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ESPResSo 3.2.0-11-g9950804-git
Extensible Simulation Package for Soft Matter Research
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ESPResSo 3.2.0-11-g9950804-git
Extensible Simulation Package for Soft Matter Research
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Struct holding all information for one particle. More...
#include <particle_data.h>
Data Fields | |
| ParticleProperties | p |
| ParticlePosition | r |
| ParticleMomentum | m |
| ParticleForce | f |
| ParticleLocal | l |
| ParticleLatticeCoupling | lc |
| IntList | bl |
| bonded interactions list. | |
| IntList | el |
| list of particles, with which this particle has no nonbonded interactions | |
Struct holding all information for one particle.
Definition at line 247 of file particle_data.h.
bonded interactions list.
The format is pretty simple: Just the bond type, and then the particle ids. The number of particle ids can be determined easily from the bonded_ia_params entry for the type.
Definition at line 265 of file particle_data.h.
Referenced by add_area_global_force(), add_bonded_energy(), add_bonded_force(), add_bonded_virials(), add_three_body_bonded_stress(), add_volume_force(), auto_exclusion(), calc_area_global(), calc_volume(), collectBonds(), compute_pos_corr_vec(), compute_vel_corr_vec(), detect_collision(), free_particle(), init_particle(), local_change_bond(), local_stress_tensor_calc(), mpi_get_particles(), mpi_get_particles_slave(), mpi_recv_part(), mpi_recv_part_slave(), print_bond_len(), recv_particles(), remove_all_bonds_to(), send_particles(), tclcommand_part_print_bond_partners(), tclcommand_part_print_bonding_structure(), tclprint_to_result_Particle(), and try_delete_bond().
list of particles, with which this particle has no nonbonded interactions
Definition at line 269 of file particle_data.h.
Referenced by do_nonbonded(), free_particle(), init_particle(), mpi_recv_part(), mpi_recv_part_slave(), recv_particles(), send_particles(), tclcommand_part_print_exclusions(), tclprint_to_result_Particle(), try_add_exclusion(), and try_delete_exclusion().
Definition at line 255 of file particle_data.h.
Referenced by add_area_global_force(), add_bonded_force(), add_buck_pair_force(), add_constraints_forces(), add_dh_coulomb_pair_force(), add_dipole_force(), add_dpd_thermo_pair_force(), add_ext_magn_field_force(), add_forces_from_recv_buffer(), add_hat_pair_force(), add_inter_dpd_pair_force(), add_interrf_pair_force(), add_kinetic_virials(), add_lj_pair_force(), add_ljangle_pair_force(), add_ljcos2_pair_force(), add_ljcos_pair_force(), add_ljgen_pair_force(), add_mdlc_force_corrections(), add_morse_pair_force(), add_non_bonded_pair_force(), add_non_bonded_pair_force_iccp3m(), add_P_force(), add_plate_force(), add_PQ_force(), add_Q_force(), add_rf_coulomb_pair_force_no_cutoff(), add_rod_force(), add_soft_pair_force(), add_thermodynamic_force(), add_tunable_slip_pair_force(), add_volume_force(), add_z_force(), app_pos_correction(), apply_mol_constraints(), apply_vel_corr(), calc_comfixed(), calc_comforce(), calc_dipole_dipole_ia(), calc_endangledist_pair_force(), calc_fene_pair_force(), calc_harmonic_pair_force(), calc_local_mol_info(), calc_overlap_bond_force(), calc_part_self_force(), calc_particle_lattice_ia(), calc_stretching_force_pair_force(), calc_subt_lj_pair_force(), calc_surface_term(), calc_tab_bond_force(), cell_cell_transfer(), check_particle_force(), comfixed_set_params(), compute_pos_corr_vec(), compute_vel_corr_vec(), convert_initial_torques(), convert_torques_body_to_space(), convert_torques_propagate_omega(), define_Qdd(), distribute_mol_force(), dp3m_add_pair_force(), dp3m_assign_forces_dip(), ELC_P3M_self_forces(), force_and_velocity_check(), force_and_velocity_display(), friction_thermo_langevin(), friction_thermo_langevin_rotation(), iccp3m_iteration(), iccp3m_revive_forces(), iccp3m_store_forces(), init_correction_vector(), init_ghost_force(), init_ghost_force_iccp3m(), init_local_particle_force(), init_local_particle_force_iccp3m(), init_particle(), lb_viscous_coupling(), local_kill_particle_forces(), maggs_calc_part_link_forces(), maggs_calc_self_influence(), maggs_compute_dipole_correction(), magnetic_dipolar_direct_sum_calculations(), meta_perform(), MMM2D_dielectric_layers_force_contribution(), mpi_send_f(), mpi_send_f_slave(), mpi_send_forces_lb(), mpi_send_forces_slave_lb(), mpi_send_torque(), mpi_send_torque_slave(), observable_blocked_com_force(), observable_com_force(), observable_particle_forces(), P3M_assign_forces(), P3M_assign_torques(), p3m_calc_dipole_term(), predict_momentum_particles(), prepare_send_buffer(), print_particle_forces(), propagate_vel(), propagate_vel_pos(), put_mol_force_on_parts(), put_recv_buffer(), rescale_forces(), rescale_forces_propagate_vel(), reset_forces(), revert_force(), tclcommand_part_print_f(), tclcommand_part_print_torque_body_frame(), tclcommand_writemd(), and transfer_force_init_vel().
Definition at line 257 of file particle_data.h.
Referenced by add_area_global_force(), add_constraints_energy(), add_constraints_forces(), add_dpd_thermo_pair_force(), add_inter_dpd_pair_force(), add_volume_force(), calc_angledist_param(), calc_area_force_local(), calc_area_global(), calc_bending_force(), calc_local_mol_info(), calc_pwdist(), calc_radial_density_map(), calc_scaling(), calc_scaling2(), calc_volume(), cell_cell_transfer(), check_resort_particles(), dd_append_particles(), dd_exchange_and_sort_particles(), fold_all(), force_and_velocity_check(), friction_thermo_langevin(), init_local_particle_force(), init_particle(), layered_append_particles(), layered_calculate_energies(), layered_calculate_ia(), layered_calculate_ia_iccp3m(), layered_calculate_virials(), layered_exchange_and_sort_particles(), lb_viscous_coupling(), local_place_particle(), maggs_sanity_checks(), magnetic_dipolar_direct_sum_calculations(), mpi_send_ext_force(), mpi_send_ext_force_slave(), mpi_send_ext_torque(), mpi_send_ext_torque_slave(), nsq_calculate_energies(), nsq_calculate_ia(), nsq_calculate_ia_iccp3m(), nsq_calculate_virials(), observable_density_profile(), observable_flux_density_profile(), observable_radial_density_profile(), observable_radial_flux_density_profile(), p3m_calc_dipole_term(), propagate_pos(), propagate_press_box_pos_and_rescale_npt(), propagate_vel_pos(), put_recv_buffer(), reflect_particle(), tclcommand_analyze_parse_and_print_check_mol(), tclcommand_part_print_ext_force(), tclcommand_part_print_ext_torque(), tclcommand_part_print_fix(), tclcommand_part_print_folded_position(), tclcommand_part_print_position(), tclcommand_writemd(), tclprint_to_result_Particle(), tscale_momentum_update(), and updatePartCfg().
Definition at line 260 of file particle_data.h.
Referenced by calc_particle_lattice_ia(), cell_cell_transfer(), lb_viscous_coupling(), prepare_send_buffer(), and put_recv_buffer().
Definition at line 253 of file particle_data.h.
Referenced by add_dpd_thermo_pair_force(), add_inter_dpd_pair_force(), add_kinetic_energy(), add_kinetic_virials(), add_tunable_slip_pair_force(), angularmomentum(), app_pos_correction(), apply_vel_corr(), calc_energy_kinetic_mol(), calc_local_mol_info(), calc_mol_vel(), cell_cell_transfer(), centermass_vel(), comfixed_set_params(), compute_vel_corr_vec(), convert_initial_torques(), convert_omega_body_to_space(), convert_torques_propagate_omega(), define_Qdd(), force_and_velocity_check(), force_and_velocity_display(), friction_thermo_langevin(), friction_thermo_langevin_rotation(), init_local_particle_force(), init_particle(), lb_viscous_coupling(), local_galilei_transform(), local_kill_particle_motion(), local_stress_tensor_calc(), local_system_CMS_velocity(), maggs_add_current_on_segment(), maggs_couple_current_to_Dfield(), momentum_flip(), mpi_get_particles_lb(), mpi_get_particles_slave_lb(), mpi_send_omega(), mpi_send_omega_slave(), mpi_send_v(), mpi_send_v_slave(), nemd_add_velocity(), nemd_change_momentum(), nemd_get_velocity(), observable_blocked_com_velocity(), observable_com_velocity(), observable_currents(), observable_flux_density_profile(), observable_particle_angular_momentum(), observable_particle_currents(), observable_particle_velocities(), observable_radial_flux_density_profile(), partial_momentum_update(), predict_momentum_particles(), prepare_send_buffer(), propagate_omega_quat_particle(), propagate_pos(), propagate_press_box_pos_and_rescale_npt(), propagate_vel(), propagate_vel_pos(), put_recv_buffer(), reflect_particle(), rescale_forces(), rescale_forces_propagate_vel(), rescale_velocities(), save_last_state(), simple_momentum_update(), tclcommand_analyze_current(), tclcommand_analyze_print_vel_distr(), tclcommand_part_print_omega_body_frame(), tclcommand_part_print_v(), tclcommand_writemd(), tscale_momentum_update(), and update_mol_vel_particle().
Definition at line 249 of file particle_data.h.
Referenced by add_area_global_force(), add_bonded_energy(), add_bonded_force(), add_bonded_virials(), add_buck_pair_force(), add_constraints_energy(), add_constraints_forces(), add_dh_coulomb_pair_force(), add_dipole_force(), add_hat_pair_force(), add_interrf_pair_force(), add_kinetic_energy(), add_lj_pair_force(), add_ljangle_pair_force(), add_ljcos2_pair_force(), add_ljcos_pair_force(), add_ljgen_pair_force(), add_morse_pair_force(), add_non_bonded_pair_energy(), add_non_bonded_pair_force(), add_non_bonded_pair_force_iccp3m(), add_non_bonded_pair_virials(), add_plate_force(), add_rf_coulomb_pair_force_no_cutoff(), add_rod_force(), add_soft_pair_force(), add_thermodynamic_force(), add_three_body_bonded_stress(), add_tunable_slip_pair_force(), add_volume_force(), add_z_force(), adress_update_weights(), adress_wf_particle(), aggregation(), analyze_cwvac(), analyze_rdfchain(), angularmomentum(), append_indexed_particle(), apply_mol_constraints(), auto_exclusion(), bilayer_density_profile(), bilayer_density_profile_sphere(), build_verlet_lists(), build_verlet_lists_and_calc_verlet_ia(), build_verlet_lists_and_calc_verlet_ia_iccp3m(), calc_area_global(), calc_bonded_force(), calc_dipole_of_molecule(), calc_endangledist_pair_force(), calc_fene_pair_force(), calc_fluctuations(), calc_g123(), calc_harmonic_pair_force(), calc_kinetic(), calc_link_cell(), calc_link_cell_iccp3m(), calc_local_mol_info(), calc_mol_center_of_mass(), calc_mol_gyr_radius2(), calc_mol_hydro_radius(), calc_mol_pos(), calc_mol_pos_cfg(), calc_mol_vel(), calc_mu_max(), calc_non_bonded_pair_energy(), calc_non_bonded_pair_force_from_partcfg_simple(), calc_non_bonded_pair_force_parts(), calc_non_bonded_pair_force_simple(), calc_overlap_bond_force(), calc_part_distribution(), calc_part_self_force(), calc_particle_lattice_ia(), calc_radial_density_map(), calc_rdf(), calc_rdf_adress(), calc_rdf_intermol_av(), calc_scaling(), calc_scaling2(), calc_stretching_force_pair_force(), calc_subt_lj_pair_force(), calc_tab_bond_force(), calc_three_body_bonded_forces(), calc_volume(), calc_wallbondyz(), calc_wallrdfyz(), calculate_link_cell_energies(), calculate_link_cell_virials(), calculate_verlet_energies(), cell_cell_transfer(), check_particle_consistency(), check_particles(), check_resort_particles(), checkIfParticlesInteractViaMolCut(), checkIfParticlesInteractViaMolCut_partcfg(), clusters_connected(), collectBonds(), compute_pos_corr_vec(), compute_vel_corr_vec(), convert_torques_propagate_omega(), dawaanr_calculations(), dd_append_particles(), dd_exchange_and_sort_particles(), dd_topology_init(), define_Qdd(), detect_collision(), dh_coulomb_pair_energy(), dipole_energy(), distribute_mol_force(), distto(), do_nonbonded(), dp3m_add_pair_force(), dp3m_dipole_assign(), ELC_p3m_charge_assign_both(), ELC_p3m_charge_assign_image(), ELC_P3M_dielectric_layers_energy_contribution(), ELC_P3M_dielectric_layers_energy_self(), ELC_P3M_dielectric_layers_force_contribution(), ELC_P3M_modify_p3m_sums_both(), ELC_P3M_modify_p3m_sums_image(), ELC_P3M_restore_p3m_sums(), ELC_P3M_self_forces(), fene_pair_energy(), fold_all(), force_and_velocity_check(), friction_thermo_langevin(), friction_thermo_langevin_rotation(), generate_constraint(), get_lipid_orients(), get_local_trapped_mols(), get_mol_com_particle(), get_mol_dist(), get_mol_dist_partcfg(), get_nonbonded_interaction(), got_particle(), iccp3m_iteration(), iccp3m_revive_forces(), iccp3m_store_forces(), ifParticleIsVirtual(), init_ghost_force(), init_local_particle_force(), init_particle(), init_type_array(), integrate_reaction(), invalidate_ghosts(), layered_append_particles(), layered_exchange_and_sort_particles(), layered_topology_init(), lb_viscous_coupling(), lipid_orientation(), ljangle_pair_energy(), local_place_particle(), local_remove_particle(), local_stress_tensor_calc(), local_system_CMS(), local_system_CMS_velocity(), maggs_accumulate_charge_from_ghosts(), maggs_add_current_on_segment(), maggs_calc_forces(), maggs_calc_self_influence(), maggs_compute_dipole_correction(), mark_neighbours(), meta_perform(), mindist(), mindist3(), mmm1d_coulomb_pair_energy(), MMM2D_dielectric_layers_energy_contribution(), MMM2D_dielectric_layers_force_contribution(), move_indexed_particle(), mpi_get_particles(), mpi_get_particles_lb(), mpi_get_particles_slave_lb(), mpi_send_dip(), mpi_send_dip_slave(), mpi_send_dipm(), mpi_send_dipm_slave(), mpi_send_mass(), mpi_send_mass_slave(), mpi_send_mol_id(), mpi_send_mol_id_slave(), mpi_send_mu_E(), mpi_send_mu_E_slave(), mpi_send_q(), mpi_send_q_slave(), mpi_send_quat(), mpi_send_quat_slave(), mpi_send_rotation(), mpi_send_rotation_slave(), mpi_send_rotational_inertia(), mpi_send_rotational_inertia_slave(), mpi_send_type(), mpi_send_type_slave(), mpi_send_virtual(), mpi_send_virtual_slave(), mpi_send_vs_relative(), mpi_send_vs_relative_slave(), mpi_set_particle_gamma(), mpi_set_particle_gamma_slave(), mpi_set_particle_temperature(), mpi_set_particle_temperature_slave(), mpi_who_has(), mpi_who_has_slave(), nbhood(), nemd_get_velocity(), observable_currents(), observable_dipole_moment(), observable_particle_currents(), p3m_calc_dipole_term(), p3m_count_charged_particles(), plate_energy(), prepare_send_buffer(), print_bond_len(), propagate_omega_quat_particle(), propagate_pos(), propagate_press_box_pos_and_rescale_npt(), propagate_vel_pos(), put_mol_force_on_parts(), put_recv_buffer(), recv_particles(), remove_particle(), rf_coulomb_pair_energy_no_cutoff(), rod_energy(), send_particles(), set_particle_type(), setup_P(), setup_PQ(), setup_Q(), setup_z_energy(), setup_z_force(), subt_lj_pair_energy(), sync_topo_part_info(), tclcommand_analyze_current(), tclcommand_analyze_parse_and_print_check_mol(), tclcommand_analyze_parse_and_print_dipole(), tclcommand_constraint_parse_cylinder(), tclcommand_constraint_parse_ext_magn_field(), tclcommand_constraint_parse_maze(), tclcommand_constraint_parse_plane_cell(), tclcommand_constraint_parse_plate(), tclcommand_constraint_parse_pore(), tclcommand_constraint_parse_rhomboid(), tclcommand_constraint_parse_rod(), tclcommand_constraint_parse_sphere(), tclcommand_constraint_parse_wall(), tclcommand_imd_parse_pos(), tclcommand_part_parse_print(), tclcommand_part_print_bond_partners(), tclcommand_part_print_mu_E(), tclcommand_part_print_rotation(), tclcommand_part_print_rotational_inertia(), tclcommand_part_print_virtual(), tclcommand_writemd(), tclprint_to_result_Constraint(), tclprint_to_result_Particle(), test_mesh_elements(), update_mol_ids_setchains(), update_mol_pos_particle(), update_mol_vel_particle(), update_particle_array(), updatePartCfg(), vs_relative_get_real_particle(), and z_energy().
Definition at line 251 of file particle_data.h.
Referenced by add_area_global_force(), add_bonded_energy(), add_bonded_force(), add_bonded_virials(), add_constraints_energy(), add_constraints_forces(), add_dipole_force(), add_ext_magn_field_force(), add_gb_pair_force(), add_ljangle_pair_force(), add_mdlc_force_corrections(), add_thermodynamic_force(), add_three_body_bonded_stress(), add_volume_force(), aggregation(), analyze_append(), analyze_formfactor(), analyze_push(), analyze_rdfchain(), analyze_replace(), angle_cosine_energy(), angle_cossquare_energy(), angle_energy(), angle_harmonic_energy(), angledist_energy(), app_pos_correction(), bilayer_density_profile(), build_verlet_lists(), build_verlet_lists_and_calc_verlet_ia(), build_verlet_lists_and_calc_verlet_ia_iccp3m(), calc_angle_3body_forces(), calc_angle_3body_tabulated_forces(), calc_angle_cosine_3body_forces(), calc_angle_cosine_force(), calc_angle_cossquare_3body_forces(), calc_angle_cossquare_force(), calc_angle_force(), calc_angle_harmonic_3body_forces(), calc_angle_harmonic_force(), calc_angledist_force(), calc_angledist_param(), calc_area_force_local(), calc_area_force_local_complicated(), calc_area_global(), calc_bending_force(), calc_bond_dist(), calc_bond_l(), calc_dihedral_angle(), calc_dipole_dipole_ia(), calc_dipole_of_molecule(), calc_endangledist_pair_force(), calc_fluctuations(), calc_force_between_mol(), calc_g123(), calc_gyration_tensor(), calc_internal_dist(), calc_link_cell(), calc_link_cell_iccp3m(), calc_local_mol_info(), calc_mol_hydro_radius(), calc_mol_pos(), calc_mol_pos_cfg(), calc_overlap_angle_force(), calc_part_distribution(), calc_particle_lattice_ia(), calc_pwangle(), calc_pwdist(), calc_rdf(), calc_re(), calc_rg(), calc_rh(), calc_scaling(), calc_scaling2(), calc_structurefactor(), calc_surface_term(), calc_tab_angle_force(), calc_volume(), calc_wallbondyz(), calc_wallrdfyz(), calc_zref(), calculate_link_cell_energies(), calculate_link_cell_virials(), calculate_verlet_energies(), calculate_verlet_ia(), calculate_verlet_ia_iccp3m(), calculate_verlet_virials(), cell_cell_transfer(), centermass(), check_particle_consistency(), clusters_connected(), compute_pos_corr_vec(), compute_vel_corr_vec(), dd_append_particles(), dd_exchange_and_sort_particles(), define_Qdd(), define_rotation_matrix(), detect_collision(), dipole_energy(), distribute_mol_force(), dp3m_add_pair_force(), dp3m_assign_forces_dip(), dp3m_dipole_assign(), dp3m_pair_energy(), ELC_p3m_charge_assign_both(), ELC_p3m_charge_assign_image(), ELC_P3M_dielectric_layers_energy_contribution(), ELC_P3M_dielectric_layers_energy_self(), ELC_P3M_dielectric_layers_force_contribution(), ELC_P3M_self_forces(), ext_magn_field_energy(), force_and_velocity_check(), gb_pair_energy(), get_DLC_dipolar(), get_DLC_energy_dipolar(), get_mol_dist(), get_mol_dist_vector_from_molid_cfg(), get_nonbonded_interaction(), init_g123(), init_ghost_force(), init_local_particle_force(), init_particle(), integrate_reaction(), layered_append_particles(), layered_calculate_energies(), layered_calculate_ia(), layered_calculate_ia_iccp3m(), layered_calculate_virials(), layered_exchange_and_sort_particles(), lb_viscous_coupling(), lipid_orientation(), ljangle_pair_energy(), local_place_particle(), local_rescale_particles(), local_stress_tensor_calc(), maggs_accumulate_charge_from_ghosts(), maggs_add_current_on_segment(), maggs_calc_forces(), maggs_calc_self_influence(), maggs_couple_current_to_Dfield(), maggs_distribute_particle_charges(), maggs_update_charge_gradients(), magnetic_dipolar_direct_sum_calculations(), mark_neighbours(), mindist(), mindist3(), mindist4(), MMM2D_dielectric_layers_energy_contribution(), MMM2D_dielectric_layers_force_contribution(), momentofinertiamatrix(), mpi_get_particles(), mpi_send_dip(), mpi_send_dip_slave(), mpi_send_dipm(), mpi_send_dipm_slave(), mpi_send_quat(), mpi_send_quat_slave(), nbhood(), nemd_add_velocity(), nemd_get_velocity(), nsq_calculate_energies(), nsq_calculate_ia(), nsq_calculate_ia_iccp3m(), nsq_calculate_virials(), observable_blocked_com_position(), observable_com_position(), observable_density_profile(), observable_dipole_moment(), observable_flux_density_profile(), observable_interacts_with(), observable_particle_positions(), observable_radial_density_profile(), observable_radial_flux_density_profile(), observable_structure_factor(), overlap_angle_energy(), P3M_assign_forces(), P3M_assign_torques(), p3m_calc_dipole_term(), p3m_charge_assign(), prepare_scx_cache(), prepare_scy_cache(), prepare_send_buffer(), print_bond_len(), print_ghost_positions(), print_local_particle_positions(), print_particle_positions(), propagate_omega_quat_particle(), propagate_pos(), propagate_press_box_pos_and_rescale_npt(), propagate_vel_pos(), put_recv_buffer(), reflect_particle(), revert_force(), save_last_state(), save_old_pos(), setup_P(), setup_PQ(), setup_Q(), setup_z_energy(), slab_dip_count_mu(), tab_angle_energy(), tclcommand_analyze_parse_and_print_check_mol(), tclcommand_analyze_parse_and_print_dipole(), tclcommand_analyze_parse_get_folded_positions(), tclcommand_analyze_parse_reference_point(), tclcommand_imd_parse_pos(), tclcommand_part_print_dip(), tclcommand_part_print_folded_position(), tclcommand_part_print_position(), tclcommand_part_print_quat(), tclcommand_part_print_quatu(), tclcommand_writemd(), transfer_force_init_vel(), update_mol_pos_particle(), update_mol_vel_particle(), vs_relate_to(), wall_sort_particles(), and z_energy().
1.7.5.1