Classes
union	_event_class

union	_stretch

struct	action_potential

struct	ap_event

struct	ap_events

struct	auxotonicStretch

struct	cell_geom

struct	Clamp

struct	d_OdeVec

struct	event_mx_rate

struct	event_mx_val

struct	event_timing

struct	event_x_threshold

struct	GVEC_DUMP

struct	IMPinfo

struct	IOCtrl

class	IonIf
	Child class of IonIfBase specialized for each ionic model type. More...

class	IonIfBase
	Represents the ionic model and plug-in (IMP) data structure. More...

class	IonType
	Abstract class representing an ionic model type. More...

struct	isoSarcoStretch

struct	isoStretch

class	LimpetData

struct	LUT
	lookup table structure More...

class	MULTI_IF

struct	pulseStretch

struct	restitute_dynamic

struct	restitute_S1S2

struct	restitution

struct	steady_state_ap

struct	SV_DUMP
	data structure to manage state variable file dumps More...

struct	SV_TAB
	array of stat variable structures More...

struct	TargetAllocator
	Allocator structure for dynamically allocating memory on multiple targets. More...

struct	tc_grp
	time constant groups More...

struct	trace
	manage input, output, resampling of traces More...

struct	Trace_Info
	data structure to manage trace dumps. Should eventually be combined with the state variable dumps, but I'm keeping it separate for now for my own sanity. More...

struct	TrgList

struct	ts
	time stepper More...

Typedefs
typedef enum limpet::_act_events	act_events

typedef enum limpet::_repol_events	repol_events

typedef enum limpet::_ampl_events	ampl_events

typedef enum limpet::_event_meth	event_meth

typedef union limpet::_event_class	event_class

typedef enum limpet::_ap_states	ap_states

typedef float	Gatetype

typedef GlobalData_t(*	SVgetfcn) (IonIfBase &, int, int)

typedef void(*	SVputfcn) (IonIfBase &, int, int, GlobalData_t)

typedef char	IIF_Mask_t

using	IonTypeList = std::vector< std::reference_wrapper< IonType > >

typedef SF_real	GlobalData_t

typedef double	LUT_data_t

typedef double	Real

typedef enum limpet::_r_protocol	r_prtcl

typedef enum limpet::_stretch_protocol	s_prtcl

typedef union limpet::_stretch	stretch

typedef enum limpet::ip_method	IpMeth_t

Enumerations
enum	_act_events { xAPD90, VmDotMx, nActEvents }

enum	_repol_events { APD90, APD30, nRepolEvents }

enum	_ampl_events { VmMX, VmMN, nAmplEvents }

enum	_event_meth { X_THRESHOLD, MX_RATE, MX_VAL }

enum	_ap_states { AP_STATE, DI_STATE }

enum	TimerIDs { CON_TM_IDX, SVD_TM_IDX, STA_TM_IDX, SSV_TM_IDX, STM_TM_IDX, LIGHT_TM_IDX, TRACE_TM_IDX, CLAMP_TM_IDX, DOPPLE_TM_IDX, RES_SAVE_TM_IDX, N_TIMERS }

enum	timingIDs { SETUP_IDX, INIT_IDX, LOOP_IDX, ODE_IDX, N_TIMINGS }

enum	DataType { dtype_Gatetype, dtype_Real, dtype_Float, dtype_Char, dtype_Integer, dtype_Double, dtype_Short, dtype_GlobalData_t, dtype_long, dtype_bool }
	data type IDs More...

enum	_r_protocol { S1S2, DYNAMIC, S1S2_fast }

enum	_stretch_protocol { STRAIN_PULSE, ISOMETRIC, ISOSARCOMETRIC, AUXOTONIC }

enum	Target { AUTO = -2, UNKNOWN = -1, CPU, MLIR_CPU, MLIR_ROCM, MLIR_CUDA, N_TARGETS }
	enum that represents different targets to run ionic models on. More...

enum	ip_method { _LINEAR_IP, _NEAREST_IP }

Functions
void	shift_vm_trace (double vm, action_potential AP, timer_manager tm)

bool	check_threshold (ap_event e, timer_manager tm)

bool	check_mx_rate (ap_event e, timer_manager tm)

bool	check_mx_val (ap_event e, timer_manager tm)

bool	update_steady_state (action_potential *AP)

void	print_AP_stats (action_potential *AP)

int	initialize_AP_analysis (action_potential *AP)

void	cleanup_AP_analysis (action_potential *AP)

void	calibrate_thresholds (action_potential *AP)

bool	check_events (double vm, action_potential AP, timer_manager tm)

bool	check_steady_state (steady_state_ap *ss)

void	print_AP_stats_header (action_potential AP, FILE outbuf)

bool	check_events (double vm, action_potential AP, opencarp::timer_manager tm)

void	determine_stim_list (char stl, TrgList trg, bool DIAs)

int	write_dump_header (GVEC_DUMP gvd, SV_DUMP svd, const char *ExpID)

void	open_globalvec_dump (FILE *fhdls, GVEC_DUMP gvd, MULTI_IF pMIIF, char base_name, IOCtrl *io)

void	globalvec_dump (FILE *fhdls, GVEC_DUMP gvd, MULTI_IF pMIIF, timer_manager tmo, IOCtrl *io, int numNode)

void	close_globalvec_dump (FILE *fhdls, GVEC_DUMP gvd, IOCtrl *io)

void	dump_all (MULTI_IF MIIF, int reg, char imp, char plugs, double t, double ddt, char fout)

void	initialize_timings (event_timing *t)

void	update_timing (event_timing *t, double event_duration)

double	getCellVal (sf_vec *v, int ind)

void	initial_SVs (MULTI_IF miif, char SVs, char imp, char plgins, int num)

void	print_param_help (IonType *im, IonTypeList &plugs)

float	determine_duration (struct gengetopt_args_info p, TrgList stim_lst)
	determine time of last stimulus More...

void	globalvec_dump (FILE *fhdls, GVEC_DUMP gvd, MULTI_IF pMIIF, opencarp::timer_manager tm, IOCtrl *io, int numNode)

double	getCellVal (opencarp::sf_vec *v, int ind)

bool	initialize_clamp (Clamp cl, double cl_val, double ini_val, double start, double dur, const char f, int trans, float *duration)

void	clamp_signal (MULTI_IF pMIIF, Clamp cl, timer_manager *tm)

void	initialize_sv_clamp (Clamp cl, const char sv, char *file, double dt)

void	sv_clamp (Clamp cl, timer_manager tm, MULTI_IF *miif, bool trigger)

void	AP_clamp (Clamp cl, timer_manager tm, sf_vec *v, bool trigger)

int	process_sv_clamps (char SVs, char files, Clamp **clamps, double dt)

void	clamp_signal (MULTI_IF pMIIF, Clamp cl, opencarp::timer_manager *tm)

void	sv_clamp (Clamp cl, opencarp::timer_manager tm, MULTI_IF *, bool trigger)

void	initialize_AP_clamp (Clamp cl, char f, double)

void	AP_clamp (Clamp cl, opencarp::timer_manager tm, opencarp::sf_vec *v, bool trigger)

char *	tokstr_r (char s1, const char s2, char **lasts)

void	initialize_ts (Target target, ts tstp, int ng, int skp, double dt)

void	update_ts (ts *ptstp)

void *	memmem (void haystack, int sz_hay, void needle, int sz_n)

char *	get_next_list (char *lst, char delimiter)

bool	verify_flags (const char flags, const char given)

bool	flag_set (const char flags, const char target)

void	initialize_ts (ts tstp, int ng, int skp, double dt)

void	SV_alloc (SV_TAB *psv, int numSeg, int struct_size)

void	SV_free (SV_TAB *psv)

void	free_sv_table (void *)

void	print_IMPs (void)

void	print_models (bool)

float	modify_param (float a, char *expr)

int	process_param_mod (char pstr, char par, char *mod)

char *	get_typename (int type)

int	load_ionic_module (const char *)

SVputfcn	getPutSV (SVgetfcn)

template<class T >
constexpr T	max (T a, T b)

template<class T >
constexpr T	min (T a, T b)

IonType *	get_ion_type (const std::string &name)

void	LUT_alloc (LUT plut, int cols, float mn, float mx, float res, const char name, Target target)

int	LUT_dump (LUT plut, const char fname)

void	destroy_lut (LUT *plut, Target target)

int	check_LUT (LUT *lut)

void	IIF_warn (const int wv, const char error[])

void	LUT_problem (LUT lt, double val, int wv, const char tabname)

int	LUT_index (LUT *tab, GlobalData_t val, int locind)

int	LUT_out_of_bounds (LUT *tab, GlobalData_t val)

LUT_data_t	LUT_interp (LUT *t, int i, int j, GlobalData_t x)

LUT_data_t	LUT_derror (LUT *t, int idx, GlobalData_t x)

LUT_data_t	LUT_interpRow (LUT const tab, GlobalData_t val, int i, LUT_data_t row)

LUT_data_t *	LUT_row (LUT *lut, GlobalData_t val, int locind)

void	LUT_interpRow_n_elements (char table, char val_ptr, int offset, int distance, int index, int n, char *row_ptr, int lut_numelements)

void	IIF_warn (const int wv, const char *error)

template<typename T >
T **	build_matrix_ns (int m, int n, int size, Target target)

void	LUT_interpRow_mlir (char table, int i, char row_ptr, int lut_num_elements, int vector_size)

void	LUT_problem_mlir (char *tab, GlobalData_t val, int locind)

void	initialize_params_MIIF (MULTI_IF *pMIIF)

void	initialize_ionic_IF (MULTI_IF *pMIIF)

void	CreateIIFLocalNodeLsts (MULTI_IF *pMIIF)

void	CreateIIFNodeLsts_ (int, char , int , int **, int)

void	alloc_MIIF (MULTI_IF *pMIIF)

void	initializeIMPData (MULTI_IF *pMIIF)

void	freeIMPData (MULTI_IF *pMIIF)

void	allocate_shared_data (MULTI_IF *)

int	getGlobalNodalIndex (IonIfBase &pIF, int relIdx)

void	CreateIIFGlobalNodeLsts (MULTI_IF *pMIIF)

bool	isIMPdata (const char *)

int	current_global_node (int local_node)

float	current_global_time ()

int	should_print_bounds_exceeded_messages ()

int	set_print_bounds_exceeded_messages (int newval)

int	int_cmp (const void a, const void b)

void	open_trace (MULTI_IF MIIF, int n_traceNodes, int traceNodes, int label, opencarp::sf_mesh imesh)
	Set up ionic model traces at some global node numbers. More...

void	dump_trace (MULTI_IF *MIIF, limpet::Real time)

void	close_trace (MULTI_IF *MIIF)

char *	get_sv (void *tab, int offset, int n, int svSize, int size, int dlo_vector_size)

int	get_plug_flag (char plgstr, int out_num_plugins, IonTypeList &out_plugins)

int	determine_write_ranges (int N, size_t offset, size_t bufsize, int *ranges)

void	free_doppel (MULTI_IF *m)

void	doppel_update (MULTI_IF orig, MULTI_IF miif_doppel)

void	doppel_MIIF (MULTI_IF orig, MULTI_IF miif_doppel)

int	IMPdataLabel2Index (const char *sv)

void	dup_IMP_node_state (IonIfBase &IF, int from, int to, GlobalData_t **localdata)

void *	get_IIF_plugparam (IonIfBase &, int)

void	ODEint_RK (GlobalData_t y, GlobalData_t ydot, void f(GlobalData_t , GlobalData_t , void ), void f_data, int len, GlobalData_t dt)

void	ODEint_FE (GlobalData_t y, GlobalData_t ydot, void f, void f_data, int len, GlobalData_t dt)

void	d_ODEint_RK (d_OdeVec y, d_OdeVec ydot, void f(GlobalData_t , d_OdeVec , void ), void f_data, GlobalData_t dt)

void	d_ODEint_FE (d_OdeVec y, d_OdeVec ydot, void f, void f_data, GlobalData_t dt)

void	get_protocol_definition (char r_file, restitution r, bool useS1S2)

int	read_restitution_protocol_def (char r_file, restitution r)

void	restitution_trigger_list (char r_file, restitution r, char protocol, int n_dop, double **t_dop)

void	restitution_save_sv (MULTI_IF miif, int R1, restitution r, action_potential *AP)

void	rbCalcKi (float K, float , float X, int ludI, void(calcDX)(float , float , void ), void *params, float h, int N, int i)

void	rbSolver (float *, float , float *, int N)

void	fludcmp0 (float *, int n, int indx, float *)

void	flubksb0 (float *, int n, int indx, float *)

void	fludcmp (float *, int, int , float *)

void	flubksb (float *, int, int , float *)

void	rbStepX (float X, void(calcDX)(float , float , void ), void(calcJ)(float *, float , void , int), void params, float h, int N)

void	apply_stretch_pulse (MULTI_IF miif, pulseStretch s, timer_manager *tm)

void	initializePulseStretch (float strain, float onset, float duration, float rise, float fall, stretch *s)

void	apply_stretch (MULTI_IF miif, stretch s, timer_manager *tm)

void	apply_stretch (MULTI_IF miif, stretch s, opencarp::timer_manager *tm)

int	read_sv (MULTI_IF , int, const char )

void	save_sv (MULTI_IF , int, const char )

void	open_trace (MULTI_IF , int, int , int *)

void	set_start_time (const float)

Target	get_target_from_string (std::string const str)
	Returns a value from the Target enum from a given string. More...

std::string	get_string_from_target (Target const target)
	Get a string representation of a given target. More...

std::string	get_target_list_string ()
	Returns a string containing the list of available targets. More...

bool	is_gpu (Target const target)
	Checks if this is a GPU target. More...

bool	is_concrete (Target const target)
	Checks if `target` is a real, concrete target. More...

template<typename T >
T *	allocate_on_target (Target target, std::size_t n, bool always_managed=false, bool do_zero=true)
	Utility function for allocating memory on a target. See TargetAllocator. More...

template<typename T >
void	deallocate_on_target (Target target, T *ptr)
	Utility function for deallocating memory on a target. See TargetAllocator. More...

bool	IsEquDistSampling (trace *tr)

int	read_trace (trace tr, const char name)

void	free_trace (trace *tr)

void	resample_trace (trace *tr, double dt)

double	trace_duration (trace tr, const char f)

void	interp1 (const double x, const float y, int N, double xi, float yi, int NI, double dxi, IpMeth_t meth)

Variables
FILE_SPEC	_nc_logf = NULL

int *	curr_node_list
	needed to determine the global node number More...

Detailed Description

Note: All numerical IDs and flags are automatically generated

Units for all IMPS must be

vm - mV (transmembrane potential) [Ca]_i - micromolar (intracellular calcium) [Ca]_b - micromolar (troponin bound calcium) t - ms (time) Lambda - normalized (stretch ratio) delLambda - 1/ms (stretch rate) Tension - kPa (active stress) [Na]_e - millimolar (extracellular sodium) [K]_e - millimolar (extracellular potassium) [Ca]_e - micromolar (extracellular calcium) Iion - uA/cm^2 (ionic current)

Typedef Documentation

◆ act_events

typedef enum limpet::_act_events limpet::act_events

◆ ampl_events

typedef enum limpet::_ampl_events limpet::ampl_events

◆ ap_states

typedef enum limpet::_ap_states limpet::ap_states

◆ event_class

typedef union limpet::_event_class limpet::event_class

◆ event_meth

typedef enum limpet::_event_meth limpet::event_meth

◆ Gatetype

typedef float limpet::Gatetype

Definition at line 45 of file ion_type.h.

◆ GlobalData_t

typedef SF_real limpet::GlobalData_t

Definition at line 27 of file limpet_types.h.

◆ IIF_Mask_t

typedef char limpet::IIF_Mask_t

Definition at line 50 of file ion_type.h.

◆ IonTypeList

using limpet::IonTypeList = typedef std::vector<std::reference_wrapper<IonType> >

Definition at line 288 of file ion_type.h.

◆ IpMeth_t

typedef enum limpet::ip_method limpet::IpMeth_t

◆ LUT_data_t

typedef double limpet::LUT_data_t

Definition at line 34 of file LUT.h.

◆ r_prtcl

typedef enum limpet::_r_protocol limpet::r_prtcl

◆ Real

typedef double limpet::Real

Definition at line 151 of file MULTI_ION_IF.h.

◆ repol_events

typedef enum limpet::_repol_events limpet::repol_events

◆ s_prtcl

typedef enum limpet::_stretch_protocol limpet::s_prtcl

◆ stretch

typedef union limpet::_stretch limpet::stretch

◆ SVgetfcn

typedef GlobalData_t(* limpet::SVgetfcn) (IonIfBase &, int, int)

Definition at line 48 of file ion_type.h.

◆ SVputfcn

typedef void(* limpet::SVputfcn) (IonIfBase &, int, int, GlobalData_t)

Definition at line 49 of file ion_type.h.

Enumeration Type Documentation

◆ _act_events

enum limpet::_act_events

Enumerator
xAPD90
VmDotMx
nActEvents

Definition at line 56 of file ap_analyzer.cc.

◆ _ampl_events

enum limpet::_ampl_events

Enumerator
VmMX
VmMN
nAmplEvents

Definition at line 58 of file ap_analyzer.cc.

◆ _ap_states

enum limpet::_ap_states

Enumerator
AP_STATE
DI_STATE

Definition at line 85 of file ap_analyzer.h.

◆ _event_meth

enum limpet::_event_meth

Enumerator
X_THRESHOLD
MX_RATE
MX_VAL

Definition at line 35 of file ap_analyzer.h.

◆ _r_protocol

enum limpet::_r_protocol

Enumerator
S1S2
DYNAMIC
S1S2_fast

Definition at line 27 of file restitute.h.

◆ _repol_events

enum limpet::_repol_events

Enumerator
APD90
APD30
nRepolEvents

Definition at line 57 of file ap_analyzer.cc.

◆ _stretch_protocol

enum limpet::_stretch_protocol

Enumerator
STRAIN_PULSE
ISOMETRIC
ISOSARCOMETRIC
AUXOTONIC

Definition at line 27 of file stretch.h.

◆ DataType

enum limpet::DataType

data type IDs

Enumerator
dtype_Gatetype
dtype_Real
dtype_Float
dtype_Char
dtype_Integer
dtype_Double
dtype_Short
dtype_GlobalData_t
dtype_long
dtype_bool

Definition at line 83 of file bench_utils.h.

◆ ip_method

enum limpet::ip_method

Enumerator
_LINEAR_IP
_NEAREST_IP

Definition at line 36 of file trace.h.

◆ Target

enum limpet::Target

enum that represents different targets to run ionic models on.

Enumerator
AUTO
UNKNOWN	special value to handle unknown targets
CPU	baseline CPU model generated with the original opencarp code generator
MLIR_CPU	vectorized CPU code generated with MLIR
MLIR_ROCM	ROCM code for AMD GPUs generated with MLIR.
MLIR_CUDA	CUDA code for NVIDIA GPUs generated with MLIR.
N_TARGETS	a token to indicate the maximum number of targets

Definition at line 45 of file target.h.

◆ TimerIDs

enum limpet::TimerIDs

Enumerator
CON_TM_IDX
SVD_TM_IDX
STA_TM_IDX
SSV_TM_IDX
STM_TM_IDX
LIGHT_TM_IDX
TRACE_TM_IDX
CLAMP_TM_IDX
DOPPLE_TM_IDX
RES_SAVE_TM_IDX
N_TIMERS

Definition at line 27 of file bench_utils.h.

◆ timingIDs

enum limpet::timingIDs

Enumerator
SETUP_IDX	timing for setup phase
INIT_IDX	timing for initialization
LOOP_IDX	timing for main loop (including IO and ODE solve)
ODE_IDX	timing for ODE solve
N_TIMINGS	number of benchmark timings we use

Definition at line 74 of file bench_utils.h.

Function Documentation

◆ alloc_MIIF()

void limpet::alloc_MIIF ( MULTI_IF * pMIIF )

allocate memory for MIIF structure

Parameters

pMIIF MIIF

Postcondition: IMPs are usable

Definition at line 221 of file MULTI_ION_IF.cc.

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◆ allocate_on_target()

template<typename T >

T* limpet::allocate_on_target	(	Target	target,
		std::size_t	n,
		bool	always_managed = `false`,
		bool	do_zero = `true`
	)

Utility function for allocating memory on a target. See TargetAllocator.

Parameters

target	target to allocate on
n	size of the memory to allocate (size of the array of type T)
always_managed	whether to use managed memory for GPU allocations

Definition at line 300 of file target.h.

◆ allocate_shared_data()

void limpet::allocate_shared_data ( MULTI_IF * miif )

allocate the global vectors which are shared amongst IMPs

They may be manually allocated. If the Vm vector is preallocated, all vectors copy its distribution

Parameters

[in] miif Multi ion IF structure

Precondition: Vm is allocated for PETsc runs

Postcondition: all required shared data vectors are allocated

Definition at line 1657 of file MULTI_ION_IF.cc.

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◆ AP_clamp() [1/2]

void limpet::AP_clamp	(	Clamp *	cl,
		opencarp::timer_manager *	tm,
		opencarp::sf_vec *	v,
		bool	trigger
	)

◆ AP_clamp() [2/2]

void limpet::AP_clamp	(	Clamp *	cl,
		timer_manager *	tm,
		sf_vec *	v,
		bool	trigger
	)

apply a Action potential clamp, let it float if outside the trace

Parameters

cl	clamp
tm	timer manager
miif	Vm
trigger	true if current stimulus started

Definition at line 178 of file clamp.cc.

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◆ apply_stretch() [1/2]

void limpet::apply_stretch	(	MULTI_IF *	miif,
		stretch *	s,
		timer_manager *	tm
	)

Definition at line 55 of file stretch.cc.

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◆ apply_stretch() [2/2]

void limpet::apply_stretch	(	MULTI_IF *	miif,
		stretch *	s,
		opencarp::timer_manager *	tm
	)

◆ apply_stretch_pulse()

void limpet::apply_stretch_pulse	(	MULTI_IF *	miif,
		pulseStretch *	s,
		timer_manager *	tm
	)

Definition at line 73 of file stretch.cc.

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◆ build_matrix_ns()

template<typename T >

T** limpet::build_matrix_ns	(	int	m,
		int	n,
		int	size,
		Target	target
	)

build an mXn matrix

Parameters

m	number of rows
n	number of columns
size	size in bytes of each entry

Returns: pointer to an array of pointers to the matrix rows

Definition at line 99 of file LUT.h.

◆ calibrate_thresholds()

void limpet::calibrate_thresholds ( action_potential * AP )

calibrate threshold values based on current AP amplitudes

Parameters

AP	action potential statistics

Postcondition: thresholds for APD90 and APD30 adjusted

Definition at line 227 of file ap_analyzer.cc.

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◆ check_events() [1/2]

bool limpet::check_events	(	double	vm,
		action_potential *	AP,
		opencarp::timer_manager *	tm
	)

◆ check_events() [2/2]

bool limpet::check_events	(	double	vm,
		action_potential *	AP,
		timer_manager *	tm
	)

check whether an event has been detected and update parameters such as APD or DI accordingly

Parameters

vm	current value of AP
AP	action potential statistics
tm	timer manager

Returns: true, if an activation has been triggered, false otherwise

Definition at line 263 of file ap_analyzer.cc.

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◆ check_LUT()

int limpet::check_LUT ( LUT * lut )

Definition at line 129 of file LUT.cc.

◆ check_mx_rate()

bool limpet::check_mx_rate	(	ap_event *	e,
		timer_manager *	tm
	)

check whether a maximum rate of change event has occurred

Parameters

e	event
tm	timer manager

Returns: true, if a maximum rate event has occured, false otherwise

Definition at line 445 of file ap_analyzer.cc.

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◆ check_mx_val()

bool limpet::check_mx_val	(	ap_event *	e,
		timer_manager *	tm
	)

check whether a maximum value event has occurred

Parameters

e	event
tm	timer manager

Returns: true, if a maximum value event has occurred, false otherwise

Definition at line 475 of file ap_analyzer.cc.

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◆ check_steady_state()

bool limpet::check_steady_state ( steady_state_ap * ss )

check whether we are in steady state

Parameters

AP	action potential statistics

Returns: true, if AP is in steady state, false otherwise

Definition at line 398 of file ap_analyzer.cc.

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◆ check_threshold()

bool limpet::check_threshold	(	ap_event *	e,
		timer_manager *	tm
	)

check whether a threshold crossing event has occurred

Parameters

e	event
tm	timer manager

Returns: true, if a threshold has been crossed, false otherwise

Definition at line 415 of file ap_analyzer.cc.

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◆ clamp_signal() [1/2]

void limpet::clamp_signal	(	MULTI_IF *	pMIIF,
		Clamp *	cl,
		opencarp::timer_manager *	tm
	)

◆ clamp_signal() [2/2]

void limpet::clamp_signal	(	MULTI_IF *	pMIIF,
		Clamp *	cl,
		timer_manager *	tm
	)

Definition at line 69 of file clamp.cc.

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◆ cleanup_AP_analysis()

void limpet::cleanup_AP_analysis ( action_potential * AP )

clean up AP analysis, free memory and close files

Parameters

AP	action potential statistics

Postcondition: dynamically allocated data freed, files closed

Definition at line 169 of file ap_analyzer.cc.

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◆ close_globalvec_dump()

void limpet::close_globalvec_dump	(	FILE **	fhdls,
		GVEC_DUMP *	gvd,
		IOCtrl *	io
	)

Definition at line 315 of file bench_utils.cc.

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◆ close_trace()

void limpet::close_trace ( MULTI_IF * MIIF )

Definition at line 452 of file MULTI_ION_IF.cc.

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◆ CreateIIFGlobalNodeLsts()

void limpet::CreateIIFGlobalNodeLsts ( MULTI_IF * pMIIF )

◆ CreateIIFLocalNodeLsts()

void limpet::CreateIIFLocalNodeLsts ( MULTI_IF * pMIIF )

map the node order to the ionic model node order

Definition at line 141 of file MULTI_ION_IF.cc.

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◆ CreateIIFNodeLsts_()

void limpet::CreateIIFNodeLsts_	(	int	N_IIF,
		IIF_Mask_t *	IIF_Mask,
		int **	N_Nodes,
		int ***	NodeLists,
		int	numNode
	)

map the node order to the ionic model node order

Parameters

	N_IIF	Number of IIFs
	IIF_Mask
[out]	N_Nodes	Number of nodes per IIF
[out]	NodeLists	List of node number for each IIF
	low	lower bound of partition
	high	higher bound of partition

Postcondition: N_Nodes and NodeLists allocated and filled in.

Definition at line 157 of file MULTI_ION_IF.cc.

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◆ current_global_node()

int limpet::current_global_node ( int local_node )

Definition at line 118 of file MULTI_ION_IF.cc.

◆ current_global_time()

float limpet::current_global_time ( )

Definition at line 122 of file MULTI_ION_IF.cc.

◆ d_ODEint_FE()

void limpet::d_ODEint_FE	(	d_OdeVec *	y,
		d_OdeVec *	ydot,
		void *	f,
		void *	f_data,
		GlobalData_t	dt
	)

ODEint_FE

Simple forward Euler ODE integrator

Integration of ydot = f(y,t)

y[t+dt] = y[t] + f(y[t])*dt

Parameters

y	value
ydot	value of f(y,t)
f	function f(y,t)
f_data	data needed for function evaluation
dt	time step

Definition at line 134 of file ODEint.cc.

◆ d_ODEint_RK()

void limpet::d_ODEint_RK	(	d_OdeVec *	y,
		d_OdeVec *	ydot,
		void	fGlobalData_t , d_OdeVec , void *,
		void *	f_data,
		GlobalData_t	dt
	)

ODEint_RK

Runge Kutta first order ODE integrator

Integration of ydot = f(y,t)

k1 = dt*f( t, y(t) ) k2 = dt*f( t+0.5*dt, y(t)+0.5*k1 ); y(t+dt) = y(t) + k2 + O(dt^3)

Parameters

y	value
ydot	value of f(y,t)
f	function f(y,t)
f_data	data needed for function evaluation
dt	time step

Definition at line 99 of file ODEint.cc.

◆ deallocate_on_target()

template<typename T >

void limpet::deallocate_on_target	(	Target	target,
		T *	ptr
	)

Utility function for deallocating memory on a target. See TargetAllocator.

Parameters

target	target to deallocate on (this should be the target on which memory was allocated)
ptr	pointer to memory to deallocate

Definition at line 314 of file target.h.

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◆ destroy_lut()

void limpet::destroy_lut	(	LUT *	plut,
		Target	target
	)

destroy LUT

Parameters

plut	pointer to lut

Definition at line 101 of file LUT.cc.

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◆ determine_duration()

float limpet::determine_duration	(	struct gengetopt_args_info *	p,
		TrgList *	stim_lst
	)

determine time of last stimulus

Parameters

p	command line options
stim_lst	stimulus list

Returns: the time of the last stimulus

Definition at line 503 of file bench_utils.cc.

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◆ determine_stim_list()

void limpet::determine_stim_list	(	char *	stl,
		TrgList *	trg,
		bool	DIAs
	)

determine the stimulation times from the list

Parameters

stl	stimulus timing list separated by commas
trg	structure to hold the info
DIAs	interpret times as diastolic intervals?

Postcondition: memory allocated in the trigger for the sorted list of stimulus times

Definition at line 101 of file bench_utils.cc.

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◆ determine_write_ranges()

int limpet::determine_write_ranges	(	int	N,
		size_t *	offset,
		size_t	bufsize,
		int **	ranges
	)

determine which variables are output each write

This troutine assumes there is an output buffer of size bufsize which is continuously filled and then output. Each node has a certain amount of data associated with it, contained in offset. This routine determines how many times the buffer must be filled and output, as well as deermining the range of nodes to be output with each buffer write

Parameters

	N	total number of nodes
	offset	byte offsets of nodes, significant only on root
	bufsize	output buffer size
[out]	ranges	node range of each write

Note: ranges is allocated and can be free()'d

Returns: the number of writes

Definition at line 993 of file MULTI_ION_IF.cc.

◆ doppel_MIIF()

void limpet::doppel_MIIF	(	MULTI_IF *	orig,
		MULTI_IF *	miif_doppel
	)

make the minimal copy of a MIIF to run independently

Parameters

orig	the original MIIF
doppel	the copy

Note: the only memory copied is that for the state variables and private data of the ionic models. All other dynamically allocated chunks are shared. Private data cannot have dynamically allocated chunks which are updated

Definition at line 1855 of file MULTI_ION_IF.cc.

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◆ doppel_update()

void limpet::doppel_update	(	MULTI_IF *	orig,
		MULTI_IF *	miif_doppel
	)

update the data of a doppel MIIF without allocating any memory

Parameters

doppel	the copy
orig	the one to copy

Postcondition: doppel will be in the same state os orig

Definition at line 1827 of file MULTI_ION_IF.cc.

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◆ dump_all()

void limpet::dump_all	(	MULTI_IF *	MIIF,
		int	reg,
		char *	imp,
		char *	plugs,
		double	t,
		double	ddt,
		char *	fout
	)

Definition at line 344 of file bench_utils.cc.

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◆ dump_trace()

void limpet::dump_trace	(	MULTI_IF *	MIIF,
		limpet::Real	time
	)

dump the traces from a node

Parameters

MIIF	the ionic region
time	time of dump

We need the trace output in a buffer so we can pass it to the root for output. The trace function of the IMPs requires a file stream for the fprintf statements and on the GPU, there is a print statement which really copies the data to the host for printing on stdout which we redirect to our desired file stream. We use fmemopen() to associate a file stream with memory and trick everyone into writing into the buffer.

Note: A maximum line length of 8196 bytes is supported

Definition at line 409 of file MULTI_ION_IF.cc.

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◆ dup_IMP_node_state()

void limpet::dup_IMP_node_state	(	IonIfBase &	IF,
		int	from,
		int	to,
		GlobalData_t **	localdata
	)

Definition at line 1912 of file MULTI_ION_IF.cc.

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◆ flag_set()

bool limpet::flag_set	(	const char *	flags,
		const char *	target
	)

determine if a flag is present in a string of flags separated by "|"

Parameters

flags	the string of all flags
target	the specific flag

Returns: true if target is in flags, false otherwise

Definition at line 551 of file ION_IF.cc.

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◆ flubksb()

void limpet::flubksb	(	float **	a,
		int	n,
		int *	indx,
		float *	b
	)

Definition at line 378 of file Rosenbrock.cc.

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◆ flubksb0()

void limpet::flubksb0	(	float **	a,
		int	n,
		int *	indx,
		float *	b
	)

solve an LU decomposed dense float matrix by back/forward substitution

Parameters

a	the matrix
n	order of a
indx	permutation vector
b	RHS

Postcondition: b is modified to the solution

Note: base 0 vectors and matrices

Definition at line 285 of file Rosenbrock.cc.

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◆ fludcmp()

void limpet::fludcmp	(	float **	a,
		int	n,
		int *	indx,
		float *	d
	)

Definition at line 301 of file Rosenbrock.cc.

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◆ fludcmp0()

void limpet::fludcmp0	(	float **	a,
		int	n,
		int *	indx,
		float *	d
	)

LU decompose a dense float matrix

Parameters

a	the matrix
n	order of a
indx	permutation vector
d	needed for the determinant

Postcondition: a is LU decomposed

Note: base 0 vectors and matrices

Definition at line 258 of file Rosenbrock.cc.

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◆ free_doppel()

void limpet::free_doppel ( MULTI_IF * m )

release the memory of the doppel

Parameters

doppel the doppel of course

Postcondition: doppel is zeroed

Definition at line 1803 of file MULTI_ION_IF.cc.

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◆ free_sv_table()

void limpet::free_sv_table ( void * )

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◆ free_trace()

void limpet::free_trace ( trace * tr )

free memory used to read trace from a file

Parameters

tr trace

Postcondition: trace memory freed.

Definition at line 76 of file trace.cc.

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◆ freeIMPData()

void limpet::freeIMPData ( MULTI_IF * pMIIF )

Definition at line 797 of file MULTI_ION_IF.cc.

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◆ get_IIF_plugparam()

void* limpet::get_IIF_plugparam	(	IonIfBase &	,
		int
	)

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◆ get_ion_type()

IonType* limpet::get_ion_type ( const std::string & name )

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◆ get_next_list()

char * limpet::get_next_list	(	char *	lst,
		char	delimiter
	)

return pointer to the next item in a list

the next delimiter in lst is replaced with a '\0'

Parameters

lst	string of separated items
delimiter	list item separator

Return values

NULL	the end of the list has been reached
pointer	to the next item in the list

Definition at line 506 of file ION_IF.cc.

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◆ get_plug_flag()

int limpet::get_plug_flag	(	char *	plgstr,
		int *	out_num_plugins,
		IonTypeList &	out_plugins
	)

determine IMP plugin flag

Parameters

plgstr	colon separated list of plugin names
out_num_plugins	number of plugins found
out_plugins	plugin array

Postcondition: out_plugins is allocated and out_num_plugins set

Returns: 1 if found and 0 if not found

Definition at line 821 of file MULTI_ION_IF.cc.

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◆ get_protocol_definition()

void limpet::get_protocol_definition	(	char *	r_file,
		restitution *	r,
		bool	useS1S2
	)

Definition at line 169 of file restitute.cc.

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◆ get_string_from_target()

std::string limpet::get_string_from_target ( Target const target )

Get a string representation of a given target.

Parameters

target target to get the string of

Returns: a string representing the given enum value target. returns "unknown" if the target is unknown.

Definition at line 46 of file target.cc.

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◆ get_sv()

char* limpet::get_sv	(	void *	tab,
		int	offset,
		int	n,
		int	svSize,
		int	size,
		int	dlo_vector_size
	)

load a particular state variable into an array

Parameters

tab	state variable array
offset	offset of variable into table
n	#nodes
svSize	size of structure holding all SVs
size	size of state variable

Returns: pointer to a buffer which must be free'd afterwards

Definition at line 530 of file MULTI_ION_IF.cc.

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◆ get_target_from_string()

Target limpet::get_target_from_string ( std::string const str )

Returns a value from the Target enum from a given string.

Parameters

str	lower case string corresponding to an enum member

Returns: an enum value corresponding to the given string, or Target::UNKNOWN if the string cannot be matched

Definition at line 36 of file target.cc.

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◆ get_target_list_string()

std::string limpet::get_target_list_string ( )

Returns a string containing the list of available targets.

Returns: a string containing a comma-separated list of targets.

Definition at line 55 of file target.cc.

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◆ get_typename()

char* limpet::get_typename ( int type )

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◆ getCellVal() [1/2]

double limpet::getCellVal	(	opencarp::sf_vec *	v,
		int	ind
	)

◆ getCellVal() [2/2]

double limpet::getCellVal	(	sf_vec *	v,
		int	ind
	)

Definition at line 392 of file bench_utils.cc.

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◆ getGlobalNodalIndex()

int limpet::getGlobalNodalIndex	(	IonIfBase &	pIF,
		int	rIdx
	)

helper function to retrieve global nodal index number from within an imp

Parameters

[in]	pIF	pointer to imp
[in]	rIdx	relative index of cell within imp

Returns: global index of cell

Definition at line 205 of file MULTI_ION_IF.cc.

◆ getPutSV()

SVputfcn limpet::getPutSV ( SVgetfcn )

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◆ globalvec_dump() [1/2]

void limpet::globalvec_dump	(	FILE **	fhdls,
		GVEC_DUMP *	gvd,
		MULTI_IF *	pMIIF,
		opencarp::timer_manager *	tm,
		IOCtrl *	io,
		int	numNode
	)

◆ globalvec_dump() [2/2]

void limpet::globalvec_dump	(	FILE **	fhdls,
		GVEC_DUMP *	gvd,
		MULTI_IF *	pMIIF,
		timer_manager *	tmo,
		IOCtrl *	io,
		int	numNode
	)

dump the global vectors

Parameters

fhdls	output file
gvd
pMIIF	IMP structure
tmo	timer
io

Definition at line 272 of file bench_utils.cc.

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◆ IIF_warn() [1/2]

void limpet::IIF_warn	(	const int	wv,
		const char *	error
	)

◆ IIF_warn() [2/2]

void limpet::IIF_warn	(	const int	wv,
		const char	error[]
	)

print an error message to the terminaldetermine why index into a lookup table failed

Parameters

error string error message.

Note: if IMP_FAST is defined, this function is implemented as a macro which does no bounds checking

Definition at line 155 of file LUT.cc.

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◆ IMPdataLabel2Index()

int limpet::IMPdataLabel2Index ( const char * sv )

figure out global IMP data vector index within array from a given name

Parameters

[in] sv name of IMP data vector

Returns: index of IMP data vector within array

Definition at line 1894 of file MULTI_ION_IF.cc.

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◆ initial_SVs()

void limpet::initial_SVs	(	MULTI_IF *	miif,
		char *	SVs,
		char *	imp,
		char *	plgins,
		int	num
	)

Definition at line 412 of file bench_utils.cc.

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◆ initialize_AP_analysis()

int limpet::initialize_AP_analysis ( action_potential * AP )

initialize AP structure for gathering AP statistics

Parameters

AP	action potential statistics

Postcondition: action potential structure initialized
Allocates : event lists

Returns: for now we return 0 only

Definition at line 71 of file ap_analyzer.cc.

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◆ initialize_AP_clamp()

void limpet::initialize_AP_clamp	(	Clamp *	cl,
		char *	f,
		double
	)

◆ initialize_clamp()

bool limpet::initialize_clamp	(	Clamp *	cl,
		double	cl_val,
		double	ini_val,
		double	start,
		double	dur,
		const char *	f,
		int	trans,
		float *	duration
	)

voltage clamp experiment

Parameters

cl	clamp structure
val	value of clamp
dur	duration
start	when to start
f	file to read for clamp signal
trans	false for clamping outside of pulse, o.w. index of timer
duration	OUT duration of clamp

Definition at line 45 of file clamp.cc.

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◆ initialize_ionic_IF()

void limpet::initialize_ionic_IF ( MULTI_IF * pMIIF )

initlaize the ionic interfaces

Parameters

pMIIF MIIF

Definition at line 261 of file MULTI_ION_IF.cc.

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◆ initialize_params_MIIF()

void limpet::initialize_params_MIIF ( MULTI_IF * pMIIF )

initialize the parameters of the ionic models with default values

Parameters

pMIIF MIIF

Definition at line 252 of file MULTI_ION_IF.cc.

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◆ initialize_sv_clamp()

void limpet::initialize_sv_clamp	(	Clamp *	cl,
		const char *	sv,
		char *	file,
		double	dt
	)

initialize a [Ca]_i transient

Parameters

cl	clamp
sv	state variable
file	file from which to read transient
dt	time step

Definition at line 117 of file clamp.cc.

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◆ initialize_timings()

void limpet::initialize_timings ( event_timing * t )

Definition at line 366 of file bench_utils.cc.

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◆ initialize_ts() [1/2]

void limpet::initialize_ts	(	Target	target,
		ts *	tstp,
		int	ng,
		int *	skp,
		double	dt
	)

initialize_ts

Initialize the time stepping structure which determines whether or not a particular time constant group needs to be updated or not.

Parameters

target	target on which data will be allocated
ts	pointer to time stepper structure
ng	number of time constant groups
skp	skip values for each group relative to the fastest group
dt	time step of fastest group

Definition at line 431 of file ION_IF.cc.

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◆ initialize_ts() [2/2]

void limpet::initialize_ts	(	ts *	tstp,
		int	ng,
		int *	skp,
		double	dt
	)

◆ initializeIMPData()

void limpet::initializeIMPData ( MULTI_IF * pMIIF )

allocate memory for the structures to hold real data for IMPs and check that all needed data is passed

Postcondition: For each Ionic model, an array of IMPDataStruct is created with each entry pointing to the local portion of the data

Definition at line 689 of file MULTI_ION_IF.cc.

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◆ initializePulseStretch()

void limpet::initializePulseStretch	(	float	strain,
		float	onset,
		float	duration,
		float	rise,
		float	fall,
		stretch *	s
	)

Definition at line 38 of file stretch.cc.

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◆ int_cmp()

int limpet::int_cmp	(	const void *	a,
		const void *	b
	)

compare 2 integers for bsearch o qsort

Definition at line 309 of file MULTI_ION_IF.cc.

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◆ interp1()

void limpet::interp1	(	const double *	x,
		const float *	y,
		int	N,
		double *	xi,
		float *	yi,
		int	NI,
		double	dxi,
		IpMeth_t	meth
	)

Interpolate function given by vectors x and y at grid xi to obtain yi where the discrete step size of xi is constant. Further, it is assumed that step size in xi is constant as well.

Parameters

x	discrete x axis
y	discrete function y
N	length of vectors x and y
xi	discrete interpolated x axis
yi	discrete interpolated y axis
NI	length of vectors xi and yi
dxi	step size of xi
meth	interpolation method, either LINEAR or NEAREST

Definition at line 189 of file trace.cc.

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◆ is_concrete()

bool limpet::is_concrete ( Target const target )

Checks if target is a real, concrete target.

Parameters

target target to check

Return values

false	if the target is not concrete (Target::UNKNOWN, Target::AUTO, ...) or invalid
true	if the target is valid and concrete

Definition at line 68 of file target.cc.

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◆ is_gpu()

bool limpet::is_gpu ( Target const target )

Checks if this is a GPU target.

Parameters

target target to check

Returns: true for GPU targets, false otherwise

Definition at line 64 of file target.cc.

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◆ IsEquDistSampling()

bool limpet::IsEquDistSampling ( trace * tr )

check whether the sampling of a trace is regular

Parameters

tr trace

Returns: true if equidistant, false otherwise

Definition at line 90 of file trace.cc.

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◆ isIMPdata()

bool limpet::isIMPdata ( const char * sv )

check whether global IMP data vector of a given name exist

Parameters

[in] sv name of IMP data vector

Returns: true, if vector exists false, otherwise

Definition at line 1883 of file MULTI_ION_IF.cc.

◆ load_ionic_module()

int limpet::load_ionic_module ( const char * )

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◆ LUT_alloc()

void limpet::LUT_alloc	(	LUT *	plut,
		int	cols,
		float	mn,
		float	mx,
		float	res,
		const char *	name,
		Target	target
	)

Definition at line 45 of file LUT.cc.

◆ LUT_derror()

LUT_data_t limpet::LUT_derror	(	LUT *	t,
		int	idx,
		GlobalData_t	x
	)

inline

compute normalized disretization error

This is defined as the distance of the lookup value from the closest lower value used by the table lookup. It is computed as $e = (X-x[i])/\Delta x$ where X is the value used in the lookup up, x[i] is the closest table value and $\Delta x$ is the table resolution

Parameters

t	table
idx	closest lower index
x	value to lookup

Returns: the normalized error

Definition at line 242 of file LUT.cc.

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◆ LUT_dump()

int limpet::LUT_dump	(	LUT *	plut,
		const char *	fname
	)

Definition at line 74 of file LUT.cc.

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◆ LUT_index()

int limpet::LUT_index	(	LUT *	tab,
		GlobalData_t	val,
		int	locind
	)

do a safe table lookup with error reporting

Parameters

tab	pointer to lookup table
val	value to lookup.
locind	index of value in its local array

Returns: the index into the table

Note: An out-of-bounds value (including infinity) will be brought to the nearest edge. NaN will die.

Definition at line 193 of file LUT.cc.

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◆ LUT_interp()

LUT_data_t limpet::LUT_interp	(	LUT *	t,
		int	i,
		int	j,
		GlobalData_t	x
	)

inline

interpolate in a lookup table

Parameters

t	the table
i	the row in the table
j	the column in the table
x	normalized discretizaton error

Returns: a linear interpolation of table values

Definition at line 223 of file LUT.cc.

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◆ LUT_interpRow()

LUT_data_t limpet::LUT_interpRow	(	LUT *const	tab,
		GlobalData_t	val,
		int	i,
		LUT_data_t *	row
	)

interpolate a row of a lookup table

Parameters

tab	the table
val	current value for which we are looking up the dependent values
i	local index of the vertex for which we are doing the lookup
row	interpolated values

Returns: discretization error

Precondition: row is allocated

Note: This is now threadsafe

Definition at line 258 of file LUT.cc.

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◆ LUT_interpRow_mlir()

void limpet::LUT_interpRow_mlir	(	char *	table,
		int	i,
		char *	row_ptr,
		int	lut_num_elements,
		int	vector_size
	)

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◆ LUT_interpRow_n_elements()

void limpet::LUT_interpRow_n_elements	(	char *	table,
		char *	val_ptr,
		int	offset,
		int	distance,
		int	index,
		int	n,
		char *	row_ptr,
		int	lut_numelements
	)

LUT function for MLIR ionic models interpolate one rows of n lookup tables

Parameters

tab	the table
val	pointer for which we are looking up the dependent values
n	number of lookup tables to fill up
row	interpolated values
lut_numelements	number of elements of this lut

Returns: discretization error

Precondition: row is allocated

Note: This is now threadsafe

Definition at line 304 of file LUT.cc.

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◆ LUT_out_of_bounds()

int limpet::LUT_out_of_bounds	(	LUT *	tab,
		GlobalData_t	val
	)

Definition at line 210 of file LUT.cc.

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◆ LUT_problem()

void limpet::LUT_problem	(	LUT *	lt,
		double	val,
		int	wv,
		const char *	tabname
	)

determine why index into a lookup table failed

Parameters

lt	lookup table
val	bad value for computing look up
wv	local index associated with val
tabname	name of table being accessed
newval	table edge boundary

Note: if IMP_FAST is defined, this function is implemented as a macro which does no bounds checking

Definition at line 171 of file LUT.cc.

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◆ LUT_problem_mlir()

void limpet::LUT_problem_mlir	(	char *	tab,
		GlobalData_t	val,
		int	locind
	)

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◆ LUT_row()

LUT_data_t * limpet::LUT_row	(	LUT *	lut,
		GlobalData_t	val,
		int	locind
	)

return the row of a lookup table

Parameters

lut	the lookup table
val	the val to index
locind	local index of val

Definition at line 280 of file LUT.cc.

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◆ max()

template<class T >

constexpr T limpet::max	(	T	a,
		T	b
	)

inline

Definition at line 31 of file ion_type.h.

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◆ memmem()

void* limpet::memmem	(	void *	haystack,
		int	sz_hay,
		void *	needle,
		int	sz_n
	)

find a byte sequence in memory

Parameters

haystack	where to look
sz_hay	size of search space
needle	object to look for
sz_n	size of object

Returns: the address if found, NULL o.w.

Definition at line 480 of file ION_IF.cc.

◆ min()

template<class T >

constexpr T limpet::min	(	T	a,
		T	b
	)

inline

Definition at line 33 of file ion_type.h.

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◆ modify_param()

float limpet::modify_param	(	float	a,
		char *	expr
	)

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◆ ODEint_FE()

void limpet::ODEint_FE	(	GlobalData_t *	y,
		GlobalData_t *	ydot,
		void *	f,
		void *	f_data,
		int	len,
		GlobalData_t	dt
	)

ODEint_FE

Simple forward Euler ODE integrator

Integration of ydot = f(y,t)

y[t+dt] = y[t] + f(y[t])*dt

Parameters

y	value
ydot	value of f(y,t)
f	function f(y,t)
f_data	data needed for function evaluation
len	length of vector
dt	time step

Definition at line 75 of file ODEint.cc.

◆ ODEint_RK()

void limpet::ODEint_RK	(	GlobalData_t *	y,
		GlobalData_t *	ydot,
		void	fGlobalData_t , GlobalData_t , void *,
		void *	f_data,
		int	len,
		GlobalData_t	dt
	)

ODEint_RK

Runge Kutta first order ODE integrator

Integration of ydot = f(y,t)

k1 = dt*f( t, y(t) ) k2 = dt*f( t+0.5*dt, y(t)+0.5*k1 ); y(t+dt) = y(t) + k2 + O(dt^3)

Parameters

y	value
ydot	value of f(y,t)
f	function f(y,t)
f_data	data needed for function evaluation
len	length of vector
dt	time step

Definition at line 40 of file ODEint.cc.

◆ open_globalvec_dump()

void limpet::open_globalvec_dump	(	FILE **	fhdls,
		GVEC_DUMP *	gvd,
		MULTI_IF *	pMIIF,
		char *	base_name,
		IOCtrl *	io
	)

Definition at line 176 of file bench_utils.cc.

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◆ open_trace() [1/2]

void limpet::open_trace	(	MULTI_IF *	,
		int	,
		int *	,
		int *
	)

◆ open_trace() [2/2]

void limpet::open_trace	(	MULTI_IF *	MIIF,
		int	n_traceNodes,
		int *	traceNodes,
		int *	label,
		opencarp::sf_mesh *	imesh
	)

Set up ionic model traces at some global node numbers.

Usage for the following three functions:

open_trace();
while(running){ if (timer_triggered) dump_trace(time); }
close_trace();

By default, each model has a NULL pointer for their trace() function. Those models that implement a trace function need only redefine this NULL pointer in their init_parameters function.

Each trace function invocation should print a list of whatever variables it wants delimited by tabs. The dumping routine will take care of inserting extra tabs between models and plugins, and will take responsibilty for printing the trailing new line on each line.

Note: This is not meant for many many nodes.

Parameters

MIIF	The MIIF state struct.
n_traceNodes	number of nodes in the following array
traceNodes	global node numbers of the nodes we want to trace.
label	output node number, if NULL, use traceNodes
imesh	The intracellular mesh, may be NULL if called from bench.

Definition at line 340 of file MULTI_ION_IF.cc.

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◆ print_AP_stats()

void limpet::print_AP_stats ( action_potential * AP )

Write AP statistic parameters to a file. Written parameters include:

Beat Number Prematurity APD DI(n) DI(n-1) Triangulation Vm_mx Vm_mn

Parameters

AP	action potential statistics data

Definition at line 498 of file ap_analyzer.cc.

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◆ print_AP_stats_header()

void limpet::print_AP_stats_header	(	action_potential *	AP,
		FILE *	outbuf
	)

Write AP statistic header to stderr

Beat Number Prematurity APD DI(n) DI(n-1) Triangulation Vm_mx Vm_mn

Parameters

AP	action potential statistics data

Definition at line 526 of file ap_analyzer.cc.

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◆ print_IMPs()

void limpet::print_IMPs ( void )

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◆ print_models()

void limpet::print_models ( bool )

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◆ print_param_help()

void limpet::print_param_help	(	IonType *	im,
		IonTypeList &	plugs
	)

Definition at line 468 of file bench_utils.cc.

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◆ process_param_mod()

int limpet::process_param_mod	(	char *	pstr,
		char *	par,
		char *	mod
	)

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◆ process_sv_clamps()

int limpet::process_sv_clamps	(	char *	SVs,
		char *	files,
		Clamp **	clamps,
		double	dt
	)

process SV clamp lists

Parameters

SVs	IN colon separated state variable list
files	IN colon separated file list of SV traces corresponding to SVs
clamps	OUT list of clamps

Returns: the number of clamps

Definition at line 197 of file clamp.cc.

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◆ rbCalcKi()

void limpet::rbCalcKi	(	float **	K,
		float **	A,
		float *	X,
		int *	ludI,
		void()(float , float , void )	calcDX,
		void *	params,
		float	h,
		int	N,
		int	i
	)

populate the i^th row of the coefficient matrix K

Parameters

K	4xN matrix K in row-major order
J	NxN Jacobian matrix in row-major order
X	N variables to be integrated
calcDX	function that populates a vector (F) with the instantaneous time derivatives of the variables in X
params	structure necessary for the calculation of F and J, defined by user
h	time step
N	number of variables to be integrated
i	row of the 4xN matrix K to be populated

Note: Typically, this function should not be called by users.

Definition at line 170 of file Rosenbrock.cc.

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◆ rbSolver()

void limpet::rbSolver	(	float **	A,
		float *	x,
		float *	b,
		int	N
	)

solve the system Ax = b

Parameters

A	pointer to the NxN matrix A
x	pointer to the Nx1 vector x
b	pointer to the Nx1 vector b
N	number of nodes in the system

Note: Typically, this function should not be called by users.; Because A tends to be near-singular in the context of the integration scheme, Gaussian elimination is employed to solve the system. It is altogether likely that this method could be improved computationally.

Definition at line 222 of file Rosenbrock.cc.

◆ rbStepX()

void limpet::rbStepX	(	float *	X,
		void()(float , float , void )	calcDX,
		void()(float , float , void *, int)	calcJ,
		void *	params,
		float	h,
		int	N
	)

semi-implicit integration of X over one time step

Parameters

X	pointer to N variables to be integrated
calcDX	pointer to a function that populates a vector (F) with the instantaneous time derivatives of the variables in X
calcJ	pointer to a function that populates the NxN Jacobian matrix (J), given by dF/dX
params	data necessary for the calculation of F and J, defined by user
h	time step
N	number of variables to be integrated

Note: The functions pointed to by calcDX and calcJ, as well as the structure pointed to by params, must be defined by the user in the context of the file calling this function. A simple example is presented at the end of this header file. A full example can be found in the Pandit ionic model.

Warning: F cannot contain any terms that are explicitly time-dependent, otherwise this implementation will fail, due to the omission of the non-autonomous gradient term.

Definition at line 101 of file Rosenbrock.cc.

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◆ read_restitution_protocol_def()

int limpet::read_restitution_protocol_def	(	char *	r_file,
		restitution *	r
	)

read restitution curve protocol definition from a file

lines of the file for S1S2 1 # prepacing beats S1 BCL longest S2 shortest S2 #S1 beats between S2's decrement of S2's

for dynamic protocols 0 #prepacing beats starting BCL ending BCL beats per BCL BCL decrement

Definition at line 222 of file restitute.cc.

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◆ read_sv()

int limpet::read_sv	(	MULTI_IF *	,
		int	,
		const char *
	)

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◆ read_trace()

int limpet::read_trace	(	trace *	tr,
		const char *	name
	)

read a trace from a file

Parameters

tr	trace
name	name of trace file

Postcondition: trace structure allocated and filled

Definition at line 43 of file trace.cc.

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◆ resample_trace()

void limpet::resample_trace	(	trace *	tr,
		double	dt
	)

resample a trace at a different sampling interval

Parameters

tr	trace
dt	time step for resampling the trace

Postcondition: the trace is assumed to start at 0

Definition at line 115 of file trace.cc.

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◆ restitution_save_sv()

void limpet::restitution_save_sv	(	MULTI_IF *	miif,
		int	R1,
		restitution *	r,
		action_potential *	AP
	)

save state vectors during restitution protocol

Parameters

[in]	miif	ionic models
[in]	R1	region ID
[in]	r	restitution protocol being used
[in]	AP	AP analysis data

Postcondition: state vector written before every step change in CI

Definition at line 275 of file restitute.cc.

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◆ restitution_trigger_list()

void limpet::restitution_trigger_list	(	char *	r_file,
		restitution *	r,
		char *	protocol,
		int *	n_dop,
		double **	t_dop
	)

determine triggers for restitution protocols

Parameters

r_file	restitution file
r	parameters for restitution protocol
protocol	use S1S2, dynamic or fast S1S2 protocol
n_dop[out]	number of resumed states
t_dop[out]	times at which to revert state

Postcondition: restitution structure filled in
Allocates : trigger lists
Assigns : restitution parameters

Definition at line 45 of file restitute.cc.

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◆ save_sv()

void limpet::save_sv	(	MULTI_IF *	,
		int	,
		const char *
	)

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◆ set_print_bounds_exceeded_messages()

int limpet::set_print_bounds_exceeded_messages ( int newval )

Definition at line 132 of file MULTI_ION_IF.cc.

◆ set_start_time()

void limpet::set_start_time ( const float )

◆ shift_vm_trace()

void limpet::shift_vm_trace	(	double	vm,
		action_potential *	AP,
		timer_manager *	tm
	)

shifts the Vm buffer by one and enters the current Vm value at position 0 of the buffer

Parameters

vm	current value of AP
AP	action potential statistics
tm	timer manager

Definition at line 207 of file ap_analyzer.cc.

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◆ should_print_bounds_exceeded_messages()

int limpet::should_print_bounds_exceeded_messages ( )

Definition at line 128 of file MULTI_ION_IF.cc.

◆ SV_alloc()

void limpet::SV_alloc	(	SV_TAB *	psv,
		int	numSeg,
		int	struct_size
	)

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◆ sv_clamp() [1/2]

void limpet::sv_clamp	(	Clamp *	cl,
		opencarp::timer_manager *	tm,
		MULTI_IF *	,
		bool	trigger
	)

◆ sv_clamp() [2/2]

void limpet::sv_clamp	(	Clamp *	cl,
		timer_manager *	tm,
		MULTI_IF *	miif,
		bool	trigger
	)

apply a state variable transient, let it float if outside the trace

Parameters

cl	clamp
tm	timer manager
miif	ionic model
trigger	true if current stimulus started

Definition at line 138 of file clamp.cc.

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◆ SV_free()

void limpet::SV_free ( SV_TAB * psv )

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◆ tokstr_r()

char * limpet::tokstr_r	(	char *	s1,
		const char *	s2,
		char **	lasts
	)

Definition at line 82 of file ION_IF.cc.

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◆ trace_duration()

double limpet::trace_duration	(	trace *	tr,
		const char *	f
	)

determine the length (duration) of a trace either from a trace file or a trace structure

Parameters

tr	trace
f	trace file where we look in the case that tr is void

Returns: duration of the trace

Definition at line 147 of file trace.cc.

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◆ update_steady_state()

bool limpet::update_steady_state ( action_potential * AP )

update data for steady state check and determine whether we are in steady state or not

Parameters

AP	action potential statistics

Returns: true, if AP is in steady state, false otherwise

Definition at line 355 of file ap_analyzer.cc.

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◆ update_timing()

void limpet::update_timing	(	event_timing *	t,
		double	event_duration
	)

Definition at line 376 of file bench_utils.cc.

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◆ update_ts()

void limpet::update_ts ( ts * ptstp )

update_ts

Update the time stepping structure, mainly increment the linear counter and compute the modulus for each time group to decide whether an update is required for the current time step.

Parameters

ptstp time step group

Definition at line 460 of file ION_IF.cc.

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◆ verify_flags()

bool limpet::verify_flags	(	const char *	flags,
		const char *	given
	)

verify that the specified flags are legal values

Parameters

flags	all possible flags
given	specified flags

Returns: true iif all given flags are found in flags

Definition at line 529 of file ION_IF.cc.

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◆ write_dump_header()

int limpet::write_dump_header	(	GVEC_DUMP *	gvd,
		SV_DUMP *	svd,
		const char *	ExpID
	)

Definition at line 135 of file bench_utils.cc.

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Variable Documentation

◆ _nc_logf

opencarp::FILE_SPEC limpet::_nc_logf = NULL

Definition at line 78 of file ION_IF.cc.

◆ curr_node_list

int* limpet::curr_node_list

needed to determine the global node number

Definition at line 108 of file ION_IF.cc.

Classes

Typedefs

Enumerations

Functions

Variables

Detailed Description

Typedef Documentation

◆ act_events

◆ ampl_events

◆ ap_states

◆ event_class

◆ event_meth

◆ Gatetype

◆ GlobalData_t

◆ IIF_Mask_t

◆ IonTypeList

◆ IpMeth_t

◆ LUT_data_t

◆ r_prtcl

◆ Real

◆ repol_events

◆ s_prtcl

◆ stretch

◆ SVgetfcn

◆ SVputfcn

Enumeration Type Documentation

◆ _act_events

◆ _ampl_events

◆ _ap_states

◆ _event_meth

◆ _r_protocol

◆ _repol_events

◆ _stretch_protocol

◆ DataType

◆ ip_method

◆ Target

◆ TimerIDs

◆ timingIDs

Function Documentation

◆ alloc_MIIF()

◆ allocate_on_target()

◆ allocate_shared_data()

◆ AP_clamp() [1/2]

◆ AP_clamp() [2/2]

◆ apply_stretch() [1/2]

◆ apply_stretch() [2/2]

◆ apply_stretch_pulse()

◆ build_matrix_ns()

◆ calibrate_thresholds()

◆ check_events() [1/2]

◆ check_events() [2/2]

◆ check_LUT()

◆ check_mx_rate()

◆ check_mx_val()

◆ check_steady_state()

◆ check_threshold()

◆ clamp_signal() [1/2]

◆ clamp_signal() [2/2]

◆ cleanup_AP_analysis()

◆ close_globalvec_dump()

◆ close_trace()

◆ CreateIIFGlobalNodeLsts()

◆ CreateIIFLocalNodeLsts()

◆ CreateIIFNodeLsts_()

◆ current_global_node()

◆ current_global_time()

◆ d_ODEint_FE()

◆ d_ODEint_RK()

◆ deallocate_on_target()

◆ destroy_lut()

◆ determine_duration()

◆ determine_stim_list()

◆ determine_write_ranges()

◆ doppel_MIIF()

◆ doppel_update()

◆ dump_all()

◆ dump_trace()

◆ dup_IMP_node_state()

◆ flag_set()

◆ flubksb()