sim_utils.cc File Reference

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>

Include dependency graph for sim_utils.cc:

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...

Detailed Description

Simulator-level utility execution control functions.

Author

Aurel Neic, Gernot Plank, Edward Vigmond

Version

Date

2019-10-25

Definition in file sim_utils.cc.