ZombiePoolInterface.cpp

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/**********************************************************************
** This program is part of 'MOOSE', the
** Messaging Object Oriented Simulation Environment.
**           Copyright (C) 2003-2010 Upinder S. Bhalla. and NCBS
** It is made available under the terms of the
** GNU Lesser General Public License version 2.1
** See the file COPYING.LIB for the full notice.
**********************************************************************/
#include "header.h"
#ifdef USE_GSL
#include <gsl/gsl_errno.h>
#include <gsl/gsl_matrix.h>
#include <gsl/gsl_odeiv2.h>
#endif

#include "VoxelPoolsBase.h"
// #include "VoxelPools.h"
#include "../mesh/VoxelJunction.h"
#include "XferInfo.h"
#include "ZombiePoolInterface.h"

#include "RateTerm.h"
#include "FuncTerm.h"
#include "SparseMatrix.h"
#include "KinSparseMatrix.h"
#include "Stoich.h"
#include "../shell/Shell.h"
#include "../mesh/MeshEntry.h"
#include "../mesh/Boundary.h"
#include "../mesh/ChemCompt.h"

ZombiePoolInterface::ZombiePoolInterface()
        : stoich_(), compartment_(),
        isBuilt_( false )
{;}

void ZombiePoolInterface::updateJunctions( double dt )
{;}
void ZombiePoolInterface::setPrev()
{;}


Id ZombiePoolInterface::getCompartment() const
{
    return compartment_;
}

void ZombiePoolInterface::setCompartment( Id compt )
{
    isBuilt_ = false; // We will have to now rebuild the whole thing.
    if ( compt.element()->cinfo()->isA( "ChemCompt" ) ) {
        compartment_ = compt;
        vector< double > vols =
            Field< vector < double > >::get( compt, "voxelVolume" );
        if ( vols.size() > 0 ) {
            setNumAllVoxels( vols.size() );
            for ( unsigned int i = 0; i < vols.size(); ++i ) {
                pools(i)->setVolume( vols[i] );
            }
        }
    }
}