Namespaces
	async

	sig

	stim_info

	user_globals

Classes
struct	Activation
	event detection data structures More...

struct	async_io_item

struct	base_timer

class	Basic_physic
	The abstract physics interface we can use to trigger all physics. More...

struct	D_Complex

class	dbc_manager
	manager for dirichlet boundary conditions More...

struct	diffMaterial

class	elec_stiffness_integrator

struct	elecMaterial

class	Electrics

class	elliptic_solver

struct	file_desc
	File descriptor struct. More...

struct	generic_timing_stats
	for analysis of the #iterations to solve CG More...

class	geom_shape
	class to store shape definitions More...

struct	gvec_data

class	igb_output_manager

class	IGBheader

class	Ionics

class	Laplace

class	LAT_detector

struct	lin_solver_stats
	for analysis of the #iterations to solve CG More...

struct	List

class	mass_integrator

struct	MaterialType
	description of materal properties in a mesh More...

struct	opticsMaterial

class	parabolic_solver

struct	phie_recovery_data

struct	physMaterial

struct	prog_stats
	for display execution progress and statistical data of electrical solve More...

struct	RegionSpecs
	region based variations of arbitrary material parameters More...

union	rgba

struct	S_Complex

struct	Salt_list
	saltatory list – memory is allocated in chunks More...

struct	Sentinel
	sentinel for checking activity in the tissue More...

class	stim_electrode

class	stim_physics

class	stim_protocol

class	stim_pulse
	define the wave form of a stimulation pulse More...

class	stimulus

struct	sv_data

struct	sync_io_item

struct	timer_eq

class	timer_manager
	centralize time managment and output triggering More...

struct	timer_neq

struct	vec3

Typedefs
typedef SF::meshdata< mesh_int_t, mesh_real_t >	sf_mesh

typedef SF::abstract_vector< mesh_int_t, double >	sf_vec

typedef SF::abstract_matrix< mesh_int_t, double >	sf_mat

typedef SF::abstract_linear_solver< mesh_int_t, double >	sf_sol

typedef file_desc *	FILE_SPEC

typedef struct opencarp::List	List

typedef unsigned char	byte

typedef unsigned char	Byte

typedef char *	String

typedef signed char	Char

typedef struct S_Complex	S_Complex

typedef double	Double

typedef struct D_Complex	D_Complex

typedef float	Float

typedef int	Int

typedef long	Long

typedef unsigned int	UInt

typedef short	Short

typedef int	BooleaN

typedef int	Flag

typedef char *	RDir

typedef char *	RFile

typedef char *	RWDir

typedef char *	RWFile

typedef char *	WDir

typedef char *	WFile

typedef char **	Text

typedef void	Any

typedef union opencarp::rgba	rgba

typedef uint16_t	short_float

typedef vec3< POINT_REAL >	Point

Enumerations
enum	IO_t { INPUT, OUTPUT, POSTPROC, CURDIR }
	The different output (directory) types. More...

enum	tagreg_t { tagreg_sphere = 1, tagreg_block = 2, tagreg_cylinder = 3, tagreg_list = 4 }
	tag regions types. must be in line with carp.prm More...

enum	physMat_t { PhysMat =0, ElecMat =1, DiffuseMat =2, MechMat =3, OpticsMat =4 }
	identifier for physical material properties More...

enum	cond_t { intra_cond, extra_cond, sum_cond, para_cond }
	description of electrical tissue properties More...

enum	mesh_t { intra_elec_msh = 0, extra_elec_msh, eikonal_msh, elasticity_msh, fluid_msh, reference_msh, phie_recv_msh, unset_msh, num_msh }
	The enum identifying the different meshes we might want to load. More...

enum	PotType { VM, PHIE }

enum	ActMethod { NONE, ACT_THRESH, ACT_DT }

enum	physic_t { ion_phys =0, elec_phys, mech_phys, diffK_phys, magnet_phys, opt_phys, fluid_phys, NUM_PHYSICS }
	Identifier for the different physics we want to set up. More...

enum	datavec_t { vm_vec, iion_vec }
	Enum used to adress the different data vectors stored in the data registry. More...

enum	waveform_t { squarePulse = 0, truncExpPulse, sinePulse, arbPulse, constPulse, unsetPulse }

enum	stim_t { I_tm =0, I_ex =1, V_ex =2, GND_ex =3, I_in =4, V_ex_ol =5, Illum =6, I_tm_grad =7, I_lat =8, Vm_clmp =9, Phie_pre =10, Ignore_stim =11 }

enum	stim_domain_t { intra_stim = 1, purk_stim = 2, all_stim = 3 }

enum	io_time { iotm_console = 0, iotm_state_var, iotm_spacedt, iotm_chkpt_list, iotm_chkpt_intv, iotm_trace, iotm_num_timers }
	The timers we always need are indexed in this enum. More...

enum	t_timer { EQUDIST, NONEQUDIST }
	We distinguish between equidistant and non-equidistant timers with an enum. More...

Functions
void	parse_params_cpy (int argc, char **argv)
	Initialize input parameters on a copy of the real command line parameters. More...

void	register_physics ()
	Register physics to the physics registry. More...

void	initialize_physics ()
	Initialize all physics in the registry. More...

void	destroy_physics ()
	Destroy all physics in the registry. More...

void	ignore_extracellular_stim (Stimulus *st, int ns, int ignore)

int	set_ignore_flags (int mode)

void	check_nullspace_ok ()

void	show_build_info ()
	show the build info, exit if -buildinfo was provided. This code runs before MPI_Init(). More...

void	check_and_convert_params ()
	Here we want to put all parameter checks, conversions and modifications that have been littered throughout the codebase. More...

void	set_io_dirs (char sim_ID, char pp_ID, IO_t init)

bool	setup_IO (int argc, char **argv)

void	update_cwd ()
	save the current working directory to curdir so that we can switch back to it if needed. More...

int	set_dir (IO_t dest)

void	basic_timer_setup ()
	Here we set up the timers that we always want to have, independent of physics. More...

void	get_protocol_column_widths (std::vector< int > &col_width, std::vector< int > &used_timer_ids)

int	plot_protocols (const char *fname)
	plot simulation protocols (I/O timers, stimuli, boundary conditions, etc) More...

void	init_console_output (const timer_manager &tm, prog_stats &p)

void	time_to_string (float time, char *str, short str_size)

void	update_console_output (const timer_manager &tm, prog_stats &p)

void	simulate ()
	Main simulate loop. More...

void	post_process ()
	do postprocessing More...

Basic_physic *	get_physics (physic_t p, bool error_if_missing=true)
	Convinience function to get a physics. More...

sf_vec *	get_data (datavec_t d)
	Retrieve a petsc data vector from the data registry. More...

void	register_data (sf_vec *dat, datavec_t d)
	Register a data vector in the global registry. More...

void	parse_mesh_types ()
	Parse the phys_type CLI parameters and set up (empty) SF::meshdata meshes. More...

void	retag_elements (sf_mesh &mesh, TagRegion *tagRegs, int ntr)

size_t	renormalise_fibres (SF::vector< mesh_real_t > &fib, size_t l_numelem)

void	setup_meshes ()
	Read in the reference mesh and use its data to populate all meshes registered in the mesh registry. More...

void	output_meshes ()

void	cleanup_and_exit ()

char *	get_file_dir (const char *file)

void	setup_petsc_err_log ()
	set up error logs for PETSc, so that it doesnt print errors to stderr. More...

short	get_mesh_dim (mesh_t id)
	get (lowest) dimension of the mesh used in the experiment More...

void	output_parameter_file (const char fname, int argc, char *argv)

void	savequit ()
	save state and quit simulator More...

unsigned int	classify_soln_methods ()

void	parse_comment_line (char *buff, const int buffsize, std::map< std::string, std::string > &metadata)

void	read_metadata (const std::string filename, std::map< std::string, std::string > &metadata, MPI_Comm comm)
	Read metadata from the header. More...

char *	skip_comments (FILE_SPEC stream, char *readbuff, size_t buffsize, MPI_Comm comm)

void	indices_from_region_tag (SF::vector< mesh_int_t > &idx, const sf_mesh &mesh, const int tag)
	Populate vertex data with the vertices of a given tag region. More...

void	indices_from_geom_shape (SF::vector< mesh_int_t > &idx, const sf_mesh &mesh, const geom_shape shape, const bool nodal)
	Populate vertex data with the vertices inside a defined box shape. More...

SF_real	get_volume_from_nodes (sf_mat &mass, SF::vector< mesh_int_t > &local_idx)

void	warn_when_passing_intra_vtx (const std::string filename)

template<class T >
void	read_indices_global (SF::vector< T > &idx, const std::string filename, MPI_Comm comm)

template<class T >
void	read_indices (SF::vector< T > &idx, const std::string filename, const hashmap::unordered_map< mesh_int_t, mesh_int_t > &dd_map, MPI_Comm comm)
	Read indices from a file. More...

template<class T >
void	read_indices (SF::vector< T > &idx, const std::string filename, const sf_mesh &mesh, const SF::SF_nbr nbr, const bool algebraic, MPI_Comm comm)
	Read indices from a file. More...

template<class T >
void	read_indices (SF::vector< T > &idx, const std::string filename, const SF::vector< mesh_int_t > &dd_nbr, MPI_Comm comm)
	Read indices from a file. More...

template<class T , class S >
void	read_indices_with_data (SF::vector< T > &idx, SF::vector< S > &dat, const std::string filename, const hashmap::unordered_map< mesh_int_t, mesh_int_t > &dd_map, const int dpn, MPI_Comm comm)
	like read_indices, but with associated data for each index More...

template<class T , class S >
void	read_indices_with_data (SF::vector< T > &idx, SF::vector< S > &dat, const std::string filename, const sf_mesh &mesh, const SF::SF_nbr nbr, const bool algebraic, const int dpn, MPI_Comm comm)
	like read_indices, but with associated data for each index More...

template<class T , class S >
void	read_indices_with_data (SF::vector< T > &idx, SF::vector< S > &dat, const std::string filename, const SF::vector< mesh_int_t > &dd_nbr, const int dpn, MPI_Comm comm)
	like read_indices, but with associated data for each index More...

sf_mesh &	get_mesh (const mesh_t gt)
	Get a mesh by specifying the gridID. More...

const char *	get_mesh_type_name (mesh_t t)
	get a char* to the name of a mesh type More...

bool	mesh_is_registered (const mesh_t gt)
	check wheter a SF mesh is set More...

SF::scattering *	register_scattering (const int from, const int to, const SF::SF_nbr nbr, const int dpn)
	Register a scattering between to grids, or between algebraic and nodal representation of data on the same grid. More...

SF::scattering *	get_scattering (const int from, const int to, const SF::SF_nbr nbr, const int dpn)
	Get a scattering from the global scatter registry. More...

bool	have_scattering (const int from, const int to, const SF::SF_nbr nbr, const int dpn)

SF::scattering *	register_permutation (const int mesh_id, const int perm_id, const int dpn)
	Register a permutation between two orderings for a mesh. More...

SF::scattering *	get_permutation (const int mesh_id, const int perm_id, const int dpn)
	Get the PETSC to canonical permutation scattering for a given mesh and number of dpn. More...

bool	have_permutation (const int mesh_id, const int perm_id, const int dpn)

SF::scattering *	register_scattering (const int from, const int to, const int dpn)

SF::scattering *	get_scattering (const int from, const int to, const int dpn)

bool	have_scattering (const int from, const int to, const int dpn)

int	get_preferred_int_order (SF::elem_t &etype, int mat_type)

void	print_element_info (const SF::element_view< mesh_int_t, mesh_real_t > &elem, const int reg, const double vol, const double eVals, const char *msg_start)

void	get_conductivity_evals (const elecMaterial &emat, const bool is_bath, double *evals)

void	get_conductivity (const double evals, const SF::Point f, const SF::Point *s, SF::dmat< double > &cond)

void	print_points (SF::Point *pts, int npts)

void	set_elec_tissue_properties (MaterialType *mtype, Electrics::grid_t g, FILE_SPEC logger)
	Fill the RegionSpec of an electrics grid with the associated inputs from the param parameters. More...

void	balance_electrode (SF::vector< stimulus > &stimuli, int balance_from, int balance_to)

void	apply_stim_to_vector (const stimulus &s, sf_vec &vec, bool add)

void	compute_restr_idx (sf_mesh &mesh, SF::vector< mesh_int_t > &inp_idx, SF::vector< mesh_int_t > &idx)

void	compute_restr_idx_async (sf_mesh &mesh, SF::vector< mesh_int_t > &inp_idx, SF::vector< mesh_int_t > &idx)

void	setup_dataout (const int dataout, std::string dataout_vtx, mesh_t grid, SF::vector< mesh_int_t > *&restr, bool async=false)

int	stimidx_from_timeridx (const SF::vector< stimulus > &stimuli, const int timer_id)
	determine link between timer and stimulus More...

void	get_kappa (sf_vec &kappa, IMPregion *ir, limpet::MULTI_IF &miif, double k)
	compute the vector $\kappa = \frac{\beta C_m}{\Delta t}$ More...

void	set_cond_type (MaterialType &m, cond_t type)

bool	have_dbc_stims (const SF::vector< stimulus > &stimuli)
	return wheter any stimuli require dirichlet boundary conditions More...

const char *	get_tsav_ext (double time)

void	print_act_log (FILE_SPEC logger, const SF::vector< Activation > &acts, int idx)

int	output_all_activations (FILE_SPEC fp, int ibuf, double act_tbuf, int nlacts)

void	recover_phie_std (sf_vec &vm, phie_recovery_data &rcv)

int	postproc_recover_phie ()

void	setup_phie_recovery_data (phie_recovery_data &data)

void	constant_total_stimulus_current (SF::vector< stimulus > &stimuli, sf_mat &mass_i, sf_mat &mass_e, limpet::MULTI_IF *miif, FILE_SPEC logger)

void	initialize_sv_dumps (limpet::MULTI_IF pmiif, IMPregion reg, int id, double t, double dump_dt)

bool	check_tags_in_elems (const SF::vector< int > &tags, SF::vector< RegionSpecs > &regspec, const char gridname, const char reglist)
	Check whether the tags in the region spec struct matches with an array of tags. More...

void	region_mask (mesh_t meshspec, SF::vector< RegionSpecs > &regspec, SF::vector< int > &regionIDs, bool mask_elem, const char *reglist)
	classify elements/points as belonging to a region More...

void	compute_IIF (limpet::IonIfBase &pIF, limpet::GlobalData_t **impdata, int n)

void *	find_SV_in_IMP (limpet::MULTI_IF miif, const int idx, const char IMP, const char SV, int offset, int *sz)

void	alloc_gvec_data (const int nGVcs, const int nRegs, GVecs *prmGVecs, gvec_data &glob_vecs)

void	init_sv_gvec (gvec_data &GVs, limpet::MULTI_IF *miif, sf_vec &tmpl, igb_output_manager &output_manager)

void	assemble_sv_gvec (gvec_data &gvecs, limpet::MULTI_IF *miif)

void	init_stim_info (void)

bool	is_voltage (stim_t type)
	uses voltage as stimulation More...

bool	is_current (stim_t type)
	uses current as stimulation More...

bool	is_dbc (stim_t type)
	whether stimulus is a dirichlet type. implies boundary conditions on matrix More...

bool	is_extra (stim_t type)
	whether stimulus is on extra grid (or on intra) More...

void	get_stim_list (const char *str_list, std::vector< double > &stlist)

void	sample_wave_form (stim_pulse &sp, int idx)
	sample a signal given in analytic form More...

void	sltlst_append (Salt_list sl, void p, int quantum)

char *	dupstr (const char *old_str)

char *	stringify (double r)

std::string	get_basename (const std::string &path)

void	log_msg (FILE_SPEC out, int level, unsigned char flag, const char *fmt,...)

bool	f_exist (const char *fname)

FILE_SPEC	f_open (const char fname, const char mode)
	Open a FILE_SPEC. More...

void	f_close (FILE_SPEC &f)
	Close a FILE_SPEC. More...

void	f_read_par (void *ptr, size_t size, size_t nmemb, FILE_SPEC stream, MPI_Comm comm=PETSC_COMM_WORLD)
	Parallel fread. Root reads, then broadcasts. More...

void	f_write_par (void *ptr, size_t size, size_t nmemb, int source_pid, FILE_SPEC stream, MPI_Comm comm=PETSC_COMM_WORLD)
	Write in parallel. Data comes from one rank, rank 0 writes. More...

char *	f_gets_par (char *s, int size, FILE_SPEC stream, MPI_Comm comm)

void	write_bin_string (FILE_SPEC out, const char *s)

char *	read_bin_string (FILE_SPEC in)

char *	read_bin_string_par (FILE_SPEC in)

bool	point_in_shape (const Point &p, const geom_shape &shape)
	test if a point is inside a simple geometric shape More...

bool	is_big_endian ()

bool	file_can_be_opened (const char *file)
	Check wheterh a file can be opened for reading. More...

bool	path_is_absolute (const char *path)
	check whether path is absolute More...

template<class STRVEC >
void	split_string (const std::string &input, const char s, STRVEC &list)
	Split a string holding a character-seperated list into a vector of strings. More...

template<typename T >
T	get_global (T in, MPI_Op OP, MPI_Comm comm=PETSC_COMM_WORLD)
	Do a global reduction on a variable. More...

template<>
int	get_global< int > (int in, MPI_Op OP, MPI_Comm comm)

template<>
long int	get_global< long int > (long int in, MPI_Op OP, MPI_Comm comm)

template<typename T >
void	get_global (SF::vector< T > &vec, int sender=0, MPI_Comm comm=PETSC_COMM_WORLD)
	Broadcast a SF::vector to all processes. More...

int	get_rank (MPI_Comm comm=PETSC_COMM_WORLD)

int	get_size (MPI_Comm comm=PETSC_COMM_WORLD)

int	get_remote_size (MPI_Comm intercomm)

void	init_iterations_logger (FILE_SPEC &logger, const char filename)
	init a logger for solver iterations More...

void	remove_preceding_char (char *buff, const int buffsize, const char c)

void	remove_char (char *buff, const int buffsize, const char c)

bool	has_char (char *buff, const int buffsize, const char c)

void	get_time (double &tm)

double	get_time ()

template<typename V >
V	timing (V &t2, const V &t1)

int	my_fputs (FILE , char )

template<class T >
int	read_IGB_data (T dp, int numt, IGBheader h, char *buf=NULL)

template<class T >
T	IGB_convert_buffer_datum (IGBheader , void buf, int a)

template<typename V >
V	det3 (const vec3< V > &a, const vec3< V > &b, const vec3< V > &c)

template<typename V >
V	dist_2 (const vec3< V > &p1, const vec3< V > &p2)

template<typename V >
V	dist (const vec3< V > &p1, const vec3< V > &p2)

template<typename V >
V	angle (const vec3< V > &v1, const vec3< V > &v2)

template<typename V >
V	dot (const vec3< V > &p1, const vec3< V > &p2)

template<typename V >
V	mag (const vec3< V > &vect)

template<typename V >
V	mag2 (const vec3< V > &vect)

template<typename V >
vec3< V >	cross (const vec3< V > &a, const vec3< V > &b)

template<typename V , typename S >
vec3< V >	scal_X (const vec3< V > &a, S k)

template<typename V >
vec3< V >	operator* (const vec3< V > &a, V k)

template<typename V >
vec3< V >	operator/ (const vec3< V > &a, V k)

template<typename V >
vec3< V >	scale3 (const vec3< V > &a, const vec3< V > &k)

template<typename V >
vec3< V >	operator- (const vec3< V > &a, const vec3< V > &b)

template<typename V >
vec3< V >	operator+ (const vec3< V > &a, const vec3< V > &b)

template<typename V >
vec3< V >	normalize (vec3< V > a)

template<typename V >
double *	v_scale (int n, double a, double k, double b)

template<typename V >
float *	v_scale_f (int n, float a, double k, double b)

template<typename V >
vec3< V >	mid_point (vec3< V > a, vec3< V > b)

template<typename V >
vec3< V >	rotate_z (vec3< V > p, double theta)

template<typename V >
vec3< V >	rotate_y (vec3< V > p, double theta)

template<typename V >
vec3< V >	rotate_x (vec3< V > p, double theta)

void	matrix_mathematica (int n, double *a, char outfile)

template<typename V >
vec3< V >	p_project (vec3< V > A, vec3< V > B)

template<typename V >
vec3< V >	p_transverse (vec3< V > A, vec3< V > B)

template<typename V >
double	triple_prod (vec3< V > a, vec3< V > b, vec3< V > c)

template<typename V >
bool	isNaN (vec3< V > a)

template<typename V >
double	infnorm (const vec3< V > &a)

Variables
const std::string	wfLabels [] = {"squarePulse", "truncExpPulse", "sinePulse", "arbPulse"}

bool	Header_Quiet = false

char	Header_Message [256]

const char *	Header_Type []

const char *	deprecated []

unsigned short	Data_Size []

int	Num_Components []

long unsigned	Header_Systeme_No []

const char *	Header_Systeme []

const uint16_t	basetable [512]

const uint16_t	shifttable [512]

const uint32_t	mantissatable [2048]

const uint16_t	offsettable [64]

const uint32_t	exponenttable [64]

Typedef Documentation

◆ Any

typedef void opencarp::Any

Definition at line 145 of file IGBheader.h.

◆ BooleaN

typedef int opencarp::BooleaN

Definition at line 136 of file IGBheader.h.

◆ byte

typedef unsigned char opencarp::byte

Definition at line 122 of file IGBheader.h.

◆ Byte

typedef unsigned char opencarp::Byte

Definition at line 124 of file IGBheader.h.

◆ Char

typedef signed char opencarp::Char

Definition at line 127 of file IGBheader.h.

◆ D_Complex

typedef struct D_Complex opencarp::D_Complex

Definition at line 130 of file IGBheader.h.

◆ Double

typedef double opencarp::Double

Definition at line 129 of file IGBheader.h.

◆ FILE_SPEC

typedef file_desc* opencarp::FILE_SPEC

Definition at line 138 of file basics.h.

◆ Flag

typedef int opencarp::Flag

Definition at line 137 of file IGBheader.h.

◆ Float

typedef float opencarp::Float

Definition at line 131 of file IGBheader.h.

◆ Int

typedef int opencarp::Int

Definition at line 132 of file IGBheader.h.

◆ List

typedef struct opencarp::List opencarp::List

◆ Long

typedef long opencarp::Long

Definition at line 133 of file IGBheader.h.

◆ Point

typedef vec3<POINT_REAL> opencarp::Point

Definition at line 93 of file vect.h.

◆ RDir

typedef char* opencarp::RDir

Definition at line 138 of file IGBheader.h.

◆ RFile

typedef char* opencarp::RFile

Definition at line 139 of file IGBheader.h.

◆ rgba

typedef union opencarp::rgba opencarp::rgba

◆ RWDir

typedef char* opencarp::RWDir

Definition at line 140 of file IGBheader.h.

◆ RWFile

typedef char* opencarp::RWFile

Definition at line 141 of file IGBheader.h.

◆ S_Complex

typedef struct S_Complex opencarp::S_Complex

Definition at line 128 of file IGBheader.h.

◆ sf_mat

typedef SF::abstract_matrix<mesh_int_t,double> opencarp::sf_mat

Shorthand for abstract matrix. Uses double value type.

Definition at line 51 of file sf_interface.h.

◆ sf_mesh

typedef SF::meshdata<mesh_int_t,mesh_real_t> opencarp::sf_mesh

Shorthand type for the mesh. Uses mesh_real_t (float) as value type.

Definition at line 47 of file sf_interface.h.

◆ sf_sol

typedef SF::abstract_linear_solver<mesh_int_t,double> opencarp::sf_sol

Shorthand for abstract linear solver. Uses double value type.

Definition at line 53 of file sf_interface.h.

◆ sf_vec

typedef SF::abstract_vector<mesh_int_t,double> opencarp::sf_vec

Shorthand for abstract vector. Uses double value type.

Definition at line 49 of file sf_interface.h.

◆ Short

typedef short opencarp::Short

Definition at line 135 of file IGBheader.h.

◆ short_float

typedef uint16_t opencarp::short_float

Definition at line 48 of file short_float.h.

◆ String

typedef char* opencarp::String

Definition at line 125 of file IGBheader.h.

◆ Text

typedef char** opencarp::Text

Definition at line 144 of file IGBheader.h.

◆ UInt

typedef unsigned int opencarp::UInt

Definition at line 134 of file IGBheader.h.

◆ WDir

typedef char* opencarp::WDir

Definition at line 142 of file IGBheader.h.

◆ WFile

typedef char* opencarp::WFile

Definition at line 143 of file IGBheader.h.

Enumeration Type Documentation

◆ ActMethod

enum opencarp::ActMethod

Enumerator
NONE
ACT_THRESH
ACT_DT

Definition at line 161 of file electrics.h.

◆ cond_t

enum opencarp::cond_t

description of electrical tissue properties

Enumerator
intra_cond
extra_cond
sum_cond
para_cond

Definition at line 42 of file fem_types.h.

◆ datavec_t

enum opencarp::datavec_t

Enum used to adress the different data vectors stored in the data registry.

Enumerator
vm_vec
iion_vec

Definition at line 99 of file physics_types.h.

◆ IO_t

enum opencarp::IO_t

The different output (directory) types.

Enumerator
INPUT
OUTPUT
POSTPROC
CURDIR

Definition at line 52 of file sim_utils.h.

◆ io_time

enum opencarp::io_time

The timers we always need are indexed in this enum.

Enumerator
iotm_console
iotm_state_var
iotm_spacedt
iotm_chkpt_list
iotm_chkpt_intv
iotm_trace
iotm_num_timers

Definition at line 44 of file timer_utils.h.

◆ mesh_t

enum opencarp::mesh_t

The enum identifying the different meshes we might want to load.

Enumerator
intra_elec_msh
extra_elec_msh
eikonal_msh
elasticity_msh
fluid_msh
reference_msh
phie_recv_msh
unset_msh
num_msh

Definition at line 58 of file sf_interface.h.

◆ physic_t

enum opencarp::physic_t

Identifier for the different physics we want to set up.

The order of the physics defines the order the in which initialize(), compute_step() and output_step() will be called.

The physic_t does not correspond directly to mesh_t, since we have multiple physics defined on one mesh (electrics).

Enumerator
ion_phys
elec_phys
mech_phys
diffK_phys
magnet_phys
opt_phys
fluid_phys
NUM_PHYSICS

Definition at line 51 of file physics_types.h.

◆ physMat_t

enum opencarp::physMat_t

identifier for physical material properties

Enumerator
PhysMat
ElecMat
DiffuseMat
MechMat
OpticsMat

Definition at line 39 of file fem_types.h.

◆ PotType

enum opencarp::PotType

Enumerator
VM
PHIE

Definition at line 160 of file electrics.h.

◆ stim_domain_t

enum opencarp::stim_domain_t

Enumerator
intra_stim
purk_stim
all_stim

Definition at line 84 of file stimulate.h.

◆ stim_t

enum opencarp::stim_t

Enumerator
I_tm
I_ex
V_ex
GND_ex
I_in
V_ex_ol
Illum
I_tm_grad
I_lat
Vm_clmp
Phie_pre
Ignore_stim

Definition at line 83 of file stimulate.h.

◆ t_timer

enum opencarp::t_timer

We distinguish between equidistant and non-equidistant timers with an enum.

Enumerator
EQUDIST
NONEQUDIST

Definition at line 49 of file timer_utils.h.

◆ tagreg_t

enum opencarp::tagreg_t

tag regions types. must be in line with carp.prm

Enumerator
tagreg_sphere
tagreg_block
tagreg_cylinder
tagreg_list

Definition at line 55 of file sim_utils.h.

◆ waveform_t

enum opencarp::waveform_t

Enumerator
squarePulse
truncExpPulse
sinePulse
arbPulse
constPulse
unsetPulse

Definition at line 79 of file stimulate.h.

Function Documentation

◆ alloc_gvec_data()

void opencarp::alloc_gvec_data	(	const int	nGVcs,
		const int	nRegs,
		GVecs *	prmGVecs,
		gvec_data &	glob_vecs
	)

Convert PrM data to internal data structures

Parameters

NGVcs	number of global (composite) state vectors
nRegs	number of IMP regions defined over entire domain
prmGVecs	Global composite vector structure to unPrM
GlobalVecs	store data needed to compose gloabl vectors

Postcondition: The GlobalVecs structure is allocated and initialized with prm values

Definition at line 506 of file ionics.cc.

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◆ angle()

template<typename V >

V opencarp::angle	(	const vec3< V > &	v1,
		const vec3< V > &	v2
	)

inline

Definition at line 120 of file vect.h.

◆ apply_stim_to_vector()

void opencarp::apply_stim_to_vector	(	const stimulus &	s,
		sf_vec &	vec,
		bool	add
	)

Definition at line 427 of file electrics.cc.

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◆ assemble_sv_gvec()

void opencarp::assemble_sv_gvec	(	gvec_data &	gvecs,
		limpet::MULTI_IF *	miif
	)

output the global vector

Parameters

Gvec	global vectors
miif	IMPs
purk	Purkinje system

Note: all Svs are converted to type real; Gvec->getsv should really be declared as a SVgetfcn but the header dependency got really ugly so it is void* and then typecast

Definition at line 628 of file ionics.cc.

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◆ balance_electrode()

void opencarp::balance_electrode	(	SF::vector< stimulus > &	stimuli,
		int	balance_from,
		int	balance_to
	)

Definition at line 366 of file electrics.cc.

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◆ basic_timer_setup()

void opencarp::basic_timer_setup ( )

Here we set up the timers that we always want to have, independent of physics.

Parameters

start_time Start time of the simulation

Definition at line 458 of file sim_utils.cc.

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◆ check_and_convert_params()

void opencarp::check_and_convert_params ( )

Here we want to put all parameter checks, conversions and modifications that have been littered throughout the codebase.

Usualy people modify param globals next to the code that is affected by that change. This works well first, but after some time a lot of state is accumulated to the initially stateless functions. As such, the code works only if the order of function calls etc is not changed. In the long term it is better to accumulate all changes and checks of globals in specific functions so that the rest of the codebase can be programmed and used stateless. -Aurel

Definition at line 227 of file sim_utils.cc.

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◆ check_nullspace_ok()

void opencarp::check_nullspace_ok ( )

check the Nullspace strategy of the setup for solving the elliptic PDE

Parameters

s	stimulus array
fGND	floating ground

Return values

true	if strategy is ok, i.e. either we specify a potential, a floating ground or a dedicated strategy (expicit enforcement of zero mean, etc)
false	system is singular

Definition at line 199 of file sim_utils.cc.

◆ check_tags_in_elems()

bool opencarp::check_tags_in_elems	(	const SF::vector< int > &	tags,
		SF::vector< RegionSpecs > &	regspec,
		const char *	gridname,
		const char *	reglist
	)

Check whether the tags in the region spec struct matches with an array of tags.

Parameters

tags	Tags vector.
regspec	Array of region spec structs
gridname	Grid name (for message output)
reglist	Name of the regspec list.

Returns: Whether all tags are present.

Definition at line 323 of file ionics.cc.

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◆ classify_soln_methods()

unsigned int opencarp::classify_soln_methods ( )

determine the solution methods

Note: We use the PrM variables

Returns: integer with solution methods bits set

◆ cleanup_and_exit()

void opencarp::cleanup_and_exit ( )

Definition at line 1216 of file sim_utils.cc.

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◆ compute_IIF()

void opencarp::compute_IIF	(	limpet::IonIfBase &	pIF,
		limpet::GlobalData_t **	impdata,
		int	n
	)

simple routine to run ionic models for prepacing

pIF ionic model

Parameters

impdata	data for ionic model
n	node to compute

Note: Only one node is run

Definition at line 458 of file ionics.cc.

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◆ compute_restr_idx()

void opencarp::compute_restr_idx	(	sf_mesh &	mesh,
		SF::vector< mesh_int_t > &	inp_idx,
		SF::vector< mesh_int_t > &	idx
	)

Definition at line 521 of file electrics.cc.

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◆ compute_restr_idx_async()

void opencarp::compute_restr_idx_async	(	sf_mesh &	mesh,
		SF::vector< mesh_int_t > &	inp_idx,
		SF::vector< mesh_int_t > &	idx
	)

Definition at line 554 of file electrics.cc.

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◆ constant_total_stimulus_current()

void opencarp::constant_total_stimulus_current	(	SF::vector< stimulus > &	simuli,
		sf_mat &	mass_i,
		sf_mat &	mass_e,
		limpet::MULTI_IF *	miif,
		FILE_SPEC	logger
	)

scale current densities to keep total injected current constant

Parameters

[in]	stimuli	The stimuli vector.
[in]	mass_i	intracellular mass matrix,
[in]	mass_e	extracellular mass matrix,
[in]	miif	ionic interface
[in]	logger	handle to output log

Note: We assume that the strength is in uA

Definition at line 2162 of file electrics.cc.

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◆ cross()

template<typename V >

vec3<V> opencarp::cross	(	const vec3< V > &	a,
		const vec3< V > &	b
	)

inline

Definition at line 144 of file vect.h.

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◆ destroy_physics()

void opencarp::destroy_physics ( )

Destroy all physics in the registry.

Definition at line 124 of file sim_utils.cc.

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◆ det3()

template<typename V >

V opencarp::det3	(	const vec3< V > &	a,
		const vec3< V > &	b,
		const vec3< V > &	c
	)

inline

Definition at line 96 of file vect.h.

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◆ dist()

template<typename V >

V opencarp::dist	(	const vec3< V > &	p1,
		const vec3< V > &	p2
	)

inline

Definition at line 114 of file vect.h.

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◆ dist_2()

template<typename V >

V opencarp::dist_2	(	const vec3< V > &	p1,
		const vec3< V > &	p2
	)

inline

Definition at line 102 of file vect.h.

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◆ dot()

template<typename V >

V opencarp::dot	(	const vec3< V > &	p1,
		const vec3< V > &	p2
	)

inline

Definition at line 125 of file vect.h.

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◆ dupstr()

char * opencarp::dupstr ( const char * old_str )

duplicates a string

Parameters

old_str string that needs to be duplicated

Returns: duplicated string

Definition at line 44 of file basics.cc.

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◆ f_close()

void opencarp::f_close ( FILE_SPEC & f )

Close a FILE_SPEC.

Parameters

f	the FILE_SPEC to close;

Definition at line 162 of file basics.cc.

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◆ f_exist()

bool opencarp::f_exist ( const char * fname )

check existence of file

Parameters

[in] fname name of file

Returns: true, if file exists false, otherwise

Definition at line 130 of file basics.cc.

◆ f_gets_par()

char * opencarp::f_gets_par	(	char *	s,
		int	size,
		FILE_SPEC	stream,
		MPI_Comm	comm
	)

Definition at line 199 of file basics.cc.

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◆ f_open()

FILE_SPEC opencarp::f_open	(	const char *	fname,
		const char *	mode
	)

Open a FILE_SPEC.

Parameters

fname	File name
mode	Mode for fopen()

Returns: The new FILE_SPEC pointer

Definition at line 135 of file basics.cc.

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◆ f_read_par()

void opencarp::f_read_par	(	void *	ptr,
		size_t	size,
		size_t	nmemb,
		FILE_SPEC	stream,
		MPI_Comm	comm = `PETSC_COMM_WORLD`
	)

Parallel fread. Root reads, then broadcasts.

Parameters

ptr	Pointer to the buffer we read into
size	Data type size_t
nmemb	Number of data members to read
stream	FILE_SPEC to use.
comm	The MPI communicator to use.

Definition at line 171 of file basics.cc.

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◆ f_write_par()

void opencarp::f_write_par	(	void *	ptr,
		size_t	size,
		size_t	nmemb,
		int	source_pid,
		FILE_SPEC	stream,
		MPI_Comm	comm = `PETSC_COMM_WORLD`
	)

Write in parallel. Data comes from one rank, rank 0 writes.

Parameters

ptr	Buffer to write. Needs only be allocated on rank source_pid.
size	Size of data type.
nmemb	Number of data members. Needs only be set on rank source_pid.
source_pid	The PID of the rank the data is on.
stream	The file we write to. Needs only be valid rank 0.
comm	The MPI communicator to use.

Definition at line 179 of file basics.cc.

◆ file_can_be_opened()

bool opencarp::file_can_be_opened ( const char * file )

Check wheterh a file can be opened for reading.

Parameters

file	Path to the file to check.

Returns: Whether the file could be opened.

Definition at line 301 of file basics.cc.

◆ find_SV_in_IMP()

void* opencarp::find_SV_in_IMP	(	limpet::MULTI_IF *	miif,
		const int	idx,
		const char *	IMP,
		const char *	SV,
		int *	offset,
		int *	sz
	)

search an IMP and its plugins for a state variable

Parameters

[in]	miif	ionic structure
[in]	inx	region index of the `miif` to search
[in]	IMP	IMP name to look in
[in]	SV	state variable to find
[out]	offset	offset into IMP state variable structure
[out]	sz	size of SV structure

Returns: the function to extract the desired SV, NULL if SV not found

Definition at line 480 of file ionics.cc.

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◆ get_basename()

std::string opencarp::get_basename ( const std::string & path )

Definition at line 61 of file basics.cc.

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◆ get_conductivity()

void opencarp::get_conductivity	(	const double *	evals,
		const SF::Point *	f,
		const SF::Point *	s,
		SF::dmat< double > &	cond
	)

Definition at line 117 of file electric_integrators.cc.

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◆ get_conductivity_evals()

void opencarp::get_conductivity_evals	(	const elecMaterial &	emat,
		const bool	is_bath,
		double *	evals
	)

Definition at line 86 of file electric_integrators.cc.

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◆ get_data()

sf_vec * opencarp::get_data ( datavec_t d )

Retrieve a petsc data vector from the data registry.

Parameters

d	The identifier of the data vector.

Returns: A pointer to the data vector.

Definition at line 834 of file sim_utils.cc.

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◆ get_file_dir()

char * opencarp::get_file_dir ( const char * file )

Definition at line 1231 of file sim_utils.cc.

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◆ get_global() [1/2]

template<typename T >

T opencarp::get_global	(	T	in,
		MPI_Op	OP,
		MPI_Comm	comm = `PETSC_COMM_WORLD`
	)

inline

Do a global reduction on a variable.

The variable gets internally cast to a double, then reduced and then cast back.

Template Parameters

T	Variable type.

Parameters

in	Local input variable.
OP	MPI operation to perform.

Returns: Globally reduced variable.

Definition at line 233 of file basics.h.

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◆ get_global() [2/2]

template<typename T >

void opencarp::get_global	(	SF::vector< T > &	vec,
		int	sender = `0`,
		MPI_Comm	comm = `PETSC_COMM_WORLD`
	)

inline

Broadcast a SF::vector to all processes.

Template Parameters

T	Datatype of vector entries

Parameters

vec	The vector we globalize
sender

Definition at line 264 of file basics.h.

◆ get_global< int >()

template<>

int opencarp::get_global< int >	(	int	in,
		MPI_Op	OP,
		MPI_Comm	comm
	)

inline

Definition at line 241 of file basics.h.

◆ get_global< long int >()

template<>

long int opencarp::get_global< long int >	(	long int	in,
		MPI_Op	OP,
		MPI_Comm	comm
	)

inline

Definition at line 249 of file basics.h.

◆ get_kappa()

void opencarp::get_kappa	(	sf_vec &	kappa,
		IMPregion *	ir,
		limpet::MULTI_IF &	miif,
		double	k
	)

compute the vector $\kappa = \frac{\beta C_m}{\Delta t}$

$\beta$ is the membrane surface area per unit tissue volume

Parameters

kappa	spatially varying kappa in vector form
ir	imp regions array provided by param
miif	miif class holding the ionic parameters
k	region-independent scaling factor

Definition at line 778 of file electrics.cc.

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◆ get_mesh()

sf_mesh & opencarp::get_mesh ( const mesh_t gt )

Get a mesh by specifying the gridID.

Parameters

gt	The grid ID.

Returns: The SF meshdata

Definition at line 33 of file sf_interface.cc.

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◆ get_mesh_dim()

short opencarp::get_mesh_dim ( mesh_t id )

get (lowest) dimension of the mesh used in the experiment

Definition at line 1255 of file sim_utils.cc.

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◆ get_mesh_type_name()

const char * opencarp::get_mesh_type_name ( mesh_t t )

get a char* to the name of a mesh type

Definition at line 46 of file sf_interface.cc.

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◆ get_permutation()

SF::scattering * opencarp::get_permutation	(	const int	mesh_id,
		const int	perm_id,
		const int	dpn
	)

Get the PETSC to canonical permutation scattering for a given mesh and number of dpn.

Parameters

mesh_id	The mesh id.
perm_id	The permutation specifier index (see sf_interface.h).
dpn	Degrees of freedom per node.

Returns: The scattering.

Definition at line 204 of file sf_interface.cc.

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◆ get_physics()

Basic_physic * opencarp::get_physics	(	physic_t	p,
		bool	error_if_missing = `true`
	)

Convinience function to get a physics.

Parameters

p	The physics type.

Returns: A pointer to the physics. NULL if physics is not present.

Definition at line 818 of file sim_utils.cc.

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◆ get_preferred_int_order()

int opencarp::get_preferred_int_order	(	SF::elem_t &	etype,
		int	mat_type
	)

inline

Definition at line 34 of file electric_integrators.cc.

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◆ get_protocol_column_widths()

void opencarp::get_protocol_column_widths	(	std::vector< int > &	col_width,
		std::vector< int > &	used_timer_ids
	)

Definition at line 493 of file sim_utils.cc.

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◆ get_rank()

int opencarp::get_rank ( MPI_Comm comm = PETSC_COMM_WORLD )

inline

get the rank of the process

Returns: the rank of the process

Definition at line 276 of file basics.h.

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◆ get_remote_size()

int opencarp::get_remote_size ( MPI_Comm intercomm )

inline

Definition at line 299 of file basics.h.

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◆ get_scattering() [1/2]

SF::scattering * opencarp::get_scattering	(	const int	from,
		const int	to,
		const SF::SF_nbr	nbr,
		const int	dpn
	)

Get a scattering from the global scatter registry.

Parameters

[in]	from	The mesh ID we scatter from.
[in]	to	The mesh ID we scatter to, or ALG_TO_NODAL.
[in]	nbr	The used numbering.
[in]	dpn	The degrees of freedom per node.

Returns: The requested scattering.

Definition at line 121 of file sf_interface.cc.

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◆ get_scattering() [2/2]

SF::scattering* opencarp::get_scattering	(	const int	from,
		const int	to,
		const int	dpn
	)

inline

Definition at line 153 of file sf_interface.h.

◆ get_size()

int opencarp::get_size ( MPI_Comm comm = PETSC_COMM_WORLD )

inline

allows to determine if we are running sequentially or in parallel.

Return values

0	sequential code
>=1	number of processes for parallel code

Definition at line 290 of file basics.h.

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◆ get_stim_list()

void opencarp::get_stim_list	(	const char *	str_list,
		std::vector< double > &	stlist
	)

Definition at line 264 of file stimulate.cc.

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◆ get_time() [1/2]

void opencarp::get_time ( double & tm )

inline

Definition at line 436 of file basics.h.

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◆ get_time() [2/2]

double opencarp::get_time ( )

inline

Definition at line 441 of file basics.h.

◆ get_tsav_ext()

const char* opencarp::get_tsav_ext ( double time )

helper function to get the tsav_ext string where the associated tsav value is closest to a given time

Definition at line 836 of file electrics.cc.

◆ get_volume_from_nodes()

SF_real opencarp::get_volume_from_nodes	(	sf_mat &	mass,
		SF::vector< mesh_int_t > &	local_idx
	)

Definition at line 202 of file fem_utils.cc.

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◆ has_char()

bool opencarp::has_char	(	char *	buff,
		const int	buffsize,
		const char	c
	)

inline

Definition at line 368 of file basics.h.

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◆ have_dbc_stims()

bool opencarp::have_dbc_stims ( const SF::vector< stimulus > & stimuli )

return wheter any stimuli require dirichlet boundary conditions

Definition at line 825 of file electrics.cc.

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◆ have_permutation()

bool opencarp::have_permutation	(	const int	mesh_id,
		const int	perm_id,
		const int	dpn
	)

Definition at line 215 of file sf_interface.cc.

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◆ have_scattering() [1/2]

bool opencarp::have_scattering	(	const int	from,
		const int	to,
		const SF::SF_nbr	nbr,
		const int	dpn
	)

Definition at line 132 of file sf_interface.cc.

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◆ have_scattering() [2/2]

bool opencarp::have_scattering	(	const int	from,
		const int	to,
		const int	dpn
	)

inline

Definition at line 157 of file sf_interface.h.

◆ IGB_convert_buffer_datum()

template<class T >

T opencarp::IGB_convert_buffer_datum	(	IGBheader *	,
		void *	buf,
		int	a
	)

◆ ignore_extracellular_stim()

void opencarp::ignore_extracellular_stim	(	Stimulus *	st,
		int	ns,
		int	ignore
	)

for monodomain simulations, ignore extracellular current and potentials and convert intracellular current injection to transmembrane

Parameters

st	specified stimuli ns #stimuli
ignore	flags type of stimuli to ignore 0: ignore extracellular GND 1: ignore extracellular voltage 2: ignore extracellular current

Postcondition: all stimuli which are not relevant for a particular mode are ignored by setting their type to Ignore_Stim

Definition at line 151 of file sim_utils.cc.

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◆ indices_from_geom_shape()

void opencarp::indices_from_geom_shape	(	SF::vector< mesh_int_t > &	idx,
		const sf_mesh &	mesh,
		const geom_shape	shape,
		const bool	nodal
	)

Populate vertex data with the vertices inside a defined box shape.

Parameters

mesh	The mesh.
shape	The shape we test against.
nodal	Whether to test mesh nodes, or mesh elements.

Postcondition: idx has been populated.

Definition at line 169 of file fem_utils.cc.

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◆ indices_from_region_tag()

void opencarp::indices_from_region_tag	(	SF::vector< mesh_int_t > &	idx,
		const sf_mesh &	mesh,
		const int	tag
	)

Populate vertex data with the vertices of a given tag region.

Parameters

mesh	The mesh.
tag	The tag region to compute the vertices for.

Postcondition: idx has been populated.

Definition at line 155 of file fem_utils.cc.

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◆ infnorm()

template<typename V >

double opencarp::infnorm ( const vec3< V > & a )

inline

Definition at line 322 of file vect.h.

◆ init_console_output()

void opencarp::init_console_output	(	const timer_manager &	tm,
		prog_stats &	p
	)

Definition at line 701 of file sim_utils.cc.

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◆ init_iterations_logger()

void opencarp::init_iterations_logger	(	FILE_SPEC *&	logger,
		const char *	filename
	)

init a logger for solver iterations

◆ init_stim_info()

void opencarp::init_stim_info ( void )

< transmembrane current

< extracellular current, volumetric source density

< extracellular voltage, closed loop

< ground (extracellular voltage)

< intracellular current

< extracellular voltage, open loop

<

< acts as transmembrane current stimulus

< clamps transmembrane voltate

< extracellular voltage, open loop

Definition at line 49 of file stimulate.cc.

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◆ init_sv_gvec()

void opencarp::init_sv_gvec	(	gvec_data &	GVs,
		limpet::MULTI_IF *	miif,
		sf_vec &	tmpl,
		igb_output_manager &	output_manager
	)

initialize the global state variable dumps

Parameters

GVs	SV dumps
miif	ionic models
purk	Purkine system
tmo	timer
grid	on what to output
tmpl	template vector to decide on parallel layout

Postcondition: more outputs are added to the grid

Definition at line 556 of file ionics.cc.

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◆ initialize_physics()

void opencarp::initialize_physics ( )

Initialize all physics in the registry.

Definition at line 100 of file sim_utils.cc.

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◆ initialize_sv_dumps()

void opencarp::initialize_sv_dumps	(	limpet::MULTI_IF *	pmiif,
		IMPregion *	reg,
		int	id,
		double	t,
		double	dump_dt
	)

wrapper function to initialize the list for sv dumping

Parameters

miif	multi-ionic interface structure
reg	region
id	ID of current region

Note: We assume that the region PrM structure is global

Definition at line 279 of file ionics.cc.

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◆ is_big_endian()

bool opencarp::is_big_endian ( )

determine endianness of a machine

Return values

true	if machine is bigendian
false	if machine is littleendian

Definition at line 290 of file basics.cc.

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◆ is_current()

bool opencarp::is_current ( stim_t type )

uses current as stimulation

Definition at line 71 of file stimulate.cc.

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◆ is_dbc()

bool opencarp::is_dbc ( stim_t type )

whether stimulus is a dirichlet type. implies boundary conditions on matrix

Definition at line 76 of file stimulate.cc.

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◆ is_extra()

bool opencarp::is_extra ( stim_t type )

whether stimulus is on extra grid (or on intra)

Definition at line 81 of file stimulate.cc.

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◆ is_voltage()

bool opencarp::is_voltage ( stim_t type )

uses voltage as stimulation

Parameters

type	uses voltage as stimulation

Definition at line 65 of file stimulate.cc.

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◆ isNaN()

template<typename V >

bool opencarp::isNaN ( vec3< V > a )

inline

check for NaN's

Definition at line 315 of file vect.h.

◆ log_msg()

void opencarp::log_msg	(	FILE_SPEC	out,
		int	level,
		unsigned char	flag,
		const char *	fmt,
			...
	)

output message into a log file

Parameters

out	output location, NULL implies ECHO
level	Severity level of message (0-5)
flags	the following may be or'ed: ECHO: print to screen LOCAL: every instance prints locally, must FLUSH to see output SYNCED: output all in order on rank 0 FLUSH: flush output, this is collective NONL: no new line at end By default, if `out` is NULL, the message is printed on the screen, and only rank 0 prints
fmt	format string for printf
...	values for format string

Note: levels range from 0 to MAX_LOG_LEVEL with 0 being normal and MAX_LOG_LEVEL indicating catastrophic failure. Levels greater than 0 are "errors" have the message prepended with the level.; a new line will be appended to the message unless NONL is specified

Precondition: _hdf5_out must be set before this routine is called

Note: to flush only, set fmt to NULL

Definition at line 72 of file basics.cc.

◆ mag()

template<typename V >

V opencarp::mag ( const vec3< V > & vect )

inline

Definition at line 131 of file vect.h.

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◆ mag2()

template<typename V >

V opencarp::mag2 ( const vec3< V > & vect )

inline

Definition at line 138 of file vect.h.

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◆ matrix_mathematica()

void opencarp::matrix_mathematica	(	int	n,
		double **	a,
		char *	outfile
	)

inline

Definition at line 264 of file vect.h.

◆ mesh_is_registered()

bool opencarp::mesh_is_registered ( const mesh_t gt )

check wheter a SF mesh is set

Definition at line 59 of file sf_interface.cc.

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◆ mid_point()

template<typename V >

vec3<V> opencarp::mid_point	(	vec3< V >	a,
		vec3< V >	b
	)

inline

Definition at line 231 of file vect.h.

◆ my_fputs()

int opencarp::my_fputs	(	FILE *	,
		char *
	)

◆ normalize()

template<typename V >

vec3<V> opencarp::normalize ( vec3< V > a )

inline

Definition at line 198 of file vect.h.

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◆ operator*()

template<typename V >

vec3<V> opencarp::operator*	(	const vec3< V > &	a,
		V	k
	)

inline

Definition at line 156 of file vect.h.

◆ operator+()

template<typename V >

vec3<V> opencarp::operator+	(	const vec3< V > &	a,
		const vec3< V > &	b
	)

inline

Definition at line 188 of file vect.h.

◆ operator-()

template<typename V >

vec3<V> opencarp::operator-	(	const vec3< V > &	a,
		const vec3< V > &	b
	)

inline

Definition at line 179 of file vect.h.

◆ operator/()

template<typename V >

vec3<V> opencarp::operator/	(	const vec3< V > &	a,
		V	k
	)

inline

Definition at line 162 of file vect.h.

◆ output_all_activations()

int opencarp::output_all_activations	(	FILE_SPEC	fp,
		int *	ibuf,
		double *	act_tbuf,
		int	nlacts
	)

Definition at line 1536 of file electrics.cc.

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◆ output_meshes()

void opencarp::output_meshes ( )

Output the meshes specified by the user

Definition at line 1164 of file sim_utils.cc.

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◆ output_parameter_file()

void opencarp::output_parameter_file	(	const char *	fname,
		int	argc,
		char **	argv
	)

output the command line and convert to a single parameter file

This involves including any parameter files specified with +F and stripping hyphens from command line options

Parameters

fname	output file name
argc	number of arguments
argv	arguments

Definition at line 1517 of file sim_utils.cc.

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◆ p_project()

template<typename V >

vec3<V> opencarp::p_project	(	vec3< V >	A,
		vec3< V >	B
	)

inline

project vector B onto unit normal A

Definition at line 292 of file vect.h.

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◆ p_transverse()

template<typename V >

vec3<V> opencarp::p_transverse	(	vec3< V >	A,
		vec3< V >	B
	)

inline

determines the orthogonal vector to the projection

Definition at line 300 of file vect.h.

◆ parse_comment_line()

void opencarp::parse_comment_line	(	char *	buff,
		const int	buffsize,
		std::map< std::string, std::string > &	metadata
	)

Definition at line 32 of file fem_utils.cc.

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◆ parse_mesh_types()

void opencarp::parse_mesh_types ( )

Parse the phys_type CLI parameters and set up (empty) SF::meshdata meshes.

Postcondition: The mesh registry is filled with SF::meshdata structs associated to the physics specified in the phys_region params.

Definition at line 854 of file sim_utils.cc.

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◆ parse_params_cpy()

void opencarp::parse_params_cpy	(	int	argc,
		char **	argv
	)

Initialize input parameters on a copy of the real command line parameters.

Parameters

argc	The true parameter count.
argv	The true cli parameters.

Definition at line 46 of file sim_utils.cc.

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◆ path_is_absolute()

bool opencarp::path_is_absolute ( const char * path )

check whether path is absolute

Definition at line 319 of file basics.cc.

◆ plot_protocols()

int opencarp::plot_protocols ( const char * )

plot simulation protocols (I/O timers, stimuli, boundary conditions, etc)

plot experimental/simulation protocols by stepping through all timers

Returns: -1, if protocol output file opening failure

Definition at line 536 of file sim_utils.cc.

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◆ point_in_shape()

bool opencarp::point_in_shape	(	const Point &	p,
		const geom_shape &	shape
	)

test if a point is inside a simple geometric shape

Definition at line 250 of file basics.cc.

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◆ post_process()

void opencarp::post_process ( )

do postprocessing

Definition at line 802 of file sim_utils.cc.

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◆ postproc_recover_phie()

int opencarp::postproc_recover_phie ( )

Definition at line 1927 of file electrics.cc.

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◆ print_act_log()

void opencarp::print_act_log	(	FILE_SPEC	logger,
		const SF::vector< Activation > &	acts,
		int	idx
	)

Definition at line 1442 of file electrics.cc.

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◆ print_element_info()

void opencarp::print_element_info	(	const SF::element_view< mesh_int_t, mesh_real_t > &	elem,
		const int *	reg,
		const double	vol,
		const double *	eVals,
		const char *	msg_start
	)

Definition at line 58 of file electric_integrators.cc.

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◆ print_points()

void opencarp::print_points	(	SF::Point *	pts,
		int	npts
	)

Definition at line 145 of file electric_integrators.cc.

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◆ read_bin_string()

char * opencarp::read_bin_string ( FILE_SPEC in )

read the length of a string followed by the string from a binary file

Parameters

in	the stream

Note: memory is allocated

Returns: the string

Definition at line 228 of file basics.cc.

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◆ read_bin_string_par()

char * opencarp::read_bin_string_par ( FILE_SPEC in )

MPI - parallel version of read_bin_string

read the length of a string followed by the string from a binary file

Parameters

in	the stream

Note: memory is allocated

Returns: the string

Definition at line 239 of file basics.cc.

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◆ read_IGB_data()

template<class T >

int opencarp::read_IGB_data	(	T *	dp,
		int	numt,
		IGBheader *	h,
		char *	buf = `NULL`
	)

◆ read_indices() [1/3]

template<class T >

void opencarp::read_indices	(	SF::vector< T > &	idx,
		const std::string	filename,
		const hashmap::unordered_map< mesh_int_t, mesh_int_t > &	dd_map,
		MPI_Comm	comm
	)

inline

Read indices from a file.

Template Parameters

T	The index type.

Parameters

[out]	idx	Vector with indices in local indexing.
[in]	filename	File path to read from.
[in]	dd_map	Global to local map.
[in]	comm	MPI communicator

Definition at line 120 of file fem_utils.h.

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◆ read_indices() [2/3]

template<class T >

void opencarp::read_indices	(	SF::vector< T > &	idx,
		const std::string	filename,
		const sf_mesh &	mesh,
		const SF::SF_nbr	nbr,
		const bool	algebraic,
		MPI_Comm	comm
	)

inline

Read indices from a file.

The global indices are mapped by a global-to-local map constrcuted from mesh, numbering and algebraic flag.

Template Parameters

T	The index type.

Parameters

[out]	idx	Vector with indices in local indexing.
[in]	filename	File path to read from.
[in]	mesh	The local mesh we localize on.
[in]	nbr	The numbering we localize for.
[in]	algebraic	Whether to keep the data nodal (overlapping) or algebraic (non-overlapping)
[in]	comm	MPI communicator

Definition at line 216 of file fem_utils.h.

◆ read_indices() [3/3]

template<class T >

void opencarp::read_indices	(	SF::vector< T > &	idx,
		const std::string	filename,
		const SF::vector< mesh_int_t > &	dd_nbr,
		MPI_Comm	comm
	)

inline

Read indices from a file.

The global indices are mapped by a global-to-local map constrcuted from a indexing vector.

Template Parameters

T	The index type.

Parameters

[out]	idx	Vector with indices in local indexing.
[in]	filename	File path to read from.
[in]	dd_nbr	Indexing vector used to construct global-to-local map.
[in]	comm	MPI communicator

Definition at line 254 of file fem_utils.h.

◆ read_indices_global()

template<class T >

void opencarp::read_indices_global	(	SF::vector< T > &	idx,
		const std::string	filename,
		MPI_Comm	comm
	)

inline

Definition at line 53 of file fem_utils.h.

◆ read_indices_with_data() [1/3]

template<class T , class S >

void opencarp::read_indices_with_data	(	SF::vector< T > &	idx,
		SF::vector< S > &	dat,
		const std::string	filename,
		const hashmap::unordered_map< mesh_int_t, mesh_int_t > &	dd_map,
		const int	dpn,
		MPI_Comm	comm
	)

inline

like read_indices, but with associated data for each index

Definition at line 269 of file fem_utils.h.

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◆ read_indices_with_data() [2/3]

template<class T , class S >

void opencarp::read_indices_with_data	(	SF::vector< T > &	idx,
		SF::vector< S > &	dat,
		const std::string	filename,
		const sf_mesh &	mesh,
		const SF::SF_nbr	nbr,
		const bool	algebraic,
		const int	dpn,
		MPI_Comm	comm
	)

inline

like read_indices, but with associated data for each index

Definition at line 375 of file fem_utils.h.

◆ read_indices_with_data() [3/3]

template<class T , class S >

void opencarp::read_indices_with_data	(	SF::vector< T > &	idx,
		SF::vector< S > &	dat,
		const std::string	filename,
		const SF::vector< mesh_int_t > &	dd_nbr,
		const int	dpn,
		MPI_Comm	comm
	)

inline

like read_indices, but with associated data for each index

Definition at line 403 of file fem_utils.h.

◆ read_metadata()

void opencarp::read_metadata	(	const std::string	filename,
		std::map< std::string, std::string > &	metadata,
		MPI_Comm	comm
	)

Read metadata from the header.

Parameters

filename	Filename to read from.
metadata	Metadata we populate.
comm	MPI communicator to use for parallel communication.

Definition at line 72 of file fem_utils.cc.

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◆ recover_phie_std()

void opencarp::recover_phie_std	(	sf_vec &	vm,
		phie_recovery_data &	rcv
	)

Definition at line 1867 of file electrics.cc.

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◆ region_mask()

void opencarp::region_mask	(	mesh_t	meshspec,
		SF::vector< RegionSpecs > &	regspec,
		SF::vector< int > &	regionIDs,
		bool	mask_elem,
		const char *	reglist
	)

classify elements/points as belonging to a region

Element tags in the elem files are grouped to construct regions. If points are to be assigned to a region, points on the boundary between regions belong to several regions. In this case, the point is assigned to the region with the highest number

Parameters

meshspec	Identifier for the mesh we work on.
regspec	Vector or region spec structs
regionIDs	Vector of element/nodal IDs (mapping into the region spec vec).
mask_elem	Whether we mask elements or points.
reglist	A string naming to region we work on for output.

Postcondition: The array holding the element region identifiers is allocated and filled. If there is only 1 region, regionIDs is set to NULL

Definition at line 356 of file ionics.cc.

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◆ register_data()

void opencarp::register_data	(	sf_vec *	dat,
		datavec_t	d
	)

Register a data vector in the global registry.

Parameters

dat	A pointer to the data vector.
d	The identifier of the data vector.

Definition at line 844 of file sim_utils.cc.

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◆ register_permutation()

SF::scattering * opencarp::register_permutation	(	const int	mesh_id,
		const int	perm_id,
		const int	dpn
	)

Register a permutation between two orderings for a mesh.

Parameters

mesh_id	The mesh we register the permutation for.
perm_id	The permutation specifier index (see sf_interface.h).
dpn	Degrees of freedom per node.

Returns: The registered permutation scattering pointer.

Definition at line 141 of file sf_interface.cc.

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◆ register_physics()

void opencarp::register_physics ( )

Register physics to the physics registry.

Definition at line 89 of file sim_utils.cc.

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◆ register_scattering() [1/2]

SF::scattering * opencarp::register_scattering	(	const int	from,
		const int	to,
		const SF::SF_nbr	nbr,
		const int	dpn
	)

Register a scattering between to grids, or between algebraic and nodal representation of data on the same grid.

Parameters

from	The mesh ID we scatter from.
to	The mesh ID we scatter to, or ALG_TO_NODAL.
nbr	The used numbering.
dpn	The degrees of freedom per node.

Definition at line 65 of file sf_interface.cc.

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◆ register_scattering() [2/2]

SF::scattering* opencarp::register_scattering	(	const int	from,
		const int	to,
		const int	dpn
	)

inline

Definition at line 123 of file sf_interface.h.

◆ remove_char()

void opencarp::remove_char	(	char *	buff,
		const int	buffsize,
		const char	c
	)

inline

Definition at line 356 of file basics.h.

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◆ remove_preceding_char()

void opencarp::remove_preceding_char	(	char *	buff,
		const int	buffsize,
		const char	c
	)

inline

Definition at line 345 of file basics.h.

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◆ renormalise_fibres()

size_t opencarp::renormalise_fibres	(	SF::vector< mesh_real_t > &	fib,
		size_t	l_numelem
	)

Definition at line 962 of file sim_utils.cc.

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◆ retag_elements()

void opencarp::retag_elements	(	sf_mesh &	mesh,
		TagRegion *	tagRegs,
		int	ntr
	)

retag elements based on user defined regions

Parameters

nl	node list
elist	Element list
tagreg	tag regions
ntr	#tag regions

Postcondition: elst->Elemtags will be altered; If there is retagging, a data file will be produced showing the element regions on the nodes

Definition at line 913 of file sim_utils.cc.

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◆ rotate_x()

template<typename V >

vec3<V> opencarp::rotate_x	(	vec3< V >	p,
		double	theta
	)

inline

Definition at line 256 of file vect.h.

◆ rotate_y()

template<typename V >

vec3<V> opencarp::rotate_y	(	vec3< V >	p,
		double	theta
	)

inline

Definition at line 247 of file vect.h.

◆ rotate_z()

template<typename V >

vec3<V> opencarp::rotate_z	(	vec3< V >	p,
		double	theta
	)

inline

Definition at line 238 of file vect.h.

◆ sample_wave_form()

void opencarp::sample_wave_form	(	stim_pulse &	sp,
		int	idx
	)

sample a signal given in analytic form

Sample a stim pulse wave form.

Parameters

sp	stimulus pulse to be sampled
idx	index of stimulus definition in stimulus array

Postcondition: data vector of stim pulse sp is filled with sampled data

Parameters

sp	Stim pulse struct.
idx	param_globals stimulus index.

Definition at line 365 of file stimulate.cc.

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◆ savequit()

void opencarp::savequit ( )

save state and quit simulator

Definition at line 1602 of file sim_utils.cc.

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◆ scal_X()

template<typename V , typename S >

vec3<V> opencarp::scal_X	(	const vec3< V > &	a,
		S	k
	)

inline

Definition at line 150 of file vect.h.

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◆ scale3()

template<typename V >

vec3<V> opencarp::scale3	(	const vec3< V > &	a,
		const vec3< V > &	k
	)

inline

Definition at line 168 of file vect.h.

◆ set_cond_type()

void opencarp::set_cond_type	(	MaterialType &	m,
		cond_t	type
	)

set conductivity tensor modifier type for each material in a grid

Parameters

[in]	m	electrical material properties
[in]	type	modifier type, rule for assembling the tensor

Postcondition: type in each material is set to selected type

Definition at line 802 of file electrics.cc.

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◆ set_dir()

int opencarp::set_dir ( IO_t dest )

set the current working directory

Parameters

dest	either INPUT, OUTPUT or POSTPROC

Postcondition: the current working directory is changed

Definition at line 446 of file sim_utils.cc.

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◆ set_elec_tissue_properties()

void opencarp::set_elec_tissue_properties	(	MaterialType *	mtype,
		Electrics::grid_t	g,
		FILE_SPEC	logger
	)

Fill the RegionSpec of an electrics grid with the associated inputs from the param parameters.

Parameters

g	The electrics grid we want to set up.

Definition at line 100 of file electrics.cc.

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◆ set_ignore_flags()

int opencarp::set_ignore_flags ( int mode )

set flags to select which extracellular stimuli types are ignored and convert intracellular current injection to transmembrane

Parameters

mode	simulation modes (MONODOMAIN, BIDOMAIN, PSEUDO_BIDM)

Returns: bits set for ignoring stimuli

Definition at line 177 of file sim_utils.cc.

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◆ set_io_dirs()

void opencarp::set_io_dirs	(	char *	sim_ID,
		char *	pp_ID,
		IO_t	init
	)

set the I/O directories

Parameters

argc	#words on command line
argv	the words
sim_ID	ID for naming output dir
pp_ID	ID for naming the postprocessing directory

Precondition: the output dir does not exist but all components in path up to it do

Postcondition: output_dir is set to sim_ID, postproc_dir to pp_ID, and input_dir is set is set to the directory from which the executable was called; the input parameter file is copied to the output directory

Definition at line 317 of file sim_utils.cc.

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◆ setup_dataout()

void opencarp::setup_dataout	(	const int	dataout,
		std::string	dataout_vtx,
		mesh_t	grid,
		SF::vector< mesh_int_t > *&	restr,
		bool	async = `false`
	)

setup the restriction indices vector. the indices we store depends on how we do output, see below.

Definition at line 591 of file electrics.cc.

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◆ setup_IO()

bool opencarp::setup_IO	(	int	argc,
		char **	argv
	)

Definition at line 388 of file sim_utils.cc.

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◆ setup_meshes()

void opencarp::setup_meshes ( )

Read in the reference mesh and use its data to populate all meshes registered in the mesh registry.

Postcondition: The meshes in the mesh registry are set up

Definition at line 986 of file sim_utils.cc.

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◆ setup_petsc_err_log()

void opencarp::setup_petsc_err_log ( )

set up error logs for PETSc, so that it doesnt print errors to stderr.

Definition at line 1240 of file sim_utils.cc.

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◆ setup_phie_recovery_data()

void opencarp::setup_phie_recovery_data ( phie_recovery_data & data )

Definition at line 2006 of file electrics.cc.

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◆ show_build_info()

void opencarp::show_build_info ( )

show the build info, exit if -buildinfo was provided. This code runs before MPI_Init().

Definition at line 219 of file sim_utils.cc.

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◆ simulate()

void opencarp::simulate ( )

Main simulate loop.

Definition at line 754 of file sim_utils.cc.

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◆ skip_comments()

char * opencarp::skip_comments	(	FILE_SPEC	stream,
		char *	readbuff,
		size_t	buffsize,
		MPI_Comm	comm
	)

Definition at line 143 of file fem_utils.cc.

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◆ sltlst_append()

void opencarp::sltlst_append	(	Salt_list *	sl,
		void *	p,
		int	quantum
	)

append to a list, allocating more memory if necessary

Parameters

sl	the list
p	item to add
quantum	size of items in bytes

Note: If the chunk size is 0, it will not work so the chunk size will be set to 1 automatically.

Definition at line 33 of file basics.cc.

◆ split_string()

template<class STRVEC >

void opencarp::split_string	(	const std::string &	input,
		const char	s,
		STRVEC &	list
	)

Split a string holding a character-seperated list into a vector of strings.

Template Parameters

STRVEC vector-of-string type, e.g. std::vector<std::string> or SF::vector<std::string>

Parameters

[in]	input	string holding list
[in]	s	character delimiting the list entries
[out]	list	the parsed list

Definition at line 103 of file basics.h.

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◆ stimidx_from_timeridx()

int opencarp::stimidx_from_timeridx	(	const SF::vector< stimulus > &	stimuli,
		const int	timer_id
	)

determine link between timer and stimulus

figure out stimulus index linked to a given timer

Definition at line 750 of file electrics.cc.

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◆ stringify()

char * opencarp::stringify ( double r )

convert a double into a string

Parameters

r	the number

Returns: a pointer to the string

Definition at line 54 of file basics.cc.

◆ time_to_string()

void opencarp::time_to_string	(	float	time,
		char *	str,
		short	str_size
	)

Definition at line 717 of file sim_utils.cc.

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◆ timing()

template<typename V >

V opencarp::timing	(	V &	t2,
		const V &	t1
	)

inline

Definition at line 448 of file basics.h.

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◆ triple_prod()

template<typename V >

double opencarp::triple_prod	(	vec3< V >	a,
		vec3< V >	b,
		vec3< V >	c
	)

inline

scalar triple product

Definition at line 308 of file vect.h.

◆ update_console_output()

void opencarp::update_console_output	(	const timer_manager &	tm,
		prog_stats &	p
	)

Definition at line 726 of file sim_utils.cc.

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◆ update_cwd()

void opencarp::update_cwd ( )

save the current working directory to curdir so that we can switch back to it if needed.

Definition at line 441 of file sim_utils.cc.

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◆ v_scale()

template<typename V >

double* opencarp::v_scale	(	int	n,
		double *	a,
		double	k,
		double *	b
	)

inline

Definition at line 209 of file vect.h.

◆ v_scale_f()

template<typename V >

float* opencarp::v_scale_f	(	int	n,
		float *	a,
		double	k,
		double *	b
	)

inline

Definition at line 220 of file vect.h.

◆ warn_when_passing_intra_vtx()

void opencarp::warn_when_passing_intra_vtx ( const std::string filename )

Definition at line 224 of file fem_utils.cc.

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◆ write_bin_string()

void opencarp::write_bin_string	(	FILE_SPEC	out,
		const char *	s
	)

write the length of a string followed by the string to a binary file

Parameters

out	the stream
s	the string

Definition at line 219 of file basics.cc.

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Variable Documentation

◆ basetable

const uint16_t opencarp::basetable

Definition at line 23 of file short_float.cc.

◆ Data_Size

unsigned short opencarp::Data_Size

Initial value:

=
  {
    0, sizeof(Byte), sizeof(char), sizeof(short), sizeof(long), sizeof(float),
    sizeof(double), 0, 0, 0, 0, sizeof(void *), 0, sizeof(int), sizeof(UInt),
    sizeof(unsigned short),
    3*sizeof(float), 3*sizeof(double), 4*sizeof(float), 4*sizeof(double),
    sizeof(short_float), 9*sizeof(float), 9*sizeof(double)
  }

Definition at line 264 of file IGBheader.cc.

◆ deprecated

const char* opencarp::deprecated[]

Initial value:

= {
    "fac_x", "fac_y", "fac_z", "fac_t"
  }

list of deprecated keywords

Definition at line 259 of file IGBheader.cc.

◆ exponenttable

const uint32_t opencarp::exponenttable

Definition at line 3171 of file short_float.cc.

◆ Header_Message

char opencarp::Header_Message

Definition at line 247 of file IGBheader.cc.

◆ Header_Quiet

bool opencarp::Header_Quiet = false

Definition at line 246 of file IGBheader.cc.

◆ Header_Systeme

const char * opencarp::Header_Systeme

Initial value:

=
  {
    "big_endian",
    "little_endian"
  }

Definition at line 289 of file IGBheader.cc.

◆ Header_Systeme_No

unsigned long opencarp::Header_Systeme_No

Initial value:

=
  {
    IGB_BIG_ENDIAN,
    IGB_LITTLE_ENDIAN
  }

Definition at line 282 of file IGBheader.cc.

◆ Header_Type

const char * opencarp::Header_Type

Initial value:

=
  {
    "", "byte", "char", "short", "long", "float", "double", "complex",
    "double_complex", "rgba", "structure", "pointer", "list","int","uint",
    "ushort",
    "vec3f","vec3d","vec4f","vec4d","hfloat","vec9f","vec9d"
  }

Definition at line 249 of file IGBheader.cc.

◆ mantissatable

const uint32_t opencarp::mantissatable

Definition at line 1053 of file short_float.cc.

◆ Num_Components

int opencarp::Num_Components

Initial value:

=
  {
    0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 1, 0, 1, 1, 1, 3, 3, 4, 4, 1, 9, 9
  }

the number of components for each data type

Definition at line 275 of file IGBheader.cc.

◆ offsettable

const uint16_t opencarp::offsettable

Definition at line 3104 of file short_float.cc.

◆ shifttable

const uint16_t opencarp::shifttable

Definition at line 538 of file short_float.cc.

◆ wfLabels

const std::string opencarp::wfLabels[] = {"squarePulse", "truncExpPulse", "sinePulse", "arbPulse"}

Definition at line 80 of file stimulate.h.

Namespaces

Classes

Typedefs

Enumerations

Functions

Variables

Typedef Documentation

◆ Any

◆ BooleaN

◆ byte

◆ Byte

◆ Char

◆ D_Complex

◆ Double

◆ FILE_SPEC

◆ Flag

◆ Float

◆ Int

◆ List

◆ Long

◆ Point

◆ RDir

◆ RFile

◆ rgba

◆ RWDir

◆ RWFile

◆ S_Complex

◆ sf_mat

◆ sf_mesh

◆ sf_sol

◆ sf_vec

◆ Short

◆ short_float

◆ String

◆ Text

◆ UInt

◆ WDir

◆ WFile

Enumeration Type Documentation

◆ ActMethod

◆ cond_t

◆ datavec_t

◆ IO_t

◆ io_time

◆ mesh_t

◆ physic_t

◆ physMat_t

◆ PotType

◆ stim_domain_t

◆ stim_t

◆ t_timer

◆ tagreg_t

◆ waveform_t

Function Documentation

◆ alloc_gvec_data()

◆ angle()

◆ apply_stim_to_vector()

◆ assemble_sv_gvec()

◆ balance_electrode()

◆ basic_timer_setup()

◆ check_and_convert_params()

◆ check_nullspace_ok()

◆ check_tags_in_elems()

◆ classify_soln_methods()

◆ cleanup_and_exit()

◆ compute_IIF()

◆ compute_restr_idx()

◆ compute_restr_idx_async()

◆ constant_total_stimulus_current()

◆ cross()

◆ destroy_physics()

◆ det3()

◆ dist()

◆ dist_2()

◆ dot()

◆ dupstr()

◆ f_close()

◆ f_exist()

◆ f_gets_par()

◆ f_open()