Molecule Struct Reference

Structure holding information about a molecule. More...

#include <topology.h>

Collaboration diagram for Molecule:

Data Fields
int	type
	Type of the molecule.
IntList	part
	List of particle identities contained in that molecule.
double	f [3]
	Total force on the molecule.
double	fav [3]
	Sum of forces on molecule over the last favcounter time steps.
int	favcounter
	counter for fav
double	mass
	Total mass of the molecule.
double	com [3]
	Center of mass position.
double	v [3]
	velocity of particle
int	trap_flag
	Whether to trap motion in a direction with a harmonic well.
double	trap_center [3]
	Location of a harmonic trap for this molecule.
double	trap_spring_constant
	Trap stiffness.
double	drag_constant
	viscous drag applied to this molecule
int	noforce_flag
	Whether to adjust forces on particles so that net force on molecule is 0.
int	isrelative
	whether trap_center is relative (i.e.
double	trap_force [3]
	the force applied by the trap on the molecule

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Detailed Description

Structure holding information about a molecule.

Definition at line 37 of file topology.h.

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Field Documentation

double Molecule::com[3]

Center of mass position.

Definition at line 53 of file topology.h.

Referenced by calc_local_mol_info(), calc_trap_force(), and mpi_comm_mol_info().

double Molecule::drag_constant

viscous drag applied to this molecule

Definition at line 63 of file topology.h.

Referenced by calc_trap_force(), and set_molecule_trap().

double Molecule::f[3]

Total force on the molecule.

Definition at line 45 of file topology.h.

Referenced by calc_local_mol_info(), calc_trap_force(), and mpi_comm_mol_info().

double Molecule::fav[3]

Sum of forces on molecule over the last favcounter time steps.

Definition at line 47 of file topology.h.

Referenced by calc_trap_force(), realloc_topology(), and tclcommand_analyze_parse_mol().

int Molecule::favcounter

counter for fav

Definition at line 49 of file topology.h.

Referenced by calc_trap_force(), realloc_topology(), and tclcommand_analyze_parse_mol().

int Molecule::isrelative

whether trap_center is relative (i.e.

fraction of box_length) (1) or absolute (0)

Definition at line 67 of file topology.h.

Referenced by calc_trap_force(), and set_molecule_trap().

double Molecule::mass

Total mass of the molecule.

Definition at line 51 of file topology.h.

Referenced by calc_local_mol_info(), and mpi_comm_mol_info().

int Molecule::noforce_flag

Whether to adjust forces on particles so that net force on molecule is 0.

Definition at line 65 of file topology.h.

Referenced by calc_trap_force(), realloc_topology(), and set_molecule_trap().

IntList Molecule::part

List of particle identities contained in that molecule.

Definition at line 41 of file topology.h.

Referenced by analyze_fold_molecules(), calc_dipole_of_molecule(), calc_force_between_mol(), calc_mol_center_of_mass(), calc_mol_gyr_radius2(), calc_mol_hydro_radius(), calc_mol_pos(), calc_mol_pos_cfg(), calc_mol_vel(), calc_trap_force(), get_lipid_orients(), get_mol_com_particle(), get_mol_com_particle_from_molid_cfg(), init_local_particle_force(), lipid_orientation(), mpi_sync_topo_part_info(), mpi_sync_topo_part_info_slave(), orient_order(), put_mol_force_on_parts(), sync_topo_part_info(), tclcommand_analyze_set_parse_topo_part_sync(), and tclcommand_analyze_set_print_all().

double Molecule::trap_center[3]

Location of a harmonic trap for this molecule.

Definition at line 59 of file topology.h.

Referenced by calc_trap_force(), and set_molecule_trap().

int Molecule::trap_flag

Whether to trap motion in a direction with a harmonic well.

Definition at line 57 of file topology.h.

Referenced by calc_trap_force(), realloc_topology(), and set_molecule_trap().

double Molecule::trap_force[3]

the force applied by the trap on the molecule

Definition at line 69 of file topology.h.

Referenced by apply_mol_constraints(), calc_trap_force(), and realloc_topology().

double Molecule::trap_spring_constant

Trap stiffness.

Definition at line 61 of file topology.h.

Referenced by calc_trap_force(), and set_molecule_trap().

int Molecule::type

Type of the molecule.

Definition at line 39 of file topology.h.

Referenced by mpi_sync_topo_part_info(), mpi_sync_topo_part_info_slave(), tclcommand_analyze_parse_generic_structure(), and tclcommand_analyze_set_parse_chain_topology().

double Molecule::v[3]

velocity of particle

Definition at line 55 of file topology.h.

Referenced by calc_local_mol_info(), calc_trap_force(), and mpi_comm_mol_info().

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The documentation for this struct was generated from the following file:

• topology.h