void testVolSort()
{
vector< unsigned int > findVolOrder( const vector< double >& vols );
vector< double > vols( 8 );
vols[0] = 7;
vols[1] = 8;
vols[2] = 6;
vols[3] = 5;
vols[4] = 1;
vols[5] = 2;
vols[6] = 3;
vols[7] = 4;
vector< unsigned int > order = findVolOrder( vols );
// The order is the rank of the volume entry, largest should be 0.
assert( order[0] == 1 );
assert( order[1] == 0 );
assert( order[2] == 2 );
assert( order[3] == 3 );
assert( order[4] == 7 );
assert( order[5] == 6 );
assert( order[6] == 5 );
assert( order[7] == 4 );
// This is a sequence which failed in a model test, despite the
// above test working.
vols.resize(5);
vols[0] = 1e-15;
vols[1] = 3e-15;
vols[2] = -1;
vols[3] = 2e-15;
vols[4] = 5e-15;
order = findVolOrder( vols );
assert( order[0] == 4 );
assert( order[1] == 1 );
assert( order[2] == 3 );
assert( order[3] == 0 );
assert( order[4] == 2 );
}
// We assume that the biggest compartment contains all the rest.
// This is not true in synapses, where they are adjacent.
void ReadKkit::assignPoolCompartments()
{
Id kinetics = Neutral::child( baseId_.eref(), "kinetics" );
assert( kinetics != Id() );
vector< unsigned int > volOrder = findVolOrder( vols_ );
assert( volCategories_.size() == vols_.size() );
assert( volCategories_.size() == volOrder.size() );
for ( unsigned int j = 0 ; j < volOrder.size(); ++j ) {
unsigned int i = volOrder[j];
if ( vols_[i] < 0 ) // Special case for enz complexes: vol == -1.
continue;
string name;
Id kinId = Neutral::child( baseId_.eref(), "kinetics" );
assert( kinId != Id() );
Id comptId;
// if ( i == maxi )
if ( j == 0 ) {
comptId = kinId;
} else {
stringstream ss;
ss << "compartment_" << j;
name = ss.str();
comptId = Neutral::child( baseId_.eref(), name );
if ( comptId == Id() )
comptId = shell_->doCreate( "CubeMesh", baseId_, name, 1 );
}
SetGet1< double >::set( comptId, "setVolumeNotRates",vols_[i]);
/*
if ( comptId.element()->cinfo()->isA( "CubeMesh" ) ) {
double side = pow( vols_[i], 1.0 / 3.0 );
vector< double > coords( 9, side );
coords[0] = coords[1] = coords[2] = 0;
// Field< double >::set( comptId, "volume", vols_[i] );
Field< vector< double > >::set( comptId, "coords", coords );
} else {
}
*/
// compartments_.push_back( comptId );
for ( vector< Id >::iterator k = volCategories_[i].begin();
k != volCategories_[i].end(); ++k ) {
if ( moveOntoCompartment_ ) {
if ( ! (getCompt( *k ).id == comptId ) )
shell_->doMove( *k, comptId );
}
}
}
}
