Dsolve.cpp File Reference

#include "header.h"
#include "ElementValueFinfo.h"
#include "SparseMatrix.h"
#include "KinSparseMatrix.h"
#include "VoxelPoolsBase.h"
#include "../mesh/VoxelJunction.h"
#include "XferInfo.h"
#include "ZombiePoolInterface.h"
#include "../kinetics/ConcChan.h"
#include "DiffPoolVec.h"
#include "ConcChanInfo.h"
#include "FastMatrixElim.h"
#include "DiffJunction.h"
#include "Dsolve.h"
#include "../mesh/Boundary.h"
#include "../mesh/MeshEntry.h"
#include "../mesh/ChemCompt.h"
#include "../mesh/MeshCompt.h"
#include "../shell/Wildcard.h"
#include "../kinetics/PoolBase.h"
#include "../kinetics/Pool.h"
#include "../kinetics/BufPool.h"
#include "../ksolve/ZombiePool.h"
#include "../ksolve/ZombieBufPool.h"

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Functions
static bool	checkJn (const vector< DiffJunction > &jn, unsigned int voxel, const string &info)
static double	integ (double myN, double rf, double rb, double dt)
static void	mapVoxelsBetweenMeshes (DiffJunction &jn, Id self, Id other)
void	printJunction (Id self, Id other, const DiffJunction &jn)

Variables
static const Cinfo *	dsolveCinfo = Dsolve::initCinfo()

Function Documentation

static bool checkJn ( const vector< DiffJunction > &  jn, unsigned int  voxel, const string &  info  )

static

Definition at line 225 of file Dsolve.cpp.

Referenced by Dsolve::getDiffScale(), Dsolve::getDiffVol1(), Dsolve::getDiffVol2(), Dsolve::setDiffScale(), Dsolve::setDiffVol1(), and Dsolve::setDiffVol2().

{
    if ( jn.size() < 1 ) {
        cout << "Warning: Dsolve::" << info << ": junctions not defined.\n";
        return false;
    }
    if ( jn[0].vj.size() < voxel + 1 ) {
        cout << "Warning: Dsolve:: " << info << ": " << voxel <<
                "out of range.\n";
        return false;
    }
    return true;
}

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static double integ ( double  myN, double  rf, double  rb, double  dt  )

static

Definition at line 295 of file Dsolve.cpp.

References EPSILON.

Referenced by Dsolve::calcJnChan(), Dsolve::calcJnDiff(), and Dsolve::calcOtherJnChan().

{
    const double EPSILON = 1e-12;
    if ( myN > EPSILON && rf > EPSILON ) {
        double C = exp( -rf * dt / myN );
        myN *= C + ( rb / rf ) * ( 1.0 - C );
    } else {
        myN += ( rb - rf ) * dt;
    }
    if ( myN < 0.0 )
        return 0.0;
    return myN;
}

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static void mapVoxelsBetweenMeshes ( DiffJunction &  jn, Id  self, Id  other  )

static

Definition at line 921 of file Dsolve.cpp.

References Eref::data(), Id::eref(), Field< A >::get(), ChemCompt::getVoxelVolume(), ChemCompt::matchMeshEntries(), and DiffJunction::vj.

Referenced by Dsolve::innerBuildMeshJunctions().

{
    Id myMesh = Field< Id >::get( self, "compartment" );
    Id otherMesh = Field< Id >::get( other, "compartment" );

    const ChemCompt* myCompt = reinterpret_cast< const ChemCompt* >(
                    myMesh.eref().data() );
    const ChemCompt* otherCompt = reinterpret_cast< const ChemCompt* >(
                    otherMesh.eref().data() );
    myCompt->matchMeshEntries( otherCompt, jn.vj );
    vector< double > myVols = myCompt->getVoxelVolume();
    vector< double > otherVols = otherCompt->getVoxelVolume();
    for ( vector< VoxelJunction >::iterator
        i = jn.vj.begin(); i != jn.vj.end(); ++i ) {
        i->firstVol = myVols[i->first];
        i->secondVol = otherVols[i->second];
    }
}

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void printJunction	(	Id	self,
		Id	other,
		const DiffJunction &	jn
	)

Definition at line 810 of file Dsolve.cpp.

References DiffJunction::myPools, DiffJunction::otherPools, Id::path(), and DiffJunction::vj.

{
    cout << "Junction between " << self.path() << ", " << other.path() << endl;
    cout << "Pool indices: myPools, otherPools\n";
    for ( unsigned int i = 0; i < jn.myPools.size(); ++i )
        cout << i << "  " << jn.myPools[i] << " " << jn.otherPools[i] << endl;
    cout << "Voxel junctions: first second  firstVol    secondVol   diffScale\n";
    for ( unsigned int i = 0; i < jn.vj.size(); ++i ) {
        cout << i << "  " << jn.vj[i].first << "    " << jn.vj[i].second <<
        "   " << jn.vj[i].firstVol << " " << jn.vj[i].secondVol <<
               "    " << jn.vj[i].diffScale <<  endl;
    }
}

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Variable Documentation

const Cinfo* dsolveCinfo = Dsolve::initCinfo()

static

Definition at line 183 of file Dsolve.cpp.

Referenced by Dsolve::initCinfo().