agox 3.7.0__tar.gz → 3.7.0rc1__tar.gz

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Files changed (461) hide show
  1. {agox-3.7.0/agox.egg-info → agox-3.7.0rc1}/PKG-INFO +1 -1
  2. {agox-3.7.0 → agox-3.7.0rc1/agox.egg-info}/PKG-INFO +1 -1
  3. {agox-3.7.0 → agox-3.7.0rc1}/LICENSE.txt +0 -0
  4. {agox-3.7.0 → agox-3.7.0rc1}/MANIFEST.in +0 -0
  5. {agox-3.7.0 → agox-3.7.0rc1}/README.md +0 -0
  6. {agox-3.7.0 → agox-3.7.0rc1}/agox/__init__.py +0 -0
  7. {agox-3.7.0 → agox-3.7.0rc1}/agox/acquisitors/ABC_acquisitor.py +0 -0
  8. {agox-3.7.0 → agox-3.7.0rc1}/agox/acquisitors/EI.py +0 -0
  9. {agox-3.7.0 → agox-3.7.0rc1}/agox/acquisitors/LCB.py +0 -0
  10. {agox-3.7.0 → agox-3.7.0rc1}/agox/acquisitors/LCB_power.py +0 -0
  11. {agox-3.7.0 → agox-3.7.0rc1}/agox/acquisitors/__init__.py +0 -0
  12. {agox-3.7.0 → agox-3.7.0rc1}/agox/candidates/ABC_candidate.py +0 -0
  13. {agox-3.7.0 → agox-3.7.0rc1}/agox/candidates/__init__.py +0 -0
  14. {agox-3.7.0 → agox-3.7.0rc1}/agox/candidates/standard.py +0 -0
  15. {agox-3.7.0 → agox-3.7.0rc1}/agox/cli/__init__.py +0 -0
  16. {agox-3.7.0 → agox-3.7.0rc1}/agox/cli/cli_analysis.py +0 -0
  17. {agox-3.7.0 → agox-3.7.0rc1}/agox/cli/cli_convert.py +0 -0
  18. {agox-3.7.0 → agox-3.7.0rc1}/agox/cli/cli_example.py +0 -0
  19. {agox-3.7.0 → agox-3.7.0rc1}/agox/cli/cli_graph_sorting.py +0 -0
  20. {agox-3.7.0 → agox-3.7.0rc1}/agox/cli/cli_notebook.py +0 -0
  21. {agox-3.7.0 → agox-3.7.0rc1}/agox/cli/main.py +0 -0
  22. {agox-3.7.0 → agox-3.7.0rc1}/agox/collectors/ABC_collector.py +0 -0
  23. {agox-3.7.0 → agox-3.7.0rc1}/agox/collectors/__init__.py +0 -0
  24. {agox-3.7.0 → agox-3.7.0rc1}/agox/collectors/ray_collector.py +0 -0
  25. {agox-3.7.0 → agox-3.7.0rc1}/agox/collectors/standard.py +0 -0
  26. {agox-3.7.0 → agox-3.7.0rc1}/agox/databases/ABC_database.py +0 -0
  27. {agox-3.7.0 → agox-3.7.0rc1}/agox/databases/__init__.py +0 -0
  28. {agox-3.7.0 → agox-3.7.0rc1}/agox/databases/concurrent_ordered.py +0 -0
  29. {agox-3.7.0 → agox-3.7.0rc1}/agox/databases/database.py +0 -0
  30. {agox-3.7.0 → agox-3.7.0rc1}/agox/databases/database_concurrent.py +0 -0
  31. {agox-3.7.0 → agox-3.7.0rc1}/agox/databases/database_utilities.py +0 -0
  32. {agox-3.7.0 → agox-3.7.0rc1}/agox/environments/ABC_environment.py +0 -0
  33. {agox-3.7.0 → agox-3.7.0rc1}/agox/environments/__init__.py +0 -0
  34. {agox-3.7.0 → agox-3.7.0rc1}/agox/environments/environment.py +0 -0
  35. {agox-3.7.0 → agox-3.7.0rc1}/agox/evaluators/ABC_evaluator.py +0 -0
  36. {agox-3.7.0 → agox-3.7.0rc1}/agox/evaluators/__init__.py +0 -0
  37. {agox-3.7.0 → agox-3.7.0rc1}/agox/evaluators/local_optimization.py +0 -0
  38. {agox-3.7.0 → agox-3.7.0rc1}/agox/evaluators/rattle.py +0 -0
  39. {agox-3.7.0 → agox-3.7.0rc1}/agox/evaluators/single_point.py +0 -0
  40. {agox-3.7.0 → agox-3.7.0rc1}/agox/generators/ABC_generator.py +0 -0
  41. {agox-3.7.0 → agox-3.7.0rc1}/agox/generators/MD.py +0 -0
  42. {agox-3.7.0 → agox-3.7.0rc1}/agox/generators/__init__.py +0 -0
  43. {agox-3.7.0 → agox-3.7.0rc1}/agox/generators/block_generators/ABC_block.py +0 -0
  44. {agox-3.7.0 → agox-3.7.0rc1}/agox/generators/block_generators/__init__.py +0 -0
  45. {agox-3.7.0 → agox-3.7.0rc1}/agox/generators/block_generators/random.py +0 -0
  46. {agox-3.7.0 → agox-3.7.0rc1}/agox/generators/block_generators/rattle.py +0 -0
  47. {agox-3.7.0 → agox-3.7.0rc1}/agox/generators/ce_generator.py +0 -0
  48. {agox-3.7.0 → agox-3.7.0rc1}/agox/generators/cog.py +0 -0
  49. {agox-3.7.0 → agox-3.7.0rc1}/agox/generators/complementary_energy/__init__.py +0 -0
  50. {agox-3.7.0 → agox-3.7.0rc1}/agox/generators/complementary_energy/attractor_methods/ABC_attractors.py +0 -0
  51. {agox-3.7.0 → agox-3.7.0rc1}/agox/generators/complementary_energy/attractor_methods/__init__.py +0 -0
  52. {agox-3.7.0 → agox-3.7.0rc1}/agox/generators/complementary_energy/attractor_methods/ce_attractors_another_structure.py +0 -0
  53. {agox-3.7.0 → agox-3.7.0rc1}/agox/generators/complementary_energy/attractor_methods/ce_attractors_current_structure.py +0 -0
  54. {agox-3.7.0 → agox-3.7.0rc1}/agox/generators/complementary_energy/attractor_methods/ce_attractors_interpolation.py +0 -0
  55. {agox-3.7.0 → agox-3.7.0rc1}/agox/generators/complementary_energy/attractor_methods/ce_attractors_kmeans.py +0 -0
  56. {agox-3.7.0 → agox-3.7.0rc1}/agox/generators/complementary_energy/ce_calculators.py +0 -0
  57. {agox-3.7.0 → agox-3.7.0rc1}/agox/generators/permutation.py +0 -0
  58. {agox-3.7.0 → agox-3.7.0rc1}/agox/generators/random.py +0 -0
  59. {agox-3.7.0 → agox-3.7.0rc1}/agox/generators/rattle.py +0 -0
  60. {agox-3.7.0 → agox-3.7.0rc1}/agox/generators/replace.py +0 -0
  61. {agox-3.7.0 → agox-3.7.0rc1}/agox/generators/reuse.py +0 -0
  62. {agox-3.7.0 → agox-3.7.0rc1}/agox/generators/sampling.py +0 -0
  63. {agox-3.7.0 → agox-3.7.0rc1}/agox/generators/steepest_descent.py +0 -0
  64. {agox-3.7.0 → agox-3.7.0rc1}/agox/generators/symmetry.py +0 -0
  65. {agox-3.7.0 → agox-3.7.0rc1}/agox/generators/symmetry_permutation.py +0 -0
  66. {agox-3.7.0 → agox-3.7.0rc1}/agox/generators/symmetry_rattle.py +0 -0
  67. {agox-3.7.0 → agox-3.7.0rc1}/agox/generators/symmetry_utils/__init__.py +0 -0
  68. {agox-3.7.0 → agox-3.7.0rc1}/agox/generators/symmetry_utils/symmetry_enforcer.py +0 -0
  69. {agox-3.7.0 → agox-3.7.0rc1}/agox/generators/symmetry_utils/symmetry_groups.py +0 -0
  70. {agox-3.7.0 → agox-3.7.0rc1}/agox/helpers/__init__.py +0 -0
  71. {agox-3.7.0 → agox-3.7.0rc1}/agox/helpers/confinement.py +0 -0
  72. {agox-3.7.0 → agox-3.7.0rc1}/agox/helpers/gpaw_io.py +0 -0
  73. {agox-3.7.0 → agox-3.7.0rc1}/agox/helpers/gpaw_subprocess.py +0 -0
  74. {agox-3.7.0 → agox-3.7.0rc1}/agox/main.py +0 -0
  75. {agox-3.7.0 → agox-3.7.0rc1}/agox/models/ABC_model.py +0 -0
  76. {agox-3.7.0 → agox-3.7.0rc1}/agox/models/GPR/GPR.py +0 -0
  77. {agox-3.7.0 → agox-3.7.0rc1}/agox/models/GPR/__init__.py +0 -0
  78. {agox-3.7.0 → agox-3.7.0rc1}/agox/models/GPR/kernels/__init__.py +0 -0
  79. {agox-3.7.0 → agox-3.7.0rc1}/agox/models/GPR/kernels/kernels.py +0 -0
  80. {agox-3.7.0 → agox-3.7.0rc1}/agox/models/GPR/local_mean.py +0 -0
  81. {agox-3.7.0 → agox-3.7.0rc1}/agox/models/GPR/priors/__init__.py +0 -0
  82. {agox-3.7.0 → agox-3.7.0rc1}/agox/models/GPR/priors/repulsive.c +0 -0
  83. {agox-3.7.0 → agox-3.7.0rc1}/agox/models/GPR/priors/repulsive.pyx +0 -0
  84. {agox-3.7.0 → agox-3.7.0rc1}/agox/models/GPR/priors/setup.py +0 -0
  85. {agox-3.7.0 → agox-3.7.0rc1}/agox/models/GPR/sGPR.py +0 -0
  86. {agox-3.7.0 → agox-3.7.0rc1}/agox/models/GPR/sGPR_ensemble.py +0 -0
  87. {agox-3.7.0 → agox-3.7.0rc1}/agox/models/__init__.py +0 -0
  88. {agox-3.7.0 → agox-3.7.0rc1}/agox/models/datasets/Ag5O3-dataset.traj +0 -0
  89. {agox-3.7.0 → agox-3.7.0rc1}/agox/models/datasets/__init__.py +0 -0
  90. {agox-3.7.0 → agox-3.7.0rc1}/agox/models/datasets/loader.py +0 -0
  91. {agox-3.7.0 → agox-3.7.0rc1}/agox/models/descriptors/ABC_descriptor.py +0 -0
  92. {agox-3.7.0 → agox-3.7.0rc1}/agox/models/descriptors/__init__.py +0 -0
  93. {agox-3.7.0 → agox-3.7.0rc1}/agox/models/descriptors/acsf.py +0 -0
  94. {agox-3.7.0 → agox-3.7.0rc1}/agox/models/descriptors/exponential_density.py +0 -0
  95. {agox-3.7.0 → agox-3.7.0rc1}/agox/models/descriptors/fingerprint.py +0 -0
  96. {agox-3.7.0 → agox-3.7.0rc1}/agox/models/descriptors/fingerprint_cython/__init__.py +0 -0
  97. {agox-3.7.0 → agox-3.7.0rc1}/agox/models/descriptors/fingerprint_cython/angular_fingerprintFeature_cy.c +0 -0
  98. {agox-3.7.0 → agox-3.7.0rc1}/agox/models/descriptors/fingerprint_cython/angular_fingerprintFeature_cy.pyx +0 -0
  99. {agox-3.7.0 → agox-3.7.0rc1}/agox/models/descriptors/fingerprint_cython/setup.py +0 -0
  100. {agox-3.7.0 → agox-3.7.0rc1}/agox/models/descriptors/scale_select_descriptor.py +0 -0
  101. {agox-3.7.0 → agox-3.7.0rc1}/agox/models/descriptors/simple_fingerprint.py +0 -0
  102. {agox-3.7.0 → agox-3.7.0rc1}/agox/models/descriptors/soap.py +0 -0
  103. {agox-3.7.0 → agox-3.7.0rc1}/agox/models/descriptors/spectral_graph_descriptor.py +0 -0
  104. {agox-3.7.0 → agox-3.7.0rc1}/agox/models/descriptors/type_descriptor.py +0 -0
  105. {agox-3.7.0 → agox-3.7.0rc1}/agox/models/descriptors/voronoi.py +0 -0
  106. {agox-3.7.0 → agox-3.7.0rc1}/agox/models/priors/constant.py +0 -0
  107. {agox-3.7.0 → agox-3.7.0rc1}/agox/models/schnetpack/__init__.py +0 -0
  108. {agox-3.7.0 → agox-3.7.0rc1}/agox/models/schnetpack/schnetpack.py +0 -0
  109. {agox-3.7.0 → agox-3.7.0rc1}/agox/module.py +0 -0
  110. {agox-3.7.0 → agox-3.7.0rc1}/agox/observer.py +0 -0
  111. {agox-3.7.0 → agox-3.7.0rc1}/agox/postprocessors/ABC_postprocess.py +0 -0
  112. {agox-3.7.0 → agox-3.7.0rc1}/agox/postprocessors/__init__.py +0 -0
  113. {agox-3.7.0 → agox-3.7.0rc1}/agox/postprocessors/centering.py +0 -0
  114. {agox-3.7.0 → agox-3.7.0rc1}/agox/postprocessors/disjoint_filtering.py +0 -0
  115. {agox-3.7.0 → agox-3.7.0rc1}/agox/postprocessors/immunizer.py +0 -0
  116. {agox-3.7.0 → agox-3.7.0rc1}/agox/postprocessors/minimum_dist.py +0 -0
  117. {agox-3.7.0 → agox-3.7.0rc1}/agox/postprocessors/optimizers/__init__.py +0 -0
  118. {agox-3.7.0 → agox-3.7.0rc1}/agox/postprocessors/optimizers/safe_bfgs.py +0 -0
  119. {agox-3.7.0 → agox-3.7.0rc1}/agox/postprocessors/ray_relax.py +0 -0
  120. {agox-3.7.0 → agox-3.7.0rc1}/agox/postprocessors/relax.py +0 -0
  121. {agox-3.7.0 → agox-3.7.0rc1}/agox/postprocessors/wrap.py +0 -0
  122. {agox-3.7.0 → agox-3.7.0rc1}/agox/samplers/ABC_sampler.py +0 -0
  123. {agox-3.7.0 → agox-3.7.0rc1}/agox/samplers/__init__.py +0 -0
  124. {agox-3.7.0 → agox-3.7.0rc1}/agox/samplers/fixed_sampler.py +0 -0
  125. {agox-3.7.0 → agox-3.7.0rc1}/agox/samplers/genetic.py +0 -0
  126. {agox-3.7.0 → agox-3.7.0rc1}/agox/samplers/kernel_similarity.py +0 -0
  127. {agox-3.7.0 → agox-3.7.0rc1}/agox/samplers/kmeans.py +0 -0
  128. {agox-3.7.0 → agox-3.7.0rc1}/agox/samplers/metropolis.py +0 -0
  129. {agox-3.7.0 → agox-3.7.0rc1}/agox/samplers/parallel_tempering_sampler.py +0 -0
  130. {agox-3.7.0 → agox-3.7.0rc1}/agox/samplers/spectral_graph.py +0 -0
  131. {agox-3.7.0 → agox-3.7.0rc1}/agox/test/.coveragerc +0 -0
  132. {agox-3.7.0 → agox-3.7.0rc1}/agox/test/__init__.py +0 -0
  133. {agox-3.7.0 → agox-3.7.0rc1}/agox/test/acquisitor_test/test_lcb.py +0 -0
  134. {agox-3.7.0 → agox-3.7.0rc1}/agox/test/conftest.py +0 -0
  135. {agox-3.7.0 → agox-3.7.0rc1}/agox/test/database_tests/database_test.py +0 -0
  136. {agox-3.7.0 → agox-3.7.0rc1}/agox/test/datasets/AgO-dataset.traj +0 -0
  137. {agox-3.7.0 → agox-3.7.0rc1}/agox/test/datasets/B12-dataset.traj +0 -0
  138. {agox-3.7.0 → agox-3.7.0rc1}/agox/test/datasets/C30-dataset.traj +0 -0
  139. {agox-3.7.0 → agox-3.7.0rc1}/agox/test/datasets/databases/mos2_databases/db1.db +0 -0
  140. {agox-3.7.0 → agox-3.7.0rc1}/agox/test/datasets/databases/mos2_databases/db2.db +0 -0
  141. {agox-3.7.0 → agox-3.7.0rc1}/agox/test/descriptor_tests/expected_outputs/SOAP_AgO.pckl +0 -0
  142. {agox-3.7.0 → agox-3.7.0rc1}/agox/test/descriptor_tests/expected_outputs/SOAP_B12.pckl +0 -0
  143. {agox-3.7.0 → agox-3.7.0rc1}/agox/test/descriptor_tests/expected_outputs/SOAP_C30.pckl +0 -0
  144. {agox-3.7.0 → agox-3.7.0rc1}/agox/test/descriptor_tests/soap_test.py +0 -0
  145. {agox-3.7.0 → agox-3.7.0rc1}/agox/test/descriptor_tests/spectral_graph_test.py +0 -0
  146. {agox-3.7.0 → agox-3.7.0rc1}/agox/test/empty_cache.py +0 -0
  147. {agox-3.7.0 → agox-3.7.0rc1}/agox/test/environment_tests/environment_test.py +0 -0
  148. {agox-3.7.0 → agox-3.7.0rc1}/agox/test/generator_tests/conftest.py +0 -0
  149. {agox-3.7.0 → agox-3.7.0rc1}/agox/test/generator_tests/expected_outputs/CenterOfGeometryGenerator_dataAgO_parameter0.pckl +0 -0
  150. {agox-3.7.0 → agox-3.7.0rc1}/agox/test/generator_tests/expected_outputs/CenterOfGeometryGenerator_dataAgO_parameter1.pckl +0 -0
  151. {agox-3.7.0 → agox-3.7.0rc1}/agox/test/generator_tests/expected_outputs/CenterOfGeometryGenerator_dataAgO_parameter2.pckl +0 -0
  152. {agox-3.7.0 → agox-3.7.0rc1}/agox/test/generator_tests/expected_outputs/CenterOfGeometryGenerator_dataB12_parameter0.pckl +0 -0
  153. {agox-3.7.0 → agox-3.7.0rc1}/agox/test/generator_tests/expected_outputs/CenterOfGeometryGenerator_dataB12_parameter1.pckl +0 -0
  154. {agox-3.7.0 → agox-3.7.0rc1}/agox/test/generator_tests/expected_outputs/CenterOfGeometryGenerator_dataB12_parameter2.pckl +0 -0
  155. {agox-3.7.0 → agox-3.7.0rc1}/agox/test/generator_tests/expected_outputs/CenterOfGeometryGenerator_dataC30_parameter0.pckl +0 -0
  156. {agox-3.7.0 → agox-3.7.0rc1}/agox/test/generator_tests/expected_outputs/CenterOfGeometryGenerator_dataC30_parameter1.pckl +0 -0
  157. {agox-3.7.0 → agox-3.7.0rc1}/agox/test/generator_tests/expected_outputs/CenterOfGeometryGenerator_dataC30_parameter2.pckl +0 -0
  158. {agox-3.7.0 → agox-3.7.0rc1}/agox/test/generator_tests/expected_outputs/PermutationGenerator_dataAgO_parameter0.pckl +0 -0
  159. {agox-3.7.0 → agox-3.7.0rc1}/agox/test/generator_tests/expected_outputs/PermutationGenerator_dataAgO_parameter1.pckl +0 -0
  160. {agox-3.7.0 → agox-3.7.0rc1}/agox/test/generator_tests/expected_outputs/PermutationGenerator_dataAgO_parameter2.pckl +0 -0
  161. {agox-3.7.0 → agox-3.7.0rc1}/agox/test/generator_tests/expected_outputs/RandomGenerator_dataAgO_parameter0.pckl +0 -0
  162. {agox-3.7.0 → agox-3.7.0rc1}/agox/test/generator_tests/expected_outputs/RandomGenerator_dataAgO_parameter1.pckl +0 -0
  163. {agox-3.7.0 → agox-3.7.0rc1}/agox/test/generator_tests/expected_outputs/RandomGenerator_dataAgO_parameter2.pckl +0 -0
  164. {agox-3.7.0 → agox-3.7.0rc1}/agox/test/generator_tests/expected_outputs/RandomGenerator_dataB12_parameter0.pckl +0 -0
  165. {agox-3.7.0 → agox-3.7.0rc1}/agox/test/generator_tests/expected_outputs/RandomGenerator_dataB12_parameter1.pckl +0 -0
  166. {agox-3.7.0 → agox-3.7.0rc1}/agox/test/generator_tests/expected_outputs/RandomGenerator_dataB12_parameter2.pckl +0 -0
  167. {agox-3.7.0 → agox-3.7.0rc1}/agox/test/generator_tests/expected_outputs/RandomGenerator_dataC30_parameter0.pckl +0 -0
  168. {agox-3.7.0 → agox-3.7.0rc1}/agox/test/generator_tests/expected_outputs/RandomGenerator_dataC30_parameter1.pckl +0 -0
  169. {agox-3.7.0 → agox-3.7.0rc1}/agox/test/generator_tests/expected_outputs/RandomGenerator_dataC30_parameter2.pckl +0 -0
  170. {agox-3.7.0 → agox-3.7.0rc1}/agox/test/generator_tests/expected_outputs/RattleGenerator_dataAgO_parameter0.pckl +0 -0
  171. {agox-3.7.0 → agox-3.7.0rc1}/agox/test/generator_tests/expected_outputs/RattleGenerator_dataAgO_parameter1.pckl +0 -0
  172. {agox-3.7.0 → agox-3.7.0rc1}/agox/test/generator_tests/expected_outputs/RattleGenerator_dataAgO_parameter2.pckl +0 -0
  173. {agox-3.7.0 → agox-3.7.0rc1}/agox/test/generator_tests/expected_outputs/RattleGenerator_dataB12_parameter0.pckl +0 -0
  174. {agox-3.7.0 → agox-3.7.0rc1}/agox/test/generator_tests/expected_outputs/RattleGenerator_dataB12_parameter1.pckl +0 -0
  175. {agox-3.7.0 → agox-3.7.0rc1}/agox/test/generator_tests/expected_outputs/RattleGenerator_dataB12_parameter2.pckl +0 -0
  176. {agox-3.7.0 → agox-3.7.0rc1}/agox/test/generator_tests/expected_outputs/RattleGenerator_dataC30_parameter0.pckl +0 -0
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  Metadata-Version: 2.1
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  Name: agox
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- Version: 3.7.0
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+ Version: 3.7.0rc1
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  Summary: Atomistic Global Optimziation X is a framework for structure optimization in materials science.
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  Author: AGOX Developers
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  Author-email: "Mads-Peter V. Christiansen" <machri@phys.au.dk>, Nikolaj Rønne <nronne@phys.au.dk>, Bjørk Hammer <hammer@phys.au.dk>
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  Metadata-Version: 2.1
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  Name: agox
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- Version: 3.7.0
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+ Version: 3.7.0rc1
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  Summary: Atomistic Global Optimziation X is a framework for structure optimization in materials science.
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  Author: AGOX Developers
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  Author-email: "Mads-Peter V. Christiansen" <machri@phys.au.dk>, Nikolaj Rønne <nronne@phys.au.dk>, Bjørk Hammer <hammer@phys.au.dk>
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