#include <tfEngine.h>

Collaboration diagram for TissueForge::engine:

[legend]

Public Attributes
unsigned int	flags = 0

unsigned int	integrator_flags

struct space	s

long	time

FPTYPE	dt

FPTYPE	temperature

FPTYPE	K

struct Potential **	p

struct Potential **	p_cluster

struct Force **	forces

struct Fluxes **	fluxes

int	nr_fluxsteps = 1

int	step_flux = 0

FPTYPE	dt_flux

pthread_mutex_t	barrier_mutex

pthread_cond_t	barrier_cond

pthread_cond_t	done_cond

int	barrier_count

int	nr_runners

struct runner *	runners

struct queue *	queues

int	nr_queues

int	nodeID

int	nr_nodes

struct engine_comm *	send

struct engine_comm *	recv

std::set< unsigned int >	pids_avail

struct Bond *	bonds

int	nr_bonds

int	nr_active_bonds

int	bonds_size

std::mutex	bonds_mutex

struct exclusion *	exclusions

int	nr_exclusions

int	exclusions_size

struct rigid *	rigids

int *	part2rigid

int	nr_rigids

int	rigids_size

int	nr_constr

int	rigids_local

int	rigids_semilocal

FPTYPE	tol_rigid

struct Angle *	angles

int	nr_angles

int	nr_active_angles

int	angles_size

struct Dihedral *	dihedrals

int	nr_dihedrals

int	nr_active_dihedrals

int	dihedrals_size

ticks	timers [engine_timer_last]

struct engine_set *	sets

int	nr_sets

FPTYPE	wall_time

uint32_t	timers_mask

long	timer_output_period

std::vector< CustomForce * >	custom_forces

FPTYPE	particle_max_dist_fraction

FPTYPE	computed_volume

EngineIntegrator	integrator

BoundaryConditions	boundary_conditions

std::vector< SubEngine * >	subengines
	Borrowed references to registered subengines.

BoundaryConditionsArgsContainer *	_init_boundary_conditions

int	_init_cells [3]

Static Public Attributes
static const int	max_type

static int	nr_types

static struct ParticleType *	types

Detailed Description

The #engine structure.

Member Data Documentation

◆ _init_boundary_conditions

BoundaryConditionsArgsContainer* TissueForge::engine::_init_boundary_conditions

saved objects from init

◆ angles

struct Angle* TissueForge::engine::angles

List of angles.

◆ angles_size

int TissueForge::engine::angles_size

Allocated size of angles array

◆ barrier_mutex

pthread_mutex_t TissueForge::engine::barrier_mutex

Mutexes, conditions and counters for the barrier

◆ bonds

struct Bond* TissueForge::engine::bonds

List of bonds.

◆ bonds_size

int TissueForge::engine::bonds_size

allocate size of bonds array

◆ custom_forces

std::vector<CustomForce*> TissueForge::engine::custom_forces

vector of constant forces. Because these forces get updates from user defined functions, we keep a copy of them here in addtion to the other copy in p_singlebody.

◆ dihedrals

struct Dihedral* TissueForge::engine::dihedrals

List of dihedrals.

◆ dihedrals_size

int TissueForge::engine::dihedrals_size

Allocated size of dihedrals array

◆ exclusions

struct exclusion* TissueForge::engine::exclusions

List of exclusions.

◆ flags

unsigned int TissueForge::engine::flags = 0

Some flags controlling how this engine works.

◆ fluxes

struct Fluxes** TissueForge::engine::fluxes

interaction matrix of pointers to fluxes, same layout as potential matrix p.

◆ forces

struct Force** TissueForge::engine::forces

vector of forces for types, indexed by type id.

◆ integrator_flags

unsigned int TissueForge::engine::integrator_flags

Internal flags related to multi-step integrators,

◆ max_type

const int TissueForge::engine::max_type

static

TODO, clean up this design for types and static engine. What is the maximum nr of types?

◆ nodeID

int TissueForge::engine::nodeID

The ID of the computational node we are on.

◆ nr_active_angles

int TissueForge::engine::nr_active_angles

number of active angles. note, active angles are not necessarily in contiguous order

◆ nr_active_bonds

int TissueForge::engine::nr_active_bonds

number of active bonds. note, active bonds are not necessarily in contigous order.

◆ nr_active_dihedrals

int TissueForge::engine::nr_active_dihedrals

number of active dihedrals. note, active dihedrals are not necessarily in contiguous order

◆ nr_angles

int TissueForge::engine::nr_angles

total number of angles, active or not.

◆ nr_bonds

int TissueForge::engine::nr_bonds

total number of bonds, active or not.

◆ nr_dihedrals

int TissueForge::engine::nr_dihedrals

total number of dihedrals, active or not.

◆ nr_exclusions

int TissueForge::engine::nr_exclusions

Nr. of exclusions.

◆ nr_rigids

int TissueForge::engine::nr_rigids

Nr. of rigids.

◆ nr_runners

int TissueForge::engine::nr_runners

Nr of runners

◆ p

struct Potential** TissueForge::engine::p

The interaction matrix

◆ part2rigid

int* TissueForge::engine::part2rigid

List linking parts to rigids.

◆ particle_max_dist_fraction

FPTYPE TissueForge::engine::particle_max_dist_fraction

particle maximum velocity as a fraction of space cell size. good values for this are around 0.2, meaning that a particle can move about 1/5th of a cell length per time step.

if this is set of infinity, means there is not max speed. if the particle speed exceeds maximum velocity, the velocity is clamped to this speed.

defaults to 0.1.

◆ pids_avail

std::set<unsigned int> TissueForge::engine::pids_avail

Recycled particle ids

◆ queues

struct queue* TissueForge::engine::queues

The queues for the runners.

◆ rigids

struct rigid* TissueForge::engine::rigids

List of rigid bodies.

◆ runners

struct runner* TissueForge::engine::runners

The runners

◆ s

struct space TissueForge::engine::s

The space on which to work

◆ send

struct engine_comm* TissueForge::engine::send

Lists of cells to exchange with other nodes.

◆ sets

struct engine_set* TissueForge::engine::sets

Bonded sets.

◆ time

long TissueForge::engine::time

Time variables

◆ timers

ticks TissueForge::engine::timers[engine_timer_last]

The Comm object for mpi. Pointers to device data for CUDA. Timers.

◆ tol_rigid

FPTYPE TissueForge::engine::tol_rigid

Rigid solver tolerance.

◆ types

struct ParticleType* TissueForge::engine::types