/**
* Generates a new set of values for the S vector that is a) random
* and b) obeys the conservation rules.
*/
void SteadyState::randomizeInitialCondition( const Eref& me )
{
#ifdef USE_GSL
Id ksolve = Field< Id >::get( stoich_, "ksolve" );
vector< double > nVec =
LookupField< unsigned int, vector< double > >::get(
ksolve,"nVec", 0 );
int numConsv = total_.size();
recalcTotal( total_, gamma_, &nVec[0] );
// The reorderRows function likes to have an I matrix at the end of
// numVarPools_, so we provide space for it, although only its first
// column is used for the total vector.
gsl_matrix* U = gsl_matrix_calloc ( numConsv, numVarPools_ + numConsv );
for ( int i = 0; i < numConsv; ++i ) {
for ( unsigned int j = 0; j < numVarPools_; ++j ) {
gsl_matrix_set( U, i, j, gsl_matrix_get( gamma_, i, j ) );
}
gsl_matrix_set( U, i, numVarPools_, total_[i] );
}
// Do the forward elimination
int rank = myGaussianDecomp( U );
assert( rank = numConsv );
vector< double > eliminatedTotal( numConsv, 0.0 );
for ( int i = 0; i < numConsv; ++i ) {
eliminatedTotal[i] = gsl_matrix_get( U, i, numVarPools_ );
}
// Put Find a vector Y that fits the consv rules.
vector< double > y( numVarPools_, 0.0 );
do {
fitConservationRules( U, eliminatedTotal, y );
} while ( !checkAboveZero( y ) );
// Sanity check. Try the new vector with the old gamma and tots
for ( int i = 0; i < numConsv; ++i ) {
double tot = 0.0;
for ( unsigned int j = 0; j < numVarPools_; ++j ) {
tot += y[j] * gsl_matrix_get( gamma_, i, j );
}
assert( fabs( tot - total_[i] ) / tot < EPSILON );
}
// Put the new values into S.
// cout << endl;
for ( unsigned int j = 0; j < numVarPools_; ++j ) {
nVec[j] = y[j];
// cout << y[j] << " ";
}
LookupField< unsigned int, vector< double > >::set(
ksolve,"nVec", 0, nVec );
#endif
}
void SteadyState::setupSSmatrix()
{
#ifdef USE_GSL
if ( numVarPools_ == 0 || nReacs_ == 0 )
return;
int nTot = numVarPools_ + nReacs_;
gsl_matrix* N = gsl_matrix_calloc (numVarPools_, nReacs_);
if ( LU_ ) { // Clear out old one.
gsl_matrix_free( LU_ );
}
LU_ = gsl_matrix_calloc (numVarPools_, nTot);
vector< int > entry = Field< vector< int > >::get(
stoich_, "matrixEntry" );
vector< unsigned int > colIndex = Field< vector< unsigned int > >::get(
stoich_, "columnIndex" );
vector< unsigned int > rowStart = Field< vector< unsigned int > >::get(
stoich_, "rowStart" );
// cout << endl << endl;
for ( unsigned int i = 0; i < numVarPools_; ++i ) {
gsl_matrix_set (LU_, i, i + nReacs_, 1 );
unsigned int k = rowStart[i];
// cout << endl << i << ": ";
for ( unsigned int j = 0; j < nReacs_; ++j ) {
double x = 0;
if ( j == colIndex[k] && k < rowStart[i+1] ) {
x = entry[k++];
}
// cout << " " << x;
gsl_matrix_set (N, i, j, x);
gsl_matrix_set (LU_, i, j, x );
}
}
cout << endl << endl;
rank_ = myGaussianDecomp( LU_ );
unsigned int nConsv = numVarPools_ - rank_;
if ( nConsv == 0 ) {
cout << "SteadyState::setupSSmatrix(): Number of conserved species == 0. Aborting\n";
return;
}
if ( Nr_ ) { // Clear out old one.
gsl_matrix_free( Nr_ );
}
Nr_ = gsl_matrix_calloc ( rank_, nReacs_ );
// Fill up Nr.
for ( unsigned int i = 0; i < rank_; i++)
for ( unsigned int j = i; j < nReacs_; j++)
gsl_matrix_set (Nr_, i, j, gsl_matrix_get( LU_, i, j ) );
if ( gamma_ ) { // Clear out old one.
gsl_matrix_free( gamma_ );
}
gamma_ = gsl_matrix_calloc (nConsv, numVarPools_ );
// Fill up gamma
for ( unsigned int i = rank_; i < numVarPools_; ++i )
for ( unsigned int j = 0; j < numVarPools_; ++j )
gsl_matrix_set( gamma_, i - rank_, j,
gsl_matrix_get( LU_, i, j + nReacs_ ) );
// Fill up boundary condition values
total_.resize( nConsv );
total_.assign( nConsv, 0.0 );
/*
cout << "S = (";
for ( unsigned int j = 0; j < numVarPools_; ++j )
cout << s_->S()[ j ] << ", ";
cout << "), Sinit = ( ";
for ( unsigned int j = 0; j < numVarPools_; ++j )
cout << s_->Sinit()[ j ] << ", ";
cout << ")\n";
*/
Id ksolve = Field< Id >::get( stoich_, "ksolve" );
vector< double > nVec =
LookupField< unsigned int, vector< double > >::get(
ksolve,"nVec", 0 );
if ( nVec.size() >= numVarPools_ ) {
for ( unsigned int i = 0; i < nConsv; ++i )
for ( unsigned int j = 0; j < numVarPools_; ++j )
total_[i] += gsl_matrix_get( gamma_, i, j ) * nVec[ j ];
isSetup_ = 1;
} else {
cout << "Error: SteadyState::setupSSmatrix(): unable to get"
"pool numbers from ksolve.\n";
isSetup_ = 0;
}
gsl_matrix_free( N );
#endif
}
