openCARP
Doxygen code documentation for the open cardiac electrophysiology simulator openCARP
|
Simulator-level utility execution control functions. More...
#include "basics.h"
#include "sim_utils.h"
#include "fem.h"
#include "physics.h"
#include "async_io.h"
#include "SF_init.h"
#include <libgen.h>
#include <fstream>
#include <iomanip>
Go to the source code of this file.
Namespaces | |
opencarp | |
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::ignore_extracellular_stim (Stimulus *st, int ns, int ignore) |
int | opencarp::set_ignore_flags (int mode) |
void | opencarp::check_nullspace_ok () |
void | opencarp::show_build_info () |
show the build info, exit if -buildinfo was provided. This code runs before MPI_Init(). More... | |
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::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... | |
void | opencarp::get_protocol_column_widths (std::vector< int > &col_width, std::vector< int > &used_timer_ids) |
int | opencarp::plot_protocols (const char *fname) |
plot simulation protocols (I/O timers, stimuli, boundary conditions, etc) More... | |
void | opencarp::init_console_output (const timer_manager &tm, prog_stats &p) |
void | opencarp::time_to_string (float time, char *str, short str_size) |
void | opencarp::update_console_output (const timer_manager &tm, prog_stats &p) |
void | opencarp::simulate () |
Main simulate loop. More... | |
void | opencarp::post_process () |
do postprocessing More... | |
Basic_physic * | opencarp::get_physics (physic_t p, bool error_if_missing=true) |
Convinience function to get a physics. More... | |
sf_vec * | opencarp::get_data (datavec_t d) |
Retrieve a petsc data vector from the data registry. More... | |
void | opencarp::register_data (sf_vec *dat, datavec_t d) |
Register a data vector in the global registry. More... | |
void | opencarp::parse_mesh_types () |
Parse the phys_type CLI parameters and set up (empty) SF::meshdata meshes. More... | |
void | opencarp::retag_elements (sf_mesh &mesh, TagRegion *tagRegs, int ntr) |
size_t | opencarp::renormalise_fibres (SF::vector< mesh_real_t > &fib, size_t l_numelem) |
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 () |
void | opencarp::cleanup_and_exit () |
char * | opencarp::get_file_dir (const char *file) |
void | opencarp::setup_petsc_err_log () |
set up error logs for PETSc, so that it doesnt print errors to stderr. More... | |
short | opencarp::get_mesh_dim (mesh_t id) |
get (lowest) dimension of the mesh used in the experiment More... | |
void | opencarp::output_parameter_file (const char *fname, int argc, char **argv) |
void | opencarp::savequit () |
save state and quit simulator More... | |
Simulator-level utility execution control functions.
Definition in file sim_utils.cc.