void testRunKsolve()
{
double simDt = 0.1;
// double plotDt = 0.1;
Shell* s = reinterpret_cast< Shell* >( Id().eref().data() );
Id kin = makeReacTest();
Id ksolve = s->doCreate( "Ksolve", kin, "ksolve", 1 );
Id stoich = s->doCreate( "Stoich", ksolve, "stoich", 1 );
Field< Id >::set( stoich, "compartment", kin );
Field< Id >::set( stoich, "ksolve", ksolve );
Field< string >::set( stoich, "path", "/kinetics/##" );
s->doUseClock( "/kinetics/ksolve", "process", 4 );
s->doSetClock( 4, simDt );
s->doReinit();
s->doStart( 20.0 );
Id plots( "/kinetics/plots" );
for ( unsigned int i = 0; i < 7; ++i ) {
stringstream ss;
ss << "plot." << i;
SetGet2< string, string >::set( ObjId( plots, i ), "xplot",
"tsr2.plot", ss.str() );
}
s->doDelete( kin );
cout << "." << flush;
}
void testReacVolumeScaling()
{
Shell* shell = reinterpret_cast< Shell* >( Id().eref().data() );
Id comptId = shell->doCreate( "CubeMesh", Id(), "cube", 1 );
Id meshId( comptId.value() + 1 );
Id subId = shell->doCreate( "Pool", comptId, "sub", 1 );
Id prdId = shell->doCreate( "Pool", comptId, "prd", 1 );
Id reacId = shell->doCreate( "Reac", comptId, "reac", 1 );
double vol1 = 1e-15;
ObjId mid = shell->doAddMsg( "OneToOne",
subId, "requestVolume", meshId, "get_volume" );
assert( mid != ObjId() );
mid = shell->doAddMsg( "OneToOne",
prdId, "requestVolume", meshId, "get_volume" );
assert( mid != ObjId() );
vector< double > coords( 9, 10.0e-6 );
coords[0] = coords[1] = coords[2] = 0;
Field< vector< double > >::set( comptId, "coords", coords );
double volume = Field< double >::get( comptId, "volume" );
assert( doubleEq( volume, vol1 ) );
ObjId ret = shell->doAddMsg( "Single", reacId, "sub", subId, "reac" );
assert( ret != ObjId() );
ret = shell->doAddMsg( "Single", reacId, "prd", prdId, "reac" );
assert( ret != ObjId() );
Field< double >::set( reacId, "Kf", 2 );
Field< double >::set( reacId, "Kb", 3 );
double x = Field< double >::get( reacId, "kf" );
assert( doubleEq( x, 2 ) );
x = Field< double >::get( reacId, "kb" );
assert( doubleEq( x, 3 ) );
ret = shell->doAddMsg( "Single", reacId, "sub", subId, "reac" );
assert( ret != ObjId() );
double conv = 1.0 / ( NA * vol1 );
x = Field< double >::get( reacId, "kf" );
assert( doubleEq( x, 2 * conv ) );
x = Field< double >::get( reacId, "kb" );
assert( doubleEq( x, 3 ) );
ret = shell->doAddMsg( "Single", reacId, "sub", subId, "reac" );
assert( ret != ObjId() );
ret = shell->doAddMsg( "Single", reacId, "prd", prdId, "reac" );
assert( ret != ObjId() );
x = Field< double >::get( reacId, "kf" );
assert( doubleEq( x, 2 * conv * conv ) );
x = Field< double >::get( reacId, "kb" );
assert( doubleEq( x, 3 * conv ) );
shell->doDelete( comptId );
cout << "." << flush;
}
void testMMenzProcess()
{
Shell* shell = reinterpret_cast< Shell* >( Id().eref().data() );
//////////////////////////////////////////////////////////////////////
// This set is the test kinetic calculation using MathFunc
//////////////////////////////////////////////////////////////////////
Id nid = shell->doCreate( "Neutral", Id(), "n", 1 );
//////////////////////////////////////////////////////////////////////
// This set is the reference kinetic calculation using MMEnz
//////////////////////////////////////////////////////////////////////
Id pid = shell->doCreate( "Pool", nid, "p", 1 ); // substrate
Id qid = shell->doCreate( "Pool", nid, "q", 1 ); // enz mol
Id rid = shell->doCreate( "Pool", nid, "r", 1 ); // product
Id mmid = shell->doCreate( "MMenz", nid, "mm", 1 ); // mmenz
Id tabid2 = shell->doCreate( "Table", nid, "tab2", 1 ); //output plot
Field< double >::set( mmid, "Km", 1.0 );
Field< double >::set( mmid, "kcat", 1.0 );
Field< double >::set( pid, "nInit", 1.0 );
Field< double >::set( qid, "nInit", 1.0 );
Field< double >::set( rid, "nInit", 0.0 );
shell->doAddMsg( "Single", ObjId( mmid ), "sub", ObjId( pid ), "reac" );
shell->doAddMsg( "Single", ObjId( mmid ), "prd", ObjId( rid ), "reac" );
shell->doAddMsg( "Single", ObjId( qid ), "nOut", ObjId( mmid ), "enzDest" );
shell->doAddMsg( "Single", ObjId( pid ), "nOut", ObjId( tabid2 ), "input" );
shell->doSetClock( 0, 0.01 );
shell->doSetClock( 1, 0.01 );
shell->doUseClock( "/n/mm,/n/tab2", "process", 0 );
shell->doUseClock( "/n/#[ISA=Pool]", "process", 1 );
//////////////////////////////////////////////////////////////////////
// Now run models and compare outputs
//////////////////////////////////////////////////////////////////////
shell->doReinit();
shell->doStart( 10 );
vector< double > vec = Field< vector< double > >::get( tabid2, "vec" );
assert( vec.size() == 1001 );
for ( unsigned int i = 0; i < vec.size(); ++i ) {
double t = 0.01 * i;
double et = estT( vec[i] );
assert( doubleApprox( t, et ) );
}
shell->doDelete( nid );
cout << "." << flush;
}
void testTaperingCylDiffn()
{
Shell* s = reinterpret_cast< Shell* >( Id().eref().data() );
double len = 25e-6;
double r0 = 2e-6;
double r1 = 1e-6;
double diffLength = 1e-6; // 1e-6 is the highest dx for which error is OK
double runtime = 10.0;
double dt = 0.1; // 0.2 is the highest dt for which the error is in bounds
double diffConst = 1.0e-12;
// Should set explicitly, currently during creation of DiffPoolVec
//double diffConst = 1.0e-12;
Id model = s->doCreate( "Neutral", Id(), "model", 1 );
Id cyl = s->doCreate( "CylMesh", model, "cyl", 1 );
Field< double >::set( cyl, "r0", r0 );
Field< double >::set( cyl, "r1", r1 );
Field< double >::set( cyl, "x0", 0 );
Field< double >::set( cyl, "x1", len );
Field< double >::set( cyl, "diffLength", diffLength );
unsigned int ndc = Field< unsigned int >::get( cyl, "numMesh" );
assert( ndc == static_cast< unsigned int >( round( len / diffLength )));
Id pool = s->doCreate( "Pool", cyl, "pool", 1 );
Field< double >::set( pool, "diffConst", diffConst );
Id dsolve = s->doCreate( "Dsolve", model, "dsolve", 1 );
Field< Id >::set( dsolve, "compartment", cyl );
s->doUseClock( "/model/dsolve", "process", 1 );
s->doSetClock( 1, dt );
// Next: build by setting the path of the dsolve.
Field< string >::set( dsolve, "path", "/model/cyl/pool" );
// Then find a way to test it.
assert( pool.element()->numData() == ndc );
Field< double >::set( ObjId( pool, 0 ), "nInit", 1.0 );
s->doReinit();
s->doStart( runtime );
double myTot = 0.0;
vector< double > poolVec;
Field< double >::getVec( pool, "n", poolVec );
for ( unsigned int i = 0; i < poolVec.size(); ++i ) {
myTot += poolVec[i];
}
assert( doubleEq( myTot, 1.0 ) );
s->doDelete( model );
cout << "." << flush;
}
/// crate test object and push it into the container vector
Id create_testobject(vector<Id> & container, string classname, Id parent, string name, vector<int> dims)
{
Shell * shell = reinterpret_cast< Shell* >( ObjId( Id(), 0 ).data() );
Id nid = shell->doCreate( classname, parent, name, dims );
container.push_back(nid);
return nid;
}
/* 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 );
}
void testPoolVolumeScaling()
{
Shell* shell = reinterpret_cast< Shell* >( Id().eref().data() );
Id comptId = shell->doCreate( "CylMesh", Id(), "cyl", 1 );
Id meshId( comptId.value() + 1 );
Id poolId = shell->doCreate( "Pool", comptId, "pool", 1 );
ObjId mid = shell->doAddMsg( "OneToOne",
ObjId( poolId, 0 ), "requestVolume",
ObjId( meshId, 0 ), "get_volume" );
assert( mid != ObjId() );
vector< double > coords( 9, 0.0 );
double x1 = 100e-6;
double r0 = 10e-6;
double r1 = 5e-6;
double lambda = x1;
coords[3] = x1;
coords[6] = r0;
coords[7] = r1;
coords[8] = lambda;
Field< vector< double > >::set( comptId, "coords", coords );
double volume = Field< double >::get( poolId, "volume" );
assert( doubleEq( volume, PI * x1 * (r0+r1) * (r0+r1) / 4.0 ) );
Field< double >::set( poolId, "n", 400 );
double volscale = 1 / ( NA * volume );
double conc = Field< double >::get( poolId, "conc" );
assert( doubleEq( conc, 400 * volscale ) );
Field< double >::set( poolId, "conc", 500 * volscale );
double n = Field< double >::get( poolId, "n" );
assert( doubleEq( n, 500 ) );
Field< double >::set( poolId, "nInit", 650 );
double concInit = Field< double >::get( poolId, "concInit" );
assert( doubleEq( concInit, 650 * volscale ) );
Field< double >::set( poolId, "concInit", 10 * volscale );
n = Field< double >::get( poolId, "nInit" );
assert( doubleEq( n, 10 ) );
shell->doDelete( comptId );
cout << "." << flush;
}
void SbmlReader::getRules() {
unsigned int nr = model_->getNumRules();
//if (nr > 0)
// cout << "\n ##### Need to populate funcpool and sumtotal which is pending due to equations \n";
Shell* shell = reinterpret_cast< Shell* >( Id().eref().data() );
for ( unsigned int r = 0; r < nr; r++ ) {
Rule * rule = model_->getRule(r);
bool assignRule = rule->isAssignment();
if ( assignRule ) {
string rule_variable = rule->getVariable();
map< string,Id >::iterator v_iter;
map< string,Id >::iterator m_iter;
v_iter = molSidMIdMap_.find( rule_variable );
if (v_iter != molSidMIdMap_.end()) {
Id rVariable = molSidMIdMap_.find(rule_variable)->second;
string rstring =molSidMIdMap_.find(rule_variable)->first;
Id sumId = shell->doCreate( "SumFunc", rVariable, "func", 1 );
rVariable.element()->zombieSwap( FuncPool::initCinfo() );
ObjId ret = shell->doAddMsg( "single",
ObjId( sumId, 0 ), "output",
ObjId( rVariable, 0 ), "input" );
assert( ret != ObjId() );
const ASTNode * ast = rule->getMath();
vector< string > ruleMembers;
ruleMembers.clear();
printMembers( ast,ruleMembers );
for ( unsigned int rm = 0; rm < ruleMembers.size(); rm++ ) {
m_iter = molSidMIdMap_.find( ruleMembers[rm] );
if ( m_iter != molSidMIdMap_.end() ) {
Id rMember = molSidMIdMap_.find(ruleMembers[rm])->second;
ObjId ret = shell->doAddMsg( "single",
ObjId( rMember, 0 ), "nOut",
ObjId( sumId, 0 ), "input" );
string test = molSidMIdMap_.find(ruleMembers[rm])->first;
} else {
cerr << "SbmlReader::getRules: Assignment rule member is not a species" << endl;
// In assignment rule there are constants instead of molecule which is yet to deal in moose.
errorFlag_ = true;
}
}
}
}
bool rateRule = rule->isRate();
if ( rateRule ) {
cout << "warning : for now Rate Rule is not handled " << endl;
errorFlag_ = true;
}
bool algebRule = rule->isAlgebraic();
if ( algebRule ) {
cout << "warning: for now Algebraic Rule is not handled" << endl;
errorFlag_ = true;
}
}
}
void testRunGsolve()
{
double simDt = 0.1;
// double plotDt = 0.1;
Shell* s = reinterpret_cast< Shell* >( Id().eref().data() );
Id kin = makeReacTest();
double volume = 1e-21;
Field< double >::set( kin, "volume", volume );
Field< double >::set( ObjId( "/kinetics/A" ), "concInit", 2 );
Field< double >::set( ObjId( "/kinetics/e1Pool" ), "concInit", 1 );
Field< double >::set( ObjId( "/kinetics/e2Pool" ), "concInit", 1 );
Id e1( "/kinetics/e1Pool/e1" );
Field< double >::set( e1, "Km", 5 );
Field< double >::set( e1, "kcat", 1 );
vector< double > stim( 100, 0.0 );
for ( unsigned int i = 0; i< 100; ++i ) {
stim[i] = volume * NA * (1.0 + sin( i * 2.0 * PI / 100.0 ) );
}
Field< vector< double > >::set( ObjId( "/kinetics/tab" ), "vector", stim );
Id gsolve = s->doCreate( "Gsolve", kin, "gsolve", 1 );
Id stoich = s->doCreate( "Stoich", gsolve, "stoich", 1 );
Field< Id >::set( stoich, "compartment", kin );
Field< Id >::set( stoich, "ksolve", gsolve );
Field< string >::set( stoich, "path", "/kinetics/##" );
s->doUseClock( "/kinetics/gsolve", "process", 4 );
s->doSetClock( 4, simDt );
s->doReinit();
s->doStart( 20.0 );
Id plots( "/kinetics/plots" );
for ( unsigned int i = 0; i < 7; ++i ) {
stringstream ss;
ss << "plot." << i;
SetGet2< string, string >::set( ObjId( plots, i ), "xplot",
"tsr3.plot", ss.str() );
}
s->doDelete( kin );
cout << "." << flush;
}
// See what Element::getNeighbors does with 2 sub <----> prd.
void testTwoReacGetNeighbors()
{
Shell* shell = reinterpret_cast< Shell* >( Id().eref().data() );
Id comptId = shell->doCreate( "CubeMesh", Id(), "cube", 1 );
Id meshId( comptId.value() + 1 );
Id subId = shell->doCreate( "Pool", comptId, "sub", 1 );
Id prdId = shell->doCreate( "Pool", comptId, "prd", 1 );
Id reacId = shell->doCreate( "Reac", comptId, "reac", 1 );
ObjId mid = shell->doAddMsg( "OneToOne",
subId, "requestVolume", meshId, "get_volume" );
assert( mid != ObjId() );
mid = shell->doAddMsg( "OneToOne",
prdId, "requestVolume", meshId, "get_volume" );
assert( mid != ObjId() );
ObjId ret = shell->doAddMsg( "Single", reacId, "sub", subId, "reac" );
assert( ret != ObjId() );
ret = shell->doAddMsg( "Single", reacId, "sub", subId, "reac" );
assert( ret != ObjId() );
ret = shell->doAddMsg( "Single", reacId, "prd", prdId, "reac" );
assert( ret != ObjId() );
vector< Id > pools;
unsigned int num = reacId.element()->getNeighbors( pools,
Reac::initCinfo()->findFinfo( "toSub" ) );
assert( num == 2 );
assert( pools[0] == subId );
assert( pools[1] == subId );
pools.clear();
num = reacId.element()->getNeighbors( pools,
Reac::initCinfo()->findFinfo( "sub" ) );
assert( num == 2 );
assert( pools[0] == subId );
assert( pools[1] == subId );
shell->doDelete( comptId );
cout << "." << flush;
}
//////////////////////////////////////////////////////////////////
// The read functions.
//////////////////////////////////////////////////////////////////
Id makeStandardElements( Id pa, const string& modelname )
{
Shell* shell = reinterpret_cast< Shell* >( Id().eref().data() );
//cout << " kkit read " << pa << " " << modelname << " "<< MooseGlobal;
string modelPath = pa.path() + "/" + modelname;
if ( pa == Id() )
modelPath = "/" + modelname;
Id mgr( modelPath );
if ( mgr == Id() )
mgr = shell->doCreate( "Neutral", pa, modelname, 1, MooseGlobal );
Id kinetics( modelPath + "/kinetics" );
if ( kinetics == Id() ) {
kinetics =
shell->doCreate( "CubeMesh", mgr, "kinetics", 1, MooseGlobal );
SetGet2< double, unsigned int >::set( kinetics, "buildDefaultMesh", 1e-15, 1 );
}
assert( kinetics != Id() );
Id graphs = shell->doCreate( "Neutral", mgr, "graphs", 1, MooseGlobal);
assert( graphs != Id() );
Id moregraphs = shell->doCreate( "Neutral", mgr, "moregraphs", 1, MooseGlobal );
Id geometry = shell->doCreate( "Neutral", mgr, "geometry", 1, MooseGlobal );
assert( geometry != Id() );
Id groups =
shell->doCreate( "Neutral", mgr, "groups", 1, MooseGlobal );
assert( groups != Id() );
return mgr;
}
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;
}
/* 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] );
}
}
}
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;
}
void testMMenz()
{
Shell* shell = reinterpret_cast< Shell* >( Id().eref().data() );
Id mmid = shell->doCreate( "MMenz", Id(), "mm", 1 ); // mmenz
MMenz m;
ProcInfo p;
m.vSetKm( mmid.eref(), 5.0 );
m.vSetKcat( mmid.eref(), 4.0 );
m.vReinit( mmid.eref(), &p );
m.vSub( 2 );
m.vEnz( 3 );
assert( doubleEq( m.vGetKm( mmid.eref() ), 5.0 ) );
assert( doubleEq( m.vGetKcat( mmid.eref() ), 4.0 ) );
m.vProcess( mmid.eref(), &p );
shell->doDelete( mmid );
cout << "." << flush;
}
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;
}
void testCylDiffnWithStoich()
{
Shell* s = reinterpret_cast< Shell* >( Id().eref().data() );
double len = 25e-6;
double r0 = 1e-6;
double r1 = 1e-6;
double diffLength = 1e-6; // 1e-6 is the highest dx for which error is OK
double runtime = 10.0;
double dt0 = 0.1; // Used for diffusion. 0.2 is the highest dt for which the error is in bounds
double dt1 = 1; // Used for chem.
double diffConst = 1.0e-12;
Id model = s->doCreate( "Neutral", Id(), "model", 1 );
Id cyl = s->doCreate( "CylMesh", model, "cyl", 1 );
Field< double >::set( cyl, "r0", r0 );
Field< double >::set( cyl, "r1", r1 );
Field< double >::set( cyl, "x0", 0 );
Field< double >::set( cyl, "x1", len );
Field< double >::set( cyl, "diffLength", diffLength );
unsigned int ndc = Field< unsigned int >::get( cyl, "numMesh" );
assert( ndc == static_cast< unsigned int >( round( len / diffLength )));
Id pool1 = s->doCreate( "Pool", cyl, "pool1", 1 );
Id pool2 = s->doCreate( "Pool", cyl, "pool2", 1 );
Field< double >::set( pool1, "diffConst", diffConst );
Field< double >::set( pool2, "diffConst", diffConst/2 );
Id stoich = s->doCreate( "Stoich", model, "stoich", 1 );
Id ksolve = s->doCreate( "Ksolve", model, "ksolve", 1 );
Id dsolve = s->doCreate( "Dsolve", model, "dsolve", 1 );
Field< Id >::set( stoich, "compartment", cyl );
Field< Id >::set( stoich, "ksolve", ksolve );
Field< Id >::set( stoich, "dsolve", dsolve );
Field< string >::set( stoich, "path", "/model/cyl/#" );
assert( pool1.element()->numData() == ndc );
// Then find a way to test it.
vector< double > poolVec;
Field< double >::set( ObjId( pool1, 0 ), "nInit", 1.0 );
Field< double >::set( ObjId( pool2, 0 ), "nInit", 1.0 );
Field< double >::getVec( pool1, "nInit", poolVec );
assert( poolVec.size() == ndc );
assert( doubleEq( poolVec[0], 1.0 ) );
assert( doubleEq( poolVec[1], 0.0 ) );
vector< double > nvec =
LookupField< unsigned int, vector< double > >::get(
dsolve, "nVec", 0);
assert( nvec.size() == ndc );
// Next: build by doing reinit
s->doUseClock( "/model/dsolve", "process", 0 );
s->doUseClock( "/model/ksolve", "process", 1 );
s->doSetClock( 0, dt0 );
s->doSetClock( 1, dt1 );
s->doReinit();
s->doStart( runtime );
nvec = LookupField< unsigned int, vector< double > >::get(
dsolve, "nVec", 0);
Field< double >::getVec( pool1, "n", poolVec );
assert( nvec.size() == poolVec.size() );
for ( unsigned int i = 0; i < nvec.size(); ++i )
assert( doubleEq( nvec[i], poolVec[i] ) );
/*
cout << endl;
for ( unsigned int i = 0; i < nvec.size(); ++i )
cout << nvec[i] << " ";
cout << endl;
*/
double dx = diffLength;
double err = 0.0;
double analyticTot = 0.0;
double myTot = 0.0;
for ( unsigned int i = 0; i < nvec.size(); ++i ) {
double x = i * dx + dx * 0.5;
// This part is the solution as a func of x,t.
double y = dx * // This part represents the init n of 1 in dx
( 1.0 / sqrt( PI * diffConst * runtime ) ) *
exp( -x * x / ( 4 * diffConst * runtime ) );
err += ( y - nvec[i] ) * ( y - nvec[i] );
//cout << i << " " << x << " " << y << " " << conc[i] << endl;
analyticTot += y;
myTot += nvec[i];
}
assert( doubleEq( myTot, 1.0 ) );
// cout << "analyticTot= " << analyticTot << ", myTot= " << myTot << endl;
assert( err < 1.0e-5 );
s->doDelete( model );
cout << "." << flush;
}
void SbmlReader::createReaction(const map< string, Id > &molSidcmptMIdMap ) {
Reaction* reac;
map< string,double > rctMap;
map< string,double >::iterator rctMap_iter;
map< string,double >prdMap;
map< string,double >::iterator prdMap_iter;
map< string,EnzymeInfo >enzInfoMap;
for ( unsigned int r = 0; r < model_->getNumReactions(); r++ ) {
Id reaction_;
reac = model_->getReaction( r );
noOfsub_ = 0;
noOfprd_ = 0;
std:: string id; //=reac->getId();
if ( reac->isSetId() )
id = reac->getId();
std::string name;
if ( reac->isSetName() ) {
name = reac->getName();
name = nameString(name);
}
if (name.empty()) {
if (id.empty())
assert("Reaction id and name is empty");
else
name = id;
}
string grpname = getAnnotation( reac,enzInfoMap );
if ( (grpname != "") && (enzInfoMap[grpname].stage == 3) ) {
setupEnzymaticReaction( enzInfoMap[grpname],grpname ,molSidcmptMIdMap,name);
}
//if (grpname != "")
// {
//cout << "\n enz matic reaction " << enzInfoMap[grpname].stage;
//setupEnzymaticReaction( enzInfoMap[grpname],grpname ,molSidcmptMIdMap);
//}
else if ( grpname == "" ) {
if (reac->getNumModifiers() > 0)
setupMMEnzymeReaction( reac,id,name ,molSidcmptMIdMap);
else {
bool rev=reac->getReversible();
bool fast=reac->getFast();
if ( fast ) {
cout<<"warning: for now fast attribute is not handled"<<endl;
errorFlag_ = true;
}
int numRcts = reac->getNumReactants();
int numPdts = reac->getNumProducts();
if ( numRcts == 0 && numPdts != 0 ) {
cout << "Reaction with zero Substrate is not possible but exist in this model";
const SpeciesReference* pdt = reac->getProduct( 0 );
std::string spName = pdt->getSpecies();
Id parent = molSidcmptMIdMap.find( spName )->second; //gives compartment of spName
cout << " \n \t ################################# Sub = 0 and prd != 0 need to the reac ############### ";
const SpeciesReference* rect=reac->getReactant(0);
std::string sp=rect->getSpecies();
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() );
reaction_ = shell->doCreate("Reac", meshEntry, name, 1);
//shell->doAddMsg( "Single", meshEntry, "remeshReacs", reaction_, "remesh");
//Get Substrate
addSubPrd(reac,reaction_,"prd");
} //if numRcts == 0
else {
const SpeciesReference* rect=reac->getReactant(0);
std::string sp=rect->getSpecies();
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() );
reaction_ = shell->doCreate("Reac", comptRef, name, 1);
//shell->doAddMsg( "Single", meshEntry, "remeshReacs", reaction_, "remesh");
//Get Substrate
addSubPrd(reac,reaction_,"sub");
//Get Product
addSubPrd(reac,reaction_,"prd");
}
if ( reac->isSetKineticLaw() ) {
KineticLaw * klaw=reac->getKineticLaw();
//vector< double > rate = getKLaw( klaw,rev );
vector< double > rate;
rate.clear();
getKLaw( klaw,rev,rate );
if ( errorFlag_ )
return;
else if ( !errorFlag_ ) {
//cout << " Reaction name " << name << " kf " << rate[0] << " kb " << rate[1]<<endl;
Field < double > :: set( reaction_, "Kf", rate[0] );
Field < double > :: set( reaction_, "Kb", rate[1] );
/*if (numRcts > 1)
rate[0] = rate[0]*pow(1e3,1.0);
cout << "Reaction " << id << " " << name << " " << rate[0] << " " << rate[1]<<endl;
Field < double > :: set( reaction_, "Kf", rate[0] );
Field < double > :: set( reaction_, "Kb", rate[1] );
*/
}
} //issetKineticLaw
} //else
} // else grpname == ""
}//for unsigned
} //reaction
/**
* @brief Reads a given SBML file and loads it into MOOSE.
*
* @param filename Name of file, std::string.
* @param location
* @param solverClass
*
* @return Id on success. Some expcetion on failure.
*/
Id SbmlReader::read( string filename, string location, string solverClass)
{
FILE * fp = fopen( filename.c_str(), "r" );
if ( fp == NULL) {
stringstream ss;
ss << "File " << filename << " does not exist." << endl;
throw runtime_error(ss.str());
}
document_ = readSBML( filename.c_str() );
unsigned num_errors = document_->getNumErrors();
if ( num_errors > 0 ) {
cerr << "Errors encountered while reading" << endl;
document_->printErrors( cerr );
errorFlag_ = true;
return baseId;
}
model_= document_->getModel();
if ( model_ == 0 ) {
cout << "SBML: Error: No model present." << endl;
errorFlag_ = true;
return baseId;
}
if ( !errorFlag_ )
getGlobalParameter();
if ( !errorFlag_ ) {
string modelName;
Id parentId;
findModelParent ( Id(), location, parentId, modelName ) ;
Id parentId2 = parentId;
Shell* s = reinterpret_cast< Shell* >( Id().eref().data() );
/* As a policy model is created under /model and all the graphs are created under /data, if this file is invoke from Gui the /model is already created and path is passed, but if readSbml is called then only modelName is taken so making sure /model is the model path */
//Id modelPath_ = s->doCreate("Neutral",parentId,"model",1,MooseGlobal);
if (parentId == Id()) {
Id parentId1 = s->doCreate("Neutral",parentId,"model",1,MooseGlobal);
parentId = parentId1;
}
Id base_ = s->doCreate( "Neutral", parentId, modelName, 1, MooseGlobal);
//Id base_ = s->doCreate( "SimManager", parentId, modelName, dims, true );
assert( base_ != Id() );
//Map Compartment's SBML id to Moose ID
map< string,Id > comptSidMIdMap;
// Map between Molecule's SBML id to which it belongs compartment Moose Id
map< string, Id > molSidcmptMIdMap;
if ( !errorFlag_ )
comptSidMIdMap = createCompartment(location, parentId, modelName, base_);
if ( !errorFlag_ )
molSidcmptMIdMap = createMolecule( comptSidMIdMap);
if ( !errorFlag_ )
getRules();
if ( !errorFlag_ )
createReaction( molSidcmptMIdMap );
// or we get
//createReaction (result);
if ( errorFlag_ )
return baseId;
else {
// SimManager* sm = reinterpret_cast< SimManager* >(baseId.eref().data());
//Shell* s = reinterpret_cast< Shell* >(baseId.eref().data());
XMLNode * annotationNode = model_->getAnnotation();
if( annotationNode != NULL ) {
unsigned int num_children = annotationNode->getNumChildren();
for( unsigned int child_no = 0; child_no < num_children; child_no++ ) {
XMLNode childNode = annotationNode->getChild( child_no );
if ( childNode.getPrefix() == "moose" && childNode.getName() == "ModelAnnotation" ) {
unsigned int num_gchildren = childNode.getNumChildren();
for( unsigned int gchild_no = 0; gchild_no < num_gchildren; gchild_no++ ) {
XMLNode &grandChildNode = childNode.getChild( gchild_no );
string nodeName = grandChildNode.getName();
if (grandChildNode.getNumChildren() == 1 ) {
string plotValue;
//double nodeValue;
if(nodeName == "plots") {
// if plots exist then will be placing at "/data"
Id graphs;
//Id dataId;
Id dataIdTest;
if (parentId2 == Id())
graphs = s->doCreate( "Neutral", parentId2, "data", 1);
else
// need to check how to put / while coming from gui as the path is /model/modelName??? 27 jun 2014
findModelParent ( Id(), modelName, dataIdTest, modelName ) ;
string test = "/data";
Id tgraphs(test);
graphs=tgraphs;
//graphs = s->doCreate("Neutral",parentId,"data",1);
//Id dataId;
//if (dataId == Id())
// cout << "Id " << dataId;
// graphs = s->doCreate( "Neutral",dataId, "data", 1);
assert( graphs != Id() );
plotValue = (grandChildNode.getChild(0).toXMLString()).c_str();
istringstream pltVal(plotValue);
string pltClean;
while (getline(pltVal,pltClean, ';')) {
pltClean.erase( remove( pltClean.begin(), pltClean.end(), ' ' ), pltClean.end() );
//string plotPath = location+pltClean;
string plotPath = base_.path()+pltClean;
Id plotSId(plotPath);
unsigned pos = pltClean.find('/');
if (pos != std::string::npos)
pltClean = pltClean.substr(pos+1,pltClean.length());
replace(pltClean.begin(),pltClean.end(),'/','_');
string plotName = pltClean + ".conc";
Id pltPath(graphs.path());
Id tab = s->doCreate( "Table", pltPath, plotName, 1 );
if (tab != Id())
s->doAddMsg("Single",tab,"requestOut",plotSId,"getConc");
}//while
/* passing /model and /data */
string comptPath =base_.path()+"/##";
s->doUseClock(comptPath,"process",4);
string tablePath = graphs.path()+"/##[TYPE=Table]";
s->doUseClock( tablePath, "process",8 );
}//plots
/*else
nodeValue = atof ((grandChildNode.getChild(0).toXMLString()).c_str());
if (nodeName == "runTime")
sm->setRunTime(nodeValue);
else if (nodeName == "simdt")
sm->setSimDt(nodeValue);
else if(nodeName == "plotdt")
sm->setPlotDt(nodeValue);
*/
} //grandChild
else
cout << "Warning: expected exactly ONE child of " << nodeName << " but none found "<<endl;
} //gchild
} //moose and modelAnnotation
}
}//annotation Node
else {
//4 for simdt and 8 for plotdt
s->doUseClock(base_.path()+"/##","process",4);
s->doUseClock(+"/data/##[TYPE=Table]","process",8);
s->doSetClock(4,0.1);
s->doSetClock(8,0.1);
}
vector< ObjId > compts;
string comptpath = base_.path()+"/##[ISA=ChemCompt]";
wildcardFind( comptpath, compts );
vector< ObjId >::iterator i = compts.begin();
string comptName = nameString(Field<string> :: get(ObjId(*i),"name"));
string simpath = base_.path() + "/##";
s->doUseClock( simpath, "process", 4 );
//wildcardFind( plotpath, plots );
//Id pathexist(base_.path()+"/kinetics");
/*
if (solverClass.empty())
{
if( pathexist != Id())
sm->build(base_.eref(),&q,"rk5");
else
sm->buildForSBML(base_.eref(),&q,"rk5");
}
else
{ if(pathexist != Id())
sm->build(base_.eref(),&q,solverClass);
else
sm->buildForSBML(base_.eref(),&q,solverClass);
}
*/
return base_;
}
} else
return baseId;
}
void testHSolveUtils( )
{
Shell* shell = reinterpret_cast< Shell* >( Id().eref().data() );
bool success;
Id n = shell->doCreate( "Neutral", Id(), "n" );
/**
* First we test the functions which return the compartments linked to a
* given compartment: adjacent(), and children().
*
* A small tree is created for this:
*
* c0
* L c1
* L c2
* L c3
* L c4
* L c5
*
* (c0 is the parent of c1. c1 is the parent of c2, c3, c4, c5.)
*/
Id c[ 6 ];
c[ 0 ] = shell->doCreate( "Compartment", n, "c0" );
c[ 1 ] = shell->doCreate( "Compartment", n, "c1" );
c[ 2 ] = shell->doCreate( "Compartment", n, "c2" );
c[ 3 ] = shell->doCreate( "Compartment", n, "c3" );
c[ 4 ] = shell->doCreate( "Compartment", n, "c4" );
c[ 5 ] = shell->doCreate( "Compartment", n, "c5" );
MsgId mid;
mid = shell->doAddMsg( "Single", c[ 0 ], "axial", c[ 1 ], "raxial" );
ASSERT( mid != Msg::bad, "Linking compartments" );
mid = shell->doAddMsg( "Single", c[ 1 ], "axial", c[ 2 ], "raxial" );
ASSERT( mid != Msg::bad, "Linking compartments" );
mid = shell->doAddMsg( "Single", c[ 1 ], "axial", c[ 3 ], "raxial" );
ASSERT( mid != Msg::bad, "Linking compartments" );
mid = shell->doAddMsg( "Single", c[ 1 ], "axial", c[ 4 ], "raxial" );
ASSERT( mid != Msg::bad, "Linking compartments" );
mid = shell->doAddMsg( "Single", c[ 1 ], "axial", c[ 5 ], "raxial" );
ASSERT( mid != Msg::bad, "Linking compartments" );
vector< Id > found;
unsigned int nFound;
/*
* Testing version 1 of HSolveUtils::adjacent.
* It finds all neighbours of given compartment.
*/
// Neighbours of c0
nFound = HSolveUtils::adjacent( c[ 0 ], found );
ASSERT( nFound == found.size(), "Finding adjacent compartments" );
// c1 is adjacent
ASSERT( nFound == 1, "Finding adjacent compartments" );
ASSERT( found[ 0 ] == c[ 1 ], "Finding adjacent compartments" );
// Neighbours of c1
found.clear();
nFound = HSolveUtils::adjacent( c[ 1 ], found );
ASSERT( nFound == 5, "Finding adjacent compartments" );
// c0 is adjacent
success =
find( found.begin(), found.end(), c[ 0 ] ) != found.end();
ASSERT( success, "Finding adjacent compartments" );
// c2 - c5 are adjacent
for ( int i = 2; i < 6; i++ ) {
success =
find( found.begin(), found.end(), c[ i ] ) != found.end();
ASSERT( success, "Finding adjacent compartments" );
}
// Neighbours of c2
found.clear();
nFound = HSolveUtils::adjacent( c[ 2 ], found );
// c1 is adjacent
ASSERT( nFound == 1, "Finding adjacent compartments" );
ASSERT( found[ 0 ] == c[ 1 ], "Finding adjacent compartments" );
/*
* Testing version 2 of HSolveUtils::adjacent.
* It finds all but one neighbours of given compartment.
* The the second argument to 'adjacent' is the one that is excluded.
*/
// Neighbours of c1 (excluding c0)
found.clear();
nFound = HSolveUtils::adjacent( c[ 1 ], c[ 0 ], found );
ASSERT( nFound == 4, "Finding adjacent compartments" );
// c2 - c5 are adjacent
for ( int i = 2; i < 6; i++ ) {
success =
find( found.begin(), found.end(), c[ i ] ) != found.end();
ASSERT( success, "Finding adjacent compartments" );
}
// Neighbours of c1 (excluding c2)
found.clear();
nFound = HSolveUtils::adjacent( c[ 1 ], c[ 2 ], found );
ASSERT( nFound == 4, "Finding adjacent compartments" );
// c0 is adjacent
success =
find( found.begin(), found.end(), c[ 0 ] ) != found.end();
ASSERT( success, "Finding adjacent compartments" );
// c3 - c5 are adjacent
for ( int i = 3; i < 6; i++ ) {
success =
find( found.begin(), found.end(), c[ i ] ) != found.end();
ASSERT( success, "Finding adjacent compartments" );
}
// Neighbours of c2 (excluding c1)
found.clear();
nFound = HSolveUtils::adjacent( c[ 2 ], c[ 1 ], found );
// None adjacent, if c1 is excluded
ASSERT( nFound == 0, "Finding adjacent compartments" );
// Neighbours of c2 (excluding c3)
found.clear();
nFound = HSolveUtils::adjacent( c[ 2 ], c[ 3 ], found );
// c1 is adjacent, while c3 is not even connected
ASSERT( nFound == 1, "Finding adjacent compartments" );
ASSERT( found[ 0 ] == c[ 1 ], "Finding adjacent compartments" );
/*
* Testing HSolveUtils::children.
* It finds all compartments which are dests for the "axial" message.
*/
// Children of c0
found.clear();
nFound = HSolveUtils::children( c[ 0 ], found );
ASSERT( nFound == 1, "Finding child compartments" );
// c1 is a child
ASSERT( found[ 0 ] == c[ 1 ], "Finding child compartments" );
// Children of c1
found.clear();
nFound = HSolveUtils::children( c[ 1 ], found );
ASSERT( nFound == 4, "Finding child compartments" );
// c2 - c5 are c1's children
for ( int i = 2; i < 6; i++ ) {
success =
find( found.begin(), found.end(), c[ i ] ) != found.end();
ASSERT( success, "Finding child compartments" );
}
// Children of c2
found.clear();
nFound = HSolveUtils::children( c[ 2 ], found );
// c2 has no children
ASSERT( nFound == 0, "Finding child compartments" );
// Clean up
shell->doDelete( n );
cout << "." << flush;
}
/**
* Tab controlled by table
* A + Tab <===> B
* A + B -sumtot--> tot1
* 2B <===> C
*
* C ---e1Pool ---> D
* D ---e2Pool ----> E
*
* All these are created on /kinetics, a cube compartment of vol 1e-18 m^3
*
*/
Id makeReacTest()
{
double simDt = 0.1;
double plotDt = 0.1;
Shell* s = reinterpret_cast< Shell* >( Id().eref().data() );
Id pools[10];
unsigned int i = 0;
// Make the objects.
Id kin = s->doCreate( "CubeMesh", Id(), "kinetics", 1 );
Id tab = s->doCreate( "StimulusTable", kin, "tab", 1 );
Id T = pools[i++] = s->doCreate( "BufPool", kin, "T", 1 );
Id A = pools[i++] = s->doCreate( "Pool", kin, "A", 1 );
Id B = pools[i++] = s->doCreate( "Pool", kin, "B", 1 );
Id C = pools[i++] = s->doCreate( "Pool", kin, "C", 1 );
Id D = pools[i++] = s->doCreate( "Pool", kin, "D", 1 );
Id E = pools[i++] = s->doCreate( "Pool", kin, "E", 1 );
Id tot1 = pools[i++] = s->doCreate( "BufPool", kin, "tot1", 1 );
Id sum = s->doCreate( "Function", tot1, "func", 1 ); // Silly that it has to have this name.
Id sumInput( sum.value() + 1 );
Id e1Pool = s->doCreate( "Pool", kin, "e1Pool", 1 );
Id e2Pool = s->doCreate( "Pool", kin, "e2Pool", 1 );
Id e1 = s->doCreate( "Enz", e1Pool, "e1", 1 );
Id cplx = s->doCreate( "Pool", e1, "cplx", 1 );
Id e2 = s->doCreate( "MMenz", e2Pool, "e2", 1 );
Id r1 = s->doCreate( "Reac", kin, "r1", 1 );
Id r2 = s->doCreate( "Reac", kin, "r2", 1 );
Id plots = s->doCreate( "Table2", kin, "plots", 7 );
// Connect them up
s->doAddMsg( "Single", tab, "output", T, "setN" );
s->doAddMsg( "Single", r1, "sub", T, "reac" );
s->doAddMsg( "Single", r1, "sub", A, "reac" );
s->doAddMsg( "Single", r1, "prd", B, "reac" );
Field< unsigned int >::set( sum, "numVars", 2 );
s->doAddMsg( "Single", A, "nOut", ObjId( sumInput, 0, 0 ), "input" );
s->doAddMsg( "Single", B, "nOut", ObjId( sumInput, 0, 1 ), "input" );
s->doAddMsg( "Single", sum, "valueOut", tot1, "setN" );
s->doAddMsg( "Single", r2, "sub", B, "reac" );
s->doAddMsg( "Single", r2, "sub", B, "reac" );
s->doAddMsg( "Single", r2, "prd", C, "reac" );
s->doAddMsg( "Single", e1, "sub", C, "reac" );
s->doAddMsg( "Single", e1, "enz", e1Pool, "reac" );
s->doAddMsg( "Single", e1, "cplx", cplx, "reac" );
s->doAddMsg( "Single", e1, "prd", D, "reac" );
s->doAddMsg( "Single", e2, "sub", D, "reac" );
s->doAddMsg( "Single", e2Pool, "nOut", e2, "enzDest" );
s->doAddMsg( "Single", e2, "prd", E, "reac" );
// Set parameters.
Field< double >::set( A, "concInit", 2 );
Field< double >::set( e1Pool, "concInit", 1 );
Field< double >::set( e2Pool, "concInit", 1 );
Field< string >::set( sum, "expr", "x0+x1" );
Field< double >::set( r1, "Kf", 0.2 );
Field< double >::set( r1, "Kb", 0.1 );
Field< double >::set( r2, "Kf", 0.1 );
Field< double >::set( r2, "Kb", 0.0 );
Field< double >::set( e1, "Km", 5 );
Field< double >::set( e1, "kcat", 1 );
Field< double >::set( e1, "ratio", 4 );
Field< double >::set( e2, "Km", 5 );
Field< double >::set( e2, "kcat", 1 );
vector< double > stim( 100, 0.0 );
double vol = Field< double >::get( kin, "volume" );
for ( unsigned int i = 0; i< 100; ++i ) {
stim[i] = vol * NA * (1.0 + sin( i * 2.0 * PI / 100.0 ) );
}
Field< vector< double > >::set( tab, "vector", stim );
Field< double >::set( tab, "stepSize", 0.0 );
Field< double >::set( tab, "stopTime", 10.0 );
Field< double >::set( tab, "loopTime", 10.0 );
Field< bool >::set( tab, "doLoop", true );
// Connect outputs
for ( unsigned int i = 0; i < 7; ++i )
s->doAddMsg( "Single", ObjId( plots,i),
"requestOut", pools[i], "getConc" );
// Schedule it.
for ( unsigned int i = 11; i < 18; ++i )
s->doSetClock( i, simDt );
s->doSetClock( 18, plotDt );
/*
s->doUseClock( "/kinetics/##[ISA=Reac],/kinetics/##[ISA=EnzBase],/kinetics/##[ISA=SumFunc]",
"process", 4 );
s->doUseClock( "/kinetics/##[ISA=PoolBase]", "process", 5 );
s->doUseClock( "/kinetics/##[ISA=StimulusTable]",
"process", 4 );
s->doUseClock( "/kinetics/##[ISA=Table]", "process", 8 );
s->doSetClock( 4, simDt );
s->doSetClock( 5, simDt );
s->doSetClock( 8, plotDt );
*/
return kin;
}
void testAssortedMsg()
{
Eref sheller = Id().eref();
Shell* shell = reinterpret_cast< Shell* >( sheller.data() );
ObjId pa = shell->doCreate( "Neutral", ObjId(), "pa", 1 );
unsigned int numData = 5;
///////////////////////////////////////////////////////////
// Set up the objects.
///////////////////////////////////////////////////////////
Id a1 = shell->doCreate( "Arith", pa, "a1", numData );
Id a2 = shell->doCreate( "Arith", pa, "a2", numData );
Id b1 = shell->doCreate( "Arith", pa, "b1", numData );
Id b2 = shell->doCreate( "Arith", pa, "b2", numData );
Id c1 = shell->doCreate( "Arith", pa, "c1", numData );
Id c2 = shell->doCreate( "Arith", pa, "c2", numData );
Id d1 = shell->doCreate( "Arith", pa, "d1", numData );
Id d2 = shell->doCreate( "Arith", pa, "d2", numData );
Id e1 = shell->doCreate( "Arith", pa, "e1", numData );
Id e2 = shell->doCreate( "Arith", pa, "e2", numData );
///////////////////////////////////////////////////////////
// Set up initial conditions
///////////////////////////////////////////////////////////
bool ret = 0;
vector< double > init; // 12345
for ( unsigned int i = 1; i < 6; ++i )
init.push_back( i );
ret = SetGet1< double >::setVec( a1, "arg1", init ); // 12345
assert( ret );
ret = SetGet1< double >::setVec( b1, "arg1", init ); // 12345
assert( ret );
ret = SetGet1< double >::setVec( c1, "arg1", init ); // 12345
assert( ret );
ret = SetGet1< double >::setVec( d1, "arg1", init ); // 12345
assert( ret );
ret = SetGet1< double >::setVec( e1, "arg1", init ); // 12345
assert( ret );
///////////////////////////////////////////////////////////
// Set up messaging
///////////////////////////////////////////////////////////
// Should give 04000
ObjId m1 = shell->doAddMsg( "Single",
ObjId( a1, 3 ), "output", ObjId( a2, 1 ), "arg1" );
assert( !m1.bad() );
// Should give 33333
ObjId m2 = shell->doAddMsg( "OneToAll",
ObjId( b1, 2 ), "output", ObjId( b2, 0 ), "arg1" );
assert( !m2.bad() );
// Should give 12345
ObjId m3 = shell->doAddMsg( "OneToOne",
ObjId( c1, 0 ), "output", ObjId( c2, 0 ), "arg1" );
assert( !m3.bad() );
// Should give 01234
ObjId m4 = shell->doAddMsg( "Diagonal",
ObjId( d1, 0 ), "output", ObjId( d2, 0 ), "arg1" );
assert( !m4.bad() );
// Should give 54321
ObjId m5 = shell->doAddMsg( "Sparse",
ObjId( e1, 0 ), "output", ObjId( e2, 0 ), "arg1" );
assert( !m5.bad() );
ret = SetGet3< unsigned int, unsigned int, unsigned int >::set(
m5, "setEntry", 0, 4, 0 );
assert( ret );
ret = SetGet3< unsigned int, unsigned int, unsigned int >::set(
m5, "setEntry", 1, 3, 0 );
assert( ret );
ret = SetGet3< unsigned int, unsigned int, unsigned int >::set(
m5, "setEntry", 2, 2, 0 );
assert( ret );
ret = SetGet3< unsigned int, unsigned int, unsigned int >::set(
m5, "setEntry", 3, 1, 0 );
assert( ret );
ret = SetGet3< unsigned int, unsigned int, unsigned int >::set(
m5, "setEntry", 4, 0, 0 );
assert( ret );
assert( ret );
///////////////////////////////////////////////////////////
// Test traversal
///////////////////////////////////////////////////////////
// Single
ObjId f = Msg::getMsg( m1 )->findOtherEnd( ObjId( a1, 3 ) );
assert( f == ObjId( a2, 1 ) );
f = Msg::getMsg( m1 )->findOtherEnd( ObjId( a2, 1 ) );
assert( f == ObjId( a1, 3 ) );
f = Msg::getMsg( m1 )->findOtherEnd( ObjId( a1, 0 ) );
assert( f.bad() );
f = Msg::getMsg( m1 )->findOtherEnd( ObjId( a2, 0 ) );
assert( f.bad() );
f = Msg::getMsg( m1 )->findOtherEnd( ObjId( b2, 1 ) );
assert( f.bad() );
// OneToAll
f = Msg::getMsg( m2 )->findOtherEnd( ObjId( b1, 2 ) );
assert( f == ObjId( b2, 0 ) );
f = Msg::getMsg( m2 )->findOtherEnd( ObjId( b2, 0 ) );
assert( f == ObjId( b1, 2 ) );
f = Msg::getMsg( m2 )->findOtherEnd( ObjId( b2, 1 ) );
assert( f == ObjId( b1, 2 ) );
f = Msg::getMsg( m2 )->findOtherEnd( ObjId( b2, 2 ) );
assert( f == ObjId( b1, 2 ) );
f = Msg::getMsg( m2 )->findOtherEnd( ObjId( b2, 3 ) );
assert( f == ObjId( b1, 2 ) );
f = Msg::getMsg( m2 )->findOtherEnd( ObjId( b2, 4 ) );
assert( f == ObjId( b1, 2 ) );
f = Msg::getMsg( m2 )->findOtherEnd( ObjId( b1, 0 ) );
assert( f.bad() );
f = Msg::getMsg( m2 )->findOtherEnd( ObjId( a2, 1 ) );
assert( f.bad() );
// OneToOne
for ( unsigned int i = 0; i < 5; ++i ) {
f = Msg::getMsg( m3 )->findOtherEnd( ObjId( c1, i ) );
assert( f == ObjId( c2, i ) );
f = Msg::getMsg( m3 )->findOtherEnd( ObjId( c2, i ) );
assert( f == ObjId( c1, i ) );
}
f = Msg::getMsg( m3 )->findOtherEnd( ObjId( a2, 1 ) );
assert( f.bad() );
// Diagonal
for ( unsigned int i = 0; i < 4; ++i ) {
f = Msg::getMsg( m4 )->findOtherEnd( ObjId( d1, i ) );
assert( f == ObjId( d2, i + 1 ) );
f = Msg::getMsg( m4 )->findOtherEnd( ObjId( d2, i + 1 ) );
assert( f == ObjId( d1, i ) );
}
f = Msg::getMsg( m4 )->findOtherEnd( ObjId( d1, 4 ) );
assert( f.bad() );
f = Msg::getMsg( m4 )->findOtherEnd( ObjId( d2, 0 ) );
assert( f.bad() );
f = Msg::getMsg( m4 )->findOtherEnd( ObjId( a2, 1 ) );
assert( f.bad() );
// Sparse
for ( unsigned int i = 0; i < 5; ++i ) {
f = Msg::getMsg( m5 )->findOtherEnd( ObjId( e1, i ) );
assert( f == ObjId( e2, 4 - i ) );
f = Msg::getMsg( m5 )->findOtherEnd( ObjId( e2, i ) );
assert( f == ObjId( e1, 4 - i ) );
}
f = Msg::getMsg( m5 )->findOtherEnd( ObjId( a2, 1 ) );
assert( f.bad() );
cout << "." << flush;
///////////////////////////////////////////////////////////
// Check lookup by funcId.
///////////////////////////////////////////////////////////
const Finfo* aFinfo = Arith::initCinfo()->findFinfo( "arg1" );
FuncId afid = dynamic_cast< const DestFinfo* >( aFinfo )->getFid();
ObjId m = a2.element()->findCaller( afid );
assert ( m == m1 );
m = b2.element()->findCaller( afid );
assert ( m == m2 );
m = c2.element()->findCaller( afid );
assert ( m == m3 );
m = d2.element()->findCaller( afid );
assert ( m == m4 );
m = e2.element()->findCaller( afid );
assert ( m == m5 );
///////////////////////////////////////////////////////////
// Clean up.
///////////////////////////////////////////////////////////
shell->doDelete( pa );
cout << "." << flush;
}
// Reported as a bug by Subha 22 Feb 2012.
void testMsgElementListing()
{
Eref sheller = Id().eref();
Shell* shell = reinterpret_cast< Shell* >( sheller.data() );
unsigned int numData = 1;
Id pa = shell->doCreate( "Neutral", Id(), "pa", numData );
numData = 5;
///////////////////////////////////////////////////////////
// Set up the objects.
///////////////////////////////////////////////////////////
Id a1 = shell->doCreate( "Arith", pa, "a1", numData );
Id a2 = shell->doCreate( "Arith", pa, "a2", numData );
Id b1 = shell->doCreate( "Arith", pa, "b1", numData );
Id b2 = shell->doCreate( "Arith", pa, "b2", numData );
Id c1 = shell->doCreate( "Arith", pa, "c1", numData );
Id c2 = shell->doCreate( "Arith", pa, "c2", numData );
Id d1 = shell->doCreate( "Arith", pa, "d1", numData );
Id d2 = shell->doCreate( "Arith", pa, "d2", numData );
Id e1 = shell->doCreate( "Arith", pa, "e1", numData );
Id e2 = shell->doCreate( "Arith", pa, "e2", numData );
///////////////////////////////////////////////////////////
// Set up messaging
///////////////////////////////////////////////////////////
ObjId m1 = shell->doAddMsg( "Single",
ObjId( a1, 3 ), "output", ObjId( a2, 1 ), "arg1" );
assert( !m1.bad() );
ObjId m2 = shell->doAddMsg( "OneToAll",
ObjId( b1, 2 ), "output", ObjId( b2, 0 ), "arg1" );
assert( !m2.bad() );
ObjId m3 = shell->doAddMsg( "OneToOne",
ObjId( c1, 0 ), "output", ObjId( c2, 0 ), "arg1" );
assert( !m3.bad() );
ObjId m4 = shell->doAddMsg( "Diagonal",
ObjId( d1, 0 ), "output", ObjId( d2, 0 ), "arg1" );
assert( !m4.bad() );
ObjId m5 = shell->doAddMsg( "Sparse",
ObjId( e1, 0 ), "output", ObjId( e2, 0 ), "arg1" );
assert( !m5.bad() );
///////////////////////////////////////////////////////////
// List messages
///////////////////////////////////////////////////////////
Id manager( "/Msgs" );
assert( manager != Id() );
vector< Id > children =
Field< vector< Id > >::get( manager, "children" );
assert( children.size() == 5 );
assert( children[0].element()->getName() == "singleMsg" );
assert( children[1].element()->getName() == "oneToOneMsg" );
assert( children[2].element()->getName() == "oneToAllMsg" );
assert( children[3].element()->getName() == "diagonalMsg" );
assert( children[4].element()->getName() == "sparseMsg" );
/*
// A remarkably large number of some message classes, including 645
// OneToAll which are used by parent-child messages. I thought they
// were cleaned out as the tests proceed.
for ( unsigned int i = 0; i < children.size(); ++i ) {
cout << "\nlocalEntries[" << i << "] = " <<
children[i].element()->dataHandler()->localEntries() << endl;
}
*/
/*
string path = children[0].path();
cout << "\nlocalEntries = " <<
children[0].element()->dataHandler()->localEntries() << endl;
assert( path == "/Msgs/singleMsg[0]" );
*/
assert( children[0].path() == "/Msgs[0]/singleMsg" );
assert( children[1].path() == "/Msgs[0]/oneToOneMsg" );
assert( children[2].path() == "/Msgs[0]/oneToAllMsg" );
assert( children[3].path() == "/Msgs[0]/diagonalMsg" );
assert( children[4].path() == "/Msgs[0]/sparseMsg" );
///////////////////////////////////////////////////////////
// Next: check that the child messages have the appropriate number
// and indices of entries.
///////////////////////////////////////////////////////////
shell->doDelete( pa );
cout << "." << flush;
}
void testBuildStoich()
{
// Matrix looks like:
// Reac Name R1 R2 e1a e1b e2
// MolName
// D -1 0 0 0 0
// A -1 0 0 0 0
// B +1 -2 0 0 0
// C 0 +1 -1 0 0
// enz1 0 0 -1 +1 0
// e1cplx 0 0 +1 -1 0
// E 0 0 0 +1 -1
// F 0 0 0 0 +1
// enz2 0 0 0 0 0
// tot1 0 0 0 0 0
//
// This has been shuffled to:
// A -1 0 0 0 0
// B +1 -2 0 0 0
// C 0 +1 -1 0 0
// E 0 0 0 +1 -1
// F 0 0 0 0 +1
// enz1 0 0 -1 +1 0
// enz2 0 0 0 0 0
// e1cplx 0 0 +1 -1 0
// D -1 0 0 0 0
// tot1 0 0 0 0 0
//
// But the reacs have also been reordered:
// Reac Name e1a e1b e2 R1 R2
// A 0 0 0 -1 0
// B 0 0 0 1 -2
// C -1 0 0 0 1
// E 0 1 -1 0 0
// F 0 0 1 0 0
// enz1 -1 1 0 0 0
// enz2 0 0 0 0 0
// e1cplx 1 -1 0 0 0
// D 0 0 0 -1 0
// tot1 0 0 0 0 0
//
// (This is the output of the print command on the sparse matrix.)
//
Shell* s = reinterpret_cast< Shell* >( Id().eref().data() );
Id kin = makeReacTest();
Id ksolve = s->doCreate( "Ksolve", kin, "ksolve", 1 );
Id stoich = s->doCreate( "Stoich", ksolve, "stoich", 1 );
Field< Id >::set( stoich, "compartment", kin );
Field< Id >::set( stoich, "ksolve", ksolve );
// Used to get at the stoich matrix from gdb.
// Stoich* stoichPtr = reinterpret_cast< Stoich* >( stoich.eref().data() );
Field< string >::set( stoich, "path", "/kinetics/##" );
unsigned int n = Field< unsigned int >::get( stoich, "numAllPools" );
assert( n == 10 );
unsigned int r = Field< unsigned int >::get( stoich, "numRates" );
assert( r == 5 ); // One each for reacs and MMenz, two for Enz.
vector< int > entries = 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" );
assert( rowStart.size() == n + 1 );
assert( entries.size() == colIndex.size() );
assert( entries.size() == 13 );
assert( entries[0] == -1 );
assert( entries[1] == 1 );
assert( entries[2] == -2 );
assert( entries[3] == -1 );
assert( entries[4] == 1 );
assert( entries[5] == 1 );
assert( entries[6] == -1 );
assert( entries[7] == 1 );
assert( entries[8] == -1 );
assert( entries[9] == 1 );
assert( entries[10] == 1 );
assert( entries[11] == -1 );
assert( entries[12] == -1 );
s->doDelete( kin );
cout << "." << flush;
}
void testHSolvePassive()
{
// TEST_BEGIN;
Shell* shell = reinterpret_cast< Shell* >( Id().eref().data() );
vector< int* > childArray;
vector< unsigned int > childArraySize;
/**
* We test passive-cable solver for the following cell:
*
* Soma---> 15 - 14 - 13 - 12
* | |
* | L 11 - 10
* |
* L 16 - 17 - 18 - 19
* |
* L 9 - 8 - 7 - 6 - 5
* | |
* | L 4 - 3
* |
* L 2 - 1 - 0
*
* The numbers are the hines indices of compartments. Compartment X is the
* child of compartment Y if X is one level further away from the soma (#15)
* than Y. So #17 is the parent of #'s 2, 9 and 18.
*/
int childArray_1[ ] =
{
/* c0 */ -1,
/* c1 */ -1, 0,
/* c2 */ -1, 1,
/* c3 */ -1,
/* c4 */ -1, 3,
/* c5 */ -1,
/* c6 */ -1, 5,
/* c7 */ -1, 4, 6,
/* c8 */ -1, 7,
/* c9 */ -1, 8,
/* c10 */ -1,
/* c11 */ -1, 10,
/* c12 */ -1,
/* c13 */ -1, 12,
/* c14 */ -1, 11, 13,
/* c15 */ -1, 14, 16,
/* c16 */ -1, 17,
/* c17 */ -1, 2, 9, 18,
/* c18 */ -1, 19,
/* c19 */ -1,
};
childArray.push_back( childArray_1 );
childArraySize.push_back( sizeof( childArray_1 ) / sizeof( int ) );
/**
* Cell 2:
*
* 3
* |
* Soma---> 2
* / \
* / \
* 1 0
*
*/
int childArray_2[ ] =
{
/* c0 */ -1,
/* c1 */ -1,
/* c2 */ -1, 0, 1, 3,
/* c3 */ -1,
};
childArray.push_back( childArray_2 );
childArraySize.push_back( sizeof( childArray_2 ) / sizeof( int ) );
/**
* Cell 3:
*
* 3
* |
* 2
* / \
* / \
* 1 0 <--- Soma
*
*/
int childArray_3[ ] =
{
/* c0 */ -1, 2,
/* c1 */ -1,
/* c2 */ -1, 1, 3,
/* c3 */ -1,
};
childArray.push_back( childArray_3 );
childArraySize.push_back( sizeof( childArray_3 ) / sizeof( int ) );
/**
* Cell 4:
*
* 3 <--- Soma
* |
* 2
* / \
* / \
* 1 0
*
*/
int childArray_4[ ] =
{
/* c0 */ -1,
/* c1 */ -1,
/* c2 */ -1, 0, 1,
/* c3 */ -1, 2,
};
childArray.push_back( childArray_4 );
childArraySize.push_back( sizeof( childArray_4 ) / sizeof( int ) );
/**
* Cell 5:
*
* 1 <--- Soma
* |
* 2
* / \
* 4 0
* / \
* 3 5
*
*/
int childArray_5[ ] =
{
/* c0 */ -1,
/* c1 */ -1, 2,
/* c2 */ -1, 0, 4,
/* c3 */ -1,
/* c4 */ -1, 3, 5,
/* c5 */ -1,
};
childArray.push_back( childArray_5 );
childArraySize.push_back( sizeof( childArray_5 ) / sizeof( int ) );
/**
* Cell 6:
*
* 3 <--- Soma
* L 4
* L 6
* L 5
* L 2
* L 1
* L 0
*
*/
int childArray_6[ ] =
{
/* c0 */ -1,
/* c1 */ -1,
/* c2 */ -1,
/* c3 */ -1, 4,
/* c4 */ -1, 0, 1, 2, 5, 6,
/* c5 */ -1,
/* c6 */ -1,
};
childArray.push_back( childArray_6 );
childArraySize.push_back( sizeof( childArray_6 ) / sizeof( int ) );
/**
* Cell 7: Single compartment
*/
int childArray_7[ ] =
{
/* c0 */ -1,
};
childArray.push_back( childArray_7 );
childArraySize.push_back( sizeof( childArray_7 ) / sizeof( int ) );
/**
* Cell 8: 3 compartments; soma is in the middle.
*/
int childArray_8[ ] =
{
/* c0 */ -1,
/* c1 */ -1, 0, 2,
/* c2 */ -1,
};
childArray.push_back( childArray_8 );
childArraySize.push_back( sizeof( childArray_8 ) / sizeof( int ) );
/**
* Cell 9: 3 compartments; first compartment is soma.
*/
int childArray_9[ ] =
{
/* c0 */ -1, 1,
/* c1 */ -1, 2,
/* c2 */ -1,
};
childArray.push_back( childArray_9 );
childArraySize.push_back( sizeof( childArray_9 ) / sizeof( int ) );
////////////////////////////////////////////////////////////////////////////
// Run tests
////////////////////////////////////////////////////////////////////////////
/*
* Solver instance.
*/
HSolvePassive HP;
/*
* This is the full reference matrix which will be compared to its sparse
* implementation.
*/
vector< vector< double > > matrix;
/*
* Model details.
*/
double dt = 1.0;
vector< TreeNodeStruct > tree;
vector< double > Em;
vector< double > B;
vector< double > V;
vector< double > VMid;
/*
* Loop over cells.
*/
int i;
int j;
//~ bool success;
int nCompt;
int* array;
unsigned int arraySize;
for ( unsigned int cell = 0; cell < childArray.size(); cell++ )
{
array = childArray[ cell ];
arraySize = childArraySize[ cell ];
nCompt = count( array, array + arraySize, -1 );
//////////////////////////////////////////
// Prepare local information on cell
//////////////////////////////////////////
tree.clear();
tree.resize( nCompt );
Em.clear();
V.clear();
for ( i = 0; i < nCompt; i++ )
{
tree[ i ].Ra = 15.0 + 3.0 * i;
tree[ i ].Rm = 45.0 + 15.0 * i;
tree[ i ].Cm = 500.0 + 200.0 * i * i;
Em.push_back( -0.06 );
V.push_back( -0.06 + 0.01 * i );
}
int count = -1;
for ( unsigned int a = 0; a < arraySize; a++ )
if ( array[ a ] == -1 )
count++;
else
tree[ count ].children.push_back( array[ a ] );
//////////////////////////////////////////
// Create cell inside moose; setup solver.
//////////////////////////////////////////
Id n = shell->doCreate( "Neutral", Id(), "n", 1 );
vector< Id > c( nCompt );
for ( i = 0; i < nCompt; i++ )
{
ostringstream name;
name << "c" << i;
c[ i ] = shell->doCreate( "Compartment", n, name.str() , 1);
Field< double >::set( c[ i ], "Ra", tree[ i ].Ra );
Field< double >::set( c[ i ], "Rm", tree[ i ].Rm );
Field< double >::set( c[ i ], "Cm", tree[ i ].Cm );
Field< double >::set( c[ i ], "Em", Em[ i ] );
Field< double >::set( c[ i ], "initVm", V[ i ] );
Field< double >::set( c[ i ], "Vm", V[ i ] );
}
for ( i = 0; i < nCompt; i++ )
{
vector< unsigned int >& child = tree[ i ].children;
for ( j = 0; j < ( int )( child.size() ); j++ )
{
ObjId mid = shell->doAddMsg(
"Single", c[ i ], "axial", c[ child[ j ] ], "raxial" );
ASSERT( ! mid.bad(), "Creating test model" );
}
}
HP.setup( c[ 0 ], dt );
/*
* Here we check if the cell was read in correctly by the solver.
* This test only checks if all the created compartments were read in.
* It doesn't check if they have been assigned hines' indices correctly.
*/
vector< Id >& hc = HP.compartmentId_;
ASSERT( ( int )( hc.size() ) == nCompt, "Tree traversal" );
for ( i = 0; i < nCompt; i++ )
ASSERT(
find( hc.begin(), hc.end(), c[ i ] ) != hc.end(), "Tree traversal"
);
//////////////////////////////////////////
// Setup local matrix
//////////////////////////////////////////
/*
* First we need to ensure that the hines' indices for the local model
* and those inside the solver match. If the numbering is different,
* then the matrices will not agree.
*
* In the following, we find out the indices assigned by the solver,
* and impose them on the local data structures.
*/
// Figure out new indices
vector< unsigned int > permutation( nCompt );
for ( i = 0; i < nCompt; i++ )
{
unsigned int newIndex =
find( hc.begin(), hc.end(), c[ i ] ) - hc.begin();
permutation[ i ] = newIndex;
}
// Shuffle compartment properties according to new order
permute< TreeNodeStruct >( tree, permutation );
permute< double >( Em, permutation );
permute< double >( V, permutation );
// Update indices of children
for ( i = 0; i < nCompt; i++ )
{
vector< unsigned int >& child = tree[ i ].children;
for ( j = 0; j < ( int )( child.size() ); j++ )
child[ j ] = permutation[ child[ j ] ];
}
// Create local reference matrix
makeFullMatrix( tree, dt, matrix );
VMid.resize( nCompt );
B.resize( nCompt );
vector< vector< double > > matrixCopy;
matrixCopy.assign( matrix.begin(), matrix.end() );
//////////////////////////////////////////
// Run comparisons
//////////////////////////////////////////
double tolerance;
/*
* Compare initial matrices
*/
tolerance = 2.0;
for ( i = 0; i < nCompt; ++i )
for ( j = 0; j < nCompt; ++j )
{
ostringstream error;
error << "Testing matrix construction:"
<< " Cell# " << cell + 1
<< " A(" << i << ", " << j << ")";
ASSERT (
isClose< double >( HP.getA( i, j ), matrix[ i ][ j ], tolerance ),
error.str()
);
}
/*
*
* Gaussian elimination
*
*/
tolerance = 4.0; // ratio to machine epsilon
for ( int pass = 0; pass < 2; pass++ )
{
/*
* First update terms in the equation. This involves setting up the B
* in Ax = B, using the latest voltage values. Also, the coefficients
* stored in A have to be restored to their original values, since
* the matrix is modified at the end of every pass of gaussian
* elimination.
*/
// Do so in the solver..
HP.updateMatrix();
// ..locally..
matrix.assign( matrixCopy.begin(), matrixCopy.end() );
for ( i = 0; i < nCompt; i++ )
B[ i ] =
V[ i ] * tree[ i ].Cm / ( dt / 2.0 ) +
Em[ i ] / tree[ i ].Rm;
// ..and compare B.
for ( i = 0; i < nCompt; ++i )
{
ostringstream error;
error << "Updating right-hand side values:"
<< " Pass " << pass
<< " Cell# " << cell + 1
<< " B(" << i << ")";
ASSERT (
isClose< double >( HP.getB( i ), B[ i ], tolerance ),
error.str()
);
}
/*
* Forward elimination..
*/
// ..in solver..
HP.forwardEliminate();
// ..and locally..
int k;
for ( i = 0; i < nCompt - 1; i++ )
for ( j = i + 1; j < nCompt; j++ )
{
double div = matrix[ j ][ i ] / matrix[ i ][ i ];
for ( k = 0; k < nCompt; k++ )
matrix[ j ][ k ] -= div * matrix[ i ][ k ];
B[ j ] -= div * B[ i ];
}
// ..then compare A..
for ( i = 0; i < nCompt; ++i )
for ( j = 0; j < nCompt; ++j )
{
ostringstream error;
error << "Forward elimination:"
<< " Pass " << pass
<< " Cell# " << cell + 1
<< " A(" << i << ", " << j << ")";
ASSERT (
isClose< double >( HP.getA( i, j ), matrix[ i ][ j ], tolerance ),
error.str()
);
}
// ..and also B.
for ( i = 0; i < nCompt; ++i )
{
ostringstream error;
error << "Forward elimination:"
<< " Pass " << pass
<< " Cell# " << cell + 1
<< " B(" << i << ")";
ASSERT (
isClose< double >( HP.getB( i ), B[ i ], tolerance ),
error.str()
);
}
/*
* Backward substitution..
*/
// ..in solver..
HP.backwardSubstitute();
// ..and full back-sub on local matrix equation..
for ( i = nCompt - 1; i >= 0; i-- )
{
VMid[ i ] = B[ i ];
for ( j = nCompt - 1; j > i; j-- )
VMid[ i ] -= VMid[ j ] * matrix[ i ][ j ];
VMid[ i ] /= matrix[ i ][ i ];
V[ i ] = 2 * VMid[ i ] - V[ i ];
}
// ..and then compare VMid.
for ( i = nCompt - 1; i >= 0; i-- )
{
ostringstream error;
error << "Back substitution:"
<< " Pass " << pass
<< " Cell# " << cell + 1
<< " VMid(" << i << ")";
ASSERT (
isClose< double >( HP.getVMid( i ), VMid[ i ], tolerance ),
error.str()
);
}
for ( i = nCompt - 1; i >= 0; i-- )
{
ostringstream error;
error << "Back substitution:"
<< " Pass " << pass
<< " Cell# " << cell + 1
<< " V(" << i << ")";
ASSERT (
isClose< double >( HP.getV( i ), V[ i ], tolerance ),
error.str()
);
}
}
// cleanup
shell->doDelete( n );
}
// TEST_END;
}
/**
* In all cases we set up the same amount of data transfer by the msgs, that
* is, equivalent to a fully recurrently connected network.
* Used in regressionTests/benchmarkTests.cpp
*/
void benchmarkMsg( unsigned int n, string msgType )
{
Eref sheller = Id().eref();
Shell* shell = reinterpret_cast< Shell* >( sheller.data() );
vector< double > init( n );
for ( unsigned int i = 0; i < n; ++i )
init[i] = (i + 1) * 1e6;
Id a1 = shell->doCreate( "Arith", Id(), "a1", n );
if ( msgType == "Single" ) {
for ( unsigned int i = 0; i < n; ++i ) {
for ( unsigned int j = 0; j < n; ++j ) {
ObjId m1 = shell->doAddMsg( "Single",
ObjId( a1, i ), "output", ObjId( a1, j ), "arg3" );
assert( !m1.bad() );
}
}
} else if ( msgType == "OneToAll" ) {
for ( unsigned int i = 0; i < n; ++i ) {
ObjId m1 = shell->doAddMsg( "OneToAll",
ObjId( a1, i ), "output", ObjId( a1, 0 ), "arg3" );
assert( !m1.bad() );
}
} else if ( msgType == "OneToOne" ) {
for ( unsigned int i = 0; i < n; ++i ) { // just repeat it n times
ObjId m1 = shell->doAddMsg( "OneToOne",
ObjId( a1, 0 ), "output", ObjId( a1, 0 ), "arg3" );
assert( !m1.bad() );
}
} else if ( msgType == "Diagonal" ) {
for ( unsigned int i = 0; i < 2 * n; ++i ) { // Set up all offsets
ObjId m1 = shell->doAddMsg( "Diagonal",
ObjId( a1, 0 ), "output", ObjId( a1, 0 ), "arg3" );
Field< int >::set( m1, "stride", n - i );
}
} else if ( msgType == "Sparse" ) {
ObjId m1 = shell->doAddMsg( "Sparse",
ObjId( a1, 0 ), "output", ObjId( a1, 0 ), "arg3" );
SetGet2< double, long >::set( m1,
"setRandomConnectivity", 1.0, 1234 );
}
shell->doUseClock( "/a1", "proc", 0 );
for ( unsigned int i = 0; i < 10; ++i )
shell->doSetClock( i, 0 );
shell->doSetClock( 0, 1 );
shell->doReinit();
SetGet1< double >::setVec( a1, "arg1", init );
shell->doStart( 100 );
for ( unsigned int i = 0; i < n; ++i )
init[i] = 0; // be sure we don't retain old info.
init.clear();
Field< double >::getVec( a1, "outputValue", init );
cout << endl;
for ( unsigned int i = 0; i < n; ++i ) {
cout << i << " " << init[i] << " ";
if ( i % 5 == 4 )
cout << endl;
}
shell->doDelete( a1 );
}
void testCellDiffn()
{
Id makeCompt( Id parentCompt, Id parentObj,
string name, double len, double dia, double theta );
Shell* s = reinterpret_cast< Shell* >( Id().eref().data() );
double len = 40e-6;
double dia = 10e-6;
double diffLength = 1e-6;
double dt = 1.0e-1;
double runtime = 100.0;
double diffConst = 1.0e-12;
Id model = s->doCreate( "Neutral", Id(), "model", 1 );
Id soma = makeCompt( Id(), model, "soma", dia, dia, 90 );
Id dend = makeCompt( soma, model, "dend", len, 3e-6, 0 );
Id branch1 = makeCompt( dend, model, "branch1", len, 2e-6, 45.0 );
Id branch2 = makeCompt( dend, model, "branch2", len, 2e-6, -45.0 );
Id twig1 = makeCompt( branch1, model, "twig1", len, 1.5e-6, 90.0 );
Id twig2 = makeCompt( branch1, model, "twig2", len, 1.5e-6, 0.0 );
Id nm = s->doCreate( "NeuroMesh", model, "neuromesh", 1 );
Field< double >::set( nm, "diffLength", diffLength );
Field< string >::set( nm, "geometryPolicy", "cylinder" );
Field< Id >::set( nm, "cell", model );
unsigned int ns = Field< unsigned int >::get( nm, "numSegments" );
assert( ns == 6 );
unsigned int ndc = Field< unsigned int >::get( nm, "numDiffCompts" );
assert( ndc == 210 );
Id pool1 = s->doCreate( "Pool", nm, "pool1", 1 );
Field< double >::set( pool1, "diffConst", diffConst );
Id pool2 = s->doCreate( "Pool", nm, "pool2", 1 );
Field< double >::set( pool2, "diffConst", diffConst );
Id dsolve = s->doCreate( "Dsolve", model, "dsolve", 1 );
Field< Id >::set( dsolve, "compartment", nm );
s->doUseClock( "/model/dsolve", "process", 1 );
s->doSetClock( 1, dt );
// Next: build by setting path
Field< string >::set( dsolve, "path", "/model/neuromesh/pool#" );
vector< double > nvec =
LookupField< unsigned int, vector< double > >::get(
dsolve, "nVec", 0);
assert( nvec.size() == ndc );
assert( pool1.element()->numData() == ndc );
Field< double >::set( ObjId( pool1, 0 ), "nInit", 1.0 );
Field< double >::set( ObjId( pool2, ndc - 1 ), "nInit", 2.0 );
s->doReinit();
s->doStart( runtime );
nvec = LookupField< unsigned int, vector< double > >::get(
dsolve, "nVec", 0);
vector< double > pool1Vec;
Field< double >::getVec( pool1, "n", pool1Vec );
assert( pool1Vec.size() == ndc );
vector< double > pool2Vec;
Field< double >::getVec( pool2, "n", pool2Vec );
assert( pool2Vec.size() == ndc );
double myTot1 = 0;
double myTot2 = 0;
for ( unsigned int i = 0; i < nvec.size(); ++i ) {
assert( doubleEq( pool1Vec[i], nvec[i] ) );
myTot1 += nvec[i];
myTot2 += pool2Vec[i];
}
assert( doubleEq( myTot1, 1.0 ) );
assert( doubleEq( myTot2, 2.0 ) );
/*
cout << endl;
cout << "Big cell: " << endl;
for ( unsigned int i = 0; i < nvec.size(); ++i )
cout << nvec[i] << ", " << pool2Vec[i] << endl;
cout << endl;
*/
s->doDelete( model );
cout << "." << flush;
}
void testCompartmentProcess()
{
Shell* shell = reinterpret_cast< Shell* >( Id().eref().data() );
unsigned int size = 100;
double Rm = 1.0;
double Ra = 0.01;
double Cm = 1.0;
double dt = 0.01;
double runtime = 10;
double lambda = sqrt( Rm / Ra );
Id cid = shell->doCreate( "Compartment", Id(), "compt", size );
assert( Id::isValid(cid));
assert( cid.eref().element()->numData() == size );
bool ret = Field< double >::setRepeat( cid, "initVm", 0.0 );
assert( ret );
Field< double >::setRepeat( cid, "inject", 0 );
// Only apply current injection in first compartment
Field< double >::set( ObjId( cid, 0 ), "inject", 1.0 );
Field< double >::setRepeat( cid, "Rm", Rm );
Field< double >::setRepeat( cid, "Ra", Ra );
Field< double >::setRepeat( cid, "Cm", Cm );
Field< double >::setRepeat( cid, "Em", 0 );
Field< double >::setRepeat( cid, "Vm", 0 );
// The diagonal message has a default stride of 1, so it connects
// successive compartments.
// Note that the src and dest elements here are identical, so we cannot
// use a shared message. The messaging system will get confused about
// direction to send data. So we split up the shared message that we
// might have used, below, into two individual messages.
// MsgId mid = shell->doAddMsg( "Diagonal", ObjId( cid ), "raxial", ObjId( cid ), "axial" );
ObjId mid = shell->doAddMsg( "Diagonal", ObjId( cid ), "axialOut", ObjId( cid ), "handleAxial" );
assert( !mid.bad());
// mid = shell->doAddMsg( "Diagonal", ObjId( cid ), "handleRaxial", ObjId( cid ), "raxialOut" );
mid = shell->doAddMsg( "Diagonal", ObjId( cid ), "raxialOut", ObjId( cid ), "handleRaxial" );
assert( !mid.bad() );
// ObjId managerId = Msg::getMsg( mid )->manager().objId();
// Make the raxial data go from high to lower index compartments.
Field< int >::set( mid, "stride", -1 );
#ifdef DO_SPATIAL_TESTS
shell->doSetClock( 0, dt );
shell->doSetClock( 1, dt );
// Ensure that the inter_compt msgs go between nodes once every dt.
shell->doSetClock( 9, dt );
shell->doUseClock( "/compt", "init", 0 );
shell->doUseClock( "/compt", "process", 1 );
shell->doReinit();
shell->doStart( runtime );
double Vmax = Field< double >::get( ObjId( cid, 0 ), "Vm" );
double delta = 0.0;
// We measure only the first 50 compartments as later we
// run into end effects because it is not an infinite cable
for ( unsigned int i = 0; i < size; i++ ) {
double Vm = Field< double >::get( ObjId( cid, i ), "Vm" );
double x = Vmax * exp( - static_cast< double >( i ) / lambda );
delta += ( Vm - x ) * ( Vm - x );
// cout << i << " (x, Vm) = ( " << x << ", " << Vm << " )\n";
}
assert( delta < 1.0e-5 );
#endif // DO_SPATIAL_TESTS
shell->doDelete( cid );
cout << "." << flush;
}
void testCalcJunction()
{
Shell* s = reinterpret_cast< Shell* >( Id().eref().data() );
// Make a neuron with same-size dend and spine. PSD is tiny.
// Put a, b, c in dend, b, c, d in spine, c, d, f in psd. No reacs.
// See settling of all concs by diffusion, pairwise.
Id model = s->doCreate( "Neutral", Id(), "model", 1 );
Id dend = s->doCreate( "Compartment", model, "dend", 1 );
Id neck = s->doCreate( "Compartment", model, "spine_neck", 1 );
Id head = s->doCreate( "Compartment", model, "spine_head", 1 );
Field< double >::set( dend, "x", 10e-6 );
Field< double >::set( dend, "diameter", 2e-6 );
Field< double >::set( dend, "length", 10e-6 );
Field< double >::set( neck, "x0", 9e-6 );
Field< double >::set( neck, "x", 9e-6 );
Field< double >::set( neck, "y", 1e-6 );
Field< double >::set( neck, "diameter", 0.5e-6 );
Field< double >::set( neck, "length", 1.0e-6 );
Field< double >::set( head, "x0", 9e-6 );
Field< double >::set( head, "x", 9e-6 );
Field< double >::set( head, "y0", 1e-6 );
Field< double >::set( head, "y", 11e-6 );
Field< double >::set( head, "diameter", 2e-6 );
Field< double >::set( head, "length", 10e-6 );
s->doAddMsg( "Single", ObjId( dend ), "raxial", ObjId( neck ), "axial");
s->doAddMsg( "Single", ObjId( neck ), "raxial", ObjId( head ), "axial");
Id nm = s->doCreate( "NeuroMesh", model, "nm", 1 );
Field< double >::set( nm, "diffLength", 10e-6 );
Field< bool >::set( nm, "separateSpines", true );
Id sm = s->doCreate( "SpineMesh", model, "sm", 1 );
Id pm = s->doCreate( "PsdMesh", model, "pm", 1 );
ObjId mid = s->doAddMsg( "Single", ObjId( nm ), "spineListOut", ObjId( sm ), "spineList" );
assert( !mid.bad() );
mid = s->doAddMsg( "Single", ObjId( nm ), "psdListOut", ObjId( pm ), "psdList" );
Field< Id >::set( nm, "cell", model );
vector< Id > pools( 9 );
static string names[] = {"a", "b", "c", "b", "c", "d", "c", "d", "e" };
static Id parents[] = {nm, nm, nm, sm, sm, sm, pm, pm, pm};
for ( unsigned int i = 0; i < 9; ++i ) {
pools[i] = s->doCreate( "Pool", parents[i], names[i], 1 );
assert( pools[i] != Id() );
Field< double >::set( pools[i], "concInit", 1.0 + 1.0 * i );
Field< double >::set( pools[i], "diffConst", 1e-11 );
if ( i < 6 ) {
double vol = Field< double >::get( pools[i], "volume" );
assert( doubleEq( vol, 10e-6 * 1e-12 * PI ) );
}
}
Id dendsolve = s->doCreate( "Dsolve", model, "dendsolve", 1 );
Id spinesolve = s->doCreate( "Dsolve", model, "spinesolve", 1 );
Id psdsolve = s->doCreate( "Dsolve", model, "psdsolve", 1 );
Field< Id >::set( dendsolve, "compartment", nm );
Field< Id >::set( spinesolve, "compartment", sm );
Field< Id >::set( psdsolve, "compartment", pm );
Field< string >::set( dendsolve, "path", "/model/nm/#" );
Field< string >::set( spinesolve, "path", "/model/sm/#" );
Field< string >::set( psdsolve, "path", "/model/pm/#" );
assert( Field< unsigned int >::get( dendsolve, "numAllVoxels" ) == 1 );
assert( Field< unsigned int >::get( spinesolve, "numAllVoxels" ) == 1 );
assert( Field< unsigned int >::get( psdsolve, "numAllVoxels" ) == 1 );
assert( Field< unsigned int >::get( dendsolve, "numPools" ) == 3 );
assert( Field< unsigned int >::get( spinesolve, "numPools" ) == 3 );
assert( Field< unsigned int >::get( psdsolve, "numPools" ) == 3 );
SetGet2< Id, Id >::set( dendsolve, "buildNeuroMeshJunctions",
spinesolve, psdsolve );
s->doSetClock( 0, 0.01 );
s->doUseClock( "/model/#solve", "process", 0 );
s->doReinit();
s->doStart( 100 );
for ( unsigned int i = 0; i < 9; ++i ) {
double c = Field< double >::get( pools[i], "conc" );
double n = Field< double >::get( pools[i], "n" );
double v = Field< double >::get( pools[i], "volume" );
cout << pools[i].path() << ": " << c << ", " << n << ", " <<
n / v << ", " <<
v << endl;
}
s->doDelete( model );
cout << "." << flush;
}
/* create MOLECULE */
const SbmlReader::sbmlStr_mooseId SbmlReader::createMolecule( map< string,Id > &comptSidMIdMap) {
Shell* shell = reinterpret_cast< Shell* >( Id().eref().data() );
map< string, Id >molSidcmptMIdMap;
double transvalue = 0.0;
int num_species = model_->getNumSpecies();
if (num_species == 0) {
baseId = Id();
errorFlag_ = true;
return molSidcmptMIdMap;
}
for ( int sindex = 0; sindex < num_species; sindex++ ) {
Species* spe = model_->getSpecies(sindex);
if (!spe) {
continue;
}
std::string compt = "";
if ( spe->isSetCompartment() ) {
compt = spe->getCompartment();
}
if (compt.length()< 1) {
//cout << "compt is empty for species "<< sindex << endl;
continue;
}
string id = spe->getId();
if (id.length() < 1) {
continue;
}
std::string name = "";
if ( spe->isSetName() ) {
name = spe->getName();
name = nameString(name);
}
if (name.empty())
name = id;
double initvalue =0.0;
if ( spe->isSetInitialConcentration() )
initvalue = spe->getInitialConcentration();
else if ( spe->isSetInitialAmount() )
initvalue = spe->getInitialAmount() ;
else {
unsigned int nr = model_->getNumRules();
bool found = false;
for ( unsigned int r = 0; r < nr; r++ ) {
Rule * rule = model_->getRule(r);
bool assignRule = rule->isAssignment();
if ( assignRule ) {
string rule_variable = rule->getVariable();
if (rule_variable.compare(id) == 0) {
found = true;
break;
}
}
}
if (found == false) {
cout << "Invalid SBML: Either initialConcentration or initialAmount must be set or it should be found in assignmentRule but non happening for " << spe->getName() <<endl;
return molSidcmptMIdMap;
}
}
Id comptEl = comptSidMIdMap[compt];
Id meshEntry = Neutral::child( comptEl.eref(), "mesh" );
bool constant = spe->getConstant();
bool boundaryCondition = spe->getBoundaryCondition();
if (boundaryCondition == true)
cout << "Pools having BoundaryCondition true " << name <<endl;
Id pool;
//If constant is true then its equivalent to BuffPool in moose
if (constant == true)
//if( (boundaryCondition == true) && (constant==false))
pool = shell->doCreate("BufPool",comptEl,name,1);
else
pool = shell->doCreate("Pool", comptEl, name ,1);
molSidcmptMIdMap[id] = comptEl;
//Map to Molecule SBML id to Moose Id
molSidMIdMap_[id] = pool;
//shell->doAddMsg( "OneToOne",pool, "mesh", meshEntry, "mesh" );
bool bcondition = spe->getBoundaryCondition();
if ( constant == true && bcondition == false)
cout <<"The species "<< name << " should not appear in reactant or product as per sbml Rules"<< endl;
unsigned int spatialDimen =Field< unsigned int >::get( comptEl, "numDimensions");
UnitDefinition * ud = spe->getDerivedUnitDefinition();
assert(ud != NULL);
bool hasonlySubUnit = spe->getHasOnlySubstanceUnits();
//double v = Field< double >::get( comptEl.path(), "volume" );
transvalue = transformUnits(1,ud,"substance",hasonlySubUnit);
if (hasonlySubUnit) {
// In Moose, no. of molecules (nInit) and unit is "item"
if (spatialDimen > 0 && spe->isSetInitialAmount() ) {
//transvalue *= initvalue;
initvalue *=transvalue;
Field < double> :: set( pool, "nInit", initvalue);
}
} else {
//transvalue *=initvalue;
initvalue *=transvalue;
Field <double> :: set(pool, "concInit",initvalue);
}
//cout << " poolMap_ "<< name << " " <<transvalue << " "<< hasonlySubUnit;
//poolMap_.insert(make_pair(id,make_tuple(name,transvalue,hasonlySubUnit)));
}
return molSidcmptMIdMap;
}
