.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/hdnnpy/preprocess/standardization.py -------------------------------------------------------------------------------- /hdnnpy/training/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/hdnnpy/training/__init__.py -------------------------------------------------------------------------------- /hdnnpy/training/extensions.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/hdnnpy/training/extensions.py -------------------------------------------------------------------------------- /hdnnpy/training/loss_function/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/hdnnpy/training/loss_function/__init__.py -------------------------------------------------------------------------------- /hdnnpy/training/loss_function/first.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/hdnnpy/training/loss_function/first.py -------------------------------------------------------------------------------- /hdnnpy/training/loss_function/loss_functions_base.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/hdnnpy/training/loss_function/loss_functions_base.py -------------------------------------------------------------------------------- /hdnnpy/training/loss_function/potential.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/hdnnpy/training/loss_function/potential.py -------------------------------------------------------------------------------- /hdnnpy/training/loss_function/zeroth.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/hdnnpy/training/loss_function/zeroth.py -------------------------------------------------------------------------------- /hdnnpy/training/manager.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/hdnnpy/training/manager.py -------------------------------------------------------------------------------- /hdnnpy/training/updater.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/hdnnpy/training/updater.py -------------------------------------------------------------------------------- /hdnnpy/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/hdnnpy/utils.py -------------------------------------------------------------------------------- /readthedocs.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/readthedocs.yml -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/requirements.txt -------------------------------------------------------------------------------- /scripts/merge_xyz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/scripts/merge_xyz -------------------------------------------------------------------------------- /scripts/outcar2xyz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/scripts/outcar2xyz -------------------------------------------------------------------------------- /scripts/poscars2xyz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/scripts/poscars2xyz -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/masayoshi-ogura/HDNNP/HEAD/setup.py --------------------------------------------------------------------------------