int Ng_GetSolidList (ClientData clientData,
Tcl_Interp * interp,
int argc, tcl_const char *argv[])
{
CSGeometry * geometry = dynamic_cast<CSGeometry*> (ng_geometry.get());
if (!geometry)
{
Tcl_SetResult (interp, err_needscsgeometry, TCL_STATIC);
return TCL_ERROR;
}
tcl_const char * valuevar = argv[1];
int i;
stringstream vst;
for (i = 1; i <= geometry->GetNSolids(); i++)
{
const Solid * sol = geometry->GetSolid(i);
if (!sol->GetPrimitive())
vst << sol->Name() << " ";
}
cout << "solnames = " << vst.str() << endl;
Tcl_SetVar (interp, valuevar, (char*)vst.str().c_str(), 0);
return TCL_OK;
}
int Ng_SetPrimitiveData (ClientData clientData,
Tcl_Interp * interp,
int argc, tcl_const char *argv[])
{
CSGeometry * geometry = dynamic_cast<CSGeometry*> (ng_geometry.get());
if (!geometry)
{
Tcl_SetResult (interp, err_needscsgeometry, TCL_STATIC);
return TCL_ERROR;
}
tcl_const char * name = argv[1];
tcl_const char * value = argv[2];
Array<double> coeffs;
cout << "Set primitive data, name = " << name
<< ", value = " << value << endl;
istringstream vst (value);
double val;
while (!vst.eof())
{
vst >> val;
coeffs.Append (val);
}
((Primitive*)
geometry->GetSolid (name)->GetPrimitive())->SetPrimitiveData (coeffs);
return TCL_OK;
}
int Ng_GetSolidData (ClientData clientData,
Tcl_Interp * interp,
int argc, tcl_const char *argv[])
{
CSGeometry * geometry = dynamic_cast<CSGeometry*> (ng_geometry.Ptr());
if (!geometry)
{
Tcl_SetResult (interp, err_needscsgeometry, TCL_STATIC);
return TCL_ERROR;
}
tcl_const char * name = argv[1];
tcl_const char * valuevar = argv[2];
ostringstream vst;
const Solid * sol = geometry->GetSolid (name);
sol->GetSolidData (vst);
cout << "GetSolidData, name = " << name << ", data = " << vst.str() << endl;
Tcl_SetVar (interp, valuevar, (char*)vst.str().c_str(), 0);
return TCL_OK;
}
int Ng_SetSolidData (ClientData clientData,
Tcl_Interp * interp,
int argc, tcl_const char *argv[])
{
CSGeometry * geometry = dynamic_cast<CSGeometry*> (ng_geometry.Ptr());
if (!geometry)
{
Tcl_SetResult (interp, err_needscsgeometry, TCL_STATIC);
return TCL_ERROR;
}
tcl_const char * name = argv[1];
tcl_const char * val = argv[2];
cout << "Set Solid Data, name = " << name
<< ", value = " << val << endl;
istringstream vst (val);
Solid * nsol = Solid::CreateSolid (vst, geometry->GetSolids());
geometry->SetSolid (name, nsol);
return TCL_OK;
}
int Ng_CreatePrimitive (ClientData clientData,
Tcl_Interp * interp,
int argc, tcl_const char *argv[])
{
CSGeometry * geometry = dynamic_cast<CSGeometry*> (ng_geometry.Ptr());
if (!geometry)
{
Tcl_SetResult (interp, err_needscsgeometry, TCL_STATIC);
return TCL_ERROR;
}
tcl_const char * classname = argv[1];
tcl_const char * name = argv[2];
cout << "Create primitive, class = " << classname
<< ", name = " << name << endl;
Primitive * nprim = Primitive::CreatePrimitive (classname);
Solid * nsol = new Solid (nprim);
char sname[100];
for (int j = 1; j <= nprim->GetNSurfaces(); j++)
{
sprintf (sname, "%s,%d", name, j);
geometry -> AddSurface (sname, &nprim->GetSurface(j));
nprim -> SetSurfaceId (j, geometry->GetNSurf());
}
geometry->SetSolid (name, nsol);
return TCL_OK;
}
CSGeometry* NGInterface::loadCSG(string data)
{
strstream in;
CSGeometry *geom;
Point<3> pmin(minX,minY,minZ),
pmax(maxX,maxY,maxZ);
Box<3> box(pmin,pmax);
in << data;
try
{
geom = ParseCSG(in);
}
catch(...)
{
cerr << "Problem in CSG-file!" << endl;
return NULL;
}
if (!geom)
{
cout << "geo-file should start with 'algebraic3d'" << endl;
return NULL;
}
else
geom->FindIdenticSurfaces(1e-8*geom->MaxSize());
geom->SetBoundingBox(box);
geom->CalcTriangleApproximation(detail,facets);
return (CSGeometry*)(geometry = geom);
}
int main()
{
std::ifstream geometry_file;
geometry_file.open("../data/half-trigate.geo");
CSGeometry * geom = ParseCSG( geometry_file );
geom->FindIdenticSurfaces(1e-8 * geom->MaxSize());
Mesh * netgen_mesh = new Mesh();
netgen::MeshingParameters mparams;
geom->GenerateMesh(netgen_mesh, mparams, 1, 5);
{
typedef viennagrid::tetrahedral_3d_mesh MeshType;
typedef viennagrid::tetrahedral_3d_segmentation SegmentationType;
MeshType mesh;
SegmentationType segmentation(mesh);
typedef viennagrid::result_of::point<MeshType>::type PointType;
typedef viennagrid::result_of::vertex_handle<MeshType>::type VertexHandleType;
typedef SegmentationType::segment_handle_type SegmentType;
int num_points = netgen_mesh->GetNP();
int num_tets = netgen_mesh->GetNE();
std::cout << "Num Points: " << num_points << std::endl;
std::cout << "Num Tets: " << num_tets << std::endl;
std::vector<VertexHandleType> vertex_handles( num_points );
for (int i = 1; i <= num_points; ++i)
{
PointType vgrid_point(netgen_mesh->Point(i)[0], netgen_mesh->Point(i)[1], netgen_mesh->Point(i)[2]);
vertex_handles[i-1] = viennagrid::make_vertex( mesh, vgrid_point );
}
for (int i = 0; i < num_tets; ++i)
{
ElementIndex ei = i;
SegmentType segment = segmentation.get_make_segment( (*netgen_mesh)[ei].GetIndex() );
viennagrid::make_tetrahedron( segment, vertex_handles[(*netgen_mesh)[ei][0]-1], vertex_handles[(*netgen_mesh)[ei][1]-1],
vertex_handles[(*netgen_mesh)[ei][2]-1], vertex_handles[(*netgen_mesh)[ei][3]-1]);
}
viennagrid::io::vtk_writer<MeshType, SegmentationType> writer;
writer(mesh, segmentation, "out");
}
}
int Ng_GeometryOptions (ClientData clientData,
Tcl_Interp * interp,
int argc, tcl_const char *argv[])
{
CSGeometry * geometry = dynamic_cast<CSGeometry*> (ng_geometry.get());
const char * command = argv[1];
if (strcmp (command, "get") == 0)
{
if (geometry)
{
char buf[20];
Point3d pmin = geometry->BoundingBox ().PMin();
Point3d pmax = geometry->BoundingBox ().PMax();
sprintf (buf, "%5.1lf", pmin.X());
Tcl_SetVar (interp, "::geooptions.minx", buf, 0);
sprintf (buf, "%5.1lf", pmin.Y());
Tcl_SetVar (interp, "::geooptions.miny", buf, 0);
sprintf (buf, "%5.1lf", pmin.Z());
Tcl_SetVar (interp, "::geooptions.minz", buf, 0);
sprintf (buf, "%5.1lf", pmax.X());
Tcl_SetVar (interp, "::geooptions.maxx", buf, 0);
sprintf (buf, "%5.1lf", pmax.Y());
Tcl_SetVar (interp, "::geooptions.maxy", buf, 0);
sprintf (buf, "%5.1lf", pmax.Z());
Tcl_SetVar (interp, "::geooptions.maxz", buf, 0);
}
}
else if (strcmp (command, "set") == 0)
{
Point<3> pmin (atof (Tcl_GetVar (interp, "::geooptions.minx", 0)),
atof (Tcl_GetVar (interp, "::geooptions.miny", 0)),
atof (Tcl_GetVar (interp, "::geooptions.minz", 0)));
Point<3> pmax (atof (Tcl_GetVar (interp, "::geooptions.maxx", 0)),
atof (Tcl_GetVar (interp, "::geooptions.maxy", 0)),
atof (Tcl_GetVar (interp, "::geooptions.maxz", 0)));
Box<3> box (pmin, pmax);
if (geometry)
geometry -> SetBoundingBox (box);
CSGeometry::SetDefaultBoundingBox (box);
}
return TCL_OK;
}
void SaveVolumeMesh (const Mesh & mesh,
const CSGeometry & geometry,
char * filename)
{
INDEX i;
ofstream outfile(filename);
outfile << "volumemesh" << endl;
outfile << mesh.GetNSE() << endl;
for (i = 1; i <= mesh.GetNSE(); i++)
{
if (mesh.SurfaceElement(i).GetIndex())
outfile << mesh.GetFaceDescriptor(mesh.SurfaceElement(i).GetIndex ()).SurfNr()
<< "\t";
else
outfile << "0" << "\t";
outfile << mesh.SurfaceElement(i)[0] << " "
<< mesh.SurfaceElement(i)[1] << " "
<< mesh.SurfaceElement(i)[2] << endl;
}
outfile << mesh.GetNE() << endl;
for (ElementIndex ei = 0; ei < mesh.GetNE(); ei++)
outfile << mesh[ei].GetIndex() << "\t"
<< mesh[ei][0] << " " << mesh[ei][1] << " "
<< mesh[ei][2] << " " << mesh[ei][3] << endl;
outfile << mesh.GetNP() << endl;
for (i = 1; i <= mesh.GetNP(); i++)
outfile << mesh.Point(i)(0) << " "
<< mesh.Point(i)(1) << " "
<< mesh.Point(i)(2) << endl;
#ifdef SOLIDGEOM
outfile << geometry.GetNSurf() << endl;
for (i = 1; i <= geometry.GetNSurf(); i++)
geometry.GetSurface(i) -> Print (outfile);
#endif
}
int Ng_GetPrimitiveData (ClientData clientData,
Tcl_Interp * interp,
int argc, tcl_const char *argv[])
{
CSGeometry * geometry = dynamic_cast<CSGeometry*> (ng_geometry.get());
if (!geometry)
{
Tcl_SetResult (interp, err_needscsgeometry, TCL_STATIC);
return TCL_ERROR;
}
tcl_const char * name = argv[1];
tcl_const char * classnamevar = argv[2];
tcl_const char * valuevar = argv[3];
const char * classname;
Array<double> coeffs;
geometry->GetSolid (name)->GetPrimitive()->GetPrimitiveData (classname, coeffs);
ostringstream vst;
for (int i = 1; i <= coeffs.Size(); i++)
vst << coeffs.Get(i) << " ";
cout << "GetPrimitiveData, name = " << name
<< ", classnamevar = " << classnamevar
<< ", classname = " << classname << endl
<< " valuevar = " << valuevar
<< ", values = " << vst.str() << endl;
Tcl_SetVar (interp, classnamevar, (char*)classname, 0);
Tcl_SetVar (interp, valuevar, (char*)vst.str().c_str(), 0);
return TCL_OK;
}
/*
* FEPP .. a finite element package developed at University Linz, Austria
*/
void WriteFEPPFormat (const Mesh & mesh,
const CSGeometry & geom,
const string & filename)
{
ofstream outfile (filename.c_str());
if (mesh.GetDimension() == 3)
{
// output for FEPP
int np = mesh.GetNP();
int ne = mesh.GetNE();
int nse = mesh.GetNSE();
int ns = mesh.GetNFD();
int i, j;
outfile.precision(5);
outfile.setf (ios::fixed, ios::floatfield);
outfile.setf (ios::showpoint);
outfile << "volumemesh4" << endl;
outfile << nse << endl;
for (i = 1; i <= nse; i++)
{
const Element2d & el = mesh.SurfaceElement(i);
// int facenr = mesh.facedecoding.Get(el.GetIndex()).surfnr;
outfile.width(4);
outfile << el.GetIndex() << " ";
outfile.width(4);
// outfile << mesh.GetFaceDescriptor(el.GetIndex()).BCProperty() << " ";
outfile << mesh.GetFaceDescriptor(el.GetIndex()).BCProperty() << " ";
outfile.width(4);
outfile << el.GetNP() << " ";
for (j = 1; j <= el.GetNP(); j++)
{
outfile.width(8);
outfile << el.PNum(j);
}
outfile << "\n";
}
outfile << ne << "\n";
for (i = 1; i <= ne; i++)
{
const Element & el = mesh.VolumeElement(i);
outfile.width(4);
outfile << el.GetIndex() << " ";
outfile.width(4);
outfile << el.GetNP() << " ";
for (j = 1; j <= el.GetNP(); j++)
{
outfile.width(8);
outfile << el.PNum(j);
}
outfile << "\n";
}
outfile << np << "\n";
for (i = 1; i <= np; i++)
{
const Point3d & p = mesh.Point(i);
outfile.width(10);
outfile << p.X() << " ";
outfile.width(9);
outfile << p.Y() << " ";
outfile.width(9);
outfile << p.Z() << "\n";
}
/*
if (typ == WRITE_FEPPML)
{
int nbn = mesh.mlbetweennodes.Size();
outfile << nbn << "\n";
for (i = 1; i <= nbn; i++)
outfile << mesh.mlbetweennodes.Get(i).I1() << " "
<< mesh.mlbetweennodes.Get(i).I2() << "\n";
// int ncon = mesh.connectedtonode.Size();
// outfile << ncon << "\n";
// for (i = 1; i <= ncon; i++)
// outfile << i << " " << mesh.connectedtonode.Get(i) << endl;
}
*/
// write CSG surfaces
if (&geom && geom.GetNSurf() >= ns)
{
outfile << ns << endl;
for (i = 1; i <= ns; i++)
geom.GetSurface(mesh.GetFaceDescriptor(i).SurfNr())->Print(outfile);
}
else
outfile << "0" << endl;
}
else
{ // 2D fepp format
;
/*
extern SplineGeometry2d * geometry2d;
if (geometry2d)
Save2DMesh (mesh, &geometry2d->GetSplines(), outfile);
else
Save2DMesh (mesh, 0, outfile);
*/
}
}
void readSpatialSBML() {
SBMLDocument *document2 = readSBML("spatial_example0.xml");
Model *model2 = document2->getModel();
Compartment *comp;
SpatialCompartmentPlugin* cplugin;
RequiredElementsSBasePlugin* reqplugin;
for (unsigned int i = 0; i < model2->getNumCompartments(); i++) {
comp = model2->getCompartment(i);
cout << "Compartment" << i << ": " << comp->getId() << endl;
reqplugin = static_cast<RequiredElementsSBasePlugin*>(comp->getPlugin("req"));
if (!reqplugin->getMathOverridden().empty()) {
cout << "Comp" << i << " req mathOverridden: " << reqplugin->getMathOverridden() << endl;
}
cplugin = static_cast<SpatialCompartmentPlugin*>(comp->getPlugin("spatial"));
if (cplugin->getCompartmentMapping()->isSetSpatialId()) {
cout << "Comp" << i << " CMSpId: " << cplugin->getCompartmentMapping()->getSpatialId() << endl;
cout << "Comp" << i << " CM_Comp: " << cplugin->getCompartmentMapping()->getCompartment() << endl;
cout << "Comp" << i << " CM_DType: " << cplugin->getCompartmentMapping()->getDomainType() << endl;
cout << "Comp" << i << " CM_UnitSz: " << cplugin->getCompartmentMapping()->getUnitSize() << endl;
}
}
Species *sp;
SpatialSpeciesRxnPlugin* srplugin;
for (unsigned int i = 0; i < model2->getNumSpecies(); i++) {
sp = model2->getSpecies(i);
cout << "Species" << i << ": " << sp->getId() << endl;
srplugin = static_cast<SpatialSpeciesRxnPlugin*>(sp->getPlugin("spatial"));
if (srplugin->getIsSpatial()) {
cout << "species" << i << " isSpatial: " << srplugin->getIsSpatial() << endl;
}
}
Parameter *param;
SpatialParameterPlugin* pplugin;
for (unsigned int i = 0; i < model2->getNumParameters(); i++) {
param = model2->getParameter(i);
cout << "Parameter" << i << ": " << param->getId() << endl;
reqplugin = static_cast<RequiredElementsSBasePlugin*>(param->getPlugin("req"));
if (!reqplugin->getMathOverridden().empty()) {
cout << "Parameter" << i << " req mathOverridden: " << reqplugin->getMathOverridden() << endl;
}
pplugin = static_cast<SpatialParameterPlugin*>(param->getPlugin("spatial"));
if (pplugin->getSpatialSymbolReference()->isSetSpatialId()) {
cout << "Parameter" << i << " SpRefId: " << pplugin->getSpatialSymbolReference()->getSpatialId() << endl;
cout << "Parameter" << i << " SpRefType: " << pplugin->getSpatialSymbolReference()->getType() << endl;
}
if (pplugin->getDiffusionCoefficient()->isSetVariable()) {
cout << "Diff_" << i << " SpeciesVarId: " << pplugin->getDiffusionCoefficient()->getVariable() << endl;
cout << "Diff_" << i << " SpCoordIndex: " << pplugin->getDiffusionCoefficient()->getCoordinateIndex() << endl;
}
if (pplugin->getAdvectionCoefficient()->isSetVariable()) {
cout << "Adv_" << i << " SpeciesVarId: " << pplugin->getAdvectionCoefficient()->getVariable() << endl;
cout << "Adv_" << i << " SpCoordIndex: " << pplugin->getAdvectionCoefficient()->getCoordinateIndex() << endl;
}
if (pplugin->getBoundaryCondition()->isSetVariable()) {
cout << "BC_" << i << " SpeciesVarId: " << pplugin->getBoundaryCondition()->getVariable() << endl;
cout << "BC_" << i << " SpCoordBoundary: " << pplugin->getBoundaryCondition()->getCoordinateBoundary() << endl;
cout << "BC_" << i << " SpBoundaryType: " << pplugin->getBoundaryCondition()->getType() << endl;
}
}
Reaction *rxn;
for (unsigned int i = 0; i < model2->getNumReactions(); i++) {
rxn = model2->getReaction(i);
cout << "Reaction" << i << ": " << rxn->getId() << endl;
srplugin = static_cast<SpatialSpeciesRxnPlugin*>(rxn->getPlugin("spatial"));
if (srplugin->getIsLocal()) {
cout << "rxn" << i << " isLocal: " << srplugin->getIsLocal() << endl;
}
}
Rule *rule;
for (unsigned int i = 0; i < model2->getNumRules(); i++) {
rule = model2->getRule(i);
cout << "Rule" << i << ": " << rule->getVariable() << endl;
}
//
// 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 cast for the
// corresponding derived class.
//
SpatialModelPlugin* mplugin2;
mplugin2 = static_cast<SpatialModelPlugin*>(model2->getPlugin("spatial"));
cout << "URI: " << mplugin2->getURI() << endl;
cout << "prefix: " << mplugin2->getPrefix() << endl;
// get a Geometry object via SpatialModelPlugin object.
Geometry* geometry2 = mplugin2->getGeometry();
cout << "Geometry coordSystem: " << geometry2->getCoordinateSystem() << endl;
// get a CoordComponent object via the Geometry object.
CoordinateComponent* coordComp = geometry2->getCoordinateComponent(0);
std::cout << "CoordComponent spatialId: " << coordComp->getSpatialId() << std::endl;
std::cout << "CoordComponent compType: " << coordComp->getComponentType() << std::endl;
std::cout << "CoordComponent sbmlUnit: " << coordComp->getSbmlUnit() << std::endl;
std::cout << "CoordComponent index: " << coordComp->getIndex() << std::endl;
BoundaryMin* minX = coordComp->getBoundaryMin();
std::cout << "minX name: " << minX->getSpatialId() << std::endl;
std::cout << "minX value: " << minX->getValue() << std::endl;
BoundaryMax* maxX = coordComp->getBoundaryMax();
std::cout << "maxX name: " << maxX->getSpatialId() << std::endl;
std::cout << "maxX value: " << maxX->getValue() << std::endl;
// get a DomainType object via the Geometry object.
DomainType* domainType2 = geometry2->getDomainType(0);
std::cout << "DomainType spatialId: " << domainType2->getSpatialId() << std::endl;
std::cout << "DomainType spatialDim: " << domainType2->getSpatialDimensions() << std::endl;
// get a Domain object via the Geometry object.
Domain* domain = geometry2->getDomain(0);
std::cout << "Domain1 spatialId: " << domain->getSpatialId() << std::endl;
std::cout << "Domain1 implicit: " << domain->getImplicit() << std::endl;
std::cout << "Domain1 domainType: " << domain->getDomainType() << std::endl;
std::cout << "Domain1 Shape: " << domain->getShapeId() << std::endl;
// get an internal point via the domain object
InteriorPoint* internalPt = domain->getInteriorPoint(0);
std::cout << "InternalPt_1 coord1: " << internalPt->getCoord1() << std::endl;
// get a Domain object via the Geometry object.
domain = geometry2->getDomain(1);
std::cout << "Domain2 spatialId: " << domain->getSpatialId() << std::endl;
std::cout << "Domain2 implicit: " << domain->getImplicit() << std::endl;
std::cout << "Domain2 domainType: " << domain->getDomainType() << std::endl;
std::cout << "Domain2 Shape: " << domain->getShapeId() << std::endl;
// get an internal point via the domain object
internalPt = domain->getInteriorPoint(0);
std::cout << "InternalPt_2 coord1: " << internalPt->getCoord1() << std::endl;
// get an AdjacentDomains object via the Geometry object.
AdjacentDomains* adjDomain = geometry2->getAdjacentDomains(0);
std::cout << "AdjDomain spatialId: " << adjDomain->getSpatialId() << std::endl;
std::cout << "AdjDomain domain1: " << adjDomain->getDomain1() << std::endl;
std::cout << "AdjDomain domain2: " << adjDomain->getDomain2() << std::endl;
// get the different GeometryDefinition objects via the Geometry object.
GeometryDefinition* gd;
for (unsigned int i = 0; i < geometry2->getNumGeometryDefinitions(); i++) {
gd = geometry2->getGeometryDefinition(i);
if (gd->isAnalyticGeometry()) {
AnalyticGeometry* analyticalGeom = static_cast<AnalyticGeometry*>(gd);
std::cout << "AnalGeom spatialId: " << analyticalGeom->getSpatialId() << std::endl;
// analVol from analGeom.
AnalyticVolume* av = analyticalGeom->getAnalyticVolume(0);
std::cout << "AnalVol spatialId: " << av->getSpatialId() << std::endl;
std::cout << "AnalVol domainType: " << av->getDomainType() << std::endl;
std::cout << "AnalVol funcType: " << av->getFunctionType() << std::endl;
std::cout << "AnalVol ordinal: " << av->getOrdinal() << std::endl;
const ASTNode* mathNode = av->getMath();
char* mathStr = writeMathMLToString(mathNode);
std::cout << "AnalVol math: " << mathStr << std::endl;
}
if (gd->isSampledFieldGeometry()) {
SampledFieldGeometry* sfGeom = static_cast<SampledFieldGeometry*>(gd);
std::cout << "SampledFieldGeom spatialId: " << sfGeom->getSpatialId() << std::endl;
// sampledField from sfGeom
SampledField* sf = sfGeom->getSampledField();
std::cout << "SampledField spatialId: " << sf->getSpatialId() << std::endl;
std::cout << "SampledField dataType: " << sf->getDataType() << std::endl;
std::cout << "SampledField interpolation: " << sf->getInterpolationType() << std::endl;
std::cout << "SampledField encoding: " << sf->getEncoding() << std::endl;
std::cout << "SampledField numSamples1: " << sf->getNumSamples1() << std::endl;
std::cout << "SampledField numSamples2: " << sf->getNumSamples2() << std::endl;
std::cout << "SampledField numSamples3: " << sf->getNumSamples3() << std::endl;
const ImageData* id = sf->getImageData();
int* samples = new int[id->getSamplesLength()];
id->getSamples(samples);
std::cout << "ImageData samples[0]: " << samples[0] << std::endl;
std::cout << "ImageData samplesLen: " << id->getSamplesLength() << std::endl;
std::cout << "ImageData dataType: " << id->getDataType() << std::endl;
// sampledVolVol from sfGeom.
SampledVolume* sv = sfGeom->getSampledVolume(0);
std::cout << "SampledVol spatialId: " << sv->getSpatialId() << std::endl;
std::cout << "SampledVol domainType: " << sv->getDomainType() << std::endl;
std::cout << "SampledVol sampledVal: " << sv->getSampledValue() << std::endl;
std::cout << "SampledVol min: " << sv->getMinValue() << std::endl;
std::cout << "SampledVol max: " << sv->getMaxValue() << std::endl;
}
if (gd->isParametricGeometry()) {
ParametricGeometry* pGeom = static_cast<ParametricGeometry*>(gd);
std::cout << "ParametricGeometry spatialId: " << pGeom->getSpatialId() << std::endl;
// parametricObject from pGeom
ParametricObject* pObj = pGeom->getParametricObject(0);
std::cout << "ParametricObj spatialId: " << pObj->getSpatialId() << std::endl;
std::cout << "ParametricObj domain: " << pObj->getDomain() << std::endl;
std::cout << "ParametricObj polygonType: " << pObj->getPolygonType() << std::endl;
const PolygonObject* po = pObj->getPolygonObject();
int* ptInd = new int[po->getIndicesLength()];
po->getPointIndices(ptInd);
std::cout << "PolygonObj ptIndices[0]: " << ptInd[0] << std::endl;
std::cout << "PolygonObj indLen: " << po->getIndicesLength() << std::endl;
// SpatialPoint from pGeom.
SpatialPoint* sp = pGeom->getSpatialPoint(0);
std::cout << "SpatialPt spatialId: " << sp->getSpatialId() << std::endl;
std::cout << "SpatialPt domain: " << sp->getDomain() << std::endl;
std::cout << "SpatialPt coord1: " << sp->getCoord1() << std::endl;
std::cout << "SpatialPt coord2: " << sp->getCoord2() << std::endl;
std::cout << "SpatialPt coord3: " << sp->getCoord3() << std::endl;
}
if (gd->isCSGeometry()) {
CSGeometry* csGeom = static_cast<CSGeometry*>(gd);
std::cout << "CSGeometry spatialId: " << csGeom->getSpatialId() << std::endl;
// CSGObject-CSGOperator from csGeom
CSGObject* csgo;
for (unsigned int i = 0; i < csGeom->getNumCSGObjects(); i++) {
csgo = csGeom->getCSGObject(i);
std::cout << "CSGObject spatialId: " << csgo->getSpatialId() << std::endl;
std::cout << "CSGObject domainType: " << csgo->getDomainType() << std::endl;
const CSGNode* csgnode = csgo->getCSGNodeRoot();
if (csgnode->isCSGTransformation()) {
CSGTransformation* transf = (CSGTransformation*)csgnode;
if (transf->isCSGScale()) {
CSGScale* scale = static_cast<CSGScale*>(transf);
std::cout << "CSGScale scaleX: " << scale->getScaleX() << std::endl;
std::cout << "CSGScale scaleY: " << scale->getScaleY() << std::endl;
std::cout << "CSGScale scaleZ: " << scale->getScaleZ() << std::endl;
const CSGNode* scaleChild = scale->getChild();
if (scaleChild->isCSGPrimitive()) {
CSGPrimitive* prim = (CSGPrimitive*)scaleChild;
std::cout << "CSGPrimitive primitiveType: " << prim->getPrimitiveType() << std::endl;
}
}
}
if (csgnode->isCSGSetOperator()) {
CSGSetOperator* setop = (CSGSetOperator*)(csgnode);
std::cout << "CSGSetOperator opType: " << setop->getOperationType() << std::endl;
for (unsigned int k = 0; k < setop->getNumCSGNodeChildren(); k++) {
CSGNode* csgNode = setop->getCSGNodeChild(k);
std::cout << "CSGNode type: " << csgNode->getTypeCode() << std::endl;
}
}
}
}
}
delete document2;
}
void writeSpatialSBML() {
/*
// SBMLNamespaces of SBML Level 3 Version 1 with Spatial Version 1
SBMLNamespaces sbmlns(3,1,"spatial",1);
// SpatialPkgNamespaces spatialns(3,1,1);
// add Required Elements package namespace
sbmlns.addPkgNamespace("req", 1);
*/
// SBMLNamespaces of SBML Level 3 Version 1 with 'req' Version 1
// then add 'spatial' package namespace.
RequiredElementsPkgNamespaces sbmlns(3,1,1);
sbmlns.addPkgNamespace("spatial",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);
dplugin = static_cast<SBMLDocumentPlugin*>(document.getPlugin("req"));
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.
// required elements package extention to parameter
RequiredElementsSBasePlugin* reqplugin;
reqplugin = static_cast<RequiredElementsSBasePlugin*>(species1->getPlugin("req"));
reqplugin->setMathOverridden("spatial");
reqplugin->setCoreHasAlternateMath(true);
SpatialSpeciesRxnPlugin* srplugin;
srplugin = static_cast<SpatialSpeciesRxnPlugin*>(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);
// required elements package extention to parameter
reqplugin = static_cast<RequiredElementsSBasePlugin*>(paramSp->getPlugin("req"));
reqplugin->setMathOverridden("spatial");
reqplugin->setCoreHasAlternateMath(true);
// spatial package extension to parameter.
SpatialParameterPlugin* pplugin;
pplugin = static_cast<SpatialParameterPlugin*>(paramSp->getPlugin("spatial"));
DiffusionCoefficient* diffCoeff = pplugin->getDiffusionCoefficient();
diffCoeff->setVariable(species1->getId());
diffCoeff->setCoordinateIndex(0);
// add parameter for adv coeff of species1
paramSp = model->createParameter();
paramSp->setId(species1->getId()+"_ac");
paramSp->setValue(1.5);
// required elements package extention to parameter
reqplugin = static_cast<RequiredElementsSBasePlugin*>(paramSp->getPlugin("req"));
reqplugin->setMathOverridden("spatial");
reqplugin->setCoreHasAlternateMath(true);
// spatial package extension to parameter.
pplugin = static_cast<SpatialParameterPlugin*>(paramSp->getPlugin("spatial"));
AdvectionCoefficient* advCoeff = pplugin->getAdvectionCoefficient();
advCoeff->setVariable(species1->getId());
advCoeff->setCoordinateIndex(0);
// add parameter for boundary condition of species1
paramSp = model->createParameter();
paramSp->setId(species1->getId()+"_bc");
paramSp->setValue(2.0);
// required elements package extention to parameter
reqplugin = static_cast<RequiredElementsSBasePlugin*>(paramSp->getPlugin("req"));
reqplugin->setMathOverridden("spatial");
reqplugin->setCoreHasAlternateMath(true);
// spatial package extension to parameter.
pplugin = static_cast<SpatialParameterPlugin*>(paramSp->getPlugin("spatial"));
BoundaryCondition* boundCon = pplugin->getBoundaryCondition();
boundCon->setVariable(species1->getId());
boundCon->setType("value");
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<SpatialSpeciesRxnPlugin*>(species2->getPlugin("spatial"));
srplugin->setIsSpatial(true);
/* // create a parameter
Parameter* param = model->createParameter();
param->setId("k_1");
param->setValue(0.24);
param->setConstant(true);
// create an assignment rule
AssignmentRule* assignRule = model->createAssignmentRule();
assignRule->setVariable(species1->getId());
assignRule->setFormula("species2+k_1");
*/
/*
reqplugin = static_cast<RequiredElementsSBasePlugin*>(assignRule->getPlugin("req"));
reqplugin->setMathOverridden("spatial");
reqplugin->setCoreHasAlternateMath(false);
*/
Reaction* reaction = model->createReaction();
reaction->setId("rxn1");
reaction->setReversible(false);
reaction->setFast(false);
reaction->setCompartment("cytosol");
srplugin = static_cast<SpatialSpeciesRxnPlugin*>(reaction->getPlugin("spatial"));
srplugin->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->getGeometry();
geometry->setCoordinateSystem("XYZ");
CoordinateComponent* coordX = geometry->createCoordinateComponent();
coordX->setSpatialId("coordComp1");
coordX->setComponentType("cartesian");
coordX->setSbmlUnit("umeter");
coordX->setIndex(1);
BoundaryMin* minX = coordX->createBoundaryMin();
minX->setSpatialId("Xmin");
minX->setValue(0.0);
BoundaryMax* maxX = coordX->createBoundaryMax();
maxX->setSpatialId("Xmax");
maxX->setValue(10.0);
Parameter* paramX = model->createParameter();
paramX->setId("x");
paramX->setValue(8.0);
// required elements package extention to parameter
// RequiredElementsSBasePlugin* reqplugin;
reqplugin = static_cast<RequiredElementsSBasePlugin*>(paramX->getPlugin("req"));
reqplugin->setMathOverridden("spatial");
reqplugin->setCoreHasAlternateMath(true);
// spatial package extension to parameter.
// SpatialParameterPlugin* pplugin;
pplugin = static_cast<SpatialParameterPlugin*>(paramX->getPlugin("spatial"));
SpatialSymbolReference* spSymRef = pplugin->getSpatialSymbolReference();
spSymRef->setSpatialId(coordX->getSpatialId());
spSymRef->setType(coordX->getElementName());
DomainType* domainType = geometry->createDomainType();
domainType->setSpatialId("dtype1");
domainType->setSpatialDimensions(3);
// Spatial package extension to compartment (mapping compartment with domainType)
// required elements package extention to compartment
reqplugin = static_cast<RequiredElementsSBasePlugin*>(compartment->getPlugin("req"));
reqplugin->setMathOverridden("spatial");
reqplugin->setCoreHasAlternateMath(true);
SpatialCompartmentPlugin* cplugin;
cplugin = static_cast<SpatialCompartmentPlugin*>(compartment->getPlugin("spatial"));
CompartmentMapping* compMapping = cplugin->getCompartmentMapping();
compMapping->setSpatialId("compMap1");
compMapping->setCompartment(compartment->getId());
compMapping->setDomainType(domainType->getSpatialId());
compMapping->setUnitSize(1.0);
Domain* domain = geometry->createDomain();
domain->setSpatialId("domain1");
domain->setDomainType("dtype1");
domain->setImplicit(false);
domain->setShapeId("circle");
InteriorPoint* internalPt1 = domain->createInteriorPoint();
internalPt1->setCoord1(1.0);
domain = geometry->createDomain();
domain->setSpatialId("domain2");
domain->setDomainType("dtype1");
domain->setImplicit(false);
domain->setShapeId("square");
InteriorPoint* internalPt2 = domain->createInteriorPoint();
internalPt2->setCoord1(5.0);
AdjacentDomains* adjDomain = geometry->createAdjacentDomains();
adjDomain->setSpatialId("adjDomain1");
adjDomain->setDomain1("domain1");
adjDomain->setDomain2("domain2");
AnalyticGeometry* analyticGeom = geometry->createAnalyticGeometry();
analyticGeom->setSpatialId("analyticGeom1");
AnalyticVolume* analyticVol = analyticGeom->createAnalyticVolume();
analyticVol->setSpatialId("analyticVol1");
analyticVol->setDomainType(domainType->getSpatialId());
analyticVol->setFunctionType("squareFn");
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->setSpatialId("sampledFieldGeom1");
SampledField* sampledField = sfg->createSampledField();
sampledField->setSpatialId("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("compressed");
id->setSamples(samples, 32);
SampledVolume* sampledVol = sfg->createSampledVolume();
sampledVol->setSpatialId("sv_1");
sampledVol->setDomainType(domainType->getSpatialId());
sampledVol->setSampledValue(128.0);
sampledVol->setMinValue(0.0);
sampledVol->setMaxValue(255.0);
ParametricGeometry* pg = geometry->createParametricGeometry();
pg->setSpatialId("parametricGeom1");
ParametricObject* paramObj = pg->createParametricObject();
paramObj->setSpatialId("po_1");
paramObj->setDomain(domain->getSpatialId());
paramObj->setPolygonType("hexagon");
int ptIndices[5] = {1, 2, 3, 4, 5};
PolygonObject* po = paramObj->createPolygonObject();
po->setPointIndices(ptIndices, 5);
SpatialPoint* spPt = pg->createSpatialPoint();
spPt->setSpatialId("sp_1");
spPt->setDomain(domain->getSpatialId());
spPt->setCoord1(1);
spPt->setCoord2(2);
spPt->setCoord3(3);
CSGeometry* csg = geometry->createCSGeometry();
csg->setSpatialId("csGeom1");
CSGObject* csgObj = csg->createCSGObject();
csgObj->setSpatialId("csg_csgo_1");
csgObj->setDomainType(domainType->getSpatialId());
csgObj->setOrdinal(1);
CSGScale* scale = csgObj->createCSGScale();
scale->setScaleX(2.0);
scale->setScaleY(3.0);
scale->setScaleZ(4.0);
CSGPrimitive* prim1 = scale->createCSGPrimitive();
prim1->setPrimitiveType("SOLID_SPHERE");
csgObj = csg->createCSGObject();
csgObj->setSpatialId("csg_csgo_2");
csgObj->setDomainType(domainType->getSpatialId());
CSGSetOperator* setUnion = csgObj->createCSGSetOperator();
setUnion->setOperationType("UNION");
/* CSGPrimitive* prim = setUnion->createCSGPrimitive();
prim->setPrimitiveType("SOLID_SPHERE");
CSGPrimitive* prim2 = setUnion->createCSGPrimitive();
prim2->setPrimitiveType("SOLID_CONE");
*/
CSGPrimitive* prim2 = new CSGPrimitive(3,1,1);
prim2->setSpatialId("cone0");
prim2->setPrimitiveType("SOLID_CONE");
CSGTranslation* translatedCone = new CSGTranslation(3,1,1);
translatedCone->setSpatialId("translation0");
translatedCone->setTranslateX(2.0);
translatedCone->setTranslateY(2.0);
translatedCone->setTranslateZ(2.0);
translatedCone->setChild(prim2);
int n = setUnion->addCSGNodeChild(translatedCone);
CSGPrimitive* prim3 = new CSGPrimitive(3,1,1);
prim3->setSpatialId("sphere0");
prim3->setPrimitiveType("SOLID_SPHERE");
n = setUnion->addCSGNodeChild(prim3);
writeSBML(&document, "spatial_example0.xml");
}
int Ng_TopLevel (ClientData clientData,
Tcl_Interp * interp,
int argc, tcl_const char *argv[])
{
CSGeometry * geometry = dynamic_cast<CSGeometry*> (ng_geometry.get());
if (!geometry)
{
Tcl_SetResult (interp, err_needscsgeometry, TCL_STATIC);
return TCL_ERROR;
}
int i;
/*
for (i = 0; i < argc; i++)
cout << argv[i] << ", ";
cout << endl;
*/
if (strcmp (argv[1], "getlist") == 0)
{
stringstream vst;
for (i = 0; i < geometry->GetNTopLevelObjects(); i++)
{
const Solid * sol;
const Surface * surf;
geometry->GetTopLevelObject (i, sol, surf);
if (!surf)
vst << "{ " << sol->Name() << " } ";
else
vst << "{ " << sol->Name() << " " << surf->Name() << " } ";
}
tcl_const char * valuevar = argv[2];
Tcl_SetVar (interp, valuevar, (char*)vst.str().c_str(), 0);
}
if (strcmp (argv[1], "set") == 0)
{
tcl_const char * solname = argv[2];
tcl_const char * surfname = argv[3];
Solid * sol = (Solid*)geometry->GetSolid (solname);
Surface * surf = (Surface*)geometry->GetSurface (surfname);
geometry->SetTopLevelObject (sol, surf);
}
if (strcmp (argv[1], "remove") == 0)
{
tcl_const char * solname = argv[2];
tcl_const char * surfname = argv[3];
Solid * sol = (Solid*)geometry->GetSolid (solname);
Surface * surf = (Surface*)geometry->GetSurface (surfname);
geometry->RemoveTopLevelObject (sol, surf);
}
if (strcmp (argv[1], "setprop") == 0)
{
tcl_const char * solname = argv[2];
tcl_const char * surfname = argv[3];
tcl_const char * propvar = argv[4];
Solid * sol = (Solid*)geometry->GetSolid (solname);
Surface * surf = (Surface*)geometry->GetSurface (surfname);
TopLevelObject * tlo = geometry->GetTopLevelObject (sol, surf);
if (!tlo) return TCL_OK;
char varname[50];
sprintf (varname, "%s(red)", propvar);
double red = atof (Tcl_GetVar (interp, varname, 0));
sprintf (varname, "%s(blue)", propvar);
double blue = atof (Tcl_GetVar (interp, varname, 0));
sprintf (varname, "%s(green)", propvar);
double green = atof (Tcl_GetVar (interp, varname, 0));
tlo -> SetRGB (red, green, blue);
sprintf (varname, "%s(visible)", propvar);
tlo -> SetVisible (bool(atoi (Tcl_GetVar (interp, varname, 0))));
sprintf (varname, "%s(transp)", propvar);
tlo -> SetTransparent (bool(atoi (Tcl_GetVar (interp, varname, 0))));
}
if (strcmp (argv[1], "getprop") == 0)
{
tcl_const char * solname = argv[2];
tcl_const char * surfname = argv[3];
tcl_const char * propvar = argv[4];
Solid * sol = (Solid*)geometry->GetSolid (solname);
Surface * surf = (Surface*)geometry->GetSurface (surfname);
TopLevelObject * tlo = geometry->GetTopLevelObject (sol, surf);
if (!tlo) return TCL_OK;
char varname[50], varval[10];
sprintf (varname, "%s(red)", propvar);
sprintf (varval, "%lf", tlo->GetRed());
Tcl_SetVar (interp, varname, varval, 0);
sprintf (varname, "%s(green)", propvar);
sprintf (varval, "%lf", tlo->GetGreen());
Tcl_SetVar (interp, varname, varval, 0);
sprintf (varname, "%s(blue)", propvar);
sprintf (varval, "%lf", tlo->GetBlue());
Tcl_SetVar (interp, varname, varval, 0);
sprintf (varname, "%s(visible)", propvar);
sprintf (varval, "%d", tlo->GetVisible());
Tcl_SetVar (interp, varname, varval, 0);
sprintf (varname, "%s(transp)", propvar);
sprintf (varval, "%d", tlo->GetTransparent());
Tcl_SetVar (interp, varname, varval, 0);
}
return TCL_OK;
}
void WriteTecPlotFormat (const Mesh & mesh,
const CSGeometry & geom,
const string & filename)
{
INDEX i;
int j, k, e, z;
Vec<3> n;
INDEX np = mesh.GetNP();
INDEX ne = mesh.GetNE();
INDEX nse = mesh.GetNSE();
ARRAY<int> sn(np);
ofstream outfile(filename.c_str());
outfile << "TITLE=\" " << filename << "\"" << endl;
// fill hashtable
INDEX_3_HASHTABLE<int> face2volelement(ne);
for (i = 1; i <= ne; i++)
{
const Element & el = mesh.VolumeElement(i);
INDEX_3 i3;
int l;
for (j = 1; j <= 4; j++) // loop over faces of tet
{
l = 0;
for (k = 1; k <= 4; k++)
if (k != j)
{
l++;
i3.I(l) = el.PNum(k);
}
i3.Sort();
face2volelement.Set (i3, i);
}
}
for (j = 1; j <= geom.GetNSurf(); j++) /* Flaeche Nummer j */
{
for (i = 1; i <= np; i++)
sn.Elem(i) = 0;
e = 0;
for (i = 1; i <= nse; i++)
{
const Element2d & el = mesh.SurfaceElement(i);
if (j == mesh.GetFaceDescriptor (el.GetIndex ()).SurfNr())
{
for (k = 1; k <= 3; k++)
sn.Elem(el.PNum(k)) = 1;
e++; /* e= Anzahl der neuen Elemente */
}
}
z = 0;
for (i = 1; i <= np; i++)
if (sn.Elem(i) == 1)
sn.Elem(i) = ++z;
outfile << "ZONE T=\" Surface " << j << " \", N=" << z
<< ", E=" << e << ", ET=TRIANGLE, F=FEPOINT" << endl;
for (i = 1; i <= np; i++)
if (sn.Elem(i) != 0)
{
n = geom.GetSurface(j) -> GetNormalVector ( mesh.Point(i) );
outfile << mesh.Point(i)(0) << " " /* Knoten Koordinaten */
<< mesh.Point(i)(1) << " "
<< mesh.Point(i)(2) << " "
<< n(0) << " "
<< n(1) << " "
<< n(2) << " "
<< i << endl;
}
for (i = 1; i <= nse; i++)
{
const Element2d & el = mesh.SurfaceElement(i);
if (j == mesh.GetFaceDescriptor(el.GetIndex ()).SurfNr())
/* FlaechenKnoten (3) */
outfile << sn.Get(el.PNum(1)) << " "
<< sn.Get(el.PNum(2)) << " "
<< sn.Get(el.PNum(3)) << endl;
/// Hier soll noch die Ausgabe der Nummer des angrenzenden
/// Vol.elements erfolgen !
for (k = 1; k <= nse; k++)
{
const Element2d & sel = mesh.SurfaceElement(k);
INDEX_3 i3;
for (j = 1; j <= 3; j++)
i3.I(j) = sel.PNum(j);
i3.Sort();
//int elind = face2volelement.Get(i3);
}
}
}
}
