42 namespace user_globals {
65 #define __FUNCT__ "main" 66 int main(
int argc,
char** argv)
69 char *help_msg = NULL;
71 initialize_PETSc(&argc, argv, DBfile, help_msg);
85 FILE_SPEC logger =
f_open(
"electrics.log", param_globals::experiment != 4 ?
"w" :
"r");
std::map< physic_t, Basic_physic * > physics_reg
the physics
description of materal properties in a mesh
std::map< mesh_t, sf_mesh > mesh_reg
Registry for the different meshes used in a multi-physics simulation.
timer_manager * tm_manager
a manager for the various physics timers
void setup_petsc_err_log()
set up error logs for PETSc, so that it doesnt print errors to stderr.
Top-level header file of numerics module.
void check_and_convert_params()
Here we want to put all parameter checks, conversions and modifications that have been littered throu...
void region_mask(mesh_t meshspec, SF::vector< RegionSpecs > ®spec, SF::vector< int > ®ionIDs, bool mask_elem, const char *reglist)
classify elements/points as belonging to a region
bool using_legacy_stimuli
flag storing whether legacy stimuli are used
FILE * petsc_error_fd
file descriptor for petsc error output
std::map< SF::quadruple< int >, SF::index_mapping< int > > map_reg
Registriy for the inter domain mappings.
Top-level header of FEM module.
void parse_params_cpy(int argc, char **argv)
Initialize input parameters on a copy of the real command line parameters.
void setup_meshes()
Read in the reference mesh and use its data to populate all meshes registered in the mesh registry...
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...
Index mapping class. This is a bijective mapping.
Top-level header of physics module.
int main(int argc, char **argv)
A vector storing arbitrary data.
std::map< datavec_t, sf_vec * > datavec_reg
important solution vectors from different physics
void rebuild_matrices(MaterialType *mtype, SF::vector< stimulus > &stimuli, FILE_SPEC logger)
SF::meshdata< mesh_int_t, mesh_real_t > sf_mesh
centralize time managment and output triggering
SF::scatter_registry scatter_reg
Registry for the different scatter objects.
The scatterer registry class.
FILE_SPEC f_open(const char *fname, const char *mode)
Open a FILE_SPEC.