void writeSpatialSBML()
{
// SBMLNamespaces of SBML Level 3 Version 1 with 'req' Version 1
// then add 'spatial' package namespace.
SpatialPkgNamespaces sbmlns(3,1,1);
// create the L3V1 document with spatial package
SBMLDocument document(&sbmlns);
// set 'required' attribute on document for 'spatial' and 'req' packages to 'T'??
SBMLDocumentPlugin* dplugin;
dplugin = static_cast<SBMLDocumentPlugin*>(document.getPlugin("spatial"));
dplugin->setRequired(true);
// create the Model
Model *model = document.createModel();
model-> setId("trial_spatial");
model-> setName("trial_spatial");
// create the Compartments
Compartment* compartment = model->createCompartment();
compartment->setId("cytosol");
compartment->setConstant(true);
// create the Species
Species* species1 = model->createSpecies();
species1->setId("ATPc");
species1->setCompartment("cytosol");
species1->setInitialConcentration(1.0);
species1->setHasOnlySubstanceUnits(false);
species1->setBoundaryCondition(false);
species1->setConstant(false);
// spatial package extension to species.
SpatialSpeciesPlugin* srplugin;
srplugin = static_cast<SpatialSpeciesPlugin*>(species1->getPlugin("spatial"));
srplugin->setIsSpatial(true);
// add parameter for diff coeff of species1
Parameter* paramSp = model->createParameter();
paramSp->setId(species1->getId()+"_dc");
paramSp->setValue(1.0);
// spatial package extension to parameter.
SpatialParameterPlugin* pplugin;
pplugin = static_cast<SpatialParameterPlugin*>(paramSp->getPlugin("spatial"));
DiffusionCoefficient* diffCoeff = pplugin->createDiffusionCoefficient();
diffCoeff->setVariable(species1->getId());
diffCoeff->setType(SPATIAL_DIFFUSIONKIND_ANISOTROPIC);
CoordinateReference* coordRef = diffCoeff->createCoordinateReference();
coordRef->setCoordinate(SPATIAL_COORDINATEKIND_CARTESIAN_X);
// add parameter for adv coeff of species1
paramSp = model->createParameter();
paramSp->setId(species1->getId()+"_ac");
paramSp->setValue(1.5);
// spatial package extension to parameter.
pplugin = static_cast<SpatialParameterPlugin*>(paramSp->getPlugin("spatial"));
AdvectionCoefficient* advCoeff = pplugin->createAdvectionCoefficient();
advCoeff->setVariable(species1->getId());
advCoeff->setCoordinate(SPATIAL_COORDINATEKIND_CARTESIAN_X);
// add parameter for boundary condition of species1
paramSp = model->createParameter();
paramSp->setId(species1->getId()+"_bc");
paramSp->setValue(2.0);
// spatial package extension to parameter.
pplugin = static_cast<SpatialParameterPlugin*>(paramSp->getPlugin("spatial"));
BoundaryCondition* boundCon = pplugin->createBoundaryCondition();
boundCon->setVariable(species1->getId());
boundCon->setType(SPATIAL_BOUNDARYKIND_DIRICHLET);
boundCon->setCoordinateBoundary("Xmin");
Species* species2 = model->createSpecies();
species2->setId("ADPc");
species2->setCompartment("cytosol");
species2->setInitialConcentration(1);
species2->setHasOnlySubstanceUnits(false);
species2->setBoundaryCondition(false);
species2->setConstant(false);
srplugin = static_cast<SpatialSpeciesPlugin*>(species2->getPlugin("spatial"));
srplugin->setIsSpatial(true);
Reaction* reaction = model->createReaction();
reaction->setId("rxn1");
reaction->setReversible(false);
reaction->setFast(false);
reaction->setCompartment("cytosol");
SpatialReactionPlugin* rplugin = static_cast<SpatialReactionPlugin*>(reaction->getPlugin("spatial"));
rplugin->setIsLocal(true);
//
// Get a SpatialModelPlugin object plugged in the model object.
//
// The type of the returned value of SBase::getPlugin() function is
// SBasePlugin*, and thus the value needs to be casted for the
// corresponding derived class.
//
SpatialModelPlugin* mplugin;
mplugin = static_cast<SpatialModelPlugin*>(model->getPlugin("spatial"));
//
// Creates a geometry object via SpatialModelPlugin object.
//
Geometry* geometry = mplugin->createGeometry();
geometry->setCoordinateSystem(SPATIAL_GEOMETRYKIND_CARTESIAN);
CoordinateComponent* coordX = geometry->createCoordinateComponent();
coordX->setId("coordComp1");
coordX->setType(SPATIAL_COORDINATEKIND_CARTESIAN_X);
coordX->setUnit("umeter");
Boundary* minX = coordX->createBoundaryMin();
minX->setId("Xmin");
minX->setValue(0.0);
Boundary* maxX = coordX->createBoundaryMax();
maxX->setId("Xmax");
maxX->setValue(10.0);
Parameter* paramX = model->createParameter();
paramX->setId("x");
paramX->setValue(8.0);
// spatial package extension to parameter.
// SpatialParameterPlugin* pplugin;
pplugin = static_cast<SpatialParameterPlugin*>(paramX->getPlugin("spatial"));
SpatialSymbolReference* spSymRef = pplugin->createSpatialSymbolReference();
spSymRef->setSpatialRef(coordX->getId());
DomainType* domainType = geometry->createDomainType();
domainType->setId("dtype1");
domainType->setSpatialDimension(3);
// Spatial package extension to compartment (mapping compartment with domainType)
SpatialCompartmentPlugin* cplugin;
cplugin = static_cast<SpatialCompartmentPlugin*>(compartment->getPlugin("spatial"));
CompartmentMapping* compMapping = cplugin->createCompartmentMapping();
compMapping->setId("compMap1");
compMapping->setDomainType(domainType->getId());
compMapping->setUnitSize(1.0);
Domain* domain = geometry->createDomain();
domain->setId("domain1");
domain->setDomainType("dtype1");
InteriorPoint* internalPt1 = domain->createInteriorPoint();
internalPt1->setCoord1(1.0);
domain = geometry->createDomain();
domain->setId("domain2");
domain->setDomainType("dtype1");
InteriorPoint* internalPt2 = domain->createInteriorPoint();
internalPt2->setCoord1(5.0);
AdjacentDomains* adjDomain = geometry->createAdjacentDomains();
adjDomain->setId("adjDomain1");
adjDomain->setDomain1("domain1");
adjDomain->setDomain2("domain2");
AnalyticGeometry* analyticGeom = geometry->createAnalyticGeometry();
analyticGeom->setId("analyticGeom1");
AnalyticVolume* analyticVol = analyticGeom->createAnalyticVolume();
analyticVol->setId("analyticVol1");
analyticVol->setDomainType(domainType->getId());
analyticVol->setFunctionType(SPATIAL_FUNCTIONKIND_LAYERED);
analyticVol->setOrdinal(1);
const char* mathMLStr = "<math xmlns=\"http://www.w3.org/1998/Math/MathML\"><apply xmlns=\"\"><plus /><apply><times /><ci>x</ci><ci>x</ci></apply><apply><minus /><cn>1.0</cn></apply></apply></math>";
ASTNode* mathNode = readMathMLFromString(mathMLStr);
analyticVol->setMath(mathNode);
SampledFieldGeometry* sfg = geometry->createSampledFieldGeometry();
sfg->setId("sampledFieldGeom1");
SampledField* sampledField = sfg->createSampledField();
sampledField->setId("sampledField1");
sampledField->setNumSamples1(4);
sampledField->setNumSamples2(4);
sampledField->setNumSamples3(2);
sampledField->setDataType("double");
sampledField->setInterpolationType("linear");
sampledField->setEncoding("encoding1");
//int samples[5] = {1, 2, 3, 4, 5};
int samples[32] = {
// z=0
0,0,0,0,
0,1,1,0,
0,1,1,0,
0,0,0,0,
// z=1
0,0,0,0,
0,1,1,0,
0,1,1,0,
0,0,0,0
};
ImageData* id = sampledField->createImageData();
id->setDataType("uint8");
id->setSamples(samples, 32);
SampledVolume* sampledVol = sfg->createSampledVolume();
sampledVol->setId("sv_1");
sampledVol->setDomainType(domainType->getId());
sampledVol->setSampledValue(128.0);
sampledVol->setMinValue(0.0);
sampledVol->setMaxValue(255.0);
writeSBML(&document, "spatial_example2.xml");
}
