- a -

• add_energy_to_cell() : three_bead_enzyme.f90

- b -

• bind_molecule() : three_bead_enzyme.f90
• buffer_particles() : chemotactic_cell.f90

- c -

• change_species() : chemotactic_cell.f90 , single_body.f90 , setup_single_catalytic_fixed_sphere.f90 , single_dimer_pbc.f90
• chemotactic_cell() : chemotactic_cell.f90
• compute_bead_energy() : three_bead_enzyme.f90
• compute_bead_force() : three_bead_enzyme.f90
• compute_cell_wise_max_v() : single_body.f90 , single_body_thermal.f90 , single_dimer.f90
• compute_force_harmonic_trap() : single_sphere_thermo_trap.f90
• compute_harmonic() : single_dimer.f90
• compute_rho_xy() : chemotactic_cell.f90
• compute_vxz_and_vxyz() : single_sphere_thermo_trap.f90
• concentration_field_cylindrical() : chemotactic_cell.f90

- d -

• detect_reaction() : single_body_thermal.f90
• div_vxyz() : single_sphere_thermo_trap.f90
• div_vxz() : single_sphere_thermo_trap.f90

- f -

• fix_neighbor_list() : three_bead_enzyme.f90
• flag_particles() : chemotactic_cell.f90 , single_body.f90
• flag_particles_nl() : setup_single_catalytic_fixed_sphere.f90 , single_dimer_pbc.f90
• flin() : test_common_0.f90
• fprime() : three_bead_enzyme.f90

- g -

• get_unit_r() : single_body.f90 , single_body_thermal.f90

- i -

• is_in_list() : test_neighbor_list_0.f90 , test_neighbor_list_1.f90

- n -

• n_colloids_pbc() : n_colloids_pbc.f90

- p -

• poiseuille_flow() : poiseuille_flow.f90

- r -

• read_links() : single_body.f90 , single_body_thermal.f90
• refuel() : single_dimer_pbc.f90 , setup_single_catalytic_fixed_sphere.f90 , single_body.f90
• rescale_at_walls() : single_sphere_thermo_trap.f90
• reset_enzyme_region_bit() : three_bead_enzyme.f90

- s -

• select_substrate() : three_bead_enzyme.f90
• setup_bulk_decay() : setup_bulk_decay.f90
• setup_fluid() : setup_thermal_fluid.f90 , setup_simple_fluid.f90
• setup_simple_colloid() : setup_single_colloid.f90
• setup_simple_colloids() : setup_simple_colloids.f90 , setup_simple_rattle.f90
• setup_single_catalytic_fixed_sphere() : setup_single_catalytic_fixed_sphere.f90
• single_body() : single_body.f90
• single_body_thermal() : single_body_thermal.f90
• single_dimer() : single_dimer.f90
• single_dimer_pbc() : single_dimer_pbc.f90
• single_sphere_thermo_trap() : single_sphere_thermo_trap.f90

- t -

• test_common_0() : test_common_0.f90
• test_common_1() : test_common_1.f90
• test_correlator_0() : test_correlator_0.f90
• test_elastic_network_0() : test_elastic_network_0.f90
• test_md_0() : test_md_0.f90
• test_neighbor_list() : test_neighbor_list_1.f90 , test_neighbor_list_0.f90
• test_particle_system_0() : test_particle_system_0.f90
• three_bead_enzyme() : three_bead_enzyme.f90
• try_all() : test_cell_system_0.f90

- u -

• unbind_molecule() : three_bead_enzyme.f90
• update_n_solvent() : setup_bulk_decay.f90
• update_polar_hist() : setup_single_catalytic_fixed_sphere.f90