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;
}
int main( int argc, char** argv )
{
bool doUnitTests = 0;
bool doRegressionTests = 0;
unsigned int benchmark = 0;
// This reorders the OpFunc to Fid mapping to ensure it is node and
// compiler independent.
Id shellId = init( argc, argv, doUnitTests, doRegressionTests, benchmark );
// Note that the main loop remains the parser loop, though it may
// spawn a lot of other stuff.
Element* shelle = shellId.element();
Shell* s = reinterpret_cast< Shell* >( shelle->data( 0 ) );
if ( doUnitTests )
nonMpiTests( s ); // These tests do not need the process loop.
if ( Shell::myNode() == 0 ) {
if ( Shell::numNodes() > 1 ) {
// Use the last clock for the postmaster, so that it is called
// after everything else has been processed and all messages
// are ready to send out.
s->doUseClock( "/postmaster", "process", 9 );
s->doSetClock( 9, 1.0 ); // Use a sensible default.
}
#ifdef DO_UNIT_TESTS
if ( doUnitTests ) {
mpiTests();
processTests( s );
}
// if ( doRegressionTests ) regressionTests();
#endif
// These are outside unit tests because they happen in optimized
// mode, using a command-line argument. As soon as they are done
// the system quits, in order to estimate timing.
if ( benchmark != 0 ) {
mooseBenchmarks( benchmark );
s->doQuit();
} else {
// Here we set off a little event loop to poll user input.
// It deals with the doQuit call too.
if(! quitFlag)
Shell::launchParser();
}
} else {
PostMaster* p = reinterpret_cast< PostMaster* >( ObjId( 3 ).data());
while ( Shell::keepLooping() ) {
p->clearPending();
}
}
Msg::clearAllMsgs();
Id::clearAllElements();
#ifdef USE_MPI
MPI_Finalize();
#endif
return 0;
}
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;
}
/**
* The readcell function implements the old GENESIS cellreader
* functionality. Although it is really a parser operation, I
* put it here in Kinetics because the cell format is independent
* of parser and is likely to remain a legacy for a while.
*/
Id ReadKkit::read(
const string& filename,
const string& modelname,
Id pa, const string& methodArg )
{
string method = methodArg;
ifstream fin( filename.c_str() );
if (!fin){
cerr << "ReadKkit::read: could not open file " << filename << endl;
return Id();
}
if ( method.substr(0, 4) == "old_" ) {
moveOntoCompartment_ = false;
method = method.substr( 4 );
}
Shell* s = reinterpret_cast< Shell* >( ObjId().data() );
Id mgr = makeStandardElements( pa, modelname );
assert( mgr != Id() );
baseId_ = mgr;
basePath_ = mgr.path();
enzCplxMols_.resize( 0 );
innerRead( fin );
assignPoolCompartments();
assignReacCompartments();
assignEnzCompartments();
assignMMenzCompartments();
convertParametersToConcUnits();
s->doSetClock( 8, plotdt_ );
string plotpath = basePath_ + "/graphs/##[TYPE=Table]," +
basePath_ + "/moregraphs/##[TYPE=Table]";
s->doUseClock( plotpath, "process", 8 );
setMethod( s, mgr, simdt_, plotdt_, method );
s->doReinit();
return mgr;
}
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;
}
/**
* 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 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;
}
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 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;
}
/**
* 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 );
}
/**
* @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;
}
