#include <electrics_eikonal.h>

Collaboration diagram for opencarp::eikonal_solver:

Classes
struct	diffusion_current

Public Types
enum	Idiff_t { FOOT = 0 , GAUSS = 1 }

Public Member Functions
	eikonal_solver ()

	~eikonal_solver ()

void	init ()
	Initialize vectors and variables in the eikonal_solver class. More...

bool	determine_model_to_run (double &time)
	Determine the next model to run in the alternation between RD and Eikonal. More...

void	set_stimuli (SF::vector< stimulus > &stimuli)
	Simple setter for stimulus vector. More...

void	clean_list ()
	Clean the list of nodes by resetting their status and tracking changes based on the time step of the RD model. More...

void	save_eikonal_state (const char *tsav_ext)
	Save the current state of variables related to the Eikonal simulation to a file to initialize a future simulation. More...

void	update_repolarization_times (const Ionics &ion)
	Estimates initial repolarization times (T_R) in Step D of DREAM. More...

void	cycFIM ()
	Implementation of the cyclical fast iterative method used in step A of the DREAM model. More...

void	FIM ()
	Standard fast iterative method to solve eikonal equation with active list approach. More...

void	update_repolarization_times_from_rd (sf_vec &Vmv, sf_vec &Vmv_old, double time)
	Updates node repolarization times based on transmembrane voltage crossing. More...

void	compute_diffusion_current (const double &time, sf_vec &vm)
	Computes the stimulus-driven diffusion current at mesh nodes. More...

void	init_imp_region_properties ()
	Initializes diffusion current models and CV restitution parameters per mesh node. More...

Public Attributes
const double	inf = std::numeric_limits<double>::infinity()

node_stats	nodeData

Idiff_t	Idiff_tech = FOOT

SF::vector< diffusion_current >	diff_cur

SF::vector< SF_real >	T_A

SF::vector< SF_real >	T_R

SF::vector< SF_real >	TA_old

SF::vector< SF_real >	D_I

SF::vector< mesh_int_t >	List

SF::vector< mesh_int_t >	num_changes

SF::vector< mesh_int_t >	nReadded2List

SF::vector< mesh_int_t >	stim_status

SF::vector< mesh_int_t >	StimulusPoints

SF::vector< SF_real >	StimulusTimes

mesh_int_t	Index_currStim

SF_real	actMIN = 0

SF_real	actMAX = 0

mesh_int_t	MESH_SIZE

bool	twoFib

size_t	num_pts

SF::vector< mesh_int_t >	e2n_con

SF::vector< mesh_int_t >	elem_start

std::vector< mesh_int_t >	n2n_connect

std::vector< mesh_int_t >	n2n_dsp

SF::vector< mesh_int_t >	e2n_cnt

SF::vector< mesh_int_t >	n2e_cnt

SF::vector< mesh_int_t >	n2e_con

SF::vector< mesh_int_t >	n2e_dsp

std::vector< SF::dmat< double > >	S

std::vector< double >	CV_L

SF::vector< SF_real >	rho_cvrest

SF::vector< SF_real >	kappa_cvrest

SF::vector< SF_real >	theta_cvrest

SF::vector< SF_real >	denom_cvrest

sf_vec *	Idiff = nullptr

sf_vec *	AT = nullptr

sf_vec *	RT = nullptr

eikonal_solver_stats	stats

Detailed Description

Definition at line 67 of file electrics_eikonal.h.

Member Enumeration Documentation

◆ Idiff_t

enum opencarp::eikonal_solver::Idiff_t

Enumerator
FOOT
GAUSS

Definition at line 78 of file electrics_eikonal.h.

Constructor & Destructor Documentation

◆ eikonal_solver()

opencarp::eikonal_solver::eikonal_solver ( )

inline

Definition at line 70 of file electrics_eikonal.h.

◆ ~eikonal_solver()

opencarp::eikonal_solver::~eikonal_solver ( )

inline

Definition at line 131 of file electrics_eikonal.h.

Member Function Documentation

◆ clean_list()

void opencarp::eikonal_solver::clean_list ( )

Clean the list of nodes by resetting their status and tracking changes based on the time step of the RD model.

This function iterates through a list of nodes and checks if their activation time (T_A[j]) is less than the current time managed by user_globals::tm_manager->time. If so, it performs the following operations:

Updates the old activation time (TA_old[j]) with the current activation time (T_A[j]).
Resets the status of the node to 0.
Resets the change counter of number of times the node reenter the list (num_changes2[j]) to 0.
If the node is marked as active in the list (List[j] == 1), it marks it as inactive (List[j] = 0).

Note: The function depends on the existence of the global variables List, T_A, TA_old, Status, and num_changes2. user_globals::tm_manager->time for the current time threshold. It makes sure that activation times behind the time step of the RD model are not considered.

Definition at line 1395 of file electrics_eikonal.cc.

◆ compute_diffusion_current()

void opencarp::eikonal_solver::compute_diffusion_current	(	const double &	time,
		sf_vec &	vm
	)

Computes the stimulus-driven diffusion current at mesh nodes.

This function evaluates the time-dependent diffusion (stimulus) current for algebraic nodes in the mesh, based on the activation times and node-specific diffusion current models. The result is stored in Idiff for later use in the parabolic solver.

Parameters

time	Current simulation time.
vm	Vector of nodal transmembrane voltages, used to evaluate voltage-dependent stimulus models.

Iterates over all algebraic nodes in the mesh.
For each node:
- Only proceeds if the node is within its stimulus-active window:
  $TA \leq time \leq TA + 5$
  and List[node] == 0.
- Computes time since activation:
  $dT = time - TA.$
- Selects the node-specific diffusion current model:
  - GAUSS: Three Gaussian pulses with parameters $\alpha_i, \beta_i, \gamma_i$ , producing:
    $I = \sum_{i=1}^3 \alpha_i \exp\!\Big(-\Big(\frac{dT - \beta_i}{\gamma_i}\Big)^2\Big).$
  - Default: Exponential form with on/off gating (foot current):
    $I = \frac{A_F}{\tau_F} \exp(dT / \tau_F) \cdot e_{\text{on}} \cdot e_{\text{off}},$
    where:
    - $e_{\text{on}} = 1$ if dT ≥ 0 else 0,
    - $e_{\text{off}} = 1$ if vm < V_th else 0.
The computed current is written to Idiff at the PETSc local index corresponding to the node.

Notes

Execution time is accumulated in stats.slvtime_B.

See also: diff_cur, Idiff, T_A

Definition at line 1499 of file electrics_eikonal.cc.

◆ cycFIM()

void opencarp::eikonal_solver::cycFIM ( )

Implementation of the cyclical fast iterative method used in step A of the DREAM model.

Definition at line 968 of file electrics_eikonal.cc.

◆ determine_model_to_run()

bool opencarp::eikonal_solver::determine_model_to_run ( double & time )

Determine the next model to run in the alternation between RD and Eikonal.

This function decides which model to run next based on the DREAM condition. If the output value is true, it will run the RD model; if false, it will run the Eikonal model.

Parameters

time	The current time step in the RD model used to evaluate the conditions.

Returns: A boolean indicating whether to run the RD model (true) or the Eikonal model (false).

Definition at line 1364 of file electrics_eikonal.cc.

◆ FIM()

void opencarp::eikonal_solver::FIM ( )

Standard fast iterative method to solve eikonal equation with active list approach.

Definition at line 866 of file electrics_eikonal.cc.

◆ init()

void opencarp::eikonal_solver::init ( )

Initialize vectors and variables in the eikonal_solver class.

Definition at line 547 of file electrics_eikonal.cc.

◆ init_imp_region_properties()

void opencarp::eikonal_solver::init_imp_region_properties ( )

Initializes diffusion current models and CV restitution parameters per mesh node.

This function prepares per-node properties required for computing stimulus-driven diffusion currents and conduction velocity restitution effects, based on region-specific parameters defined in param_globals::imp_region.

Allocates and resizes per-node storage arrays:
- diff_cur : diffusion current model parameters
- rho_cvrest, kappa_cvrest, theta_cvrest, denom_cvrest : restitution parameters
Builds a mapping from local nodes to imp regions:
- If only one imp region exists, all nodes are assigned to region 0.
- Otherwise, calls region_mask() to resolve region IDs from tags.
For each node (in parallel):
- Reads region-specific stimulus current model:
  - GAUSS model: initializes three Gaussian terms ( $\alpha_i, \beta_i, \gamma_i$ ).
  - Default model: initializes exponential stimulus parameters ( $A_F, \tau_F, V_{th}$ ).
- Reads CV restitution parameters:
  - $\rho, \kappa, \theta$
  - Precomputes $\text{denom} = \log(\rho) / \psi$
Logs a warning if an imp region has incomplete subregion IDs.
Prints timing information if output_level is enabled.

Note: Each vertex is initialized exactly once in parallel.

See also: compute_diffusion_current, diff_cur, rho_cvrest, kappa_cvrest, theta_cvrest, denom_cvrest

Definition at line 613 of file electrics_eikonal.cc.

◆ save_eikonal_state()

void opencarp::eikonal_solver::save_eikonal_state ( const char * tsav_ext )

Save the current state of variables related to the Eikonal simulation to a file to initialize a future simulation.

This function saves the current state of variables, including activation times (T_A), repolazitaion times (T_R), old activation times (TA_old), and other required variables

The data is saved in a structured format where each line corresponds to a node: The file is named based on the param_globals::write_statef and tsav_ext parameters.

Parameters

tsav_ext Extension to append to the file name.

Definition at line 1545 of file electrics_eikonal.cc.

◆ set_stimuli()

void opencarp::eikonal_solver::set_stimuli ( SF::vector< stimulus > & stimuli )

inline

Simple setter for stimulus vector.

Definition at line 153 of file electrics_eikonal.h.

◆ update_repolarization_times()

void opencarp::eikonal_solver::update_repolarization_times ( const Ionics & ion )

Estimates initial repolarization times (T_R) in Step D of DREAM.

This function performs a short run of the ionic model (not a full RD simulation) to update T_R. It only iterates over nodes that do not have an up to date value of T_R. When detected, the current simulation time is stored in T_R[ind_nodes]. The function resets state variables to their pre-call values.

Parameters

ion	The Ionics object containing information about the ionic model.

Definition at line 1433 of file electrics_eikonal.cc.

◆ update_repolarization_times_from_rd()

void opencarp::eikonal_solver::update_repolarization_times_from_rd	(	sf_vec &	Vmv,
		sf_vec &	Vmv_old,
		double	time
	)

Updates node repolarization times based on transmembrane voltage crossing.

This function scans all mesh nodes and records the time at which each node’s transmembrane potential falls below a given threshold, marking the end of its action potential (repolarization). Uses Vm from the parabolic solver.

Parameters

Vmv	Vector of current transmembrane voltages at all nodes.
Vmv_old	Vector of transmembrane voltages from the previous timestep.
time	Current simulation time, recorded as the repolarization time for nodes that cross the threshold during this step.

The threshold value is taken from param_globals::dream.repol_time_thresh.
For each node ind_nodes:
- If Vmv_old[ind_nodes] ≥ threshold and Vmv[ind_nodes] < threshold, the repolarization time T_R[ind_nodes] is set to time.
Memory pointers to Vmv and Vmv_old are explicitly managed via ptr() and release_ptr().

See also: T_R

Definition at line 1416 of file electrics_eikonal.cc.

Member Data Documentation

◆ actMAX

SF_real opencarp::eikonal_solver::actMAX = 0

Definition at line 105 of file electrics_eikonal.h.

◆ actMIN

SF_real opencarp::eikonal_solver::actMIN = 0

Definition at line 105 of file electrics_eikonal.h.

◆ AT

sf_vec* opencarp::eikonal_solver::AT = nullptr

Definition at line 125 of file electrics_eikonal.h.

◆ CV_L

std::vector<double> opencarp::eikonal_solver::CV_L

Definition at line 118 of file electrics_eikonal.h.

◆ D_I

SF::vector<SF_real> opencarp::eikonal_solver::D_I

Definition at line 100 of file electrics_eikonal.h.

◆ denom_cvrest

SF::vector<SF_real> opencarp::eikonal_solver::denom_cvrest

Definition at line 121 of file electrics_eikonal.h.

◆ diff_cur

SF::vector<diffusion_current> opencarp::eikonal_solver::diff_cur

Definition at line 99 of file electrics_eikonal.h.

◆ e2n_cnt

SF::vector<mesh_int_t> opencarp::eikonal_solver::e2n_cnt

Definition at line 114 of file electrics_eikonal.h.

◆ e2n_con

SF::vector<mesh_int_t> opencarp::eikonal_solver::e2n_con

Definition at line 111 of file electrics_eikonal.h.

◆ elem_start

SF::vector<mesh_int_t> opencarp::eikonal_solver::elem_start

Definition at line 112 of file electrics_eikonal.h.

◆ Idiff

sf_vec* opencarp::eikonal_solver::Idiff = nullptr

Definition at line 124 of file electrics_eikonal.h.

◆ Idiff_tech

Idiff_t opencarp::eikonal_solver::Idiff_tech = FOOT

Definition at line 80 of file electrics_eikonal.h.

◆ Index_currStim

mesh_int_t opencarp::eikonal_solver::Index_currStim

Definition at line 104 of file electrics_eikonal.h.

◆ inf

const double opencarp::eikonal_solver::inf = std::numeric_limits<double>::infinity()

Definition at line 72 of file electrics_eikonal.h.

◆ kappa_cvrest

SF::vector<SF_real> opencarp::eikonal_solver::kappa_cvrest

Definition at line 121 of file electrics_eikonal.h.

◆ List

SF::vector<mesh_int_t> opencarp::eikonal_solver::List

Definition at line 101 of file electrics_eikonal.h.

◆ MESH_SIZE

mesh_int_t opencarp::eikonal_solver::MESH_SIZE

Definition at line 108 of file electrics_eikonal.h.

◆ n2e_cnt

SF::vector<mesh_int_t> opencarp::eikonal_solver::n2e_cnt

Definition at line 114 of file electrics_eikonal.h.

◆ n2e_con

SF::vector<mesh_int_t> opencarp::eikonal_solver::n2e_con

Definition at line 114 of file electrics_eikonal.h.

◆ n2e_dsp

SF::vector<mesh_int_t> opencarp::eikonal_solver::n2e_dsp

Definition at line 114 of file electrics_eikonal.h.

◆ n2n_connect

std::vector<mesh_int_t> opencarp::eikonal_solver::n2n_connect

Definition at line 113 of file electrics_eikonal.h.

◆ n2n_dsp

std::vector<mesh_int_t> opencarp::eikonal_solver::n2n_dsp

Definition at line 113 of file electrics_eikonal.h.

◆ nodeData

node_stats opencarp::eikonal_solver::nodeData

Definition at line 75 of file electrics_eikonal.h.

◆ nReadded2List

SF::vector<mesh_int_t> opencarp::eikonal_solver::nReadded2List

Definition at line 101 of file electrics_eikonal.h.

◆ num_changes

SF::vector<mesh_int_t> opencarp::eikonal_solver::num_changes

Definition at line 101 of file electrics_eikonal.h.

◆ num_pts

size_t opencarp::eikonal_solver::num_pts

Definition at line 110 of file electrics_eikonal.h.

◆ rho_cvrest

SF::vector<SF_real> opencarp::eikonal_solver::rho_cvrest

Definition at line 121 of file electrics_eikonal.h.

◆ RT

sf_vec* opencarp::eikonal_solver::RT = nullptr

Definition at line 126 of file electrics_eikonal.h.

◆ S

std::vector<SF::dmat<double> > opencarp::eikonal_solver::S

Definition at line 117 of file electrics_eikonal.h.

◆ stats

eikonal_solver_stats opencarp::eikonal_solver::stats

Definition at line 129 of file electrics_eikonal.h.

◆ stim_status

SF::vector<mesh_int_t> opencarp::eikonal_solver::stim_status

Definition at line 101 of file electrics_eikonal.h.

◆ StimulusPoints

SF::vector<mesh_int_t> opencarp::eikonal_solver::StimulusPoints

Definition at line 102 of file electrics_eikonal.h.

◆ StimulusTimes

SF::vector<SF_real> opencarp::eikonal_solver::StimulusTimes

Definition at line 103 of file electrics_eikonal.h.

◆ T_A

SF::vector<SF_real> opencarp::eikonal_solver::T_A

Definition at line 100 of file electrics_eikonal.h.

◆ T_R

SF::vector<SF_real> opencarp::eikonal_solver::T_R

Definition at line 100 of file electrics_eikonal.h.

◆ TA_old

SF::vector<SF_real> opencarp::eikonal_solver::TA_old

Definition at line 100 of file electrics_eikonal.h.

◆ theta_cvrest

SF::vector<SF_real> opencarp::eikonal_solver::theta_cvrest

Definition at line 121 of file electrics_eikonal.h.

◆ twoFib

bool opencarp::eikonal_solver::twoFib

Definition at line 109 of file electrics_eikonal.h.

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

physics/electrics_eikonal.h
physics/electrics_eikonal.cc

Classes

Public Types

Public Member Functions

Public Attributes

Detailed Description

Member Enumeration Documentation

◆ Idiff_t

Constructor & Destructor Documentation

◆ eikonal_solver()

◆ ~eikonal_solver()

Member Function Documentation

◆ clean_list()

◆ compute_diffusion_current()

Notes

◆ cycFIM()

◆ determine_model_to_run()

◆ FIM()

◆ init()

◆ init_imp_region_properties()

◆ save_eikonal_state()

◆ set_stimuli()

◆ update_repolarization_times()

◆ update_repolarization_times_from_rd()

Member Data Documentation

◆ actMAX

◆ actMIN

◆ AT

◆ CV_L

◆ D_I

◆ denom_cvrest

◆ diff_cur

◆ e2n_cnt

◆ e2n_con

◆ elem_start

◆ Idiff

◆ Idiff_tech

◆ Index_currStim

◆ inf

◆ kappa_cvrest

◆ List

◆ MESH_SIZE

◆ n2e_cnt

◆ n2e_con

◆ n2e_dsp

◆ n2n_connect

◆ n2n_dsp

◆ nodeData

◆ nReadded2List

◆ num_changes

◆ num_pts

◆ rho_cvrest

◆ RT

◆ S

◆ stats

◆ stim_status

◆ StimulusPoints

◆ StimulusTimes

◆ T_A

◆ T_R

◆ TA_old

◆ theta_cvrest

◆ twoFib