NEURON
Public Member Functions | Public Attributes | List of all members
ECS_Grid_node Class Reference

#include <grids.h>

Inheritance diagram for ECS_Grid_node:
Grid_node

Public Member Functions

 ECS_Grid_node ()
 
 ECS_Grid_node (PyHocObject *, int, int, int, double, double, double, double, double, double, PyHocObject *, PyHocObject *, int, double, double)
 
 ~ECS_Grid_node ()
 
void set_num_threads (const int n)
 
void do_grid_currents (double *, double, int)
 
void apply_node_flux3D (double dt, double *states)
 
void volume_setup ()
 
int dg_adi ()
 
void variable_step_diffusion (const double *states, double *ydot)
 
void variable_step_ode_solve (double *RHS, double dt)
 
void variable_step_hybrid_connections (const double *cvode_states_3d, double *const ydot_3d, const double *cvode_states_1d, double *const ydot_1d)
 
void scatter_grid_concentrations ()
 
void hybrid_connections ()
 
void set_diffusion (double *, int)
 
void set_tortuosity (PyHocObject *)
 
void set_volume_fraction (PyHocObject *)
 
void do_multicompartment_reactions (double *)
 
void initialize_multicompartment_reaction ()
 
void clear_multicompartment_reaction ()
 
int add_multicompartment_reaction (int, int *, int)
 
double * set_rxd_currents (int, int *, PyHocObject **)
 
- Public Member Functions inherited from Grid_node
int insert (int grid_list_index)
 
virtual ~Grid_node ()
 

Public Attributes

struct ECSAdiGridData * ecs_tasks
 
struct ECSAdiDirection * ecs_adi_dir_x
 
struct ECSAdiDirection * ecs_adi_dir_y
 
struct ECSAdiDirection * ecs_adi_dir_z
 
int induced_idx
 
int * react_offsets
 
int react_offset_count
 
int * reaction_indices
 
int * all_reaction_indices
 
int * proc_num_reactions
 
int * proc_num_reaction_states
 
int total_reaction_states
 
unsigned char multicompartment_inititalized
 
int * induced_currents_index
 
int induced_current_count
 
int * proc_induced_current_count
 
int * proc_induced_current_offset
 
double * all_reaction_states
 
double * induced_currents
 
double * local_induced_currents
 
double * induced_currents_scale
 
- Public Attributes inherited from Grid_node
Grid_node * next
 
double * states
 
double * states_x
 
double * states_y
 
double * states_z
 
double * states_cur
 
int size_x
 
int size_y
 
int size_z
 
double dc_x
 
double dc_y
 
double dc_z
 
double dx
 
double dy
 
double dz
 
bool diffusable
 
bool hybrid
 
BoundaryConditions * bc
 
Hybrid_data * hybrid_data
 
Concentration_Pair * concentration_list
 
Current_Triple * current_list
 
ssize_t num_concentrations
 
ssize_t num_currents
 
int num_all_currents
 
int * proc_offsets
 
int * proc_num_currents
 
int * proc_flux_offsets
 
int * proc_num_fluxes
 
long * current_dest
 
double * all_currents
 
unsigned char VARIABLE_ECS_VOLUME
 
double * permeability
 
double * alpha
 
double(* get_alpha )(double *, int)
 
double(* get_permeability )(double *, int)
 
double atolscale
 
int64_t * ics_surface_nodes_per_seg
 
int64_t * ics_surface_nodes_per_seg_start_indices
 
double ** ics_concentration_seg_ptrs
 
double ** ics_current_seg_ptrs
 
double * ics_scale_factors
 
int ics_num_segs
 
int node_flux_count
 
long * node_flux_idx
 
double * node_flux_scale
 
PyObject ** node_flux_src
 

Detailed Description

Definition at line 186 of file grids.h.

Constructor & Destructor Documentation

◆ ECS_Grid_node() [1/2]

ECS_Grid_node::ECS_Grid_node ( )

Definition at line 53 of file grids.cpp.

◆ ECS_Grid_node() [2/2]

ECS_Grid_node::ECS_Grid_node ( PyHocObject *  my_states,
int  my_num_states_x,
int  my_num_states_y,
int  my_num_states_z,
double  my_dc_x,
double  my_dc_y,
double  my_dc_z,
double  my_dx,
double  my_dy,
double  my_dz,
PyHocObject *  my_alpha,
PyHocObject *  my_permeability,
int  bc_type,
double  bc_value,
double  atolscale 
)

Definition at line 54 of file grids.cpp.

◆ ~ECS_Grid_node()

ECS_Grid_node::~ECS_Grid_node ( )

Definition at line 1229 of file grids.cpp.

Member Function Documentation

◆ add_multicompartment_reaction()

int ECS_Grid_node::add_multicompartment_reaction ( int  nstates,
int *  indices,
int  step 
)

Definition at line 1034 of file grids.cpp.

◆ apply_node_flux3D()

void ECS_Grid_node::apply_node_flux3D ( double  dt,
double *  states 
)
virtual

Implements Grid_node.

Definition at line 919 of file grids.cpp.

◆ clear_multicompartment_reaction()

void ECS_Grid_node::clear_multicompartment_reaction ( )

Definition at line 1062 of file grids.cpp.

◆ dg_adi()

int ECS_Grid_node::dg_adi ( )
virtual

Implements Grid_node.

Definition at line 968 of file grids.cpp.

◆ do_grid_currents()

void ECS_Grid_node::do_grid_currents ( double *  output,
double  dt,
int  grid_id 
)
virtual

Implements Grid_node.

Definition at line 828 of file grids.cpp.

◆ do_multicompartment_reactions()

void ECS_Grid_node::do_multicompartment_reactions ( double *  result)

Definition at line 1198 of file grids.cpp.

◆ hybrid_connections()

void ECS_Grid_node::hybrid_connections ( )
virtual

Implements Grid_node.

Definition at line 1026 of file grids.cpp.

◆ initialize_multicompartment_reaction()

void ECS_Grid_node::initialize_multicompartment_reaction ( )

Definition at line 1080 of file grids.cpp.

◆ scatter_grid_concentrations()

void ECS_Grid_node::scatter_grid_concentrations ( )
virtual

Implements Grid_node.

Definition at line 1014 of file grids.cpp.

◆ set_diffusion()

void ECS_Grid_node::set_diffusion ( double *  dc,
int   
)
virtual

Implements Grid_node.

Definition at line 529 of file grids.cpp.

◆ set_num_threads()

void ECS_Grid_node::set_num_threads ( const int  n)
virtual

Implements Grid_node.

Definition at line 777 of file grids.cpp.

◆ set_rxd_currents()

double * ECS_Grid_node::set_rxd_currents ( int  current_count,
int *  current_indices,
PyHocObject **  ptrs 
)

Definition at line 891 of file grids.cpp.

◆ set_tortuosity()

void ECS_Grid_node::set_tortuosity ( PyHocObject *  my_permeability)

Definition at line 408 of file grids.cpp.

◆ set_volume_fraction()

void ECS_Grid_node::set_volume_fraction ( PyHocObject *  my_alpha)

Definition at line 473 of file grids.cpp.

◆ variable_step_diffusion()

void ECS_Grid_node::variable_step_diffusion ( const double *  states,
double *  ydot 
)
virtual

Implements Grid_node.

Definition at line 999 of file grids.cpp.

◆ variable_step_hybrid_connections()

void ECS_Grid_node::variable_step_hybrid_connections ( const double *  cvode_states_3d,
double *const  ydot_3d,
const double *  cvode_states_1d,
double *const  ydot_1d 
)
virtual

Implements Grid_node.

Definition at line 1030 of file grids.cpp.

◆ variable_step_ode_solve()

void ECS_Grid_node::variable_step_ode_solve ( double *  RHS,
double  dt 
)
virtual

Implements Grid_node.

Definition at line 1224 of file grids.cpp.

◆ volume_setup()

void ECS_Grid_node::volume_setup ( )
virtual

Implements Grid_node.

Definition at line 953 of file grids.cpp.

Member Data Documentation

◆ all_reaction_indices

int* ECS_Grid_node::all_reaction_indices

Definition at line 204 of file grids.h.

◆ all_reaction_states

double* ECS_Grid_node::all_reaction_states

Definition at line 213 of file grids.h.

◆ ecs_adi_dir_x

struct ECSAdiDirection* ECS_Grid_node::ecs_adi_dir_x

Definition at line 195 of file grids.h.

◆ ecs_adi_dir_y

struct ECSAdiDirection* ECS_Grid_node::ecs_adi_dir_y

Definition at line 196 of file grids.h.

◆ ecs_adi_dir_z

struct ECSAdiDirection* ECS_Grid_node::ecs_adi_dir_z

Definition at line 197 of file grids.h.

◆ ecs_tasks

struct ECSAdiGridData* ECS_Grid_node::ecs_tasks

Definition at line 194 of file grids.h.

◆ induced_current_count

int ECS_Grid_node::induced_current_count

Definition at line 210 of file grids.h.

◆ induced_currents

double* ECS_Grid_node::induced_currents

Definition at line 214 of file grids.h.

◆ induced_currents_index

int* ECS_Grid_node::induced_currents_index

Definition at line 209 of file grids.h.

◆ induced_currents_scale

double* ECS_Grid_node::induced_currents_scale

Definition at line 216 of file grids.h.

◆ induced_idx

int ECS_Grid_node::induced_idx

Definition at line 200 of file grids.h.

◆ local_induced_currents

double* ECS_Grid_node::local_induced_currents

Definition at line 215 of file grids.h.

◆ multicompartment_inititalized

unsigned char ECS_Grid_node::multicompartment_inititalized

Definition at line 208 of file grids.h.

◆ proc_induced_current_count

int* ECS_Grid_node::proc_induced_current_count

Definition at line 211 of file grids.h.

◆ proc_induced_current_offset

int* ECS_Grid_node::proc_induced_current_offset

Definition at line 212 of file grids.h.

◆ proc_num_reaction_states

int* ECS_Grid_node::proc_num_reaction_states

Definition at line 206 of file grids.h.

◆ proc_num_reactions

int* ECS_Grid_node::proc_num_reactions

Definition at line 205 of file grids.h.

◆ react_offset_count

int ECS_Grid_node::react_offset_count

Definition at line 202 of file grids.h.

◆ react_offsets

int* ECS_Grid_node::react_offsets

Definition at line 201 of file grids.h.

◆ reaction_indices

int* ECS_Grid_node::reaction_indices

Definition at line 203 of file grids.h.

◆ total_reaction_states

int ECS_Grid_node::total_reaction_states

Definition at line 207 of file grids.h.

The documentation for this class was generated from the following files: