├── .gitignore ├── .gitmodules ├── LICENSE ├── README.md ├── asset ├── mesh │ ├── README.md │ ├── armadillo_10k.ele │ ├── armadillo_10k.node │ ├── armadillo_high_res.obj │ ├── armadillo_low_res.obj │ ├── bob.obj │ ├── bunny_watertight.obj │ ├── bunny_watertight_simplified.obj │ ├── bunny_watertight_simplified2.obj │ ├── curved_ground.obj │ ├── fixed.obj │ ├── flat_ground.obj │ ├── lock.obj │ ├── lock.py │ ├── lock_tri_mesh.obj │ ├── plant.obj │ ├── plant.py │ ├── plant_tri_mesh.obj │ ├── plant_watertight.obj │ ├── sphere.obj │ ├── spot.obj │ ├── starfish.obj │ ├── starfish.stl │ ├── starfish_half.obj │ ├── starfish_half_simplified.obj │ ├── starfish_simplified.obj │ ├── starfish_simplified2.obj │ ├── torus.obj │ ├── torus_analytic.obj │ └── torus_tri_mesh.obj ├── texture │ ├── lightmap.exr │ ├── lines.exr │ ├── siggraph_logo.jpg │ └── uffizi-large.exr └── video │ └── tennis_09.mov ├── cpp ├── .gitignore ├── CMakeLists.txt ├── core │ ├── include │ │ ├── common │ │ │ ├── common.h │ │ │ ├── config.h │ │ │ ├── exception_with_call_stack.h │ │ │ ├── file_helper.h │ │ │ └── geometry.h │ │ ├── fem │ │ │ ├── deformable.h │ │ │ ├── finite_element_sample.h │ │ │ ├── hex_deformable.h │ │ │ ├── quad_deformable.h │ │ │ ├── tet_deformable.h │ │ │ └── tri_deformable.h │ │ ├── friction │ │ │ ├── frictional_boundary.h │ │ │ ├── planar_frictional_boundary.h │ │ │ └── spherical_frictional_boundary.h │ │ ├── material │ │ │ ├── corotated.h │ │ │ ├── linear.h │ │ │ ├── material.h │ │ │ └── neohookean.h │ │ ├── mesh │ │ │ └── mesh.h │ │ ├── pd_energy │ │ │ ├── corotated_pd_element_energy.h │ │ │ ├── deformation_gradient_auxiliary_data.h │ │ │ ├── pd_element_energy.h │ │ │ ├── pd_muscle_energy.h │ │ │ ├── pd_vertex_energy.h │ │ │ ├── planar_collision_pd_vertex_energy.h │ │ │ └── volume_pd_element_energy.h │ │ ├── solver │ │ │ ├── deformable_preconditioner.h │ │ │ ├── matrix_op.h │ │ │ └── pardiso_spd_solver.h │ │ └── state_force │ │ │ ├── arc_contact_state_force.h │ │ │ ├── billiard_ball_state_force.h │ │ │ ├── gravitational_state_force.h │ │ │ ├── hydrodynamics_state_force.h │ │ │ ├── planar_contact_state_force.h │ │ │ └── state_force.h │ └── src │ │ ├── .gitignore │ │ ├── common │ │ ├── common.cpp │ │ ├── exception_with_call_stack.cpp │ │ ├── file_helper.cpp │ │ └── geometry.cpp │ │ ├── fem │ │ ├── deformable.cpp │ │ ├── deformable_actuation.cpp │ │ ├── deformable_friction.cpp │ │ ├── deformable_newton_backward.cpp │ │ ├── deformable_newton_forward.cpp │ │ ├── deformable_pd_energy.cpp │ │ ├── deformable_projective_dynamics_backward.cpp │ │ ├── deformable_projective_dynamics_forward.cpp │ │ ├── deformable_quasi_static.cpp │ │ ├── deformable_semi_implicit.cpp │ │ ├── deformable_state_force.cpp │ │ ├── finite_element_sample.cpp │ │ ├── hex_deformable.cpp │ │ ├── quad_deformable.cpp │ │ ├── tet_deformable.cpp │ │ └── tri_deformable.cpp │ │ ├── friction │ │ ├── planar_frictional_boundary.cpp │ │ └── spherical_frictional_boundary.cpp │ │ ├── material │ │ ├── corotated.cpp │ │ ├── linear.cpp │ │ ├── material.cpp │ │ └── neohookean.cpp │ │ ├── mesh │ │ └── mesh.cpp │ │ ├── pd_energy │ │ ├── corotated_pd_element_energy.cpp │ │ ├── deformation_gradient_auxiliary_data.cpp │ │ ├── pd_element_energy.cpp │ │ ├── pd_muscle_energy.cpp │ │ ├── pd_vertex_energy.cpp │ │ ├── planar_collision_pd_vertex_energy.cpp │ │ └── volume_pd_element_energy.cpp │ │ ├── py_diff_pd_core.i │ │ ├── solver │ │ └── pardiso_spd_solver.cpp │ │ └── state_force │ │ ├── arc_contact_state_force.cpp │ │ ├── billiard_ball_state_force.cpp │ │ ├── gravitational_state_force.cpp │ │ ├── hydrodynamics_state_force.cpp │ │ ├── planar_contact_state_force.cpp │ │ └── state_force.cpp └── main.cpp ├── environment.yml ├── external └── .gitignore ├── install.sh └── python ├── arm_model ├── README.md ├── _utils.py ├── arm_data_sep_4 │ └── README.md ├── colearning_resphy │ ├── _utils.py │ ├── hyperparam_opt.py │ ├── model.py │ ├── sopra_residual_physics.py │ ├── test_residual_physics.py │ ├── training.py │ └── validate_residual_physics.py ├── env_arm.py ├── markermatch.py ├── preprocess_data │ ├── _utils.py │ └── build_augmented_data.py ├── sopra_model │ └── sopra_494.vtk └── test_experiments │ ├── _visualization.py │ ├── chamber_calibration.py │ └── identify_chamber_ordering.ipynb ├── beam_model ├── _utils.py ├── _visualization.py ├── sim2real_beam_model │ ├── README.md │ ├── beam_residual_physics.py │ ├── beam_sys_all.py │ ├── beam_sys_grid_search.py │ ├── damping_opt.py │ ├── env_base.py │ ├── env_cantilever.py │ ├── generate_augmented_data.py │ ├── hyperparam_opt.py │ ├── init_beam.py │ ├── model.py │ ├── optimize_trajectory.py │ ├── test_residual_physics.py │ ├── training.py │ └── validate_residual_physics.py └── sim2sim_beam_model │ ├── README.md │ ├── beam_residual_physics.py │ ├── env_base.py │ ├── env_cantilever.py │ ├── sim2real_prep │ ├── marker_ablation.py │ └── plot_marker_ablation.py │ ├── twist │ ├── data_generation.py │ ├── optimize_trajectory.py │ ├── test_residual_physics.py │ └── training.py │ └── vibration │ ├── data_generation.py │ ├── optimize_trajectory.py │ ├── test_residual_physics.py │ └── training.py ├── paper_figures ├── fig4_markerexp_data │ └── plot.py ├── fig5_gridsearch │ └── plot.py ├── fig5_trajectorydata │ └── plot.py ├── fig6_sim2realbeam │ ├── plot.py │ └── plotError.py ├── fig7_3dplot │ └── plot3D.py ├── fig7_sim2realsopra │ ├── plot.py │ ├── plotError.py │ ├── plotXY.py │ └── plotXYphase.py └── fig8_generalization │ └── plotError.py ├── py_diff_pd ├── .gitignore ├── __init__.py ├── common │ ├── .gitignore │ ├── __init__.py │ ├── common.py │ ├── controller.py │ ├── display.py │ ├── grad_check.py │ ├── hex_mesh.py │ ├── parallel.py │ ├── quad_mesh.py │ ├── renderer.py │ ├── rl_sim.py │ ├── sim.py │ ├── tet_mesh.py │ └── tri_mesh.py ├── core │ ├── .gitignore │ └── __init__.py └── env │ ├── armadillo_env_3d.py │ ├── billiard_ball_env_3d.py │ ├── bouncing_ball_env_3d.py │ ├── bunny_env_3d.py │ ├── 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