void HSolve::zombify( Eref hsolve ) const
{
vector< Id >::const_iterator i;
vector< ObjId > temp;
for ( i = compartmentId_.begin(); i != compartmentId_.end(); ++i )
temp.push_back( ObjId( *i, 0 ) );
for ( i = compartmentId_.begin(); i != compartmentId_.end(); ++i )
CompartmentBase::zombify( i->eref().element(),
ZombieCompartment::initCinfo(), hsolve.id() );
temp.clear();
for ( i = caConcId_.begin(); i != caConcId_.end(); ++i )
temp.push_back( ObjId( *i, 0 ) );
// Shell::dropClockMsgs( temp, "process" );
for ( i = caConcId_.begin(); i != caConcId_.end(); ++i )
CaConcBase::zombify( i->eref().element(), ZombieCaConc::initCinfo(), hsolve.id() );
temp.clear();
for ( i = channelId_.begin(); i != channelId_.end(); ++i )
temp.push_back( ObjId( *i, 0 ) );
for ( i = channelId_.begin(); i != channelId_.end(); ++i )
HHChannelBase::zombify( i->eref().element(),
ZombieHHChannel::initCinfo(), hsolve.id() );
}
void HHGate::setTableA( const Eref& e, vector< double > v )
{
if ( v.size() < 2 ) {
cout << "Warning: HHGate::setTableA: size must be >= 2 entries on "
<< e.id().path() << endl;
return;
}
if ( checkOriginal( e.id(), "tableA" ) ) {
isDirectTable_ = 1;
A_ = v;
unsigned int xdivs = A_.size() - 1;
invDx_ = static_cast< double >( xdivs ) / ( xmax_ - xmin_ );
}
}
void HHGate::setAlpha( const Eref& e, vector< double > val )
{
if ( val.size() != 5 ) {
cout << "Error: HHGate::setAlpha on " << e.id().path() <<
": Number of entries on argument vector should be 5, was " <<
val.size() << endl;
return;
}
if ( checkOriginal( e.id(), "alpha" ) ) {
alpha_ = val;
updateTauMinf();
updateTables();
}
}
void HHGate::setMinfinity( const Eref& e, vector< double > val )
{
if ( val.size() != 5 ) {
cout << "Error: HHGate::setMinfinity on " << e.id().path() <<
": Number of entries on argument vector should be 5, was " <<
val.size() << endl;
return;
}
if ( checkOriginal( e.id(), "mInfinity" ) ) {
mInfinity_ = val;
updateAlphaBeta();
updateTables();
}
}
/* Enzymatic Reaction */
void SbmlReader::setupEnzymaticReaction( const EnzymeInfo & einfo,string name )
{
static const Cinfo* enzymeCinfo = initEnzymeCinfo();
static const Finfo* k1Finfo = enzymeCinfo->findFinfo( "k1" );
static const Finfo* k2Finfo = enzymeCinfo->findFinfo( "k2" );
static const Finfo* k3Finfo = enzymeCinfo->findFinfo( "k3" );
Eref E = ( einfo.enzyme )();
Element* enzyme_ = Neutral::create( "Enzyme",name,E.id(),Id::scratchId() );//create Enzyme
Eref complx = einfo.complex();
Eref(enzyme_).add( "enz",E,"reac",ConnTainer::Default );
Eref(enzyme_).add( "cplx",complx,"reac",ConnTainer::Default );
vector< Id >::const_iterator sub_itr;
for ( sub_itr = einfo.substrates.begin(); sub_itr != einfo.substrates.end(); sub_itr++ )
{ Eref S = (*sub_itr)();
Eref( enzyme_ ).add( "sub",S,"reac",ConnTainer::Default );
}
vector< Id >::const_iterator prd_itr;
for ( prd_itr = einfo.products.begin(); prd_itr != einfo.products.end(); prd_itr++ )
{ Eref P = (*prd_itr)();
Eref( enzyme_ ).add( "prd",P,"prd",ConnTainer::Default );
}
::set< double >( enzyme_, k1Finfo, einfo.k1 );
::set< double >( enzyme_, k2Finfo, einfo.k2 );
::set< double >( enzyme_, k3Finfo, einfo.k3 );
::set< bool >( enzyme_,"mode",0 );
::set( complx,"destroy" );
}
void OutputEventPort::innerInitialiseFunc( Eref e,
unsigned int width,
unsigned int offset,
MUSIC::EventOutputPort*
mPort)
{
myWidth_ = width;
myOffset_ = offset;
mPort_ = mPort;
for(unsigned int i = 0; i < width; i++)
{
ostringstream name;
name << "channel[" << i + offset << "]";
Element* channel = Neutral::create( "OutputEventChannel", name.str(),
e.id(), Id::scratchId() );
channels_.push_back(channel);
set< unsigned int, MUSIC::EventOutputPort* >
(channel, "initialise", i, mPort);
}
}
void Neutral::setName( const Eref& e, string name )
{
if ( e.id().value() <= 3 ) {
cout << "Warning: Neutral::setName on '" << e.id().path() <<
"'.Cannot rename core objects\n";
return;
}
ObjId pa = parent( e );
Id sibling = Neutral::child( pa.eref(), name );
if ( sibling == Id() ) { // OK, no existing object with same name.
e.element()->setName( name );
} else {
cout << "Warning: Neutral::setName: an object with the name '" <<
name << "'\n already exists on the same parent. Not changed\n";
}
}
void GslStoich::setNinit( const Eref& e, double v )
{
unsigned int i = e.index().value();
unsigned int j = coreStoich()->convertIdToPoolIndex( e.id() );
assert( i < pools_.size() );
assert( j < pools_[i].size() );
pools_[i].varSinit()[j] = v;
}
double GslStoich::getNinit( const Eref& e ) const
{
unsigned int i = e.index().value();
unsigned int j = coreStoich()->convertIdToPoolIndex( e.id() );
assert( i < pools_.size() );
assert( j < pools_[i].size() );
return pools_[i].Sinit()[j];
}
/// Utility function to find the size of a pool. We assume one-to-one
/// match between pool indices and mesh indices: that is what they are for.
double lookupVolumeFromMesh( const Eref& e )
{
ObjId compt = getCompt( e.id() );
if ( compt == ObjId() )
return 1.0;
return LookupField< unsigned int, double >::
get( compt, "oneVoxelVolume", e.dataIndex() );
}
void HHChannel2D::destroyGate( const Eref& e, const Qinfo* q,
string gateType )
{
if ( !checkOriginal( e.id() ) ) {
cout << "Warning: HHChannel2D::destroyGate: Not allowed from copied channel:\n" << e.id().path() << "\n";
return;
}
if ( gateType == "X" )
innerDestroyGate( "xGate", &xGate_, e.id() );
else if ( gateType == "Y" )
innerDestroyGate( "yGate", &yGate_, e.id() );
else if ( gateType == "Z" )
innerDestroyGate( "zGate", &zGate_, e.id() );
else
cout << "Warning: HHChannel2D::destroyGate: Unknown gate type '" <<
gateType << "'. Ignored\n";
}
void HHGate::setTableB( const Eref& e, vector< double > v )
{
if ( checkOriginal( e.id(), "tableB" ) ) {
isDirectTable_ = 1;
if ( A_.size() != v.size() ) {
cout << "Warning: HHGate::setTableB: size should be same as table A: " << v.size() << " != " << A_.size() << ". Ignoring.\n";
return;
}
B_ = v;
}
}
void GslStoich::setN( const Eref& e, double v )
{
unsigned int i = e.index().value(); // Later: Handle node location.
unsigned int j = coreStoich()->convertIdToPoolIndex( e.id() );
assert( i < pools_.size() );
assert( j < pools_[i].size() );
pools_[i].varS()[j] = v;
assert( i < y_.size() );
assert( j < y_[i].size() );
y_[i][j] = v;
}
void HHGate::setupTau( const Eref& e,
vector< double > parms )
{
if ( checkOriginal( e.id(), "setupTau" ) ) {
if ( parms.size() != 13 ) {
cout << "HHGate::setupTau: Error: parms.size() != 13\n";
return;
}
setupTables( parms, true );
}
}
vector< Id > Neutral::getNeighbors( const Eref& e, string field ) const
{
vector< Id > ret;
const Finfo* finfo = e.element()->cinfo()->findFinfo( field );
if ( finfo )
e.element()->getNeighbors( ret, finfo );
else
cout << "Warning: Neutral::getNeighbors: Id.Field '" <<
e.id().path() << "." << field <<
"' not found\n";
return ret;
}
void Cell::reinit( const Eref& cell, ProcPtr p )
//~ void Cell::reinit( const Eref& cell, const Qinfo* q )
{
cout << ".. Cell::reinit()" << endl;
//~ if ( q->protectedAddToStructuralQ() )
//~ return;
// Delete existing solver
//~ string solverPath = cell.id().path() + "/" + solverName_;
//~ Id solver( solverPath );
//~ if ( solver.path() == solverPath )
//~ solver.destroy();
if ( method_ == "ee" )
return;
// Find any compartment that is a descendant of this cell
Id seed = findCompt( cell.id() );
if ( seed == Id() ) // No compartment found.
return;
setupSolver( cell.id(), seed );
}
void HHGate::setMin( const Eref& e, double val )
{
if ( checkOriginal( e.id(), "min" ) ) {
xmin_ = val;
unsigned int xdivs = A_.size() - 1;
if ( isDirectTable_ && xdivs > 0 ) {
// Stuff here to stretch out table using interpolation.
invDx_ = static_cast< double >( xdivs ) / ( xmax_ - val );
tabFill( A_, xdivs, val, xmax_ );
tabFill( B_, xdivs, val, xmax_ );
} else {
updateTables();
}
}
}
//////////////////////////////////////////////////////////////
// init operations.
//////////////////////////////////////////////////////////////
void Gsolve::initProc( const Eref& e, ProcPtr p )
{
// vector< vector< double > > values( xfer_.size() );
for ( unsigned int i = 0; i < xfer_.size(); ++i ) {
XferInfo& xf = xfer_[i];
unsigned int size = xf.xferPoolIdx.size() * xf.xferVoxel.size();
// values[i].resize( size, 0.0 );
vector< double > values( size, 0.0 );
for ( unsigned int j = 0; j < xf.xferVoxel.size(); ++j ) {
unsigned int vox = xf.xferVoxel[j];
pools_[vox].xferOut( j, values, xf.xferPoolIdx );
}
xComptOut()->sendTo( e, xf.ksolve, e.id(), values );
}
}
void HHGate::setMax( const Eref& e, double val )
{
if ( checkOriginal( e.id(), "max" ) ) {
xmax_ = val;
unsigned int xdivs = A_.size() - 1;
if ( isDirectTable_ && xdivs > 0 ) {
// Set up using direct assignment of table values.
invDx_ = static_cast< double >( xdivs ) / ( val - xmin_ );
tabFill( A_, xdivs, xmin_, val );
tabFill( B_, xdivs, xmin_, val );
} else {
// Set up using functional form. here we just recalculate.
updateTables();
}
}
}
void HHGate::setDivs( const Eref& e, unsigned int val )
{
if ( checkOriginal( e.id(), "divs" ) ) {
if ( isDirectTable_ ) {
invDx_ = static_cast< double >( val ) / ( xmax_ - xmin_ );
tabFill( A_, val, xmin_, xmax_ );
tabFill( B_, val, xmin_, xmax_ );
} else {
/// Stuff here to redo sizes.
A_.resize( val + 1 );
B_.resize( val + 1 );
invDx_ = static_cast< double >( val ) / ( xmax_ - xmin_ );
updateTables();
}
}
}
void HHChannel::vCreateGate( const Eref& e,
string gateType )
{
if ( !checkOriginal( e.id() ) ) {
cout << "Warning: HHChannel::createGate: Not allowed from copied channel:\n" << e.id().path() << "\n";
return;
}
if ( gateType == "X" )
innerCreateGate( "xGate", &xGate_, e.id(), Id(e.id().value() + 1) );
else if ( gateType == "Y" )
innerCreateGate( "yGate", &yGate_, e.id(), Id(e.id().value() + 2) );
else if ( gateType == "Z" )
innerCreateGate( "zGate", &zGate_, e.id(), Id(e.id().value() + 3) );
else
cout << "Warning: HHChannel::createGate: Unknown gate type '" <<
gateType << "'. Ignored\n";
}
void HHGate::setupAlpha( const Eref& e,
vector< double > parms )
{
if ( checkOriginal( e.id(), "setupAlpha" ) ) {
if ( parms.size() != 13 ) {
cout << "HHGate::setupAlpha: Error: parms.size() != 13\n";
return;
}
setupTables( parms, false );
alpha_.resize( 5, 0 );
beta_.resize( 5, 0 );
for ( unsigned int i = 0; i < 5; ++i )
alpha_[i] = parms[i];
for ( unsigned int i = 5; i < 10; ++i )
beta_[i - 5] = parms[i];
}
}
/*
* set up Michalies Menten reaction
*/
void SbmlReader::setupMMEnzymeReaction( Reaction * reac,string rid )
{
string::size_type loc = rid.find( "_MM_Reaction_" );
if( loc != string::npos ){
int strlen = rid.length();
rid.erase( loc,strlen-loc );
}
static const Cinfo* enzymeCinfo = initEnzymeCinfo();
static const Finfo* kmFinfo = enzymeCinfo->findFinfo( "Km" );
static const Finfo* kcatFinfo = enzymeCinfo->findFinfo( "kcat" );
unsigned int num_modifr = reac->getNumModifiers();
for ( unsigned int m = 0; m < num_modifr; m++ )
{
const ModifierSpeciesReference* modifr=reac->getModifier( m );
string sp = modifr->getSpecies();
Eref E = elmtMap_.find(sp)->second;
Element* enzyme_ = Neutral::create( "Enzyme",rid,E.id(),Id::scratchId() );//create Enzyme
KineticLaw * klaw=reac->getKineticLaw();
vector< double > rate;
rate.clear();
getKLaw( klaw,true,rate );
if ( errorFlag_ )
return;
else if ( !errorFlag_ ){
::set< bool >( enzyme_,"mode",1 );
Eref(enzyme_).add( "enz",E,"reac",ConnTainer::Default );
for ( unsigned int rt = 0; rt < reac->getNumReactants(); rt++ )
{
const SpeciesReference* rct = reac->getReactant( rt );
sp=rct->getSpecies();
Eref S = elmtMap_.find(sp)->second;
Eref(enzyme_).add( "sub",S,"reac",ConnTainer::Default );
}
for ( unsigned int pt = 0; pt < reac->getNumProducts(); pt++ )
{
const SpeciesReference* pdt = reac->getProduct(pt);
sp = pdt->getSpecies();
Eref P = elmtMap_.find(sp)->second;
Eref(enzyme_).add( "prd",P,"prd",ConnTainer::Default );
}
::set< double >( enzyme_, kcatFinfo, rate[0] );
::set< double >( enzyme_, kmFinfo, rate[1] );
}
}
}
void Gsolve::initReinit( const Eref& e, ProcPtr p )
{
for ( unsigned int i = 0 ; i < pools_.size(); ++i ) {
pools_[i].reinit( &sys_ );
}
// vector< vector< double > > values( xfer_.size() );
for ( unsigned int i = 0; i < xfer_.size(); ++i ) {
XferInfo& xf = xfer_[i];
unsigned int size = xf.xferPoolIdx.size() * xf.xferVoxel.size();
xf.lastValues.assign( size, 0.0 );
for ( unsigned int j = 0; j < xf.xferVoxel.size(); ++j ) {
unsigned int vox = xf.xferVoxel[j];
pools_[ vox ].xferOut( j, xf.lastValues, xf.xferPoolIdx );
// values[i] = xf.lastValues;
}
xComptOut()->sendTo( e, xf.ksolve, e.id(), xf.lastValues );
}
}
vector< string > Neutral::getMsgDestFunctions( const Eref& e, string field ) const
{
vector< string > ret( 0 );
const Finfo* finfo = e.element()->cinfo()->findFinfo( field );
const SrcFinfo* sf = dynamic_cast< const SrcFinfo* >( finfo );
if ( sf ) {
vector< ObjId > tgt;
vector< string > func;
e.element()->getMsgTargetAndFunctions( e.dataIndex(), sf,
tgt, func );
return func;
} else {
cout << "Warning: Neutral::getMsgDestFunctions: Id.Field '" <<
e.id().path() << "." << field <<
"' not found or not a SrcFinfo\n";
}
return ret;
}
/**
* @brief Reinitialize
*
* @param e
* @param p
*/
void Table::reinit( const Eref& e, ProcPtr p )
{
tablePath_ = e.id().path();
unsigned int numTick = e.element()->getTick();
Clock* clk = reinterpret_cast<Clock*>(Id(1).eref().data());
dt_ = clk->getTickDt( numTick );
/** Create the default filepath for this table. */
if( useStreamer_ )
{
// The first column is variable time.
columns_.push_back( "time" );
// And the second column name is the name of the table.
columns_.push_back( moose::moosePathToUserPath( tablePath_ ) );
// If user has not set the filepath, then use the table path prefixed
// with rootdit as path.
if( ! outfileIsSet_ )
setOutfile( rootdir_ +
moose::moosePathToUserPath(tablePath_) + '.' + format_
);
}
input_ = 0.0;
vec().resize( 0 );
lastTime_ = 0;
vector< double > ret;
requestOut()->send( e, &ret );
vec().insert( vec().end(), ret.begin(), ret.end() );
if( useStreamer_ )
{
zipWithTime( vec(), data_, lastTime_ );
StreamerBase::writeToOutFile( outfile_, format_, "w", data_, columns_);
clearVec();
data_.clear();
clearVec();
}
}
void SigNeur::innerBuildTree( unsigned int parent, Eref paE, Eref e,
int msg1, int msg2 )
{
unsigned int paIndex = tree_.size();
TreeNode t( e.id(), parent, guessCompartmentCategory( e ) );
tree_.push_back( t );
// cout << e.name() << endl;
Conn* c = e->targets( msg1, e.i );
// Things are messy here because src/dest directions are flawed
// in Element::targets.
// The parallel moose fixes this mess, simply by checking against
// which the originating element is. Here we need to do the same
// explicitly.
for ( ; c->good(); c->increment() ) {
Eref tgtE = c->target();
if ( tgtE == e )
tgtE = c->source();
if ( !( tgtE == paE ) ) {
// cout << "paE=" << paE.name() << ", e=" << e.name() << ", msg1,2= " << msg1 << "," << msg2 << ", src=" << c->source().name() << ", tgt= " << tgtE.name() << endl;
innerBuildTree( paIndex, e, tgtE, msg1, msg2 );
}
}
delete c;
c = e->targets( msg2, e.i );
for ( ; c->good(); c->increment() ) {
Eref tgtE = c->target();
if ( tgtE == e )
tgtE = c->source();
if ( !( tgtE == paE ) ) {
// cout << "paE=" << paE.name() << ", e=" << e.name() << ", msg1,2= " << msg1 << "," << msg2 << ", src=" << c->source().name() << ", tgt= " << tgtE.name() << endl;
innerBuildTree( paIndex, e, tgtE, msg1, msg2 );
}
}
delete c;
}
double GslStoich::getDiffConst( const Eref& e ) const
{
unsigned int j = coreStoich()->convertIdToPoolIndex( e.id() );
assert( j < pools_[ e.index().value() ].size() );
return coreStoich()->getDiffConst( j );
}
void GslStoich::setDiffConst( const Eref& e, double v )
{
unsigned int j = coreStoich()->convertIdToPoolIndex( e.id() );
assert( j < pools_[ e.index().value() ].size() );
coreStoich_.setDiffConst( j, v );
}
unsigned int GslStoich::getSpecies( const Eref& e )
{
unsigned int j = coreStoich()->convertIdToPoolIndex( e.id() );
assert( j < pools_[ e.index().value() ].size() );
return coreStoich()->getSpecies( j );
}