#include <MULTI_ION_IF.h>

Collaboration diagram for limpet::MULTI_IF:

Public Member Functions
	MULTI_IF ()

	~MULTI_IF ()

void	zero_data ()

void	initialize_MIIF ()

void	initialize_currents (double, int)

void	compute_ionic_current (bool flag_send=1, bool flag_receive=1)
	GPU kernel to emulate the `add_scaled` call made to adjust the Vm values when the update to Vm is not made externally. This is to avoid computing the Vm update on CPU when runnign a GPU model. More...

void	free_MIIF ()

void	sv_dump_add (int, const IonType &, int, int, int, const char , const char )

int	sv_dump_add_by_name (int, char , char , char , char )

void	sv_dump_add_by_name_list (int, char , char , char , char , char *, double, double)

int	dump_svs (opencarp::base_timer *)

void	close_svs_dumps ()

void	dump_luts_MIIF (bool)

void	dump_state (char *, float, opencarp::mesh_t gid, bool, unsigned int)

void	transmem_stim_species (float, const char , float, int , int)

float	restore_state (const char *, opencarp::mesh_t gid, bool)

void	releaseRealData ()

void	releaseRealDataDuringInit ()

void	getRealData ()

int	adjust_MIIF_variables (const char *variable, const SF::vector< int > &indices, const SF::vector< double > &values)

void	MIIF_change_dt (double)

bool	use_stretch ()

void *	thread_initialize_MIIF ()

Public Attributes
std::string	name
	name for MIIF region More...

bool	doppel
	is this a shallow clone? More...

int *	N_Nodes
	#nodes for each IMP More...

int **	NodeLists
	local partitioned node lists for each IMP stored More...

std::vector< IonIfBase * >	IIF
	array of IIF's More...

SV_DUMP	svd
	state variable dump More...

GlobalData_t *	procdata [NUM_IMP_DATA_TYPES]
	data for this processor More...

GlobalData_t ***	ldata
	data local to each IMP More...

bool *	contiguous
	whether a region is contiguously numbered More...

Trace_Info *	trace_info
	Information about traces. More...

bool	extUpdateVm
	flag indicating update function for Vm More...

int *	numplugs
	number of plugins for each region More...

int	numNode
	local number of nodes More...

int	N_IIF
	how many different IIF's More...

IonTypeList	iontypes
	type for each region More...

std::vector< Target >	targets
	target for each region More...

IIF_Mask_t *	IIFmask
	region for each node More...

std::vector< IonTypeList >	plugtypes
	plugins types for each region More...

opencarp::sf_vec *	gdata [NUM_IMP_DATA_TYPES]
	data used by all IMPs More...

opencarp::FILE_SPEC	logger

double	dt
	time step (ms) More...

int	numSubDt
	number of sub-dt time steps More...

Detailed Description

hold different ionic model information

Definition at line 195 of file MULTI_ION_IF.h.

Constructor & Destructor Documentation

◆ MULTI_IF()

limpet::MULTI_IF::MULTI_IF ( )

inline

Definition at line 226 of file MULTI_ION_IF.h.

◆ ~MULTI_IF()

limpet::MULTI_IF::~MULTI_IF ( )

inline

Definition at line 231 of file MULTI_ION_IF.h.

Member Function Documentation

◆ adjust_MIIF_variables()

int limpet::MULTI_IF::adjust_MIIF_variables	(	const char *	variable,
		const SF::vector< int > &	indices,
		const SF::vector< double > &	values
	)

adjust a state variable within a model.

Right now, state variables are the only variables in a model that vary on a nodal basis. By setting state variables, we can adjust some parameters on a per-node basis in individual ionic models. This will allow people to run simulations that would otherwise be impossible without using thousands of regions.

Parameters

pMIIF	multi-ion interface
name	Name of parameter to adjust. The name should be in the format "external_var" or "Model_name.state_variable", i.e. "Lambda" or "LRDII_F.m"
numNodes	Size of the following two arrays
indices	Array of local node numbers, mapping into our local mesh
values	Array of values we want to be setting.

Returns: the number of items set

Definition at line 869 of file MULTI_ION_IF.cc.

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◆ close_svs_dumps()

void limpet::MULTI_IF::close_svs_dumps ( )

close sv table IO files

Parameters

MIIF	pointer to MULTI_IF structure

Definition at line 509 of file MULTI_ION_IF.cc.

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◆ compute_ionic_current()

void limpet::MULTI_IF::compute_ionic_current	(	bool	flag_send = `1`,
		bool	flag_receive = `1`
	)

GPU kernel to emulate the add_scaled call made to adjust the Vm values when the update to Vm is not made externally. This is to avoid computing the Vm update on CPU when runnign a GPU model.

Definition at line 586 of file MULTI_ION_IF.cc.

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◆ dump_luts_MIIF()

void limpet::MULTI_IF::dump_luts_MIIF ( bool zipped )

dump LUTs of all IIFs

Parameters

MIIF	pointer to MULTI_IF structure
zipped	toggle between zipped\|\|unzipped dump

Definition at line 483 of file MULTI_ION_IF.cc.

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◆ dump_state()

void limpet::MULTI_IF::dump_state	(	char *	,
		float	,
		opencarp::mesh_t	gid,
		bool	,
		unsigned	int
	)

dump the IIF's to a file so that they can later be restored

the following is output as binary data in order:

dump identifier (char *)
format version (unsigned int)
program version number (unsigned int)
time file is created (time_t)
simulation time (float)
total #nodes in model (int)
number of used global data vectors (int)
for each used global data vector
1. the length of its name (int)
2. its name (char *)
3. the array (Real *) in canonical order
number of IIF regions (int)
for each IIF region
1. length of the IMP name (int)
2. IMP name (char *)
3. size of state variable info (int)
4. number of plug-ins (int)
5. for each plug-in
  1. length of the IMP name (int)
  2. IMP name (char *)
  3. size of state variable info (int)
the node mask specifying the regions (IIF_Mask_t *) in canonical order
for each node
1. state variables for the base IMP (IMP_SV)
2. for each plug-in
  1. state variables (PLUGIN_SV)

Parameters

fname	output file name
simtime	simulation time at which dump occurs
gid	ID of the mesh we operate on
append	true to append to existing file
revision	calling program version

Definition at line 1057 of file MULTI_ION_IF.cc.

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◆ dump_svs()

int limpet::MULTI_IF::dump_svs ( opencarp::base_timer * )

dump state variables

Parameters

MIIF	pointer to MULTI_IF structure
iot	IO timer

Returns: the number of data written per dump variable

Definition at line 551 of file MULTI_ION_IF.cc.

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◆ free_MIIF()

void limpet::MULTI_IF::free_MIIF ( )

Definition at line 673 of file MULTI_ION_IF.cc.

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◆ getRealData()

void limpet::MULTI_IF::getRealData ( )

for each IMP data vector, get the local portion corresponding to each ionic model

If PETSc is used, we need to get the local data first

If nodes for a particular region are noncontigous in the original vector, they must be copied to a local contiguous vector

Definition at line 725 of file MULTI_ION_IF.cc.

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◆ initialize_currents()

void limpet::MULTI_IF::initialize_currents	(	double	idt,
		int	subDt
	)

initialize the computation functions

Parameters

MIIF	pointer to MULTI_IF structure
dt	time step (milliseconds)
subDt	number of sub time steps per global time step

Definition at line 468 of file MULTI_ION_IF.cc.

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◆ initialize_MIIF()

void limpet::MULTI_IF::initialize_MIIF ( )

create lists and allocate memory for IMPs

Parameters

MIIF	multi yyion interface

Definition at line 295 of file MULTI_ION_IF.cc.

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◆ MIIF_change_dt()

void limpet::MULTI_IF::MIIF_change_dt ( double Dt )

change the time step

Parameters

miif	the ionic model iinterface
Dt	the new time step

Definition at line 1779 of file MULTI_ION_IF.cc.

◆ releaseRealData()

void limpet::MULTI_IF::releaseRealData ( )

copy data back into original vectors

If the data passed from the main is noncontiguous in memory, the data values must first be copied from the local contiguous array

If PETSc is used, the vector must be restored

Definition at line 761 of file MULTI_ION_IF.cc.

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◆ releaseRealDataDuringInit()

void limpet::MULTI_IF::releaseRealDataDuringInit ( )

Copy both reqqed and modded data back into the global vectors.

Parameters

m MIIF

Definition at line 274 of file MULTI_ION_IF.cc.

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◆ restore_state()

float limpet::MULTI_IF::restore_state	(	const char *	,
		opencarp::mesh_t	gid,
		bool
	)

restore the IIF's from a file

The model saved must agree with the model being run. This is checked by ensuring the #nodes agree. See dump_state()

Compatible IIF's are restored. To be compatible, the ionic model and ionic model size for an IIF must match. Plug-ins and their order may change. Only compatible plug-ins (matching type and size) are restored, others are ignored.

Parameters

fname	input file name, if NULL use open file stream
gid	the ID of the mesh we operate on (usually intra_elec_msh)
close	close the file stream afterwards?

Precondition: The IMPs have all been allocated

Note: all ranks process the file; There are static variables, the input file stream and file name

Returns: the time at which the simulation was saved

Definition at line 1272 of file MULTI_ION_IF.cc.

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◆ sv_dump_add()

void limpet::MULTI_IF::sv_dump_add	(	int	region,
		const IonType &	type,
		int	offset,
		int	size,
		int	dtype,
		const char *	filename,
		const char *	regname
	)

add a state variable to the list to be dumped

Parameters

miif	Multi ion IF structure
region	region containing the state variable
imp	ID of IMP within the region
offset	offset of SV within the IMP SV structure
size	size of the SV
dtype	ID of data type
filename	output file name
impname	string specifying the IMP
regname	name of the region

Note: It is much easier to call this function with the ::SV_add macro or with the ::sv_dump_add_by_name function than directly.

Definition at line 1555 of file MULTI_ION_IF.cc.

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◆ sv_dump_add_by_name()

int limpet::MULTI_IF::sv_dump_add_by_name	(	int	region,
		char *	impname,
		char *	svname,
		char *	regname,
		char *	filename
	)

add a state variable by name to the list to be dumped

Parameters

miif	Multi ion IF structure
region	region containing the state variable
impname	string specifying the IMP
svname	string specifying the state variable to dump
regname	name of the region
filename	output file name

Definition at line 1624 of file MULTI_ION_IF.cc.

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◆ sv_dump_add_by_name_list()

void limpet::MULTI_IF::sv_dump_add_by_name_list	(	int	region,
		char *	imp_name,
		char *	reg_name,
		char *	sv_lst,
		char *	plg_lst,
		char *	plg_sv_lst,
		double	t,
		double	dump_dt
	)

wrapper function to add sv's for dumping using a colon separated list

Parameters

pmiif	multi-ionic interface structure
region	IIF number
imp_name	name of IMP
reg_name	name of region
sv_lst	ionic model state variable list we want to dump
plg_lst	plugin list of this ionic model
plg_sv_lst	plugin state variable list we want to dump

Definition at line 1496 of file MULTI_ION_IF.cc.

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◆ thread_initialize_MIIF()

void* limpet::MULTI_IF::thread_initialize_MIIF ( )

◆ transmem_stim_species()

void limpet::MULTI_IF::transmem_stim_species	(	float	charge,
		const char *	species,
		float	beta,
		int *	node,
		int	numnode
	)

assign transmembrane current stimulus to an ionic species and adjust concentration of species

Parameters

miif	ionic models
charge	transmembrane charge=currentdt (µAms/cm^2)
species	ionic species carrying current
beta	effective surface to volume ratio of cells (per micrometer)
node	list of stimulated nodes
numnode	#nodes in list

Note: extracellular concentrations are not affected since it is assumed that electrons at the electrode interface cause depletion/creation of ions and the ground electrode is located far away; The voltage is NOT affected. This must be done separately.

Definition at line 1708 of file MULTI_ION_IF.cc.

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◆ use_stretch()

bool limpet::MULTI_IF::use_stretch ( )

test whether we have any mechanics enabled

Parameters

[in] miif Multi ion IF structure

Returns: true, if mechanics is used false, otherwise

Definition at line 1677 of file MULTI_ION_IF.cc.

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◆ zero_data()

void limpet::MULTI_IF::zero_data ( )

inline

Definition at line 233 of file MULTI_ION_IF.h.

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Member Data Documentation

◆ contiguous

bool* limpet::MULTI_IF::contiguous

whether a region is contiguously numbered

Definition at line 206 of file MULTI_ION_IF.h.

◆ doppel

bool limpet::MULTI_IF::doppel

is this a shallow clone?

Definition at line 199 of file MULTI_ION_IF.h.

◆ dt

double limpet::MULTI_IF::dt

time step (ms)

Definition at line 219 of file MULTI_ION_IF.h.

◆ extUpdateVm

bool limpet::MULTI_IF::extUpdateVm

flag indicating update function for Vm

Definition at line 208 of file MULTI_ION_IF.h.

◆ gdata

opencarp::sf_vec* limpet::MULTI_IF::gdata[NUM_IMP_DATA_TYPES]

data used by all IMPs

Definition at line 216 of file MULTI_ION_IF.h.

◆ IIF

std::vector<IonIfBase*> limpet::MULTI_IF::IIF

array of IIF's

Definition at line 202 of file MULTI_ION_IF.h.

◆ IIFmask

IIF_Mask_t* limpet::MULTI_IF::IIFmask

region for each node

Definition at line 214 of file MULTI_ION_IF.h.

◆ iontypes

IonTypeList limpet::MULTI_IF::iontypes

type for each region

Definition at line 212 of file MULTI_ION_IF.h.

◆ ldata

GlobalData_t*** limpet::MULTI_IF::ldata

data local to each IMP

Definition at line 205 of file MULTI_ION_IF.h.

◆ logger

opencarp::FILE_SPEC limpet::MULTI_IF::logger

Definition at line 217 of file MULTI_ION_IF.h.

◆ N_IIF

int limpet::MULTI_IF::N_IIF

how many different IIF's

Definition at line 211 of file MULTI_ION_IF.h.

◆ N_Nodes

int* limpet::MULTI_IF::N_Nodes

#nodes for each IMP

Definition at line 200 of file MULTI_ION_IF.h.

◆ name

std::string limpet::MULTI_IF::name

name for MIIF region

Definition at line 198 of file MULTI_ION_IF.h.

◆ NodeLists

int** limpet::MULTI_IF::NodeLists

local partitioned node lists for each IMP stored

Definition at line 201 of file MULTI_ION_IF.h.

◆ numNode

int limpet::MULTI_IF::numNode

local number of nodes

Definition at line 210 of file MULTI_ION_IF.h.

◆ numplugs

int* limpet::MULTI_IF::numplugs

number of plugins for each region

Definition at line 209 of file MULTI_ION_IF.h.

◆ numSubDt

int limpet::MULTI_IF::numSubDt

number of sub-dt time steps

Definition at line 220 of file MULTI_ION_IF.h.

◆ plugtypes

std::vector<IonTypeList> limpet::MULTI_IF::plugtypes

plugins types for each region

Definition at line 215 of file MULTI_ION_IF.h.

◆ procdata

GlobalData_t* limpet::MULTI_IF::procdata[NUM_IMP_DATA_TYPES]

data for this processor

Definition at line 204 of file MULTI_ION_IF.h.

◆ svd

SV_DUMP limpet::MULTI_IF::svd

state variable dump

Definition at line 203 of file MULTI_ION_IF.h.

◆ targets

std::vector<Target> limpet::MULTI_IF::targets

target for each region

Definition at line 213 of file MULTI_ION_IF.h.

◆ trace_info

Trace_Info* limpet::MULTI_IF::trace_info

Information about traces.

Definition at line 207 of file MULTI_ION_IF.h.

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

physics/limpet/src/MULTI_ION_IF.h
physics/limpet/src/MULTI_ION_IF.cc

Public Member Functions

Public Attributes

Detailed Description

Constructor & Destructor Documentation

◆ MULTI_IF()

◆ ~MULTI_IF()

Member Function Documentation

◆ adjust_MIIF_variables()

◆ close_svs_dumps()

◆ compute_ionic_current()

◆ dump_luts_MIIF()

◆ dump_state()

◆ dump_svs()

◆ free_MIIF()

◆ getRealData()

◆ initialize_currents()

◆ initialize_MIIF()

◆ MIIF_change_dt()

◆ releaseRealData()

◆ releaseRealDataDuringInit()

◆ restore_state()

◆ sv_dump_add()

◆ sv_dump_add_by_name()

◆ sv_dump_add_by_name_list()

◆ thread_initialize_MIIF()

◆ transmem_stim_species()

◆ use_stretch()

◆ zero_data()

Member Data Documentation

◆ contiguous

◆ doppel

◆ dt

◆ extUpdateVm

◆ gdata

◆ IIF

◆ IIFmask

◆ iontypes

◆ ldata

◆ logger

◆ N_IIF

◆ N_Nodes

◆ name

◆ NodeLists

◆ numNode

◆ numplugs

◆ numSubDt

◆ plugtypes

◆ procdata

◆ svd

◆ targets

◆ trace_info