Data structures for bonded interactions. More...

#include "angle_common.hpp"
#include "angle_cosine.hpp"
#include "angle_cossquare.hpp"
#include "angle_harmonic.hpp"
#include "bonded_coulomb.hpp"
#include "bonded_coulomb_sr.hpp"
#include "bonded_tab.hpp"
#include "dihedral.hpp"
#include "fene.hpp"
#include "harmonic.hpp"
#include "immersed_boundary/ibm_tribend.hpp"
#include "immersed_boundary/ibm_triel.hpp"
#include "immersed_boundary/ibm_volcons.hpp"
#include "object-in-fluid/oif_global_forces_params.hpp"
#include "object-in-fluid/oif_local_forces.hpp"
#include "quartic.hpp"
#include "rigid_bond.hpp"
#include "thermalized_bond.hpp"
#include "TabulatedPotential.hpp"
#include <boost/serialization/access.hpp>
#include <boost/serialization/variant.hpp>
#include <boost/variant.hpp>
#include <algorithm>
#include <cassert>
#include <cmath>
#include <stdexcept>
#include <unordered_map>
#include <vector>

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Classes
struct	NoneBond
	Interaction type for unused bonded interaction slots. More...

struct	VirtualBond
	Interaction type for virtual bonds. More...

class	BondNumPartners
	Visitor to get the number of bound partners from the bond parameter variant. More...

class	BondedInteractionsMap

Typedefs
using	Bonded_IA_Parameters = boost::variant< NoneBond, FeneBond, HarmonicBond, QuarticBond, BondedCoulomb, BondedCoulombSR, AngleHarmonicBond, AngleCosineBond, AngleCossquareBond, DihedralBond, TabulatedDistanceBond, TabulatedAngleBond, TabulatedDihedralBond, ThermalizedBond, RigidBond, IBMTriel, IBMVolCons, IBMTribend, OifGlobalForcesBond, OifLocalForcesBond, VirtualBond >
	Variant in which to store the parameters of an individual bonded interaction.

Functions
double	maximal_cutoff_bonded ()
	Calculate the maximal cutoff of bonded interactions, required to determine the cell size for communication.

int	number_of_partners (Bonded_IA_Parameters const &iaparams)
	Return the number of bonded partners for the specified bond.

Variables
static constexpr double	BONDED_INACTIVE_CUTOFF = -1.

BondedInteractionsMap	bonded_ia_params
	Field containing the parameters of the bonded ia types.

Detailed Description

Data structures for bonded interactions.

For more information on how to add new interactions, see Adding new interactions.

Definition in file bonded_interaction_data.hpp.

Typedef Documentation

◆ Bonded_IA_Parameters

Variant in which to store the parameters of an individual bonded interaction.

Definition at line 95 of file bonded_interaction_data.hpp.

Function Documentation

◆ maximal_cutoff_bonded()

double maximal_cutoff_bonded ( )

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

Bond angle and dihedral potentials do not contain a cutoff intrinsically. The cutoff for these potentials depends on the bond length potentials (it is assumed that particles participating in a bond angle or dihedral potential are bound to each other by some bond length potential). For bond angle potentials nothing has to be done. For dihedral potentials the cutoff is set to twice the maximal cutoff because the particle in which the bond is stored is only bonded to the first two partners, one of which has an additional bond to the third partner.

Definition at line 43 of file bonded_interaction_data.cpp.

References BondedInteractionsMap::begin(), bonded_ia_params, BONDED_INACTIVE_CUTOFF, and BondedInteractionsMap::end().

Referenced by System::System::calculate_energy(), System::System::calculate_forces(), System::System::calculate_pressure(), ScriptInterface::CellSystem::CellSystem::CellSystem(), and System::System::maximal_cutoff().