Implementation of interaction_data.h. More...

#include <string.h>
#include <stdlib.h>
#include "utils.h"
#include "rattle.h"
#include "interaction_data.h"
#include "errorhandling.h"
#include "communication.h"
#include "grid.h"
#include "pressure.h"
#include "p3m.h"
#include "debye_hueckel.h"
#include "reaction_field.h"
#include "mmm1d.h"
#include "mmm2d.h"
#include "maggs.h"
#include "elc.h"
#include "lj.h"
#include "ljgen.h"
#include "ljangle.h"
#include "steppot.h"
#include "hertzian.h"
#include "gaussian.h"
#include "buckingham.h"
#include "soft_sphere.h"
#include "hat.h"
#include "tab.h"
#include "overlap.h"
#include "ljcos.h"
#include "ljcos2.h"
#include "gb.h"
#include "cells.h"
#include "comforce.h"
#include "comfixed.h"
#include "morse.h"
#include "dpd.h"
#include "tunable_slip.h"
#include "magnetic_non_p3m_methods.h"
#include "mdlc_correction.h"
#include "initialize.h"

Include dependency graph for interaction_data.c:

Go to the source code of this file.

Functions
static void	recalc_global_maximal_nonbonded_cutoff ()
	calculates and returns the maximal global nonbonded cutoff that is required.
static void	recalc_maximal_cutoff_bonded ()
	calculate the maximal cutoff of bonded interactions, required to determine the cell size for communication.
void	force_and_energy_tables_init ()
	Initialize force and energy tables.
void	tf_tables_init ()
void	initialize_ia_params (IA_parameters *params)
	Initialize interaction parameters.
void	copy_ia_params (IA_parameters dst, IA_parameters src)
	Copy interaction parameters.
IA_parameters *	get_ia_param_safe (int i, int j)
	get interaction parameters between particle sorts i and j.
void	initialize_tf_params (TF_parameters *params)
void	copy_tf_params (TF_parameters dst, TF_parameters src)
int	checkIfTF (TF_parameters *data)
static void	recalc_maximal_cutoff_nonbonded ()
void	recalc_maximal_cutoff ()
	calculates the maximal cutoff of all real space interactions.
char *	get_name_of_bonded_ia (int i)
void	realloc_ia_params (int nsize)
	This function increases the LOCAL ia_params field for non-bonded interactions to the given size.
void	realloc_tf_params (int nsize)
void	make_particle_type_exist (int type)
	Makes sure that ia_params is large enough to cover interactions for this particle type.
void	make_bond_type_exist (int type)
	Makes sure that bonded_ia_params is large enough to cover the parameters for the bonded interaction type.
int	check_obs_calc_initialized ()
	check whether all force calculation routines are properly initialized.
int	coulomb_set_bjerrum (double bjerrum)
int	dipolar_set_Dbjerrum (double bjerrum)
void	recalc_coulomb_prefactor ()
	call when the temperature changes, for Bjerrum length adjusting.
int	virtual_set_params (int bond_type)
Variables
int	n_particle_types = 0
	Maximal particle type seen so far.
int	n_interaction_types = 0
IA_parameters *	ia_params = NULL
TF_parameters *	tf_params = NULL
Coulomb_parameters	coulomb
	Structure containing the coulomb parameters.
Debye_hueckel_params	dh_params = { 0.0, 0.0 }
	Structure containing the Debye-Hueckel parameters.
Reaction_field_params	rf_params = { 0.0, 0.0 }
	Structure containing the Reaction Field parameters.
int	n_bonded_ia = 0
	number of bonded interactions.
Bonded_ia_parameters *	bonded_ia_params = NULL
	Field containing the paramters of the bonded ia types.
double	min_global_cut = 0.0
	Minimal global interaction cutoff.
double	max_cut
	Maximal interaction cutoff.
double	max_cut_nonbonded
	Maximal interaction cutoff (real space/short range non-bonded interactions).
double	max_cut_bonded
	Maximal interaction cutoff (real space/short range bonded interactions).
double	max_cut_global
	maximal cutoff of type-independent short range ia, mainly electrostatics and DPD
DoubleList	tabulated_forces
	Array containing all tabulated forces.
DoubleList	tabulated_energies
	Corresponding array containing all tabulated energies.
DoubleList	thermodynamic_forces
	Array containing the thermodynamic forces.
DoubleList	thermodynamic_f_energies

Detailed Description

Implementation of interaction_data.h.

Definition in file interaction_data.c.

Function Documentation

int check_obs_calc_initialized ( )

check whether all force calculation routines are properly initialized.

Definition at line 886 of file interaction_data.c.

References COULOMB_ELC_P3M, COULOMB_MMM1D, COULOMB_MMM2D, COULOMB_P3M, COULOMB_P3M_GPU, DIPOLAR_DS, DIPOLAR_MDLC_DS, DIPOLAR_MDLC_P3M, DIPOLAR_P3M, Coulomb_parameters::Dmethod, dp3m_sanity_checks(), ELC_sanity_checks(), magnetic_dipolar_direct_sum_sanity_checks(), mdlc_sanity_checks(), Coulomb_parameters::method, MMM1D_sanity_checks(), MMM2D_sanity_checks(), and p3m_sanity_checks().

Referenced by energy_calc(), on_integration_start(), and pressure_calc().

int checkIfTF ( TF_parameters * data )

Definition at line 402 of file interaction_data.c.

References TF_parameters::TF_TAB_maxval.

void copy_ia_params	(	IA_parameters *	dst,
		IA_parameters *	src
	)

Copy interaction parameters.

copy a set of interaction parameters.

Definition at line 376 of file interaction_data.c.

Referenced by mpi_bcast_ia_params(), mpi_bcast_ia_params_slave(), and realloc_ia_params().

void copy_tf_params	(	TF_parameters *	dst,
		TF_parameters *	src
	)

Definition at line 398 of file interaction_data.c.

Referenced by realloc_tf_params().

int coulomb_set_bjerrum ( double bjerrum )

int dipolar_set_Dbjerrum ( double bjerrum )

Definition at line 972 of file interaction_data.c.

References Coulomb_parameters::Dbjerrum, DIPOLAR_MDLC_P3M, DIPOLAR_NONE, DIPOLAR_P3M, Coulomb_parameters::Dmethod, dp3m_set_bjerrum(), ES_ERROR, ES_OK, and mpi_bcast_coulomb_params().

Referenced by tclcommand_inter_parse_magnetic().

void force_and_energy_tables_init ( )

Initialize force and energy tables.

Function for initializing force and energy tables.

Definition at line 142 of file interaction_data.c.

References init_doublelist().

Referenced by on_program_start().

IA_parameters* get_ia_param_safe	(	int	i,
		int	j
	)

get interaction parameters between particle sorts i and j.

Slower than get_ia_param, but can also be used on not yet present particle types

Definition at line 380 of file interaction_data.c.

References get_ia_param(), imax(), and make_particle_type_exist().

Referenced by BMHTF_set_params(), buckingham_set_params(), comfixed_set_params(), comforce_set_params(), gaussian_set_params(), gay_berne_set_params(), hat_set_params(), hertzian_set_params(), inter_dpd_set_params(), interrf_set_params(), lennard_jones_set_params(), lj_cos_set_params(), ljangle_set_params(), ljcos2_set_params(), ljgen_set_params(), local_setup_reaction(), molcut_set_params(), morse_set_params(), smooth_step_set_params(), soft_sphere_set_params(), tabulated_set_params(), and tunable_slip_set_params().

char* get_name_of_bonded_ia ( int i )

void initialize_ia_params ( IA_parameters * params )

Initialize interaction parameters.

Definition at line 165 of file interaction_data.c.

Referenced by realloc_ia_params().

void initialize_tf_params ( TF_parameters * params )

Definition at line 387 of file interaction_data.c.

References TF_parameters::TF_prefactor, TF_parameters::TF_TAB_filename, TF_parameters::TF_TAB_maxval, TF_parameters::TF_TAB_minval, TF_parameters::TF_TAB_npoints, TF_parameters::TF_TAB_startindex, and TF_parameters::TF_TAB_stepsize.

Referenced by realloc_tf_params().

void make_bond_type_exist ( int type )

Makes sure that bonded_ia_params is large enough to cover the parameters for the bonded interaction type.

Attention: 1: There is no initialization done here. 2: Use only in connection with creating new or overwriting old bond types

Definition at line 854 of file interaction_data.c.

References BONDED_IA_NONE, BONDED_IA_OVERLAPPED, BONDED_IA_TABULATED, free, i, n_bonded_ia, Bonded_ia_parameters::overlap, realloc, and Bonded_ia_parameters::tab.

Referenced by angle_cosine_set_params(), angle_cossquare_set_params(), angle_harmonic_set_params(), angle_set_params(), angledist_set_params(), area_force_global_set_params(), area_force_local_set_params(), bending_force_set_params(), dihedral_set_params(), endangledist_set_params(), fene_set_params(), harmonic_set_params(), mpi_bcast_ia_params_slave(), overlapped_bonded_set_params(), rigid_bond_set_params(), stretching_force_set_params(), subt_lj_set_params(), tabulated_bonded_set_params(), virtual_set_params(), and volume_force_set_params().

void make_particle_type_exist ( int type )

Makes sure that ia_params is large enough to cover interactions for this particle type.

The interactions are initialized with values such that no physical interaction occurs.

Definition at line 846 of file interaction_data.c.

References mpi_bcast_n_particle_types(), and n_particle_types.

Referenced by collision_detection_set_params(), get_ia_param_safe(), local_setup_reaction(), on_program_start(), set_particle_type(), tclcommand_constraint_parse_cylinder(), tclcommand_constraint_parse_maze(), tclcommand_constraint_parse_plane_cell(), tclcommand_constraint_parse_pore(), tclcommand_constraint_parse_rhomboid(), tclcommand_constraint_parse_sphere(), tclcommand_constraint_parse_wall(), tclcommand_inter_print_non_bonded(), tf_print(), and tf_set_params().

void realloc_ia_params ( int nsize )

This function increases the LOCAL ia_params field for non-bonded interactions to the given size.

This function increases the LOCAL ia_params field to the given size.

This function is not exported since it does not do this on all nodes. Use make_particle_type_exist for that.

Definition at line 781 of file interaction_data.c.

References copy_ia_params(), free, i, initialize_ia_params(), malloc, and n_particle_types.

Referenced by mpi_bcast_n_particle_types_slave().

void realloc_tf_params ( int nsize )

Definition at line 814 of file interaction_data.c.

References copy_tf_params(), free, i, initialize_tf_params(), malloc, and n_particle_types.

Referenced by mpi_bcast_n_particle_types_slave().

void recalc_coulomb_prefactor ( )

call when the temperature changes, for Bjerrum length adjusting.

Definition at line 1002 of file interaction_data.c.

References Coulomb_parameters::bjerrum, Coulomb_parameters::Dbjerrum, Coulomb_parameters::Dprefactor, Coulomb_parameters::prefactor, and temperature.

Referenced by on_coulomb_change().

static void recalc_global_maximal_nonbonded_cutoff ( ) [static]

calculates and returns the maximal global nonbonded cutoff that is required.

Currently, this are just the cutoffs from the electrostatics method and some dpd cutoffs.

Definition at line 489 of file interaction_data.c.

References box_l, COULOMB_DH, COULOMB_ELC_P3M, COULOMB_INTER_RF, COULOMB_P3M, COULOMB_P3M_GPU, COULOMB_RF, DIPOLAR_MDLC_P3M, DIPOLAR_P3M, Coulomb_parameters::Dmethod, dp3m, dpd_r_cut, dpd_tr_cut, elc_params, max_cut_global, Coulomb_parameters::method, min_global_cut, p3m, dp3m_data_struct::params, p3m_data_struct::params, Debye_hueckel_params::r_cut, Reaction_field_params::r_cut, p3m_parameter_struct::r_cut_iL, and ELC_struct::space_layer.

Referenced by recalc_maximal_cutoff_nonbonded().

void recalc_maximal_cutoff ( )

calculates the maximal cutoff of all real space interactions.

these are: bonded, non bonded + real space electrostatics. The result is stored in the global variable max_cut. The maximal cutoff of the non-bonded + real space electrostatic interactions is stored in max_cut_non_bonded. This value is used in the verlet pair list algorithm (see verlet.h).

Definition at line 714 of file interaction_data.c.

References max_cut, max_cut_bonded, max_cut_nonbonded, recalc_maximal_cutoff_bonded(), and recalc_maximal_cutoff_nonbonded().

Referenced by on_parameter_change(), on_short_range_ia_change(), and propagate_press_box_pos_and_rescale_npt().

static void recalc_maximal_cutoff_bonded ( ) [static]

calculate the maximal cutoff of bonded interactions, required to determine the cell size for communication.

Definition at line 410 of file interaction_data.c.

References BONDED_IA_DIHEDRAL, BONDED_IA_FENE, BONDED_IA_HARMONIC, BONDED_IA_OVERLAPPED, BONDED_IA_RIGID_BOND, BONDED_IA_SUBT_LJ, BONDED_IA_TABULATED, Bonded_ia_parameters::fene, Bonded_ia_parameters::harmonic, i, max_cut_bonded, n_bonded_ia, Bonded_ia_parameters::overlap, OVERLAP_BOND_DIHEDRAL, OVERLAP_BOND_LENGTH, Bonded_ia_parameters::p, Bonded_ia_parameters::rigid_bond, Bonded_ia_parameters::subt_lj, Bonded_ia_parameters::tab, TAB_BOND_DIHEDRAL, and TAB_BOND_LENGTH.

Referenced by recalc_maximal_cutoff().

static void recalc_maximal_cutoff_nonbonded ( ) [static]

Definition at line 561 of file interaction_data.c.

References IA_parameters::BMHTF_cut, IA_parameters::BUCK_cut, CELL_TRACE, IA_parameters::dpd_r_cut, IA_parameters::dpd_tr_cut, IA_parameters::Gaussian_cut, IA_parameters::GB_cut, get_ia_param(), IA_parameters::HAT_r, IA_parameters::Hertzian_sig, i, IA_parameters::LJ_cut, IA_parameters::LJ_offset, IA_parameters::LJANGLE_cut, IA_parameters::LJCOS2_cut, IA_parameters::LJCOS2_offset, IA_parameters::LJCOS_cut, IA_parameters::LJCOS_offset, IA_parameters::LJGEN_cut, IA_parameters::LJGEN_offset, IA_parameters::max_cut, max_cut_bonded, max_cut_global, max_cut_nonbonded, IA_parameters::mol_cut_cutoff, IA_parameters::mol_cut_type, IA_parameters::MORSE_cut, n_particle_types, IA_parameters::particlesInteract, IA_parameters::REACTION_range, recalc_global_maximal_nonbonded_cutoff(), IA_parameters::SmSt_cut, IA_parameters::soft_cut, IA_parameters::TAB_maxval, this_node, and IA_parameters::TUNABLE_SLIP_r_cut.

Referenced by recalc_maximal_cutoff().

void tf_tables_init ( )

Definition at line 157 of file interaction_data.c.

References init_doublelist().

Referenced by on_program_start().

int virtual_set_params ( int bond_type )

Definition at line 1020 of file interaction_data.c.

References BONDED_IA_VIRTUAL_BOND, ES_ERROR, ES_OK, make_bond_type_exist(), mpi_bcast_ia_params(), Bonded_ia_parameters::num, and Bonded_ia_parameters::type.

Referenced by tclcommand_inter_parse_virtual_bonds().

Variable Documentation

Bonded_ia_parameters* bonded_ia_params = NULL

Field containing the paramters of the bonded ia types.

Definition at line 94 of file interaction_data.c.

Referenced by add_area_global_force(), add_bonded_energy(), add_bonded_force(), add_bonded_virials(), add_three_body_bonded_stress(), add_volume_force(), angle_cosine_set_params(), angle_cossquare_set_params(), angle_harmonic_set_params(), angle_set_params(), angledist_set_params(), area_force_global_set_params(), area_force_local_set_params(), auto_exclusion(), bending_force_set_params(), calc_area_global(), calc_volume(), collectBonds(), collision_detection_set_params(), compute_pos_corr_vec(), compute_vel_corr_vec(), detect_collision(), dihedral_set_params(), endangledist_set_params(), fene_set_params(), handle_collisions(), harmonic_set_params(), local_change_bond(), local_stress_tensor_calc(), mpi_bcast_ia_params(), mpi_bcast_ia_params_slave(), mpi_send_bond(), overlapped_bonded_set_params(), polymerC(), print_bond_len(), remove_all_bonds_to(), rigid_bond_set_params(), stretching_force_set_params(), subt_lj_set_params(), tabulated_bonded_set_params(), tclcommand_analyze_print_all(), tclcommand_analyze_print_pressure_all(), tclcommand_analyze_print_stress_tensor_all(), tclcommand_diamond(), tclcommand_icosaeder(), tclcommand_inter_print_all(), tclcommand_inter_print_partner_num(), tclcommand_part_parse_bond(), tclcommand_part_print_bond_partners(), tclcommand_part_print_bonding_structure(), tclprint_to_result_BondedIA(), try_delete_bond(), and volume_force_set_params().

Coulomb_parameters coulomb

Initial value:

 { 

  0.0, 0.0, COULOMB_NONE,


  0.0, 0.0, DIPOLAR_NONE,

}

Structure containing the coulomb parameters.

Definition at line 78 of file interaction_data.c.

Referenced by add_dh_coulomb_pair_force(), add_dipole_force(), add_mdlc_energy_corrections(), add_mdlc_force_corrections(), add_mmm1d_coulomb_pair_force(), add_mmm2d_coulomb_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_z_force(), calc_dipole_dipole_ia(), calc_long_range_energies(), calc_long_range_forces(), calc_long_range_forces_iccp3m(), calc_long_range_virials(), calc_surface_term(), cuda_mpi_get_particles(), cuda_mpi_get_particles_slave(), dawaanr_set_params(), dh_coulomb_pair_energy(), dipole_energy(), dp3m_add_pair_force(), dp3m_calc_kspace_forces(), dp3m_get_accuracy(), dp3m_init(), dp3m_mc_time(), dp3m_mcr_time(), dp3m_pair_energy(), dp3m_scaleby_box_l(), dp3m_set_params(), dp3m_set_tune_params(), ELC_init(), ELC_set_params(), get_nonbonded_interaction(), iccp3m_iteration(), iccp3m_sanity_check(), init_energies(), init_p_tensor(), init_virials(), integrate_vv(), maggs_init(), magnetic_dipolar_direct_sum_calculations(), mdds_set_params(), mdlc_set_params(), mmm1d_coulomb_pair_energy(), MMM1D_set_params(), MMM1D_setup_constants(), mmm1d_tune(), mmm2d_coulomb_pair_energy(), MMM2D_dielectric_layers_energy_contribution(), MMM2D_init(), MMM2D_self_energy(), MMM2D_set_params(), mpi_bcast_coulomb_params_slave(), on_boxl_change(), on_cell_structure_change(), on_coulomb_change(), on_ghost_flags_change(), on_integration_start(), on_observable_calc(), on_resort_particles(), p3m_add_pair_force(), p3m_calc_dipole_term(), p3m_calc_kspace_forces(), p3m_calc_kspace_stress(), p3m_get_accuracy(), p3m_init(), p3m_mc_time(), p3m_mcr_time(), p3m_pair_energy(), p3m_scaleby_box_l(), p3m_set_params(), p3m_set_tune_params(), plate_energy(), rf_coulomb_pair_energy_no_cutoff(), rod_energy(), setup_P(), setup_PQ(), setup_Q(), setup_z_energy(), setup_z_force(), tclcommand_analyze_print_all(), tclcommand_analyze_print_pressure_all(), tclcommand_analyze_print_stress_tensor_all(), tclcommand_integrate_set_npt_isotropic(), tclcommand_inter_coulomb_parse_dh(), tclcommand_inter_coulomb_parse_maggs(), tclcommand_inter_coulomb_parse_p3m(), tclcommand_inter_coulomb_parse_rf(), tclcommand_inter_parse_coulomb(), tclcommand_inter_parse_magnetic(), tclcommand_inter_print_all(), tclprint_to_result_CoulombIA(), tclprint_to_result_DipolarIA(), tclprint_to_result_p3m(), and z_energy().

Debye_hueckel_params dh_params = { 0.0, 0.0 }

Structure containing the Debye-Hueckel parameters.

Definition at line 89 of file interaction_data.c.

Referenced by dh_set_params(), mpi_bcast_coulomb_params_slave(), and tclprint_to_result_dh().

double max_cut

Maximal interaction cutoff.

Maximal interaction cutoff (real space/short range interactions).

Definition at line 98 of file interaction_data.c.

Referenced by cells_on_geometry_change(), dd_create_cell_grid(), dd_on_geometry_change(), incubewithskin(), local_stress_tensor_calc(), on_integration_start(), and recalc_maximal_cutoff().

double max_cut_bonded

Maximal interaction cutoff (real space/short range bonded interactions).

Definition at line 100 of file interaction_data.c.

Referenced by recalc_maximal_cutoff(), recalc_maximal_cutoff_bonded(), and recalc_maximal_cutoff_nonbonded().

double max_cut_global

maximal cutoff of type-independent short range ia, mainly electrostatics and DPD

Definition at line 103 of file interaction_data.c.

Referenced by initialize_ia_params(), recalc_global_maximal_nonbonded_cutoff(), and recalc_maximal_cutoff_nonbonded().

double max_cut_nonbonded

Maximal interaction cutoff (real space/short range non-bonded interactions).

Definition at line 99 of file interaction_data.c.

Referenced by build_verlet_lists(), build_verlet_lists_and_calc_verlet_ia(), build_verlet_lists_and_calc_verlet_ia_iccp3m(), calculate_verlet_energies(), calculate_verlet_virials(), recalc_maximal_cutoff(), recalc_maximal_cutoff_nonbonded(), and tclcommand_analyze_parse_aggregation().

double min_global_cut = 0.0

Minimal global interaction cutoff.

Particles with a distance smaller than this are guaranteed to be available on the same node (through ghosts).

Definition at line 96 of file interaction_data.c.

Referenced by recalc_global_maximal_nonbonded_cutoff(), tclcallback_min_global_cut(), and vs_relate_to().

int n_interaction_types = 0

Definition at line 68 of file interaction_data.c.

int n_particle_types = 0

Maximal particle type seen so far.

Definition at line 67 of file interaction_data.c.

Reaction_field_params rf_params = { 0.0, 0.0 }

Structure containing the Reaction Field parameters.

Definition at line 90 of file interaction_data.c.

Referenced by mpi_bcast_coulomb_params_slave(), rf_set_params(), and tclprint_to_result_rf().

DoubleList tabulated_energies

Corresponding array containing all tabulated energies.

Array containing all tabulated energies.

Definition at line 108 of file interaction_data.c.

Referenced by mpi_bcast_ia_params(), mpi_bcast_ia_params_slave(), tabulated_pair_energy(), and tabulated_set_params().

DoubleList tabulated_forces

Array containing all tabulated forces.

Definition at line 106 of file interaction_data.c.

Referenced by add_tabulated_pair_force(), check_tab_forcecap(), mpi_bcast_ia_params(), mpi_bcast_ia_params_slave(), tabulated_pair_energy(), and tabulated_set_params().

TF_parameters* tf_params = NULL

Definition at line 73 of file interaction_data.c.

Referenced by add_thermodynamic_force(), and get_tf_param().

DoubleList thermodynamic_f_energies

Definition at line 121 of file interaction_data.c.

Referenced by mpi_bcast_tf_params(), mpi_bcast_tf_params_slave(), and tf_set_params().

DoubleList thermodynamic_forces

Array containing the thermodynamic forces.

Definition at line 120 of file interaction_data.c.

Referenced by mpi_bcast_tf_params(), mpi_bcast_tf_params_slave(), tf_profile(), and tf_set_params().

Functions

Variables

Detailed Description

Function Documentation

Variable Documentation