integrate.cpp File Reference

Molecular dynamics integrator. More...

#include "integrate.hpp"
#include "integrators/Propagation.hpp"
#include "integrators/brownian_inline.hpp"
#include "integrators/steepest_descent.hpp"
#include "integrators/stokesian_dynamics_inline.hpp"
#include "integrators/symplectic_euler_inline.hpp"
#include "integrators/velocity_verlet_inline.hpp"
#include "integrators/velocity_verlet_npt.hpp"
#include "BoxGeometry.hpp"
#include "PropagationMode.hpp"
#include "accumulators/AutoUpdateAccumulators.hpp"
#include "bond_breakage/bond_breakage.hpp"
#include "bonded_interactions/bonded_interaction_data.hpp"
#include "cell_system/CellStructure.hpp"
#include "cell_system/for_each_particle.hpp"
#include "cells.hpp"
#include "collision_detection/CollisionDetection.hpp"
#include "communication.hpp"
#include "errorhandling.hpp"
#include "lb/particle_coupling.hpp"
#include "lb/utils.hpp"
#include "lees_edwards/lees_edwards.hpp"
#include "nonbonded_interactions/nonbonded_interaction_data.hpp"
#include "npt.hpp"
#include "rattle.hpp"
#include "rotation.hpp"
#include "signalhandling.hpp"
#include "stokesian_dynamics/sd_interface.hpp"
#include "system/System.hpp"
#include "system/System.impl.hpp"
#include "thermostat.hpp"
#include "thermostats/langevin_inline.hpp"
#include "virtual_sites/com.hpp"
#include "virtual_sites/lb_tracers.hpp"
#include "virtual_sites/relative.hpp"
#include <instrumentation/fe_trap.hpp>
#include <boost/mpi/collectives/all_reduce.hpp>
#include "caliper_utils.hpp"
#include <callgrind.h>
#include <algorithm>
#include <cassert>
#include <cmath>
#include <csignal>
#include <functional>
#include <limits>
#include <sstream>
#include <stdexcept>
#include <string>
#include <utility>

Include dependency graph for integrate.cpp:

Go to the source code of this file.

Namespaces
namespace	anonymous_namespace{integrate.cpp}
namespace	LeesEdwards

Functions
void	walberla_tau_sanity_checks (std::string const &method, double tau, double time_step)
void	walberla_agrid_sanity_checks (std::string const &method, Utils::Vector3d const &geo_left, Utils::Vector3d const &geo_right, Utils::Vector3d const &lattice_left, Utils::Vector3d const &lattice_right, double agrid)
static void	resort_particles_if_needed (System::System &system)
static bool	integrator_step_1 (CellStructure &cell_structure, Propagation const &propagation, System::System &system, double time_step)
	Calls the hook for propagation kernels before the force calculation.
static auto	make_step2_particle_kernel (Propagation const &propagation, double time_step)
	Build the per-particle half-kick callable for step_2.
static void	integrator_step_2 (CellStructure &cell_structure, Propagation const &propagation, System::System &system, double time_step)
static void	integrator_step_2_filtered (CellStructure &cell_structure, Propagation const &propagation, double time_step, bool interior_pass)
	Restricted step_2 for the split-phase ghost-force-reduce overlap.

Variables
volatile std::sig_atomic_t	anonymous_namespace{integrate.cpp}::ctrl_C = 0

Detailed Description

Molecular dynamics integrator.

For more information about the integrator see integrate.hpp.

Definition in file integrate.cpp.

Function Documentation

integrator_step_1()

static bool integrator_step_1 ( CellStructure &  cell_structure, Propagation const &  propagation, System::System &  system, double  time_step  )

static

Calls the hook for propagation kernels before the force calculation.

Returns

whether or not to stop the integration loop early.

Definition at line 397 of file integrate.cpp.

References brownian_dynamics_propagator(), brownian_dynamics_rotator(), Propagation::default_propagation, ESPRESSO_CALI_MARK_FUNCTION, ParticleRange::filter(), CellStructure::for_each_local_particle(), INTEG_METHOD_NPT_ISO_AND, INTEG_METHOD_NPT_ISO_MTK, INTEG_METHOD_STEEPEST_DESCENT, INTEG_METHOD_SYMPLECTIC_EULER, Propagation::integ_switch, Particle::is_virtual(), CellStructure::local_particles(), PropagationMode::ROT_BROWNIAN, PropagationMode::ROT_EULER, PropagationMode::ROT_LANGEVIN, Propagation::should_propagate_with(), System::System::steepest_descent, System::System::stokesian_dynamics, stokesian_dynamics_step_1(), symplectic_euler_propagator_1(), symplectic_euler_rotator_1(), System::System::thermostat, PropagationMode::TRANS_BROWNIAN, PropagationMode::TRANS_LANGEVIN, PropagationMode::TRANS_LANGEVIN_NPT, PropagationMode::TRANS_LB_MOMENTUM_EXCHANGE, PropagationMode::TRANS_NEWTON, PropagationMode::TRANS_STOKESIAN, Propagation::used_propagations, velocity_verlet_npt_Andersen_step_1(), velocity_verlet_npt_MTK_step_1(), velocity_verlet_propagator_1(), and velocity_verlet_rotator_1().

Referenced by System::System::integrate().

integrator_step_2()

static void integrator_step_2 ( CellStructure &  cell_structure, Propagation const &  propagation, System::System &  system, double  time_step  )

static

Definition at line 545 of file integrate.cpp.

References Propagation::default_propagation, ESPRESSO_CALI_MARK_FUNCTION, ParticleRange::filter(), CellStructure::for_each_local_particle(), INTEG_METHOD_NPT_ISO_AND, INTEG_METHOD_NPT_ISO_MTK, INTEG_METHOD_STEEPEST_DESCENT, Propagation::integ_switch, CellStructure::local_particles(), make_step2_particle_kernel(), PropagationMode::TRANS_LANGEVIN_NPT, Propagation::used_propagations, velocity_verlet_npt_Andersen_step_2(), and velocity_verlet_npt_MTK_step_2().

Referenced by System::System::integrate().

integrator_step_2_filtered()

static void integrator_step_2_filtered ( CellStructure &  cell_structure, Propagation const &  propagation, double  time_step, bool  interior_pass  )

static

Restricted step_2 for the split-phase ghost-force-reduce overlap.

Called twice per step: once with interior_pass = true (while the ghost reduce is in flight) and once with interior_pass = false (after CellStructure::ghosts_reduce_forces_finish completes). The per-particle kernel is identical to the one used by integrator_step_2 — shared via make_step2_particle_kernel.

NPT is absent here: the eligibility check in calculate_forces() guarantees TRANS_LANGEVIN_NPT is never active when this path runs.

Definition at line 585 of file integrate.cpp.

References ESPRESSO_CALI_MARK_FUNCTION, CellStructure::for_each_boundary_particle(), CellStructure::for_each_interior_particle(), INTEG_METHOD_STEEPEST_DESCENT, Propagation::integ_switch, make_step2_particle_kernel(), PropagationMode::TRANS_LANGEVIN_NPT, and Propagation::used_propagations.

Referenced by System::System::integrate().

make_step2_particle_kernel()

static auto make_step2_particle_kernel ( Propagation const &  propagation, double  time_step  )

static

Build the per-particle half-kick callable for step_2.

Returns a lambda that captures propagation and time_step by reference and applies the velocity (and torque, if ROTATION is enabled) update for a single particle. Virtual sites are skipped.

Shared verbatim by integrator_step_2 (full pass) and integrator_step_2_filtered (interior / boundary passes): the lambda is constructed once, then handed to for_each_local_particle, for_each_interior_particle, or for_each_boundary_particle.

NPT particles are intentionally absent: the NPT arm must run only on the ineligible (full-reduce-then-step_2) path and is handled separately inside integrator_step_2.

Definition at line 501 of file integrate.cpp.

References INTEG_METHOD_SYMPLECTIC_EULER, Propagation::integ_switch, PropagationMode::ROT_EULER, PropagationMode::ROT_LANGEVIN, Propagation::should_propagate_with(), symplectic_euler_propagator_2(), symplectic_euler_rotator_2(), PropagationMode::TRANS_LANGEVIN, PropagationMode::TRANS_LB_MOMENTUM_EXCHANGE, PropagationMode::TRANS_NEWTON, velocity_verlet_propagator_2(), and velocity_verlet_rotator_2().

Referenced by integrator_step_2(), and integrator_step_2_filtered().

resort_particles_if_needed()

static void resort_particles_if_needed ( System::System &  system )

static

Definition at line 382 of file integrate.cpp.

References System::System::box_geo, System::System::cell_structure, ESPRESSO_CALI_MARK_FUNCTION, Cells::RESORT_LOCAL, and LeesEdwards::verlet_list_offset().

Referenced by System::System::integrate().

walberla_agrid_sanity_checks()

void walberla_agrid_sanity_checks	(	std::string const &	method,
		Utils::Vector3d const &	geo_left,
		Utils::Vector3d const &	geo_right,
		Utils::Vector3d const &	lattice_left,
		Utils::Vector3d const &	lattice_right,
		double	agrid
	)

Definition at line 358 of file integrate.cpp.

References this_node.

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

walberla_tau_sanity_checks()

void walberla_tau_sanity_checks	(	std::string const &	method,
		double	tau,
		double	time_step
	)

Definition at line 338 of file integrate.cpp.

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