├── .gitignore ├── .gitmodules ├── LICENSE.txt ├── Laplace_kernels ├── Laplace_kernels_numba.py └── Laplace_kernels_stkfmm.py ├── Lubrication ├── Lub_Solver.py ├── Lubrication_Class.cc ├── Lubrication_Examples │ ├── Colloidal_Quasicrystal │ │ ├── Ladder_to_Ring │ │ │ ├── inputfile_suspension.dat │ │ │ ├── main_chain.py │ │ │ └── suspension_ladder_N_6_random.clones │ │ ├── Plot_Data.m │ │ ├── README.md │ │ ├── Rhombus_to_Sigma │ │ │ ├── inputfile_suspension.dat │ │ │ ├── main_chain.py │ │ │ ├── random_states │ │ │ │ ├── .random_state │ │ │ │ ├── suspension_rhombus_N_12_random.random_state │ │ │ │ ├── suspension_rhombus_N_12_random_eq1.random_state │ │ │ │ └── suspension_rhombus_N_12_random_eq2.random_state │ │ │ ├── suspension_rhombus_N_12_random.clones │ │ │ ├── suspension_rhombus_N_12_random_eq1.clones │ │ │ └── suspension_rhombus_N_12_random_eq2.clones │ │ ├── Rot_From_Q.m │ │ ├── Square_to_Diamond │ │ │ ├── inputfile_suspension.dat │ │ │ ├── main_chain.py │ │ │ └── suspension_diamond_N_4_random.clones │ │ ├── blob.vertex │ │ ├── data │ │ │ └── README.md │ │ ├── mArrow3.m │ │ └── multi_bodies_functions.py │ ├── Colloidal_Sheets │ │ ├── README.md │ │ ├── blob.vertex │ │ ├── coors_50_layer10_rotxz30.clones │ │ ├── data │ │ │ └── README.md │ │ ├── inputfile_suspension.dat │ │ ├── main_chain.py │ │ └── multi_bodies_functions.py │ ├── Magnetic_Chain_With_Twist │ │ ├── README.md │ │ ├── Rot_From_Q.m │ │ ├── S_curve_60.clones │ │ ├── blob.vertex │ │ ├── chain_60.clones │ │ ├── chain_gen.m │ │ ├── chain_plot.m │ │ ├── hairpin_60.clones │ │ ├── inputfile_chain.dat │ │ ├── main_chain.py │ │ └── multi_bodies_functions.py │ └── Uniform_Rollers │ │ ├── README.md │ │ ├── big_a_8kt_experiment_hard_phi_0.4_n_2048_eq.clones │ │ ├── blob.vertex │ │ ├── inputfile_rollers_exp.dat │ │ ├── main_rollers.py │ │ └── multi_bodies_functions.py ├── Makefile ├── README.md ├── Resistance_Coefs │ ├── MATtoTXT.m │ ├── Resolved_Wall_Resistance_Compare.m │ ├── Resolved_Wall_Resistance_Compare_single_entry.m │ ├── Wall_Resistance_Eig_Modify.m │ ├── midfield_scalars_AT.mat │ ├── midfield_scalars_AT.txt │ ├── mob_scalars_MB_1.mat │ ├── mob_scalars_MB_1.txt │ ├── mob_scalars_MB_12.mat │ ├── mob_scalars_MB_12.txt │ ├── mob_scalars_MB_162.mat │ ├── mob_scalars_MB_162.txt │ ├── mob_scalars_MB_2562.mat │ ├── mob_scalars_MB_2562.txt │ ├── mob_scalars_MB_42.mat │ ├── mob_scalars_MB_42.txt │ ├── mob_scalars_MB_642.mat │ ├── mob_scalars_MB_642.txt │ ├── mob_scalars_WS.mat │ ├── mob_scalars_WS.txt │ ├── mob_scalars_wall_MB_10242_full.txt │ ├── mob_scalars_wall_MB_10242_full_take_2.txt │ ├── mob_scalars_wall_MB_10242_running.txt │ ├── mob_scalars_wall_MB_10242_running_take_2.txt │ ├── mob_scalars_wall_MB_12.mat │ ├── mob_scalars_wall_MB_12.txt │ ├── mob_scalars_wall_MB_162.mat │ ├── mob_scalars_wall_MB_162.txt │ ├── mob_scalars_wall_MB_2562.mat │ ├── mob_scalars_wall_MB_2562.txt │ ├── mob_scalars_wall_MB_2562_eig_thresh.txt │ ├── mob_scalars_wall_MB_2562_new_dp.txt │ ├── mob_scalars_wall_MB_42.mat │ ├── mob_scalars_wall_MB_42.txt │ ├── mob_scalars_wall_MB_642.mat │ ├── mob_scalars_wall_MB_642.txt │ ├── nearfield_scalars_AT.mat │ ├── nearfield_scalars_AT.txt │ ├── res_scalars_JO.txt │ ├── res_scalars_MB_1.txt │ ├── res_scalars_WS.txt │ ├── res_scalars_wall_MB.txt │ ├── res_scalars_wall_MB_10242_full.txt │ ├── res_scalars_wall_MB_10242_full_take_2.txt │ └── res_scalars_wall_MB_2562_new_dp.txt └── test_Lub_Class_CC.py ├── README.md ├── articulated └── articulated.py ├── body ├── __init__.py └── body.py ├── boomerang ├── README.md ├── __init__.py ├── boomerang.py ├── boomerang_test.py ├── calculate_boomerang_msd_from_trajectories.py ├── evaluate_com_mobility.py ├── plot_boomerang_msd.py └── plot_boomerang_trajectory.py ├── cRigid_cFibers ├── Carpet_of_Fibers.py ├── Clamp_fiber_Data │ └── plot_fibers.m ├── Free_Fiber_Data │ ├── MCMC_data │ │ ├── MCMC_alpha_stat_0.2_N_10.mat │ │ ├── MCMC_alpha_stat_0.2_N_20.mat │ │ ├── MCMC_alpha_stat_0.2_N_40.mat │ │ ├── MCMC_alpha_stat_0.2_N_5.mat │ │ ├── MCMC_alpha_stat_0.5_N_10.mat │ │ ├── MCMC_alpha_stat_0.5_N_20.mat │ │ ├── MCMC_alpha_stat_0.5_N_40.mat │ │ ├── MCMC_alpha_stat_0.5_N_5.mat │ │ ├── MCMC_alpha_stat_16_N_10.mat │ │ ├── MCMC_alpha_stat_16_N_20.mat │ │ ├── MCMC_alpha_stat_16_N_40.mat │ │ ├── MCMC_alpha_stat_16_N_5.mat │ │ ├── MCMC_alpha_stat_1_N_10.mat │ │ ├── MCMC_alpha_stat_1_N_20.mat │ │ ├── MCMC_alpha_stat_1_N_40.mat │ │ ├── MCMC_alpha_stat_1_N_5.mat │ │ ├── MCMC_alpha_stat_2_N_10.mat │ │ ├── MCMC_alpha_stat_2_N_20.mat │ │ ├── MCMC_alpha_stat_2_N_40.mat │ │ ├── MCMC_alpha_stat_2_N_5.mat │ │ ├── MCMC_alpha_stat_4_N_10.mat │ │ ├── MCMC_alpha_stat_4_N_20.mat │ │ ├── MCMC_alpha_stat_4_N_40.mat │ │ ├── MCMC_alpha_stat_4_N_5.mat │ │ ├── MCMC_alpha_stat_8_N_10.mat │ │ ├── MCMC_alpha_stat_8_N_20.mat │ │ ├── MCMC_alpha_stat_8_N_40.mat │ │ └── MCMC_alpha_stat_8_N_5.mat │ └── Plot_End_2_End.m ├── GridAndKernelConfig.py ├── Makefile ├── Many_Free_Fibers.py ├── README.md ├── Rigid_Object_Main.py ├── Rigid_Rods │ ├── DP_config.clones │ ├── Rod_Plot.m │ ├── SC_config.clones │ ├── data │ │ ├── DP_run.inputfile │ │ └── Rod_Plot.m │ ├── multi_bodies_functions.py │ └── rods_input.dat ├── c_fibers_obj.cpp └── c_rigid_obj.cpp ├── config.py ├── constraint └── constraint.py ├── doc ├── Obstacles.pdf ├── README.md └── TechDemo_Bilbao2022.pdf ├── general_application_utils.py ├── many_bodyMCMC ├── examples │ └── boomerang_suspension │ │ ├── README.md │ │ ├── boomerang_suspension_N_15.clones │ │ ├── inputfile_boomerang_suspension.dat │ │ └── potential_pycuda_user_defined.py ├── inputMCMC.dat ├── many_body_MCMC.py ├── many_body_potential_pycuda.py └── many_body_rejection.py ├── mobility ├── Makefile ├── Makefile.in ├── __init__.py ├── mobility.cpp ├── mobility.hpp ├── mobility.py ├── mobility_ext.cc ├── mobility_fmm.f90 ├── mobility_numba.py ├── mobility_pycuda.py ├── mobility_test.py ├── test.py ├── test_blobs.py ├── test_double_layer_finite.py ├── test_double_layer_rpy_stkfmm.py ├── test_rods.py └── test_source_target.py ├── multi_bodies ├── Makefile ├── Makefile.in ├── Makefile.in-boost-1.58 ├── Structures │ ├── Cylinder_N_14_Lg_1_9295_Rg_0_18323.clones │ ├── Cylinder_N_14_Lg_1_9295_Rg_0_18323.vertex │ ├── Cylinder_N_324_Lg_2_0299_Rg_0_1554.clones │ ├── Cylinder_N_324_Lg_2_0299_Rg_0_1554.vertex │ ├── Cylinder_N_86_Lg_1_9384_Rg_0_1484.clones │ ├── Cylinder_N_86_Lg_1_9384_Rg_0_1484.vertex │ ├── bacteria.clones │ ├── bacteria.list_vertex │ ├── bacteria_active.const │ ├── bacteria_constant_torque.clones │ ├── bacteria_passive.const │ ├── blob.clones │ ├── blob.vertex │ ├── boomerang_N_15.clones │ ├── boomerang_N_15.vertex │ ├── create_3d_sphere.cpp │ ├── flagellum_L_10_alpha_0.35.vertex │ ├── robot_arm_N_7.clones │ ├── robot_arm_N_7.const │ ├── rod_Lg_1.845_Rg_0.1308_Nx_16_Ntheta_6.vertex │ ├── shell_N_12_Rg_0.3960_Rh_0.5.vertex │ ├── shell_N_12_Rg_0_7921_Rh_1.vertex │ ├── shell_N_12_Rg_1.clones │ ├── shell_N_12_Rg_1.vertex │ ├── shell_N_12_Rg_1_Rh_1_2625.vertex │ ├── shell_N_162_Rg_0_9497_Rh_1.vertex │ ├── shell_N_162_Rg_1_Rh_1_0530.vertex │ ├── shell_N_162_Rg_1_slip_length_1e+03.slip_length │ ├── shell_N_2562_Rg_0_9888_Rh_1.vertex │ ├── shell_N_2562_Rg_1_Rh_1_0113.vertex │ ├── shell_N_42_Rg_0_225.clones │ ├── shell_N_42_Rg_0_225.vertex │ ├── shell_N_42_Rg_0_8913_Rh_1.vertex │ ├── shell_N_42_Rg_1_Rh_1_1220.vertex │ ├── shell_N_642_Rg_0_9767_Rh_1.vertex │ ├── shell_N_642_Rg_1_Rh_1_0239.vertex │ ├── sprinkler_N_72_La_5_00_Lb_5_00_W_1_00.vertex │ ├── sprinkler_N_72_La_5_00_Lb_5_00_W_1_00_k_0_00_alpha_1_00_surf_mob_1_00.Laplace │ └── two_sprinklers.clones ├── create_random_suspension.py ├── data │ └── README ├── examples │ ├── FreeSlip │ │ ├── README.md │ │ ├── create_slip_length_file.py │ │ ├── inputfile.dat │ │ ├── multi_bodies.py │ │ ├── quaternion_integrator_multi_bodies.py │ │ ├── snippet_stkfmm.py │ │ └── user_defined_functions.py │ ├── HydroGrid │ │ ├── README.md │ │ ├── Structures │ │ │ └── rollers.clones │ │ ├── hydroGridOptions.nml │ │ └── inputfile.dat │ ├── Laplace_sphere │ │ ├── README.md │ │ ├── create_laplace_file_janus_sphere.py │ │ ├── inputfile.dat │ │ ├── multi_bodies_stkfmm.py │ │ ├── snippet_stkfmm.py │ │ └── snippet_vtk.py │ ├── Mobility_Prod_Timing │ │ ├── Const_Torque_t_15.clones │ │ ├── Multiblob.inputfile │ │ ├── README.txt │ │ └── main.py │ ├── Multi_Blob_Two_Rollers │ │ ├── README.md │ │ ├── inputfile_rollers.dat │ │ ├── inputfile_rollers_42.dat │ │ ├── multi_bodies.py │ │ ├── roller_pngs │ │ │ └── README.md │ │ ├── run_two_rollers │ │ │ ├── Rot_From_Q.m │ │ │ ├── plot_config.m │ │ │ └── plot_config_42.m │ │ ├── two_rollers.clones │ │ └── user_defined_functions.py │ ├── Pillars │ │ ├── README.md │ │ ├── inputfile.dat │ │ ├── notesMixedKinematics.tex │ │ ├── pillar.clones │ │ ├── pillar_R_2_h_2_Ntheta_96_Nz_17_caps_4.vertex │ │ ├── rod_resolved.clones │ │ └── rod_resolved.slip │ ├── Radial_Dist_Test │ │ ├── G_of_R.clones │ │ ├── G_of_R.inputfile │ │ ├── MCMC_G_of_R_data.dat │ │ ├── Makefile │ │ ├── README │ │ ├── gr_pseudo2D_single_blob.cpp │ │ └── user_defined_functions.py │ ├── Rollers_Small_Example │ │ ├── 16_lines.clones │ │ ├── README.md │ │ ├── clones_gen.m │ │ ├── inputfile_rollers.dat │ │ ├── multi_bodies.py │ │ ├── roller_pngs │ │ │ └── README.md │ │ └── run_rollers │ │ │ └── plot_config.m │ ├── Spectral_Multiblob_Roller │ │ ├── 16_lines.clones │ │ ├── Const_Torque_t_15.clones │ │ ├── FCMJoint_MB.py │ │ ├── README.md │ │ ├── bug_check.py │ │ ├── inputfile_2048_rollers.dat │ │ ├── inputfile_lines.dat │ │ ├── inputfile_rollers.dat │ │ ├── inputfile_rollers_42.dat │ │ ├── main.py │ │ ├── multi_bodies.py │ │ ├── multi_bodies_functions.py │ │ ├── roller_HIst_MAT_file.m │ │ ├── roller_pngs │ │ │ └── README.md │ │ └── two_rollers.clones │ ├── bacteria │ │ ├── README.md │ │ ├── inputfile_bacteria_constant_angular_velocity.dat │ │ ├── inputfile_bacteria_constant_torque.dat │ │ └── user_defined_functions.py │ ├── bacteria_run_and_tumble │ │ ├── README.md │ │ ├── Structures │ │ │ ├── bacteria.clones │ │ │ ├── bacteria.const │ │ │ ├── bacteria.list_vertex │ │ │ └── flagellum_L_10_alpha_1_a_0.0245_d_0.0245.vertex │ │ ├── inputfile.dat │ │ └── user_defined_functions.py │ ├── boomerang_suspension │ │ ├── README.md │ │ ├── Two_Booms_Data │ │ │ ├── MCMC.1-16.histogram.r.dat │ │ │ └── MCMC.1-16.histogram.z.dat │ │ ├── boomerang_suspension_N_15.clones │ │ ├── cross_point_r.py │ │ ├── forces_numba_user_defined.py │ │ ├── forces_pycuda_user_defined.py │ │ ├── inputfile_boomerang_suspension.dat │ │ ├── inputfile_two_boomerangs.dat │ │ ├── scriptAnalyze_twoBoomerangs │ │ ├── two_boomerangs_N_15.clones │ │ └── user_defined_functions.py │ ├── chiral_phoretic_particle │ │ ├── README.md │ │ ├── create_sprinkler_vertex_file.py │ │ └── inputfile_chiral_phoretic_particle.dat │ ├── mapping │ │ ├── README.md │ │ ├── Structures │ │ │ ├── bacteria_rigid.clones │ │ │ ├── bacteria_rigid.shell_N_162_flagellum_L_10_alpha_0.35_d_0.262_shift_1.262.vertex │ │ │ └── swimmer.clones │ │ ├── average_files_sphere.py │ │ ├── average_vtk.py │ │ ├── compute_flow.py │ │ ├── compute_slip_from_flow.py │ │ ├── difference_vtk.py │ │ ├── get_final_speed_Higdon.py │ │ ├── inputfile_flagellated.dat │ │ ├── inputfile_slip.dat │ │ ├── snippet.py │ │ ├── squirmer_slip_generation.py │ │ └── user_defined_functions.py │ ├── optimisation_mobility_sphere │ │ ├── README.md │ │ ├── create_vertex_file_sphere.py │ │ ├── optimize_grid.py │ │ └── optimize_grid_general.py │ ├── pair_active_rods │ │ ├── README.md │ │ ├── __init__.py │ │ ├── force_high_resolution.dat │ │ ├── force_low_resolution.dat │ │ ├── force_mid_resolution.dat │ │ ├── inputfile_high_resolution.dat │ │ ├── inputfile_low_resolution.dat │ │ ├── inputfile_mid_resolution.dat │ │ ├── run_high_res.velocity.dat.reference │ │ ├── run_low_res.velocity.dat.reference │ │ ├── run_mid_res.velocity.dat.reference │ │ ├── slip_function.py │ │ └── user_defined_functions.py │ ├── radii │ │ ├── README.md │ │ ├── inputfile.dat │ │ ├── shell_1.clones │ │ └── shell_2.clones │ ├── robot_arm_sedimentation_example │ │ ├── Body_Plot.m │ │ ├── Generate_list_vertex_clones_const_files.m │ │ ├── Rot_From_Q.m │ │ ├── blob.vertex │ │ ├── inputfile_robot_arm_N_15_Mx_10_Mz_10_single_blob.dat │ │ ├── robot_arm_N_15_Mx_10_Mz_10.clones │ │ ├── robot_arm_N_15_Mx_10_Mz_10.const │ │ ├── robot_arm_N_15_Mx_10_Mz_10_single_blob.list_vertex │ │ └── shell_N_12_Rg_0_7921_Rh_1.vertex │ ├── rollers │ │ ├── README.md │ │ ├── inputfile_rollers.dat │ │ └── rollers.clones │ ├── rollers_pillars │ │ ├── README.md │ │ ├── Structures │ │ │ ├── Lattice_blobs_Np_2000_a_0_19134_Z_1_2a_dx_dy_2_2_2_2a.clones │ │ │ ├── blob.vertex │ │ │ ├── pillar_R_0_5_h_4_64_Ntheta_8_Nz_15.vertex │ │ │ ├── pillars.clones │ │ │ ├── slip_zero_N1536.dat │ │ │ └── velocities_zero.dat │ │ ├── inputfile_rollers_pillars.in │ │ └── user_defined_functions.py │ └── squirmer │ │ ├── README.md │ │ ├── inputfile_squirmer.dat │ │ ├── inputfile_squirmer_velocity_field.dat │ │ ├── squirmer.clones │ │ └── squirmer.slip ├── force.dat ├── forces.cpp ├── forces.hpp ├── forces_ext.cc ├── forces_ext.cc-boost-1.58 ├── forces_numba.py ├── forces_pycuda.py ├── inputfile.dat ├── inputfile_body_mobility.dat ├── inputfile_dynamic.dat ├── multi_bodies.py ├── multi_bodies_functions.py ├── multi_bodies_utilities.py └── test_force.py ├── plot ├── __init__.py └── plot_velocity_field.py ├── quaternion_integrator ├── __init__.py ├── gmres.py ├── quaternion.py ├── quaternion_integrator.py ├── quaternion_integrator_multi_bodies.py ├── quaternion_integrator_rollers.py └── quaternion_test.py ├── read_input ├── __init__.py ├── read_clones_file.py ├── read_constraints_file.py ├── read_input.py ├── read_slip_file.py ├── read_velocity_file.py ├── read_vertex_file.py └── read_vertex_file_list.py ├── single_non_sphere ├── non_sphere.py └── ns_rejection.py ├── single_sphere ├── single_sphere_rejection.py └── sphere.py ├── sphere ├── __init__.py ├── checkSPD.py ├── mobility.162-blob.dat ├── plot_sphere_rotational_msd.py ├── selfMobilityFaucheux.py ├── selfMobilityGoldman.py ├── selfMobilityHuang.py ├── sphere.py ├── sphere_rotational_msd.py ├── sphere_test.py └── splines.py ├── stochastic_forcing ├── Makefile.in ├── __init__.py ├── icc_cuda.cu ├── icc_cuda.h ├── stochastic_forcing.py └── test.py ├── tools ├── Body_Plot.m ├── Rot_From_Q.m ├── articulated_to_xyz.py ├── averageFiles.py ├── bodies_to_xyz.py ├── create_soft_articulated.py ├── get_body.py ├── histogram.py └── velocity_linear_angular.py └── visit ├── Makefile.in ├── Makefile.in-boost-1.58 ├── __init__.py ├── test_visit.py ├── visit_writer.c ├── visit_writer.h ├── visit_writer.py ├── visit_writer_interface.cc └── visit_writer_interface.cc-boost-1.58 /.gitignore: -------------------------------------------------------------------------------- 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