#include <diffusion_grid.h>

Inheritance diagram for bdm::DiffusionGrid:

Collaboration diagram for bdm::DiffusionGrid:

Public Member Functions
	DiffusionGrid ()=default

	DiffusionGrid (const TRootIOCtor *)

	DiffusionGrid (int substance_id, const std::string &substance_name, real_t dc, real_t mu, int resolution=10)

	~DiffusionGrid () override=default

	DiffusionGrid (const DiffusionGrid &)=delete

DiffusionGrid &	operator= (const DiffusionGrid &)=delete

	DiffusionGrid (DiffusionGrid &&)=delete

DiffusionGrid &	operator= (DiffusionGrid &&)=delete

void	Initialize () override

void	Update () override

void	Step (real_t dt) override

void	Diffuse (real_t dt)

virtual void	DiffuseWithClosedEdge (real_t dt)=0

virtual void	DiffuseWithOpenEdge (real_t dt)=0

virtual void	DiffuseWithDirichlet (real_t dt)=0

virtual void	DiffuseWithNeumann (real_t dt)=0

virtual void	DiffuseWithPeriodic (real_t dt)=0

void	CalculateGradient ()

void	RunInitializers ()

void	ChangeConcentrationBy (const Real3 &position, real_t amount, InteractionMode mode=InteractionMode::kAdditive, bool scale_with_resolution=false)

void	ChangeConcentrationBy (size_t idx, real_t amount, InteractionMode mode=InteractionMode::kAdditive, bool scale_with_resolution=false)
	See ChangeConcentrationBy(const Real3&, real_t, InteractionMode, bool). More...

real_t	GetValue (const Real3 &position) const override
	Get the value of the scalar field at specified position. More...

real_t	GetConcentration (const Real3 &position) const

real_t	GetConcentration (const size_t idx) const
	Get the concentration at specified index. More...

Real3	GetGradient (const Real3 &position) const override

virtual void	GetGradient (const Real3 &position, Real3 *gradient, bool normalize=true) const

std::array< uint32_t, 3 >	GetBoxCoordinates (const Real3 &position) const
	Get the coordinates of the box at the specified position. More...

std::array< uint32_t, 3 >	GetBoxCoordinates (const size_t idx) const

size_t	GetBoxIndex (const std::array< uint32_t, 3 > &box_coord) const
	Calculates the box index at specified box coordinates. More...

size_t	GetBoxIndex (const Real3 &position) const
	Calculates the box index of the substance at specified position. More...

std::array< size_t, 6 >	GetNeighboringBoxes (size_t index) const

std::array< size_t, 6 >	GetNeighboringBoxes (size_t index, const std::array< uint32_t, 3 > &box_coord) const

void	SetDecayConstant (real_t mu)

real_t	GetLastTimestep () const
	Return the last timestep `dt` that was used to run `Diffuse(dt)` More...

void	SetUpperThreshold (real_t t)

real_t	GetUpperThreshold () const

void	SetLowerThreshold (real_t t)

real_t	GetLowerThreshold () const

const real_t *	GetAllConcentrations () const

const real_t *	GetAllGradients () const

std::array< size_t, 3 >	GetNumBoxesArray () const

size_t	GetNumBoxes () const

real_t	GetBoxLength () const

int	GetSubstanceId () const

const std::string &	GetSubstanceName () const

real_t	GetDecayConstant () const

const int32_t *	GetDimensionsPtr () const

std::array< int32_t, 6 >	GetDimensions () const

std::array< int32_t, 3 >	GetGridSize () const

const std::array< real_t, 7 > &	GetDiffusionCoefficients () const

size_t	GetResolution () const

real_t	GetBoxVolume () const

template<typename F >
void	AddInitializer (F function)

bool	IsFixedSubstance ()
	Return if a substance is stationary, e.g. (mu == 0 && dc == 0) More...

void	SetBoundaryCondition (std::unique_ptr< BoundaryCondition > bc)
	Set the boundary condition, takes ownership of the object. More...

BoundaryCondition *	GetBoundaryCondition () const
	Returns the boundary condition. Does not transfer ownership. More...

void	SetBoundaryConditionType (BoundaryConditionType bc_type)
	Sets boundary condition type. More...

BoundaryConditionType	GetBoundaryConditionType () const
	Returns the BoundaryConditionType, see `BoundaryConditionType` More...

void	PrintInfo (std::ostream &out=std::cout)
	Print information about the Diffusion Grid. More...

void	PrintInfoWithInitialization ()
	Print the information after initialization. More...

bool	IsInitialized () const
	Returns if the grid has been initialized. More...

void	TurnOffGradientCalculation ()

Public Member Functions inherited from bdm::ScalarField
	ScalarField ()=default

	ScalarField (const TRootIOCtor *)

	~ScalarField () override=default

	BDM_CLASS_DEF_OVERRIDE (ScalarField, 1)

Public Member Functions inherited from bdm::Continuum
	Continuum ()=default

	Continuum (const TRootIOCtor *)

virtual	~Continuum ()=default

void	IntegrateTimeAsynchronously (real_t dt)

int	GetContinuumId () const
	Returns the ID of the continuum. More...

void	SetContinuumId (int id)
	Sets the ID of the continuum. More...

const std::string &	GetContinuumName () const
	Returns the name of the continuum. More...

void	SetContinuumName (const std::string &name)
	Sets the name of the continuum. More...

real_t	GetSimulatedTime () const
	Returns the time simulated by the continuum. More...

void	SetTimeStep (real_t dt)

real_t	GetTimeStep () const
	Returns the time step for the continuum. More...

Private Member Functions
void	ParametersCheck (real_t dt)

void	CopyOldData (const ParallelResizeVector< real_t > &old_c1, const ParallelResizeVector< Real3 > &old_gradients, size_t old_resolution)

	BDM_CLASS_DEF_OVERRIDE (DiffusionGrid, 1)

Private Attributes
real_t	box_length_ = 0
	The side length of each box. More...

real_t	box_volume_ = 0
	the volume of each box More...

ParallelResizeVector< Spinlock >	locks_ = {}

ParallelResizeVector< real_t >	c1_ = {}
	The array of concentration values. More...

ParallelResizeVector< real_t >	c2_ = {}
	An extra concentration data buffer for faster value updating. More...

ParallelResizeVector< Real3 >	gradients_ = {}
	The array of gradients (x, y, z) More...

real_t	upper_threshold_ = 1e15
	The maximum concentration value that a box can have. More...

real_t	lower_threshold_ = 0.0
	The minimum concentration value that a box can have. More...

std::array< real_t, 7 >	dc_ = {{0}}
	The diffusion coefficients [cc, cw, ce, cs, cn, cb, ct]. More...

real_t	mu_ = 0
	The decay constant. More...

std::array< int32_t, 2 >	grid_dimensions_ = {{0}}
	The grid dimensions of the diffusion grid (cubic shaped) More...

uint64_t	num_boxes_axis_ = 0
	The number of boxes at each axis [x, y, z] (same along each axis) More...

size_t	total_num_boxes_ = 0
	The total number of boxes in the diffusion grid. More...

size_t	resolution_ = 0

real_t	last_dt_ = 0.0
	The last timestep `dt` used for the diffusion grid update `Diffuse(dt)` More...

bool	parity_ = false
	If false, grid dimensions are even; if true, they are odd. More...

std::vector< std::function< real_t(real_t, real_t, real_t)> >	initializers_

bool	init_gradient_ = false

BoundaryConditionType	bc_type_ = BoundaryConditionType::kDirichlet
	Type of boundary conditions. More...

std::unique_ptr< BoundaryCondition >	boundary_condition_ = nullptr
	Object that implements the boundary conditions. More...

bool	initialized_ = false
	Flag to indicate if the grid is initialized. More...

bool	print_info_with_initialization_ = false

bool	precompute_gradients_ = true

Friends
class	EulerGrid

class	EulerDepletionGrid

class	TestGrid

Detailed Description

Definition at line 90 of file diffusion_grid.h.

Constructor & Destructor Documentation

◆ DiffusionGrid() [1/5]

bdm::DiffusionGrid::DiffusionGrid ( )

default

◆ DiffusionGrid() [2/5]

bdm::DiffusionGrid::DiffusionGrid ( const TRootIOCtor * )

inlineexplicit

Definition at line 93 of file diffusion_grid.h.

◆ DiffusionGrid() [3/5]

bdm::DiffusionGrid::DiffusionGrid	(	int	substance_id,
		const std::string &	substance_name,
		real_t	dc,
		real_t	mu,
		int	resolution = `10`
	)

Definition at line 61 of file diffusion_grid.cc.

◆ ~DiffusionGrid()

bdm::DiffusionGrid::~DiffusionGrid ( )

overridedefault

◆ DiffusionGrid() [4/5]

bdm::DiffusionGrid::DiffusionGrid ( const DiffusionGrid & )

delete

◆ DiffusionGrid() [5/5]

bdm::DiffusionGrid::DiffusionGrid ( DiffusionGrid && )

delete

Member Function Documentation

◆ AddInitializer()

template<typename F >

void bdm::DiffusionGrid::AddInitializer ( F function )

inline

Definition at line 311 of file diffusion_grid.h.

◆ BDM_CLASS_DEF_OVERRIDE()

bdm::DiffusionGrid::BDM_CLASS_DEF_OVERRIDE	(	DiffusionGrid	,
		1
	)

private

◆ CalculateGradient()

void bdm::DiffusionGrid::CalculateGradient ( )

Calculates the gradient for each box in the diffusion grid. The gradient is calculated in each direction (x, y, z) as following:

c(x + box_length_) - c(x - box_length) / (2 * box_length_),

where c(x) implies the concentration at position x

At the edges the gradient is the same as the box next to it

Definition at line 317 of file diffusion_grid.cc.

◆ ChangeConcentrationBy() [1/2]

void bdm::DiffusionGrid::ChangeConcentrationBy	(	const Real3 &	position,
		real_t	amount,
		InteractionMode	mode = `InteractionMode::kAdditive`,
		bool	scale_with_resolution = `false`
	)

Increase the concentration at a specified position a with specified amount. The InteractionMode defines how the new concentration is calculated. If the interaction mode is kAdditive, the new concentration is the sum of the old concentration and the amount. If the interaction mode is kExponential, the new concentration is the product of the old concentration and the amount. If the interaction mode is kLogistic, the new concentration is the logistic function of the old concentration and the amount, e.g. additive but scaled with (upper_threshold_ - u) or (u - lower_threshold_) if amount is positive or negative, respectively. Should be used with thresholds 1.0 and 0.0. The parameter scale_with_resolution scales the amount with the inverse of the voxel volume. This is useful if the amount is given in units of, for instance, [mg] but the diffusion grid is in units of [mg / um^3]. It's helpful to model this way to obtain similar/identical results independent of the resolution of the diffusion grid.

Definition at line 355 of file diffusion_grid.cc.

◆ ChangeConcentrationBy() [2/2]

void bdm::DiffusionGrid::ChangeConcentrationBy	(	size_t	idx,
		real_t	amount,
		InteractionMode	mode = `InteractionMode::kAdditive`,
		bool	scale_with_resolution = `false`
	)

See ChangeConcentrationBy(const Real3&, real_t, InteractionMode, bool).

Increase the concentration at specified box with specified amount.

Definition at line 363 of file diffusion_grid.cc.

◆ CopyOldData()

void bdm::DiffusionGrid::CopyOldData	(	const ParallelResizeVector< real_t > &	old_c1,
		const ParallelResizeVector< Real3 > &	old_gradients,
		size_t	old_resolution
	)

private

Copies the concentration and gradients values to the new (larger) grid. In the 2D case it looks like the following:

                        [0 0  0  0]
          [v1 v2]  -->  [0 v1 v2 0]
          [v3 v4]  -->  [0 v3 v4 0]
                        [0 0  0  0]

The dimensions are doubled in this case from 2x2 to 4x4 If the dimensions would be increased from 2x2 to 3x3, it will still be increased to 4x4 in order for GetBoxIndex to function correctly

Definition at line 211 of file diffusion_grid.cc.

◆ Diffuse()

void bdm::DiffusionGrid::Diffuse ( real_t dt )

Definition at line 125 of file diffusion_grid.cc.

◆ DiffuseWithClosedEdge()

virtual void bdm::DiffusionGrid::DiffuseWithClosedEdge ( real_t dt )

pure virtual

Implemented in bdm::EulerGrid, and bdm::EulerDepletionGrid.

◆ DiffuseWithDirichlet()

virtual void bdm::DiffusionGrid::DiffuseWithDirichlet ( real_t dt )

pure virtual

Compute the diffusion of the substance with Dirichlet boundary conditions ( u = const on the boundary) for a given time step dt.

Implemented in bdm::EulerDepletionGrid, and bdm::EulerGrid.

◆ DiffuseWithNeumann()

virtual void bdm::DiffusionGrid::DiffuseWithNeumann ( real_t dt )

pure virtual

Compute the diffusion of the substance with Neumann boundary conditions (du/dn = const on the boundary) for a given time step dt.

Implemented in bdm::EulerDepletionGrid, and bdm::EulerGrid.

◆ DiffuseWithOpenEdge()

virtual void bdm::DiffusionGrid::DiffuseWithOpenEdge ( real_t dt )

pure virtual

Implemented in bdm::EulerDepletionGrid, and bdm::EulerGrid.

◆ DiffuseWithPeriodic()

virtual void bdm::DiffusionGrid::DiffuseWithPeriodic ( real_t dt )

pure virtual

Compute the diffusion of the substance with Periodic boundary conditions (u_{-1} = {u_N-1}, u_{N} = u_{0}) for a given time step dt.

Implemented in bdm::EulerDepletionGrid, and bdm::EulerGrid.

◆ GetAllConcentrations()

const real_t* bdm::DiffusionGrid::GetAllConcentrations ( ) const

inline

Definition at line 256 of file diffusion_grid.h.

◆ GetAllGradients()

const real_t* bdm::DiffusionGrid::GetAllGradients ( ) const

inline

Definition at line 258 of file diffusion_grid.h.

◆ GetBoundaryCondition()

BoundaryCondition * bdm::DiffusionGrid::GetBoundaryCondition ( ) const

Returns the boundary condition. Does not transfer ownership.

Returns: const Pointer to the boundary condition

Definition at line 536 of file diffusion_grid.cc.

◆ GetBoundaryConditionType()

BoundaryConditionType bdm::DiffusionGrid::GetBoundaryConditionType ( ) const

Returns the BoundaryConditionType, see BoundaryConditionType

Definition at line 548 of file diffusion_grid.cc.

◆ GetBoxCoordinates() [1/2]

std::array< uint32_t, 3 > bdm::DiffusionGrid::GetBoxCoordinates ( const Real3 & position ) const

Get the coordinates of the box at the specified position.

Definition at line 463 of file diffusion_grid.cc.

◆ GetBoxCoordinates() [2/2]

std::array< uint32_t, 3 > bdm::DiffusionGrid::GetBoxCoordinates ( const size_t idx ) const

Definition at line 485 of file diffusion_grid.cc.

◆ GetBoxIndex() [1/2]

size_t bdm::DiffusionGrid::GetBoxIndex ( const Real3 & position ) const

Calculates the box index of the substance at specified position.

Definition at line 505 of file diffusion_grid.cc.

◆ GetBoxIndex() [2/2]

size_t bdm::DiffusionGrid::GetBoxIndex ( const std::array< uint32_t, 3 > & box_coord ) const

Calculates the box index at specified box coordinates.

Definition at line 497 of file diffusion_grid.cc.

◆ GetBoxLength()

real_t bdm::DiffusionGrid::GetBoxLength ( ) const

inline

Definition at line 270 of file diffusion_grid.h.

◆ GetBoxVolume()

real_t bdm::DiffusionGrid::GetBoxVolume ( ) const

inline

Definition at line 308 of file diffusion_grid.h.

◆ GetConcentration() [1/2]

real_t bdm::DiffusionGrid::GetConcentration ( const Real3 & position ) const

inline

Definition at line 170 of file diffusion_grid.h.

◆ GetConcentration() [2/2]

real_t bdm::DiffusionGrid::GetConcentration ( const size_t idx ) const

Get the concentration at specified index.

Get the concentration at specified voxel.

Parameters

idx	Flat index of the grid

Returns: c1_[idx]

Definition at line 407 of file diffusion_grid.cc.

◆ GetDecayConstant()

real_t bdm::DiffusionGrid::GetDecayConstant ( ) const

inline

Definition at line 281 of file diffusion_grid.h.

◆ GetDiffusionCoefficients()

const std::array<real_t, 7>& bdm::DiffusionGrid::GetDiffusionCoefficients ( ) const

inline

Definition at line 304 of file diffusion_grid.h.

◆ GetDimensions()

std::array<int32_t, 6> bdm::DiffusionGrid::GetDimensions ( ) const

inline

Definition at line 285 of file diffusion_grid.h.

◆ GetDimensionsPtr()

const int32_t* bdm::DiffusionGrid::GetDimensionsPtr ( ) const

inline

Definition at line 283 of file diffusion_grid.h.

◆ GetGradient() [1/2]

Real3 bdm::DiffusionGrid::GetGradient ( const Real3 & position ) const

inlineoverridevirtual

Get the gradient at a specified position. By default, the obtained gradient is scaled to norm 1, but with normalize = false one can obtain the full gradient information (e.g. the un-normalized gradient). If the gradient is zero and normalize = true, this method returns a zero vector. The gradient is computed via a central difference scheme on the underlying spatial discretization (central difference for inner boxes, forward/backward difference for edge boxes). The gradients can either be computed once for all boxes (set Param::calculate_gradients to true) or on the fly (set Param::calculate_gradients to false). Depending on the use case, one of the two options might be more efficient (e.g. if the gradient is only needed for a few boxes, 'on the fly' might be more efficient). Please note that the on the fly evaluation of the gradient is done on the current state of the diffusion grid (c1_), thus, it interferes with ChangeConcentrationBy() (e.g. Adding to the substance will change the gradient: evaluating the gradient during the same iteration may yield different results). Further, if you need to visualize the gradient with Paraview, you must set Param::calculate_gradients to true.

Implements bdm::ScalarField.

Definition at line 196 of file diffusion_grid.h.

◆ GetGradient() [2/2]

void bdm::DiffusionGrid::GetGradient	(	const Real3 &	position,
		Real3 *	gradient,
		bool	normalize = `true`
	)		const

virtual

Get the gradient at a specified position. See GetGradient(Real3) for details. Note that the pointer to the gradient is passed as an argument and is dereferenced in the method. Thus the gradient must be initialized before calling this method and must not be nullptr.

Definition at line 419 of file diffusion_grid.cc.

◆ GetGridSize()

std::array<int32_t, 3> bdm::DiffusionGrid::GetGridSize ( ) const

inline

Definition at line 296 of file diffusion_grid.h.

◆ GetLastTimestep()

real_t bdm::DiffusionGrid::GetLastTimestep ( ) const

inline

Return the last timestep dt that was used to run Diffuse(dt)

Definition at line 242 of file diffusion_grid.h.

◆ GetLowerThreshold()

real_t bdm::DiffusionGrid::GetLowerThreshold ( ) const

inline

Definition at line 254 of file diffusion_grid.h.

◆ GetNeighboringBoxes() [1/2]

std::array< size_t, 6 > bdm::DiffusionGrid::GetNeighboringBoxes ( size_t index ) const

Determines the indices of the neighboring boxes of a given box index. Order: x-, x+, y-, y+, z-, z+. If the box is on the edge of the grid, the index itself is returned. E.g. if the box is on the left edge of the grid, x- is the same as index.

Definition at line 510 of file diffusion_grid.cc.

◆ GetNeighboringBoxes() [2/2]

std::array< size_t, 6 > bdm::DiffusionGrid::GetNeighboringBoxes	(	size_t	index,
		const std::array< uint32_t, 3 > &	box_coord
	)		const

Determines the indices of the neighboring boxes of given box coordinates. Order: x-, x+, y-, y+, z-, z+. If the box is on the edge of the grid, the index itself is returned. E.g. if the box is on the left edge of the grid, x- is the same as index.

Definition at line 515 of file diffusion_grid.cc.

◆ GetNumBoxes()

size_t bdm::DiffusionGrid::GetNumBoxes ( ) const

inline

Definition at line 268 of file diffusion_grid.h.

◆ GetNumBoxesArray()

std::array<size_t, 3> bdm::DiffusionGrid::GetNumBoxesArray ( ) const

inline

Definition at line 260 of file diffusion_grid.h.

◆ GetResolution()

size_t bdm::DiffusionGrid::GetResolution ( ) const

inline

Definition at line 306 of file diffusion_grid.h.

◆ GetSubstanceId()

int bdm::DiffusionGrid::GetSubstanceId ( ) const

inline

Definition at line 272 of file diffusion_grid.h.

◆ GetSubstanceName()

const std::string& bdm::DiffusionGrid::GetSubstanceName ( ) const

inline

Definition at line 277 of file diffusion_grid.h.

◆ GetUpperThreshold()

real_t bdm::DiffusionGrid::GetUpperThreshold ( ) const

inline

Definition at line 248 of file diffusion_grid.h.

◆ GetValue()

real_t bdm::DiffusionGrid::GetValue ( const Real3 & position ) const

overridevirtual

Get the value of the scalar field at specified position.

Get the concentration at specified position.

Parameters

position 3D position of

Returns: c1_[idx[position]]

Implements bdm::ScalarField.

Definition at line 401 of file diffusion_grid.cc.

◆ Initialize()

void bdm::DiffusionGrid::Initialize ( )

overridevirtual

Initializes the continuum. This method is called via Scheduler::Initialize. For some implementations, this method may be useful, other may not require it. A possibly use case is that agents move in a stationary continuum that is the solution to a timeindependent PDE. In this case, the Initialize method could be used to solve the PDE once at the beginning of the simulation.

Implements bdm::Continuum.

Definition at line 77 of file diffusion_grid.cc.

◆ IsFixedSubstance()

bool bdm::DiffusionGrid::IsFixedSubstance ( )

inline

Return if a substance is stationary, e.g. (mu == 0 && dc == 0)

Definition at line 316 of file diffusion_grid.h.

◆ IsInitialized()

bool bdm::DiffusionGrid::IsInitialized ( ) const

inline

Returns if the grid has been initialized.

Definition at line 345 of file diffusion_grid.h.

◆ operator=() [1/2]

DiffusionGrid& bdm::DiffusionGrid::operator= ( const DiffusionGrid & )

delete

◆ operator=() [2/2]

DiffusionGrid& bdm::DiffusionGrid::operator= ( DiffusionGrid && )

delete

◆ ParametersCheck()

void bdm::DiffusionGrid::ParametersCheck ( real_t dt )

private

Definition at line 593 of file diffusion_grid.cc.

◆ PrintInfo()

void bdm::DiffusionGrid::PrintInfo ( std::ostream & out = std::cout )

Print information about the Diffusion Grid.

Definition at line 552 of file diffusion_grid.cc.

◆ PrintInfoWithInitialization()

void bdm::DiffusionGrid::PrintInfoWithInitialization ( )

inline

Print the information after initialization.

Definition at line 340 of file diffusion_grid.h.

◆ RunInitializers()

void bdm::DiffusionGrid::RunInitializers ( )

Initialize the diffusion grid according to the initialization functions. Note that if your initializers our outside the defined bounds (lower and upper threshold), they will be clamped to the bounds.

Definition at line 253 of file diffusion_grid.cc.

◆ SetBoundaryCondition()

void bdm::DiffusionGrid::SetBoundaryCondition ( std::unique_ptr< BoundaryCondition > bc )

Set the boundary condition, takes ownership of the object.

Parameters

bc	object that implements the boundary condition, see for example `ConstantBoundaryCondition`

Definition at line 531 of file diffusion_grid.cc.

◆ SetBoundaryConditionType()

void bdm::DiffusionGrid::SetBoundaryConditionType ( BoundaryConditionType bc_type )

Sets boundary condition type.

Definition at line 540 of file diffusion_grid.cc.

◆ SetDecayConstant()

void bdm::DiffusionGrid::SetDecayConstant ( real_t mu )

inline

Definition at line 236 of file diffusion_grid.h.

◆ SetLowerThreshold()

void bdm::DiffusionGrid::SetLowerThreshold ( real_t t )

inline

Definition at line 251 of file diffusion_grid.h.

◆ SetUpperThreshold()

void bdm::DiffusionGrid::SetUpperThreshold ( real_t t )

inline

Definition at line 245 of file diffusion_grid.h.

◆ Step()

void bdm::DiffusionGrid::Step ( real_t dt )

inlineoverridevirtual

This method integrates the continuum model in time by dt. Typically, the continuum is the solution of a partial differential equation (PDE). Thus, the step method is used to advance the solution in time. If your numerical scheme has requirements for it's parameters depending on dt, make sure to verify them in this method.

Implements bdm::Continuum.

Definition at line 110 of file diffusion_grid.h.

◆ TurnOffGradientCalculation()

void bdm::DiffusionGrid::TurnOffGradientCalculation ( )

inline

Turn off the gradient calculation. Gradients are not precomputed but can be calculated on the fly.

Definition at line 349 of file diffusion_grid.h.

◆ Update()

void bdm::DiffusionGrid::Update ( )

overridevirtual

Updates the grid dimensions, based on the given threshold values. The diffusion grid dimensions need always be larger than the neighbor grid dimensions, so that each simulation object can obtain its local concentration / gradient

Implements bdm::Continuum.

Definition at line 156 of file diffusion_grid.cc.

Friends And Related Function Documentation

◆ EulerDepletionGrid

friend class EulerDepletionGrid

friend

Definition at line 353 of file diffusion_grid.h.

◆ EulerGrid

friend class EulerGrid

friend

Definition at line 352 of file diffusion_grid.h.

◆ TestGrid

friend class TestGrid

friend

Definition at line 354 of file diffusion_grid.h.

Member Data Documentation

◆ bc_type_

BoundaryConditionType bdm::DiffusionGrid::bc_type_ = BoundaryConditionType::kDirichlet

private

Type of boundary conditions.

Definition at line 415 of file diffusion_grid.h.

◆ boundary_condition_

std::unique_ptr<BoundaryCondition> bdm::DiffusionGrid::boundary_condition_ = nullptr

private

Object that implements the boundary conditions.

Definition at line 417 of file diffusion_grid.h.

◆ box_length_

real_t bdm::DiffusionGrid::box_length_ = 0

private

The side length of each box.

Definition at line 375 of file diffusion_grid.h.

◆ box_volume_

real_t bdm::DiffusionGrid::box_volume_ = 0

private

the volume of each box

Definition at line 377 of file diffusion_grid.h.

◆ c1_

ParallelResizeVector<real_t> bdm::DiffusionGrid::c1_ = {}

private

The array of concentration values.

Definition at line 382 of file diffusion_grid.h.

◆ c2_

ParallelResizeVector<real_t> bdm::DiffusionGrid::c2_ = {}

private

An extra concentration data buffer for faster value updating.

Definition at line 384 of file diffusion_grid.h.

◆ dc_

std::array<real_t, 7> bdm::DiffusionGrid::dc_ = {{0}}

private

The diffusion coefficients [cc, cw, ce, cs, cn, cb, ct].

Definition at line 392 of file diffusion_grid.h.

◆ gradients_

ParallelResizeVector<Real3> bdm::DiffusionGrid::gradients_ = {}

private

The array of gradients (x, y, z)

Definition at line 386 of file diffusion_grid.h.

◆ grid_dimensions_

std::array<int32_t, 2> bdm::DiffusionGrid::grid_dimensions_ = {{0}}

private

The grid dimensions of the diffusion grid (cubic shaped)

Definition at line 396 of file diffusion_grid.h.

◆ init_gradient_

bool bdm::DiffusionGrid::init_gradient_ = false

private

Definition at line 413 of file diffusion_grid.h.

◆ initialized_

bool bdm::DiffusionGrid::initialized_ = false

private

Flag to indicate if the grid is initialized.

Definition at line 419 of file diffusion_grid.h.

◆ initializers_

std::vector<std::function<real_t(real_t, real_t, real_t)> > bdm::DiffusionGrid::initializers_

private

Initial value:

=

{}

A list of functions that initialize this diffusion grid ROOT currently doesn't support IO of std::function

Definition at line 410 of file diffusion_grid.h.

◆ last_dt_

real_t bdm::DiffusionGrid::last_dt_ = 0.0

private

The last timestep dt used for the diffusion grid update Diffuse(dt)

Definition at line 405 of file diffusion_grid.h.

◆ locks_

ParallelResizeVector<Spinlock> bdm::DiffusionGrid::locks_ = {}

mutableprivate

Lock for each voxel used to prevent race conditions between multiple threads

Definition at line 380 of file diffusion_grid.h.

◆ lower_threshold_

real_t bdm::DiffusionGrid::lower_threshold_ = 0.0

private

The minimum concentration value that a box can have.

Definition at line 390 of file diffusion_grid.h.

◆ mu_

real_t bdm::DiffusionGrid::mu_ = 0

private

The decay constant.

Definition at line 394 of file diffusion_grid.h.

◆ num_boxes_axis_

uint64_t bdm::DiffusionGrid::num_boxes_axis_ = 0

private

The number of boxes at each axis [x, y, z] (same along each axis)

Definition at line 398 of file diffusion_grid.h.

◆ parity_

bool bdm::DiffusionGrid::parity_ = false

private

If false, grid dimensions are even; if true, they are odd.

Definition at line 407 of file diffusion_grid.h.

◆ precompute_gradients_

bool bdm::DiffusionGrid::precompute_gradients_ = true

private

Flag to avoid gradient computation if not needed. (E.g. if multiple DGs are used but the gradient is only needed for one of them.)

Definition at line 425 of file diffusion_grid.h.

◆ print_info_with_initialization_

bool bdm::DiffusionGrid::print_info_with_initialization_ = false

private

Flag to indicate if we want to print information about the grid after initialization

Definition at line 422 of file diffusion_grid.h.

◆ resolution_

size_t bdm::DiffusionGrid::resolution_ = 0

private

The resolution of the diffusion grid (i.e. number of boxes along each axis)

Definition at line 403 of file diffusion_grid.h.

◆ total_num_boxes_

size_t bdm::DiffusionGrid::total_num_boxes_ = 0

private

The total number of boxes in the diffusion grid.

Definition at line 400 of file diffusion_grid.h.

◆ upper_threshold_

real_t bdm::DiffusionGrid::upper_threshold_ = 1e15

private

The maximum concentration value that a box can have.

Definition at line 388 of file diffusion_grid.h.

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

core/diffusion/diffusion_grid.h
core/diffusion/diffusion_grid.cc

Public Member Functions

Private Member Functions

Private Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

◆ DiffusionGrid() [1/5]

◆ DiffusionGrid() [2/5]

◆ DiffusionGrid() [3/5]

◆ ~DiffusionGrid()

◆ DiffusionGrid() [4/5]

◆ DiffusionGrid() [5/5]

Member Function Documentation

◆ AddInitializer()

◆ BDM_CLASS_DEF_OVERRIDE()

◆ CalculateGradient()

◆ ChangeConcentrationBy() [1/2]

◆ ChangeConcentrationBy() [2/2]

◆ CopyOldData()

◆ Diffuse()

◆ DiffuseWithClosedEdge()

◆ DiffuseWithDirichlet()

◆ DiffuseWithNeumann()

◆ DiffuseWithOpenEdge()

◆ DiffuseWithPeriodic()

◆ GetAllConcentrations()

◆ GetAllGradients()

◆ GetBoundaryCondition()

◆ GetBoundaryConditionType()

◆ GetBoxCoordinates() [1/2]

◆ GetBoxCoordinates() [2/2]

◆ GetBoxIndex() [1/2]

◆ GetBoxIndex() [2/2]

◆ GetBoxLength()

◆ GetBoxVolume()

◆ GetConcentration() [1/2]

◆ GetConcentration() [2/2]

◆ GetDecayConstant()

◆ GetDiffusionCoefficients()

◆ GetDimensions()

◆ GetDimensionsPtr()

◆ GetGradient() [1/2]

◆ GetGradient() [2/2]

◆ GetGridSize()

◆ GetLastTimestep()

◆ GetLowerThreshold()

◆ GetNeighboringBoxes() [1/2]

◆ GetNeighboringBoxes() [2/2]

◆ GetNumBoxes()

◆ GetNumBoxesArray()

◆ GetResolution()

◆ GetSubstanceId()

◆ GetSubstanceName()

◆ GetUpperThreshold()

◆ GetValue()

◆ Initialize()

◆ IsFixedSubstance()

◆ IsInitialized()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ ParametersCheck()

◆ PrintInfo()

◆ PrintInfoWithInitialization()

◆ RunInitializers()

◆ SetBoundaryCondition()

◆ SetBoundaryConditionType()

◆ SetDecayConstant()

◆ SetLowerThreshold()

◆ SetUpperThreshold()

◆ Step()

◆ TurnOffGradientCalculation()

◆ Update()

Friends And Related Function Documentation

◆ EulerDepletionGrid

◆ EulerGrid

◆ TestGrid

Member Data Documentation

◆ bc_type_

◆ boundary_condition_

◆ box_length_