void HSolveUtils::rates(
Id gateId,
HSolveUtils::Grid grid,
vector< double >& A,
vector< double >& B )
{
double min = HSolveUtils::get< HHGate, double >( gateId, "min" );
double max = HSolveUtils::get< HHGate, double >( gateId, "max" );
unsigned int divs = HSolveUtils::get< HHGate, unsigned int >(
gateId, "divs" );
if ( grid == Grid( min, max, divs ) ) {
A = HSolveUtils::get< HHGate, vector< double > >( gateId, "tableA" );
B = HSolveUtils::get< HHGate, vector< double > >( gateId, "tableB" );
return;
}
A.resize( grid.size() );
B.resize( grid.size() );
/*
* Getting Id of original (prototype) gate, so that we can set fields on
* it. Copied gates are read-only.
*/
HHGate* gate = reinterpret_cast< HHGate* >( gateId.eref().data() );
gateId = gate->originalGateId();
/*
* Setting interpolation flag on. Will set back to its original value once
* we're done.
*/
bool useInterpolation = HSolveUtils::get< HHGate, bool >
( gateId, "useInterpolation" );
//~ HSolveUtils::set< HHGate, bool >( gateId, "useInterpolation", true );
Qinfo* qDummy = NULL;
gate->setUseInterpolation( gateId.eref(), qDummy, true );
unsigned int igrid;
double* ia = &A[ 0 ];
double* ib = &B[ 0 ];
for ( igrid = 0; igrid < grid.size(); ++igrid ) {
gate->lookupBoth( grid.entry( igrid ), ia, ib );
++ia, ++ib;
}
// Setting interpolation flag back to its original value.
//~ HSolveUtils::set< HHGate, bool >
//~ ( gateId, "useInterpolation", useInterpolation );
gate->setUseInterpolation( gateId.eref(), qDummy, useInterpolation );
}
bool Shell::isRunning() const
{
static Id clockId( 1 );
assert( clockId.element() != 0 );
return ( reinterpret_cast< const Clock* >( clockId.eref().data() ) )->isRunning();
}
/* Enzymatic Reaction */
void SbmlReader::setupEnzymaticReaction( const EnzymeInfo & einfo,string enzname, const map< string, Id > &molSidcmptMIdMap,string name1) {
string enzPool = einfo.enzyme;
Id comptRef = molSidcmptMIdMap.find(enzPool)->second; //gives compartment of sp
Id meshEntry = Neutral::child( comptRef.eref(), "mesh" );
Shell* shell = reinterpret_cast< Shell* >( Id().eref().data() );
//Creating enz pool to enzyme site
Id enzPoolId = molSidMIdMap_.find(enzPool)->second;
Id enzyme_ = shell->doCreate("Enz", enzPoolId, name1, 1);
//shell->doAddMsg( "Single", meshEntry, "remeshReacs", enzyme_, "remesh");
Id complex = einfo.complex;
//Moving enzyme site under enzyme
shell->doMove(complex,enzyme_);
shell->doAddMsg("OneToAll",enzyme_,"cplx",complex,"reac");
shell->doAddMsg("OneToOne",enzyme_,"enz",enzPoolId,"reac");
vector< Id >::const_iterator sub_itr;
for ( sub_itr = einfo.substrates.begin(); sub_itr != einfo.substrates.end(); sub_itr++ ) {
Id S = (*sub_itr);
Id b = shell->doAddMsg( "OneToOne", enzyme_, "sub" ,S , "reac" );
}
vector< Id >::const_iterator prd_itr;
for ( prd_itr = einfo.products.begin(); prd_itr != einfo.products.end(); prd_itr++ ) {
Id P = (*prd_itr);
shell->doAddMsg ("OneToOne",enzyme_,"prd", P,"reac");
}
// populate k3,k2,k1 in this order only.
Field < double > :: set( enzyme_, "k3", einfo.k3 );
Field < double > :: set( enzyme_, "k2", einfo.k2 );
Field < double > :: set( enzyme_, "k1", einfo.k1 );
}
bool isDoingReinit()
{
static Id clockId( 1 );
assert( clockId.element() != 0 );
return ( reinterpret_cast< const Clock* >(
clockId.eref().data() ) )->isDoingReinit();
}
void testSpikeGen()
{
Shell* shell = reinterpret_cast< Shell* >( Id().eref().data() );
Id sid = shell->doCreate( "SpikeGen", Id(), "spike", 1, MooseGlobal );
SpikeGen& sg = *( reinterpret_cast< SpikeGen* >( sid.eref().data() ) );
Eref er( sid.eref() );
ProcInfo p;
p.dt = 0.001;
p.currTime = 0.0;
sg.setThreshold( 1.0 );
sg.setRefractT( 0.005 );
sg.reinit( er, &p );
sg.handleVm( 0.5 );
sg.process( er, &p );
assert( !sg.getFired() );
p.currTime += p.dt;
sg.handleVm( 0.999 );
sg.process( er, &p );
assert( !sg.getFired() );
p.currTime += p.dt;
sg.handleVm( 1.001 );
sg.process( er, &p );
assert( sg.getFired() );
p.currTime += p.dt;
sg.handleVm( 0.999 );
sg.process( er, &p );
assert( !sg.getFired() );
p.currTime += p.dt;
sg.handleVm( 2.0 ); // Too soon, refractory
sg.process( er, &p );
assert( !sg.getFired() );
p.currTime += 0.005; // Now post-refractory
sg.handleVm( 2.0 ); // Now not refractory
sg.process( er, &p );
assert( sg.getFired() );
sid.destroy();
cout << "." << flush;
}
/////////////////////////////////////////////////////////////////
// Now test 'get' across nodes.
// Normally the 'get' call is invoked by the parser, which expects a
// value to come back. Note that the return must be asynchronous:
// the parser cannot block since we need to execute MPI polling
// operations on either side.
/////////////////////////////////////////////////////////////////
void testParGet( Id tnId, vector< Id >& testIds )
{
unsigned int myNode = MuMPI::INTRA_COMM().Get_rank();
unsigned int numNodes = MuMPI::INTRA_COMM().Get_size();
Slot parGetSlot = initShellCinfo()->getSlot( "parallel.getSrc" );
char name[20];
string sname;
if ( myNode == 0 ) {
cout << "\ntesting parallel get" << flush;
} else {
sprintf( name, "foo%d", myNode * 2 );
sname = name;
set< string >( tnId.eref(), "name", sname );
}
MuMPI::INTRA_COMM().Barrier();
Eref e = Id::shellId().eref();
Shell* sh = static_cast< Shell* >( e.data() );
vector< unsigned int > rids( numNodes, 0 );
vector< string > ret( numNodes );
unsigned int origSize = sh->freeRidStack_.size();
ASSERT( origSize > 0 , "Stack initialized properly" );
if ( myNode == 0 ) {
for ( unsigned int i = 1; i < numNodes; i++ ) {
rids[i] =
openOffNodeValueRequest< string >( sh, &ret[i], 1 );
ASSERT( sh->freeRidStack_.size() == origSize - i, "stack in use" );
sendTo3< Id, string, unsigned int >(
Id::shellId().eref(), parGetSlot, i - 1,
testIds[i - 1], "name", rids[i]
);
}
}
// Here we explicitly do what the closeOffNodeValueRequest handles.
MuMPI::INTRA_COMM().Barrier();
// Cycle a few times to make sure all data gets back to node 0
for ( unsigned int i = 0; i < 5; i++ ) {
pollPostmaster();
MuMPI::INTRA_COMM().Barrier();
}
// Now go through to check all values have come back.
if ( myNode == 0 ) {
ASSERT( sh->freeRidStack_.size() == 1 + origSize - numNodes,
"Stack still waiting" );
for ( unsigned int i = 1; i < numNodes; i++ ) {
sprintf( name, "foo%d", i * 2 );
sname = name;
ASSERT( sh->offNodeData_[ rids[i] ].numPending == 0,
"Pending requests cleared" );
ASSERT( sh->offNodeData_[ rids[i] ].data ==
static_cast< void* >( &ret[i] ), "Pointing to strings" );
ASSERT( ret[ i ] == sname, "All values returned correctly" );
// Clean up the debris
sh->offNodeData_[ rids[i] ].data = 0;
sh->freeRidStack_.push_back( rids[i] );
}
}
}
// Utility function: return the compartment in which the specified
// object is located.
// Simply traverses the tree toward the root till it finds a
// compartment. Pools use a special msg, but this works for reacs too.
ObjId getCompt( Id id )
{
ObjId pa = Neutral::parent( id.eref() ).id;
if ( pa == ObjId() )
return pa;
else if ( pa.element()->cinfo()->isA( "ChemCompt" ) )
return pa;
return getCompt( pa );
}
static Id makeCompt( Id parent,
const SwcSegment& seg, const SwcSegment& pa,
double RM, double RA, double CM,
unsigned int i, unsigned int j )
{
Shell* shell = reinterpret_cast< Shell* >( Id().eref().data() );
double len = seg.radius() * 2.0;
string name = "soma";
Id compt;
double x0, y0, z0;
if ( seg.parent() != ~0U ) {
len = seg.distance( pa );
stringstream ss;
ss << SwcSegment::typeName[ seg.type() ] << "_" << i << "_" << j;
name = ss.str();
x0 = pa.vec().a0();
y0 = pa.vec().a1();
z0 = pa.vec().a2();
} else {
x0 = seg.vec().a0() - len;
y0 = seg.vec().a1();
z0 = seg.vec().a2();
}
assert( len > 0.0 );
compt = shell->doCreate( "Compartment", parent, name, 1 );
Eref er = compt.eref();
moose::CompartmentBase *cptr = reinterpret_cast< moose::CompartmentBase* >(
compt.eref().data() );
double xa = seg.radius() * seg.radius() * PI * 1e-12;
len *= 1e-6;
double dia = seg.radius() * 2.0e-6;
cptr->setRm( er, RM / ( len * dia * PI ) );
cptr->setRa( er, RA * len / xa );
cptr->setCm( er, CM * ( len * dia * PI ) );
cptr->setDiameter( dia );
cptr->setLength( len );
cptr->setX0( x0 * 1e-6 );
cptr->setY0( y0 * 1e-6 );
cptr->setZ0( z0 * 1e-6 );
cptr->setX( seg.vec().a0() * 1e-6 );
cptr->setY( seg.vec().a1() * 1e-6 );
cptr->setZ( seg.vec().a2() * 1e-6 );
return compt;
}
/**
* Creates objects on remote nodes.
* Also tests that objects on /library get created on all nodes.
* \todo: Needs to be extended by creating objects on remote nodes with
* parents on different remote nodes.
*/
Id testParCreate( vector< Id >& testIds )
{
unsigned int myNode = MuMPI::INTRA_COMM().Get_rank();
unsigned int numNodes = MuMPI::INTRA_COMM().Get_size();
if ( myNode == 0 )
cout << flush << "\nTest ParCreate";
MuMPI::INTRA_COMM().Barrier();
cout << "b" << myNode << flush;
MuMPI::INTRA_COMM().Barrier();
Eref shellE = Id::shellId().eref();
assert( shellE.e != 0 );
if ( myNode == 0 ) {
Slot remoteCreateSlot =
initShellCinfo()->getSlot( "parallel.createSrc" );
for ( unsigned int i = 1; i < numNodes; i++ ) {
char name[20];
sprintf( name, "tn%d", i );
string sname = name;
unsigned int tgt = ( i < myNode ) ? i : i - 1;
Id newId = Id::makeIdOnNode( i );
testIds.push_back( newId );
// cout << "Create op: sendTo4( shellId, slot, " << tgt << ", " << "Neutral, " << sname << ", root, " << newId << endl;
sendTo4< string, string, Nid, Nid >(
shellE, remoteCreateSlot, tgt,
"Neutral", sname,
Id(), newId
);
}
Id libid = Id::localId( "/library" ); // a global
ASSERT( libid.good(), "create libkids" );
ASSERT( libid.isGlobal(), "create libkids" );
SetConn c( shellE );
Shell::staticCreate( &c, "Neutral", "foo", Id::UnknownNode, libid );
}
MuMPI::INTRA_COMM().Barrier();
pollPostmaster(); // There is a barrier in the polling operation itself
MuMPI::INTRA_COMM().Barrier();
pollPostmaster();
MuMPI::INTRA_COMM().Barrier();
pollPostmaster();
MuMPI::INTRA_COMM().Barrier();
char name[20];
sprintf( name, "/tn%d", myNode );
string sname = name;
Id kidid = Id::localId( "/library/foo" );
ASSERT( kidid.good(), "create libkids" );
ASSERT( kidid.isGlobal(), "create libkids" );
bool ret = set( kidid.eref(), "destroy" );
ASSERT( ret, "destroy libkids" );
if ( myNode != 0 ) {
Id tnId = Id::localId( sname );
ASSERT( tnId.good(), "postmaster created obj on remote node" );
return tnId;
}
return Id();
}
vector< Id > HSolve::children( Id obj )
{
//~ return Field< vector< Id > >::get( obj, "children" );
//~ return Field< vector< Id > >::fastGet( obj.eref(), "children" );
//~ return localGet< Neutral, vector< Id > >( obj.eref(), "children" );
vector< Id > c;
Neutral::children( obj.eref(), c );
return c;
}
void ZombieCaConc::vSetSolver( const Eref& e, Id hsolve )
{
if ( !hsolve.element()->cinfo()->isA( "HSolve" ) ) {
cout << "Error: ZombieCaConc::vSetSolver: Object: " <<
hsolve.path() << " is not an HSolve. Aborted\n";
hsolve_ = 0;
return;
}
hsolve_ = reinterpret_cast< HSolve* >( hsolve.eref().data() );
}
/**
* This routine tests sending many packets over in one go. Tests
* how many polls are needed for everything to execute, and whether
* the execution order is clean.
*/
void testParCommandSequence()
{
const unsigned int numSeq = 10;
unsigned int myNode = MuMPI::INTRA_COMM().Get_rank();
unsigned int numNodes = MuMPI::INTRA_COMM().Get_size();
Eref shellE = Id::shellId().eref();
char name[20];
string sname;
if ( myNode == 0 ) {
cout << "\ntesting parallel command sequence" << flush;
}
if ( myNode == 0 ) {
Slot remoteCreateSlot =
initShellCinfo()->getSlot( "parallel.createSrc" );
Slot parSetSlot =
initShellCinfo()->getSlot( "parallel.setSrc" );
for ( unsigned int j = 0; j < numSeq; j++ ) {
for ( unsigned int i = 1; i < numNodes; i++ ) {
char name[20];
sprintf( name, "zug%d.%d", i, j );
string sname = name;
unsigned int tgt = ( i < myNode ) ? i : i - 1;
Id newId = Id::makeIdOnNode( i );
// cout << "Create op: sendTo4( shellId, slot, " << tgt << ", " << "Neutral, " << sname << ", root, " << newId << endl;
sendTo4< string, string, Nid, Nid >(
Id::shellId().eref(), remoteCreateSlot, tgt,
"Table", sname,
Id(), newId
);
sname = sname + ".extra";
sendTo3< Id, string, string >(
Id::shellId().eref(), parSetSlot, tgt,
newId, "name", sname
);
}
}
}
for ( unsigned int i = 0 ; i < 5; i++ ) {
pollPostmaster();
MuMPI::INTRA_COMM().Barrier();
}
if ( myNode != 0 ) {
for ( unsigned int j = 0; j < numSeq; j++ ) {
sprintf( name, "/zug%d.%d.extra", myNode, j );
sname = name;
Id checkId = Id::localId( sname );
// cout << "On " << myNode << ", checking id for " << sname << ": " << checkId << endl;
ASSERT( checkId.good(), "parallel command sequencing" );
// Clean up.
set( checkId.eref(), "destroy" );
}
cout << myNode << flush;
}
}
void Gsolve::setStoich( Id stoich )
{
// This call is done _before_ setting the path on stoich
assert( stoich.element()->cinfo()->isA( "Stoich" ) );
stoich_ = stoich;
stoichPtr_ = reinterpret_cast< Stoich* >( stoich.eref().data() );
sys_.stoich = stoichPtr_;
sys_.isReady = false;
for ( unsigned int i = 0; i < pools_.size(); ++i )
pools_[i].setStoich( stoichPtr_ );
}
void checkChildren( Id parent, const string& info )
{
vector< Id > ret;
Neutral::children( parent.eref(), ret );
cout << info << " checkChildren of " <<
parent.element()->getName() << ": " <<
ret.size() << " children\n";
for ( vector< Id >::iterator i = ret.begin(); i != ret.end(); ++i )
{
cout << i->element()->getName() << endl;
}
}
void SigNeur::buildTree( Id soma, const vector< Id >& compts )
{
const Finfo* axialFinfo;
const Finfo* raxialFinfo;
if ( soma.eref().e->cinfo() == initSymCompartmentCinfo() ) {
axialFinfo = initSymCompartmentCinfo()->findFinfo( "raxial1" );
raxialFinfo = initSymCompartmentCinfo()->findFinfo( "raxial2" );
} else {
axialFinfo = initCompartmentCinfo()->findFinfo( "axial" );
raxialFinfo = initCompartmentCinfo()->findFinfo( "raxial" );
}
assert( axialFinfo != 0 );
assert( raxialFinfo != 0 );
// Soma may be in middle of messaging structure for cell, so we need
// to traverse both ways. But nothing below soma should
// change direction in the traversal.
innerBuildTree( 0, soma.eref(), soma.eref(),
axialFinfo->msg(), raxialFinfo->msg() );
// innerBuildTree( 0, soma.eref(), soma.eref(), raxialFinfo->msg() );
}
/**
* For now don't deal with taper
*/
unsigned int numSegments( Id compt, double lambda )
{
double length = 0.0;
// double dia = 0.0;
assert( compt.good() );
bool ret = get< double >( compt.eref(), "length", length );
assert( ret );
// ret = get< double >( compt.eref(), "diameter", dia );
assert( ret );
assert( length > 0.0 && lambda > 0.0 );
return ( 1 + length / lambda );
}
void Cell::setupSolver( Id cell, Id seed ) const
{
Id solver = Id::nextId();
vector< int > dims( 1, 1 );
dims.push_back( 0 ); // isGlobal
shell_->innerCreate( "HSolve", cell, solver, solverName_, dims );
//~ Id solver = shell_->doCreate( "HSolve", cell, solverName_ );
HSolve* data = reinterpret_cast< HSolve* >( solver.eref().data() );
data->setSeed( seed );
//~ shell_->doUseClock( solver.path(), "proc", solverClock_ );
}
void ZombieMMenz::setSolver( Id solver, Id orig )
{
static const DestFinfo* enz = dynamic_cast< const DestFinfo* >(
EnzBase::initCinfo()->findFinfo( "enzDest" ) );
static const SrcFinfo* sub = dynamic_cast< const SrcFinfo* >(
EnzBase::initCinfo()->findFinfo( "toSub" ) );
static const SrcFinfo* prd = dynamic_cast< const SrcFinfo* >(
EnzBase::initCinfo()->findFinfo( "toPrd" ) );
assert( enz );
assert( sub );
assert( prd );
stoich_ = reinterpret_cast< Stoich* >( solver.eref().data() );
/// Now set up the RateTerm
vector< Id > subvec;
vector< Id > prdvec;
unsigned int rateIndex = stoich_->convertIdToReacIndex( orig );
unsigned int num = orig.element()->getNeighbours( subvec, enz );
unsigned int enzIndex = stoich_->convertIdToPoolIndex( subvec[0] );
MMEnzymeBase* meb;
double numKm = 1.0; // Dummy default initial values, later to be reset
double kcat = 1.0;
/*
double numKm = base->zGetNumKm( orig.eref(), 0 );
double kcat = base->zGetKcat( orig.eref(), 0 );
*/
num = orig.element()->getNeighbours( subvec, sub );
if ( num == 1 ) {
unsigned int subIndex = stoich_->convertIdToPoolIndex( subvec[0] );
meb = new MMEnzyme1( numKm, kcat, enzIndex, subIndex );
} else if ( num > 1 ) {
vector< unsigned int > v;
for ( unsigned int i = 0; i < num; ++i )
v.push_back( stoich_->convertIdToPoolIndex( subvec[i] ) );
ZeroOrder* rateTerm = new NOrder( 1.0, v );
meb = new MMEnzyme( numKm, kcat, enzIndex, rateTerm );
} else {
cout << "Error: ZombieMMenz::zombify: No substrates for " <<
orig.path() << endl;
cout << "Will ignore and continue, but don't be surprised if "
"simulation fails.\n";
// assert( 0 );
return;
}
num = orig.element()->getNeighbours( prdvec, prd );
stoich_->installMMenz( meb, rateIndex, subvec, prdvec );
}
/**
* Recursive function to compare all descendants and cram matches into ret.
* Returns number of matches.
*/
int allChildren( Id start, const string& insideBrace, unsigned int index,
vector< Id >& ret )
{
unsigned int nret = ret.size();
vector< Id > kids;
Neutral::getChildren( start.eref(), kids );
vector< Id >::iterator i;
for ( i = kids.begin(); i != kids.end(); i++ ) {
if ( matchName( start, *i, "#", insideBrace, index ) )
ret.push_back( *i );
allChildren( *i, insideBrace, index, ret );
}
return ret.size() - nret;
}
void SigNeur::schedule( Eref me )
{
static const Finfo* lookupChildFinfo =
initNeutralCinfo()->findFinfo( "lookupChild" );
Id kinId;
lookupGet< Id, string >( me, lookupChildFinfo, kinId, "kinetics" );
assert( kinId.good() );
Id cellId;
lookupGet< Id, string >( me, lookupChildFinfo, cellId, "cell" );
assert( cellId.good() );
SetConn c( Id::shellId().eref() );
Shell::setClock( &c, 0, cellDt_, 0 );
Shell::setClock( &c, 1, cellDt_, 1 );
Shell::setClock( &c, 2, cellDt_, 2 );
Shell::setClock( &c, 3, sigDt_, 0 );
Shell::setClock( &c, 4, sigDt_, 1 );
set< string >( cellId.eref(), "method", cellMethod_ );
set< string >( kinId.eref(), "method", dendMethod_ );
if ( separateSpineSolvers_ ) {
vector< Id > kids;
get< vector< Id > >( spine_.eref(), "childList", kids );
cout << "Setting separate spine method " << spineMethod_ <<
" to " << kids.size() << " spines\n";
for ( vector< Id >::iterator i = kids.begin();
i != kids.end(); ++i )
set< string >( i->eref(), "method", spineMethod_ );
}
Shell::useClock( &c, "t3", "/sig/kinetics", "process" );
Shell::useClock( &c, "t3", "/sig/kinetics/solve/hub", "process" );
Shell::useClock( &c, "t3", "/sig/kinetics/solve/integ", "process" );
Shell::useClock( &c, "t4", "/sig/cell/##[][TYPE==Adaptor]", "process" );
}
/**
* wildcardFieldComparison returns true if the value of the
* specified field matches the value in the comparsion string mid.
* Format is FIELD(name)=val
* If the format or the value does not match, return 0
*/
static bool wildcardFieldComparison( Id id, const string& mid )
{
// where = could be the usual comparison operators and val
// could be a number. No strings yet
string::size_type pos = mid.find(')');
if ( pos == string::npos )
return 0;
string fieldName = mid.substr( 0, pos );
string::size_type pos2 = mid.find_last_of( "=<>" );
if ( pos2 == string::npos )
return 0;
string op = mid.substr( pos + 1, pos2 - pos );
string testValue = mid.substr( pos2 + 1 );
if ( testValue.length() == 0 )
return 0;
const Finfo* f = id()->findFinfo( fieldName );
if ( !f )
return 0;
// At this point we don't want to compare multivalue fields.
if ( f->ftype()->nValues() != 1 )
return 0;
string actualValue;
bool ret = f->strGet( id.eref(), actualValue );
if ( ret == 0 )
return 0;
if ( op == "==" || op == "=" )
return ( testValue == actualValue );
if ( op == "!=" )
return ( testValue != actualValue );
double v1 = atof( actualValue.c_str() );
double v2 = atof( testValue.c_str() );
if ( op == ">" )
return ( v1 > v2 );
if ( op == ">=" )
return ( v1 >= v2 );
if ( op == "<" )
return ( v1 < v2 );
if ( op == "<=" )
return ( v1 <= v2 );
return 0;
}
void Gsolve::setDsolve( Id dsolve )
{
if ( dsolve == Id () ) {
dsolvePtr_ = 0;
dsolve_ = Id();
} else if ( dsolve.element()->cinfo()->isA( "Dsolve" ) ) {
dsolve_ = dsolve;
dsolvePtr_ = reinterpret_cast< ZombiePoolInterface* >(
dsolve.eref().data() );
} else {
cout << "Warning: Gsolve::setDsolve: Object '" << dsolve.path() <<
"' should be class Dsolve, is: " <<
dsolve.element()->cinfo()->name() << endl;
}
}
void testCompartment()
{
unsigned int size = 1;
Eref sheller( Id().eref() );
Shell* shell = reinterpret_cast< Shell* >( sheller.data() );
Id comptId = shell->doCreate("Compartment", Id(), "compt", size);
assert( Id::isValid(comptId));
Eref compter = comptId.eref();
Compartment* c = reinterpret_cast< Compartment* >( comptId.eref().data() );
ProcInfo p;
p.dt = 0.002;
c->setInject( compter, 1.0 );
c->setRm( compter, 1.0 );
c->setRa( compter, 0.0025 );
c->setCm( compter, 1.0 );
c->setEm( compter, 0.0 );
c->setVm( compter, 0.0 );
// First, test charging curve for a single compartment
// We want our charging curve to be a nice simple exponential
// Vm = 1.0 - 1.0 * exp( - t / 1.0 );
double delta = 0.0;
double Vm = 0.0;
double tau = 1.0;
double Vmax = 1.0;
for ( p.currTime = 0.0; p.currTime < 2.0; p.currTime += p.dt )
{
Vm = c->getVm( compter );
double x = Vmax - Vmax * exp( -p.currTime / tau );
delta += ( Vm - x ) * ( Vm - x );
c->process( compter, &p );
}
assert( delta < 1.0e-6 );
shell->doDelete(comptId);
cout << "." << flush;
}
// static function
bool Neutral::isDescendant( Id me, Id ancestor )
{
static const Finfo* pf = neutralCinfo->findFinfo( "parentMsg" );
static const DestFinfo* pf2 = dynamic_cast< const DestFinfo* >( pf );
static const FuncId pafid = pf2->getFid();
Eref e = me.eref();
while ( e.element()->id() != Id() && e.element()->id() != ancestor ) {
ObjId mid = e.element()->findCaller( pafid );
assert( mid != ObjId() );
ObjId fid = Msg::getMsg( mid )->findOtherEnd( e.objId() );
e = fid.eref();
}
return ( e.element()->id() == ancestor );
}
/**
* Launches Parser. Blocking when the parser blocks.
*/
void Shell::launchParser()
{
Id shellId;
Shell* s = reinterpret_cast< Shell* >( shellId.eref().data() );
bool quit = 0;
cout << "moose : " << flush;
while ( !quit ) {
string temp;
cin >> temp;
if ( temp == "quit" || temp == "q" ) {
s->doQuit();
quit = 1;
}
}
cout << "\nQuitting Moose\n" << flush;
}
/* set up Michalies Menten reaction */
void SbmlReader::setupMMEnzymeReaction( Reaction * reac,string rid,string rname,const map< string, Id > &molSidcmptMIdMap ) {
string::size_type loc = rid.find( "_MM_Reaction_" );
if( loc != string::npos ) {
int strlen = rid.length();
rid.erase( loc,strlen-loc );
}
unsigned int num_modifr = reac->getNumModifiers();
for ( unsigned int m = 0; m < num_modifr; m++ ) {
const ModifierSpeciesReference* modifr=reac->getModifier( m );
std::string sp = modifr->getSpecies();
Id enzyme_;
Id E = molSidMIdMap_.find(sp)->second;
Id comptRef = molSidcmptMIdMap.find(sp)->second; //gives compartment of sp
Id meshEntry = Neutral::child( comptRef.eref(), "mesh" );
Shell* shell = reinterpret_cast< Shell* >( Id().eref().data() );
enzyme_ = shell->doCreate("MMenz",E,rname,1);
//shell->doAddMsg( "Single", meshEntry, "remeshReacs", enzyme_, "remesh");
shell->doAddMsg("Single",E,"nOut",enzyme_,"enzDest");
KineticLaw * klaw=reac->getKineticLaw();
vector< double > rate;
rate.clear();
getKLaw( klaw,true,rate );
if ( errorFlag_ )
return;
else if ( !errorFlag_ ) {
for ( unsigned int rt = 0; rt < reac->getNumReactants(); rt++ ) {
const SpeciesReference* rct = reac->getReactant( rt );
sp=rct->getSpecies();
Id S = molSidMIdMap_.find(sp)->second;
shell->doAddMsg( "OneToOne", enzyme_, "sub" ,S , "reac" );
}
for ( unsigned int pt = 0; pt < reac->getNumProducts(); pt++ ) {
const SpeciesReference* pdt = reac->getProduct(pt);
sp = pdt->getSpecies();
Id P = molSidMIdMap_.find(sp)->second;
shell->doAddMsg( "OneToOne", enzyme_, "prd" ,P, "reac" );
}
Field < double > :: set( enzyme_, "kcat", rate[0] );
Field < double > :: set( enzyme_, "numKm", rate[1] );
}
}
}
void Ksolve::setStoich( Id stoich )
{
assert( stoich.element()->cinfo()->isA( "Stoich" ) );
stoich_ = stoich;
stoichPtr_ = reinterpret_cast< Stoich* >( stoich.eref().data() );
if ( !isBuilt_ )
{
OdeSystem ode;
ode.epsAbs = epsAbs_;
ode.epsRel = epsRel_;
// ode.initStepSize = getEstimatedDt();
ode.initStepSize = 0.01; // This will be overridden at reinit.
ode.method = method_;
#ifdef USE_GSL
ode.gslSys.dimension = stoichPtr_->getNumAllPools();
if ( ode.gslSys.dimension == 0 )
return; // No pools, so don't bother.
innerSetMethod( ode, method_ );
ode.gslSys.function = &VoxelPools::gslFunc;
ode.gslSys.jacobian = 0;
innerSetMethod( ode, method_ );
unsigned int numVoxels = pools_.size();
for ( unsigned int i = 0 ; i < numVoxels; ++i )
{
ode.gslSys.params = &pools_[i];
pools_[i].setStoich( stoichPtr_, &ode );
// pools_[i].setIntDt( ode.initStepSize ); // We're setting it up anyway
}
#elif USE_BOOST
ode.dimension = stoichPtr_->getNumAllPools();
ode.boostSys.epsAbs = epsAbs_;
ode.boostSys.epsRel = epsRel_;
ode.boostSys.method = method_;
if ( ode.dimension == 0 )
return; // No pools, so don't bother.
unsigned int numVoxels = pools_.size();
for ( unsigned int i = 0 ; i < numVoxels; ++i )
{
ode.boostSys.params = &pools_[i];
pools_[i].setStoich( stoichPtr_, &ode );
}
#endif
isBuilt_ = true;
}
}
void ReadCell::addChannelMessage( Id chan )
{
/*
* Get child objects of type Mstring, named addmsg1, 2, etc.
* These define extra messages to be assembled at setup.
* Similar to what was done with GENESIS.
*/
vector< Id > kids;
Neutral::children( chan.eref(), kids );
Shell *shell = reinterpret_cast< Shell* >( Id().eref().data() );
Id cwe = shell->getCwe();
shell->setCwe( chan );
for ( vector< Id >::iterator i = kids.begin(); i != kids.end(); ++i )
{
// Ignore kid if its name does not begin with "addmsg"..
const string& name = i->element()->getName();
if ( name.find( "addmsg", 0 ) != 0 )
continue;
string s = Field< string >::get( *i, "value" );
vector< string > token;
tokenize( s, " ", token );
assert( token.size() == 4 );
ObjId src = shell->doFind( token[0] );
ObjId dest = shell->doFind( token[2] );
// I would like to assert, or warn here, but there are legitimate
// cases where not all possible messages are actually available
// to set up. So I just bail.
if ( src.bad() || dest.bad()) {
#ifndef NDEBUG
/*
cout << "ReadCell::addChannelMessage( " << chan.path() <<
"): " << name << " " << s <<
": Bad src " << src << " or dest " << dest << endl;
*/
#endif
continue;
}
ObjId mid =
shell->doAddMsg( "single", src, token[1], dest, token[3] );
assert( !mid.bad());
}
shell->setCwe( cwe );
}
/**
* @brief Add a table to streamer.
*
* @param table Id of table.
*/
void Streamer::addTable( Id table )
{
// If this table is not already in the vector, add it.
for( size_t i = 0; i < tableIds_.size(); i++)
if( table.path() == tableIds_[i].path() )
return; /* Already added. */
Table* t = reinterpret_cast<Table*>(table.eref().data());
tableIds_.push_back( table );
tables_.push_back( t );
tableTick_.push_back( table.element()->getTick() );
// NOTE: If user can make sure that names are unique in table, using name is
// better than using the full path.
if( t->getColumnName().size() > 0 )
columns_.push_back( t->getColumnName( ) );
else
columns_.push_back( moose::moosePathToUserPath( table.path() ) );
}
void SteadyState::setStoich( Id value ) {
if ( !value.element()->cinfo()->isA( "Stoich" ) ) {
cout << "Error: SteadyState::setStoich: Must be of Stoich class\n";
return;
}
stoich_ = value;
Stoich* stoichPtr = reinterpret_cast< Stoich* >( value.eref().data());
numVarPools_ = Field< unsigned int >::get( stoich_, "numVarPools" );
nReacs_ = Field< unsigned int >::get( stoich_, "numRates" );
setupSSmatrix();
double vol = LookupField< unsigned int, double >::get(
stoichPtr->getCompartment(), "oneVoxelVolume", 0 );
pool_.setVolume( vol );
pool_.setStoich( stoichPtr, 0 );
pool_.updateAllRateTerms( stoichPtr->getRateTerms(),
stoichPtr->getNumCoreRates() );
isInitialized_ = 1;
}