ionics.h

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// ----------------------------------------------------------------------------
// openCARP is an open cardiac electrophysiology simulator.
//
// Copyright (C) 2020 openCARP project
//
// This program is licensed under the openCARP Academic Public License (APL)
// v1.0: You can use and redistribute it and/or modify it in non-commercial
// academic environments under the terms of APL as published by the openCARP
// project v1.0, or (at your option) any later version. Commercial use requires
// a commercial license (info@opencarp.org).
//
// This program is distributed without any warranty; see the openCARP APL for
// more details.
//
// You should have received a copy of the openCARP APL along with this program
// and can find it online: http://www.opencarp.org/license
// ----------------------------------------------------------------------------

#ifndef _IONICS_H
#define _IONICS_H

#include "physics_types.h"
#include "sim_utils.h"
#include "stimulate.h"
#include "IGBheader.h"
#include "timers.h"

#include "sf_interface.h"
#include "MULTI_ION_IF.h"
#include "sv_init.h"

namespace opencarp {


void region_mask(mesh_t meshspec, SF::vector<RegionSpecs> & regspec,
                 SF::vector<int> & regionIDs, bool mask_elem, const char* reglist);

class Ionics : public Basic_physic
{
  public:
  limpet::MULTI_IF* miif = NULL;
  mesh_t    ion_domain;

  generic_timing_stats comp_stats;

  Ionics(mesh_t gid) : ion_domain(gid)
  {
    switch(ion_domain) {
      case intra_elec_msh:
        name = "Myocard Ionics"; break;
      default:
        name = "Ionics"; break;
    }
  }

  void initialize();
  void destroy();
  void compute_step();
  void output_step();
  ~Ionics() = default;

  double timer_val(const int timer_id);
  std::string timer_unit(const int timer_id);

  private:
  double setup_MIIF(int nnodes, int nreg, IMPregion* impreg, int* mask,
             const char *start_fn, int numadjust, IMPVariableAdjustment *adjust,
             double time_step, bool close);

};

void compute_IIF(limpet::IonIfBase& pIF, limpet::GlobalData_t** impdata, int n);

struct sv_data {
  char*        name;        
  char**       imps;        
  char**       svNames;     
  int*         svInds;      
  int*         svSizes;     
  int*         svOff;       
  FILE_SPEC    outf;        
  void**       getsv;       
  sf_vec* ordered;     
  char*        units;       
  float        bogus;       
};

struct gvec_data {
  unsigned int           nRegs;        
  bool                   inclPS;       
  SF::vector<sv_data>    vecs;         
  SF::vector<int>        plugin_idx;   
  bool                   rm_dumps;     
};

void init_sv_gvec(gvec_data& GVs, limpet::MULTI_IF* miif, sf_vec & tmpl,
                  igb_output_manager & output_manager);
void assemble_sv_gvec(gvec_data & gvecs, limpet::MULTI_IF *miif);
}
#endif