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openCARP
Doxygen code documentation for the open cardiac electrophysiology simulator openCARP
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Simulator-level utility execution control functions. More...
#include <cstdio>#include <cstdlib>#include <cstring>#include "Typedefs.h"#include "sf_interface.h"#include "timer_utils.h"#include "physics_types.h"#include "build_info.h"#include "openCARP_p.h"#include "openCARP_d.h"#include "IGBheader.h"Go to the source code of this file.
Classes | |
| struct | opencarp::prog_stats |
| for display execution progress and statistical data of electrical solve More... | |
| struct | opencarp::sync_io_item |
| struct | opencarp::async_io_item |
| class | opencarp::igb_output_manager |
Namespaces | |
| opencarp | |
| opencarp::user_globals | |
Macros | |
| #define | CARP_PARAMS |
| #define | DATAOUT_NONE 0 |
| #define | DATAOUT_SURF 1 |
| #define | DATAOUT_VOL 2 |
| #define | DATAOUT_VTX 3 |
| #define | SOLV_METH(A, B) (B & A##_FLAG) |
| #define | MONODOMAIN_FLAG 1 |
| #define | ITERATE_FLAG 2 |
| #define | CN_PARAB_FLAG 4 |
| #define | PURKINJE_FLAG 8 |
| #define | O2dT_PARAB_FLAG 16 |
| #define | PSEUDO_BIDM_FLAG 32 |
| #define | MONODOMAIN 0 |
| #define | BIDOMAIN 1 |
| #define | PSEUDO_BIDM 2 |
| #define | RECOVER_PHIE 1 |
| #define | OPTICAL_MAP 2 |
| #define | ACTIVATING_FUNCTION 4 |
| #define | AXIAL_CURRENTS 8 |
| #define | FILAMENTS 16 |
| #define | CURRENT_DENSITIES 32 |
| #define | EXP_NORMAL 0 |
| #define | EXP_OUTPUT_FEM 1 |
| #define | EXP_LAPLACE 2 |
| #define | EXP_SETUP_MESH 3 |
| #define | EXP_POSTPROCESS 4 |
Enumerations | |
| enum | opencarp::IO_t { opencarp::INPUT , opencarp::OUTPUT , opencarp::POSTPROC , opencarp::CURDIR } |
| The different output (directory) types. More... | |
| enum | opencarp::tagreg_t { opencarp::tagreg_sphere = 1 , opencarp::tagreg_block = 2 , opencarp::tagreg_cylinder = 3 , opencarp::tagreg_list = 4 } |
| tag regions types. must be in line with carp.prm More... | |
Functions | |
| void | opencarp::parse_params_cpy (int argc, char **argv) |
| Initialize input parameters on a copy of the real command line parameters. More... | |
| void | opencarp::register_physics () |
| Register physics to the physics registry. More... | |
| void | opencarp::initialize_physics () |
| Initialize all physics in the registry. More... | |
| void | opencarp::destroy_physics () |
| Destroy all physics in the registry. More... | |
| void | opencarp::simulate () |
| Main simulate loop. More... | |
| void | opencarp::post_process () |
| do postprocessing More... | |
| void | opencarp::parse_mesh_types () |
| Parse the phys_type CLI parameters and set up (empty) SF::meshdata meshes. More... | |
| void | opencarp::setup_meshes () |
| Read in the reference mesh and use its data to populate all meshes registered in the mesh registry. More... | |
| void | opencarp::output_meshes () |
| unsigned int | opencarp::classify_soln_methods () |
| void | opencarp::check_and_convert_params () |
| Here we want to put all parameter checks, conversions and modifications that have been littered throughout the codebase. More... | |
| void | opencarp::setup_petsc_err_log () |
| set up error logs for PETSc, so that it doesnt print errors to stderr. More... | |
| void | opencarp::set_io_dirs (char *sim_ID, char *pp_ID, IO_t init) |
| bool | opencarp::setup_IO (int argc, char **argv) |
| void | opencarp::update_cwd () |
| save the current working directory to curdir so that we can switch back to it if needed. More... | |
| int | opencarp::set_dir (IO_t dest) |
| void | opencarp::basic_timer_setup () |
| Here we set up the timers that we always want to have, independent of physics. More... | |
| int | opencarp::plot_protocols (const char *fname) |
| plot simulation protocols (I/O timers, stimuli, boundary conditions, etc) More... | |
| Basic_physic * | opencarp::get_physics (physic_t p, bool error_if_missing=true) |
| Convinience function to get a physics. More... | |
| short | opencarp::get_mesh_dim (mesh_t id) |
| get (lowest) dimension of the mesh used in the experiment More... | |
| void | opencarp::register_data (sf_vec *dat, datavec_t d) |
| Register a data vector in the global registry. More... | |
| void | opencarp::cleanup_and_exit () |
| char * | opencarp::get_file_dir (const char *file) |
| sf_vec * | opencarp::get_data (datavec_t d) |
| Retrieve a petsc data vector from the data registry. More... | |
| void | opencarp::output_parameter_file (const char *fname, int argc, char **argv) |
| void | opencarp::savequit () |
| save state and quit simulator More... | |
| void | opencarp::show_build_info () |
| show the build info, exit if -buildinfo was provided. This code runs before MPI_Init(). More... | |
Simulator-level utility execution control functions.
Definition in file sim_utils.h.
| #define ACTIVATING_FUNCTION 4 |
Definition at line 151 of file sim_utils.h.
| #define AXIAL_CURRENTS 8 |
Definition at line 152 of file sim_utils.h.
| #define BIDOMAIN 1 |
Definition at line 144 of file sim_utils.h.
| #define CARP_PARAMS |
Definition at line 42 of file sim_utils.h.
| #define CN_PARAB_FLAG 4 |
Definition at line 137 of file sim_utils.h.
| #define CURRENT_DENSITIES 32 |
Definition at line 154 of file sim_utils.h.
| #define DATAOUT_NONE 0 |
Definition at line 57 of file sim_utils.h.
| #define DATAOUT_SURF 1 |
Definition at line 58 of file sim_utils.h.
| #define DATAOUT_VOL 2 |
Definition at line 59 of file sim_utils.h.
| #define DATAOUT_VTX 3 |
Definition at line 60 of file sim_utils.h.
| #define EXP_LAPLACE 2 |
Definition at line 159 of file sim_utils.h.
| #define EXP_NORMAL 0 |
Definition at line 157 of file sim_utils.h.
| #define EXP_OUTPUT_FEM 1 |
Definition at line 158 of file sim_utils.h.
| #define EXP_POSTPROCESS 4 |
Definition at line 161 of file sim_utils.h.
| #define EXP_SETUP_MESH 3 |
Definition at line 160 of file sim_utils.h.
| #define FILAMENTS 16 |
Definition at line 153 of file sim_utils.h.
| #define ITERATE_FLAG 2 |
Definition at line 136 of file sim_utils.h.
| #define MONODOMAIN 0 |
Definition at line 143 of file sim_utils.h.
| #define MONODOMAIN_FLAG 1 |
Definition at line 135 of file sim_utils.h.
| #define O2dT_PARAB_FLAG 16 |
Definition at line 139 of file sim_utils.h.
| #define OPTICAL_MAP 2 |
Definition at line 150 of file sim_utils.h.
| #define PSEUDO_BIDM 2 |
Definition at line 145 of file sim_utils.h.
| #define PSEUDO_BIDM_FLAG 32 |
Definition at line 140 of file sim_utils.h.
| #define PURKINJE_FLAG 8 |
Definition at line 138 of file sim_utils.h.
| #define RECOVER_PHIE 1 |
Definition at line 149 of file sim_utils.h.
| #define SOLV_METH | ( | A, | |
| B | |||
| ) | (B & A##_FLAG) |
Definition at line 134 of file sim_utils.h.
1.9.1