DiffPoolVec Class Reference

#include <DiffPoolVec.h>

Collaboration diagram for DiffPoolVec:

Public Member Functions
void	advance (double dt)
	DiffPoolVec ()
double	getDiffConst () const
unsigned int	getId () const
double	getMotorConst () const
double	getN (unsigned int vox) const
double	getNinit (unsigned int vox) const
unsigned int	getNumVoxels () const
const vector< double > &	getNvec () const
	Used by parent solver to manipulate 'n'. More...
double	getPrev (unsigned int vox) const
void	process ()
void	reinit ()
void	setDiffConst (double value)
void	setId (unsigned int id)
void	setMotorConst (double value)
void	setN (unsigned int vox, double value)
void	setNinit (unsigned int vox, double value)
void	setNumVoxels (unsigned int num)
void	setNvec (const vector< double > &n)
	Used by parent solver to manipulate 'n'. More...
void	setNvec (unsigned int start, unsigned int num, vector< double >::const_iterator q)
void	setOps (const vector< Triplet< double > > &ops_, const vector< double > &diagVal_)
	Assigns prev_ = n_. More...
void	setPrevVec ()

Private Attributes
vector< double >	diagVal_
double	diffConst_
	Boundary condition: Initial 'n'. More...
unsigned int	id_
	Assign operations. More...
double	motorConst_
	Diffusion const, assumed uniform. More...
vector< double >	n_
	Integer conversion of Id of pool handled. More...
vector< double >	nInit_
	molecules of pool on previous timestep More...
vector< Triplet< double > >	ops_
	Motor const, ie, transport rate. More...
vector< double >	prev_
	Number of molecules of pool in each voxel. More...

Detailed Description

This is a FieldElement of the Dsolve class. It manages (ie., zombifies) a specific pool, and the pool maintains a pointer to it. For accessing volumes, this maintains a pointer to the relevant ChemCompt.

Definition at line 18 of file DiffPoolVec.h.

Constructor & Destructor Documentation

DiffPoolVec::DiffPoolVec

(

)

Default is to create it with a single compartment, independent of any solver, so that we can set it up as a dummy DiffPool for the Pool to work on in single-compartment models.

Definition at line 25 of file DiffPoolVec.cpp.

    : id_( 0 ), n_( 1, 0.0 ), nInit_( 1, 0.0 ),
      diffConst_( 1.0e-12 ), motorConst_( 0.0 )
{
    ;
}

Member Function Documentation

void DiffPoolVec::advance

(

double

dt

)

Definition at line 144 of file DiffPoolVec.cpp.

References diagVal_, n_, and ops_.

{
    if ( ops_.size() == 0 ) return;
    for ( vector< Triplet< double > >::const_iterator
            i = ops_.begin(); i != ops_.end(); ++i )
        n_[i->c_] -= n_[i->b_] * i->a_;

    assert( n_.size() == diagVal_.size() );
    vector< double >::iterator iy = n_.begin();
    for ( vector< double >::const_iterator
            i = diagVal_.begin(); i != diagVal_.end(); ++i )
        *iy++ *= *i;
}

double DiffPoolVec::getDiffConst

(

)

const

Definition at line 87 of file DiffPoolVec.cpp.

References diffConst_.

Referenced by Dsolve::calcJnDiff().

{
    return diffConst_;
}

Here is the caller graph for this function:

unsigned int DiffPoolVec::getId

(

)

const

Definition at line 123 of file DiffPoolVec.cpp.

References id_.

{
    return id_;
}

double DiffPoolVec::getMotorConst

(

)

const

Definition at line 97 of file DiffPoolVec.cpp.

References motorConst_.

{
    return motorConst_;
}

double DiffPoolVec::getN

(

unsigned int

vox

)

const

Definition at line 44 of file DiffPoolVec.cpp.

References n_.

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

{
    assert( voxel < n_.size() );
    return n_[ voxel ];
}

Here is the caller graph for this function:

double DiffPoolVec::getNinit

(

unsigned int

vox

)

const

Definition at line 32 of file DiffPoolVec.cpp.

References nInit_.

{
    assert( voxel < nInit_.size() );
    return nInit_[ voxel ];
}

unsigned int DiffPoolVec::getNumVoxels

(

)

const

Definition at line 113 of file DiffPoolVec.cpp.

References n_.

{
    return n_.size();
}

const vector< double > & DiffPoolVec::getNvec

(

)

const

Used by parent solver to manipulate 'n'.

Definition at line 62 of file DiffPoolVec.cpp.

References n_.

{
    return n_;
}

double DiffPoolVec::getPrev

(

unsigned int

vox

)

const

Definition at line 56 of file DiffPoolVec.cpp.

References n_, and prev_.

Referenced by Dsolve::calcJnXfer().

{
    assert( voxel < n_.size() );
    return prev_[ voxel ];
}

Here is the caller graph for this function:

void DiffPoolVec::process

(

)

void DiffPoolVec::reinit

(

)

Definition at line 158 of file DiffPoolVec.cpp.

References n_, nInit_, and prev_.

{
    assert( n_.size() == nInit_.size() );
    prev_ = n_ = nInit_;
}

void DiffPoolVec::setDiffConst

(

double

value

)

Definition at line 92 of file DiffPoolVec.cpp.

References diffConst_.

{
    diffConst_ = v;
}

void DiffPoolVec::setId

(

unsigned int

id

)

Definition at line 118 of file DiffPoolVec.cpp.

References id, and id_.

{
    id_ = id;
}

void DiffPoolVec::setMotorConst

(

double

value

)

Definition at line 102 of file DiffPoolVec.cpp.

References motorConst_.

{
    motorConst_ = v;
}

void DiffPoolVec::setN	(	unsigned int	vox,
		double	value
	)

Definition at line 50 of file DiffPoolVec.cpp.

References n_.

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

{
    assert( voxel < n_.size() );
    n_[ voxel ] = v;
}

Here is the caller graph for this function:

void DiffPoolVec::setNinit	(	unsigned int	vox,
		double	value
	)

Definition at line 38 of file DiffPoolVec.cpp.

References nInit_.

{
    assert( voxel < nInit_.size() );
    nInit_[ voxel ] = v;
}

void DiffPoolVec::setNumVoxels

(

unsigned int

num

)

Definition at line 107 of file DiffPoolVec.cpp.

References n_, and nInit_.

{
    nInit_.resize( num, 0.0 );
    n_.resize( num, 0.0 );
}

void DiffPoolVec::setNvec

(

const vector< double > &

n

)

Used by parent solver to manipulate 'n'.

Definition at line 67 of file DiffPoolVec.cpp.

References n_.

{
    assert( vec.size() == n_.size() );
    n_ = vec;
}

void DiffPoolVec::setNvec	(	unsigned int	start,
		unsigned int	num,
		vector< double >::const_iterator	q
	)

Definition at line 73 of file DiffPoolVec.cpp.

References n_.

{
    assert( start + num <= n_.size() );
    vector< double >::iterator p = n_.begin() + start;
    for ( unsigned int i = 0; i < num; ++i )
        *p++ = *q++;
}

void DiffPoolVec::setOps	(	const vector< Triplet< double > > &	ops_,
		const vector< double > &	diagVal_
	)

Assigns prev_ = n_.

Definition at line 128 of file DiffPoolVec.cpp.

References diagVal_, n_, and ops_.

{
    if ( ops.size() > 0 )
    {
        assert( diagVal.size() == n_.size() );
        ops_ = ops;
        diagVal_ = diagVal;
    }
    else
    {
        ops_.clear();
        diagVal_.clear();
    }
}

void DiffPoolVec::setPrevVec

(

)

Definition at line 82 of file DiffPoolVec.cpp.

References n_, and prev_.

{
    prev_ = n_;
}

Member Data Documentation

vector< double > DiffPoolVec::diagVal_

private

Definition at line 63 of file DiffPoolVec.h.

Referenced by advance(), and setOps().

double DiffPoolVec::diffConst_

private

Boundary condition: Initial 'n'.

Definition at line 60 of file DiffPoolVec.h.

Referenced by getDiffConst(), and setDiffConst().

unsigned int DiffPoolVec::id_

private

Assign operations.

Definition at line 56 of file DiffPoolVec.h.

Referenced by getId(), and setId().

double DiffPoolVec::motorConst_

private

Diffusion const, assumed uniform.

Definition at line 61 of file DiffPoolVec.h.

Referenced by getMotorConst(), and setMotorConst().

vector< double > DiffPoolVec::n_

private

Integer conversion of Id of pool handled.

Definition at line 57 of file DiffPoolVec.h.

Referenced by advance(), getN(), getNumVoxels(), getNvec(), getPrev(), reinit(), setN(), setNumVoxels(), setNvec(), setOps(), and setPrevVec().

vector< double > DiffPoolVec::nInit_

private

molecules of pool on previous timestep

Definition at line 59 of file DiffPoolVec.h.

Referenced by getNinit(), reinit(), setNinit(), and setNumVoxels().

vector< Triplet< double > > DiffPoolVec::ops_

private

Motor const, ie, transport rate.

Definition at line 62 of file DiffPoolVec.h.

Referenced by advance(), and setOps().

vector< double > DiffPoolVec::prev_

private

Number of molecules of pool in each voxel.

Definition at line 58 of file DiffPoolVec.h.

Referenced by getPrev(), reinit(), and setPrevVec().

---

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

• moose-core/diffusion/DiffPoolVec.h
• moose-core/diffusion/DiffPoolVec.cpp