BondedInteractionsMap Class Reference

container for bonded interactions. More...

#include <bonded_interaction_data.hpp>

Inheritance diagram for BondedInteractionsMap:

Collaboration diagram for BondedInteractionsMap:

Public Types
using	key_type = container_type::key_type
using	mapped_type = container_type::mapped_type
using	value_type = container_type::value_type
using	iterator = container_type::iterator
using	const_iterator = container_type::const_iterator

Public Member Functions
	BondedInteractionsMap ()=default
virtual	~BondedInteractionsMap ()=default
iterator	begin ()
iterator	end ()
const_iterator	begin () const
const_iterator	end () const
void	insert (key_type const &key, mapped_type const &ptr)
key_type	insert (mapped_type const &ptr)
auto	erase (key_type const &key)
virtual void	activate_bond (mapped_type const &ptr)
virtual void	deactivate_bond (mapped_type const &ptr)
mapped_type const &	at (key_type const &key) const
bool	contains (key_type const &key) const
bool	empty () const
auto	size () const
DEVICE_QUALIFIER auto	get_next_key () const
auto	get_zero_based_type (int bond_id) const
DEVICE_QUALIFIER auto	get_n_thermalized_bonds () const
DEVICE_QUALIFIER auto	get_n_rigid_bonds () const
std::optional< key_type >	find_bond_id (mapped_type const &target_bond) const
double	maximal_cutoff () const
	Calculate the maximal cutoff of bonded interactions, required to determine the cell size for communication.
template<typename BondType >
bool	pair_bond_exists_on (Particle const &p, Particle const &p_partner) const
	Checks both particles for a specific bond, even on ghost particles.
template<typename BondType >
bool	pair_bond_exists_between (Particle const &p1, Particle const &p2) const
	Checks both particles for a specific bond, even on ghost particles.
void	on_ia_change ()
Public Member Functions inherited from System::Leaf< BondedInteractionsMap >
void	bind_system (std::shared_ptr< System > const &system)
void	detach_system (std::shared_ptr< System > const &system)

Public Attributes
std::vector< Utils::Vector9d >	rigid_bond_virial
	Per-bond-type RATTLE constraint virial.

Additional Inherited Members
Protected Member Functions inherited from System::Leaf< BondedInteractionsMap >
auto &	get_system ()
auto &	get_system () const
Protected Attributes inherited from System::Leaf< BondedInteractionsMap >
std::weak_ptr< System >	m_system

Detailed Description

container for bonded interactions.

Definition at line 89 of file bonded_interaction_data.hpp.

Member Typedef Documentation

const_iterator

using BondedInteractionsMap::const_iterator = container_type::const_iterator

Definition at line 98 of file bonded_interaction_data.hpp.

iterator

using BondedInteractionsMap::iterator = container_type::iterator

Definition at line 97 of file bonded_interaction_data.hpp.

key_type

using BondedInteractionsMap::key_type = container_type::key_type

Definition at line 94 of file bonded_interaction_data.hpp.

mapped_type

using BondedInteractionsMap::mapped_type = container_type::mapped_type

Definition at line 95 of file bonded_interaction_data.hpp.

value_type

using BondedInteractionsMap::value_type = container_type::value_type

Definition at line 96 of file bonded_interaction_data.hpp.

Constructor & Destructor Documentation

BondedInteractionsMap()

BondedInteractionsMap::BondedInteractionsMap ( )

default

~BondedInteractionsMap()

virtual BondedInteractionsMap::~BondedInteractionsMap ( )

virtualdefault

Member Function Documentation

activate_bond()

void BondedInteractionsMap::activate_bond ( mapped_type const &  ptr )

virtual

Definition at line 71 of file bonded_interaction_data.cpp.

References System::Leaf< BondedInteractionsMap >::get_system(), and stream.

Referenced by insert(), and insert().

at()

mapped_type const & BondedInteractionsMap::at ( key_type const &  key ) const

inline

Definition at line 134 of file bonded_interaction_data.hpp.

References stream.

Referenced by add_oif_global_forces(), calc_oif_mesh(), compute_correction_vector(), Mpiio::dump_info(), get_zero_based_type(), and vol_cons_parameters().

begin() [1/2]

iterator BondedInteractionsMap::begin ( )

inline

Definition at line 103 of file bonded_interaction_data.hpp.

Referenced by maximal_cutoff().

begin() [2/2]

const_iterator BondedInteractionsMap::begin ( ) const

inline

Definition at line 105 of file bonded_interaction_data.hpp.

contains()

bool BondedInteractionsMap::contains ( key_type const &  key ) const

inline

Definition at line 135 of file bonded_interaction_data.hpp.

References stream.

Referenced by Mpiio::dump_info(), and get_zero_based_type().

deactivate_bond()

void BondedInteractionsMap::deactivate_bond ( mapped_type const &  ptr )

virtual

Definition at line 87 of file bonded_interaction_data.cpp.

References stream.

Referenced by erase(), and insert().

empty()

bool BondedInteractionsMap::empty ( ) const

inline

Definition at line 136 of file bonded_interaction_data.hpp.

Referenced by create_kokkos_bonds_kernel_data().

end() [1/2]

iterator BondedInteractionsMap::end ( )

inline

Definition at line 104 of file bonded_interaction_data.hpp.

Referenced by maximal_cutoff().

end() [2/2]

const_iterator BondedInteractionsMap::end ( ) const

inline

Definition at line 106 of file bonded_interaction_data.hpp.

erase()

auto BondedInteractionsMap::erase ( key_type const &  key )

inline

Definition at line 124 of file bonded_interaction_data.hpp.

References deactivate_bond(), on_ia_change(), and stream.

find_bond_id()

std::optional< key_type > BondedInteractionsMap::find_bond_id ( mapped_type const &  target_bond ) const

inline

Definition at line 166 of file bonded_interaction_data.hpp.

References stream.

get_n_rigid_bonds()

DEVICE_QUALIFIER auto BondedInteractionsMap::get_n_rigid_bonds ( ) const

inline

Definition at line 150 of file bonded_interaction_data.hpp.

References stream.

get_n_thermalized_bonds()

DEVICE_QUALIFIER auto BondedInteractionsMap::get_n_thermalized_bonds ( ) const

inline

Definition at line 144 of file bonded_interaction_data.hpp.

References stream.

get_next_key()

DEVICE_QUALIFIER auto BondedInteractionsMap::get_next_key ( ) const

inline

Definition at line 139 of file bonded_interaction_data.hpp.

Referenced by correct_position_shake(), and Mpiio::dump_info().

get_zero_based_type()

auto BondedInteractionsMap::get_zero_based_type ( int  bond_id ) const

inline

Definition at line 140 of file bonded_interaction_data.hpp.

References at(), and contains().

insert() [1/2]

void BondedInteractionsMap::insert ( key_type const &  key, mapped_type const &  ptr  )

inline

Definition at line 108 of file bonded_interaction_data.hpp.

References activate_bond(), deactivate_bond(), on_ia_change(), and stream.

insert() [2/2]

key_type BondedInteractionsMap::insert ( mapped_type const &  ptr )

inline

Definition at line 117 of file bonded_interaction_data.hpp.

References activate_bond(), on_ia_change(), and stream.

maximal_cutoff()

double BondedInteractionsMap::maximal_cutoff

(

)

const

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 32 of file bonded_interaction_data.cpp.

References begin(), bonded_inactive_cutoff, end(), and stream.

Referenced by create_cabana_neighbor_kernel().

on_ia_change()

void BondedInteractionsMap::on_ia_change

(

)

Definition at line 50 of file bonded_interaction_data.cpp.

References System::Leaf< BondedInteractionsMap >::m_system, and stream.

Referenced by erase(), insert(), and insert().

pair_bond_exists_between()

template<typename BondType >

bool BondedInteractionsMap::pair_bond_exists_between ( Particle const &  p1, Particle const &  p2  ) const

inline

Checks both particles for a specific bond, even on ghost particles.

Parameters

p1	particle on which the bond may be stored
p2	particle on which the bond may be stored

Template Parameters

BondType

Bond type to check for.

Definition at line 218 of file bonded_interaction_data.hpp.

References stream.

Referenced by thole_pair_energy(), and thole_pair_force().

pair_bond_exists_on()

template<typename BondType >

bool BondedInteractionsMap::pair_bond_exists_on ( Particle const &  p, Particle const &  p_partner  ) const

inline

Checks both particles for a specific bond, even on ghost particles.

Parameters

p	particle to check for the bond
p_partner	possible bond partner

Template Parameters

BondType

Bond type to check for. Must be of one of the types in Bonded_IA_Parameters.

Definition at line 199 of file bonded_interaction_data.hpp.

References Particle::bonds(), and stream.

size()

auto BondedInteractionsMap::size ( ) const

inline

Definition at line 137 of file bonded_interaction_data.hpp.

Referenced by Mpiio::dump_info().

Member Data Documentation

rigid_bond_virial

std::vector<Utils::Vector9d> BondedInteractionsMap::rigid_bond_virial

Per-bond-type RATTLE constraint virial.

Accumulated bond-by-bond inside correct_position_shake() (indexed by bond id, same convention as Observable_stat::bonded_contribution()), where the pairwise correction/mass/bond-vector are all unambiguous, regardless of how many rigid bonds a particle participates in. Reset at the start of every SHAKE call; consumed by System::System::calculate_pressure().

Definition at line 164 of file bonded_interaction_data.hpp.

Referenced by correct_position_shake().

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The documentation for this class was generated from the following files:

• bonded_interaction_data.hpp
• bonded_interaction_data.cpp