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.

void	rebuild_aosoa ()

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.

unsigned	get_force_reduce_ghost_flags () const
	Returns the ghost flags for the force-reduce step.

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

Observable_stat const &	calculate_energy ()
	Calculate the total energy.

Observable_stat const &	calculate_pressure ()
	Calculate the pressure from a virial expansion.

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)

bool	has_npt_enabled () const

Utils::Vector3d *	get_npt_virial () const

void	calculate_forces ()
	Calculate all forces.

void	calculate_long_range_fields ()
	Calculate dipole fields.

bool	has_collision_detection_enabled () const

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	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
std::shared_ptr< 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< SteepestDescent >	steepest_descent

std::shared_ptr< StokesianDynamics >	stokesian_dynamics

std::shared_ptr< NptIsoParameters >	nptiso

std::shared_ptr< InstantaneousPressure >	npt_inst_pressure

Protected Member Functions
void	update_local_geo ()

void	update_icc_particles ()

bool	has_icc_enabled () const

void	integrate_magnetodynamics ()
	Run magnetodynamics update for local virtual 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.

std::shared_ptr< EnergyObservable >	m_obs_energy

std::shared_ptr< PressureObservable >	m_obs_pressure

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 87 of file core/system/System.hpp.

Constructor & Destructor Documentation

◆ System()

System::System::System ( Private )

Definition at line 75 of file core/system/System.cpp.

References inactive_cutoff, and kokkos_handle.

Member Function Documentation

◆ calculate_energy()

Observable_stat const & System::System::calculate_energy ( )

Calculate the total energy.

Definition at line 64 of file energy.cpp.

References cabana_short_range(), ESPRESSO_CALI_MARK_BEGIN, ESPRESSO_CALI_MARK_END, get_ptr(), inactive_cutoff, kokkos_deep_copy(), reduce_cabana_energy(), rotational_kinetic_energy(), translational_kinetic_energy(), and update_verlet_state().

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

◆ calculate_forces()

void System::System::calculate_forces ( )

Calculate all forces.

Definition at line 414 of file forces.cpp.

References cabana_short_range(), create_cabana_neighbor_kernel(), create_kokkos_bonds_kernel_data(), create_specialized_verlet_pair_loop(), ESPRESSO_CALI_MARK_BEGIN, ESPRESSO_CALI_MARK_END, ESPRESSO_CALI_MARK_FUNCTION, force_capping(), gay_berne_active(), GayBerne, get_ptr(), ghost_reduce_overlap_eligible(), GHOSTTRANS_TORQUE, inactive_cutoff, init_forces_and_thermostat(), INTEG_METHOD_STEEPEST_DESCENT, reduce_cabana_forces_and_torques(), reinit_dip_fld(), PropagationMode::ROT_VS_INDEPENDENT, PropagationMode::ROT_VS_RELATIVE, this_node, PropagationMode::TRANS_LANGEVIN_NPT, PropagationMode::TRANS_LB_MOMENTUM_EXCHANGE, PropagationMode::TRANS_VS_CENTER_OF_MASS, PropagationMode::TRANS_VS_RELATIVE, update_verlet_state(), vs_com_back_transfer_forces_and_torques(), and vs_relative_back_transfer_forces_and_torques().

◆ calculate_long_range_fields()

void System::System::calculate_long_range_fields ( )

Calculate dipole fields.

◆ calculate_pressure()

Observable_stat const & System::System::calculate_pressure ( )

Calculate the pressure from a virial expansion.

Definition at line 60 of file pressure.cpp.

References cabana_short_range(), PressureKernel::dpd, Utils::flatten(), get_ptr(), inactive_cutoff, kokkos_deep_copy(), reduce_cabana_pressure(), Utils::sqr(), Utils::tensor_product(), update_verlet_state(), 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 163 of file core/system/System.cpp.

◆ create()

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

static

Definition at line 69 of file core/system/System.cpp.

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

◆ get_force_cap()

auto System::System::get_force_cap ( ) const

inline

Get force_cap.

Definition at line 115 of file core/system/System.hpp.

Referenced by ghost_reduce_overlap_eligible().

◆ get_force_reduce_ghost_flags()

unsigned System::System::get_force_reduce_ghost_flags ( ) const

Returns the ghost flags for the force-reduce step.

Always includes GHOSTTRANS_FORCE; adds GHOSTTRANS_TORQUE when orientation physics is active (same whitelist as get_global_ghost_flags for QUAT).

Definition at line 664 of file core/system/System.cpp.

References GHOSTTRANS_FORCE, GHOSTTRANS_TORQUE, and System::orientation_ghosts_needed().

◆ 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 634 of file core/system/System.cpp.

References Cells::DATA_PART_BONDS, Cells::DATA_PART_MOMENTUM, Cells::DATA_PART_POSITION, Cells::DATA_PART_PROPERTIES, Cells::DATA_PART_QUAT, System::orientation_ghosts_needed(), THERMO_BOND, and THERMO_DPD.

Referenced by BondBreakage::BondBreakage::execute_bond_breakage().

◆ get_interaction_range()

double System::System::get_interaction_range ( ) const

Get the interaction range.

Definition at line 479 of file core/system/System.cpp.

References inactive_cutoff.

Referenced by update_verlet_state().

◆ get_min_global_cut()

auto System::System::get_min_global_cut ( ) const

inline

Get min_global_cut.

Definition at line 121 of file core/system/System.hpp.

Referenced by CollisionDetection::BindAtPointOfCollision::handle_collisions(), and CollisionDetection::GlueToSurface::handle_collisions().

◆ get_npt_virial()

Utils::Vector3d * System::System::get_npt_virial ( ) const

Definition at line 681 of file core/system/System.cpp.

◆ get_sim_time()

auto System::System::get_sim_time ( ) const

inline

Get sim_time.

Definition at line 109 of file core/system/System.hpp.

◆ get_time_step()

auto System::System::get_time_step ( ) const

inline

Get time_step.

Definition at line 103 of file core/system/System.hpp.

Referenced by init_forces_and_thermostat(), EK::EKWalberla::sanity_checks(), and LB::LBWalberla::sanity_checks().

◆ has_collision_detection_enabled()

bool System::System::has_collision_detection_enabled ( ) const

Definition at line 691 of file core/system/System.cpp.

◆ has_icc_enabled()

bool System::System::has_icc_enabled ( ) const

protected

Definition at line 315 of file icc.cpp.

◆ has_npt_enabled()

bool System::System::has_npt_enabled ( ) const

Definition at line 675 of file core/system/System.cpp.

References INTEG_METHOD_NPT_ISO_AND, and INTEG_METHOD_NPT_ISO_MTK.

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

◆ 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, or 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 609 of file integrate.cpp.

References check_runtime_errors(), comm_cart, convert_initial_torques(), correct_position_shake(), correct_velocity_shake(), Cells::DATA_PART_PROPERTIES, ESPRESSO_CALI_MARK_BEGIN, ESPRESSO_CALI_MARK_END, ESPRESSO_CALI_MARK_FUNCTION, CellStructure::ghosts_reduce_forces_finish(), CellStructure::has_pending_ghost_reduce(), INTEG_ERROR_RUNTIME, INTEG_ERROR_SIGINT, INTEG_METHOD_BD, INTEG_METHOD_STEEPEST_DESCENT, INTEG_REUSE_FORCES_ALWAYS, INTEG_REUSE_FORCES_NEVER, integrator_step_1(), integrator_step_2(), integrator_step_2_filtered(), EspressoCaliLoop::iteration(), lb_tracers_add_particle_force_to_fluid(), lb_tracers_propagate(), LEES_EDWARDS, Cells::RESORT_LOCAL, resort_particles_if_needed(), PropagationMode::ROT_VS_INDEPENDENT, PropagationMode::ROT_VS_RELATIVE, runtimeErrorMsg, save_old_position(), PropagationMode::TRANS_LB_MOMENTUM_EXCHANGE, PropagationMode::TRANS_LB_TRACER, PropagationMode::TRANS_VS_CENTER_OF_MASS, PropagationMode::TRANS_VS_RELATIVE, vs_com_update_particles(), and vs_relative_update_particles().

Referenced by run_full_force_calc(), and time_calc().

◆ integrate_magnetodynamics()

void System::System::integrate_magnetodynamics ( )

protected

Run magnetodynamics update for local virtual particles.

Iterate over local particles and update the dipole moment of virtual particles according to the thermal Stoner-Wohlfarth model. Collect active homogeneous external magnetic fields from constraints and add the per-particle dipolar contribution before performing either the simplified no-field update or the full thermal Stoner-Wohlfarth update.

Definition at line 258 of file stoner_wohlfarth_thermal.cpp.

References Particle::dip_fld(), get_external_field(), get_reference_particle(), Particle::id(), Particle::is_virtual(), Particle::stoner_wohlfarth_is_enabled(), stoner_wohlfarth_main(), stoner_wohlfarth_no_field(), THERMO_LANGEVIN, and Utils::uniform().

◆ integrate_with_signal_handler()

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

Definition at line 1005 of file integrate.cpp.

References comm_cart, INTEG_ERROR_RUNTIME, and INTEG_REUSE_FORCES_ALWAYS.

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

◆ lb_couple_particles()

void System::System::lb_couple_particles ( )

Calculate particle-lattice interactions.

Definition at line 348 of file particle_coupling.cpp.

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

◆ 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 464 of file core/system/System.cpp.

References runtimeErrorMsg.

◆ maximal_cutoff()

double System::System::maximal_cutoff ( ) const

Calculate the maximal cutoff of all interactions.

Definition at line 446 of file core/system/System.cpp.

References communicator, and inactive_cutoff.

Referenced by create_cabana_neighbor_kernel(), and create_specialized_verlet_pair_loop().

◆ npt_add_virial_contribution()

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

Definition at line 137 of file npt.cpp.

Referenced by CoulombP3MImpl< FloatType, Architecture, FFTConfig >::add_long_range_forces_gpu(), CoulombP3MImpl< FloatType, Architecture, FFTConfig >::long_range_kernel(), and DipolarP3MHeffte< FloatType, Architecture, FFTConfig >::npt_add_virial_contribution().

◆ npt_ensemble_init()

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

Reinitialize the NpT state.

Definition at line 101 of file npt.cpp.

References comm_cart, Utils::Mpi::gather_buffer(), Utils::Vector< T, N >::size(), 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 212 of file core/system/System.cpp.

Referenced by velocity_verlet_npt_propagate_AVOVA_And(), and velocity_verlet_npt_propagate_AVOVA_MTK().

◆ on_cell_structure_change()

void System::System::on_cell_structure_change ( )

Definition at line 276 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 338 of file core/system/System.cpp.

◆ on_coulomb_change()

void System::System::on_coulomb_change ( )

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

Referenced by CoulombTuningAlgorithm< FloatType, Architecture, FFTConfig >::on_solver_change(), and CoulombP3MImpl< FloatType, Architecture, FFTConfig >::tune().

◆ on_dipoles_change()

void System::System::on_dipoles_change ( )

Definition at line 331 of file core/system/System.cpp.

Referenced by DipolarTuningAlgorithm< FloatType, Architecture, FFTConfig >::on_solver_change(), and DipolarP3MHeffte< FloatType, Architecture, FFTConfig >::tune().

◆ on_integration_start()

void System::System::on_integration_start ( )

Definition at line 491 of file core/system/System.cpp.

References Utils::Mpi::all_compare(), comm_cart, INTEG_METHOD_NPT_ISO_AND, INTEG_METHOD_NPT_ISO_MTK, invalidate_fetch_cache(), and runtimeErrorMsg.

◆ 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 340 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 438 of file core/system/System.cpp.

◆ on_node_grid_change()

void System::System::on_node_grid_change ( )

Definition at line 244 of file core/system/System.cpp.

◆ on_non_bonded_ia_change()

void System::System::on_non_bonded_ia_change ( )

Definition at line 317 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 410 of file core/system/System.cpp.

References clear_particle_node().

Referenced by dpd_pressure_local().

◆ on_particle_change()

void System::System::on_particle_change ( )

Called every time a particle property changes.

Definition at line 350 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(), Galilei::galilei_transform(), Galilei::kill_particle_forces(), Galilei::kill_particle_motion(), make_new_particle(), 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 370 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 344 of file core/system/System.cpp.

◆ on_periodicity_change()

void System::System::on_periodicity_change ( )

Definition at line 257 of file core/system/System.cpp.

References INTEG_METHOD_SD, and runtimeErrorMsg.

◆ on_short_range_ia_change()

void System::System::on_short_range_ia_change ( )

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

◆ on_temperature_change()

void System::System::on_temperature_change ( )

Definition at line 301 of file core/system/System.cpp.

◆ on_thermostat_param_change()

void System::System::on_thermostat_param_change ( )

Definition at line 288 of file core/system/System.cpp.

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

◆ on_timestep_change()

void System::System::on_timestep_change ( )

Definition at line 306 of file core/system/System.cpp.

◆ on_verlet_skin_change()

void System::System::on_verlet_skin_change ( )

Definition at line 290 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 219 of file energy.cpp.

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

◆ 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 195 of file energy.cpp.

References calc_non_bonded_pair_energy(), and do_nonbonded().

◆ rebuild_aosoa()

void System::System::rebuild_aosoa ( )

Definition at line 428 of file core/system/System.cpp.

References inactive_cutoff, and update_verlet_state().

◆ rebuild_cell_structure()

void System::System::rebuild_cell_structure ( )

Rebuild cell lists.

Use e.g. after a skin change.

Definition at line 208 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 486 of file core/system/System.cpp.

◆ set_cell_structure_topology()

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

Change cell structure topology.

Definition at line 182 of file core/system/System.cpp.

References HYBRID, NSQUARE, and REGULAR.

◆ set_force_cap()

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

Set force_cap.

Definition at line 172 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 177 of file core/system/System.cpp.

◆ set_sim_time()

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

Set sim_time.

Definition at line 1054 of file integrate.cpp.

◆ set_time_step()

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

Set time_step.

Definition at line 150 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 44 of file npt.cpp.

References comm_cart.

◆ 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 125 of file tuning.cpp.

References 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 376 of file core/system/System.cpp.

References PropagationMode::ROT_VS_INDEPENDENT, PropagationMode::ROT_VS_RELATIVE, PropagationMode::TRANS_VS_CENTER_OF_MASS, PropagationMode::TRANS_VS_RELATIVE, vs_com_update_particles(), and vs_relative_update_particles().

◆ update_icc_particles()

void System::System::update_icc_particles ( )

protected

Definition at line 321 of file icc.cpp.

References get_ptr().

◆ update_local_geo()

void System::System::update_local_geo ( )

protected

Definition at line 440 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 189 of file integrate.cpp.

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

Referenced by CollisionDetection::BindAtPointOfCollision::handle_collisions(), and CollisionDetection::GlueToSurface::handle_collisions().

◆ veto_boxl_change()

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

Definition at line 230 of file core/system/System.cpp.

References comm_cart.

Member Data Documentation

◆ auto_update_accumulators

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

Definition at line 342 of file core/system/System.hpp.

◆ bond_breakage

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

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

Referenced by create_kokkos_bonds_kernel_data().

◆ bonded_ias

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

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

Referenced by create_cabana_neighbor_kernel(), create_kokkos_bonds_kernel_data(), PairCriteria::EnergyCriterion::decide(), ScriptInterface::Particles::ParticleHandle::do_call_method(), CollisionDetection::BindAtPointOfCollision::handle_collisions(), CollisionDetection::BindAtPointOfCollision::initialize(), CollisionDetection::BindCenters::initialize(), and CollisionDetection::GlueToSurface::initialize().

◆ box_geo

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

Definition at line 325 of file core/system/System.hpp.

◆ cell_structure

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

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

Referenced by CollisionDetection::add_bind_centers(), add_bond(), angular_momentum(), calc_linear_momentum(), calc_re(), calc_rg(), calc_rh(), Galilei::calc_system_cms_position(), Galilei::calc_system_cms_velocity(), center_of_mass(), Coulomb::check_charge_neutrality(), DipolarP3MHeffte< FloatType, Architecture, FFTConfig >::count_magnetic_particles(), create_cabana_neighbor_kernel(), create_kokkos_bonds_kernel_data(), create_specialized_verlet_pair_loop(), TuningAlgorithm::determine_r_cut_limits(), ScriptInterface::System::System::do_call_method(), dpd_pressure_local(), BondBreakage::BondBreakage::execute_bond_breakage(), Galilei::galilei_transform(), gather_traits_for_types(), get_cell_structure(), get_interacting_neighbors(), TuningAlgorithm::get_mc_time(), get_neighbor_pids(), get_pairs_filtered(), get_short_range_neighbors(), CollisionDetection::BindAtPointOfCollision::handle_collisions(), CollisionDetection::GlueToSurface::handle_collisions(), init_forces_and_thermostat(), is_valid_position(), Galilei::kill_particle_forces(), Galilei::kill_particle_motion(), mindist(), moment_of_inertia_matrix(), nbhood(), non_bonded_loop_trace(), reduce_cabana_forces_and_torques(), resort_particles_if_needed(), update_verlet_state(), velocity_verlet_npt_propagate_AVOVA_And(), and velocity_verlet_npt_propagate_AVOVA_MTK().

◆ cleanup_queue

ResourceCleanup System::System::cleanup_queue

Definition at line 100 of file core/system/System.hpp.

◆ collision_detection

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

Definition at line 337 of file core/system/System.hpp.

◆ comfixed

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

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

Referenced by ghost_reduce_overlap_eligible().

◆ constraints

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

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

Referenced by is_valid_position().

◆ coulomb

Coulomb::Solver System::System::coulomb

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

Referenced by create_cabana_neighbor_kernel(), create_specialized_verlet_pair_loop(), PairCriteria::EnergyCriterion::decide(), CoulombP3MImpl< FloatType, Architecture, FFTConfig >::init_gpu_kernels(), CoulombTuningAlgorithm< FloatType, Architecture, FFTConfig >::layer_correction_veto_r_cut(), and update_verlet_state().

◆ dipoles

Dipoles::Solver System::System::dipoles

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

Referenced by ghost_reduce_overlap_eligible(), init_forces_and_thermostat(), and update_verlet_state().

◆ ek

EK::Solver System::System::ek

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

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

◆ force_cap

double System::System::force_cap

protected

Molecular dynamics integrator force capping.

Definition at line 362 of file core/system/System.hpp.

◆ galilei

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

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

◆ gpu

std::shared_ptr<GpuParticleData> System::System::gpu

Definition at line 98 of file core/system/System.hpp.

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

◆ immersed_boundaries

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

Definition at line 335 of file core/system/System.hpp.

◆ lb

LB::Solver System::System::lb

Definition at line 323 of file core/system/System.hpp.

Referenced by calc_linear_momentum(), ScriptInterface::walberla::LBFluid::do_call_method(), Observables::LBFluidPressureTensor::operator()(), and EK::EKWalberla::propagate().

◆ lees_edwards

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

Definition at line 340 of file core/system/System.hpp.

◆ local_geo

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

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

Referenced by TuningAlgorithm::determine_r_cut_limits(), TuningAlgorithm::get_mc_time(), EK::EKWalberla::sanity_checks(), LB::LBWalberla::sanity_checks(), CoulombP3M::sanity_checks_boxl(), and DipolarP3M::sanity_checks_boxl().

◆ m_obs_energy

std::shared_ptr<EnergyObservable> System::System::m_obs_energy

protected

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

◆ m_obs_pressure

std::shared_ptr<PressureObservable> System::System::m_obs_pressure

protected

Definition at line 370 of file core/system/System.hpp.

◆ 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 368 of file core/system/System.hpp.

◆ nonbonded_ias

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

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

Referenced by create_cabana_neighbor_kernel(), create_specialized_verlet_pair_loop(), PairCriteria::EnergyCriterion::decide(), dpd_pressure_local(), CollisionDetection::BindAtPointOfCollision::initialize(), CollisionDetection::GlueToSurface::initialize(), GetNonbondedCutoff::operator()(), ScriptInterface::Particles::ParticleHandle::ParticleHandle(), Thermostat::Thermostat::recalc_prefactors(), and VerletCriterion< CutoffGetter, ShortRangeOnly >::VerletCriterion().

◆ npt_inst_pressure

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

Definition at line 350 of file core/system/System.hpp.

Referenced by velocity_verlet_npt_Andersen_step_1(), velocity_verlet_npt_Andersen_step_2(), velocity_verlet_npt_MTK_step_1(), velocity_verlet_npt_MTK_step_2(), and velocity_verlet_npt_propagate_AVOVA_And().

◆ nptiso

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

Definition at line 349 of file core/system/System.hpp.

Referenced by ScriptInterface::Integrators::VelocityVerletIsoNPT::activate(), velocity_verlet_npt_Andersen_step_1(), velocity_verlet_npt_Andersen_step_2(), velocity_verlet_npt_MTK_step_1(), velocity_verlet_npt_MTK_step_2(), velocity_verlet_npt_propagate_AVOVA_And(), and velocity_verlet_npt_propagate_AVOVA_MTK().

◆ oif_global

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

Definition at line 334 of file core/system/System.hpp.

◆ propagation

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

Definition at line 328 of file core/system/System.hpp.

Referenced by ScriptInterface::Integrators::BrownianDynamics::activate(), ScriptInterface::Integrators::SteepestDescent::activate(), ScriptInterface::Integrators::SymplecticEuler::activate(), ScriptInterface::Integrators::VelocityVerlet::activate(), ScriptInterface::Integrators::VelocityVerletIsoNPT::activate(), ghost_reduce_overlap_eligible(), init_forces_and_thermostat(), and update_verlet_state().

◆ reinit_thermo

bool System::System::reinit_thermo

protected

Whether the thermostat has to be reinitialized before integration.

Definition at line 356 of file core/system/System.hpp.

◆ sim_time

double System::System::sim_time

protected

Molecular dynamics integrator simulation time.

Definition at line 360 of file core/system/System.hpp.

◆ steepest_descent

std::shared_ptr<SteepestDescent> System::System::steepest_descent

Definition at line 344 of file core/system/System.hpp.

Referenced by ScriptInterface::Integrators::SteepestDescent::activate(), and integrator_step_1().

◆ stokesian_dynamics

std::shared_ptr<StokesianDynamics> System::System::stokesian_dynamics

Definition at line 346 of file core/system/System.hpp.

Referenced by integrator_step_1().

◆ thermostat

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

Definition at line 331 of file core/system/System.hpp.

Referenced by create_cabana_neighbor_kernel(), dpd_pressure_local(), init_forces_and_thermostat(), and integrator_step_1().

◆ time_step

double System::System::time_step

protected

Molecular dynamics integrator time step.

Definition at line 358 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_force_reduce_ghost_flags()

◆ get_global_ghost_flags()

◆ get_interaction_range()

◆ get_min_global_cut()

◆ get_npt_virial()

◆ get_sim_time()

◆ get_time_step()

◆ has_collision_detection_enabled()

◆ has_icc_enabled()

◆ has_npt_enabled()

◆ integrate()

◆ integrate_magnetodynamics()

◆ integrate_with_signal_handler()

◆ lb_couple_particles()

◆ long_range_interactions_sanity_checks()

◆ maximal_cutoff()

◆ npt_add_virial_contribution()

◆ 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_aosoa()

◆ 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()

◆ 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