├── .gitattributes ├── .github └── workflows │ ├── Build-with-Nuitka.yml │ ├── pytest.yml │ └── python-publish.yml ├── .gitignore ├── .readthedocs.yml ├── CHANGELOG.md ├── LICENSE ├── MANIFEST.in ├── README.md ├── THIRD_PARTY_NOTICES.md ├── docs ├── Makefile ├── make.bat ├── requirements.txt └── source │ ├── _static │ ├── css │ │ └── custom.css │ └── image │ │ ├── alignment.svg │ │ ├── auto_distance.svg │ │ ├── check.svg │ │ ├── data_range.svg │ │ ├── delete.svg │ │ ├── dft_d3.png │ │ ├── discovery.svg │ │ ├── edit_info.svg │ │ ├── example │ │ ├── display │ │ │ ├── config1.gif │ │ │ ├── config2.gif │ │ │ ├── fps.gif │ │ │ ├── import.gif │ │ │ ├── main.png │ │ │ ├── maxerror.gif │ │ │ ├── mouse.gif │ │ │ ├── play.gif │ │ │ └── save.gif │ │ └── plot_descriptor │ │ │ ├── click_export.png │ │ │ ├── descriptor_scatter_plot.png │ │ │ ├── main_ui.png │ │ │ ├── select_path.png │ │ │ └── select_structure.png │ │ ├── export.svg │ │ ├── export1.svg │ │ ├── find_max.svg │ │ ├── index.svg │ │ ├── information.png │ │ ├── init.svg │ │ ├── interface.png │ │ ├── inverse.svg │ │ ├── open.svg │ │ ├── pan.svg │ │ ├── pen.svg │ │ ├── play.svg │ │ ├── revoke.svg │ │ ├── save.svg │ │ ├── search.svg │ │ ├── show_bond.svg │ │ ├── sparse.svg │ │ ├── toolbar.png │ │ ├── uncheck.svg │ │ ├── view_change.svg │ │ ├── visualization.png │ │ └── xyz.svg │ ├── api │ └── index.rst │ ├── changelog.md │ ├── conf.py │ ├── example │ ├── NEP-display.md │ ├── Plot-descriptor.md │ └── index.rst │ ├── formats.md │ ├── index.rst │ ├── module │ ├── NEP-dataset-display.md │ ├── data-management.md │ ├── index.rst │ ├── make-dataset.md │ └── settings.md │ └── quickstart.md ├── pyproject.toml ├── pyrightconfig.json ├── requirements.txt ├── setup.py ├── src ├── NepTrainKit │ ├── Config │ │ ├── config.sqlite │ │ ├── nep.json │ │ ├── nep89.txt │ │ └── ptable.json │ ├── __init__.py │ ├── config.py │ ├── core │ │ ├── __init__.py │ │ ├── _fastxyz.cp310-win_amd64.pyd │ │ ├── _fastxyz.cpp │ │ ├── calculator.py │ │ ├── card_manager.py │ │ ├── dataset │ │ │ ├── __init__.py │ │ │ ├── database.py │ │ │ ├── manager.py │ │ │ ├── models.py │ │ │ └── services.py │ │ ├── energy_shift.py │ │ ├── fast_float.h │ │ ├── io │ │ │ ├── __init__.py │ │ │ ├── base.py │ │ │ ├── deepmd.py │ │ │ ├── importers.py │ │ │ ├── nep.py │ │ │ ├── registry.py │ │ │ └── sampler.py │ │ ├── message.py │ │ ├── structure.py │ │ ├── torsion_guard_pbc.py │ │ ├── types.py │ │ └── utils.py │ ├── cudart64_12-f95273031fc5ea44cdb37e0a696a1b15.dll │ ├── main.py │ ├── msvcp140-173e0efa998dc33612e518408bfd190c.dll │ ├── nep_cpu.cp310-win_amd64.pyd │ ├── nep_gpu.cp310-win_amd64.pyd │ ├── paths.py │ ├── src.qrc │ ├── src │ │ ├── images │ │ │ ├── alignment.svg │ │ │ ├── auto_distance.svg │ │ │ ├── auto_load.svg │ │ │ ├── check.svg │ │ │ ├── collapse.svg │ │ │ ├── copy_figure.svg │ │ │ ├── data_range.svg │ │ │ ├── dataset.svg │ │ │ ├── defect.svg │ │ │ ├── delete.svg │ │ │ ├── dft_d3.png │ │ │ ├── discovery.svg │ │ │ ├── edit_info.svg │ │ │ ├── enlarge.svg │ │ │ ├── expand.svg │ │ │ ├── export.svg │ │ │ ├── export1.svg │ │ │ ├── find_max.svg │ │ │ ├── fps.svg │ │ │ ├── gpu.svg │ │ │ ├── gpumd.png │ │ │ ├── gpumd_new.png │ │ │ ├── group.svg │ │ │ ├── hide.svg │ │ │ ├── hide_bond.svg │ │ │ ├── index.svg │ │ │ ├── init.svg │ │ │ ├── inverse.svg │ │ │ ├── logo.png │ │ │ ├── logo.svg │ │ │ ├── make.svg │ │ │ ├── open.svg │ │ │ ├── pan.svg │ │ │ ├── pause.svg │ │ │ ├── pen.svg │ │ │ ├── perturb.svg │ │ │ ├── play.svg │ │ │ ├── revoke.svg │ │ │ ├── run.svg │ │ │ ├── save.svg │ │ │ ├── scaling.svg │ │ │ ├── search.svg │ │ │ ├── show.svg │ │ │ ├── show_bond.svg │ │ │ ├── show_nep.svg │ │ │ ├── sort.svg │ │ │ ├── sparse.svg │ │ │ ├── stop.svg │ │ │ ├── supercell.svg │ │ │ ├── uncheck.svg │ │ │ ├── view_change.svg │ │ │ └── xyz.svg │ │ └── qss │ │ │ └── theme.qss │ ├── src_rc.py │ ├── ui │ │ ├── __init__.py │ │ ├── canvas │ │ │ ├── __init__.py │ │ │ ├── base │ │ │ │ ├── __init__.py │ │ │ │ └── canvas.py │ │ │ ├── pyqtgraph │ │ │ │ ├── __init__.py │ │ │ │ ├── canvas.py │ │ │ │ └── structure.py │ │ │ └── vispy │ │ │ │ ├── __init__.py │ │ │ │ ├── canvas.py │ │ │ │ └── structure.py │ │ ├── dialogs.py │ │ ├── messages.py │ │ ├── pages │ │ │ ├── __init__.py │ │ │ ├── data_manager.py │ │ │ ├── makedata.py │ │ │ ├── settings.py │ │ │ └── show_nep.py │ │ ├── threads.py │ │ ├── update.py │ │ ├── updater.py │ │ ├── views │ │ │ ├── __init__.py │ │ │ ├── _card │ │ │ │ ├── __init__.py │ │ │ │ ├── card_group.py │ │ │ │ ├── cell_scaling_card.py │ │ │ │ ├── cell_strain_card.py │ │ │ │ ├── fps_filter_card.py │ │ │ │ ├── interstitial_adsorbate_card.py │ │ │ │ ├── magmom_rotation_card.py │ │ │ │ ├── organic_mol_config_pbc_card.py │ │ │ │ ├── perturb_card.py │ │ │ │ ├── random_doping_card.py │ │ │ │ ├── random_slab_card.py │ │ │ │ ├── random_vacancy_card.py │ │ │ │ ├── shear_angle_card.py │ │ │ │ ├── shear_matrix_card.py │ │ │ │ ├── stacking_fault_card.py │ │ │ │ ├── super_cell_card.py │ │ │ │ ├── vacancy_defect_card.py │ │ │ │ └── vibration_perturb_card.py │ │ │ ├── cards.py │ │ │ ├── dataset_widget.py │ │ │ ├── nep.py │ │ │ ├── project_view.py │ │ │ ├── structure.py │ │ │ └── toolbar.py │ │ └── widgets │ │ │ ├── __init__.py │ │ │ ├── button.py │ │ │ ├── card_widget.py │ │ │ ├── completer.py │ │ │ ├── dialog.py │ │ │ ├── docker.py │ │ │ ├── doping_rule.py │ │ │ ├── input.py │ │ │ ├── label.py │ │ │ ├── layout.py │ │ │ ├── search_widget.py │ │ │ ├── settingscard.py │ │ │ ├── table.py │ │ │ ├── tree.py │ │ │ └── vacancy_rule.py │ ├── update.exe │ ├── upx.exe │ ├── utils.py │ ├── vcomp140-55aba23cdcd6484fbb06f4155b8ca75a.dll │ └── version.py ├── nep_cpu │ ├── README.md │ ├── dftd3para.h │ ├── nep.cpp │ ├── nep.h │ └── nep_cpu.cpp └── nep_gpu │ ├── README.md │ ├── main_nep │ ├── dataset.cu │ ├── dataset.cuh │ ├── fitness.cu │ ├── fitness.cuh │ ├── main.cu │ ├── mic.cuh │ ├── nep.cu │ ├── nep.cuh │ ├── nep_charge.cu │ ├── nep_charge.cuh │ ├── parameters.cu │ ├── parameters.cuh │ ├── potential.cuh │ ├── snes.cu │ ├── snes.cuh │ ├── structure.cu │ ├── structure.cuh │ ├── tnep.cu │ └── tnep.cuh │ ├── nep_desc.cu │ ├── nep_desc.cuh │ ├── nep_gpu.cu │ ├── nep_parameters.cu │ ├── nep_parameters.cuh │ └── utilities │ ├── common.cuh │ ├── cusolver_wrapper.cu │ ├── cusolver_wrapper.cuh │ ├── error.cu │ ├── error.cuh │ ├── gnep_utilities.cuh │ ├── gpu_macro.cuh │ ├── gpu_vector.cuh │ ├── least_square.cuh │ ├── main_common.cu │ ├── main_common.cuh │ ├── nep_utilities.cuh │ ├── read_file.cu │ └── read_file.cuh ├── tests ├── data │ ├── Si2.vasp │ ├── dipole │ │ ├── nep.txt │ │ └── train.xyz │ ├── nep │ │ ├── descriptor.npy │ │ ├── energy.npy │ │ ├── forces.npy │ │ ├── nep.txt │ │ ├── train.xyz │ │ └── virial.npy │ └── polarizability │ │ ├── nep.txt │ │ └── train.xyz ├── test_base.py ├── test_calculator.py ├── test_card.py ├── test_nep.py ├── test_structure.py └── test_utils.py └── tools ├── dimensionality_reduction.py ├── plot_descriptor.py └── xyz2dp.py /.gitattributes: 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