KinSparseMatrix Class Reference
#include <KinSparseMatrix.h>
Public Member Functions | |
| double | computeRowRate (unsigned int row, const vector< double > &v) const |
| void | getGillespieDependence (unsigned int row, vector< unsigned int > &cols) const |
| void | fireReac (unsigned int reacIndex, vector< double > &S) const |
| void | truncateRow (unsigned int maxColumnIndex) |
| vector< int > | matrixEntry () const |
| Here we expose the sparse matrix for MOOSE use. | |
| vector< unsigned int > | colIndex () const |
| vector< unsigned int > | rowStart () const |
Member Function Documentation
| vector< unsigned int > KinSparseMatrix::colIndex | ( | ) | const |
References SparseMatrix< int >::colIndex_.
Referenced by Stoich::getColIndex().
| 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.
Referenced by VoxelPools::updateRates().
| void KinSparseMatrix::fireReac | ( | unsigned int | reacIndex, | |
| vector< double > & | S | |||
| ) | const |
Fires a stochastic reaction: It undergoes a single transition This operation updates the mol concs due to the reacn.
Referenced by GssaVoxelPools::advance().
| void KinSparseMatrix::getGillespieDependence | ( | unsigned int | row, | |
| vector< unsigned int > & | cols | |||
| ) | 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.
Referenced by Gsolve::rebuildGssaSystem().
| vector< int > KinSparseMatrix::matrixEntry | ( | ) | const |
Here we expose the sparse matrix for MOOSE use.
References SparseMatrix< int >::N_.
Referenced by Stoich::getMatrixEntry().
| vector< unsigned int > KinSparseMatrix::rowStart | ( | ) | const |
References SparseMatrix< int >::rowStart_.
Referenced by Stoich::getRowStart().
| 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.
References SparseMatrix< int >::colIndex_, and SparseMatrix< int >::rowStart_.
Referenced by Gsolve::rebuildGssaSystem().
The documentation for this class was generated from the following files:
- ksolve/KinSparseMatrix.h
- ksolve/KinSparseMatrix.cpp
