BUCToolkit 1.0b0__py3-none-any.whl

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Files changed (88) hide show
  1. BUCToolkit/BatchGenerate/CheckStructures.py +198 -0
  2. BUCToolkit/BatchGenerate/__init__.py +6 -0
  3. BUCToolkit/BatchGenerate/coords_interp.py +127 -0
  4. BUCToolkit/BatchGenerate/initial_ads_structures.py +351 -0
  5. BUCToolkit/BatchGenerate/random_replace.py +88 -0
  6. BUCToolkit/BatchMC/MetropolisMC.py +210 -0
  7. BUCToolkit/BatchMC/_BaseMC.py +863 -0
  8. BUCToolkit/BatchMC/__init__.py +8 -0
  9. BUCToolkit/BatchMD/BiasedMD.py +276 -0
  10. BUCToolkit/BatchMD/NVE.py +92 -0
  11. BUCToolkit/BatchMD/NVT.py +510 -0
  12. BUCToolkit/BatchMD/_BaseMD.py +1251 -0
  13. BUCToolkit/BatchMD/__init__.py +18 -0
  14. BUCToolkit/BatchMD/constrained_md/BiasedMD.py +273 -0
  15. BUCToolkit/BatchMD/constrained_md/ConstrNVE.py +169 -0
  16. BUCToolkit/BatchMD/constrained_md/ConstrNVT.py +462 -0
  17. BUCToolkit/BatchMD/constrained_md/NVE.py +78 -0
  18. BUCToolkit/BatchMD/constrained_md/NVT.py +346 -0
  19. BUCToolkit/BatchMD/constrained_md/_BaseMD.py +440 -0
  20. BUCToolkit/BatchMD/constrained_md/_ConstrBaseMD.py +607 -0
  21. BUCToolkit/BatchMD/constrained_md/__init__.py +18 -0
  22. BUCToolkit/BatchOptim/TS/CI_NEB.py +286 -0
  23. BUCToolkit/BatchOptim/TS/Dimer.py +950 -0
  24. BUCToolkit/BatchOptim/TS/__init__.py +10 -0
  25. BUCToolkit/BatchOptim/_BaseOpt.py +702 -0
  26. BUCToolkit/BatchOptim/__init__.py +22 -0
  27. BUCToolkit/BatchOptim/_utils/__init__.py +6 -0
  28. BUCToolkit/BatchOptim/_utils/_line_search.py +972 -0
  29. BUCToolkit/BatchOptim/_utils/_warnings.py +11 -0
  30. BUCToolkit/BatchOptim/frequency.py +496 -0
  31. BUCToolkit/BatchOptim/minimize/CG.py +256 -0
  32. BUCToolkit/BatchOptim/minimize/FIRE.py +310 -0
  33. BUCToolkit/BatchOptim/minimize/QN.py +205 -0
  34. BUCToolkit/BatchOptim/minimize/__init__.py +17 -0
  35. BUCToolkit/BatchStructures/BatchStructuresBase.py +2261 -0
  36. BUCToolkit/BatchStructures/StructuresIO.py +1394 -0
  37. BUCToolkit/BatchStructures/__init__.py +15 -0
  38. BUCToolkit/Preprocessing/__init__.py +7 -0
  39. BUCToolkit/Preprocessing/load_files.py +1680 -0
  40. BUCToolkit/Preprocessing/preprocessing.py +923 -0
  41. BUCToolkit/Preprocessing/sampling.py +299 -0
  42. BUCToolkit/Preprocessing/supercells.py +140 -0
  43. BUCToolkit/Preprocessing/write_files.py +524 -0
  44. BUCToolkit/StandardTemplate.py +417 -0
  45. BUCToolkit/__init__.py +33 -0
  46. BUCToolkit/_version.py +7 -0
  47. BUCToolkit/api/ConstrainedMolecularDynamics.py +347 -0
  48. BUCToolkit/api/DataLoaders.py +321 -0
  49. BUCToolkit/api/Losses.py +170 -0
  50. BUCToolkit/api/Metrics.py +84 -0
  51. BUCToolkit/api/ModelOptims.py +296 -0
  52. BUCToolkit/api/MolecularDynamics.py +282 -0
  53. BUCToolkit/api/MonteCarlo.py +280 -0
  54. BUCToolkit/api/NEB.py +325 -0
  55. BUCToolkit/api/Predictor.py +292 -0
  56. BUCToolkit/api/StructureOptimization.py +484 -0
  57. BUCToolkit/api/Trainer.py +635 -0
  58. BUCToolkit/api/VibrationAnalysis.py +279 -0
  59. BUCToolkit/api/__init__.py +38 -0
  60. BUCToolkit/api/_io.py +1026 -0
  61. BUCToolkit/cli/__init__.py +20 -0
  62. BUCToolkit/cli/cli.py +934 -0
  63. BUCToolkit/cli/input_stub.py +140 -0
  64. BUCToolkit/cli/main.py +368 -0
  65. BUCToolkit/cli/print_logo.py +149 -0
  66. BUCToolkit/cli/template_model.py +6 -0
  67. BUCToolkit/io.py +30 -0
  68. BUCToolkit/utils/AtomSelector.py +64 -0
  69. BUCToolkit/utils/AtomicNumber2Properties.py +39 -0
  70. BUCToolkit/utils/ElemListReduce.py +52 -0
  71. BUCToolkit/utils/Ewald.py +210 -0
  72. BUCToolkit/utils/IrregularTensorReformat.py +59 -0
  73. BUCToolkit/utils/_CheckModules.py +30 -0
  74. BUCToolkit/utils/_Element_info.py +527 -0
  75. BUCToolkit/utils/__init__.py +22 -0
  76. BUCToolkit/utils/_para_flatt_list.py +131 -0
  77. BUCToolkit/utils/_print_formatter.py +59 -0
  78. BUCToolkit/utils/check_structures.py +204 -0
  79. BUCToolkit/utils/function_utils.py +147 -0
  80. BUCToolkit/utils/grad_functions.py +69 -0
  81. BUCToolkit/utils/index_ops.py +432 -0
  82. BUCToolkit/utils/setup_loggers.py +137 -0
  83. buctoolkit-1.0b0.dist-info/METADATA +28 -0
  84. buctoolkit-1.0b0.dist-info/RECORD +88 -0
  85. buctoolkit-1.0b0.dist-info/WHEEL +5 -0
  86. buctoolkit-1.0b0.dist-info/entry_points.txt +6 -0
  87. buctoolkit-1.0b0.dist-info/licenses/LICENSE +21 -0
  88. buctoolkit-1.0b0.dist-info/top_level.txt +1 -0
BUCToolkit/BatchStructures/__init__.py ADDED
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+ # Copyright (c) 2024-2025.7.4, BUCToolkit.
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+ # Authors: Pu Pengxin, Song Xin
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+ # Version: 0.9a
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+ # File: __init__.py
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+ # Environment: Python 3.12
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+
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+ from BUCToolkit.BatchStructures.StructuresIO import read_opt_structures, read_md_traj, read_mc_traj, ArrayDumper, ArrayDumpReader
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+
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+ __all__ = [
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+ "read_opt_structures",
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+ "read_md_traj",
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+ "read_mc_traj",
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+ "ArrayDumper",
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+ "ArrayDumpReader",
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+ ]
BUCToolkit/Preprocessing/__init__.py ADDED
@@ -0,0 +1,7 @@
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+ # Copyright (c) 2024-2025.7.4, BUCToolkit.
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+ # Authors: Pu Pengxin, Song Xin
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+ # Version: 0.9a
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+ # File: __init__.py
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+ # Environment: Python 3.12
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+
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+