├── .github └── workflows │ └── pythonpackage.yml ├── .gitignore ├── ASAP-logo.png ├── LICENSE ├── README.md ├── asaplib ├── __init__.py ├── cli │ ├── __init__.py │ ├── cmd_asap.py │ ├── cmd_cli_options.py │ └── func_asap.py ├── cluster │ ├── __init__.py │ ├── ml_cluster_base.py │ ├── ml_cluster_fit.py │ └── ml_cluster_tools.py ├── compressor │ ├── __init__.py │ ├── cur.py │ ├── fps.py │ ├── reweight.py │ ├── sparsifier.py │ └── split.py ├── data │ ├── __init__.py │ ├── design_matrix.py │ └── xyz.py ├── descriptors │ ├── __init__.py │ ├── atomic_descriptors.py │ ├── atomic_to_global.py │ └── global_descriptors.py ├── fit │ ├── __init__.py │ ├── base.py │ ├── getscore.py │ ├── krr.py │ ├── ridgeregression.py │ └── sparse_krr_wrapper.py ├── hypers │ ├── __init__.py │ ├── hyper_acsf.py │ ├── hyper_soap.py │ └── univeral_length_scales.py ├── io │ ├── __init__.py │ ├── cscope.py │ ├── io_cell.py │ └── io_parse.py ├── kde │ ├── __init__.py │ ├── density_estimation.py │ └── density_estimation_internal.py ├── kernel │ ├── __init__.py │ ├── kernel_transforms.py │ └── ml_kernel_operations.py ├── plot │ ├── __init__.py │ ├── plot_colors.py │ ├── plot_styles.py │ └── plotters.py ├── reducedim │ ├── __init__.py │ ├── dim_reducer.py │ ├── ml_kpca.py │ ├── ml_pca.py │ └── sparse_kpca.py └── util │ ├── __init__.py │ ├── util_fft.py │ └── util_gettcv.py ├── deprecated ├── clustering_deprecated.py ├── frame_select_deprecated.py ├── gen_ACSF_descriptors_deprecated.py ├── gen_CM_descriptors_deprecated.py ├── gen_FCHL19_descriptors_deprecated.py ├── gen_LMBTR_descriptors_deprecated.py ├── gen_soap_descriptors_deprecated.py ├── gen_soap_kmat_deprecated.py ├── kernel_density_estimation_deprecated.py ├── kpca_deprecated.py ├── kpca_for_projection_viewer_deprecated.py ├── kpca_sparse_deprecated.py ├── krr_deprecated.py ├── pca_deprecated.py ├── ridge_regression_deprecated.py ├── tsne_deprecated.py └── umap_reducer_deprecated.py ├── doc ├── Makefile ├── make.bat └── source │ ├── TiO2-ASAP-KPCA.png │ ├── advance.rst │ ├── asaplib.cli.rst │ ├── asaplib.cluster.rst │ ├── asaplib.compressor.rst │ ├── asaplib.data.rst │ ├── asaplib.descriptors.rst │ ├── asaplib.fit.rst │ ├── asaplib.hypers.rst │ ├── asaplib.io.rst │ ├── asaplib.kde.rst │ ├── asaplib.kernel.rst │ ├── asaplib.plot.rst │ ├── asaplib.reducedim.rst │ ├── asaplib.rst │ ├── asaplib.util.rst │ ├── cluster.rst │ ├── conf.py │ ├── example.rst │ ├── fit.rst │ ├── gen_desc.rst │ ├── howto_asaplib.rst │ ├── index.rst │ ├── install.rst │ ├── kde.rst │ ├── map.rst │ ├── modules.rst │ ├── select.rst │ └── tutorials.rst ├── examples ├── B-RSS-train-set │ ├── README.md │ └── sps_all.xyz ├── Lennard-Jones-nucleus │ ├── FCCUBIC.list │ ├── README.md │ └── lj-nucleus.xyz ├── Ni-icosahedral-np │ ├── Ni-icosa.xyz │ └── README.md ├── README.md ├── TiO2-knownphases │ ├── README.md │ └── knownphases.xyz ├── Tungstun-train-set │ ├── README.md │ └── Tungstun_GAP_6.xyz ├── ice-phases │ ├── README.md │ ├── ice-dataset.xyz │ └── ice-properties.dat ├── molecular-photoswitches │ ├── photoswitches.csv │ └── photoswitches.xyz └── singlet-triplet-fission │ ├── README.md │ └── all.xyz ├── install.sh ├── scripts ├── asap_completion.sh ├── cif2xyz.py ├── frame-split.py ├── gen_universal_acsf_hypers.py ├── gen_universal_soap_hypers.py └── get_symmetry.py ├── setup.py └── tests ├── Makefile ├── ice_test.xyz ├── small_molecules-1000.xyz ├── small_molecules-SOAP.xyz ├── test_cli.py ├── test_frame_select.py ├── test_gen_descriptors.py ├── test_kpca.py ├── test_krr_sparse.py ├── test_pca.py └── test_ridge_regression.py /.github/workflows/pythonpackage.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BingqingCheng/ASAP/HEAD/.github/workflows/pythonpackage.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 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