private static Tuple <Model, IModelReader> CreateCancerTransportModel(double[] k, double[][] U, double[] TumcElement)
{
string filename = Path.Combine(Directory.GetCurrentDirectory(), "InputFiles", "TumorGrowthModel", "mesh.mphtxt");
var modelReader = new ComsolMeshReader2(filename, k, U, L);
Model model = modelReader.CreateModelFromFile();
var materials = new ConvectionDiffusionMaterial[] { new ConvectionDiffusionMaterial(k[0], U[0], L[0]), new ConvectionDiffusionMaterial(k[1], U[1], L[1]) };
if (TumcElement == null)
{
TumcElement = new double[model.Elements.Count];
for (int i = 0; i < model.Elements.Count; i++)
{
TumcElement[i] = 0.96;
}
}
double[] f = new double[model.Elements.Count];
int domainID = 1;
foreach (Element element in modelReader.elementDomains[domainID])
{
f[element.ID] = 1;
var nodes = (IReadOnlyList <Node>)element.Nodes;
var domainLoad = new ConvectionDiffusionDomainLoad(materials[domainID], f[element.ID], ThermalDof.Temperature);
var bodyLoadElementFactory = new BodyLoadElementFactory(domainLoad, model);
var bodyLoadElement = bodyLoadElementFactory.CreateElement(CellType.Tet4, nodes);
model.BodyLoads.Add(bodyLoadElement);
}
return(new Tuple <Model, IModelReader>(model, modelReader));
}
private static void RunTest()
{
Model model = CreateModel(1, new double[] { 2, 2, 2 }, 0).Item1;
ComsolMeshReader2 modelReader = CreateModel(1, new double[] { 2, 2, 2 }, 0).Item2;
IVectorView solution = SolveModel(model, modelReader);
Assert.True(CompareResults(solution));
}
private static void RunTest()
{
double diff = 1e-4;
double conv = 2e-4;
Model model = CreateModel(diff, new double[] { conv, conv, conv }, 0).Item1;
ComsolMeshReader2 modelReader = CreateModel(diff, new double[] { conv, conv, conv }, 0).Item2;
IVectorView solution = SolveModel(model, modelReader);
Assert.True(CompareResults(solution));
}
private static IVectorView SolveModel(Model model, ComsolMeshReader2 modelReader)
{
//var initialTemp = Vector.CreateZero(model.Nodes.Count);
double[] temp0 = new double[model.Nodes.Count];
int[] boundaryIDs = new int[] { 0 };
foreach (int boundaryID in boundaryIDs)
{
foreach (IList <Node> nodes in modelReader.triBoundaries[boundaryID])
{
foreach (Node node in nodes)
{
temp0[node.ID] = 1;
}
}
}
boundaryIDs = new int[] { 5 };
foreach (int boundaryID in boundaryIDs)
{
foreach (IList <Node> nodes in modelReader.triBoundaries[boundaryID])
{
foreach (Node node in nodes)
{
temp0[node.ID] = 0;
}
}
}
Vector initialTemp = Vector.CreateFromArray(temp0);
var builder = new DenseMatrixSolver.Builder();
builder.IsMatrixPositiveDefinite = false;
var solver = builder.BuildSolver(model);
var provider = new ProblemConvectionDiffusion(model, solver);
var childAnalyzer = new LinearAnalyzer(model, solver, provider);
//var parentAnalyzer = new BDF(model, solver, provider, childAnalyzer, 1, 10, 1, initialTemp);
var parentAnalyzer = new ConvectionDiffusionExplicitDynamicAnalyzer(model, solver, provider, childAnalyzer, 2.5e-3, 5, initialTemp);
parentAnalyzer.Initialize();
parentAnalyzer.Solve();
return(parentAnalyzer.temperature[subdomainID]);
//return parentAnalyzer.temperature[1][subdomainID];
// return solver.LinearSystems[subdomainID].Solution;
}
private static Tuple <Model, IModelReader> CreateGrowthModel(double k, double[] U, double L, double[] lgr)
{
string filename = Path.Combine(Directory.GetCurrentDirectory(), "InputFiles", "TumorGrowthModel", "mesh.mphtxt");
var modelReader = new ComsolMeshReader2(filename, new double[] { k, k }, new double[][] { U, U }, new double[] { L, 0 });
Model model = modelReader.CreateModelFromFile();
if (lgr == null)
{
lgr = new double[model.Elements.Count];
for (int i = 0; i < model.Elements.Count; i++)
{
lgr[i] = 1;
}
}
if (c_oxElement == null)
{
c_oxElement = new double[model.Elements.Count];
for (int i = 0; i < model.Elements.Count; i++)
{
c_oxElement[i] = 0;/* 0.9673;*/
}
}
var materialODE = new ConvectionDiffusionMaterial(k, U, L);
double[] Grox = new double[model.Elements.Count];
double[] fg = new double[model.Elements.Count];
int[] domainIDs = new int[] { 0, };
foreach (int domainID in domainIDs)
{
foreach (Element element in modelReader.elementDomains[domainID])
{
Grox[element.ID] = (loxc[domainID] * cvox * c_oxElement[element.ID]) / (cvox * c_oxElement[element.ID] + Koxc[domainID]);
fg[element.ID] = 24d * 3600d * Grox[element.ID] * lgr[element.ID] / 3d;
var nodes = (IReadOnlyList <Node>)element.Nodes;
var domainLoad = new ConvectionDiffusionDomainLoad(materialODE, fg[element.ID], ThermalDof.Temperature);
var bodyLoadElementFactory = new BodyLoadElementFactory(domainLoad, model);
var bodyLoadElement = bodyLoadElementFactory.CreateElement(CellType.Tet4, nodes);
model.BodyLoads.Add(bodyLoadElement);
}
}
return(new Tuple <Model, IModelReader>(model, modelReader));
}
private static Tuple <Model, IModelReader> CreateOxygenTransportModel(double[] k, double[][] U, double[] L, double[] coxElement)
{
string filename = Path.Combine(Directory.GetCurrentDirectory(), "InputFiles", "TumorGrowthModel", "mesh.mphtxt");
var modelReader = new ComsolMeshReader2(filename, k, U, L);
Model model = modelReader.CreateModelFromFile();
var materials = new ConvectionDiffusionMaterial[] { new ConvectionDiffusionMaterial(k[0], U[0], L[0]), new ConvectionDiffusionMaterial(k[1], U[1], L[1]) };
if (coxElement == null)
{
coxElement = new double[model.Elements.Count];
for (int i = 0; i < model.Elements.Count; i++)
{
coxElement[i] = 0;/* 0.9673;*/
}
}
double[] fox = new double[model.Elements.Count];
int[] domainIDs = new int[] { 0, 1 };
foreach (int domainID in domainIDs)
{
foreach (Element element in modelReader.elementDomains[domainID])
{
if (domainID == 0)
{
fox[element.ID] = (Dox[domainID] / Lwv * 7e3 - ((Aox[domainID] * coxElement[element.ID]) / (kox[domainID] + coxElement[element.ID] * cvox)) * 0.3) * (24d * 3600d);
}
else
{
fox[element.ID] = Dox[domainID] / Lwv * 7e3 * (24d * 3600d);
}
var nodes = (IReadOnlyList <Node>)element.Nodes;
var domainLoad = new ConvectionDiffusionDomainLoad(materials[domainID], fox[element.ID], ThermalDof.Temperature);
var bodyLoadElementFactory = new BodyLoadElementFactory(domainLoad, model);
var bodyLoadElement = bodyLoadElementFactory.CreateElement(CellType.Tet4, nodes);
model.BodyLoads.Add(bodyLoadElement);
}
}
return(new Tuple <Model, IModelReader>(model, modelReader));
}
private static Tuple <Model, IModelReader> CreateConvectionDiffusionModel2(double k, double[] U, double L, double b, double f, double bl)
{
string filename = Path.Combine(Directory.GetCurrentDirectory(), "InputFiles", "TumorGrowthModel", "9hexa.mphtxt");
var modelReader = new ComsolMeshReader2(filename, k, U, L);
Model model = modelReader.CreateModelFromFile();
var material = new ConvectionDiffusionMaterial(k, U, L);
//Boundary Conditions
var flux1 = new FluxLoad(f);
var dir1 = new DirichletDistribution(list => {
return(Vector.CreateWithValue(list.Count, b));
});
//var dir2 = new DirichletDistribution(list =>
//{
// return Vector.CreateWithValue(list.Count, b2);
//});
var weakDirichlet1 = new WeakDirichlet(dir1, k);
//var weakDirichlet2 = new WeakDirichlet(dir2, k);
var dirichletFactory1 = new SurfaceLoadElementFactory(weakDirichlet1);
//var dirichletFactory2 = new SurfaceLoadElementFactory(weakDirichlet2);
var fluxFactory1 = new SurfaceLoadElementFactory(flux1);
var boundaryFactory3D = new SurfaceBoundaryFactory3D(0,
new ConvectionDiffusionMaterial(k, new double[] { 0, 0, 0 }, 0));
int[] domainIDs = new int[] { 0, };
foreach (int domainID in domainIDs)
{
foreach (Element element in modelReader.elementDomains[domainID])
{
////IReadOnlyList<Node> nodes = (IReadOnlyList<Node>)element.Nodes;
//var fluxElement1 = fluxFactory1.CreateElement(CellType.Quad4, nodes);
//model.SurfaceLoads.Add(fluxElement1);
var bodyLoadElementCellType = element.ElementType.CellType;
var nodes = (IReadOnlyList <Node>)element.Nodes;
var domainLoad = new ConvectionDiffusionDomainLoad(material, bl, ThermalDof.Temperature);
var bodyLoadElementFactory = new BodyLoadElementFactory(domainLoad, model);
var bodyLoadElement = bodyLoadElementFactory.CreateElement(CellType.Hexa8, nodes);
model.BodyLoads.Add(bodyLoadElement);
//var surfaceElement = new SurfaceLoadElement();
//element.ID = TriID;
//surfaceElement.ElementType = DirichletElement1;
//model.SubdomainsDictionary[0].Elements.Add(dirichletElement1);
//model.ElementsDictionary.Add(TriID, surfaceElement);
//model.NodesDictionary[surfaceElement.ID].Constraints.Add(new Constraint() { DOF = ThermalDof.Temperature, Amount = 100 });
}
}
//foreach (Node node in model.Nodes)
//{
// model.Loads.Add(new Load() { Amount = bl[node.ID], Node = node, DOF = ThermalDof.Temperature });
//}
int[] boundaryIDs = new int[] { 0, };
int QuadID = model.ElementsDictionary.Count + 1;
foreach (int boundaryID in boundaryIDs)
{
foreach (IReadOnlyList <Node> nodes in modelReader.quadBoundaries[boundaryID])
{
//var fluxElement1 = fluxFactory1.CreateElement(CellType.Quad4, nodes);
//model.SurfaceLoads.Add(fluxElement1);
//var dirichletElement1 = dirichletFactory1.CreateElement(CellType.Quad4, nodes);
//model.SurfaceLoads.Add(dirichletElement1);
//var SurfaceBoundaryElement = boundaryFactory3D.CreateElement(CellType.Quad4, nodes);
//var element = new Element();
//element.ID = QuadID;
//element.ElementType = SurfaceBoundaryElement;
//model.SubdomainsDictionary[0].Elements.Add(element);
//model.ElementsDictionary.Add(QuadID, element);
//foreach (Node node in nodes)
//{
// element.AddNode(node);
//}
//QuadID += 1;
}
}
boundaryIDs = new int[] { 5 };
foreach (int boundaryID in boundaryIDs)
{
foreach (IReadOnlyList <Node> nodes in modelReader.quadBoundaries[boundaryID])
{
//var fluxElement1 = fluxFactory1.CreateElement(CellType.Quad4, nodes);
//model.SurfaceLoads.Add(fluxElement1);
//var bodyLoadElement = bodyLoadElementFactory.CreateElement(CellType.Quad4, nodes);
//model.SurfaceLoads.Add(bodyLoadElement);
//var SurfaceBoundaryElement = boundaryFactory3D.CreateElement(CellType.Quad4, nodes);
//var element = new Element();
//element.ID = QuadID;
//element.ElementType = SurfaceBoundaryElement;
//model.SubdomainsDictionary[0].Elements.Add(element);
//model.ElementsDictionary.Add(QuadID, element);
//foreach (Node node in nodes)
//{
// element.AddNode(node);
//}
//QuadID += 1;
}
}
return(new Tuple <Model, IModelReader>(model, modelReader));
}
private static Tuple <Model, ComsolMeshReader2> CreateModel(double k, double[] U, double L)
{
string filename = Path.Combine(Directory.GetCurrentDirectory(), "InputFiles", "TumorGrowthModel", "mesh.mphtxt");
ComsolMeshReader2 modelReader = new ComsolMeshReader2(filename, k, U, L);
Model model = modelReader.CreateModelFromFile();
//Boundary Conditions
var flux1 = new FluxLoad(6.9e08);
var flux2 = new FluxLoad(10);
var dir1 = new DirichletDistribution(list => {
return(Vector.CreateWithValue(list.Count, 1));
});
var dir2 = new DirichletDistribution(list => {
return(Vector.CreateWithValue(list.Count, 0));
});
var weakDirichlet1 = new WeakDirichlet(dir1, k);
var weakDirichlet2 = new WeakDirichlet(dir2, k);
var dirichletFactory1 = new SurfaceLoadElementFactory(weakDirichlet1);
var dirichletFactory2 = new SurfaceLoadElementFactory(weakDirichlet2);
var fluxFactory1 = new SurfaceLoadElementFactory(flux1);
var fluxFactory2 = new SurfaceLoadElementFactory(flux2);
var boundaryFactory3D = new SurfaceBoundaryFactory3D(0,
new ConvectionDiffusionMaterial(k, new double[] { 0, 0, 0 }, 0));
int[] boundaryIDs = new int[] { 0, 1, 2 };
//int numberOfQuadElements = 0;
//for ( int i = 0; i<boundaryIDs.Length; i++)
//{
// numberOfQuadElements += modelReader.quadBoundaries[boundaryIDs[i]].Count;
//}
int TriID = model.ElementsDictionary.Count + 1;
foreach (int boundaryID in boundaryIDs)
{
foreach (IReadOnlyList <Node> nodes in modelReader.triBoundaries[boundaryID])
{
//var fluxElement1 = fluxFactory1.CreateElement(CellType.Tri3, nodes);
//model.SurfaceLoads.Add(fluxElement1);
var dirichletElement1 = dirichletFactory1.CreateElement(CellType.Tri3, nodes);
model.SurfaceLoads.Add(dirichletElement1);
var SurfaceBoundaryElement = boundaryFactory3D.CreateElement(CellType.Tri3, nodes);
var element = new Element();
element.ID = TriID;
element.ElementType = SurfaceBoundaryElement;
model.SubdomainsDictionary[0].Elements.Add(element);
model.ElementsDictionary.Add(TriID, element);
foreach (Node node in nodes)
{
element.AddNode(node);
}
TriID += 1;
// var surfaceElement = new SurfaceLoadElement();
//element.ID = TriID;
//surfaceElement.ElementType = DirichletElement1;
//model.SubdomainsDictionary[0].Elements.Add(dirichletElement1);
//model.ElementsDictionary.Add(TriID, surfaceElement);
//model.NodesDictionary[surfaceElement.ID].Constraints.Add(new Constraint() { DOF = ThermalDof.Temperature, Amount = 100 });
}
}
boundaryIDs = new int[] { 5 };
foreach (int boundaryID in boundaryIDs)
{
foreach (IReadOnlyList <Node> nodes in modelReader.quadBoundaries[boundaryID])
{
// //IReadOnlyList<Node> nodes = (IReadOnlyList<Node>)element.Nodes;
// //var fluxElement1 = fluxFactory1.CreateElement(CellType.Quad4, nodes);
// //model.SurfaceLoads.Add(fluxElement1);
var dirichletElement2 = dirichletFactory2.CreateElement(CellType.Quad4, nodes);
model.SurfaceLoads.Add(dirichletElement2);
var SurfaceBoundaryElement = boundaryFactory3D.CreateElement(CellType.Quad4, nodes);
var element = new Element();
element.ID = TriID;
element.ElementType = SurfaceBoundaryElement;
model.SubdomainsDictionary[0].Elements.Add(element);
model.ElementsDictionary.Add(TriID, element);
foreach (Node node in nodes)
{
element.AddNode(node);
}
TriID += 1;
// // var surfaceElement = new SurfaceLoadElement();
// //element.ID = TriID;
// //surfaceElement.ElementType = DirichletElement1;
// //model.SubdomainsDictionary[0].Elements.Add(dirichletElement1);
// //model.ElementsDictionary.Add(TriID, surfaceElement);
// //model.NodesDictionary[surfaceElement.ID].Constraints.Add(new Constraint() { DOF = ThermalDof.Temperature, Amount = 100 });
}
}
//boundaryIDs = new int[] { 1, 2, 3, 4 };
//foreach (int boundaryID in boundaryIDs)
//{
// foreach (Element element in modelReader.elementBoundaries[boundaryID])
// {
// IReadOnlyList<Node> nodes = (IReadOnlyList<Node>)element.Nodes;
// var fluxElement = fluxFactory.CreateElement(CellType.Quad4, nodes);
// model.SurfaceLoads.Add(fluxElement);
// }
//}
return(new Tuple <Model, ComsolMeshReader2>(model, modelReader));
}
private static void RunTest()
{
Model model = CreateModel(1, new double[] { 2, 2, 2 }, 0).Item1;
ComsolMeshReader2 modelReader = CreateModel(1, new double[] { 2, 2, 2 }, 0).Item2;
string path0 = @"C:\Users\Ody\Documents\Marie Curie\comsolModels\MsolveOutput";
string path3 = Path.Combine(Directory.GetCurrentDirectory(), "CDcubeOutput.vtu");
//var path2 = Path.Combine(path0, $"nodes.txt");
IVectorView solution = SolveModel(model, modelReader);
var numberOfPoints = model.Nodes.Count;
var numberOfCells = model.Elements.Count;
using (StreamWriter outputFile = new StreamWriter(path3))
{
outputFile.WriteLine("<VTKFile type=\"UnstructuredGrid\" version=\"0.1\" byte_order=\"LittleEndian\">");
outputFile.WriteLine(" <UnstructuredGrid>");
outputFile.WriteLine($" <Piece NumberOfPoints=\"{numberOfPoints}\" NumberOfCells=\"{numberOfCells}\">");
outputFile.WriteLine(" <Points>");
outputFile.WriteLine(" <DataArray type=\"Float64\" Name=\"position\" NumberOfComponents=\"3\" format =\"ascii\">");
for (int i = 0; i < numberOfPoints; i++)
{
outputFile.WriteLine($"{model.Nodes[i].X} {model.Nodes[i].Y} {model.Nodes[i].Z} ");
}
outputFile.WriteLine(" </DataArray>");
outputFile.WriteLine(" </Points>");
outputFile.WriteLine(" <PointData>");
outputFile.WriteLine(" <DataArray type=\"Int32\" Name=\"node_ID\" NumberOfComponents=\"1\" format=\"ascii\">");
for (int i = 0; i < numberOfPoints; i++)
{
outputFile.WriteLine($"{i + 1}");
}
outputFile.WriteLine(" </DataArray>");
outputFile.WriteLine(" <DataArray type=\"Float64\" Name=\"solution\" NumberOfComponents=\"1\" format=\"ascii\">");
for (int i = 0; i < numberOfPoints; i++)
{
outputFile.WriteLine($"{solution[i]} ");
}
outputFile.WriteLine(" </DataArray>");
outputFile.WriteLine(" </PointData>");
outputFile.WriteLine(" <CellData>");
outputFile.WriteLine(" <DataArray type=\"Int32\" Name=\"element_ID\" NumberOfComponents=\"1\" format=\"ascii\">");
for (int i = 0; i < numberOfCells; i++)
{
outputFile.WriteLine($"{i + 1}");
}
outputFile.WriteLine(" </DataArray>");
outputFile.WriteLine(" </CellData>");
outputFile.WriteLine(" <Cells>");
outputFile.WriteLine(" <DataArray type=\"Int32\" Name=\"connectivity\">");
for (int i = 0; i < numberOfCells; i++)
{
for (int j = 0; j < model.Elements[i].Nodes.Count; j++)
{
outputFile.Write($"{model.Elements[i].Nodes[j].ID} ");
}
outputFile.WriteLine("");
}
outputFile.WriteLine(" </DataArray>");
outputFile.WriteLine(" <DataArray type=\"Int32\" Name=\"offsets\" NumberOfComponents=\"1\" format=\"ascii\">");
var offset = 0;
for (int i = 0; i < numberOfCells; i++)
{
offset += model.Elements[i].Nodes.Count;
outputFile.WriteLine($"{offset} ");
}
outputFile.WriteLine(" </DataArray>");
outputFile.WriteLine(" <DataArray type=\"Int32\" Name =\"types\" NumberOfComponents =\"1\" format=\"ascii\">");
for (int i = 0; i < numberOfCells; i++)
{
if (model.Elements[i].Nodes.Count == 4)
{
outputFile.WriteLine($"{10} ");
}
else
{
outputFile.WriteLine($"{5} ");
}
}
outputFile.WriteLine(" </DataArray>");
outputFile.WriteLine(" </Cells>");
outputFile.WriteLine(" </Piece>");
outputFile.WriteLine(" </UnstructuredGrid>");
outputFile.WriteLine("</VTKFile>");
}
Assert.True(CompareResults(solution));
}
private static Tuple <Model, ComsolMeshReader2> CreateModel(double k, double[] U, double L, double b1, double b2, double f1, double f2, double[] bl)
{
string filename = Path.Combine(Directory.GetCurrentDirectory(), "InputFiles", "TumorGrowthModel", "9hexa.mphtxt");
ComsolMeshReader2 modelReader = new ComsolMeshReader2(filename, k, U, L);
Model model = modelReader.CreateModelFromFile();
//Boundary Conditions
var flux1 = new FluxLoad(f1);
var flux2 = new FluxLoad(f2);
var dir1 = new DirichletDistribution(list => {
return(Vector.CreateWithValue(list.Count, b1));
});
var dir2 = new DirichletDistribution(list => {
return(Vector.CreateWithValue(list.Count, b2));
});
var weakDirichlet1 = new WeakDirichlet(dir1, k);
var weakDirichlet2 = new WeakDirichlet(dir2, k);
var dirichletFactory1 = new SurfaceLoadElementFactory(weakDirichlet1);
var dirichletFactory2 = new SurfaceLoadElementFactory(weakDirichlet2);
var fluxFactory1 = new SurfaceLoadElementFactory(flux1);
var fluxFactory2 = new SurfaceLoadElementFactory(flux2);
var boundaryFactory3D = new SurfaceBoundaryFactory3D(0,
new ConvectionDiffusionMaterial(k, new double[] { 0, 0, 0 }, 0));
foreach (Node node in model.Nodes)
{
model.Loads.Add(new Load()
{
Amount = bl[node.ID], Node = node, DOF = ThermalDof.Temperature
});
}
int[] boundaryIDs = new int[] { 0, };
int QuadID = model.ElementsDictionary.Count + 1;
foreach (int boundaryID in boundaryIDs)
{
foreach (IReadOnlyList <Node> nodes in modelReader.quadBoundaries[boundaryID])
{
var fluxElement1 = fluxFactory1.CreateElement(CellType.Quad4, nodes);
model.SurfaceLoads.Add(fluxElement1);
var dirichletElement1 = dirichletFactory1.CreateElement(CellType.Quad4, nodes);
model.SurfaceLoads.Add(dirichletElement1);
var SurfaceBoundaryElement = boundaryFactory3D.CreateElement(CellType.Quad4, nodes);
var element = new Element();
element.ID = QuadID;
element.ElementType = SurfaceBoundaryElement;
model.SubdomainsDictionary[0].Elements.Add(element);
model.ElementsDictionary.Add(QuadID, element);
foreach (Node node in nodes)
{
element.AddNode(node);
}
QuadID += 1;
}
}
boundaryIDs = new int[] { 5 };
foreach (int boundaryID in boundaryIDs)
{
foreach (IReadOnlyList <Node> nodes in modelReader.quadBoundaries[boundaryID])
{
var fluxElement1 = fluxFactory1.CreateElement(CellType.Quad4, nodes);
model.SurfaceLoads.Add(fluxElement1);
var dirichletElement2 = dirichletFactory2.CreateElement(CellType.Quad4, nodes);
model.SurfaceLoads.Add(dirichletElement2);
var SurfaceBoundaryElement = boundaryFactory3D.CreateElement(CellType.Quad4, nodes);
var element = new Element();
element.ID = QuadID;
element.ElementType = SurfaceBoundaryElement;
model.SubdomainsDictionary[0].Elements.Add(element);
model.ElementsDictionary.Add(QuadID, element);
foreach (Node node in nodes)
{
element.AddNode(node);
}
QuadID += 1;
}
}
return(new Tuple <Model, ComsolMeshReader2>(model, modelReader));
}
private static Tuple <Model, IModelReader> CreateOxygenTransportModel(double[] k, double[][] U, double[] L, double[] cox)
{
string filename = Path.Combine(Directory.GetCurrentDirectory(), "InputFiles", "TumorGrowthModel", "mesh.mphtxt");
var modelReader = new ComsolMeshReader2(filename, k, U, L);
Model model = modelReader.CreateModelFromFile();
var materials = new ConvectionDiffusionMaterial[] { new ConvectionDiffusionMaterial(k[0], U[0], L[0]), new ConvectionDiffusionMaterial(k[1], U[1], L[1]) };
//Boundary Conditions
//var flux1 = new FluxLoad(f);
//var dir1 = new DirichletDistribution(list => {
// return Vector.CreateWithValue(list.Count, b);
//});
//var dir2 = new DirichletDistribution(list =>
//{
// return Vector.CreateWithValue(list.Count, b2);
//});
//var weakDirichlet1 = new WeakDirichlet(dir1, k);
//var weakDirichlet2 = new WeakDirichlet(dir2, k);
//var dirichletFactory1 = new SurfaceLoadElementFactory(weakDirichlet1);
//var dirichletFactory2 = new SurfaceLoadElementFactory(weakDirichlet2);
//var fluxFactory1 = new SurfaceLoadElementFactory(flux1);
//var boundaryFactory3D = new SurfaceBoundaryFactory3D(0,
// new ConvectionDiffusionMaterial(k, new double[] { 0, 0, 0 }, 0));
if (cox == null)
{
cox = new double[model.Nodes.Count];
for (int i = 0; i < model.Nodes.Count; i++)
{
cox[i] = 0;/* 0.9673;*/
}
}
double[] fox = new double[model.Elements.Count];
int[] domainIDs = new int[] { 0, 1 };
var coxElement = new double[model.Elements.Count];
foreach (var e in model.Elements)
{
coxElement[e.ID] = 0;
for (int i = 0; i < e.Nodes.Count; i++)
{
coxElement[e.ID] += cox[i] / (e.Nodes.Count);
}
}
foreach (int domainID in domainIDs)
{
//foreach (Element element in modelReader.nodeDomains[domainID])
//{
// if (domainID == 0)
// {
// fox[element.ID] = (Dox[domainID]/Lwv * (1 - coxElement[element.ID])-((Aox[domainID]* coxElement[element.ID])/(kox[domainID]+ coxElement[element.ID]*cvox))*0.3)*(24d * 3600d);
// }
// else
// {
// fox[element.ID] = Dox[domainID] / Lwv * (1 - cox[element.ID])*(24d*3600d);
// }
// model.Loads.Add(new Load() { Node = element, DOF = ThermalDof.Temperature, Amount = fox[element.ID] });
//}
foreach (Element element in modelReader.elementDomains[domainID])
{
//IReadOnlyList<Node> nodes = (IReadOnlyList<Node>)element.Nodes;
//var fluxElement1 = fluxFactory1.CreateElement(CellType.Quad4, nodes);
//model.SurfaceLoads.Add(fluxElement1);
if (domainID == 0)
{
fox[element.ID] = (Dox[domainID] / Lwv * 7e3 - ((Aox[domainID] * coxElement[element.ID]) / (kox[domainID] + coxElement[element.ID] * cvox)) * 0.3) * (24d * 3600d);
}
else
{
fox[element.ID] = Dox[domainID] / Lwv * 7e3 * (24d * 3600d);
}
var nodes = (IReadOnlyList <Node>)element.Nodes;
var domainLoad = new ConvectionDiffusionDomainLoad(materials[domainID], fox[element.ID], ThermalDof.Temperature);
var bodyLoadElementFactory = new BodyLoadElementFactory(domainLoad, model);
var bodyLoadElement = bodyLoadElementFactory.CreateElement(CellType.Tet4, nodes);
model.BodyLoads.Add(bodyLoadElement);
//var surfaceElement = new SurfaceLoadElement();
//element.ID = TriID;
//surfaceElement.ElementType = DirichletElement1;
//model.SubdomainsDictionary[0].Elements.Add(dirichletElement1);
//model.ElementsDictionary.Add(TriID, surfaceElement);
//model.NodesDictionary[surfaceElement.ID].Constraints.Add(new Constraint() { DOF = ThermalDof.Temperature, Amount = 100 });
}
}
//foreach (Node node in model.Nodes)
//{
// model.Loads.Add(new Load() { Amount = bl[node.ID], Node = node, DOF = ThermalDof.Temperature });
//}
//int[] boundaryIDs = new int[] { 0, };
//int QuadID = model.ElementsDictionary.Count + 1;
//foreach (int boundaryID in boundaryIDs)
//{
// foreach (IReadOnlyList<Node> nodes in modelReader.quadBoundaries[boundaryID])
// {
// //var fluxElement1 = fluxFactory1.CreateElement(CellType.Quad4, nodes);
// //model.SurfaceLoads.Add(fluxElement1);
// //var dirichletElement1 = dirichletFactory1.CreateElement(CellType.Quad4, nodes);
// //model.SurfaceLoads.Add(dirichletElement1);
// //var SurfaceBoundaryElement = boundaryFactory3D.CreateElement(CellType.Quad4, nodes);
// //var element = new Element();
// //element.ID = QuadID;
// //element.ElementType = SurfaceBoundaryElement;
// //model.SubdomainsDictionary[0].Elements.Add(element);
// //model.ElementsDictionary.Add(QuadID, element);
// //foreach (Node node in nodes)
// //{
// // element.AddNode(node);
// //}
// //QuadID += 1;
// }
//}
//boundaryIDs = new int[] { 5 };
//foreach (int boundaryID in boundaryIDs)
//{
// foreach (IReadOnlyList<Node> nodes in modelReader.quadBoundaries[boundaryID])
// {
// //var fluxElement1 = fluxFactory1.CreateElement(CellType.Quad4, nodes);
// //model.SurfaceLoads.Add(fluxElement1);
// //var bodyLoadElement = bodyLoadElementFactory.CreateElement(CellType.Quad4, nodes);
// //model.SurfaceLoads.Add(bodyLoadElement);
// //var SurfaceBoundaryElement = boundaryFactory3D.CreateElement(CellType.Quad4, nodes);
// //var element = new Element();
// //element.ID = QuadID;
// //element.ElementType = SurfaceBoundaryElement;
// //model.SubdomainsDictionary[0].Elements.Add(element);
// //model.ElementsDictionary.Add(QuadID, element);
// //foreach (Node node in nodes)
// //{
// // element.AddNode(node);
// //}
// //QuadID += 1;
// }
//}
return(new Tuple <Model, IModelReader>(model, modelReader));
}
private static Tuple <Model, ComsolMeshReader2> CreateModel(double k, double[] U, double L)
{
string filename = Path.Combine(Directory.GetCurrentDirectory(), "InputFiles", "TumorGrowthModel", "fullModel.mphtxt");
ComsolMeshReader2 modelReader = new ComsolMeshReader2(filename, new double[] { k }, new double[][] { U }, new double[] { L });
Model model = modelReader.CreateModelFromFile();
//Boundary Conditions
var bodyLoad = new ConvectionDiffusionDomainLoad(new ConvectionDiffusionMaterial(k, U, L), 1, ThermalDof.Temperature);
var flux1 = new FluxLoad(1);
var flux2 = new FluxLoad(10);
var dir1 = new DirichletDistribution(list => {
return(Vector.CreateWithValue(list.Count, 1));
});
var dir2 = new DirichletDistribution(list => {
return(Vector.CreateWithValue(list.Count, 0));
});
var weakDirichlet1 = new WeakDirichlet(dir1, k);
var weakDirichlet2 = new WeakDirichlet(dir2, k);
var bodyLoadElementFactory = new BodyLoadElementFactory(bodyLoad, model);
var dirichletFactory1 = new SurfaceLoadElementFactory(weakDirichlet1);
var dirichletFactory2 = new SurfaceLoadElementFactory(weakDirichlet2);
var fluxFactory1 = new SurfaceLoadElementFactory(flux1);
var fluxFactory2 = new SurfaceLoadElementFactory(flux2);
var boundaryFactory3D = new SurfaceBoundaryFactory3D(0,
new ConvectionDiffusionMaterial(k, new double[] { 0, 0, 0 }, 0));
int[] domainIDs = new int[] { 0, };
foreach (int domainID in domainIDs)
{
foreach (Element element in modelReader.elementDomains[domainID])
{
//IReadOnlyList<Node> nodes = (IReadOnlyList<Node>)element.Nodes;
//var fluxElement1 = fluxFactory1.CreateElement(CellType.Quad4, nodes);
//model.SurfaceLoads.Add(fluxElement1);
//var bodyLoadElementCellType = element.ElementType.CellType;
//var nodes = (IReadOnlyList<Node>)element.Nodes;
//var bodyLoadElement = bodyLoadElementFactory.CreateElement(CellType.Hexa8, nodes);
//model.BodyLoads.Add(bodyLoadElement);
// var surfaceElement = new SurfaceLoadElement();
//element.ID = TriID;
//surfaceElement.ElementType = DirichletElement1;
//model.SubdomainsDictionary[0].Elements.Add(dirichletElement1);
//model.ElementsDictionary.Add(TriID, surfaceElement);
//model.NodesDictionary[surfaceElement.ID].Constraints.Add(new Constraint() { DOF = ThermalDof.Temperature, Amount = 100 });
}
}
//foreach (Node node in model.Nodes)
//{
// model.Loads.Add(new Load() { Amount = .25, Node = node, DOF = ThermalDof.Temperature });
//}
int[] boundaryIDs = new int[] { 0, 1, 2, 3, 4, 7 };
int TriID = model.ElementsDictionary.Count + 1;
foreach (int boundaryID in boundaryIDs)
{
foreach (IReadOnlyList <Node> nodes in modelReader.triBoundaries[boundaryID])
{
//IReadOnlyList<Node> nodes = (IReadOnlyList<Node>)element.Nodes;
//var fluxElement1 = fluxFactory1.CreateElement(CellType.Quad4, nodes);
//model.SurfaceLoads.Add(fluxElement1);
var dirichletElement1 = dirichletFactory1.CreateElement(CellType.Tri3, nodes);
model.SurfaceLoads.Add(dirichletElement1);
var surfaceBoundaryElement = boundaryFactory3D.CreateElement(CellType.Tri3, nodes);
var element = new Element();
element.ID = TriID;
element.ElementType = surfaceBoundaryElement;
model.SubdomainsDictionary[0].Elements.Add(element);
model.ElementsDictionary.Add(TriID, element);
foreach (Node node in nodes)
{
element.AddNode(node);
}
TriID += 1;
// var surfaceElement = new SurfaceLoadElement();
//element.ID = TriID;
//surfaceElement.ElementType = DirichletElement1;
//model.SubdomainsDictionary[0].Elements.Add(dirichletElement1);
//model.ElementsDictionary.Add(TriID, surfaceElement);
//model.NodesDictionary[surfaceElement.ID].Constraints.Add(new Constraint() { DOF = ThermalDof.Temperature, Amount = 100 });
}
}
boundaryIDs = new int[] { 6, 8, 9 };
foreach (int boundaryID in boundaryIDs)
{
foreach (IReadOnlyList <Node> nodes in modelReader.triBoundaries[boundaryID])
{
//IReadOnlyList<Node> nodes = (IReadOnlyList<Node>)element.Nodes;
//var fluxElement2 = fluxFactory2.CreateElement(CellType.Quad4, nodes);
//model.SurfaceLoads.Add(fluxElement2);
var dirichletElement2 = dirichletFactory2.CreateElement(CellType.Tri3, nodes);
model.SurfaceLoads.Add(dirichletElement2);
var surfaceBoundaryElement = boundaryFactory3D.CreateElement(CellType.Tri3, nodes);
var element = new Element();
element.ID = TriID;
element.ElementType = surfaceBoundaryElement;
model.SubdomainsDictionary[0].Elements.Add(element);
model.ElementsDictionary.Add(TriID, element);
foreach (Node node in nodes)
{
element.AddNode(node);
}
TriID += 1;
// var surfaceElement = new SurfaceLoadElement();
//element.ID = TriID;
//surfaceElement.ElementType = DirichletElement1;
//model.SubdomainsDictionary[0].Elements.Add(dirichletElement1);
//model.ElementsDictionary.Add(TriID, surfaceElement);
//model.NodesDictionary[surfaceElement.ID].Constraints.Add(new Constraint() { DOF = ThermalDof.Temperature, Amount = 100 });
}
}
//boundaryIDs = new int[] { 1, 2, 3, 4 };
//foreach (int boundaryID in boundaryIDs)
//{
// foreach (Element element in modelReader.elementBoundaries[boundaryID])
// {
// IReadOnlyList<Node> nodes = (IReadOnlyList<Node>)element.Nodes;
// var fluxElement = fluxFactory.CreateElement(CellType.Quad4, nodes);
// model.SurfaceLoads.Add(fluxElement);
// }
//}
return(new Tuple <Model, ComsolMeshReader2>(model, modelReader));
}
