├── .gitignore ├── CMakeBoostSetup.txt ├── CMakeCFlagsSetup.txt ├── CMakeCGALSetup.txt ├── CMakeGSLSetup.txt ├── CMakeLists.txt ├── CMakeMiscSetup.txt ├── CMakeSRCSetup.txt ├── CMakeVTKSetup.txt ├── FormerAnalysis ├── Patches_stresses_defects_lib.py ├── StressEnergy_plot.py ├── cells_patches_stresses_defects.py ├── cells_patches_stresses_defects_cells.py ├── energy_profile_lib.py ├── energy_profile_lib_flat.py ├── energy_profile_lib_v.py ├── flat_patches_stresses_defects.py ├── nematic_analysis.py ├── nematic_analysis_version_silke.py ├── nematic_defects_analysis.py ├── particle.py ├── polar_defects_analysis.py ├── polar_defects_analysis_debug.py ├── read_conf.py ├── read_data.py ├── read_param.py ├── sphere_analysis_lib.py └── sphere_patches_stresses_defects.py ├── GPATH ├── GRTAGS ├── GTAGS ├── LICENSE.txt ├── README.md ├── analysis ├── batch_nematic │ ├── batch_analyze_nematic.py │ ├── batch_analyze_nematic_R16.py │ ├── batch_analyze_nematic_R16a.py │ ├── batch_analyze_nematic_R16b.py │ ├── batch_analyze_nematic_R30a.py │ ├── batch_analyze_nematic_R30b.py │ ├── batch_analyze_nematic_R30c.py │ ├── batch_analyze_nematic_R40a.py │ ├── batch_analyze_nematic_R40b.py │ ├── batch_analyze_nematic_R40c.py │ ├── batch_analyze_nematic_R40d.py │ ├── batch_analyze_nematic_R40m.py │ ├── batch_analyze_nematic_R8.py │ ├── batch_analyze_nematic_R8a.py │ ├── batch_analyze_nematic_R8b.py │ ├── batch_analyze_nematic_long16_a.py │ ├── batch_analyze_nematic_long16_b.py │ ├── batch_analyze_nematic_long5_a.py │ ├── batch_analyze_nematic_long5_b.py │ ├── batch_analyze_nematic_long5_c.py │ ├── batch_analyze_nematic_long5_d.py │ ├── batch_analyze_nematic_long5_e.py │ ├── batch_analyze_nematic_longa.py │ ├── batch_analyze_nematic_longb.py │ ├── batch_analyze_nematic_phi0.75.py │ ├── batch_analyze_nematic_phi0.75a.py │ ├── batch_analyze_nematic_phi0.75b.py │ ├── batch_analyze_nematic_phi1.0a.py │ ├── batch_analyze_nematic_phi1.0b.py │ ├── batch_analyze_nematic_v0p2.py │ ├── batch_analyze_nematic_v1p0.py │ └── batch_analyze_nematic_v5p0.py ├── batch_polar │ ├── batch_analyze.py │ ├── batch_analyze_J0.01.py │ ├── batch_analyze_J0.1.py │ ├── batch_analyze_J0.1_0702.py │ ├── batch_analyze_J0.1_0702_a.py │ ├── batch_analyze_J0.1_0702_b.py │ ├── batch_analyze_J1.py │ ├── batch_analyze_J10.py │ ├── batch_analyze_J10_0702.py │ ├── batch_analyze_J10_0702_a.py │ ├── batch_analyze_J10_0702_b.py │ ├── batch_analyze_flat.py │ ├── batch_analyze_flat_J0.01.py │ ├── batch_analyze_flat_J0.1.py │ ├── batch_analyze_flat_J1.py │ ├── batch_analyze_flat_J10.py │ ├── batch_defects_J1_v0.01.py │ ├── batch_defects_J1_v0.05.py │ ├── batch_defects_J1_v0.1.py │ └── batch_defects_J1_v0.5.py ├── plot_analysis_nematic │ ├── angle_plot.py │ ├── angle_plot_pretty.py │ ├── angle_plot_pretty_long.py │ ├── angle_plot_pretty_long_jvar.py │ └── angle_plot_pretty_phi.py ├── plot_analysis_polar │ ├── plot_compare_rvary.py │ ├── plot_order_PRE.py │ ├── plot_order_everything.py │ ├── plot_order_rebuttal.py │ ├── plot_profiles.py │ ├── plot_profiles0120.py │ ├── plot_profiles070.py │ ├── plot_profiles0703.py │ ├── plot_profiles_Rastko.py │ ├── plot_profiles_flat.py │ ├── plot_profiles_oneJ.py │ ├── plot_profiles_polar_v2.py │ ├── plot_profiles_polar_v2_jslices.py │ ├── plot_profiles_polar_v2_nuslices.py │ ├── plot_profiles_polar_v2_vslices.py │ └── plot_profiles_rebuttal.py └── polar_analytics │ ├── profiles_compare_PRE.py │ ├── profiles_compare_silke.py │ ├── profiles_compare_silke0714.py │ └── sphere_chain_order1_compare_analytics.py ├── configurations ├── Cornea │ └── cornea.conf ├── Cornea_flat │ ├── cornea_testing_arrows.pvsm │ ├── plane_circle_cornea.txt │ └── plane_circle_homeo_three_groups.conf ├── MakeConfigurations │ ├── TestRods.dat │ ├── TissueWithObstacle │ │ ├── circle.py │ │ ├── make_initial.py │ │ ├── obstacle.py │ │ ├── particle.py │ │ ├── polygon_test.py │ │ ├── tissue.py │ │ └── wall.py │ ├── cornea.dat │ ├── cornea.py │ ├── cornea.txt │ ├── hexagonal_patch.py │ ├── make_regular_torus.py │ ├── particle.py │ ├── particle_SH.py │ ├── plane_circle.py │ ├── plane_circle_cornea.py │ ├── plane_circle_epithelial.py │ ├── plane_from_file.py │ ├── plane_rod_from_file.py │ ├── random_cylinder.py │ ├── random_peanut.py │ ├── random_plane.py │ ├── random_plane_poly.py │ ├── random_sphere.py │ ├── random_torus.py │ ├── regular_rods.py │ ├── rod_stacks.dat │ ├── stacked_rods.py │ ├── test.dat │ └── triangular_plane.py ├── cells_fixed │ ├── cells_fixed.conf │ ├── fixed.boundary │ └── fixed.input ├── circular_patch │ ├── Cells_patch.conf │ ├── Cells_patch_v2.conf │ ├── cell.log │ ├── make_circular_patch.py │ ├── messages.msg │ ├── particle_tess_dual_cell.pvsm │ └── patch.dat ├── filaments_on_plane │ ├── README │ ├── active_poly.conf │ ├── filaments.angles │ ├── filaments.bonds │ ├── filaments.input │ ├── make_filament.py │ ├── make_filaments.py │ └── make_many.inp ├── gaussian_bump │ ├── README │ ├── bump.dat │ └── soft_on_bump.conf ├── growth │ ├── growth.conf │ ├── sfinal.boundary │ └── sfinal.input ├── lj_langevin │ ├── CellList.py │ ├── CellList2D.py │ ├── langevin_lj.conf │ ├── make_cube.py │ ├── make_planar.py │ └── particles.dat ├── plot_polardefects.psvm ├── population_on_plane │ ├── plane.dat │ └── population_on_plane.conf ├── population_slow_periodic │ ├── flat_velocites.pvsm │ ├── population_on_plane.conf │ └── soft_plane.txt ├── pulling_patch │ ├── epithelial_circle2.txt │ ├── flat_velocites_directors.pvsm │ ├── patches_pressure_director_defects.pvsm │ ├── patches_pressure_velocity_defects.pvsm │ ├── population_on_plane_circle.conf │ └── pulling_patch_10000_pretty.png ├── relax │ ├── out.input │ └── relax.conf ├── rods_on_plane │ ├── rods_on_plane.conf │ └── rods_on_plane.pvsm ├── rods_on_sphere │ ├── rods_on_sphere.conf │ └── rods_on_sphere_aspect4.pvsm ├── soft_on_hourglass │ ├── hourglass.dat │ └── soft_on_hourglass.conf ├── soft_on_plane │ ├── plane.dat │ └── soft_on_plane.conf ├── soft_on_sphere │ ├── soft_on_sphere.conf │ └── sphere.dat ├── two_component_plane │ ├── plane.dat │ └── two_component_plane.conf ├── vicsek_on_plane │ ├── plane.dat │ └── vicsek_on_plane.conf └── vicsek_on_sphere │ ├── sphere.dat │ └── vicsek_on_sphere.conf ├── doc ├── CMakeLists.txt ├── Doxyfile.in ├── DoxygenLayout.xml └── tutorial │ ├── css │ ├── .DS_Store │ ├── bootstrap-theme.css │ ├── bootstrap-theme.css.map │ ├── bootstrap-theme.min.css │ ├── bootstrap-theme.min.css.map │ ├── bootstrap.css │ ├── bootstrap.css.map │ ├── bootstrap.min.css │ └── bootstrap.min.css.map │ ├── docs │ ├── .DS_Store │ └── assets │ │ ├── .DS_Store │ │ └── css │ │ ├── docs.css │ │ └── pygments-manni.css │ ├── examples │ ├── cells_fixed │ │ ├── cells_fixed.conf │ │ ├── fixed.boundary │ │ └── fixed.input │ ├── growth │ │ ├── growth.conf │ │ ├── sfinal.boundary │ │ └── sfinal.input │ ├── relax │ │ ├── out.input │ │ └── relax.conf │ ├── soft_on_sphere │ │ ├── soft_on_sphere.conf │ │ └── sphere.dat │ └── types │ │ ├── epi.boundary │ │ ├── epi.input │ │ └── sorting.conf │ ├── fonts │ ├── glyphicons-halflings-regular.eot │ ├── glyphicons-halflings-regular.svg │ ├── glyphicons-halflings-regular.ttf │ ├── glyphicons-halflings-regular.woff │ └── glyphicons-halflings-regular.woff2 │ ├── images │ ├── boundary_edge_flip.png │ ├── boundary_particle_removal.png │ ├── boundary_topology.png │ ├── fixed_final.png │ ├── grow_export_800.png │ ├── grow_line.png │ ├── model.png │ ├── polar_sphere.jpg │ ├── polar_sphere.png │ ├── samos_organisation.png │ ├── tempsort.png │ ├── tissue_example.jpg │ └── triangle_circumcenter.png │ ├── js │ ├── .DS_Store │ ├── bootstrap.js │ ├── bootstrap.min.js │ ├── menu.js │ └── npm.js │ ├── tissues.html │ └── tutorial.html ├── doxy.conf ├── src ├── CMakeLists.txt ├── aligner │ ├── CMakeLists.txt │ ├── aligner.cpp │ ├── aligner.hpp │ ├── external │ │ ├── CMakeLists.txt │ │ ├── external_ajnematic_aligner.cpp │ │ ├── external_ajnematic_aligner.hpp │ │ ├── external_ajpolar_aligner.cpp │ │ ├── external_ajpolar_aligner.hpp │ │ ├── external_aligner.hpp │ │ ├── external_field_aligner.cpp │ │ ├── external_field_aligner.hpp │ │ ├── external_kenotaxis_aligner.cpp │ │ ├── external_kenotaxis_aligner.hpp │ │ ├── external_piv_aligner.cpp │ │ ├── external_piv_aligner.hpp │ │ ├── external_radial_aligner.cpp │ │ ├── external_radial_aligner.hpp │ │ ├── external_shape_aligner.cpp │ │ ├── external_shape_aligner.hpp │ │ ├── external_tangent_aligner.cpp │ │ └── external_tangent_aligner.hpp │ └── pair │ │ ├── CMakeLists.txt │ │ ├── pair_aligner.hpp │ │ ├── pair_nematic_aligner.cpp │ │ ├── pair_nematic_aligner.hpp │ │ ├── pair_polar_aligner.cpp │ │ ├── pair_polar_aligner.hpp │ │ ├── pair_velocity_aligner.cpp │ │ ├── pair_velocity_aligner.hpp │ │ ├── pair_vicsek_aligner.cpp │ │ └── pair_vicsek_aligner.hpp ├── constraints │ ├── CMakeLists.txt │ ├── constrainer.hpp │ ├── constraint.cpp │ ├── constraint.hpp │ ├── constraint_actomyo.cpp │ ├── constraint_actomyo.hpp │ ├── constraint_cylinder.cpp │ ├── constraint_cylinder.hpp │ ├── constraint_ellipsoid.cpp │ ├── constraint_ellipsoid.hpp │ ├── constraint_gaussian_bump.cpp │ ├── constraint_gaussian_bump.hpp │ ├── constraint_gyroid.cpp │ ├── constraint_gyroid.hpp │ ├── constraint_hourglass.cpp │ ├── constraint_hourglass.hpp │ ├── constraint_none.hpp │ ├── constraint_peanut.cpp │ ├── constraint_peanut.hpp │ ├── constraint_plane.cpp │ ├── constraint_plane.hpp │ ├── constraint_plane_walls.cpp │ ├── constraint_plane_walls.hpp │ ├── constraint_slab.cpp │ ├── constraint_slab.hpp │ ├── constraint_sphere.cpp │ ├── constraint_sphere.hpp │ ├── constraint_tetrahedron.cpp │ ├── constraint_tetrahedron.hpp │ ├── constraint_torus.cpp │ └── constraint_torus.hpp ├── dump │ ├── CMakeLists.txt │ ├── dump.cpp │ └── dump.hpp ├── integrators │ ├── CMakeLists.txt │ ├── integrator.hpp │ ├── integrator_actomyo.cpp │ ├── integrator_actomyo.hpp │ ├── integrator_brownian.cpp │ ├── integrator_brownian.hpp │ ├── integrator_brownian_align.cpp │ ├── integrator_brownian_align.hpp │ ├── integrator_brownian_pos.cpp │ ├── integrator_brownian_pos.hpp │ ├── integrator_brownian_rod.cpp │ ├── integrator_brownian_rod.hpp │ ├── integrator_fire.cpp │ ├── integrator_fire.hpp │ ├── integrator_langevin.cpp │ ├── integrator_langevin.hpp │ ├── integrator_nematic.cpp │ ├── integrator_nematic.hpp │ ├── integrator_nve.cpp │ ├── integrator_nve.hpp │ ├── integrator_sepulveda.cpp │ ├── integrator_sepulveda.hpp │ ├── integrator_vicsek.cpp │ └── integrator_vicsek.hpp ├── log │ ├── CMakeLists.txt │ ├── log.hpp │ ├── log_angle_eng.hpp │ ├── log_area.hpp │ ├── log_bond_eng.hpp │ ├── log_external_eng.hpp │ ├── log_kinetic_eng.hpp │ ├── log_pair_align.hpp │ ├── log_pair_eng.hpp │ ├── log_perim.hpp │ ├── log_size.hpp │ ├── log_step.hpp │ ├── log_vec_velocity.hpp │ ├── log_velocity.hpp │ ├── logger.cpp │ └── logger.hpp ├── messenger │ ├── CMakeLists.txt │ ├── messenger.cpp │ └── messenger.hpp ├── parser │ ├── CMakeLists.txt │ ├── parse_align.hpp │ ├── parse_angle.hpp │ ├── parse_aux.hpp │ ├── parse_bond.hpp │ ├── parse_box.hpp │ ├── parse_command.hpp │ ├── parse_constraint.hpp │ ├── parse_disable.hpp │ ├── parse_external.hpp │ ├── parse_external_align.hpp │ ├── parse_group.hpp │ ├── parse_input.hpp │ ├── parse_integrator.hpp │ ├── parse_log_dump.hpp │ ├── parse_parameters.hpp │ ├── parse_population.hpp │ ├── parse_population_disable.hpp │ ├── parse_potential.hpp │ ├── parse_rng_seed.hpp │ ├── parse_run.hpp │ └── parse_timestep.hpp ├── population │ ├── CMakeLists.txt │ ├── population.hpp │ ├── population_actomyosin.cpp │ ├── population_actomyosin.hpp │ ├── population_actomyosin_head.cpp │ ├── population_actomyosin_head.hpp │ ├── population_actomyosin_molecule.cpp │ ├── population_actomyosin_molecule.hpp │ ├── population_actomyosin_poisson.cpp │ ├── population_actomyosin_poisson.hpp │ ├── population_cell.cpp │ ├── population_cell.hpp │ ├── population_density.cpp │ ├── population_density.hpp │ ├── population_elongation.cpp │ ├── population_elongation.hpp │ ├── population_growth.cpp │ ├── population_growth.hpp │ ├── population_random.cpp │ ├── population_random.hpp │ ├── population_region.cpp │ └── population_region.hpp ├── potentials │ ├── CMakeLists.txt │ ├── angle │ │ ├── CMakeLists.txt │ │ ├── angle_cosine_potential.cpp │ │ ├── angle_cosine_potential.hpp │ │ ├── angle_harmonic_potential.cpp │ │ ├── angle_harmonic_potential.hpp │ │ └── angle_potential.hpp │ ├── bond │ │ ├── CMakeLists.txt │ │ ├── bond_active_force.cpp │ │ ├── bond_active_force.hpp │ │ ├── bond_fene_potential.cpp │ │ ├── bond_fene_potential.hpp │ │ ├── bond_harmonic_potential.cpp │ │ ├── bond_harmonic_potential.hpp │ │ └── bond_potential.hpp │ ├── external │ │ ├── CMakeLists.txt │ │ ├── external_boundary_pull.cpp │ │ ├── external_boundary_pull.hpp │ │ ├── external_gravity_potential.cpp │ │ ├── external_gravity_potential.hpp │ │ ├── external_harmonic_potential.cpp │ │ ├── external_harmonic_potential.hpp │ │ ├── external_potential.hpp │ │ ├── external_self_propulsion.cpp │ │ └── external_self_propulsion.hpp │ ├── pair │ │ ├── CMakeLists.txt │ │ ├── pair_active_nematic_potential.cpp │ │ ├── pair_active_nematic_potential.hpp │ │ ├── pair_active_potential.cpp │ │ ├── pair_active_potential.hpp │ │ ├── pair_bare_coulomb_potential.cpp │ │ ├── pair_bare_coulomb_potential.hpp │ │ ├── pair_boundary_attraction_potential.cpp │ │ ├── pair_boundary_attraction_potential.hpp │ │ ├── pair_boundary_bending_potential.cpp │ │ ├── pair_boundary_bending_potential.hpp │ │ ├── pair_coulomb3_potential.cpp │ │ ├── pair_coulomb3_potential.hpp │ │ ├── pair_coulomb_potential.cpp │ │ ├── pair_coulomb_potential.hpp │ │ ├── pair_gaussian_potential.cpp │ │ ├── pair_gaussian_potential.hpp │ │ ├── pair_line_tension_potential.cpp │ │ ├── pair_line_tension_potential.hpp │ │ ├── pair_lj_potential.cpp │ │ ├── pair_lj_potential.hpp │ │ ├── pair_ljrod_potential.cpp │ │ ├── pair_ljrod_potential.hpp │ │ ├── pair_morse_potential.cpp │ │ ├── pair_morse_potential.hpp │ │ ├── pair_motor_potential.cpp │ │ ├── pair_motor_potential.hpp │ │ ├── pair_potential.hpp │ │ ├── pair_rod_potential.cpp │ │ ├── pair_rod_potential.hpp │ │ ├── pair_soft_attractive_potential.cpp │ │ ├── pair_soft_attractive_potential.hpp │ │ ├── pair_soft_potential.cpp │ │ ├── pair_soft_potential.hpp │ │ ├── pair_vertex_particle_potential.cpp │ │ ├── pair_vertex_particle_potential.hpp │ │ ├── pair_yukawa_potential.cpp │ │ └── pair_yukawa_potential.hpp │ ├── potential.cpp │ └── potential.hpp ├── samos.cpp ├── samos.hpp ├── system │ ├── CMakeLists.txt │ ├── angle.hpp │ ├── bond.hpp │ ├── box.hpp │ ├── cell.hpp │ ├── cell_list.cpp │ ├── cell_list.hpp │ ├── defaults.hpp │ ├── edge.cpp │ ├── edge.hpp │ ├── face.cpp │ ├── face.hpp │ ├── group.hpp │ ├── matrix3d.cpp │ ├── matrix3d.hpp │ ├── mesh.cpp │ ├── mesh.hpp │ ├── neighbour_list.cpp │ ├── neighbour_list.hpp │ ├── particle.cpp │ ├── particle.hpp │ ├── system.cpp │ ├── system.hpp │ ├── value.hpp │ ├── vector3d.cpp │ ├── vector3d.hpp │ ├── vertex.cpp │ └── vertex.hpp └── utils │ ├── CMakeLists.txt │ ├── class_factory.hpp │ ├── factory_types.hpp │ ├── register.hpp │ ├── register_angle_potentials.cpp │ ├── register_bond_potentials.cpp │ ├── register_constraints.cpp │ ├── register_external_aligners.cpp │ ├── register_external_potentials.cpp │ ├── register_integrators.cpp │ ├── register_pair_aligners.cpp │ ├── register_pair_potentials.cpp │ ├── register_populations.cpp │ ├── register_values.cpp │ ├── rng.cpp │ └── rng.hpp └── utils ├── AnalyzeCellConfiguration.py ├── AnalyzeConfiguration.py ├── AnalyzeConfigurationDebug.py ├── AnalyzeConfigurationSingle.py ├── AnalyzeConfiguration_helper.py ├── AnalyzeGlassy.py ├── AnalyzeModes.py ├── CellConfiguration.py ├── CellGlassy.py ├── CellList.py ├── CellList2D.py ├── Configuration.py ├── ConfigurationNoParameters.py ├── Defects.py ├── Detailed_tracking.py ├── Geometry.py ├── GetConfigurationData_sphere.py ├── Glassy.py ├── Hessian.py ├── Hessian2d.py ├── InitialAnalysis ├── dat2vtk.py ├── energy_profile.py ├── find_dist.py ├── inertia.py ├── interparticle_dist.py ├── op.py ├── order_param.py ├── plane_vel_correl.py ├── sphere_vel_correl.py ├── vel_histo.py └── vtktools.py ├── Interaction.py ├── NematicTracking.py ├── OneConfiguration.py ├── Profiles.py ├── RastkoVisu ├── dat2vtp.py ├── dir2mol2.py ├── msd.py ├── particle_tracking.py ├── pot_energy_plot.py ├── read_data.py ├── read_data.pyc ├── read_data_SH.py └── vel2pov.py ├── Tesselation.py ├── Writer.py ├── make_circular_patch.py ├── particle.py ├── patch_configurations.py ├── pvmodel ├── README ├── analyse_cells.py ├── build_epithilial.py ├── cellmesh.py ├── cmplotting.py ├── constructmesh.py ├── ioutils.py ├── maingen.py ├── old_cmplotting.py ├── particle.py ├── read_data.py ├── senario.py ├── test_cellmesh.py ├── test_construct.py ├── tmp_read_data.py ├── transitions.py └── writemesh.py ├── read_conf.py ├── read_data.py ├── 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