MeshEntry Class Reference

#include <MeshEntry.h>

Collaboration diagram for MeshEntry:

Public Member Functions
void	extent (DataId di, double volume, double area, double perimeter)
vector< double >	getCoordinates (const Eref &e) const
vector< double >	getDiffusionArea (const Eref &e) const
vector< double >	getDiffusionScaling (const Eref &e) const
unsigned int	getDimensions (const Eref &e) const
unsigned int	getMeshType (const Eref &e) const
vector< unsigned int >	getNeighbors (const Eref &e) const
double	getVolume (const Eref &e) const
	MeshEntry ()
	MeshEntry (const ChemCompt *parent)
void	process (const Eref &e, ProcPtr info)
void	reinit (const Eref &e, ProcPtr info)
void	triggerRemesh (const Eref &e, double oldvol, unsigned int startEntry, const vector< unsigned int > &localIndices, const vector< double > &vols)

Static Public Member Functions
static const Cinfo *	initCinfo ()

Private Attributes
const ChemCompt *	parent_
	Volume or area. More...
double	volume_

Detailed Description

The MeshEntry is a single 'compartment' in the mathematical sense, that is, all properties are assumed homogenous within it. It is a FieldElement, so it gets all its values from the parent ChemCompt.

Definition at line 33 of file MeshEntry.h.

Constructor & Destructor Documentation

MeshEntry::MeshEntry

(

)

Definition at line 183 of file MeshEntry.cpp.

    : parent_( 0 )
{;}

MeshEntry::MeshEntry

(

const ChemCompt *

parent

)

Definition at line 187 of file MeshEntry.cpp.

    : parent_( parent )
{;}

Member Function Documentation

void MeshEntry::extent	(	DataId	di,
		double	volume,
		double	area,
		double	perimeter
	)

vector< double > MeshEntry::getCoordinates

(

const Eref &

e

)

const

Coords that define current MeshEntry. Usually generated on the fly by passing the current Field Index to the parent ChemCompt subclass, which will figure it out.

Definition at line 242 of file MeshEntry.cpp.

References Eref::fieldIndex(), ChemCompt::getCoordinates(), and parent_.

Referenced by initCinfo().

{
    return parent_->getCoordinates( e.fieldIndex() );
}

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vector< double > MeshEntry::getDiffusionArea

(

const Eref &

e

)

const

Diffusion scaling for area

Definition at line 253 of file MeshEntry.cpp.

References Eref::fieldIndex(), ChemCompt::getDiffusionArea(), and parent_.

Referenced by initCinfo().

{
    return parent_->getDiffusionArea( e.fieldIndex() );
}

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vector< double > MeshEntry::getDiffusionScaling

(

const Eref &

e

)

const

Diffusion scaling for geometry of interface

Definition at line 259 of file MeshEntry.cpp.

References Eref::fieldIndex(), ChemCompt::getDiffusionScaling(), and parent_.

Referenced by initCinfo().

{
    return parent_->getDiffusionScaling( e.fieldIndex() );
}

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unsigned int MeshEntry::getDimensions

(

const Eref &

e

)

const

returns number of dimension

Definition at line 232 of file MeshEntry.cpp.

References Eref::fieldIndex(), ChemCompt::getMeshDimensions(), and parent_.

Referenced by initCinfo().

{
    return parent_->getMeshDimensions( e.fieldIndex() );
}

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unsigned int MeshEntry::getMeshType

(

const Eref &

e

)

const

The MeshType defines the shape of the mesh entry. 0: Not assigned 1: cuboid 2: cylinder

1. cylindrical shell 4: cylindrical shell segment 5: sphere 6: spherical shell 7: spherical shell segment 8: Tetrahedral 9: EndoMesh

Definition at line 237 of file MeshEntry.cpp.

References Eref::fieldIndex(), ChemCompt::getMeshType(), and parent_.

Referenced by initCinfo().

{
    return parent_->getMeshType( e.fieldIndex() );
}

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vector< unsigned int > MeshEntry::getNeighbors

(

const Eref &

e

)

const

Indices of other Entries that this one connects to, for diffusion

Definition at line 247 of file MeshEntry.cpp.

References Eref::fieldIndex(), ChemCompt::getNeighbors(), and parent_.

Referenced by initCinfo().

{
    return parent_->getNeighbors( e.fieldIndex() );
}

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double MeshEntry::getVolume

(

const Eref &

e

)

const

Definition at line 226 of file MeshEntry.cpp.

References Eref::fieldIndex(), ChemCompt::getMeshEntryVolume(), and parent_.

Referenced by initCinfo().

{
    //return parent_->getMeshEntryVolume( e.dataIndex() );
    return parent_->getMeshEntryVolume( e.fieldIndex() );
}

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const Cinfo * MeshEntry::initCinfo ( )

static

Definition at line 47 of file MeshEntry.cpp.

References getCoordinates(), getDiffusionArea(), getDiffusionScaling(), getDimensions(), ValueFinfoBase::getFinfo(), getMeshType(), getNeighbors(), getVolume(), Neutral::initCinfo(), meshEntryCinfo, process(), reinit(), remeshOut(), and remeshReacsOut().

Referenced by ChemCompt::initCinfo().

{
        // Field Definitions
        static ReadOnlyElementValueFinfo< MeshEntry, double > volume(
            "volume",
            "Volume of this MeshEntry",
            &MeshEntry::getVolume
        );

        static ReadOnlyElementValueFinfo< MeshEntry, unsigned int >
            dimensions (
            "dimensions",
            "number of dimensions of this MeshEntry",
            &MeshEntry::getDimensions
        );

        static ReadOnlyElementValueFinfo< MeshEntry, unsigned int >
            meshType(
            "meshType",
            " The MeshType defines the shape of the mesh entry."
            " 0: Not assigned"
            " 1: cuboid"
            " 2: cylinder"
            " 3. cylindrical shell"
            " 4: cylindrical shell segment"
            " 5: sphere"
            " 6: spherical shell"
            " 7: spherical shell segment"
            " 8: Tetrahedral",
            &MeshEntry::getMeshType
        );

        static ReadOnlyElementValueFinfo< MeshEntry, vector< double >  >
            coordinates (
            "Coordinates",
            "Coordinates that define current MeshEntry. Depend on MeshType.",
            &MeshEntry::getCoordinates
        );

        static ReadOnlyElementValueFinfo< MeshEntry, vector< unsigned int >  >
            neighbors (
            "neighbors",
            "Indices of other MeshEntries that this one connects to",
            &MeshEntry::getNeighbors
        );

        static ReadOnlyElementValueFinfo< MeshEntry, vector< double >  >
            diffusionArea (
            "DiffusionArea",
            "Diffusion area for geometry of interface",
            &MeshEntry::getDiffusionArea
        );

        static ReadOnlyElementValueFinfo< MeshEntry, vector< double >  >
            diffusionScaling (
            "DiffusionScaling",
            "Diffusion scaling for geometry of interface",
            &MeshEntry::getDiffusionScaling
        );

        // MsgDest Definitions
        static DestFinfo process( "process",
            "Handles process call",
            new ProcOpFunc< MeshEntry >( &MeshEntry::process ) );
        static DestFinfo reinit( "reinit",
            "Handles reinit call",
            new ProcOpFunc< MeshEntry >( &MeshEntry::reinit ) );
        // Shared definitions
        static Finfo* procShared[] = {
            &process, &reinit
        };
        static SharedFinfo proc( "proc",
            "Shared message for process and reinit",
            procShared, sizeof( procShared ) / sizeof( const Finfo* )
        );

        static Finfo* meshShared[] = {
            remeshOut(), volume.getFinfo()
        };

        static SharedFinfo mesh( "mesh",
            "Shared message for updating mesh volumes and subdivisions,"
            "typically controls pool volumes",
            meshShared, sizeof( meshShared ) / sizeof( const Finfo* )
        );


        // SrcFinfo Definitions

    static Finfo* meshFinfos[] = {
        &volume,        // Readonly Value
        &dimensions,    // Readonly Value
        &meshType,      // Readonly Value
        &coordinates,   // Readonly Value
        &neighbors,     // Readonly Value
        &diffusionArea, // Readonly Value
        &diffusionScaling,  // Readonly Value
        &proc,          // SharedFinfo
        &mesh,          // SharedFinfo
        remeshReacsOut(),   // SrcFinfo
    };

    static string doc[] =
    {
            "Name", "MeshEntry",
            "Author", "Upi Bhalla",
            "Description", "One voxel in a chemical reaction compartment",
    };
    static Dinfo< MeshEntry > dinfo;
    static Cinfo meshEntryCinfo (
        "MeshEntry",
        Neutral::initCinfo(),
        meshFinfos,
        sizeof( meshFinfos ) / sizeof ( Finfo* ),
        &dinfo,
        doc,
        sizeof(doc)/sizeof( string ),
        true // This IS a FieldElement, not be be created directly.
    );

    return &meshEntryCinfo;
}

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void MeshEntry::process	(	const Eref &	e,
		ProcPtr	info
	)

Update the diffusion rate terms. Note that these stay the same through the entire clock tick, even if the GSL solver takes many intermediate steps. The assumption is that the concs change slowly enough that the diffusion terms are not hugely changed over the duration of one tick. Also assume that diffusion itself is slow. The latter assumption is OK for suitable grid sizes. The first assumption is OK with a sensible tick step.

Definition at line 204 of file MeshEntry.cpp.

Referenced by initCinfo().

{
    // cout << "updateDiffusion for " << e.fieldIndex() << ", at t = " << info->currTime << ", on thr = " << info->threadIndexInGroup << endl << flush;
    // parent_->updateDiffusion( e.fieldIndex() );
}

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void MeshEntry::reinit	(	const Eref &	e,
		ProcPtr	info
	)

Assigns the Stoich Id to the parent.

Definition at line 213 of file MeshEntry.cpp.

References Eref::dataIndex(), and Neutral::parent().

Referenced by initCinfo().

{
    if ( e.dataIndex() == 0 ) {
        ObjId pa = Neutral::parent( e );
        // parent_->lookupStoich( pa );
    }
}

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void MeshEntry::triggerRemesh	(	const Eref &	e,
		double	oldvol,
		unsigned int	startEntry,
		const vector< unsigned int > &	localIndices,
		const vector< double > &	vols
	)

Definition at line 267 of file MeshEntry.cpp.

References ChemCompt::getNumEntries(), parent_, remeshOut(), remeshReacsOut(), and SrcFinfo0::send().

Referenced by PsdMesh::handlePsdList(), and SpineMesh::handleSpineList().

{
    // cout << "MeshEntry::triggerRemesh on " << e.element()->getName() << endl;
    remeshOut()->send( e, oldvol, parent_->getNumEntries(),
        startEntry, localIndices, vols );
    remeshReacsOut()->send( e );
}

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Member Data Documentation

const ChemCompt* MeshEntry::parent_

private

Volume or area.

Definition at line 127 of file MeshEntry.h.

Referenced by getCoordinates(), getDiffusionArea(), getDiffusionScaling(), getDimensions(), getMeshType(), getNeighbors(), getVolume(), and triggerRemesh().

double MeshEntry::volume_

private

Definition at line 126 of file MeshEntry.h.

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

• moose-core/mesh/MeshEntry.h
• moose-core/mesh/MeshEntry.cpp