Main system class. More...

#include <System.hpp>

Inheritance diagram for System::System:

Collaboration diagram for System::System:

Public Member Functions
	System (Private)

auto	get_time_step () const
	Get time_step.

void	set_time_step (double value)
	Set time_step.

auto	get_sim_time () const
	Get sim_time.

void	set_sim_time (double value)
	Set sim_time.

auto	get_force_cap () const
	Get force_cap.

void	set_force_cap (double value)
	Set force_cap.

auto	get_min_global_cut () const
	Get min_global_cut.

void	set_min_global_cut (double value)
	Set min_global_cut.

void	set_box_l (Utils::Vector3d const &box_l)
	Change the box dimensions.

void	tune_verlet_skin (double min_skin, double max_skin, double tol, int int_steps, bool adjust_max_skin)
	Tune the Verlet skin.

void	set_cell_structure_topology (CellStructureType topology)
	Change cell structure topology.

void	rebuild_cell_structure ()
	Rebuild cell lists.

double	maximal_cutoff () const
	Calculate the maximal cutoff of all interactions.

double	get_interaction_range () const
	Get the interaction range.

unsigned	get_global_ghost_flags () const
	Returns the ghost flags required for running pair kernels for the global state, e.g.

bool	long_range_interactions_sanity_checks () const
	Check electrostatic and magnetostatic methods are properly initialized.

std::shared_ptr< Observable_stat >	calculate_energy ()
	Calculate the total energy.

std::shared_ptr< Observable_stat >	calculate_pressure ()
	Calculate the pressure from a virial expansion.

double	get_instantaneous_pressure ()
	get the instantaneous pressure with (q(t+dt), p(t+dt/2))

double	get_instantaneous_pressure_virial ()
	get the instantaneous virial pressure with q(t+dt)

void	synchronize_npt_state ()
	Synchronize NpT state such as instantaneous and average pressure.

void	npt_ensemble_init (bool recalc_forces)
	Reinitialize the NpT state.

void	npt_add_virial_contribution (double energy)

void	npt_add_virial_contribution (Utils::Vector3d const &force, Utils::Vector3d const &d)

void	calculate_forces ()
	Calculate all forces.

void	calculate_long_range_fields ()
	Calculate dipole fields.

double	particle_short_range_energy_contribution (int pid)
	Compute the short-range energy of a particle.

std::optional< double >	particle_bond_energy (int pid, int bond_id, std::vector< int > partners)
	Compute the energy of a given bond which has to exist on the given particle.

int	integrate (int n_steps, int reuse_forces)
	Integrate equations of motion.

int	integrate_with_signal_handler (int n_steps, int reuse_forces, bool update_accumulators)

void	thermostat_force_init ()
	Calculate initial particle forces from active thermostats.

void	lb_couple_particles ()
	Calculate particle-lattice interactions.

void	update_dependent_particles ()
	Update particles with properties depending on other particles, namely virtual sites and ICC charges.

void	update_used_propagations ()
	Update the global propagation bitmask.

void	check_kT (double value) const
	Veto temperature change.

Hook procedures
These procedures are called if several significant changes to the system happen which may make a reinitialization of subsystems necessary.
void	on_boxl_change (bool skip_method_adaption=false)
	Called when the box length has changed.

void	on_node_grid_change ()

void	on_periodicity_change ()

void	on_cell_structure_change ()

void	on_thermostat_param_change ()

void	on_temperature_change ()

void	on_verlet_skin_change ()

void	on_timestep_change ()

void	on_integration_start ()

void	on_short_range_ia_change ()

void	on_non_bonded_ia_change ()

void	on_coulomb_change ()

void	on_dipoles_change ()

void	on_constraint_change ()
	Called every time a constraint is changed.

void	on_lb_boundary_conditions_change ()
	Called when the LB boundary conditions change (geometry, slip velocity, or both).

void	on_particle_local_change ()
	Called every time a particle local property changes.

void	on_particle_change ()
	Called every time a particle property changes.

void	on_particle_charge_change ()
	Called every time a particle charge changes.

void	on_observable_calc ()
	called before calculating observables, i.e.

void	on_lees_edwards_change ()

void	veto_boxl_change (bool skip_particle_checks=false) const

Static Public Member Functions
static std::shared_ptr< System >	create ()

Public Attributes
GpuParticleData	gpu

ResourceCleanup	cleanup_queue

Coulomb::Solver	coulomb

Dipoles::Solver	dipoles

LB::Solver	lb

EK::Solver	ek

std::shared_ptr< BoxGeometry >	box_geo

std::shared_ptr< LocalBox >	local_geo

std::shared_ptr< CellStructure >	cell_structure

std::shared_ptr< Propagation >	propagation

std::shared_ptr< BondedInteractionsMap >	bonded_ias

std::shared_ptr< InteractionsNonBonded >	nonbonded_ias

std::shared_ptr< Thermostat::Thermostat >	thermostat

std::shared_ptr< ComFixed >	comfixed

std::shared_ptr< Galilei >	galilei

std::shared_ptr< OifGlobal >	oif_global

std::shared_ptr< ImmersedBoundaries >	immersed_boundaries

std::shared_ptr< CollisionDetection::CollisionDetection >	collision_detection

std::shared_ptr< BondBreakage::BondBreakage >	bond_breakage

std::shared_ptr< LeesEdwards::LeesEdwards >	lees_edwards

std::shared_ptr< Accumulators::AutoUpdateAccumulators >	auto_update_accumulators

std::shared_ptr< Constraints::Constraints >	constraints

std::shared_ptr< NptIsoParameters >	nptiso

std::shared_ptr< InstantaneousPressure >	npt_inst_pressure

Protected Member Functions
void	update_local_geo ()

void	update_icc_particles ()

Protected Attributes
bool	reinit_thermo
	Whether the thermostat has to be reinitialized before integration.

double	time_step
	Molecular dynamics integrator time step.

double	sim_time
	Molecular dynamics integrator simulation time.

double	force_cap
	Molecular dynamics integrator force capping.

double	min_global_cut
	Minimal global interaction cutoff.

Detailed Description

Main system class.

Most components follow the composite pattern and the opaque pointer pattern. See System class design for more details.

Definition at line 79 of file core/system/System.hpp.

Constructor & Destructor Documentation

◆ System()

System::System::System ( Private )

Definition at line 65 of file core/system/System.cpp.

References INACTIVE_CUTOFF.

Member Function Documentation

◆ calculate_energy()

std::shared_ptr< Observable_stat > System::System::calculate_energy ( )

Calculate the total energy.

Definition at line 39 of file energy.cpp.

References add_non_bonded_pair_energy(), calc_bonded_energy(), get_ptr(), rotational_kinetic_energy(), short_range_loop(), stream, and translational_kinetic_energy().

Referenced by Observables::Energy::operator()().

◆ calculate_forces()

void System::System::calculate_forces ( )

Calculate all forces.

Definition at line 119 of file forces.cpp.

References add_bonded_force(), add_non_bonded_pair_force(), calc_long_range_forces(), force_capping(), get_ptr(), INACTIVE_CUTOFF, init_forces(), PropagationMode::ROT_VS_RELATIVE, short_range_loop(), stream, this_node, PropagationMode::TRANS_LANGEVIN_NPT, PropagationMode::TRANS_LB_MOMENTUM_EXCHANGE, PropagationMode::TRANS_VS_RELATIVE, and vs_relative_back_transfer_forces_and_torques().

◆ calculate_long_range_fields()

void System::System::calculate_long_range_fields ( )

Calculate dipole fields.

Definition at line 162 of file energy.cpp.

Referenced by Observables::ParticleDipoleFields::evaluate().

◆ calculate_pressure()

std::shared_ptr< Observable_stat > System::System::calculate_pressure ( )

Calculate the pressure from a virial expansion.

Definition at line 47 of file pressure.cpp.

References add_kinetic_virials(), add_non_bonded_pair_virials(), Utils::Array< T, N >::begin(), calc_bonded_pressure_tensor(), Dipoles::Solver::calc_pressure_long_range(), dpd_pressure_local(), Utils::flatten(), Dipoles::get_dipoles(), get_ptr(), short_range_loop(), stream, and vs_relative_pressure_tensor().

Referenced by Observables::Pressure::operator()(), and Observables::PressureTensor::operator()().

◆ check_kT()

void System::System::check_kT ( double value ) const

Veto temperature change.

Definition at line 141 of file core/system/System.cpp.

◆ create()

std::shared_ptr< System > System::System::create ( )

static

Definition at line 59 of file core/system/System.cpp.

References stream.

Referenced by ScriptInterface::System::System::do_construct().

◆ get_force_cap()

auto System::System::get_force_cap ( ) const

inline

Get force_cap.

Definition at line 107 of file core/system/System.hpp.

◆ get_global_ghost_flags()

unsigned System::System::get_global_ghost_flags ( ) const

Returns the ghost flags required for running pair kernels for the global state, e.g.

the force calculation.

Returns: Required data parts;

Definition at line 495 of file core/system/System.cpp.

References Cells::DATA_PART_BONDS, Cells::DATA_PART_MOMENTUM, Cells::DATA_PART_POSITION, Cells::DATA_PART_PROPERTIES, stream, THERMO_BOND, and THERMO_DPD.

◆ get_instantaneous_pressure()

double System::System::get_instantaneous_pressure ( )

get the instantaneous pressure with (q(t+dt), p(t+dt/2))

◆ get_instantaneous_pressure_virial()

double System::System::get_instantaneous_pressure_virial ( )

get the instantaneous virial pressure with q(t+dt)

◆ get_interaction_range()

double System::System::get_interaction_range ( ) const

Get the interaction range.

Definition at line 431 of file core/system/System.cpp.

References INACTIVE_CUTOFF, and stream.

◆ get_min_global_cut()

auto System::System::get_min_global_cut ( ) const

inline

Get min_global_cut.

Definition at line 113 of file core/system/System.hpp.

◆ get_sim_time()

auto System::System::get_sim_time ( ) const

inline

Get sim_time.

Definition at line 101 of file core/system/System.hpp.

◆ get_time_step()

auto System::System::get_time_step ( ) const

inline

Get time_step.

Definition at line 95 of file core/system/System.hpp.

◆ integrate()

int System::System::integrate	(	int	n_steps,
		int	reuse_forces
	)

Integrate equations of motion.

Parameters

n_steps	Number of integration steps, can be zero
reuse_forces	Decide when to re-calculate forces

This function calls two hooks for propagation kernels such as velocity verlet, velocity verlet + npt box changes, and steepest_descent. One hook is called before and one after the force calculation. It is up to the propagation kernels to increment the simulation time.

This function propagates the system according to the choice of integrator stored in Propagation::integ_switch. The general structure is:

if reuse_forces is zero, recalculate the forces based on the current state of the system
Loop over the number of simulation steps:
1. initialization (e.g., RATTLE)
2. First hook for propagation kernels
3. Update dependent particles and properties (RATTLE, virtual sites)
4. Calculate forces for the current state of the system. This includes forces added by the Langevin thermostat and the Lattice-Boltzmann-particle coupling
5. Second hook for propagation kernels
6. Update dependent properties (Virtual sites, RATTLE)
7. Run single step algorithms (Lattice-Boltzmann propagation, collision detection, NpT update)
Final update of dependent properties and statistics/counters

High-level documentation of the integration and thermostatting schemes can be found in doc/sphinx/system_setup.rst and /doc/sphinx/running.rst

Returns: number of steps that have been integrated, or a negative error code

Definition at line 441 of file integrate.cpp.

References check_runtime_errors(), comm_cart, convert_initial_torques(), correct_position_shake(), correct_velocity_shake(), Cells::DATA_PART_PROPERTIES, INTEG_ERROR_RUNTIME, INTEG_ERROR_SIGINT, INTEG_METHOD_BD, INTEG_METHOD_NPT_ISO, INTEG_METHOD_STEEPEST_DESCENT, INTEG_REUSE_FORCES_ALWAYS, INTEG_REUSE_FORCES_NEVER, integrator_step_1(), integrator_step_2(), lb_tracers_add_particle_force_to_fluid(), lb_tracers_propagate(), LEES_EDWARDS, Cells::RESORT_LOCAL, resort_particles_if_needed(), PropagationMode::ROT_VS_RELATIVE, runtimeErrorMsg, save_old_position(), stream, PropagationMode::TRANS_LB_MOMENTUM_EXCHANGE, PropagationMode::TRANS_LB_TRACER, PropagationMode::TRANS_VS_RELATIVE, and vs_relative_update_particles().

◆ integrate_with_signal_handler()

int System::System::integrate_with_signal_handler	(	int	n_steps,
		int	reuse_forces,
		bool	update_accumulators
	)

Definition at line 722 of file integrate.cpp.

References comm_cart, INTEG_ERROR_RUNTIME, INTEG_REUSE_FORCES_ALWAYS, and stream.

Referenced by ScriptInterface::Integrators::SteepestDescent::integrate().

◆ lb_couple_particles()

void System::System::lb_couple_particles ( )

Calculate particle-lattice interactions.

Definition at line 354 of file particle_coupling.cpp.

References LB::is_tracer(), LB::lb_coupling_sanity_checks(), runtimeErrorMsg, and stream.

◆ long_range_interactions_sanity_checks()

bool System::System::long_range_interactions_sanity_checks ( ) const

Check electrostatic and magnetostatic methods are properly initialized.

Returns: true if sanity checks failed.

Definition at line 416 of file core/system/System.cpp.

References runtimeErrorMsg, and stream.

◆ maximal_cutoff()

double System::System::maximal_cutoff ( ) const

Calculate the maximal cutoff of all interactions.

Definition at line 394 of file core/system/System.cpp.

References communicator, and INACTIVE_CUTOFF.

◆ npt_add_virial_contribution() [1/2]

void System::System::npt_add_virial_contribution ( double energy )

Definition at line 122 of file npt.cpp.

References INTEG_METHOD_NPT_ISO.

Referenced by CoulombP3MImpl< FloatType, Architecture >::add_long_range_forces_gpu(), CoulombP3MImpl< FloatType, Architecture >::long_range_kernel(), DipolarP3MImpl< FloatType, Architecture >::long_range_kernel(), DipolarP3MImpl< FloatType, Architecture >::npt_add_virial_contribution(), and npt_add_virial_force_contribution().

◆ npt_add_virial_contribution() [2/2]

void System::System::npt_add_virial_contribution	(	Utils::Vector3d const &	force,
		Utils::Vector3d const &	d
	)

Definition at line 128 of file npt.cpp.

References INTEG_METHOD_NPT_ISO.

◆ npt_ensemble_init()

void System::System::npt_ensemble_init ( bool recalc_forces )

Reinitialize the NpT state.

Definition at line 98 of file npt.cpp.

References comm_cart, Utils::Mpi::gather_buffer(), and this_node.

◆ on_boxl_change()

void System::System::on_boxl_change ( bool skip_method_adaption = false )

Called when the box length has changed.

This routine is relatively fast, and changing the box length every time step as for example necessary for NpT is more or less ok.

Parameters

skip_method_adaption skip the long-range methods adaptions

Definition at line 190 of file core/system/System.cpp.

References stream.

◆ on_cell_structure_change()

void System::System::on_cell_structure_change ( )

Definition at line 254 of file core/system/System.cpp.

References clear_particle_node().

◆ on_constraint_change()

void System::System::on_constraint_change ( )

Called every time a constraint is changed.

Definition at line 316 of file core/system/System.cpp.

◆ on_coulomb_change()

void System::System::on_coulomb_change ( )

Definition at line 302 of file core/system/System.cpp.

Referenced by CoulombTuningAlgorithm< FloatType, Architecture >::on_solver_change().

◆ on_dipoles_change()

void System::System::on_dipoles_change ( )

Definition at line 309 of file core/system/System.cpp.

Referenced by DipolarTuningAlgorithm< FloatType, Architecture >::on_solver_change().

◆ on_integration_start()

void System::System::on_integration_start ( )

Definition at line 443 of file core/system/System.cpp.

References Utils::Mpi::all_compare(), comm_cart, INTEG_METHOD_NPT_ISO, invalidate_fetch_cache(), runtimeErrorMsg, and stream.

◆ on_lb_boundary_conditions_change()

void System::System::on_lb_boundary_conditions_change ( )

Called when the LB boundary conditions change (geometry, slip velocity, or both).

Definition at line 318 of file core/system/System.cpp.

Referenced by ScriptInterface::walberla::LBFluid::do_call_method().

◆ on_lees_edwards_change()

void System::System::on_lees_edwards_change ( )

Definition at line 386 of file core/system/System.cpp.

◆ on_node_grid_change()

void System::System::on_node_grid_change ( )

Definition at line 222 of file core/system/System.cpp.

◆ on_non_bonded_ia_change()

void System::System::on_non_bonded_ia_change ( )

Definition at line 295 of file core/system/System.cpp.

◆ on_observable_calc()

void System::System::on_observable_calc ( )

called before calculating observables, i.e.

energy, pressure or the integrator (forces). Initialize any methods here which are not initialized immediately (P3M etc.).

Definition at line 369 of file core/system/System.cpp.

References clear_particle_node().

◆ on_particle_change()

void System::System::on_particle_change ( )

Called every time a particle property changes.

Definition at line 327 of file core/system/System.cpp.

References HYBRID, invalidate_fetch_cache(), Cells::RESORT_GLOBAL, and Cells::RESORT_LOCAL.

Referenced by ScriptInterface::Particles::ParticleHandle::do_call_method(), make_new_particle(), ReactionMethods::ReactionAlgorithm::make_reaction_attempt(), remove_all_particles(), remove_particle(), and set_particle_pos().

◆ on_particle_charge_change()

void System::System::on_particle_charge_change ( )

Called every time a particle charge changes.

Definition at line 345 of file core/system/System.cpp.

◆ on_particle_local_change()

void System::System::on_particle_local_change ( )

Called every time a particle local property changes.

Definition at line 322 of file core/system/System.cpp.

Referenced by ReactionMethods::ReactionAlgorithm::make_reaction_attempt().

◆ on_periodicity_change()

void System::System::on_periodicity_change ( )

Definition at line 235 of file core/system/System.cpp.

References INTEG_METHOD_SD, runtimeErrorMsg, and stream.

◆ on_short_range_ia_change()

void System::System::on_short_range_ia_change ( )

Definition at line 290 of file core/system/System.cpp.

◆ on_temperature_change()

void System::System::on_temperature_change ( )

Definition at line 279 of file core/system/System.cpp.

◆ on_thermostat_param_change()

void System::System::on_thermostat_param_change ( )

Definition at line 266 of file core/system/System.cpp.

Referenced by ScriptInterface::Integrators::VelocityVerletIsoNPT::activate().

◆ on_timestep_change()

void System::System::on_timestep_change ( )

Definition at line 284 of file core/system/System.cpp.

◆ on_verlet_skin_change()

void System::System::on_verlet_skin_change ( )

Definition at line 268 of file core/system/System.cpp.

◆ particle_bond_energy()

std::optional< double > System::System::particle_bond_energy	(	int	pid,
		int	bond_id,
		std::vector< int >	partners
	)

Compute the energy of a given bond which has to exist on the given particle.

Requires that bond partners are visible on the same MPI rank as the primary particle. Returns nothing if the primary particle is not owned by this MPI rank.

Parameters

pid	Particle id
bond_id	Bond id
partners	Particle ids of the bond partners

Returns: energy of the bond given the primary particle and bond partners

Definition at line 139 of file energy.cpp.

References bond_broken_error(), calc_bonded_energy(), get_ptr(), Particle::id(), Particle::is_ghost(), and stream.

◆ particle_short_range_energy_contribution()

double System::System::particle_short_range_energy_contribution ( int pid )

Compute the short-range energy of a particle.

Iterate through particles inside cell and neighboring cells and compute energy contribution for a specific particle.

Parameters

pid	Particle id

Returns: Non-bonded energy of the particle.

Definition at line 114 of file energy.cpp.

References calc_non_bonded_pair_energy(), do_nonbonded(), get_ptr(), and stream.

◆ rebuild_cell_structure()

void System::System::rebuild_cell_structure ( )

Rebuild cell lists.

Use e.g. after a skin change.

Definition at line 186 of file core/system/System.cpp.

◆ set_box_l()

void System::System::set_box_l ( Utils::Vector3d const & box_l )

Change the box dimensions.

Definition at line 438 of file core/system/System.cpp.

References stream.

◆ set_cell_structure_topology()

void System::System::set_cell_structure_topology ( CellStructureType topology )

Change cell structure topology.

Definition at line 160 of file core/system/System.cpp.

References HYBRID, NSQUARE, REGULAR, and stream.

◆ set_force_cap()

void System::System::set_force_cap ( double value )

Set force_cap.

Definition at line 150 of file core/system/System.cpp.

◆ set_min_global_cut()

void System::System::set_min_global_cut ( double value )

Set min_global_cut.

Definition at line 155 of file core/system/System.cpp.

◆ set_sim_time()

void System::System::set_sim_time ( double value )

Set sim_time.

Definition at line 771 of file integrate.cpp.

◆ set_time_step()

void System::System::set_time_step ( double value )

Set time_step.

Definition at line 128 of file core/system/System.cpp.

◆ synchronize_npt_state()

void System::System::synchronize_npt_state ( )

Synchronize NpT state such as instantaneous and average pressure.

Definition at line 41 of file npt.cpp.

References comm_cart.

◆ thermostat_force_init()

void System::System::thermostat_force_init ( )

Calculate initial particle forces from active thermostats.

Definition at line 319 of file integrate.cpp.

References convert_vector_body_to_space(), Particle::force(), friction_thermo_langevin(), friction_thermo_langevin_rotation(), PropagationMode::ROT_LANGEVIN, stream, Particle::torque(), and PropagationMode::TRANS_LANGEVIN.

◆ tune_verlet_skin()

void System::System::tune_verlet_skin	(	double	min_skin,
		double	max_skin,
		double	tol,
		int	int_steps,
		bool	adjust_max_skin
	)

Tune the Verlet skin.

Choose the optimal Verlet list skin between min_skin and max_skin by bisection to tolerance tol.

Definition at line 126 of file tuning.cpp.

References stream, and time_calc().

◆ update_dependent_particles()

void System::System::update_dependent_particles ( )

Update particles with properties depending on other particles, namely virtual sites and ICC charges.

Definition at line 351 of file core/system/System.cpp.

References vs_relative_update_particles().

◆ update_icc_particles()

void System::System::update_icc_particles ( )

protected

Definition at line 292 of file icc.cpp.

References get_ptr(), and stream.

◆ update_local_geo()

void System::System::update_local_geo ( )

protected

Definition at line 388 of file core/system/System.cpp.

References Communicator::calc_node_index(), communicator, LocalBox::make_regular_decomposition(), and Communicator::node_grid.

◆ update_used_propagations()

void System::System::update_used_propagations ( )

Update the global propagation bitmask.

Definition at line 181 of file integrate.cpp.

References comm_cart, PropagationMode::NONE, and PropagationMode::SYSTEM_DEFAULT.

◆ veto_boxl_change()

void System::System::veto_boxl_change ( bool skip_particle_checks = false ) const

Definition at line 208 of file core/system/System.cpp.

References comm_cart, and stream.

Member Data Documentation

◆ auto_update_accumulators

std::shared_ptr<Accumulators::AutoUpdateAccumulators> System::System::auto_update_accumulators

Definition at line 329 of file core/system/System.hpp.

◆ bond_breakage

std::shared_ptr<BondBreakage::BondBreakage> System::System::bond_breakage

Definition at line 326 of file core/system/System.hpp.

◆ bonded_ias

std::shared_ptr<BondedInteractionsMap> System::System::bonded_ias

Definition at line 316 of file core/system/System.hpp.

Referenced by PairCriteria::EnergyCriterion::decide(), and ScriptInterface::Particles::ParticleHandle::do_call_method().

◆ box_geo

std::shared_ptr<BoxGeometry> System::System::box_geo

Definition at line 312 of file core/system/System.hpp.

◆ cell_structure

std::shared_ptr<CellStructure> System::System::cell_structure

Definition at line 314 of file core/system/System.hpp.

Referenced by CoulombP3MImpl< FloatType, Architecture >::count_charged_particles(), DipolarP3MImpl< FloatType, Architecture >::count_magnetic_particles(), TuningAlgorithm::determine_r_cut_limits(), get_cell_structure(), TuningAlgorithm::get_mc_time(), and steepest_descent_step().

◆ cleanup_queue

ResourceCleanup System::System::cleanup_queue

Definition at line 92 of file core/system/System.hpp.

◆ collision_detection

std::shared_ptr<CollisionDetection::CollisionDetection> System::System::collision_detection

Definition at line 324 of file core/system/System.hpp.

◆ comfixed

std::shared_ptr<ComFixed> System::System::comfixed

Definition at line 319 of file core/system/System.hpp.

◆ constraints

std::shared_ptr<Constraints::Constraints> System::System::constraints

Definition at line 330 of file core/system/System.hpp.

◆ coulomb

Coulomb::Solver System::System::coulomb

Definition at line 308 of file core/system/System.hpp.

Referenced by PairCriteria::EnergyCriterion::decide(), Coulomb::get_coulomb(), and CoulombTuningAlgorithm< FloatType, Architecture >::layer_correction_veto_r_cut().

◆ dipoles

Dipoles::Solver System::System::dipoles

Definition at line 309 of file core/system/System.hpp.

Referenced by Dipoles::get_dipoles().

◆ ek

EK::Solver System::System::ek

Definition at line 311 of file core/system/System.hpp.

Referenced by ScriptInterface::walberla::EKContainer::do_call_method(), and EK::Solver::reset().

◆ force_cap

double System::System::force_cap

protected

Molecular dynamics integrator force capping.

Definition at line 345 of file core/system/System.hpp.

◆ galilei

std::shared_ptr<Galilei> System::System::galilei

Definition at line 320 of file core/system/System.hpp.

◆ gpu

GpuParticleData System::System::gpu

Definition at line 90 of file core/system/System.hpp.

Referenced by CoulombP3MImpl< FloatType, Architecture >::add_long_range_forces_gpu(), and CoulombP3MImpl< FloatType, Architecture >::request_gpu().

◆ immersed_boundaries

std::shared_ptr<ImmersedBoundaries> System::System::immersed_boundaries

Definition at line 322 of file core/system/System.hpp.

◆ lb

LB::Solver System::System::lb

Definition at line 310 of file core/system/System.hpp.

Referenced by ScriptInterface::walberla::LBFluid::do_call_method(), Observables::CylindricalLBVelocityProfile::operator()(), Observables::LBFluidPressureTensor::operator()(), Observables::LBVelocityProfile::operator()(), EK::EKWalberla::propagate(), and LB::Solver::reset().

◆ lees_edwards

std::shared_ptr<LeesEdwards::LeesEdwards> System::System::lees_edwards

Definition at line 327 of file core/system/System.hpp.

◆ local_geo

std::shared_ptr<LocalBox> System::System::local_geo

Definition at line 313 of file core/system/System.hpp.

Referenced by TuningAlgorithm::determine_r_cut_limits(), and TuningAlgorithm::get_mc_time().

◆ min_global_cut

double System::System::min_global_cut

protected

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 351 of file core/system/System.hpp.

◆ nonbonded_ias

std::shared_ptr<InteractionsNonBonded> System::System::nonbonded_ias

Definition at line 317 of file core/system/System.hpp.

Referenced by PairCriteria::EnergyCriterion::decide(), dpd_init(), init_type_map(), GetNonbondedCutoff::operator()(), and ScriptInterface::Particles::ParticleHandle::ParticleHandle().

◆ npt_inst_pressure

std::shared_ptr<InstantaneousPressure> System::System::npt_inst_pressure

Definition at line 333 of file core/system/System.hpp.

Referenced by velocity_verlet_npt_propagate_vel().

◆ nptiso

std::shared_ptr<NptIsoParameters> System::System::nptiso

Definition at line 332 of file core/system/System.hpp.

Referenced by ScriptInterface::Integrators::VelocityVerletIsoNPT::activate(), and velocity_verlet_npt_propagate_vel().

◆ oif_global

std::shared_ptr<OifGlobal> System::System::oif_global

Definition at line 321 of file core/system/System.hpp.

◆ propagation

std::shared_ptr<Propagation> System::System::propagation

Definition at line 315 of file core/system/System.hpp.

Referenced by ScriptInterface::Integrators::BrownianDynamics::activate(), ScriptInterface::Integrators::SteepestDescent::activate(), ScriptInterface::Integrators::StokesianDynamics::activate(), ScriptInterface::Integrators::VelocityVerlet::activate(), ScriptInterface::Integrators::VelocityVerletIsoNPT::activate(), and CoulombP3MImpl< FloatType, Architecture >::add_long_range_forces_gpu().

◆ reinit_thermo

bool System::System::reinit_thermo

protected

Whether the thermostat has to be reinitialized before integration.

Definition at line 339 of file core/system/System.hpp.

◆ sim_time

double System::System::sim_time

protected

Molecular dynamics integrator simulation time.

Definition at line 343 of file core/system/System.hpp.

◆ thermostat

std::shared_ptr<Thermostat::Thermostat> System::System::thermostat

Definition at line 318 of file core/system/System.hpp.

◆ time_step

double System::System::time_step

protected

Molecular dynamics integrator time step.

Definition at line 341 of file core/system/System.hpp.

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

Public Member Functions

Static Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ System()

Member Function Documentation

◆ calculate_energy()

◆ calculate_forces()

◆ calculate_long_range_fields()

◆ calculate_pressure()

◆ check_kT()

◆ create()

◆ get_force_cap()

◆ get_global_ghost_flags()

◆ get_instantaneous_pressure()

◆ get_instantaneous_pressure_virial()

◆ get_interaction_range()

◆ get_min_global_cut()

◆ get_sim_time()

◆ get_time_step()

◆ integrate()

◆ integrate_with_signal_handler()

◆ lb_couple_particles()

◆ long_range_interactions_sanity_checks()

◆ maximal_cutoff()

◆ npt_add_virial_contribution() [1/2]

◆ npt_add_virial_contribution() [2/2]

◆ npt_ensemble_init()

◆ on_boxl_change()

◆ on_cell_structure_change()

◆ on_constraint_change()

◆ on_coulomb_change()

◆ on_dipoles_change()

◆ on_integration_start()

◆ on_lb_boundary_conditions_change()

◆ on_lees_edwards_change()

◆ on_node_grid_change()

◆ on_non_bonded_ia_change()

◆ on_observable_calc()

◆ on_particle_change()

◆ on_particle_charge_change()

◆ on_particle_local_change()

◆ on_periodicity_change()

◆ on_short_range_ia_change()

◆ on_temperature_change()

◆ on_thermostat_param_change()

◆ on_timestep_change()

◆ on_verlet_skin_change()

◆ particle_bond_energy()

◆ particle_short_range_energy_contribution()

◆ rebuild_cell_structure()

◆ set_box_l()

◆ set_cell_structure_topology()

◆ set_force_cap()

◆ set_min_global_cut()

◆ set_sim_time()

◆ set_time_step()

◆ synchronize_npt_state()

◆ thermostat_force_init()

◆ tune_verlet_skin()

◆ update_dependent_particles()

◆ update_icc_particles()

◆ update_local_geo()

◆ update_used_propagations()

◆ veto_boxl_change()

Member Data Documentation

◆ auto_update_accumulators

◆ bond_breakage

◆ bonded_ias

◆ box_geo

◆ cell_structure

◆ cleanup_queue

◆ collision_detection

◆ comfixed

◆ constraints

◆ coulomb

◆ dipoles