/**
* In this destructor we need to put messages back to process,
* and we need to replace the SolveFinfos on zombies with the
* original ThisFinfo. This should really just use the clearFunc.
*/
void HSolveHub::destroy( const Conn* c )
{
static Finfo* origCompartmentFinfo =
const_cast< Finfo* >(
initCompartmentCinfo()->getThisFinfo() );
static Finfo* origHHChannelFinfo =
const_cast< Finfo* >(
initHHChannelCinfo()->getThisFinfo() );
Element* hub = c->target().e;
unsigned int eIndex = c->target().i;
Conn* i = hub->targets( compartmentSolveFinfo->msg(), eIndex );
while ( i->good() ) {
i->target().e->setThisFinfo( origCompartmentFinfo );
i->increment();
}
delete i;
i = hub->targets( hhchannelSolveFinfo->msg(), eIndex );
while ( i->good() ) {
i->target().e->setThisFinfo( origHHChannelFinfo );
i->increment();
}
delete i;
Neutral::destroy( c );
}
Finfo* initHHChannelZombieFinfo()
{
static Finfo* hhchannelFields[] =
{
new ValueFinfo( "Gbar", ValueFtype1< double >::global(),
GFCAST( &HSolveHub::getHHChannelGbar ),
RFCAST( &HSolveHub::setHHChannelGbar )
),
new ValueFinfo( "Ek", ValueFtype1< double >::global(),
GFCAST( &HSolveHub::getEk ),
RFCAST( &HSolveHub::setEk )
),
new ValueFinfo( "Gk", ValueFtype1< double >::global(),
GFCAST( &HSolveHub::getGk ),
RFCAST( &HSolveHub::setGk )
),
new ValueFinfo( "Ik", ValueFtype1< double >::global(),
GFCAST( &HSolveHub::getIk ),
&dummyFunc
),
new ValueFinfo( "X", ValueFtype1< double >::global(),
GFCAST( &HSolveHub::getX ),
RFCAST( &HSolveHub::setX )
),
new ValueFinfo( "Y", ValueFtype1< double >::global(),
GFCAST( &HSolveHub::getY ),
RFCAST( &HSolveHub::setY )
),
new ValueFinfo( "Z", ValueFtype1< double >::global(),
GFCAST( &HSolveHub::getZ ),
RFCAST( &HSolveHub::setZ )
),
};
static const ThisFinfo* tf = dynamic_cast< const ThisFinfo* >(
initHHChannelCinfo()->getThisFinfo() );
assert( tf != 0 );
static SolveFinfo hhchannelZombieFinfo(
hhchannelFields,
sizeof( hhchannelFields ) / sizeof( Finfo* ),
tf
);
return &hhchannelZombieFinfo;
}
static const Finfo* hubCompartmentChannelFinfo = initHSolveHubCinfo()->findFinfo( "compartmentChannel" ); /* * Finfos from biophysical objects. Needed so that 'set' operations are done * on the solver as well as the objects. Also needed for redirecting any dest * messages on these finfos to the solver (e.g.: to the inject field). */ static const Finfo* compartmentInjectFinfo = initCompartmentCinfo()->findFinfo( "injectMsg" ); static const Finfo* compartmentChannelFinfo = initCompartmentCinfo()->findFinfo( "channel" ); static const Finfo* compartmentVmFinfo = initCompartmentCinfo()->findFinfo( "Vm" ); static const Finfo* channelGbarFinfo = initHHChannelCinfo()->findFinfo( "Gbar" ); static const Finfo* channelEkFinfo = initHHChannelCinfo()->findFinfo( "Ek" ); static const Finfo* channelGkFinfo = initHHChannelCinfo()->findFinfo( "Gk" ); static const Finfo* channelXFinfo = initHHChannelCinfo()->findFinfo( "X" ); static const Finfo* channelYFinfo = initHHChannelCinfo()->findFinfo( "Y" ); static const Finfo* channelZFinfo = initHHChannelCinfo()->findFinfo( "Z" ); static const Finfo* caConcCaFinfo = initCaConcCinfo()->findFinfo( "Ca" ); ///////////////////////////////////////////////////////////////////////// // Replacement fields for aspiring zombies /////////////////////////////////////////////////////////////////////////
void adaptSig2Chan( TreeNode& t,
map< string, Element* >& m,
unsigned int offset,
const string& mol, Id chanId )
{
static const Finfo* inputFinfo =
initAdaptorCinfo()->findFinfo( "input" );
static const Finfo* outputFinfo =
initAdaptorCinfo()->findFinfo( "outputSrc" );
static const Finfo* scaleFinfo =
initAdaptorCinfo()->findFinfo( "scale" );
static const Finfo* inputOffsetFinfo =
initAdaptorCinfo()->findFinfo( "inputOffset" );
static const Finfo* outputOffsetFinfo =
initAdaptorCinfo()->findFinfo( "outputOffset" );
// Not sure if these update when solved
static const Finfo* molNumFinfo =
initMoleculeCinfo()->findFinfo( "nSrc" );
static const Finfo* nInitFinfo =
initMoleculeCinfo()->findFinfo( "nInit" );
// This isn't yet a separate destMsg. Again, issue with update.
static const Finfo* hhChanGbarFinfo =
initHHChannelCinfo()->findFinfo( "Gbar" );
static const Finfo* synChanGbarFinfo =
initSynChanCinfo()->findFinfo( "Gbar" );
// Set up the correct Finfo. Complain if we try to connect up an
// unknown chan type.
const Finfo* gbarFinfo = 0;
if ( chanId()->cinfo()->isA( initHHChannelCinfo() ) )
gbarFinfo = hhChanGbarFinfo;
if ( chanId()->cinfo()->isA( initSynChanCinfo() ) )
gbarFinfo = synChanGbarFinfo;
if ( gbarFinfo == 0 ) {
cout << "Error: attempt to set up adaptor from signaling to \n" <<
" biophysics for an unknown channel type: " <<
chanId()->cinfo()->name() << endl <<
"for channel " << chanId.path() << endl;
return;
}
// Look up matching molecule
map< string, Element* >::iterator i = m.find( mol );
if ( i != m.end() ) {
Element* e = i->second;
// cout << "Adding adaptor from " << e->name() << " to " << chanId.path() << endl;
assert( t.sigStart >= offset );
assert( t.sigEnd - offset <= e->numEntries() );
// Create the adaptor
string name = "adapt_" + mol + "_2_" + chanId.eref().e->name();
Element* adaptor = Neutral::create( "Adaptor", name,
t.compt, Id::childId( t.compt ) );
assert( adaptor != 0 );
Eref adaptorE( adaptor, 0 );
double n = 0.00;
Eref MolE( e, t.sigStart - offset );
bool ret = get< double >( e, nInitFinfo, n );
assert( ret );
if ( n > 0.0 ) {
double gbar = 0.0;
ret = get< double >( chanId.eref(), gbarFinfo, gbar );
assert( ret );
double scale = gbar / n;
ret = set< double >( adaptorE, scaleFinfo, scale );
assert( ret );
}
ret = set< double >( adaptorE, inputOffsetFinfo, 0.0 );
assert( ret );
ret = set< double >( adaptorE, outputOffsetFinfo, 0.0 );
assert( ret );
for ( unsigned int j = t.sigStart; j < t.sigEnd; ++j ) {
// Connect up the adaptor.
Eref molE( e, j - offset );
ret = molE.add( molNumFinfo->msg(), adaptorE,
inputFinfo->msg(), ConnTainer::Default );
assert( ret );
// Here we set the parameters of the adaptor.
}
ret = adaptorE.add( outputFinfo->msg(), chanId.eref(),
gbarFinfo->msg(), ConnTainer::Default );
assert( ret );
}
}
