#include <KinSparseMatrix.h>

Inheritance diagram for KinSparseMatrix:

Collaboration diagram for KinSparseMatrix:

Public Member Functions
double	computeRowRate (unsigned int row, const vector< double > &v) const

void	fireReac (unsigned int reacIndex, vector< double > &S, double direction) const

void	getGillespieDependence (unsigned int row, vector< unsigned int > &cols) const

void	truncateRow (unsigned int maxColumnIndex)

Public Member Functions inherited from SparseMatrix< int >
void	addRow (unsigned int rowNum, const vector< int > &row)

void	addRow (unsigned int rowNum, const vector< int > &entry, const vector< unsigned int > &colIndexArg)

void	clear ()

const vector< unsigned int > &	colIndex () const

int	get (unsigned int row, unsigned int column) const

unsigned int	getColumn (unsigned int col, vector< int > &entry, vector< unsigned int > &rowIndex) const

unsigned int	getRow (unsigned int row, const int entry, const unsigned int colIndex) const

unsigned int	getRow (unsigned int row, vector< int > &e, vector< unsigned int > &c) const

const vector< int > &	matrixEntry () const
	Here we expose the sparse matrix for MOOSE use. More...

unsigned int	nColumns () const

unsigned int	nEntries () const

unsigned int	nRows () const

void	pairFill (const vector< unsigned int > &row, const vector< unsigned int > &col, intvalue)

void	print () const

void	printInternal () const

void	printTriplet (const vector< Triplet< int > > &t)

void	reorderColumns (const vector< unsigned int > &colMap)

const vector< unsigned int > &	rowStart () const

void	set (unsigned int row, unsigned int column, intvalue)

void	setSize (unsigned int nrows, unsigned int ncolumns)

	SparseMatrix ()

	SparseMatrix (unsigned int nrows, unsigned int ncolumns)

void	transpose ()

void	tripletFill (const vector< unsigned int > &row, const vector< unsigned int > &col, const vector< int > &z, bool retainSize=false)

void	unset (unsigned int row, unsigned int column)

Private Attributes
vector< unsigned int >	rowTruncated_

Additional Inherited Members
Protected Attributes inherited from SparseMatrix< int >
vector< unsigned int >	colIndex_
	Non-zero entries in the SparseMatrix. More...

vector< int >	N_

unsigned int	ncolumns_

unsigned int	nrows_

vector< unsigned int >	rowStart_
	Start index in the N_ and colIndex_ vectors, of each row. More...

Detailed Description

Definition at line 13 of file KinSparseMatrix.h.

Member Function Documentation

double KinSparseMatrix::computeRowRate	(	unsigned int	row,
		const vector< double > &	v
	)		const

Returns all non-zero column indices, for the specified row. This gives reac #s in orig matrix, and molecule #s in the transposed matrix Not needed. The getRow function does all this, more efficiently. int getRowIndices( unsigned int row, vector< unsigned int >& indices ); Returns the dot product of the specified row with the vector v. v corresponds to the vector of reaction rates. v must have nColumns entries.

Returns the dot product of the specified row with the vector v. v corresponds to the vector of reaction rates. v must have nColumns entries.

Definition at line 28 of file KinSparseMatrix.cpp.

References numEntries.

Referenced by VoxelPools::updateRates().

 {
     assert( nColumns() == 0 || row < nRows() );
     assert( v.size() == nColumns() );
     const int* entry = 0;
     const unsigned int* colIndex = 0;
     unsigned int numEntries = getRow( row, &entry, &colIndex );
     const int* end = entry + numEntries;
 
     double ret = 0.0;
     for ( const int* i = entry; i != end; ++i ) {
         ret += *i * v[ *colIndex++ ];
     }
 
 /*
     for ( unsigned int i = 0; i < numEntries; ++i ) {
         ret += entry[i] * v[ colIndex[i] ];
 
     }
 
     vector< int >::const_iterator i;
     unsigned int rs = rowStart_[ row ];
     vector< unsigned int >::const_iterator j = colIndex_.begin() + rs;
     vector< int >::const_iterator end = N_.begin() + rowStart_[ row + 1 ];
 
     double ret = 0.0;
     for ( i = N_.begin() + rs; i != end; i++ )
         ret += *i * v[ *j++ ];
 
     // assert ( !( ret !<>= 0.0 ) );
     */
 
     assert ( !( std::isnan( ret ) ) );
     return ret;
 }

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void KinSparseMatrix::fireReac	(	unsigned int	reacIndex,
		vector< double > &	S,
		double	direction
	)		const

Fires a stochastic reaction: It undergoes a single transition This operation updates the mol concs due to the reacn. Direction is +1 or -1, specifies direction of reaction

This too operates on the transposed matrix, because we need to get all the molecules for a given reac: a column in the original N matrix. Direction [-1,+1] specifies whether the reaction is forward or backward.

Definition at line 113 of file KinSparseMatrix.cpp.

Referenced by GssaVoxelPools::advance().

 {
     assert( ncolumns_ == S.size() && reacIndex < nrows_ );
     unsigned int rowBeginIndex = rowStart_[ reacIndex ];
     // vector< int >::const_iterator rowEnd = N_.begin() + rowStart_[ reacIndex + 1];
     vector< int >::const_iterator rowBegin =
         N_.begin() + rowBeginIndex;
     vector< int >::const_iterator rowEnd =
         N_.begin() + rowTruncated_[ reacIndex ];
     vector< unsigned int >::const_iterator molIndex =
         colIndex_.begin() + rowBeginIndex;
 
     for ( vector< int >::const_iterator i = rowBegin; i != rowEnd; ++i ) {
         double& x = S[ *molIndex++ ];
         x += *i * direction;
         x *= (x > 0 );
         // assert( S[ *molIndex ] + *i * direction >= 0.0 );
         // S[ *molIndex++ ] += *i * direction;
     }
 }

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void KinSparseMatrix::getGillespieDependence	(	unsigned int	row,
		vector< unsigned int > &	deps
	)		const

Does a special self-product of the specified row. Output is the set of nonzero indices in the product abs( Rij ) * neg( Rjk ) for the specified index i, where neg( val ) is true only if val < 0.

Has to operate on transposed matrix row argument refers to reac# in this transformed situation. Fills up 'deps' with reac::s that depend on the row argument. Does NOT ensure that list is unique.

Definition at line 73 of file KinSparseMatrix.cpp.

Referenced by Gsolve::rebuildGssaSystem().

 {
     deps.resize( 0 );
     // vector< unsigned int > deps;
     for ( unsigned int i = 0; i < nrows_; ++i ) {
         // i is index for reac # here. Note that matrix is transposed.
         unsigned int j = rowStart_[ row ];
         unsigned int jend = rowStart_[ row + 1 ];
         unsigned int k = rowStart_[ i ];
         unsigned int kend = rowStart_[ i + 1 ];
 
         while ( j < jend && k < kend ) {
             if ( colIndex_[ j ] == colIndex_[ k ] ) {
                 /* Pre 28 Nov 2015. Why below zero? Shouldn't it be any?
                 if ( N_[ k ] < 0 ) {
                     deps.push_back( i );
                 }
                 */
                 assert( round( N_[k] ) != 0 );
                 deps.push_back( i );
                 ++j;
                 ++k;
             } else if ( colIndex_[ j ] < colIndex_[ k ] ) {
                 ++j;
             } else if ( colIndex_[ j ] > colIndex_[ k ] ) {
                 ++k;
             } else {
                 assert( 0 );
             }
         }
     }
 }

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void KinSparseMatrix::truncateRow ( unsigned int maxColumnIndex )

This function generates a new internal list of rowEnds, such that they are all less than the maxColumnIndex. It is used because in fireReac we don't want to update all the molecules, only those that are variable.

Definition at line 141 of file KinSparseMatrix.cpp.

Referenced by Gsolve::rebuildGssaSystem().

 {
     rowTruncated_.resize( nrows_, 0 );
     if ( colIndex_.size() == 0 )
         return;
     for ( unsigned int i = 0; i < nrows_; ++i ) {
         unsigned int endCol = rowStart_[ i ];
         for ( unsigned int j = rowStart_[ i ];
             j < rowStart_[ i + 1 ]; ++j ) {
             if ( colIndex_[ j ] < maxColumnIndex ) {
                 endCol = j + 1;
             } else {
                 break;
             }
         }
         rowTruncated_[ i ] = endCol;
     }
 }

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Member Data Documentation

vector< unsigned int > KinSparseMatrix::rowTruncated_

private

End colIndex for rows (molecules in the transposed matrix) so that only variable molecules are below the colIndex.

Definition at line 69 of file KinSparseMatrix.h.

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

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

Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Function Documentation

Member Data Documentation