mdapy 0.9.2__tar.gz → 0.9.4__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (188) hide show
  1. {mdapy-0.9.2 → mdapy-0.9.4}/.gitignore +0 -0
  2. {mdapy-0.9.2 → mdapy-0.9.4}/.readthedocs.yaml +0 -0
  3. {mdapy-0.9.2 → mdapy-0.9.4}/LICENSE +0 -0
  4. {mdapy-0.9.2/mdapy.egg-info → mdapy-0.9.4}/PKG-INFO +333 -320
  5. {mdapy-0.9.2 → mdapy-0.9.4}/README.rst +17 -2
  6. {mdapy-0.9.2 → mdapy-0.9.4}/benchmark/Identify_SFs_TBs/SFTB_mdapy_ovito.py +146 -146
  7. {mdapy-0.9.2 → mdapy-0.9.4}/benchmark/aja/aja_mdapy_ovito.py +114 -114
  8. {mdapy-0.9.2 → mdapy-0.9.4}/benchmark/atomic_entropy/entropy_mdapy_ovito.py +192 -192
  9. {mdapy-0.9.2 → mdapy-0.9.4}/benchmark/average_rdf/rdf_benchmark.gsd +0 -0
  10. {mdapy-0.9.2 → mdapy-0.9.4}/benchmark/average_rdf/rdf_mdapy_mdanalysis_mdtraj.py +158 -158
  11. {mdapy-0.9.2 → mdapy-0.9.4}/benchmark/cluster/cluster_mdapy_ovito.py +115 -115
  12. {mdapy-0.9.2 → mdapy-0.9.4}/benchmark/cna/cna_mdapy_ovito.py +120 -120
  13. {mdapy-0.9.2 → mdapy-0.9.4}/benchmark/csp/csp_mdapy_ovito.py +110 -110
  14. {mdapy-0.9.2 → mdapy-0.9.4}/benchmark/lattice_maker/latticemaker_mdapy_freud.py +110 -110
  15. {mdapy-0.9.2 → mdapy-0.9.4}/benchmark/msd/msd_mdapy_mdanalysis_mdtraj.py +138 -138
  16. {mdapy-0.9.2 → mdapy-0.9.4}/benchmark/neighbor/neighbor_mdapy_ovito_freud.py +139 -139
  17. {mdapy-0.9.2 → mdapy-0.9.4}/benchmark/neighbor_threads/neighbor_thread.py +100 -100
  18. {mdapy-0.9.2 → mdapy-0.9.4}/benchmark/pair_distribution/pair_mdapy_ovito_freud.py +170 -170
  19. {mdapy-0.9.2 → mdapy-0.9.4}/benchmark/polyhedra_template_match/ptm_mdapy_ovito.py +93 -93
  20. {mdapy-0.9.2 → mdapy-0.9.4}/benchmark/steinhardt_order/steinhardt_mdapy_freud.py +108 -108
  21. {mdapy-0.9.2 → mdapy-0.9.4}/compile.sh +5 -2
  22. {mdapy-0.9.2 → mdapy-0.9.4}/doc/Makefile +0 -0
  23. {mdapy-0.9.2 → mdapy-0.9.4}/doc/environment.yml +0 -2
  24. {mdapy-0.9.2 → mdapy-0.9.4}/doc/source/conf.py +2 -2
  25. mdapy-0.9.4/doc/source/gettingstarted/benchmark.ipynb +232 -0
  26. {mdapy-0.9.2 → mdapy-0.9.4}/doc/source/gettingstarted/examples.rst +8 -10
  27. {mdapy-0.9.2 → mdapy-0.9.4}/doc/source/gettingstarted/installation.rst +0 -0
  28. {mdapy-0.9.2 → mdapy-0.9.4}/doc/source/gettingstarted/main_features.rst +0 -0
  29. mdapy-0.9.4/doc/source/gettingstarted/quicklystart.ipynb +955 -0
  30. mdapy-0.9.4/doc/source/gettingstarted/reading_and_saving_file.ipynb +774 -0
  31. mdapy-0.9.4/doc/source/gettingstarted/use_mdapy_efficiently.ipynb +322 -0
  32. {mdapy-0.9.2 → mdapy-0.9.4}/doc/source/images/mdapy_favico.ico +0 -0
  33. {mdapy-0.9.2 → mdapy-0.9.4}/doc/source/images/mdapy_favico_white.ico +0 -0
  34. {mdapy-0.9.2 → mdapy-0.9.4}/doc/source/images/mdapy_logo.png +0 -0
  35. {mdapy-0.9.2 → mdapy-0.9.4}/doc/source/images/mdapy_logo_white.png +0 -0
  36. {mdapy-0.9.2 → mdapy-0.9.4}/doc/source/index.rst +1 -2
  37. {mdapy-0.9.2 → mdapy-0.9.4}/doc/source/mdapy.rst +0 -0
  38. {mdapy-0.9.2 → mdapy-0.9.4}/doc/source/modules.rst +0 -0
  39. {mdapy-0.9.2 → mdapy-0.9.4}/example/Al_DFT.eam.alloy +0 -0
  40. {mdapy-0.9.2 → mdapy-0.9.4}/example/CoCuFeNiPd-4M.data +0 -0
  41. {mdapy-0.9.2 → mdapy-0.9.4}/example/CoCuFeNiPd-4M.dump +0 -0
  42. {mdapy-0.9.2 → mdapy-0.9.4}/example/CoNiFeAlCu.eam.alloy +0 -0
  43. {mdapy-0.9.2 → mdapy-0.9.4}/example/FCC.data +0 -0
  44. {mdapy-0.9.2 → mdapy-0.9.4}/example/ISF.dump +0 -0
  45. {mdapy-0.9.2 → mdapy-0.9.4}/example/ISFsTBs.py +0 -1
  46. {mdapy-0.9.2 → mdapy-0.9.4}/example/analyze_trajectories.py +0 -0
  47. {mdapy-0.9.2 → mdapy-0.9.4}/example/calculate_eos.py +0 -1
  48. {mdapy-0.9.2 → mdapy-0.9.4}/example/create_polycrystalline.py +0 -0
  49. {mdapy-0.9.2 → mdapy-0.9.4}/example/get_WCP.py +1 -1
  50. {mdapy-0.9.2 → mdapy-0.9.4}/example/solidliquid.dump +0 -0
  51. {mdapy-0.9.2 → mdapy-0.9.4}/example/solidliquid.py +0 -0
  52. {mdapy-0.9.2 → mdapy-0.9.4}/example/test_cpp_module.py +2 -1
  53. {mdapy-0.9.2 → mdapy-0.9.4}/mdapy/__init__.py +1 -1
  54. {mdapy-0.9.2 → mdapy-0.9.4}/mdapy/ackland_jones_analysis.py +0 -0
  55. {mdapy-0.9.2 → mdapy-0.9.4}/mdapy/calculator.py +0 -0
  56. {mdapy-0.9.2 → mdapy-0.9.4}/mdapy/centro_symmetry_parameter.py +0 -0
  57. {mdapy-0.9.2 → mdapy-0.9.4}/mdapy/cluser_analysis.py +0 -0
  58. {mdapy-0.9.2 → mdapy-0.9.4}/mdapy/cluster/_cluster.cpp +0 -0
  59. {mdapy-0.9.2 → mdapy-0.9.4}/mdapy/common_neighbor_analysis.py +0 -0
  60. {mdapy-0.9.2 → mdapy-0.9.4}/mdapy/common_neighbor_parameter.py +0 -0
  61. {mdapy-0.9.2 → mdapy-0.9.4}/mdapy/create_polycrystalline.py +13 -4
  62. {mdapy-0.9.2 → mdapy-0.9.4}/mdapy/eam_average.py +0 -0
  63. {mdapy-0.9.2 → mdapy-0.9.4}/mdapy/eam_generate.py +6 -35
  64. {mdapy-0.9.2 → mdapy-0.9.4}/mdapy/entropy.py +0 -0
  65. {mdapy-0.9.2 → mdapy-0.9.4}/mdapy/identify_SFs_TBs.py +0 -0
  66. {mdapy-0.9.2 → mdapy-0.9.4}/mdapy/lattice_maker.py +86 -9
  67. {mdapy-0.9.2 → mdapy-0.9.4}/mdapy/lindemann_parameter.py +0 -0
  68. {mdapy-0.9.2 → mdapy-0.9.4}/mdapy/load_save_data.py +39 -19
  69. {mdapy-0.9.2 → mdapy-0.9.4}/mdapy/mean_squared_displacement.py +0 -0
  70. {mdapy-0.9.2 → mdapy-0.9.4}/mdapy/nearest_neighbor.py +0 -0
  71. {mdapy-0.9.2 → mdapy-0.9.4}/mdapy/neigh/_neigh.cpp +0 -0
  72. {mdapy-0.9.2 → mdapy-0.9.4}/mdapy/neighbor.py +0 -0
  73. {mdapy-0.9.2 → mdapy-0.9.4}/mdapy/pair_distribution.py +0 -0
  74. {mdapy-0.9.2 → mdapy-0.9.4}/mdapy/pigz.py +0 -0
  75. {mdapy-0.9.2 → mdapy-0.9.4}/mdapy/plotset.py +0 -0
  76. {mdapy-0.9.2 → mdapy-0.9.4}/mdapy/polyhedral_template_matching.py +0 -0
  77. {mdapy-0.9.2 → mdapy-0.9.4}/mdapy/potential.py +0 -0
  78. {mdapy-0.9.2 → mdapy-0.9.4}/mdapy/ptm/_ptm.cpp +0 -0
  79. {mdapy-0.9.2 → mdapy-0.9.4}/mdapy/rdf/_rdf.cpp +0 -0
  80. {mdapy-0.9.2 → mdapy-0.9.4}/mdapy/replicate.py +0 -0
  81. {mdapy-0.9.2 → mdapy-0.9.4}/mdapy/spatial_binning.py +0 -0
  82. {mdapy-0.9.2 → mdapy-0.9.4}/mdapy/steinhardt_bond_orientation.py +0 -0
  83. {mdapy-0.9.2 → mdapy-0.9.4}/mdapy/system.py +132 -53
  84. {mdapy-0.9.2 → mdapy-0.9.4}/mdapy/temperature.py +0 -0
  85. {mdapy-0.9.2 → mdapy-0.9.4}/mdapy/timer.py +0 -0
  86. {mdapy-0.9.2 → mdapy-0.9.4}/mdapy/tool_function.py +3 -2
  87. {mdapy-0.9.2 → mdapy-0.9.4}/mdapy/void_distribution.py +15 -25
  88. {mdapy-0.9.2 → mdapy-0.9.4}/mdapy/voronoi/_voro.cpp +0 -0
  89. {mdapy-0.9.2 → mdapy-0.9.4}/mdapy/voronoi_analysis.py +0 -0
  90. {mdapy-0.9.2 → mdapy-0.9.4}/mdapy/warren_cowley_parameter.py +0 -0
  91. {mdapy-0.9.2 → mdapy-0.9.4/mdapy.egg-info}/PKG-INFO +333 -320
  92. {mdapy-0.9.2 → mdapy-0.9.4}/mdapy.egg-info/SOURCES.txt +21 -1
  93. {mdapy-0.9.2 → mdapy-0.9.4}/mdapy.egg-info/dependency_links.txt +0 -0
  94. {mdapy-0.9.2 → mdapy-0.9.4}/mdapy.egg-info/not-zip-safe +0 -0
  95. {mdapy-0.9.2 → mdapy-0.9.4}/mdapy.egg-info/requires.txt +0 -2
  96. {mdapy-0.9.2 → mdapy-0.9.4}/mdapy.egg-info/top_level.txt +0 -0
  97. {mdapy-0.9.2 → mdapy-0.9.4}/pyproject.toml +0 -0
  98. {mdapy-0.9.2 → mdapy-0.9.4}/requirements.txt +0 -2
  99. {mdapy-0.9.2 → mdapy-0.9.4}/setup.cfg +4 -4
  100. {mdapy-0.9.2 → mdapy-0.9.4}/setup.py +4 -4
  101. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/ptm/LICENSE +0 -0
  102. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/ptm/README +0 -0
  103. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/ptm/ptm_alloy_types.cpp +0 -0
  104. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/ptm/ptm_alloy_types.h +0 -0
  105. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/ptm/ptm_alt_templates.h +0 -0
  106. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/ptm/ptm_canonical_coloured.cpp +0 -0
  107. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/ptm/ptm_canonical_coloured.h +0 -0
  108. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/ptm/ptm_constants.cpp +0 -0
  109. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/ptm/ptm_constants.h +0 -0
  110. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/ptm/ptm_convex_hull_incremental.cpp +0 -0
  111. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/ptm/ptm_convex_hull_incremental.h +0 -0
  112. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/ptm/ptm_deformation_gradient.cpp +0 -0
  113. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/ptm/ptm_deformation_gradient.h +0 -0
  114. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/ptm/ptm_functions.h +0 -0
  115. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/ptm/ptm_fundamental_mappings.h +0 -0
  116. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/ptm/ptm_graph_data.cpp +0 -0
  117. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/ptm/ptm_graph_data.h +0 -0
  118. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/ptm/ptm_graph_tools.cpp +0 -0
  119. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/ptm/ptm_graph_tools.h +0 -0
  120. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/ptm/ptm_index.cpp +0 -0
  121. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/ptm/ptm_initialize_data.cpp +0 -0
  122. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/ptm/ptm_initialize_data.h +0 -0
  123. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/ptm/ptm_neighbour_ordering.cpp +0 -0
  124. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/ptm/ptm_neighbour_ordering.h +0 -0
  125. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/ptm/ptm_normalize_vertices.cpp +0 -0
  126. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/ptm/ptm_normalize_vertices.h +0 -0
  127. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/ptm/ptm_polar.cpp +0 -0
  128. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/ptm/ptm_polar.h +0 -0
  129. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/ptm/ptm_quat.cpp +0 -0
  130. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/ptm/ptm_quat.h +0 -0
  131. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/ptm/ptm_structure_matcher.cpp +0 -0
  132. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/ptm/ptm_structure_matcher.h +0 -0
  133. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/ptm/ptm_voronoi_cell.cpp +0 -0
  134. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/ptm/ptm_voronoi_cell.h +0 -0
  135. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/ptm/ptm_voronoi_config.h +0 -0
  136. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/voro++/LICENSE +0 -0
  137. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/voro++/README +0 -0
  138. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/voro++/c_info.hh +0 -0
  139. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/voro++/cell_2d.cc +0 -0
  140. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/voro++/cell_2d.hh +0 -0
  141. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/voro++/cell_3d.cc +0 -0
  142. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/voro++/cell_3d.hh +0 -0
  143. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/voro++/cmd_line.cc +0 -0
  144. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/voro++/common.cc +0 -0
  145. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/voro++/common.hh +0 -0
  146. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/voro++/config.hh +0 -0
  147. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/voro++/container_2d.cc +0 -0
  148. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/voro++/container_2d.hh +0 -0
  149. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/voro++/container_3d.cc +0 -0
  150. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/voro++/container_3d.hh +0 -0
  151. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/voro++/container_tri.cc +0 -0
  152. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/voro++/container_tri.hh +0 -0
  153. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/voro++/iter_2d.cc +0 -0
  154. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/voro++/iter_2d.hh +0 -0
  155. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/voro++/iter_3d.cc +0 -0
  156. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/voro++/iter_3d.hh +0 -0
  157. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/voro++/particle_list.cc +0 -0
  158. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/voro++/particle_list.hh +0 -0
  159. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/voro++/particle_order.hh +0 -0
  160. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/voro++/rad_option.hh +0 -0
  161. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/voro++/unitcell.cc +0 -0
  162. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/voro++/unitcell.hh +0 -0
  163. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/voro++/v_base_2d.cc +0 -0
  164. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/voro++/v_base_2d.hh +0 -0
  165. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/voro++/v_base_3d.cc +0 -0
  166. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/voro++/v_base_3d.hh +0 -0
  167. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/voro++/v_base_wl_2d.cc +0 -0
  168. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/voro++/v_base_wl_3d.cc +0 -0
  169. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/voro++/v_compute_2d.cc +0 -0
  170. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/voro++/v_compute_2d.hh +0 -0
  171. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/voro++/v_compute_3d.cc +0 -0
  172. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/voro++/v_compute_3d.hh +0 -0
  173. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/voro++/voro++.cc +0 -0
  174. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/voro++/voro++.hh +0 -0
  175. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/voro++/wall.cc +0 -0
  176. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/voro++/wall.hh +0 -0
  177. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/voro++/wall_2d.cc +0 -0
  178. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/voro++/wall_2d.hh +0 -0
  179. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/voro++/wall_3d.cc +0 -0
  180. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/voro++/wall_3d.hh +0 -0
  181. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/voro++/worklist_2d.hh +0 -0
  182. {mdapy-0.9.2 → mdapy-0.9.4}/thirdparty/voro++/worklist_3d.hh +0 -0
  183. mdapy-0.9.2/doc/source/gettingstarted/benchmark.ipynb +0 -227
  184. mdapy-0.9.2/doc/source/gettingstarted/quicklystart.ipynb +0 -1135
  185. mdapy-0.9.2/doc/source/gettingstarted/reading_and_saving_file.ipynb +0 -772
  186. mdapy-0.9.2/doc/source/gettingstarted/use_mdapy_efficiently.ipynb +0 -502
  187. mdapy-0.9.2/example/Al-heat.in +0 -44
  188. {mdapy-0.9.2 → mdapy-0.9.4}/doc/make.bat +0 -0
{mdapy-0.9.2 → mdapy-0.9.4}/.gitignore RENAMED
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{mdapy-0.9.2 → mdapy-0.9.4}/.readthedocs.yaml RENAMED
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{mdapy-0.9.2 → mdapy-0.9.4}/LICENSE RENAMED
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