├── .gitignore ├── AUTHORS.md ├── CHANGELOG.md ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── EXTERNAL_DEPENDENCIES.md ├── FACTORY.md ├── HOWTO_EVENT_HANDLER.md ├── LICENSE ├── README.md ├── References.bib ├── jellyfysh ├── __init__.py ├── activator │ ├── __init__.py │ ├── activator.py │ ├── internal_state │ │ ├── __init__.py │ │ ├── cell_occupancy │ │ │ ├── __init__.py │ │ │ ├── cell_occupancy.py │ │ │ └── cells │ │ │ │ ├── __init__.py │ │ │ │ ├── cells.py │ │ │ │ ├── cuboid_cells.py │ │ │ │ ├── cuboid_periodic_cells.py │ │ │ │ └── periodic_cells.py │ │ ├── internal_state.py │ │ └── single_active_cell_occupancy.py │ ├── tag_activator.py │ └── tagger │ │ ├── __init__.py │ │ ├── abstracts.py │ │ ├── active_global_state_in_state_tagger.py │ │ ├── active_root_unit_in_state_tagger.py │ │ ├── cell_boundary_tagger.py │ │ ├── cell_bounding_potential_tagger.py │ │ ├── cell_veto_tagger.py │ │ ├── excluded_cells_tagger.py │ │ ├── factor_type_map_in_state_tagger.py │ │ ├── factor_type_maps.py │ │ ├── no_in_state_tagger.py │ │ ├── surplus_cells_tagger.py │ │ └── tagger.py ├── base │ ├── __init__.py │ ├── exceptions.py │ ├── factory.py │ ├── initializer.py │ ├── logging.py │ ├── node.py │ ├── particle.py │ ├── strings.py │ ├── time.py │ ├── unit.py │ ├── uuid.py │ └── vectors.py ├── config_files │ ├── 2018_JCP_149_064113 │ │ ├── coulomb_atoms │ │ │ ├── cell_bounded.ini │ │ │ ├── cell_veto.ini │ │ │ ├── power_bounded.ini │ │ │ └── power_bounded_dump.ini │ │ ├── dipoles │ │ │ ├── atom_factors.ini │ │ │ ├── cell_bounded.ini │ │ │ ├── cell_veto.ini │ │ │ ├── dipole_factors_inside_first.ini │ │ │ ├── dipole_factors_outside_first.ini │ │ │ ├── dipole_factors_ratio.ini │ │ │ └── dipole_motion.ini │ │ └── water │ │ │ ├── coulomb_cell_veto_lj_cell_veto.ini │ │ │ ├── coulomb_cell_veto_lj_inverted.ini │ │ │ ├── coulomb_power_bounded_lj_cell_bounded.ini │ │ │ ├── coulomb_power_bounded_lj_inverted.ini │ │ │ └── single_molecule.ini │ ├── factor_set_files │ │ ├── factor_set_coulomb_atoms.txt │ │ ├── factor_set_dipoles_atomic.txt │ │ ├── factor_set_dipoles_dipole.txt │ │ ├── factor_set_hard_disk_dipoles.txt │ │ ├── factor_set_water.txt │ │ └── factor_set_water_atomic.txt │ └── hard_disk_dipoles │ │ ├── 81dipoles_min0.952380952380952_max1.047619047619048.pdb │ │ ├── hard_disk_dipoles.ini │ │ ├── hard_disk_dipoles_cells.ini │ │ └── single_hard_disk_dipole.ini ├── create_examples.py ├── estimator │ ├── __init__.py │ ├── boundary_point_estimator.py │ ├── dipole_inner_point_estimator.py │ ├── dipole_monte_carlo_estimator.py │ ├── estimator.py │ └── inner_point_estimator.py ├── event_handler │ ├── __init__.py │ ├── abstracts │ │ ├── __init__.py │ │ ├── abstracts.py │ │ ├── cell_bounding_potential_event_handler.py │ │ ├── cell_veto_event_handler.py │ │ ├── composite_objects.py │ │ ├── dumping_event_handler.py │ │ ├── end_of_chain_event_handler.py │ │ ├── end_of_run_event_handler.py │ │ ├── event_handler_with_bounding_potential.py │ │ ├── sampling_event_handler.py │ │ └── start_of_run_event_handler.py │ ├── cell_boundary_event_handler.py │ ├── composite_object_cell_veto_event_handler.py │ ├── event_handler.py │ ├── final_time_end_of_run_event_handler.py │ ├── fixed_interval_dumping_event_handler.py │ ├── fixed_interval_sampling_event_handler.py │ ├── fixed_separations_event_handler_with_piecewise_constant_bounding_potential.py │ ├── initial_chain_start_of_run_event_handler.py │ ├── leaf_unit_cell_veto_event_handler.py │ ├── root_leaf_unit_active_switcher.py │ ├── root_unit_active_two_composite_object_summed_bounding_potential_event_handler.py │ ├── root_unit_active_two_leaf_unit_event_handler.py │ ├── single_independent_active_periodic_direction_end_of_chain_event_handler.py │ ├── single_independent_active_sequential_direction_end_of_chain_event_handler.py │ ├── two_composite_object_cell_bounding_potential_event_handler.py │ ├── two_composite_object_summed_bounding_potential_event_handler.py │ ├── two_leaf_unit_bounding_potential_event_handler.py │ ├── two_leaf_unit_cell_bounding_potential_event_handler.py │ ├── two_leaf_unit_event_handler.py │ ├── two_leaf_unit_event_handler_with_piecewise_constant_bounding_potential.py │ └── walker.py ├── input_output_handler │ ├── __init__.py │ ├── input_handler │ │ ├── __init__.py │ │ ├── charge_values.py │ │ ├── input_handler.py │ │ ├── pdb_input_handler.py │ │ ├── random_input_handler.py │ │ └── random_node_creator │ │ │ ├── __init__.py │ │ │ ├── atom_random_node_creator.py │ │ │ ├── dipole_random_node_creator.py │ │ │ ├── random_node_creator.py │ │ │ └── water_random_node_creator.py │ ├── input_output_handler.py │ ├── mdanalysis_import.py │ └── output_handler │ │ ├── __init__.py │ │ ├── abstracts.py │ │ ├── bond_length_and_angle_output_handler.py │ │ ├── dcd_output_handler.py │ │ ├── dummy_output_handler.py │ │ ├── dumping_output_handler.py │ │ ├── output_handler.py │ │ ├── oxygen_oxygen_separation_output_handler.py │ │ ├── pdb_output_handler.py │ │ ├── polarization_output_handler.py │ │ └── separation_output_handler.py ├── lifting │ ├── __init__.py │ ├── inside_first_lifting.py │ ├── lifting.py │ ├── outside_first_lifting.py │ └── ratio_lifting.py ├── mediator │ ├── __init__.py │ ├── mediator.py │ ├── multi_process_mediator │ │ ├── __init__.py │ │ ├── multi_process_mediator.py │ │ └── or_event.py │ └── single_process_mediator.py ├── output │ ├── 2018_JCP_149_064113 │ │ ├── coulomb_atoms │ │ │ ├── ReferenceDataCoulombAtoms.dat │ │ │ └── plot_histogram_coulomb_atoms.py │ │ ├── dipoles │ │ │ ├── ReferenceDataDipoles_13.dat │ │ │ ├── ReferenceDataDipoles_14.dat │ │ │ └── plot_histogram_dipoles.py │ │ └── water │ │ │ ├── ReferenceAngleSingleMolecule.dat │ │ │ ├── ReferenceLengthSingleMolecule.dat │ │ │ ├── ReferenceOOSeparation.dat │ │ │ ├── plot_histogram_single_molecule.py │ │ │ └── plot_histogram_water.py │ ├── __init__.py │ ├── correct_dcd_file.py │ ├── hard_disk_dipoles │ │ ├── ReferenceDataPx_81Dipoles_NewtonianECMC.dat │ │ ├── ReferenceDataPy_81Dipoles_NewtonianECMC.dat │ │ ├── plot_histogram_hard_disk_dipoles.py │ │ ├── plot_histogram_single_hard_disk_dipole.py │ │ └── vmd_trajectory.tcl │ └── plotting_functions.py ├── potential │ ├── __init__.py │ ├── abstracts.py │ ├── bending_potential.py │ ├── cell_bounding_potential.py │ ├── displaced_even_power_potential.py │ ├── hard_dipole_potential.py │ ├── hard_sphere_potential.py │ ├── inverse_power_coulomb_bounding_potential │ │ ├── __init__.py │ │ ├── inverse_power_coulomb_bounding_potential.c │ │ ├── inverse_power_coulomb_bounding_potential.h │ │ ├── inverse_power_coulomb_bounding_potential.py │ │ └── inverse_power_coulomb_bounding_potential_build.py │ ├── inverse_power_potential.py │ ├── lennard_jones_potential.py │ ├── merged_image_coulomb_potential │ │ ├── __init__.py │ │ ├── merged_image_coulomb_potential.c │ │ ├── merged_image_coulomb_potential.h │ │ ├── merged_image_coulomb_potential.py │ │ └── merged_image_coulomb_potential_build.py │ └── potential.py ├── resume.py ├── run.py ├── scheduler │ ├── __init__.py │ ├── heap_scheduler │ │ ├── __init__.py │ │ ├── heap.c │ │ ├── heap.h │ │ ├── heap_build.py │ │ └── heap_scheduler.py │ ├── list_scheduler.py │ └── scheduler.py ├── setting │ ├── __init__.py │ ├── hypercubic_setting.py │ ├── hypercuboid_setting.py │ ├── periodic_boundaries.py │ └── setting.py ├── state_handler │ ├── __init__.py │ ├── lifting_state │ │ ├── __init__.py │ │ ├── lifting_state.py │ │ └── tree_lifting_state.py │ ├── physical_state │ │ ├── __init__.py │ │ ├── physical_state.py │ │ └── tree_physical_state.py │ ├── state_handler.py │ └── tree_state_handler.py └── version.py ├── setup.py └── unittests ├── expanded_test_case.py ├── run_tests.py ├── test_activator ├── __init__.py └── test_internal_state │ ├── __init__.py │ └── test_cell_occupancy │ ├── __init__.py │ └── test_cells │ ├── __init__.py │ ├── test_cuboid_cells.py │ └── test_cuboid_periodic_cells.py ├── test_base ├── __init__.py ├── test_classes_for_factory │ ├── __init__.py │ ├── class_with_list_of_simple_type.py │ ├── custom_class_default_constructable.py │ ├── custom_class_with_abstract_class.py │ ├── simple_abstract_class │ │ ├── __init__.py │ │ ├── simple_abstract_class.py │ │ └── simple_inheriting_class.py │ ├── simple_class_default_constructable.py │ ├── simple_class_in_package │ │ ├── __init__.py │ │ └── simple_class_in_package.py │ └── simple_class_not_default_constructable.py ├── test_factory.py ├── test_initializer.py ├── test_node.py ├── test_particle.py ├── test_strings.py ├── test_time.py ├── test_unit.py ├── test_uuid.py └── test_vectors.py ├── test_config_files ├── __init__.py ├── test_2018_JCP_149_064113 │ ├── __init__.py │ ├── test_coulomb_atoms │ │ ├── __init__.py │ │ ├── test_cell_bounded.py │ │ ├── test_cell_veto.py │ │ └── test_power_bounded.py │ ├── test_dipoles │ │ ├── __init__.py │ │ ├── test_atom_factors.py │ │ ├── test_cell_bounded.py │ │ ├── test_cell_veto.py │ │ ├── test_dipole_factors_inside_first.py │ │ ├── test_dipole_factors_outside_first.py │ │ ├── test_dipole_factors_ratio.py │ │ └── test_dipole_motion.py │ └── test_water │ │ ├── __init__.py │ │ ├── test_coulomb_cell_veto_lj_cell_veto.py │ │ ├── test_coulomb_cell_veto_lj_inverted.py │ │ ├── test_coulomb_power_bounded_lj_cell_bounded.py │ │ ├── test_coulomb_power_bounded_lj_inverted.py │ │ └── test_single_molecule.py └── test_hard_disk_dipoles │ ├── __init__.py │ ├── test_hard_disk_dipoles.py │ ├── test_hard_disk_dipoles_cells.py │ └── test_single_hard_disk_dipole.py ├── test_event_handler ├── __init__.py ├── test_cell_boundary_event_handler.py ├── test_final_time_end_of_run_event_handler.py ├── test_fixed_interval_dumping_event_handler.py ├── test_fixed_interval_sampling_event_handler.py ├── test_fixed_separations_event_handler_with_piecewise_constant_bounding_potential.py ├── test_initial_chain_start_of_run_event_handler.py ├── test_leaf_unit_cell_veto_event_handler.py ├── test_root_leaf_unit_active_switcher.py ├── test_single_independent_active_periodic_direction_end_of_chain_event_handler.py ├── test_single_independent_active_sequential_direction_end_of_chain_event_handler.py ├── test_two_leaf_unit_bounding_potential_event_handler.py ├── test_two_leaf_unit_cell_bounding_potential_event_handler.py ├── test_two_leaf_unit_event_handler.py └── test_two_leaf_unit_event_handler_with_piecewise_constant_bounding_potential.py ├── test_expanded_test_case.py ├── test_input_output_handler ├── __init__.py └── test_input_handler │ ├── __init__.py │ ├── pdb_test_files │ ├── atom_test_2D.pdb │ ├── atom_test_2D_wrong_positions.pdb │ ├── atom_test_2D_wrong_system_box.pdb │ ├── atom_test_origin_0.pdb │ ├── atom_test_origin_l2.pdb │ ├── test_non_equal_composite_point_objects.pdb │ ├── water_test_origin_0.pdb │ ├── water_test_origin_0.wrong_ending │ └── water_test_origin_l2.pdb │ └── test_pdb_input_handler.py ├── test_lifting ├── __init__.py ├── test_inside_first_lifting.py ├── test_outside_first_lifting.py └── 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