TB2J 0.9.9.4__tar.gz → 0.9.9.7__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 (228) hide show
  1. tb2j-0.9.9.7/.github/workflows/pylint.yml.bak +23 -0
  2. tb2j-0.9.9.7/.github/workflows/python-app.yml +44 -0
  3. tb2j-0.9.9.7/.gitignore +131 -0
  4. tb2j-0.9.9.7/.pre-commit-config.yaml +11 -0
  5. tb2j-0.9.9.7/.readthedocs.yml +28 -0
  6. tb2j-0.9.9.7/.ruff.toml +78 -0
  7. tb2j-0.9.9.7/.travis.yml +33 -0
  8. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/PKG-INFO +2 -3
  9. tb2j-0.9.9.7/TB2J/.gitignore +5 -0
  10. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/Jdownfolder.py +3 -2
  11. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/MAEGreen.py +22 -17
  12. tb2j-0.9.9.7/TB2J/downfold/Hdownfolder.py +233 -0
  13. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/exchange.py +1 -1
  14. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/exchange_params.py +1 -2
  15. tb2j-0.9.9.7/TB2J/interfaces/abacus/.gitignore +2 -0
  16. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/interfaces/abacus/abacus_wrapper.py +0 -3
  17. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/interfaces/abacus/gen_exchange_abacus.py +3 -0
  18. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/interfaces/abacus/orbital_api.py +1 -0
  19. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/interfaces/siesta_interface.py +15 -7
  20. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/io_exchange/__init__.py +2 -0
  21. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/io_exchange/io_exchange.py +40 -12
  22. tb2j-0.9.9.7/TB2J/magnon/__init__.py +3 -0
  23. tb2j-0.9.9.7/TB2J/magnon/io_exchange2.py +695 -0
  24. tb2j-0.9.9.7/TB2J/magnon/magnon3.py +334 -0
  25. tb2j-0.9.9.7/TB2J/magnon/magnon_io.py +48 -0
  26. tb2j-0.9.9.7/TB2J/magnon/magnon_math.py +53 -0
  27. tb2j-0.9.9.7/TB2J/magnon/plot.py +58 -0
  28. tb2j-0.9.9.7/TB2J/magnon/structure.py +348 -0
  29. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/mathutils/__init__.py +2 -0
  30. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/mathutils/fibonacci_sphere.py +1 -1
  31. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/mathutils/rotate_spin.py +0 -3
  32. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/symmetrize_J.py +1 -1
  33. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J.egg-info/PKG-INFO +2 -3
  34. tb2j-0.9.9.7/TB2J.egg-info/SOURCES.txt +225 -0
  35. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J.egg-info/requires.txt +1 -2
  36. tb2j-0.9.9.7/buildimage.sh +51 -0
  37. tb2j-0.9.9.7/docs/Makefile +20 -0
  38. tb2j-0.9.9.7/docs/_static/Logo-ULG.png +0 -0
  39. tb2j-0.9.9.7/docs/_static/logo_TB2J_horizon.png +0 -0
  40. tb2j-0.9.9.7/docs/conf.py +67 -0
  41. tb2j-0.9.9.7/docs/index.rst +44 -0
  42. tb2j-0.9.9.7/docs/make.bat +35 -0
  43. tb2j-0.9.9.7/docs/requirements.txt +3 -0
  44. tb2j-0.9.9.7/docs/src/BFOvarT.png +0 -0
  45. tb2j-0.9.9.7/docs/src/Contributors.rst +44 -0
  46. tb2j-0.9.9.7/docs/src/ReleaseNotes.md +226 -0
  47. tb2j-0.9.9.7/docs/src/SrMnO3_DOS.png +0 -0
  48. tb2j-0.9.9.7/docs/src/abacus.md +103 -0
  49. tb2j-0.9.9.7/docs/src/applications.rst +9 -0
  50. tb2j-0.9.9.7/docs/src/convention.rst +18 -0
  51. tb2j-0.9.9.7/docs/src/development.md +22 -0
  52. tb2j-0.9.9.7/docs/src/downfold.md +28 -0
  53. tb2j-0.9.9.7/docs/src/ecosystem.md +49 -0
  54. tb2j-0.9.9.7/docs/src/eigen.rst +34 -0
  55. tb2j-0.9.9.7/docs/src/extend.rst +45 -0
  56. tb2j-0.9.9.7/docs/src/faq.rst +79 -0
  57. tb2j-0.9.9.7/docs/src/install.rst +86 -0
  58. tb2j-0.9.9.7/docs/src/mae.md +127 -0
  59. tb2j-0.9.9.7/docs/src/magnon_band.assets/exchange_magnon-1593690872101.png +0 -0
  60. tb2j-0.9.9.7/docs/src/magnon_band.assets/exchange_magnon.png +0 -0
  61. tb2j-0.9.9.7/docs/src/magnon_band.assets/magnon_dos.png +0 -0
  62. tb2j-0.9.9.7/docs/src/magnon_band.rst +98 -0
  63. tb2j-0.9.9.7/docs/src/multibinit.rst +89 -0
  64. tb2j-0.9.9.7/docs/src/openmx.rst +27 -0
  65. tb2j-0.9.9.7/docs/src/orbital_contribution.md +80 -0
  66. tb2j-0.9.9.7/docs/src/output.rst +52 -0
  67. tb2j-0.9.9.7/docs/src/parameters.rst +89 -0
  68. tb2j-0.9.9.7/docs/src/references.rst +36 -0
  69. tb2j-0.9.9.7/docs/src/roadmap.md +8 -0
  70. tb2j-0.9.9.7/docs/src/rotate_and_merge.rst +54 -0
  71. tb2j-0.9.9.7/docs/src/siesta.rst +38 -0
  72. tb2j-0.9.9.7/docs/src/spin_model_assets/canting_DMI.png +0 -0
  73. tb2j-0.9.9.7/docs/src/spin_model_assets/tmulti5_2.png +0 -0
  74. tb2j-0.9.9.7/docs/src/symmetry.md +42 -0
  75. tb2j-0.9.9.7/docs/src/tutorial.rst +18 -0
  76. tb2j-0.9.9.7/docs/src/wannier.rst +228 -0
  77. tb2j-0.9.9.7/examples/Siesta/BccFe/Fe.1.psml +1181 -0
  78. tb2j-0.9.9.7/examples/Siesta/BccFe/TB2J_results/EigenJq.txt +119 -0
  79. tb2j-0.9.9.7/examples/Siesta/BccFe/TB2J_results/Multibinit/exchange.xml +4126 -0
  80. tb2j-0.9.9.7/examples/Siesta/BccFe/TB2J_results/Multibinit/exchange_kpth.txt +8 -0
  81. tb2j-0.9.9.7/examples/Siesta/BccFe/TB2J_results/Multibinit/exchange_magnon.png +0 -0
  82. tb2j-0.9.9.7/examples/Siesta/BccFe/TB2J_results/Multibinit/magnon.py +3 -0
  83. tb2j-0.9.9.7/examples/Siesta/BccFe/TB2J_results/Multibinit/magnon_band.json +3332 -0
  84. tb2j-0.9.9.7/examples/Siesta/BccFe/TB2J_results/Multibinit/magnon_band.pdf +0 -0
  85. tb2j-0.9.9.7/examples/Siesta/BccFe/TB2J_results/Multibinit/magnon_dos.png +0 -0
  86. tb2j-0.9.9.7/examples/Siesta/BccFe/TB2J_results/Multibinit/magnon_dos.txt +302 -0
  87. tb2j-0.9.9.7/examples/Siesta/BccFe/TB2J_results/Multibinit/mb.files +3 -0
  88. tb2j-0.9.9.7/examples/Siesta/BccFe/TB2J_results/Multibinit/mb.in +33 -0
  89. tb2j-0.9.9.7/examples/Siesta/BccFe/TB2J_results/Multibinit/plot.sh +1 -0
  90. tb2j-0.9.9.7/examples/Siesta/BccFe/TB2J_results/Multibinit/plot_magnon_dos.sh +1 -0
  91. tb2j-0.9.9.7/examples/Siesta/BccFe/TB2J_results/Multibinit/plot_magnon_from_json_file.py +73 -0
  92. tb2j-0.9.9.7/examples/Siesta/BccFe/TB2J_results/TB2J.pickle +0 -0
  93. tb2j-0.9.9.7/examples/Siesta/BccFe/TB2J_results/TomASD/exchange.exch +1381 -0
  94. tb2j-0.9.9.7/examples/Siesta/BccFe/TB2J_results/TomASD/exchange.ucf +3 -0
  95. tb2j-0.9.9.7/examples/Siesta/BccFe/TB2J_results/exchange.out +3097 -0
  96. tb2j-0.9.9.7/examples/Siesta/BccFe/getJ.sh +2 -0
  97. tb2j-0.9.9.7/examples/Siesta/BccFe/run.sh +3 -0
  98. tb2j-0.9.9.7/examples/Siesta/BccFe/siesta.fdf +61 -0
  99. tb2j-0.9.9.7/examples/Siesta/HcpCo/Co.1.psml +3174 -0
  100. tb2j-0.9.9.7/examples/Siesta/HcpCo/TB2J_results/Multibinit/exchange.xml +7610 -0
  101. tb2j-0.9.9.7/examples/Siesta/HcpCo/TB2J_results/Multibinit/mb.files +3 -0
  102. tb2j-0.9.9.7/examples/Siesta/HcpCo/TB2J_results/Multibinit/mb.in +33 -0
  103. tb2j-0.9.9.7/examples/Siesta/HcpCo/TB2J_results/TB2J.pickle +0 -0
  104. tb2j-0.9.9.7/examples/Siesta/HcpCo/TB2J_results/TomASD/exchange.exch +2556 -0
  105. tb2j-0.9.9.7/examples/Siesta/HcpCo/TB2J_results/TomASD/exchange.ucf +4 -0
  106. tb2j-0.9.9.7/examples/Siesta/HcpCo/TB2J_results/Vampire/input +42 -0
  107. tb2j-0.9.9.7/examples/Siesta/HcpCo/TB2J_results/Vampire/vampire.UCF +644 -0
  108. tb2j-0.9.9.7/examples/Siesta/HcpCo/TB2J_results/Vampire/vampire.mat +24 -0
  109. tb2j-0.9.9.7/examples/Siesta/HcpCo/TB2J_results/exchange.out +5708 -0
  110. tb2j-0.9.9.7/examples/Siesta/HcpCo/TB2J_results/summary.txt +10 -0
  111. tb2j-0.9.9.7/examples/Siesta/HcpCo/getJ.sh +1 -0
  112. tb2j-0.9.9.7/examples/Siesta/HcpCo/run.sh +3 -0
  113. tb2j-0.9.9.7/examples/Siesta/HcpCo/siesta.fdf +63 -0
  114. tb2j-0.9.9.7/examples/abinit-w90/SrMnO3/TB2J_results/JvsR.pdf +0 -0
  115. tb2j-0.9.9.7/examples/abinit-w90/SrMnO3/TB2J_results/Multibinit/exchange.xml +533 -0
  116. tb2j-0.9.9.7/examples/abinit-w90/SrMnO3/TB2J_results/Multibinit/mb.files +3 -0
  117. tb2j-0.9.9.7/examples/abinit-w90/SrMnO3/TB2J_results/Multibinit/mb.in +33 -0
  118. tb2j-0.9.9.7/examples/abinit-w90/SrMnO3/TB2J_results/TB2J.pickle +0 -0
  119. tb2j-0.9.9.7/examples/abinit-w90/SrMnO3/TB2J_results/TomASD/exchange.exch +509 -0
  120. tb2j-0.9.9.7/examples/abinit-w90/SrMnO3/TB2J_results/TomASD/exchange.ucf +3 -0
  121. tb2j-0.9.9.7/examples/abinit-w90/SrMnO3/TB2J_results/Vampire/input +42 -0
  122. tb2j-0.9.9.7/examples/abinit-w90/SrMnO3/TB2J_results/Vampire/vampire.UCF +135 -0
  123. tb2j-0.9.9.7/examples/abinit-w90/SrMnO3/TB2J_results/Vampire/vampire.mat +13 -0
  124. tb2j-0.9.9.7/examples/abinit-w90/SrMnO3/TB2J_results/assigned_basis.txt +14 -0
  125. tb2j-0.9.9.7/examples/abinit-w90/SrMnO3/TB2J_results/exchange.out +406 -0
  126. tb2j-0.9.9.7/examples/abinit-w90/SrMnO3/TB2J_results/exchange_orb_decomposition.out +1274 -0
  127. tb2j-0.9.9.7/examples/abinit-w90/SrMnO3/abinit.files +8 -0
  128. tb2j-0.9.9.7/examples/abinit-w90/SrMnO3/abinit.in +83 -0
  129. tb2j-0.9.9.7/examples/abinit-w90/SrMnO3/abinito_w90_down.win +113 -0
  130. tb2j-0.9.9.7/examples/abinit-w90/SrMnO3/abinito_w90_down_centres.xyz +21 -0
  131. tb2j-0.9.9.7/examples/abinit-w90/SrMnO3/abinito_w90_down_hr.dat +24512 -0
  132. tb2j-0.9.9.7/examples/abinit-w90/SrMnO3/abinito_w90_up.win +113 -0
  133. tb2j-0.9.9.7/examples/abinit-w90/SrMnO3/abinito_w90_up_centres.xyz +21 -0
  134. tb2j-0.9.9.7/examples/abinit-w90/SrMnO3/abinito_w90_up_hr.dat +24512 -0
  135. tb2j-0.9.9.7/examples/abinit-w90/SrMnO3/get_J.sh +1 -0
  136. tb2j-0.9.9.7/examples/abinit-w90/SrMnO3/psp/Mn.GGA-PBESOL-JTH.xml +16818 -0
  137. tb2j-0.9.9.7/examples/abinit-w90/SrMnO3/psp/O.GGA-PBESOL-JTH.xml +12782 -0
  138. tb2j-0.9.9.7/examples/abinit-w90/SrMnO3/psp/Sr.GGA-PBESOL-JTH.xml +12646 -0
  139. tb2j-0.9.9.7/examples/abinit-w90/SrMnO3/run.sh +6 -0
  140. tb2j-0.9.9.7/requirements.txt +11 -0
  141. tb2j-0.9.9.7/scripts/TB2J_magnon2.py +78 -0
  142. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/scripts/abacus2J.py +0 -1
  143. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/setup.py +3 -3
  144. tb2j-0.9.9.7/upload_to_pip.sh +5 -0
  145. tb2j-0.9.9.4/TB2J.egg-info/SOURCES.txt +0 -101
  146. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/LICENSE +0 -0
  147. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/README.md +0 -0
  148. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/Jtensor.py +0 -0
  149. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/MAE.py +0 -0
  150. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/Oiju.py +0 -0
  151. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/Oiju_epc.py +0 -0
  152. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/__init__.py +0 -0
  153. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/anisotropy.py +0 -0
  154. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/basis.py +0 -0
  155. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/citation.py +0 -0
  156. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/contour.py +0 -0
  157. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/density_matrix.py +0 -0
  158. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/epc.py +0 -0
  159. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/exchangeCL2.py +0 -0
  160. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/exchange_pert.py +0 -0
  161. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/exchange_qspace.py +0 -0
  162. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/external/__init__.py +0 -0
  163. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/external/p_tqdm.py +0 -0
  164. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/gpaw_wrapper.py +0 -0
  165. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/green.py +0 -0
  166. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/greentest.py +0 -0
  167. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/interfaces/__init__.py +0 -0
  168. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/interfaces/abacus/__init__.py +0 -0
  169. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/interfaces/abacus/abacus_api.py +0 -0
  170. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/interfaces/abacus/stru_api.py +0 -0
  171. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/interfaces/abacus/test_density_matrix.py +0 -0
  172. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/interfaces/abacus/test_read_HRSR.py +0 -0
  173. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/interfaces/abacus/test_read_stru.py +0 -0
  174. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/interfaces/gpaw_interface.py +0 -0
  175. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/interfaces/lawaf_interface.py +0 -0
  176. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/interfaces/manager.py +0 -0
  177. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/interfaces/wannier90_interface.py +0 -0
  178. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/io_exchange/io_multibinit.py +0 -0
  179. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/io_exchange/io_tomsasd.py +0 -0
  180. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/io_exchange/io_txt.py +0 -0
  181. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/io_exchange/io_uppasd.py +0 -0
  182. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/io_exchange/io_vampire.py +0 -0
  183. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/io_merge.py +0 -0
  184. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/kpoints.py +0 -0
  185. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/mathutils/fermi.py +0 -0
  186. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/mathutils/kR_convert.py +0 -0
  187. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/mathutils/lowdin.py +0 -0
  188. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/myTB.py +0 -0
  189. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/mycfr.py +0 -0
  190. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/orbital_magmom.py +0 -0
  191. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/orbmap.py +0 -0
  192. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/pauli.py +0 -0
  193. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/pert.py +0 -0
  194. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/plot.py +0 -0
  195. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/rotate_atoms.py +0 -0
  196. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/rotate_siestaDM.py +0 -0
  197. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/sisl_wrapper.py +0 -0
  198. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/spinham/__init__.py +0 -0
  199. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/spinham/base_parser.py +0 -0
  200. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/spinham/constants.py +0 -0
  201. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/spinham/hamiltonian.py +0 -0
  202. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/spinham/hamiltonian_terms.py +0 -0
  203. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/spinham/plot.py +0 -0
  204. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/spinham/qsolver.py +0 -0
  205. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/spinham/spin_api.py +0 -0
  206. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/spinham/spin_xml.py +0 -0
  207. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/spinham/supercell.py +0 -0
  208. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/tensor_rotate.py +0 -0
  209. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/thetaphi.py +0 -0
  210. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/utest.py +0 -0
  211. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/utils.py +0 -0
  212. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/versioninfo.py +0 -0
  213. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/wannier/__init__.py +0 -0
  214. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/wannier/w90_parser.py +0 -0
  215. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J/wannier/w90_tb_parser.py +0 -0
  216. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J.egg-info/dependency_links.txt +0 -0
  217. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J.egg-info/entry_points.txt +0 -0
  218. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/TB2J.egg-info/top_level.txt +0 -0
  219. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/scripts/TB2J_downfold.py +0 -0
  220. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/scripts/TB2J_eigen.py +0 -0
  221. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/scripts/TB2J_magnon.py +0 -0
  222. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/scripts/TB2J_magnon_dos.py +0 -0
  223. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/scripts/TB2J_merge.py +0 -0
  224. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/scripts/TB2J_rotate.py +0 -0
  225. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/scripts/TB2J_rotateDM.py +0 -0
  226. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/scripts/siesta2J.py +0 -0
  227. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/scripts/wann2J.py +0 -0
  228. {tb2j-0.9.9.4 → tb2j-0.9.9.7}/setup.cfg +0 -0
@@ -0,0 +1,23 @@
1
+ name: Pylint
2
+
3
+ on: [push]
4
+
5
+ jobs:
6
+ build:
7
+ runs-on: ubuntu-latest
8
+ strategy:
9
+ matrix:
10
+ python-version: ["3.8", "3.9", "3.10"]
11
+ steps:
12
+ - uses: actions/checkout@v3
13
+ - name: Set up Python ${{ matrix.python-version }}
14
+ uses: actions/setup-python@v3
15
+ with:
16
+ python-version: ${{ matrix.python-version }}
17
+ - name: Install dependencies
18
+ run: |
19
+ python -m pip install --upgrade pip
20
+ pip install pylint
21
+ - name: Analysing the code with pylint
22
+ run: |
23
+ pylint $(git ls-files '*.py')
@@ -0,0 +1,44 @@
1
+ # This workflow will install Python dependencies, run tests and lint with a single version of Python
2
+ # For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
3
+
4
+ name: Python application
5
+
6
+ on:
7
+ push:
8
+ branches: [ "master" ]
9
+ pull_request:
10
+ branches: [ "master" ]
11
+
12
+ permissions:
13
+ contents: read
14
+
15
+ jobs:
16
+ build:
17
+ runs-on: ubuntu-latest
18
+ steps:
19
+ - uses: actions/checkout@v4
20
+ - name: Set up Python 3.10
21
+ uses: actions/setup-python@v5
22
+ with:
23
+ python-version: "3.10"
24
+ - name: Install dependencies
25
+ run: |
26
+ python -m pip install --upgrade pip
27
+ pip install flake8 pytest
28
+ if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
29
+ - name: Lint with flake8
30
+ run: |
31
+ # stop the build if there are Python syntax errors or undefined names
32
+ flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
33
+ # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
34
+ flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
35
+ - name: Test with pytest
36
+ run: |
37
+ #pytest
38
+ # - pwd
39
+ python -m pip install .
40
+ cd examples/abinit-w90/SrMnO3
41
+ ls -lah
42
+ sh get_J.sh
43
+ cd TB2J_results/Multibinit
44
+ TB2J_magnon.py --figfname magnon.png
@@ -0,0 +1,131 @@
1
+ doc/refs/*.pdf
2
+
3
+
4
+ *.swp
5
+
6
+ # Latex
7
+ *.aux
8
+
9
+ # xyz files
10
+
11
+ .DS_Store
12
+
13
+ # Byte-compiled / optimized / DLL files
14
+ __pycache__/
15
+ *.py[cod]
16
+ *$py.class
17
+
18
+ # numpy results
19
+ *.npy
20
+
21
+ # png files
22
+
23
+ # C extensions
24
+ *.so
25
+ *.a
26
+
27
+ # Fortran extensions
28
+ *.fpp
29
+ *.mod
30
+ *.o
31
+
32
+ # F90wrap files
33
+ *.plist
34
+
35
+ # Distribution / packaging
36
+ .Python
37
+ env/
38
+ build/
39
+ develop-eggs/
40
+ dist/
41
+ downloads/
42
+ eggs/
43
+ .eggs/
44
+ lib/
45
+ lib64/
46
+ parts/
47
+ sdist/
48
+ var/
49
+ wheels/
50
+ *.egg-info/
51
+ *.egg-info/*
52
+ .installed.cfg
53
+ *.egg
54
+
55
+ # temporary files
56
+ temp/
57
+
58
+ # PyInstaller
59
+ # Usually these files are written by a python script from a template
60
+ # before PyInstaller builds the exe, so as to inject date/other infos into it.
61
+ *.manifest
62
+ *.spec
63
+
64
+ # Installer logs
65
+ pip-log.txt
66
+ pip-delete-this-directory.txt
67
+
68
+ # Unit test / coverage reports
69
+ htmlcov/
70
+ .tox/
71
+ .coverage
72
+ .coverage.*
73
+ .cache
74
+ nosetests.xml
75
+ coverage.xml
76
+ *.cover
77
+ .hypothesis/
78
+
79
+ # Translations
80
+ *.mo
81
+ *.pot
82
+
83
+ # Django stuff:
84
+ *.log
85
+ local_settings.py
86
+
87
+ # Flask stuff:
88
+ instance/
89
+ .webassets-cache
90
+
91
+ # Scrapy stuff:
92
+ .scrapy
93
+
94
+ # Sphinx documentation
95
+ docs/_build/
96
+
97
+ # PyBuilder
98
+ target/
99
+
100
+ # Jupyter Notebook
101
+ .ipynb_checkpoints
102
+
103
+ # pyenv
104
+ .python-version
105
+
106
+ # celery beat schedule file
107
+ celerybeat-schedule
108
+
109
+ # SageMath parsed files
110
+ *.sage.py
111
+
112
+ # dotenv
113
+ .env
114
+
115
+ # virtualenv
116
+ .venv
117
+ venv/
118
+ ENV/
119
+
120
+ # Spyder project settings
121
+ .spyderproject
122
+ .spyproject
123
+
124
+ # Rope project settings
125
+ .ropeproject
126
+
127
+ # mkdocs documentation
128
+ /site
129
+
130
+ # mypy
131
+ .mypy_cache/
@@ -0,0 +1,11 @@
1
+ repos:
2
+ - repo: https://github.com/astral-sh/ruff-pre-commit
3
+ # Ruff version.
4
+ rev: v0.3.5
5
+ hooks:
6
+ # Run the linter.
7
+ - id: ruff
8
+ # --select I sorts imports
9
+ args: [ --fix, --extend-select, I ]
10
+ # Run the formatter.
11
+ - id: ruff-format
@@ -0,0 +1,28 @@
1
+ # .readthedocs.yml
2
+ # Read the Docs configuration file
3
+ # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
4
+
5
+ # Required
6
+ version: 2
7
+ build:
8
+ os: "ubuntu-22.04"
9
+ tools:
10
+ python: "3.11"
11
+
12
+ # Build documentation in the docs/ directory with Sphinx
13
+ sphinx:
14
+ configuration: docs/conf.py
15
+
16
+ # Build documentation with MkDocs
17
+ #mkdocs:
18
+ # configuration: mkdocs.yml
19
+
20
+ # Optionally build your docs in additional formats such as PDF
21
+ formats:
22
+ - pdf
23
+
24
+ # Optionally set the version of Python and requirements required to build your docs
25
+ python:
26
+ install:
27
+ - requirements: requirements.txt
28
+ - requirements: docs/requirements.txt
@@ -0,0 +1,78 @@
1
+ # Exclude a variety of commonly ignored directories.
2
+ exclude = [
3
+ ".bzr",
4
+ ".direnv",
5
+ ".eggs",
6
+ ".git",
7
+ ".git-rewrite",
8
+ ".hg",
9
+ ".ipynb_checkpoints",
10
+ ".mypy_cache",
11
+ ".nox",
12
+ ".pants.d",
13
+ ".pyenv",
14
+ ".pytest_cache",
15
+ ".pytype",
16
+ ".ruff_cache",
17
+ ".svn",
18
+ ".tox",
19
+ ".venv",
20
+ ".vscode",
21
+ "__pypackages__",
22
+ "_build",
23
+ "buck-out",
24
+ "build",
25
+ "dist",
26
+ "node_modules",
27
+ "site-packages",
28
+ "venv",
29
+ ]
30
+
31
+ # Same as Black.
32
+ line-length = 88
33
+ indent-width = 4
34
+
35
+ # Assume Python 3.8
36
+ target-version = "py38"
37
+
38
+ [lint]
39
+ # Enable Pyflakes (`F`) and a subset of the pycodestyle (`E`) codes by default.
40
+ # Unlike Flake8, Ruff doesn't enable pycodestyle warnings (`W`) or
41
+ # McCabe complexity (`C901`) by default.
42
+ select = ["E4", "E7", "E9", "F"]
43
+ ignore = ["E741"]
44
+
45
+ # Allow fix for all enabled rules (when `--fix`) is provided.
46
+ fixable = ["ALL"]
47
+ unfixable = []
48
+
49
+ # Allow unused variables when underscore-prefixed.
50
+ dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
51
+
52
+ [format]
53
+ # Like Black, use double quotes for strings.
54
+ quote-style = "double"
55
+
56
+ # Like Black, indent with spaces, rather than tabs.
57
+ indent-style = "space"
58
+
59
+ # Like Black, respect magic trailing commas.
60
+ skip-magic-trailing-comma = false
61
+
62
+ # Like Black, automatically detect the appropriate line ending.
63
+ line-ending = "auto"
64
+
65
+ # Enable auto-formatting of code examples in docstrings. Markdown,
66
+ # reStructuredText code/literal blocks and doctests are all supported.
67
+ #
68
+ # This is currently disabled by default, but it is planned for this
69
+ # to be opt-out in the future.
70
+ docstring-code-format = false
71
+
72
+ # Set the line length limit used when formatting code snippets in
73
+ # docstrings.
74
+ #
75
+ # This only has an effect when the `docstring-code-format` setting is
76
+ # enabled.
77
+ docstring-code-line-length = "dynamic"
78
+
@@ -0,0 +1,33 @@
1
+ language: python
2
+ python:
3
+ - "3.7"
4
+ - "3.8"
5
+ - "3.9"
6
+ - "3.10"
7
+ - "3.11"
8
+ cache: pip
9
+
10
+ addons:
11
+ apt:
12
+ packages: &common_packages
13
+ - gfortran
14
+ - libatlas-base-dev
15
+ - liblapack-dev
16
+ - libnetcdf-dev
17
+ - libnetcdff-dev
18
+ - eatmydata
19
+ - ccache
20
+ before_install:
21
+ - if [[ $TRAVIS_PYTHON_VERSION == 3.7 ]]; then pip install -U importlib_metadata; fi
22
+
23
+ install:
24
+ - pip install -r requirements.txt
25
+ - pip install sisl
26
+ - pip install -e .
27
+ script:
28
+ - pwd
29
+ - cd examples/abinit-w90/SrMnO3
30
+ - ls -lah
31
+ - sh get_J.sh
32
+ - cd TB2J_results/Multibinit
33
+ - TB2J_magnon.py --figfname magnon.png
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: TB2J
3
- Version: 0.9.9.4
3
+ Version: 0.9.9.7
4
4
  Summary: TB2J: First principle to Heisenberg exchange J using tight-binding Green function method
5
5
  Author: Xu He
6
6
  Author-email: mailhexu@gmail.com
@@ -21,11 +21,10 @@ Requires-Dist: ase>=3.19
21
21
  Requires-Dist: tqdm
22
22
  Requires-Dist: pathos
23
23
  Requires-Dist: packaging>=20.0
24
- Requires-Dist: HamiltonIO>=0.2.1
24
+ Requires-Dist: HamiltonIO>=0.2.3
25
25
  Requires-Dist: pre-commit
26
26
  Requires-Dist: sympair>0.1.0
27
27
  Requires-Dist: sisl>=0.9.0
28
- Requires-Dist: netcdf4
29
28
  Dynamic: author
30
29
  Dynamic: author-email
31
30
  Dynamic: classifier
@@ -0,0 +1,5 @@
1
+ *.o
2
+ *.x
3
+ *.mod
4
+ exchanges.sublime-project
5
+ exchanges.sublime-workspace
@@ -136,7 +136,7 @@ class JDownfolder_pickle:
136
136
  outpath,
137
137
  qmesh=[7, 7, 7],
138
138
  iso_only=False,
139
- method="pwf",
139
+ method="lowdin",
140
140
  **kwargs,
141
141
  ):
142
142
  self.exc = SpinIO.load_pickle(path=inpath, fname="TB2J.pickle")
@@ -146,6 +146,7 @@ class JDownfolder_pickle:
146
146
  self.ligands = ligands
147
147
  self.outpath = outpath
148
148
  self.method = method
149
+ print("Using method:", self.method)
149
150
 
150
151
  # read atomic structure
151
152
  self.atoms = self.exc.atoms
@@ -176,7 +177,7 @@ class JDownfolder_pickle:
176
177
 
177
178
  def _downfold(self, **kwargs):
178
179
  JR2 = self.exc.get_full_Jtensor_for_Rlist(asr=True)
179
- if self.method == "lowdin":
180
+ if self.method.lower() == "lowdin":
180
181
  d = JDownfolder(
181
182
  JR2,
182
183
  self.exc.Rlist,
@@ -1,7 +1,6 @@
1
1
  import gc
2
2
  from pathlib import Path
3
3
 
4
- import matplotlib.pyplot as plt
5
4
  import numpy as np
6
5
  import tqdm
7
6
  from HamiltonIO.abacus.abacus_wrapper import AbacusSplitSOCParser
@@ -32,7 +31,9 @@ class MAEGreen(ExchangeNCL):
32
31
  """
33
32
  super().__init__(**kwargs)
34
33
  self.natoms = len(self.atoms)
35
- if angles is None or angles == "axis":
34
+ if angles is None or angles == "xyz":
35
+ self.set_angles_xyz()
36
+ elif angles == "axis":
36
37
  self.set_angles_axis()
37
38
  elif angles == "scan":
38
39
  self.set_angles_scan()
@@ -51,6 +52,11 @@ class MAEGreen(ExchangeNCL):
51
52
  self.es_atom = np.zeros((nangles, self.natoms), dtype=complex)
52
53
  self.es_atom_orb = DefaultDict(lambda: 0)
53
54
 
55
+ def set_angles_xyz(self):
56
+ """theta and phi are defined as the x, y, z, xy, yz, xz, xyz, x-yz, -xyz, -x-yz axis."""
57
+ self.thetas = [np.pi / 2, np.pi / 2, 0.0]
58
+ self.phis = [np.pi / 2, 0, 0.0]
59
+
54
60
  def set_angles_axis(self):
55
61
  """theta and phi are defined as the x, y, z, xy, yz, xz, xyz, x-yz, -xyz, -x-yz axis."""
56
62
  self.thetas = [0, np.pi / 2, np.pi / 2, np.pi / 2, np.pi, 0, np.pi / 2, 0, 0, 0]
@@ -75,7 +81,6 @@ class MAEGreen(ExchangeNCL):
75
81
  self.thetas = thetas
76
82
  self.phis = phis
77
83
  self.angle_pairs = list(zip(thetas, phis))
78
- # remove duplicates of angles using sets.
79
84
  self.angle_pairs = list(set(self.angle_pairs))
80
85
  self.thetas, self.phis = zip(*self.angle_pairs)
81
86
 
@@ -248,11 +253,11 @@ class MAEGreen(ExchangeNCL):
248
253
  Path(output_path).mkdir(exist_ok=True)
249
254
  fname = f"{output_path}/MAE.dat"
250
255
  fname_orb = f"{output_path}/MAE_orb.dat"
251
- fname_tensor = f"{output_path}/MAE_tensor.dat"
252
- if figure3d is not None:
253
- fname_fig3d = f"{output_path}/{figure3d}"
254
- if figure_contourf is not None:
255
- fname_figcontourf = f"{output_path}/{figure_contourf}"
256
+ # fname_tensor = f"{output_path}/MAE_tensor.dat"
257
+ # if figure3d is not None:
258
+ # fname_fig3d = f"{output_path}/{figure3d}"
259
+ # if figure_contourf is not None:
260
+ # fname_figcontourf = f"{output_path}/{figure_contourf}"
256
261
 
257
262
  # ouput with eigenvalues.
258
263
  if with_eigen:
@@ -277,18 +282,18 @@ class MAEGreen(ExchangeNCL):
277
282
  f.write(f"{ea*1e3:.8f} ")
278
283
  f.write("\n")
279
284
 
280
- self.ani = self.fit_anisotropy_tensor()
281
- with open(fname_tensor, "w") as f:
282
- f.write("# Anisotropy tensor in meV\n")
283
- f.write(f"{self.ani.tensor_strings(include_isotropic=False)}\n")
285
+ # self.ani = self.fit_anisotropy_tensor()
286
+ # with open(fname_tensor, "w") as f:
287
+ # f.write("# Anisotropy tensor in meV\n")
288
+ # f.write(f"{self.ani.tensor_strings(include_isotropic=False)}\n")
284
289
 
285
- if figure3d is not None:
286
- self.ani.plot_3d(figname=fname_fig3d, show=False)
290
+ # if figure3d is not None:
291
+ # self.ani.plot_3d(figname=fname_fig3d, show=False)
287
292
 
288
- if figure_contourf is not None:
289
- self.ani.plot_contourf(figname=fname_figcontourf, show=False)
293
+ # if figure_contourf is not None:
294
+ # self.ani.plot_contourf(figname=fname_figcontourf, show=False)
290
295
 
291
- plt.close()
296
+ # plt.close()
292
297
  gc.collect()
293
298
 
294
299
  with open(fname_orb, "w") as f: