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Extensible Simulation Package for Research on Soft Matter Systems
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Classes | Public Member Functions | Static Public Member Functions | Public Attributes | Protected Member Functions | Protected Attributes | List of all members
System::System Class Reference

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.
 
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)
 
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

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 ()
 
bool has_icc_enabled () const
 

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 68 of file core/system/System.cpp.

References inactive_cutoff, and kokkos_handle.

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(), translational_kinetic_energy(), and Particle::type().

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

◆ calculate_forces()

void System::System::calculate_forces ( )

Calculate all forces.

Definition at line 165 of file forces.cpp.

References add_bonded_force(), add_non_bonded_pair_force(), cabana_short_range(), calc_long_range_forces(), force_capping(), get_ptr(), inactive_cutoff, init_forces_and_thermostat(), reinit_dip_fld(), PropagationMode::ROT_VS_INDEPENDENT, PropagationMode::ROT_VS_RELATIVE, short_range_loop(), this_node, PropagationMode::TRANS_LANGEVIN_NPT, PropagationMode::TRANS_LB_MOMENTUM_EXCHANGE, PropagationMode::TRANS_VS_CENTER_OF_MASS, PropagationMode::TRANS_VS_RELATIVE, update_cabana_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()

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::Vector< 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(), Particle::type(), 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 147 of file core/system/System.cpp.

◆ create()

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

Definition at line 62 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 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 535 of file core/system/System.cpp.

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

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

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

References inactive_cutoff.

◆ 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.

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 566 of file core/system/System.cpp.

◆ 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.

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

◆ has_collision_detection_enabled()

bool System::System::has_collision_detection_enabled ( ) const

Definition at line 576 of file core/system/System.cpp.

◆ has_icc_enabled()

bool System::System::has_icc_enabled ( ) const
protected

Definition at line 321 of file icc.cpp.

◆ has_npt_enabled()

bool System::System::has_npt_enabled ( ) const

Definition at line 560 of file core/system/System.cpp.

References INTEG_METHOD_NPT_ISO_AND, and INTEG_METHOD_NPT_ISO_MTK.

Referenced by CoulombP3MHeffte< 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_stepsNumber of integration steps, can be zero
reuse_forcesDecide 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 495 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_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_INDEPENDENT, PropagationMode::ROT_VS_RELATIVE, run_magnetodynamics(), 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_with_signal_handler()

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

Definition at line 842 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 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 452 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 434 of file core/system/System.cpp.

References communicator, and inactive_cutoff.

◆ npt_add_virial_contribution()

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

Definition at line 137 of file npt.cpp.

Referenced by CoulombP3MHeffte< FloatType, Architecture, FFTConfig >::add_long_range_forces_gpu(), CoulombP3MHeffte< 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 100 of file npt.cpp.

References cell_structure, comm_cart, Utils::Mpi::gather_buffer(), System::get_system(), get_time_step(), 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_adaptionskip the long-range methods adaptions

Definition at line 196 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 260 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 322 of file core/system/System.cpp.

◆ on_coulomb_change()

void System::System::on_coulomb_change ( )

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

Referenced by CoulombTuningAlgorithm< FloatType, Architecture, FFTConfig >::on_solver_change(), and CoulombP3MHeffte< FloatType, Architecture, FFTConfig >::tune().

◆ on_dipoles_change()

void System::System::on_dipoles_change ( )

Definition at line 315 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 479 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 324 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 426 of file core/system/System.cpp.

◆ on_node_grid_change()

void System::System::on_node_grid_change ( )

Definition at line 228 of file core/system/System.cpp.

◆ on_non_bonded_ia_change()

void System::System::on_non_bonded_ia_change ( )

Definition at line 301 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 386 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 333 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(), 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 354 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 328 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 241 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 296 of file core/system/System.cpp.

◆ on_temperature_change()

void System::System::on_temperature_change ( )

Definition at line 285 of file core/system/System.cpp.

◆ on_thermostat_param_change()

void System::System::on_thermostat_param_change ( )

Definition at line 272 of file core/system/System.cpp.

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

◆ on_timestep_change()

void System::System::on_timestep_change ( )

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

◆ on_verlet_skin_change()

void System::System::on_verlet_skin_change ( )

Definition at line 274 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
pidParticle id
bond_idBond id
partnersParticle ids of the bond partners
Returns
energy of the bond given the primary particle and bond partners

Definition at line 141 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
pidParticle id
Returns
Non-bonded energy of the particle.

Definition at line 116 of file energy.cpp.

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

◆ rebuild_aosoa()

void System::System::rebuild_aosoa ( )

Definition at line 407 of file core/system/System.cpp.

References inactive_cutoff, and update_cabana_state().

◆ rebuild_cell_structure()

void System::System::rebuild_cell_structure ( )

Rebuild cell lists.

Use e.g. after a skin change.

Definition at line 192 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 474 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 166 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 156 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 161 of file core/system/System.cpp.

◆ set_sim_time()

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

Set sim_time.

Definition at line 891 of file integrate.cpp.

◆ set_time_step()

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

Set time_step.

Definition at line 134 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 43 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 126 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 360 of file core/system/System.cpp.

References vs_com_update_particles(), and vs_relative_update_particles().

◆ update_icc_particles()

void System::System::update_icc_particles ( )
protected

Definition at line 327 of file icc.cpp.

References get_ptr().

◆ update_local_geo()

void System::System::update_local_geo ( )
protected

Definition at line 428 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 186 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 214 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 334 of file core/system/System.hpp.

◆ bond_breakage

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

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

◆ bonded_ias

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

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

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

◆ box_geo

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

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

Referenced by Constraints::Constraints::add_energy(), Constraints::Constraints::add_forces(), angular_momentum(), DipolarP3MHeffte< FloatType, Architecture, FFTConfig >::calc_average_self_energy_k_space(), DipolarP3MHeffte< FloatType, Architecture, FFTConfig >::calc_energy_correction(), CoulombP3MHeffte< FloatType, Architecture, FFTConfig >::calc_influence_function_energy(), DipolarP3MHeffte< FloatType, Architecture, FFTConfig >::calc_influence_function_energy(), CoulombP3MHeffte< FloatType, Architecture, FFTConfig >::calc_influence_function_force(), DipolarP3MHeffte< FloatType, Architecture, FFTConfig >::calc_influence_function_force(), calc_part_distribution(), calc_re(), calc_rg(), calc_rh(), DipolarP3MHeffte< FloatType, Architecture, FFTConfig >::calc_surface_term(), Galilei::calc_system_cms_position(), DipolarTuningAlgorithm< FloatType, Architecture, FFTConfig >::calculate_accuracy(), center_of_mass(), TuningAlgorithm::commit(), PairCriteria::DistanceCriterion::decide(), PairCriteria::EnergyCriterion::decide(), TuningAlgorithm::determine_r_cut_limits(), ScriptInterface::walberla::LBFluid::do_call_method(), ScriptInterface::walberla::LatticeWalberla::do_construct(), dpd_stress(), draw_polymer_positions(), Observables::BondAngles::evaluate(), Observables::BondDihedrals::evaluate(), Observables::CosPersistenceAngles::evaluate(), Observables::CylindricalDensityProfile::evaluate(), Observables::CylindricalFluxDensityProfile::evaluate(), Observables::CylindricalVelocityProfile::evaluate(), Observables::DensityProfile::evaluate(), Observables::FluxDensityProfile::evaluate(), Observables::ForceDensityProfile::evaluate(), Observables::ParticleDistances::evaluate(), BondBreakage::BondBreakage::execute_bond_breakage(), LB::Solver::get_interpolated_densities(), LB::Solver::get_interpolated_density(), LB::Solver::get_interpolated_velocity(), TuningAlgorithm::get_mc_time(), ReactionMethods::ReactionAlgorithm::get_random_position_in_box(), gyration_tensor(), CollisionDetection::BindAtPointOfCollision::handle_collisions(), CollisionDetection::GlueToSurface::handle_collisions(), CoulombP3MHeffte< FloatType, Architecture, FFTConfig >::init_gpu_kernels(), CoulombP3MHeffte< FloatType, Architecture, FFTConfig >::long_range_pressure(), LB::Solver::make_lattice_position_checker(), maybe_insert_particle(), mindist(), moment_of_inertia_matrix(), nbhood(), pack_particles(), ScriptInterface::Particles::ParticleHandle::ParticleHandle(), ParticleObservables::traits< Particle >::position(), register_integrator(), resort_particles_if_needed(), EK::EKWalberla::sanity_checks(), CoulombP3M::sanity_checks_boxl(), DipolarP3M::sanity_checks_boxl(), CoulombP3MHeffte< FloatType, Architecture, FFTConfig >::scaleby_box_l(), DipolarP3MHeffte< FloatType, Architecture, FFTConfig >::scaleby_box_l(), ReactionMethods::ReactionAlgorithm::set_cyl_constraint(), ReactionMethods::ReactionAlgorithm::set_slab_constraint(), CoulombTuningAlgorithm< FloatType, Architecture, FFTConfig >::setup_logger(), DipolarTuningAlgorithm< FloatType, Architecture, FFTConfig >::setup_logger(), structure_factor(), CoulombP3MHeffte< FloatType, Architecture, FFTConfig >::tune(), DipolarP3MHeffte< FloatType, Architecture, FFTConfig >::tune(), ReactionMethods::ReactionAlgorithm::update_volume(), velocity_verlet_npt_propagate_AVOVA_And(), and velocity_verlet_npt_propagate_AVOVA_MTK().

◆ cell_structure

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

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

Referenced by CollisionDetection::add_bind_centers(), add_bond(), angular_momentum(), calc_linear_momentum(), calc_mu_max(), 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(), count_magnetic_particles(), TuningAlgorithm::determine_r_cut_limits(), 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(), npt_ensemble_init(), resort_particles_if_needed(), steepest_descent_step(), velocity_verlet_npt_propagate_AVOVA_And(), and velocity_verlet_npt_propagate_AVOVA_MTK().

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

◆ comfixed

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

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

◆ constraints

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

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

Referenced by is_valid_position().

◆ coulomb

Coulomb::Solver System::System::coulomb

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

Referenced by PairCriteria::EnergyCriterion::decide(), Coulomb::get_coulomb(), CoulombP3MHeffte< FloatType, Architecture, FFTConfig >::init_gpu_kernels(), and CoulombTuningAlgorithm< FloatType, Architecture, FFTConfig >::layer_correction_veto_r_cut().

◆ dipoles

Dipoles::Solver System::System::dipoles

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

Referenced by Dipoles::get_dipoles().

◆ ek

EK::Solver System::System::ek

Definition at line 316 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 350 of file core/system/System.hpp.

◆ galilei

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

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

◆ gpu

GpuParticleData System::System::gpu

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

Referenced by CoulombP3MHeffte< FloatType, Architecture, FFTConfig >::add_long_range_forces_gpu(), CoulombP3MHeffte< FloatType, Architecture, FFTConfig >::init_gpu_kernels(), and CoulombP3MHeffte< FloatType, Architecture, FFTConfig >::request_gpu().

◆ immersed_boundaries

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

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

◆ lb

LB::Solver System::System::lb

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

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

◆ lees_edwards

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

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

◆ local_geo

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

Definition at line 318 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().

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

◆ nonbonded_ias

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

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

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

◆ npt_inst_pressure

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

Definition at line 338 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 337 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 326 of file core/system/System.hpp.

◆ propagation

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

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

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

◆ reinit_thermo

bool System::System::reinit_thermo
protected

Whether the thermostat has to be reinitialized before integration.

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

◆ sim_time

double System::System::sim_time
protected

Molecular dynamics integrator simulation time.

Definition at line 348 of file core/system/System.hpp.

◆ thermostat

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

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

Referenced by init_forces_and_thermostat(), and integrator_step_1().

◆ time_step

double System::System::time_step
protected

Molecular dynamics integrator time step.

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

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