#include <model_initializer.h>

Static Public Member Functions
template<typename Function >
static void	Grid3D (size_t agents_per_dim, real_t space, Function agent_builder)

template<typename Function >
static void	Grid3D (const std::array< size_t, 3 > &agents_per_dim, real_t space, Function agent_builder)

template<typename Function >
static void	CreateAgents (const std::vector< Real3 > &positions, Function agent_builder)

template<typename Function >
static void	CreateAgentsRandom (real_t min, real_t max, uint64_t num_agents, Function agent_builder, DistributionRng< real_t > *rng=nullptr)

template<typename Function >
static void	CreateAgentsOnSurface (real_t(f)(const real_t , const real_t *), const FixedSizeVector< real_t, 10 > &fn_params, real_t xmin, real_t xmax, real_t deltax, real_t ymin, real_t ymax, real_t deltay, Function agent_builder)

template<typename Function >
static void	CreateAgentsOnSurfaceRndm (real_t(f)(const real_t , const real_t *), const FixedSizeVector< real_t, 10 > &fn_params, real_t xmin, real_t xmax, real_t ymin, real_t ymax, uint64_t num_agents, Function agent_builder)

template<typename Function >
static void	CreateAgentsOnSphereRndm (const Real3 &center, real_t radius, uint64_t num_agents, Function agent_builder)

template<typename Function >
static void	CreateAgentsInSphereRndm (const Real3 &center, real_t radius, uint64_t num_agents, Function agent_builder)

static void	DefineSubstance (int substance_id, const std::string &substance_name, real_t diffusion_coeff, real_t decay_constant, int resolution=10, const std::vector< real_t > &binding_coefficients={}, const std::vector< int > &binding_substances={})

template<typename F >
static void	InitializeSubstance (int substance_id, F function)

static void	AddBoundaryConditions (int substance_id, BoundaryConditionType bc_type, std::unique_ptr< BoundaryCondition > bc)

Detailed Description

Definition at line 35 of file model_initializer.h.

Member Function Documentation

◆ AddBoundaryConditions()

static void bdm::ModelInitializer::AddBoundaryConditions	(	int	substance_id,
		BoundaryConditionType	bc_type,
		std::unique_ptr< BoundaryCondition >	bc
	)

inlinestatic

Sets the boundary condition for the specified substance. Transfers the ownership of the boundary condition to the diffusion grid.

Parameters

[in]	substance_id	The substance identifier
[in]	bc_type	The boundary condition type
[in]	bc	The boundary condition

Definition at line 411 of file model_initializer.h.

◆ CreateAgents()

template<typename Function >

static void bdm::ModelInitializer::CreateAgents	(	const std::vector< Real3 > &	positions,
		Function	agent_builder
	)

inlinestatic

Creates agents on the given positions and adds them to the ExecutionContext.

Parameters

positions	positions of the agents to be
agent_builder	function containing the logic to instantiate a new agent. Takes `const Real3&` as input parameter

Definition at line 122 of file model_initializer.h.

◆ CreateAgentsInSphereRndm()

template<typename Function >

static void bdm::ModelInitializer::CreateAgentsInSphereRndm	(	const Real3 &	center,
		real_t	radius,
		uint64_t	num_agents,
		Function	agent_builder
	)

inlinestatic

Creates agents with random positions in a sphere and adds them to the ExecutionContext. Agents are distributed uniformly inside the sphere. Agent creation is parallelized. Algorithm: Knop, 1970, 10.1145/362349.362377 (doi).

Parameters

[in]	center	Center of the sphere
[in]	radius	Radius of the sphere
[in]	num_agents	The number of agents
[in]	agent_builder	function containing the logic to instantiate a new agent. Takes `const Real3&` as input parameter

Definition at line 335 of file model_initializer.h.

◆ CreateAgentsOnSphereRndm()

template<typename Function >

static void bdm::ModelInitializer::CreateAgentsOnSphereRndm	(	const Real3 &	center,
		real_t	radius,
		uint64_t	num_agents,
		Function	agent_builder
	)

inlinestatic

Creates agents with random positions on a sphere and adds them to the ExecutionContext. The agents' positions are uniformly distributed across the surface. Agent creation is parallelized. Algorithm: Knop, 1970, 10.1145/362349.362377 (doi).

Parameters

[in]	center	Center of the sphere
[in]	radius	Radius of the sphere
[in]	num_agents	The number of agents
[in]	agent_builder	function containing the logic to instantiate a new agent. Takes `const Real3&` as input parameter

Definition at line 305 of file model_initializer.h.

◆ CreateAgentsOnSurface()

template<typename Function >

static void bdm::ModelInitializer::CreateAgentsOnSurface	(	real_t()(const real_t , const real_t *)	f,
		const FixedSizeVector< real_t, 10 > &	fn_params,
		real_t	xmin,
		real_t	xmax,
		real_t	deltax,
		real_t	ymin,
		real_t	ymax,
		real_t	deltay,
		Function	agent_builder
	)

inlinestatic

Creates agents on surface and adds them to the ExecutionContext. The x and y positions are defined by xmin, xmax, deltax and ymin, ymax, deltay. The z position is calculated using f. Agent creation is parallelized.

auto construct = [](const Real3& position) {
  Cell* cell = new Cell(position);
  cell->SetDiameter(10);
  return cell;
};
auto f = [](const real_t* x, const real_t* params) {
    // 10 * sin(x/20) + 10 * sin(y/20)
    return 10 * std::sin(x[0] / 20.) + 10 * std::sin(x[1] / 20.0);
};
ModelInitializer::CreateAgentsOnSurface(f, {}, -100, 100, 10, -100,
100, 10, construct);

Parameters

[in]	f	function that defines the surface
[in]	fn_params	Parameters that will be passed to `f` as second argument.
[in]	xmin	Minimum x coordinate on which a agent will be created.
[in]	xmax	Maximum x coordinate on which a agent will be created.
[in]	deltax	Space between two agents on the x-axis.
[in]	ymin	Minimum y coordinate on which a agent will be created.
[in]	ymax	Maximum y coordinate on which a agent will be created.
[in]	deltay	Space between two agents on the y-axis.
[in]	agent_builder	function containing the logic to instantiate a new agent. Takes `const Real3&` as input parameter

Definition at line 214 of file model_initializer.h.

◆ CreateAgentsOnSurfaceRndm()

template<typename Function >

static void bdm::ModelInitializer::CreateAgentsOnSurfaceRndm	(	real_t()(const real_t , const real_t *)	f,
		const FixedSizeVector< real_t, 10 > &	fn_params,
		real_t	xmin,
		real_t	xmax,
		real_t	ymin,
		real_t	ymax,
		uint64_t	num_agents,
		Function	agent_builder
	)

inlinestatic

Creates agents on surface and adds them to the ExecutionContext. The x and y positions are determined by a uniform distribution [xmin, xmax[ and [ymin, ymax[. The z position is calculated using f. Agent creation is parallelized.

auto construct = [](const Real3& position) {
  Cell* cell = new Cell(position);
  cell->SetDiameter(10);
  return cell;
};
auto f = [](const real_t* x, const real_t* params) {
    // 10 * sin(x/20) + 10 * sin(y/20)
    return 10 * std::sin(x[0] / 20.) + 10 * std::sin(x[1] / 20.0);
};
ModelInitializer::CreateAgentsOnSurfaceRndm(f, {}, -100, 100, -100,
100, construct);

Parameters

[in]	f	function that defines the surface
[in]	fn_params	Parameters that will be passed to `f` as second argument.
[in]	xmin	Minimum x coordinate on which a agent will be created.
[in]	xmax	Maximum x coordinate on which a agent will be created.
[in]	ymin	Minimum y coordinate on which a agent will be created.
[in]	ymax	Maximum y coordinate on which a agent will be created.
[in]	agent_builder	function containing the logic to instantiate a new agent. Takes `const Real3&` as input parameter

Definition at line 274 of file model_initializer.h.

◆ CreateAgentsRandom()

template<typename Function >

static void bdm::ModelInitializer::CreateAgentsRandom	(	real_t	min,
		real_t	max,
		uint64_t	num_agents,
		Function	agent_builder,
		DistributionRng< real_t > *	rng = `nullptr`
	)

inlinestatic

Creates agents with random positions and adds them to the ExecutionContext. Agent creation is parallelized.

Parameters

[in]	min	The minimum position value
[in]	max	The maximum position value
[in]	num_agents	The number agents
[in]	agent_builder	function containing the logic to instantiate a new agent. Takes `const Real3&` as input parameter
[in]	rng	Uses the given DistributionRng. if rng is a nullptr, this function uses a uniform distribution between [min, max[

Definition at line 151 of file model_initializer.h.

◆ DefineSubstance()

void bdm::ModelInitializer::DefineSubstance	(	int	substance_id,
		const std::string &	substance_name,
		real_t	diffusion_coeff,
		real_t	decay_constant,
		int	resolution = `10`,
		const std::vector< real_t > &	binding_coefficients = `{}`,
		const std::vector< int > &	binding_substances = `{}`
	)

static

Allows agents to secrete the specified substance. Diffusion throughout the simulation space is automatically taken care of by the DiffusionGrid class

Parameters

[in]	substance_id	The substance identifier
[in]	substance_name	The substance name
[in]	diffusion_coeff	The diffusion coefficient
[in]	decay_constant	The decay constant
[in]	resolution	The resolution of the diffusion grid
[in]	binding_coefficients	The binding coefficients of the depleting substances
[in]	binding_substances	The depleting substances

Definition at line 23 of file model_initializer.cc.

◆ Grid3D() [1/2]

template<typename Function >

static void bdm::ModelInitializer::Grid3D	(	const std::array< size_t, 3 > &	agents_per_dim,
		real_t	space,
		Function	agent_builder
	)

inlinestatic

Creates a 3D grid of agents and adds them to the ExecutionContext. Type of the agent is determined by the return type of parameter agent_builder.

ModelInitializer::Grid3D({8,6,4}, 10, [](const Real3&
pos){ return Cell(pos); });

Parameters

agents_per_dim	number of agents on each axis. Number of generated agents = `agents_per_dim[0] * agents_per_dim[1] * agents_per_dim[2]`
space	space between the positions - e.g space = 10: positions = `{(0, 0, 0), (0, 0, 10), (0, 0, 20), ... }`
agent_builder	function containing the logic to instantiate a new agent. Takes `const Real3&` as input parameter

Definition at line 92 of file model_initializer.h.

◆ Grid3D() [2/2]

template<typename Function >

static void bdm::ModelInitializer::Grid3D	(	size_t	agents_per_dim,
		real_t	space,
		Function	agent_builder
	)

inlinestatic

Creates a 3D cubic grid of agents and adds them to the ExecutionContext. Type of the agent is determined by the return type of parameter agent_builder.

ModelInitializer::Grid3D(8, 10, [](const Real3& pos){
return Cell(pos); });

Parameters

agents_per_dim	number of agents on each axis. Number of generated agents = `agents_per_dim ^ 3`
space	space between the positions - e.g space = 10: positions = `{(0, 0, 0), (0, 0, 10), (0, 0, 20), ... }`
agent_builder	function containing the logic to instantiate a new agent. Takes `const Real3&` as input parameter

Definition at line 53 of file model_initializer.h.

◆ InitializeSubstance()

template<typename F >

static void bdm::ModelInitializer::InitializeSubstance	(	int	substance_id,
		F	function
	)

inlinestatic

Definition at line 399 of file model_initializer.h.

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

core/model_initializer.h
core/model_initializer.cc

Static Public Member Functions

Detailed Description

Member Function Documentation

◆ AddBoundaryConditions()

◆ CreateAgents()

◆ CreateAgentsInSphereRndm()

◆ CreateAgentsOnSphereRndm()

◆ CreateAgentsOnSurface()

◆ CreateAgentsOnSurfaceRndm()

◆ CreateAgentsRandom()

◆ DefineSubstance()

◆ Grid3D() [1/2]

◆ Grid3D() [2/2]

◆ InitializeSubstance()