BidomainProblem.cpp

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/*~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   This file is part of CEPS.
 
   CEPS is free software: you can redistribute it and/or modify
   it under the terms of the GNU General Public License as published by
   the Free Software Foundation, either version 3 of the License, or
   (at your option) any later version.
 
   CEPS is distributed in the hope that it will be useful,
   but WITHOUT ANY WARRANTY; without even the implied warranty of
   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
   GNU General Public License for more details.
 
   You should have received a copy of the GNU General Public License
   along with CEPS (see file LICENSE at root of project).
   If not, see <https://www.gnu.org/licenses/>.
 
 
   Copyright 2019-2024 Inria, Universite de Bordeaux
 
   Authors, in alphabetical order:
 
     Pierre-Elliott BECUE, Florian CARO, Yves COUDIERE(*), Andjela DAVIDOVIC, 
     Charlie DOUANLA-LONTSI, Marc FUENTES, Mehdi JUHOOR, Michael LEGUEBE(*), 
     Pauline MIGERDITICHAN, Valentin PANNETIER(*), Nejib ZEMZEMI.
     * : currently active authors
 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~*/
#include "cardiac/problem/BidomainProblem.hpp"
#include "cardiac/solver/BidomainSolver.hpp"
 
 
 
BidomainProblem::
BidomainProblem(Geometry* g, InputParameters* params)
  : CardiacProblem(g,params)
{
  setProblemName("Bidomain");
}
 
void
BidomainProblem::defineUnknowns()
{
  addUnknown(UnknownsName::vm, getTissueAttributes());
  addUnknown(UnknownsName::ue, getTissueAttributes());
  addUnknownInteraction(UnknownsName::vm, UnknownsName::ue, getTissueAttributes());
}
 
CepsVector<Unknown*>
BidomainProblem::getTMVUnknowns() const
{
  return {getTMVUnknown()};
}
 
CepsVector<Unknown*>
BidomainProblem::getCardiacUnknowns() const
{
  return {getTMVUnknown(), getUeUnknown()};
}
 
Unknown*
BidomainProblem::getTMVUnknown() const
{
  return getUnknown(UnknownsName::vm);
}
 
Unknown*
BidomainProblem::getUeUnknown() const
{
  return getUnknown(UnknownsName::ue);
}
 
void
BidomainProblem::getInitialCondition(DHVecPtr vm) const
{
  CardiacProblem::getInitialCondition(vm);
  // vm->getLocalData();
  // CepsReal v = 0.;
  // if (ceps::isMaster())
  //   v = (*vm)[0];
  // MPI_Bcast(&v,1,CEPS_MPI_REAL,0,ceps::getCommunicator()); 
  // for (auto toParse: {m_discr->getOwnedDofs(),m_discr->getHaloDofs()})
  // for (DegreeOfFreedom* dof: toParse)
  //   (*vm)[dof->getGlobalIndex()] = v;
  // vm->releaseLocalData();
}
 
void
BidomainProblem::run()
{
  if (ceps::isProfiling()) 
    getProfiler()->start("whole","solving the bidomain problem");
 
  initializeEquation();
 
  BidomainSolver solver(this);
  
  solver.solve(); 
 
  if (hasAnalyticSolution())
    m_errors = solver.getErrors();
 
  if (ceps::isProfiling())
    getProfiler()->stop("whole");  
 
}