#include <VoxelPoolsBase.h>

Inheritance diagram for VoxelPoolsBase:

Collaboration diagram for VoxelPoolsBase:

Public Member Functions
void	addProxyTransferIndex (unsigned int comptIndex, unsigned int transferIndex)

void	addProxyVoxy (unsigned int comptIndex, Id comptId, unsigned int voxel)
	Adds the index of a voxel to which proxy data should go. More...

void	backwardReacVolumeFactor (unsigned int i, double volume)

void	filterCrossRateTerms (const vector< Id > &offSolverReacs, const vector< pair< Id, Id > > &offSolverReacCompts)

void	forwardReacVolumeFactor (unsigned int i, double volume)

double	getDiffConst (unsigned int) const

double	getN (unsigned int) const

double	getNinit (unsigned int) const

double	getVolume () const
	Return the volume of the voxel. More...

double	getXreacScaleProducts (unsigned int i) const

double	getXreacScaleSubstrates (unsigned int i) const

bool	hasXfer (unsigned int comptIndex) const
	True when this voxel has data to be transferred. More...

bool	isVoxelJunctionPresent (Id i1, Id i2) const

void	print () const
	Debugging utility. More...

void	reinit ()

void	resetXreacScale (unsigned int size)

void	resizeArrays (unsigned int totNumPools)
	Allocate # of pools. More...

const double *	S () const

void	scaleVolsBufsRates (double ratio, const Stoich *stoichPtr)

void	setDiffConst (unsigned int, double v)

void	setN (unsigned int i, double v)

void	setNinit (unsigned int, double v)

void	setVolume (double vol)
	Just assigns the volume without any cascading to other values. More...

virtual void	setVolumeAndDependencies (double vol)

const double *	Sinit () const

unsigned int	size () const

vector< double > &	Svec ()
	Returns a handle to the mol # vector. More...

virtual void	updateAllRateTerms (const vector< RateTerm * > &rates, unsigned int numCoreRates)=0

virtual void	updateRateTerms (const vector< RateTerm * > &rates, unsigned int numCoreRates, unsigned int index)=0

double *	varS ()

double *	varSinit ()

	VoxelPoolsBase ()

void	xferIn (const vector< unsigned int > &poolIndex, const vector< double > &values, const vector< double > &lastValues, unsigned int voxelIndex)

void	xferInOnlyProxies (const vector< unsigned int > &poolIndex, const vector< double > &values, unsigned int numProxyPools, unsigned int voxelIndex)

void	xferOut (unsigned int voxelIndex, vector< double > &values, const vector< unsigned int > &poolIndex)
	Assembles data values for sending out for x-compt reacs. More...

virtual	~VoxelPoolsBase ()

Protected Attributes
vector< RateTerm * >	rates_

const Stoich *	stoichPtr_

Private Attributes
map< Id, unsigned int >	proxyComptMap_

vector< vector< unsigned int > >	proxyPoolVoxels_

vector< vector< unsigned int > >	proxyTransferIndex_

vector< double >	S_

vector< double >	Sinit_

double	volume_

vector< double >	xReacScaleProducts_

vector< double >	xReacScaleSubstrates_

Detailed Description

This is the base class for voxels used in reac-diffusion systems. Each voxel manages all the molecular pools that live in it. This is the S_ and Sinit_ vectors. Additionally, the last set of entries in S_ and Sinit_ refer to the proxy pools that participate in cross-node reactions, but are really located on other compartments.

Definition at line 31 of file VoxelPoolsBase.h.

Constructor & Destructor Documentation

VoxelPoolsBase::VoxelPoolsBase ( )

Definition at line 25 of file VoxelPoolsBase.cpp.

                                :
     stoichPtr_( 0 ),
     S_(1),
     Sinit_(1),
     volume_(1.0)
 {
     ;
 }

VoxelPoolsBase::~VoxelPoolsBase ( )

virtual

Definition at line 34 of file VoxelPoolsBase.cpp.

35 {}

Member Function Documentation

void VoxelPoolsBase::addProxyTransferIndex	(	unsigned int	comptIndex,
		unsigned int	transferIndex
	)

Definition at line 253 of file VoxelPoolsBase.cpp.

References proxyTransferIndex_.

 {
     if ( comptIndex >= proxyTransferIndex_.size() )
         proxyTransferIndex_.resize( comptIndex + 1 );
     proxyTransferIndex_[comptIndex].push_back( transferIndex );
 }

void VoxelPoolsBase::addProxyVoxy	(	unsigned int	comptIndex,
		Id	comptId,
		unsigned int	voxel
	)

Adds the index of a voxel to which proxy data should go.

Definition at line 241 of file VoxelPoolsBase.cpp.

References proxyComptMap_, and proxyPoolVoxels_.

 {
     if ( comptIndex >= proxyPoolVoxels_.size() )
     {
         proxyPoolVoxels_.resize( comptIndex + 1 );
     }
 
     proxyPoolVoxels_[comptIndex].push_back( voxel );
     proxyComptMap_[otherComptId] = comptIndex;
 }

void VoxelPoolsBase::backwardReacVolumeFactor	(	unsigned int	i,
		double	volume
	)

Multiply in scale factor for different cross-reac volumes, to be applied to specified RateTerm in the rates_ vector. Applies to backward reaction terms

Definition at line 299 of file VoxelPoolsBase.cpp.

References getVolume(), and xReacScaleProducts_.

 {
     assert( i < xReacScaleProducts_.size() );
     xReacScaleProducts_[i] *= volume / getVolume();
     // cout << "backwardReacVolumeFactor[" << i << "] = "<< xReacScaleProducts_[i] <<endl;
 }

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void VoxelPoolsBase::filterCrossRateTerms	(	const vector< Id > &	offSolverReacs,
		const vector< pair< Id, Id > > &	offSolverReacCompts
	)

Changes cross rate terms to zero if there is no junction

Zeroes out rate terms that are involved in cross-reactions that are not present on current voxel.

Definition at line 320 of file VoxelPoolsBase.cpp.

References Element::cinfo(), Stoich::convertIdToReacIndex(), Id::element(), Stoich::getOneWay(), Cinfo::isA(), isVoxelJunctionPresent(), rates_, reacCinfo, and stoichPtr_.

 {
     assert (offSolverReacs.size() == offSolverReacCompts.size() );
     // unsigned int numCoreRates = stoichPtr_->getNumCoreRates();
     for ( unsigned int i = 0; i < offSolverReacCompts.size(); ++i )
     {
         const pair< Id, Id >& p = offSolverReacCompts[i];
         if ( !isVoxelJunctionPresent( p.first, p.second) )
         {
             Id reacId = offSolverReacs[i];
             const Cinfo* reacCinfo = reacId.element()->cinfo();
             unsigned int k = stoichPtr_->convertIdToReacIndex( offSolverReacs[i] );
             // Start by replacing the immediate cross reaction term.
             if ( rates_[k] )
                 delete rates_[k];
             rates_[k] = new ExternReac;
             if ( stoichPtr_->getOneWay() )
             {
                 k++; // Delete the next entry too, it is the reverse reacn.
                 assert( k < rates_.size() );
                 if ( reacCinfo->isA( "ReacBase" ) )
                 {
                     if ( rates_[k] )
                         delete rates_[k];
                     rates_[k] = new ExternReac;
                 }
                 if ( reacCinfo->isA( "CplxEnzBase" ) )   // Delete next two.
                 {
                     if ( rates_[k] )
                         delete rates_[k];
                     rates_[k] = new ExternReac;
                     k++;
                     assert( k < rates_.size() );
                     if ( rates_[k] )
                         delete rates_[k];
                     rates_[k] = new ExternReac;
                 }
             }
             else
             {
                 if ( reacCinfo->isA( "CplxEnzBase" ) )   // Delete next one.
                 {
                     k++;
                     assert( k < rates_.size() );
                     if ( rates_[k] )
                         delete rates_[k];
                     rates_[k] = new ExternReac;
                 }
             }
         }
     }
 }

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void VoxelPoolsBase::forwardReacVolumeFactor	(	unsigned int	i,
		double	volume
	)

Multiply in scale factor for different cross-reac volumes, to be applied to specified RateTerm in the rates_ vector. Applies to forward reaction terms

Definition at line 292 of file VoxelPoolsBase.cpp.

References getVolume(), and xReacScaleSubstrates_.

 {
     assert( i < xReacScaleSubstrates_.size() );
     xReacScaleSubstrates_[i] *= volume / getVolume();
     // cout << "forwardReacVolumeFactor[" << i << "] = " << xReacScaleSubstrates_[i] <<endl;
 }

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double VoxelPoolsBase::getDiffConst ( unsigned int i ) const

Definition at line 179 of file VoxelPoolsBase.cpp.

 {
     return 0;
 }

double VoxelPoolsBase::getN ( unsigned int i ) const

Definition at line 157 of file VoxelPoolsBase.cpp.

References S_.

 {
     return S_[i];
 }

double VoxelPoolsBase::getNinit ( unsigned int i ) const

Definition at line 169 of file VoxelPoolsBase.cpp.

References Sinit_.

 {
     return Sinit_[i];
 }

double VoxelPoolsBase::getVolume ( ) const

Return the volume of the voxel.

Definition at line 90 of file VoxelPoolsBase.cpp.

References volume_.

Referenced by backwardReacVolumeFactor(), forwardReacVolumeFactor(), scaleVolsBufsRates(), GssaVoxelPools::updateAllRateTerms(), and GssaVoxelPools::updateRateTerms().

 {
     return volume_;
 }

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double VoxelPoolsBase::getXreacScaleProducts ( unsigned int i ) const

Return scale factor for specified entry on rate terms. Index is # of cross-compartment rate term.

Definition at line 311 of file VoxelPoolsBase.cpp.

References xReacScaleProducts_.

Referenced by scaleVolsBufsRates(), GssaVoxelPools::updateAllRateTerms(), and GssaVoxelPools::updateRateTerms().

 {
     return xReacScaleProducts_[i];
 }

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double VoxelPoolsBase::getXreacScaleSubstrates ( unsigned int i ) const

Return scale factor for specified entry on rate terms. Index is # of cross-compartment rate term.

Definition at line 306 of file VoxelPoolsBase.cpp.

References xReacScaleSubstrates_.

Referenced by scaleVolsBufsRates(), GssaVoxelPools::updateAllRateTerms(), and GssaVoxelPools::updateRateTerms().

 {
     return xReacScaleSubstrates_[i];
 }

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bool VoxelPoolsBase::hasXfer ( unsigned int comptIndex ) const

True when this voxel has data to be transferred.

Assigns the Id and volume of the specified x-reac coupled compartment void setComptVolume( unsigned int comptIndex, Id id, double vol );

Definition at line 261 of file VoxelPoolsBase.cpp.

References proxyPoolVoxels_, and size().

 {
     if ( comptIndex >= proxyPoolVoxels_.size() )
         return false;
     return (proxyPoolVoxels_[ comptIndex ].size() > 0);
 }

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bool VoxelPoolsBase::isVoxelJunctionPresent	(	Id	i1,
		Id	i2
	)		const

True when there is a junction. i1 must match, and if i2 is non-zero then it too must match.

Definition at line 268 of file VoxelPoolsBase.cpp.

References proxyComptMap_.

Referenced by filterCrossRateTerms().

 {
     if ( i1 == Id () )
         return false;
     if ( proxyComptMap_.find( i1 ) == proxyComptMap_.end() )
         return false;
     if ( i2 == Id() ) // This is intentionally blank, only one jn.
         return true;
     // If there is an i2 but it isn't on the map, then not connected.
     if ( proxyComptMap_.find( i2 ) == proxyComptMap_.end() )
         return false;
     return true;
 }

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void VoxelPoolsBase::print ( ) const

Debugging utility.

Definition at line 376 of file VoxelPoolsBase.cpp.

References proxyPoolVoxels_, proxyTransferIndex_, rates_, S_, volume_, xReacScaleProducts_, and xReacScaleSubstrates_.

Referenced by VoxelPools::print().

 {
     cout << "S_.size=" << S_.size() << ", volume = " << volume_ << endl;
     cout << "proxyPoolsVoxels.size()=" << proxyPoolVoxels_.size() <<
          ", proxyTransferIndex.size()=" << proxyTransferIndex_.size() <<
          endl;
     assert( proxyPoolVoxels_.size() == proxyTransferIndex_.size() );
     for ( unsigned int i = 0; i < proxyPoolVoxels_.size(); ++i )
     {
         cout << "ppv[" << i << "]=";
         const vector< unsigned int >& ppv = proxyPoolVoxels_[i];
         for ( unsigned int j = 0; j < ppv.size(); ++j )
         {
             cout << "   " << ppv[j];
         }
         cout << endl;
     }
     for ( unsigned int i = 0; i < proxyTransferIndex_.size(); ++i )
     {
         cout << "pti[" << i << "]=";
         const vector< unsigned int >& pti = proxyTransferIndex_[i];
         for ( unsigned int j = 0; j < pti.size(); ++j )
         {
             cout << "   " << pti[j];
         }
         cout << endl;
     }
     cout <<
          "xReacScaleSubstrates.size()=" << xReacScaleSubstrates_.size() <<
          ", xReacScaleProducts.size()=" << xReacScaleProducts_.size() <<
          endl;
     assert( xReacScaleSubstrates_.size() == xReacScaleProducts_.size() );
     for ( unsigned int i = 0; i < xReacScaleSubstrates_.size(); ++i )
     {
         cout << i << "  " << xReacScaleSubstrates_[i] << "  " <<
              xReacScaleProducts_[i] << endl;
     }
     cout << "##############    RATES    ######################\n";
     for ( unsigned int i = 0; i < rates_.size(); ++i )
     {
         cout << i << "  :   " << rates_[i]->getR1() << ",   " <<
              rates_[i]->getR2() << endl;
     }
 }

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void VoxelPoolsBase::reinit ( )

Assigns S = Sinit and sets up initial dt.

Definition at line 47 of file VoxelPoolsBase.cpp.

References S_, and Sinit_.

Referenced by VoxelPools::reinit(), GssaVoxelPools::reinit(), and VoxelPools::setStoich().

 {
     S_ = Sinit_;
 }

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void VoxelPoolsBase::resetXreacScale ( unsigned int size )

Initialize/reset the vector xReacScaling_ for scale factors for each cross reaction in this voxel.

Definition at line 286 of file VoxelPoolsBase.cpp.

References xReacScaleProducts_, and xReacScaleSubstrates_.

 {
     xReacScaleSubstrates_.assign( size, 1.0 );
     xReacScaleProducts_.assign( size, 1.0 );
 }

void VoxelPoolsBase::resizeArrays ( unsigned int totNumPools )

Allocate # of pools.

Using the computed array sizes, now allocate space for them.

Definition at line 41 of file VoxelPoolsBase.cpp.

References S_, and Sinit_.

 {
     S_.resize( totNumPools, 0.0 );
     Sinit_.resize( totNumPools, 0.0);
 }

const double * VoxelPoolsBase::S ( ) const

Returns the array of doubles of current mol #s at the specified mesh index

Definition at line 55 of file VoxelPoolsBase.cpp.

References S_.

Referenced by GssaVoxelPools::refreshAtot(), and GssaVoxelPools::updateDependentRates().

 {
     return &S_[0];
 }

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void VoxelPoolsBase::scaleVolsBufsRates	(	double	ratio,
		const Stoich *	stoichPtr
	)

Definition at line 111 of file VoxelPoolsBase.cpp.

References Stoich::getNumBufPools(), Stoich::getNumCoreRates(), Stoich::getNumVarPools(), Stoich::getRateTerms(), getVolume(), getXreacScaleProducts(), getXreacScaleSubstrates(), Stoich::isFuncTarget(), rates_, S_, Sinit_, stoichPtr_, and volume_.

Referenced by Stoich::scaleBufsAndRates().

 {
     volume_ *= ratio; // Scale vol
     for ( vector< double >::iterator
             i = Sinit_.begin(); i != Sinit_.end(); ++i )
         *i *= ratio; // Scale Bufs
     // Here we also need to set the Ns for the buffered pools.
     unsigned int start = stoichPtr_->getNumVarPools();
     unsigned int end = start + stoichPtr_->getNumBufPools();
     assert( end == Sinit_.size() );
     for ( unsigned int i = start; i < end; ++i )
     {
         // Must not reassign pools that are controlled by functions.
         if ( !stoichPtr->isFuncTarget(i) )
             S_[i] = Sinit_[i];
     }
 
     // Scale rates. Start by clearing out old rates if any
     for ( unsigned int i = 0; i < rates_.size(); ++i )
         delete( rates_[i] );
 
     unsigned int numCoreRates = stoichPtr->getNumCoreRates();
     const vector< RateTerm* >& rates = stoichPtr->getRateTerms();
     rates_.resize( rates.size() );
     for ( unsigned int i = 0; i < numCoreRates; ++i )
         rates_[i] = rates[i]->copyWithVolScaling( getVolume(), 1, 1 );
     for ( unsigned int i = numCoreRates; i < rates.size(); ++i )
     {
         rates_[i] = rates[i]->copyWithVolScaling(  getVolume(),
                     getXreacScaleSubstrates(i - numCoreRates),
                     getXreacScaleProducts(i - numCoreRates ) );
     }
 }

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void VoxelPoolsBase::setDiffConst	(	unsigned int	i,
		double	v
	)

Definition at line 174 of file VoxelPoolsBase.cpp.

 {
     ; // Do nothing.
 }

void VoxelPoolsBase::setN	(	unsigned int	i,
		double	v
	)

Definition at line 150 of file VoxelPoolsBase.cpp.

References S_.

 {
     S_[i] = v;
     if ( S_[i] < 0.0 )
         S_[i] = 0.0;
 }

void VoxelPoolsBase::setNinit	(	unsigned int	i,
		double	v
	)

Definition at line 162 of file VoxelPoolsBase.cpp.

References Sinit_.

 {
     Sinit_[i] = v;
     if ( Sinit_[i] < 0.0 )
         Sinit_[i] = 0.0;
 }

void VoxelPoolsBase::setVolume ( double vol )

Just assigns the volume without any cascading to other values.

Definition at line 85 of file VoxelPoolsBase.cpp.

References volume_.

Referenced by ZombiePoolInterface::setCompartment(), and SteadyState::setStoich().

 {
     volume_ = vol;
 }

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void VoxelPoolsBase::setVolumeAndDependencies ( double vol )

virtual

Assign the volume, and handle the cascading effects by scaling all the dependent values of nInit and rates if applicable.

Reimplemented in VoxelPools, and GssaVoxelPools.

Definition at line 95 of file VoxelPoolsBase.cpp.

References S_, Sinit_, and volume_.

Referenced by GssaVoxelPools::setVolumeAndDependencies(), and VoxelPools::setVolumeAndDependencies().

 {
     double ratio = vol / volume_;
     volume_ = vol;
     for ( vector< double >::iterator
             i = Sinit_.begin(); i != Sinit_.end(); ++i )
         *i *= ratio;
 
     for ( vector< double >::iterator i = S_.begin(); i != S_.end(); ++i )
         *i *= ratio;
 
     // I would like to update the xReacScaleSubstreates and Products here,
     // but I don't know the order of their reactions. So leave it to
     // a subsequent call via Ksolve or Stoich.
 }

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const double * VoxelPoolsBase::Sinit ( ) const

Returns the array of doubles of initial mol #s at the specified mesh index

Definition at line 70 of file VoxelPoolsBase.cpp.

References Sinit_.

 {
     return &Sinit_[0];
 }

unsigned int VoxelPoolsBase::size ( ) const

Returns # of pools

Definition at line 80 of file VoxelPoolsBase.cpp.

References Sinit_.

Referenced by hasXfer().

 {
     return Sinit_.size();
 }

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vector< double > & VoxelPoolsBase::Svec ( )

Returns a handle to the mol # vector.

Definition at line 60 of file VoxelPoolsBase.cpp.

References S_.

Referenced by GssaVoxelPools::advance(), Gsolve::getNvec(), and Ksolve::getNvec().

 {
     return S_;
 }

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virtual void VoxelPoolsBase::updateAllRateTerms	(	const vector< RateTerm * > &	rates,
		unsigned int	numCoreRates
	)

pure virtual

Reassign entire rate vector.

Implemented in VoxelPools, and GssaVoxelPools.

virtual void VoxelPoolsBase::updateRateTerms	(	const vector< RateTerm * > &	rates,
		unsigned int	numCoreRates,
		unsigned int	index
	)

pure virtual

Update specified index on rate terms. The entire rates vector is passed in for the source values, the index specifies which entry on the local rate vector is to be updated.

Implemented in VoxelPools, and GssaVoxelPools.

double * VoxelPoolsBase::varS ( )

Returns the array of doubles of current mol #s at the specified mesh index. Dangerous, allows one to modify the values.

Definition at line 65 of file VoxelPoolsBase.cpp.

References S_.

Referenced by GssaVoxelPools::advance(), GssaVoxelPools::refreshAtot(), GssaVoxelPools::reinit(), GssaVoxelPools::updateDependentMathExpn(), and GssaVoxelPools::xferIn().

 {
     return &S_[0];
 }

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double * VoxelPoolsBase::varSinit ( )

Returns the array of doubles of initial mol #s at the specified mesh index, as a writable array.

Definition at line 75 of file VoxelPoolsBase.cpp.

References Sinit_.

 {
     return &Sinit_[0];
 }

void VoxelPoolsBase::xferIn	(	const vector< unsigned int > &	poolIndex,
		const vector< double > &	values,
		const vector< double > &	lastValues,
		unsigned int	voxelIndex
	)

Digests incoming data values for cross-compt reactions. Sums the changes in the values onto the specified pools.

Definition at line 187 of file VoxelPoolsBase.cpp.

References S_.

 {
     unsigned int offset = voxelIndex * poolIndex.size();
     vector< double >::const_iterator i = values.begin() + offset;
     vector< double >::const_iterator j = lastValues.begin() + offset;
     for ( vector< unsigned int >::const_iterator
             k = poolIndex.begin(); k != poolIndex.end(); ++k )
     {
         S_[*k] += *i++ - *j++;
     }
 }

void VoxelPoolsBase::xferInOnlyProxies	(	const vector< unsigned int > &	poolIndex,
		const vector< double > &	values,
		unsigned int	numProxyPools,
		unsigned int	voxelIndex
	)

Used during initialization: Takes only the proxy pool values from the incoming transfer data, and assigns it to the proxy pools on current solver

Definition at line 203 of file VoxelPoolsBase.cpp.

References Stoich::getNumProxyPools(), Stoich::getNumVarPools(), S_, Sinit_, and stoichPtr_.

 {
     unsigned int offset = voxelIndex * poolIndex.size();
     vector< double >::const_iterator i = values.begin() + offset;
     unsigned int proxyEndIndex = stoichPtr_->getNumVarPools() +
                                  stoichPtr_->getNumProxyPools();
     for ( vector< unsigned int >::const_iterator
             k = poolIndex.begin(); k != poolIndex.end(); ++k )
     {
         // if ( *k >= S_.size() - numProxyPools )
         if ( *k >= stoichPtr_->getNumVarPools() && *k < proxyEndIndex )
         {
             // cout << S_[*k] << ", " << Sinit_[*k] << ", " << *i <<  endl;
             Sinit_[*k] = *i;
             S_[*k] = *i;
         }
         i++;
     }
 }

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void VoxelPoolsBase::xferOut	(	unsigned int	voxelIndex,
		vector< double > &	values,
		const vector< unsigned int > &	poolIndex
	)

Assembles data values for sending out for x-compt reacs.

Definition at line 227 of file VoxelPoolsBase.cpp.

References S_.

 {
     unsigned int offset = voxelIndex * poolIndex.size();
     vector< double >::iterator i = values.begin() + offset;
     for ( vector< unsigned int >::const_iterator
             k = poolIndex.begin(); k != poolIndex.end(); ++k )
     {
         *i++ = S_[*k];
     }
 }

Member Data Documentation

map< Id, unsigned int > VoxelPoolsBase::proxyComptMap_

private

Looks up comptIndex from compt. Actually just a set would do.

Definition at line 263 of file VoxelPoolsBase.h.

Referenced by addProxyVoxy(), and isVoxelJunctionPresent().

vector< vector< unsigned int > > VoxelPoolsBase::proxyPoolVoxels_

private

The number of pools (at the end of S and Sinit) that are here just as proxies for some off-compartment pools that participate in cross-compartment reactions. unsigned int numProxyPools_; proxyPoolVoxels_[comptIndex][#] Used to build the transfer vector. Stores the voxels of proxy pools in specified compartment,

Definition at line 251 of file VoxelPoolsBase.h.

Referenced by addProxyVoxy(), hasXfer(), and print().

vector< vector< unsigned int > > VoxelPoolsBase::proxyTransferIndex_

private

proxyTransferIndex_[comptIndex][#] Stores the index in the transfer vector for proxy pools that live on this voxel. The poolIndex and # of pools is known from the xferPoolIdx_ vector stored on the Ksolve.

Definition at line 258 of file VoxelPoolsBase.h.

Referenced by addProxyTransferIndex(), and print().

vector< RateTerm* > VoxelPoolsBase::rates_

protected

Definition at line 212 of file VoxelPoolsBase.h.

Referenced by filterCrossRateTerms(), GssaVoxelPools::getReacVelocity(), print(), scaleVolsBufsRates(), GssaVoxelPools::updateAllRateTerms(), GssaVoxelPools::updateRateTerms(), GssaVoxelPools::updateReacVelocities(), and GssaVoxelPools::~GssaVoxelPools().

vector< double > VoxelPoolsBase::S_

private

S_ is the array of molecules. Stored as n, number of molecules per mesh entry. The poolIndex specifies which molecular species pool to use.

The first numVarPools_ in the poolIndex are state variables and are integrated using the ODE solver or the GSSA solver. The next numBufPools_ are fixed but can be changed by the script. The next numFuncPools_ are computed using arbitrary functions of any of the molecule levels, and the time. The functions evaluate before the solver. The functions should not cascade as there is no guarantee of execution order.

Definition at line 229 of file VoxelPoolsBase.h.

Referenced by getN(), print(), reinit(), resizeArrays(), S(), scaleVolsBufsRates(), setN(), setVolumeAndDependencies(), Svec(), varS(), xferIn(), xferInOnlyProxies(), and xferOut().

vector< double > VoxelPoolsBase::Sinit_

private

Sinit_ specifies initial conditions at t = 0. Whenever the reac system is rebuilt or reinited, all S_ values become set to Sinit. Also used for buffered molecules as the fixed values of these molecules.

Definition at line 237 of file VoxelPoolsBase.h.

Referenced by getNinit(), reinit(), resizeArrays(), scaleVolsBufsRates(), setNinit(), setVolumeAndDependencies(), Sinit(), size(), varSinit(), and xferInOnlyProxies().

const Stoich* VoxelPoolsBase::stoichPtr_

protected

Definition at line 211 of file VoxelPoolsBase.h.

Referenced by VoxelPools::advance(), filterCrossRateTerms(), scaleVolsBufsRates(), GssaVoxelPools::setStoich(), GssaVoxelPools::setVolumeAndDependencies(), and xferInOnlyProxies().

double VoxelPoolsBase::volume_

private

This is what I would need to fully identify proxy compts and voxels for each proxy reac. vector< Id, Id, unsigned int, unsigned int> proxyComptVoxel Volume of voxel.

Definition at line 273 of file VoxelPoolsBase.h.

Referenced by getVolume(), print(), scaleVolsBufsRates(), setVolume(), and setVolumeAndDependencies().

vector< double > VoxelPoolsBase::xReacScaleProducts_

private

xReacScaleProducts_[crossRateTermIndex] Product of productVol/voxelVol for each of the products, for reverse reacs. Applied to R2 of the RateTerm. Used only for cross reactions.

Definition at line 289 of file VoxelPoolsBase.h.

Referenced by backwardReacVolumeFactor(), getXreacScaleProducts(), print(), and resetXreacScale().

vector< double > VoxelPoolsBase::xReacScaleSubstrates_

private

xReacScaleSubstrates_[crossRateTermIndex] Product of substrateVol/voxelVol for each of the substrates, for forward reacs. Applied to R1 of the RateTerm. Used only for cross reactions.

Definition at line 281 of file VoxelPoolsBase.h.

Referenced by forwardReacVolumeFactor(), getXreacScaleSubstrates(), print(), and resetXreacScale().

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

moose-core/ksolve/VoxelPoolsBase.h
moose-core/ksolve/VoxelPoolsBase.cpp

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