SteadyStateBoost.cpp File Reference

#include "header.h"
#include "global.h"
#include "SparseMatrix.h"
#include "KinSparseMatrix.h"
#include "RateTerm.h"
#include "FuncTerm.h"
#include "VoxelPoolsBase.h"
#include "../mesh/VoxelJunction.h"
#include "XferInfo.h"
#include "ZombiePoolInterface.h"
#include "Stoich.h"
#include "../randnum/RNG.h"
#include "NonlinearSystem.h"
#include "boost/numeric/bindings/lapack/lapack.hpp"
#include "boost/numeric/bindings/lapack/geev.hpp"
#include "OdeSystem.h"
#include "VoxelPools.h"
#include "SteadyStateBoost.h"

Include dependency graph for SteadyStateBoost.cpp:

Go to the source code of this file.

Classes
struct	reac_info

Functions
static bool	checkAboveZero (const vector< double > &y)
void	eliminateRowsBelow (ublas::matrix< double > &U, int start, int leftCol)
static bool	isSolutionValid (const vector< double > &x)
unsigned int	rankUsingBoost (ublas::matrix< double > &U)
void	recalcTotal (vector< double > &tot, ublas::matrix< double > &g, const double *S)
	Utility funtion to doing scans for steady states. More...
int	reorderRows (ublas::matrix< double > &U, int start, int leftCol)
void	ss_func (const vector_type &x, void *params, vector_type &f)
void	swapRows (ublas::matrix< double > &mat, unsigned int r1, unsigned int r2)
	Swap row r1 and r2. More...

Variables
static const Cinfo *	steadyStateCinfo = SteadyState::initCinfo()

Function Documentation

static bool checkAboveZero ( const vector< double > &  y )

static

Definition at line 934 of file SteadyStateBoost.cpp.

Referenced by SteadyState::randomizeInitialCondition().

{
    for ( vector< double >::const_iterator
            i = y.begin(); i != y.end(); ++i )
    {
        if ( *i < 0.0 )
            return false;
    }
    return true;
}

Here is the caller graph for this function:

void eliminateRowsBelow	(	ublas::matrix< double > &	U,
		int	start,
		int	leftCol
	)

Definition at line 890 of file SteadyStateBoost.cpp.

References SteadyState::EPSILON.

Referenced by rankUsingBoost().

{
    int numMols = U.size1();
    double pivot = U( start, leftCol );
    assert( fabs( pivot ) > SteadyState::EPSILON );
    for ( int i = start + 1; i < numMols; ++i )
    {
        double factor = U(i, leftCol);
        if( fabs ( factor ) > SteadyState::EPSILON )
        {
            factor = factor / pivot;
            for ( size_t j = leftCol + 1; j < U.size2(); ++j )
            {
                double x = U(i,j);
                double y = U( start, j );
                x -= y * factor;
                if ( fabs( x ) < SteadyState::EPSILON )
                    x = 0.0;
                U( i, j ) = x;
            }
        }
        U(i, leftCol) = 0.0;
    }
}

Here is the caller graph for this function:

static bool isSolutionValid ( const vector< double > &  x )

static

Definition at line 712 of file SteadyStateBoost.cpp.

Referenced by SteadyState::settle().

{
    for( size_t i = 0; i < x.size(); i++ )
    {
        double v = x[i];
        if ( std::isnan( v ) or std::isinf( v ) )
        {
            cout << "Warning: SteadyState iteration gave nan/inf concs\n";
            return false;
        }
        else if( v < 0.0 )
        {
            cout << "Warning: SteadyState iteration gave negative concs\n";
            return false;
        }
    }
    return true;
}

Here is the caller graph for this function:

unsigned int rankUsingBoost

(

ublas::matrix< double > &

U

)

Definition at line 915 of file SteadyStateBoost.cpp.

References eliminateRowsBelow(), and reorderRows().

Referenced by SteadyState::randomizeInitialCondition(), and SteadyState::setupSSmatrix().

{
    int numMols = U.size1();
    int numReacs = U.size2() - numMols;
    int i;
    // Start out with a nonzero entry at 0,0
    int leftCol = reorderRows( U, 0, 0 );

    for ( i = 0; i < numMols - 1; ++i )
    {
        eliminateRowsBelow( U, i, leftCol );
        leftCol = reorderRows( U, i + 1, leftCol );
        if ( leftCol == numReacs )
            break;
    }
    return i + 1;
}

Here is the call graph for this function:

Here is the caller graph for this function:

void recalcTotal	(	vector< double > &	tot,
		ublas::matrix< double > &	g,
		const double *	S
	)

Utility funtion to doing scans for steady states.

Parameters

tot
g
S

Definition at line 952 of file SteadyStateBoost.cpp.

Referenced by SteadyState::randomizeInitialCondition().

{
    assert( g.size1() == tot.size() );
    for ( size_t i = 0; i < g.size1(); ++i )
    {
        double t = 0.0;
        for ( unsigned int j = 0; j < g.size2(); ++j )
            t += g( i, j ) * S[j];
        tot[ i ] = t;
    }
}

Here is the caller graph for this function:

int reorderRows	(	ublas::matrix< double > &	U,
		int	start,
		int	leftCol
	)

Definition at line 863 of file SteadyStateBoost.cpp.

References SteadyState::EPSILON, and swapRows().

Referenced by rankUsingBoost().

{
    int leftMostRow = start;
    int numReacs = U.size2() - U.size1();
    int newLeftCol = numReacs;
    for ( size_t i = start; i < U.size1(); ++i )
    {
        for ( int j = leftCol; j < numReacs; ++j )
        {
            if ( fabs( U(i,j )) > SteadyState::EPSILON )
            {
                if ( j < newLeftCol )
                {
                    newLeftCol = j;
                    leftMostRow = i;
                }
                break;
            }
        }
    }

    if ( leftMostRow != start )   // swap them.
        swapRows( U, start, leftMostRow );

    return newLeftCol;
}

Here is the call graph for this function:

Here is the caller graph for this function:

void ss_func	(	const vector_type &	x,
		void *	params,
		vector_type &	f
	)

void swapRows	(	ublas::matrix< double > &	mat,
		unsigned int	r1,
		unsigned int	r2
	)

Swap row r1 and r2.

Parameters

mat	Matrix input
r1	index of row 1
r2	index of row 2

Definition at line 849 of file SteadyStateBoost.cpp.

Referenced by reorderRows().

{
    ublas::vector<value_type> temp( mat.size2() );
    for (size_t i = 0; i < mat.size2(); i++)
    {
        temp[i] = mat(r1, i );
        mat(r1, i ) = mat(r2, i );
    }

    for (size_t i = 0; i < mat.size2(); i++)
        mat(r2, i) = temp[i];
}

Here is the caller graph for this function:

Variable Documentation

const Cinfo* steadyStateCinfo = SteadyState::initCinfo()

static

Definition at line 316 of file SteadyStateBoost.cpp.

Referenced by SteadyState::initCinfo().