Abstract active stress class. More...

#include <ActiveStress.h>

Inheritance diagram for ActiveStress:

Public Member Functions
	ActiveStress (const unsigned int n_states_, const bool needs_fiber_stretch, const bool needs_fiber_stretch_rate)
	Constructor.

virtual	~ActiveStress ()=default
	Virtual destructor.

virtual std::unique_ptr< ActiveStressModelParameters >	get_parameters () const =0
	Construct an instance of model parameters for this model.

void	read_parameters (const ActiveStressParameters &params)
	Read model parameters from a parameter object.

void	distribute_parameters (const CmMod &cm_mod, const cmType &cm)
	Distribute model parameters to all parallel processes.

double	get_tension_fibers (const int idx) const
	Get the tension along fibers \(\eta_f \Tact\) at a given point.

double	get_tension_sheets (const int idx) const
	Get the tension along sheets \(\eta_s \Tact\) at a given point.

double	get_tension_sheet_normals (const int idx) const
	Get the tension along sheet normals \(\eta_n \Tact\) at a given point.

virtual void	init (const unsigned int tnNo)
	Initialize the model.

virtual void	advance_time_step (const double t, const double dt, const Vector< double > &calcium, const Vector< double > &fiber_stretch, const Vector< double > &fiber_stretch_rate)
	Advance in time.

bool	needs_fiber_stretch () const
	Whether this model uses the fiber stretch passed to advance_time_step. This flag can be used to determine whether fiber stretch computation can be skipped for efficiency.

bool	needs_fiber_stretch_rate () const
	Whether this model uses the fiber stretch rate passed to advance_time_step. This flag can be used to determine whether fiber stretch rate computation can be skipped for efficiency.

Public Attributes
const unsigned int	n_states
	Number of state variables for this model.

Protected Member Functions
virtual void	read_model_specific_parameters (const ActiveStressModelParameters &params)=0
	Read model parameters from a parameter object.

virtual void	distribute_model_specific_parameters (const CmMod &cm_mod, const cmType &cm)=0
	Distribute model parameters to all parallel processes.

virtual void	init_local (Vector< double > &state) const =0
	Initialize the state vector for a single node.

virtual void	advance_time_step_local (const double t, const double dt, const double calcium, const double fiber_stretch, const double fiber_stretch_rate, Vector< double > &state) const =0
	Advance in time for a single node.

virtual double	compute_active_tension_local (const Vector< double > &state, const double fiber_stretch) const =0
	Compute the active tension for a single node.

Protected Attributes
bool	needs_fiber_stretch_
	Backing store for needs_fiber_stretch.

bool	needs_fiber_stretch_rate_
	Backing store for needs_fiber_stretch_rate.

double	time
	Current time. Updated whenever calling advance_time_step.

Array< double >	states
	State variables for the model.

Vector< double >	active_tension
	Active tension at every node.

double	eta_f
	Active tension coefficient along the fiber direction.

double	eta_s
	Active tension coefficient along the sheet direction.

double	eta_n
	Active tension coefficient along the sheet-normal direction.

Detailed Description

Abstract active stress class.

This class provides an interface for defining active stress models, i.e. models that, in the context of structural mechanics of muscular tissue, compute an active tension representing the contribution of muscular contraction to the constitiutive law.

The class assumes that the active tension can be expressed as

\[ \Tact = \Tact(t, \calcium, \fiberstretch, \fiberstretchrate, \astressstate), \]

where \(\calcium\) is the intracellular calcium concentration, \(\fiberstretch\) is the fiber stretch, \(\fiberstretchrate\) is the fiber stretch rate, and \(\astressstate\) is a vector of internal state variables, representing the state of contraction.

The expression assumed above implies that the active tension is a local function of the variables it depends on, that is the active tension at a given point only depends on the value of other variables at that same point. Accordingly, this class works nodally, by evaluating the active tension at every mesh node and storing it in a vector, whose values can be accessed through ActiveStress::get_tension_fibers.

Directional distribution of active stress

In muscular mechanics models, active stress normally acts only along the direction of fibers \(\fiberdirection\), reflecting the fact that contractile units are aligned with fibers. However, one might want to account for fiber dispersion, i.e. the fact that fibers are not perfectly and regularly aligned, but rather have a certain distribution of orientations centered around the principal direction \(\fiberdirection\).

This can be surrogated by defining the active stress tensor as

\[ S_\text{act} = \Tact \left( \eta_f \fiberdirection \otimes \fiberdirection + \eta_s \sheetdirection \otimes \sheetdirection + \eta_n \sheetnormaldirection \otimes \sheetnormaldirection \right), \]

where \(\sheetdirection\) and \(\sheetnormaldirection\) are the sheet and sheet-normal directions, respectively, and \(\eta_f\), \(\eta_s\), and \(\eta_n\) are coefficients that define the distribution the active tension along the three principal directions. The coefficients must be such that \(\eta_f + \eta_s + \eta_n = 1\).

This class stores the values of \(\eta_f\), \(\eta_s\) and \(\eta_n\), and provides the functions ActiveStress::get_tension_fibers, ActiveStress::get_tension_sheets and ActiveStress::get_tension_sheet_normals to access \(\eta_f \Tact\), \(\eta_s \Tact\) and \(\eta_n \Tact\), respectively.

Implementing concrete active stress models

To implement a new active stress model, the following steps need to be taken:

Create a new class derived from ActiveStress.
Override the methods init_local, advance_time_step_local and compute_active_tension_local, defining the initial condition, time evolution and active tension computation, respectively, for a single node.
Create a new class derived from ActiveStressModelParameters to store the parameters specific to the new active stress model.
Override the methods get_parameters, read_model_specific_parameters and distribute_model_specific_parameters to manage the parameters of the new active stress model.
Register the new class into the active stress model factory by using the macro REGISTER_ACTIVE_STRESS_MODEL. The macro should be called in a .cpp file, not in a header file.

Notice that if the model is expressed in terms of a system of ODEs, it can be implemented by deriving from ActiveStressODE, which already addresses some of the points above.

Constructor & Destructor Documentation

◆ ActiveStress()

ActiveStress::ActiveStress	(	const unsigned int	n_states_,
		const bool	needs_fiber_stretch,
		const bool	needs_fiber_stretch_rate
	)

inline

Constructor.

Parameters

n_states_	Number of state variables for this model.
needs_fiber_stretch	Whether this model uses the fiber stretch passed to advance_time_step. This flag can be used to determine whether fiber stretch computation can be skipped for efficiency.
needs_fiber_stretch_rate	Whether this model uses the fiber stretch rate passed to advance_time_step. This flag can be used to determine whether fiber stretch rate computation can be skipped for efficiency.

◆ ~ActiveStress()

virtual ActiveStress::~ActiveStress ( )

virtualdefault

Virtual destructor.

Member Function Documentation

◆ advance_time_step()

void ActiveStress::advance_time_step	(	const double	t,
		const double	dt,
		const Vector< double > &	calcium,
		const Vector< double > &	fiber_stretch,
		const Vector< double > &	fiber_stretch_rate
	)

virtual

Advance in time.

Parameters

[in]	t	Current time (i.e. the time instant being advanced to).
[in]	dt	Time step size.
[in]	calcium	Calcium concentration at every node.
[in]	fiber_stretch	Fiber stretch at every node. This is usually computed with post::fib_stretch.
[in]	fiber_stretch_rate	Fiber stretch rate at every node. This is usually computed with post::fib_stretch_rate.

◆ advance_time_step_local()

virtual void ActiveStress::advance_time_step_local	(	const double	t,
		const double	dt,
		const double	calcium,
		const double	fiber_stretch,
		const double	fiber_stretch_rate,
		Vector< double > &	state
	)		const

protectedpure virtual

Advance in time for a single node.

Parameters

[in]	t	Current time (i.e. the time instant being advanced to).
[in]	dt	Time step size.
[in]	calcium	Calcium concentration at the current node.
[in]	fiber_stretch	Fiber stretch at the current node.
[in]	fiber_stretch_rate	Fiber stretch rate at the current node.
[in,out]	state	State vector for a single node, to be updated by this function.

Implemented in ActiveStressODE, ActiveStressRegazzoni, ActiveStressUniformSteady, and ActiveStressUniformUnsteady.

◆ compute_active_tension_local()

virtual double ActiveStress::compute_active_tension_local	(	const Vector< double > &	state,
		const double	fiber_stretch
	)		const

protectedpure virtual

Compute the active tension for a single node.

Parameters

[in]	state	State vector for a single node.
[in]	fiber_stretch	Fiber stretch at the current node.

Implemented in ActiveStressNashPanfilov, ActiveStressRegazzoni, ActiveStressUniformSteady, and ActiveStressUniformUnsteady.

◆ distribute_model_specific_parameters()

virtual void ActiveStress::distribute_model_specific_parameters	(	const CmMod &	cm_mod,
		const cmType &	cm
	)

protectedpure virtual

Distribute model parameters to all parallel processes.

This method needs to be overridden by derived classes to distribute the parameters specific to the concrete model they implement to all parallel processes.

Implemented in ActiveStressNashPanfilov, ActiveStressODE, ActiveStressRegazzoni, ActiveStressUniformSteady, and ActiveStressUniformUnsteady.

◆ distribute_parameters()

void ActiveStress::distribute_parameters	(	const CmMod &	cm_mod,
		const cmType &	cm
	)

Distribute model parameters to all parallel processes.

◆ get_parameters()

virtual std::unique_ptr< ActiveStressModelParameters > ActiveStress::get_parameters ( ) const

pure virtual

Construct an instance of model parameters for this model.

Implemented in ActiveStressNashPanfilov, ActiveStressRegazzoni, ActiveStressUniformSteady, and ActiveStressUniformUnsteady.

◆ get_tension_fibers()

double ActiveStress::get_tension_fibers ( const int idx ) const

inline

Get the tension along fibers \(\eta_f \Tact\) at a given point.

◆ get_tension_sheet_normals()

double ActiveStress::get_tension_sheet_normals ( const int idx ) const

inline

Get the tension along sheet normals \(\eta_n \Tact\) at a given point.

◆ get_tension_sheets()

double ActiveStress::get_tension_sheets ( const int idx ) const

inline

Get the tension along sheets \(\eta_s \Tact\) at a given point.

◆ init()

void ActiveStress::init ( const unsigned int tnNo )

virtual

Initialize the model.

Allocates the internal state vector and initializes it with the model's initial conditions.

Parameters

[in] tnNo Total number of mesh nodes for the current rank.

Reimplemented in ActiveStressUniformUnsteady.

◆ init_local()

virtual void ActiveStress::init_local ( Vector< double > & state ) const

protectedpure virtual

Initialize the state vector for a single node.

Parameters

[out] state State vector for a single node, to be initialized by this function.

Implemented in ActiveStressNashPanfilov, ActiveStressRegazzoni, ActiveStressUniformSteady, and ActiveStressUniformUnsteady.

◆ needs_fiber_stretch()

bool ActiveStress::needs_fiber_stretch ( ) const

inline

Whether this model uses the fiber stretch passed to advance_time_step. This flag can be used to determine whether fiber stretch computation can be skipped for efficiency.

◆ needs_fiber_stretch_rate()

bool ActiveStress::needs_fiber_stretch_rate ( ) const

inline

Whether this model uses the fiber stretch rate passed to advance_time_step. This flag can be used to determine whether fiber stretch rate computation can be skipped for efficiency.

◆ read_model_specific_parameters()

virtual void ActiveStress::read_model_specific_parameters ( const ActiveStressModelParameters & params )

protectedpure virtual

Read model parameters from a parameter object.

This method needs to be overridden by derived classes to read the parameters specific to the concrete model they implement.

Implemented in ActiveStressNashPanfilov, ActiveStressODE, ActiveStressRegazzoni, ActiveStressUniformSteady, and ActiveStressUniformUnsteady.

◆ read_parameters()

void ActiveStress::read_parameters ( const ActiveStressParameters & params )

Read model parameters from a parameter object.

Member Data Documentation

◆ active_tension

Vector<double> ActiveStress::active_tension

protected

Active tension at every node.

◆ eta_f

double ActiveStress::eta_f

protected

Active tension coefficient along the fiber direction.

◆ eta_n

double ActiveStress::eta_n

protected

Active tension coefficient along the sheet-normal direction.

◆ eta_s

double ActiveStress::eta_s

protected

Active tension coefficient along the sheet direction.

◆ n_states

const unsigned int ActiveStress::n_states

Number of state variables for this model.

◆ needs_fiber_stretch_

bool ActiveStress::needs_fiber_stretch_

protected

Backing store for needs_fiber_stretch.

◆ needs_fiber_stretch_rate_

bool ActiveStress::needs_fiber_stretch_rate_

protected

Backing store for needs_fiber_stretch_rate.

◆ states

Array<double> ActiveStress::states

protected

State variables for the model.

◆ time

double ActiveStress::time

protected

Current time. Updated whenever calling advance_time_step.

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

solver/ActiveStress.h
solver/ActiveStress.cpp

Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Detailed Description

Directional distribution of active stress

Implementing concrete active stress models

Constructor & Destructor Documentation

◆ ActiveStress()

◆ ~ActiveStress()

Member Function Documentation

◆ advance_time_step()

◆ advance_time_step_local()

◆ compute_active_tension_local()

◆ distribute_model_specific_parameters()

◆ distribute_parameters()

◆ get_parameters()

◆ get_tension_fibers()

◆ get_tension_sheet_normals()

◆ get_tension_sheets()

◆ init()

◆ init_local()

◆ needs_fiber_stretch()

◆ needs_fiber_stretch_rate()

◆ read_model_specific_parameters()

◆ read_parameters()

Member Data Documentation

◆ active_tension

◆ eta_f

◆ eta_n

◆ eta_s

◆ n_states

◆ needs_fiber_stretch_

◆ needs_fiber_stretch_rate_

◆ states

◆ time