private static Tuple <Model, ComsolMeshReader> CreateModel()
{
string filename = Path.Combine(Directory.GetCurrentDirectory(), "InputFiles", "TumorGrowthModel", "mesh1.mphtxt");
ComsolMeshReader modelReader = new ComsolMeshReader(filename);
Model model = modelReader.CreateModelFromFile();
//Boundary Conditions
var flux = new FluxLoad(10);
var dir1 = new DirichletDistribution(list => {
return(Vector.CreateWithValue(list.Count, 0));
});
var dir2 = new DirichletDistribution(list => {
return(Vector.CreateWithValue(list.Count, 1));
});
var weakDirichlet1 = new WeakDirichlet(dir1, modelReader.diffusionCeoff);
var weakDirichlet2 = new WeakDirichlet(dir2, modelReader.diffusionCeoff);
var dirichletFactory1 = new SurfaceLoadElementFactory(weakDirichlet1);
var dirichletFactory2 = new SurfaceLoadElementFactory(weakDirichlet2);
var fluxFactory = new SurfaceLoadElementFactory(flux);
int[] boundaryIDs = new int[] { 2, 7, 8, 9 };
foreach (int boundaryID in boundaryIDs)
{
foreach (Element element in modelReader.elementBoundaries[boundaryID])
{
IReadOnlyList <Node> nodes = (IReadOnlyList <Node>)element.Nodes;
var dirichletElement1 = dirichletFactory1.CreateElement(CellType.Tri3, nodes);
model.SurfaceLoads.Add(dirichletElement1);
//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[] { 0, 1, 3, 4, 6 };
foreach (int boundaryID in boundaryIDs)
{
foreach (Element element in modelReader.elementBoundaries[boundaryID])
{
IReadOnlyList <Node> nodes = (IReadOnlyList <Node>)element.Nodes;
var dirichletElement2 = dirichletFactory2.CreateElement(CellType.Tri3, nodes);
model.SurfaceLoads.Add(dirichletElement2);
}
}
return(new Tuple <Model, ComsolMeshReader>(model, modelReader));
}
public void ConstructorTest4()
{
// Create a Dirichlet with the following concentrations
var dirich = new DirichletDistribution(0.42, 0.57, 1.2);
// Common measures
double[] mean = dirich.Mean; // { 0.19, 0.26, 0.54 }
double[] median = dirich.Median; // { 0.19, 0.26, 0.54 }
double[] var = dirich.Variance; // { 0.048, 0.060, 0.077 }
double[,] cov = dirich.Covariance; // see below
// 0.0115297440926238 0.0156475098399895 0.0329421259789253
// cov = 0.0156475098399895 0.0212359062114143 0.0447071709713986
// 0.0329421259789253 0.0447071709713986 0.0941203599397865
// (the above matrix representation has been transcribed to text using)
string str = cov.ToString(DefaultMatrixFormatProvider.InvariantCulture);
// Probability mass functions
double pdf1 = dirich.ProbabilityDensityFunction(new double[] { 2, 5 }); // 0.12121671541846207
double pdf2 = dirich.ProbabilityDensityFunction(new double[] { 4, 2 }); // 0.12024840322466089
double pdf3 = dirich.ProbabilityDensityFunction(new double[] { 3, 7 }); // 0.082907634905068528
double lpdf = dirich.LogProbabilityDensityFunction(new double[] { 3, 7 }); // -2.4900281233124044
Assert.AreEqual(0.19178082191780821, mean[0]);
Assert.AreEqual(0.26027397260273971, mean[1]);
Assert.AreEqual(0.547945205479452, median[2]);
Assert.AreEqual(0.19178082191780821, median[0]);
Assert.AreEqual(0.26027397260273971, median[1]);
Assert.AreEqual(0.547945205479452, median[2]);
Assert.AreEqual(0.048589635818914775, var[0]);
Assert.AreEqual(0.060354680811388089, var[1]);
Assert.AreEqual(0.077649296950323854, var[2]);
Assert.AreEqual(0.011529744092623844, cov[0, 0]);
Assert.AreEqual(0.015647509839989502, cov[0, 1]);
Assert.AreEqual(0.015647509839989502, cov[1, 0]);
Assert.AreEqual(0.021235906211414326, cov[1, 1]);
Assert.AreEqual(0.12121671541846207, pdf1);
Assert.AreEqual(0.12024840322466089, pdf2);
Assert.AreEqual(0.082907634905068528, pdf3);
Assert.AreEqual(-2.4900281233124044, lpdf);
}
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, 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, 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 Model CreateModel()
{
IList <IList <Node> > nodeBoundaries;
IList <IList <Element> > elementBoundaries;
double density = 1.0;
double[] U = { 2, 2, 2 };
double k = 1.0;
double L = .0;
var elementFactory3D = new ConvectionDiffusionElement3DFactory(new ConvectionDiffusionMaterial(k, U, L));
var boundaryFactory3D = new SurfaceBoundaryFactory3D(0, new ConvectionDiffusionMaterial(k, U, L));
var model = new Model();
model.SubdomainsDictionary[0] = new Subdomain(0);
elementBoundaries = new List <IList <Element> >();
nodeBoundaries = new List <IList <Node> >();
for (int i = 0; i < 10; i++)
{
elementBoundaries.Add(new List <Element>());
nodeBoundaries.Add(new List <Node>());
}
double[,] nodeData = new double[, ] {
{ 0, 0, 0 },
{ 0, 1, 0 },
{ 0, 1, 1 },
{ 0, 0, 1 },
{ 1, 0, 0 },
{ 1, 1, 0 },
{ 1, 1, 1 },
{ 1, 0, 1 }
};
for (int nNode = 0; nNode < nodeData.GetLength(0); nNode++)
{
model.NodesDictionary.Add(nNode, new Node(id: nNode, x: nodeData[nNode, 0], y: nodeData[nNode, 1], z: nodeData[nNode, 2]));
}
IReadOnlyList <Node> nodes = new List <Node>
{
model.NodesDictionary[0],
model.NodesDictionary[1],
model.NodesDictionary[2],
model.NodesDictionary[3],
model.NodesDictionary[4],
model.NodesDictionary[5],
model.NodesDictionary[6],
model.NodesDictionary[7],
};
IList <IReadOnlyList <Node> > face = new List <IReadOnlyList <Node> >();
//face = new List<IReadOnlyList<Node>>();
for (int i = 0; i < 6; i++)
{
face.Add(new List <Node>());
}
face[0] = new List <Node>
{
model.NodesDictionary[0],
model.NodesDictionary[1],
model.NodesDictionary[2],
model.NodesDictionary[3],
};
face[1] = new List <Node>
{
model.NodesDictionary[4],
model.NodesDictionary[5],
model.NodesDictionary[6],
model.NodesDictionary[7],
};
face[2] = new List <Node>
{
model.NodesDictionary[0],
model.NodesDictionary[1],
model.NodesDictionary[5],
model.NodesDictionary[4],
};
face[3] = new List <Node>
{
model.NodesDictionary[1],
model.NodesDictionary[2],
model.NodesDictionary[6],
model.NodesDictionary[5],
};
face[4] = new List <Node>
{
model.NodesDictionary[2],
model.NodesDictionary[6],
model.NodesDictionary[7],
model.NodesDictionary[3],
};
face[5] = new List <Node>
{
model.NodesDictionary[0],
model.NodesDictionary[4],
model.NodesDictionary[7],
model.NodesDictionary[3],
};
int[] elementData = new int[] { 0, 1, 2, 3, 4, 5, 6, 7 };// the last line will not be used. We assign only one element
var Hexa8 = elementFactory3D.CreateElement(CellType.Hexa8, nodes);
var element = new Element();
element.ID = 0;
element.ElementType = Hexa8;
for (int j = 0; j < 8; j++)
{
element.NodesDictionary.Add(elementData[j], model.NodesDictionary[elementData[j]]);
}
model.SubdomainsDictionary[0].Elements.Add(element);
model.ElementsDictionary.Add(0, element);
var flux1 = new FluxLoad(1);
var flux2 = new FluxLoad(10);
var dir1 = new DirichletDistribution(list => {
return(Vector.CreateWithValue(list.Count, 0));
});
var dir2 = new DirichletDistribution(list => {
return(Vector.CreateWithValue(list.Count, 10));
});
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);
//foreach (int i in new int[] { 1 })
//{
// var Quad = boundaryFactory3D.CreateElement(CellType.Quad4, face[i - 1]);
// var faceElement = new Element();
// faceElement.ID = i;
// faceElement.ElementType = Quad;
// foreach (Node node in face[i - 1])
// {
// faceElement.AddNode(node);
// }
// model.SubdomainsDictionary[0].Elements.Add(faceElement);
// model.ElementsDictionary.Add(i, faceElement);
// var dirichletElement = dirichletFactory1.CreateElement(CellType.Quad4, face[i - 1]);
// //var fluxElement = fluxFactory.CreateElement(CellType.Quad4, face[i - 1]);
// model.SurfaceLoads.Add(dirichletElement);
// //model.SurfaceLoads.Add(fluxElement);
//}
foreach (int i in new int[] { 0 })
{
//var Quad = boundaryFactory3D.CreateElement(CellType.Quad4, face[i]);
//var faceElement = new Element();
//faceElement.ID = 1;
//faceElement.ElementType = Quad;
//foreach (Node node in face[i])
//{
// faceElement.AddNode(node);
//}
//model.SubdomainsDictionary[0].Elements.Add(faceElement);
//model.ElementsDictionary.Add(1, faceElement);
//var dirichletElement = dirichletFactory2.CreateElement(CellType.Quad4, face[i]);
//model.SurfaceLoads.Add(dirichletElement);
var fluxElement = fluxFactory1.CreateElement(CellType.Quad4, face[i]);
model.SurfaceLoads.Add(fluxElement);
}
foreach (int i in new int[] { 1 })
{
//var Quad = boundaryFactory3D.CreateElement(CellType.Quad4, face[i]);
//var faceElement = new Element();
//faceElement.ID = 2;
//faceElement.ElementType = Quad;
//foreach (Node node in face[i])
//{
// faceElement.AddNode(node);
//}
//model.SubdomainsDictionary[0].Elements.Add(faceElement);
//model.ElementsDictionary.Add(2, faceElement);
//var dirichletElement = dirichletFactory2.CreateElement(CellType.Quad4, face[i]);
//model.SurfaceLoads.Add(dirichletElement);
var fluxElement = fluxFactory2.CreateElement(CellType.Quad4, face[i]);
model.SurfaceLoads.Add(fluxElement);
}
//constraints
//foreach (int i in new int[] { 4, 5, 6, 7 })
//{
// model.NodesDictionary[i].Constraints.Add(new Constraint()
// {
// Amount = 0,
// DOF = ThermalDof.Temperature
// });
//}
//// loads
//Load load1;
//foreach (int i in new int[] {0, 1, 2, 3})
//{
// load1 = new Load()
// {
// Node = model.NodesDictionary[i],
// DOF = ThermalDof.Temperature,
// Amount = 12.5
// };
// model.Loads.Add(load1);
//}
return(model);
}
public WeakDirichlet(DirichletDistribution distribution, double diffusionCoeff)
{
_distribution = distribution;
_diffusionCoeff = diffusionCoeff;
}
protected void DoLearning(LearningTask learningTask)
{
if (learningTask.LearningState == ComputationState.Done)
{
return;
}
// Grab options.
var options = learningTask.Options;
// Grab training set.
var trainingSet = learningTask.TrainingSet;
// Grab variable names.
var firstObservation = learningTask.TrainingSet.First();
var variableNames = firstObservation.VariableNames;
// Build a starter Bayesian network.
var bn = new BayesianNetwork(learningTask.TrainingSet.Name);
// Build variables for each variable in the training set.
foreach (var variableName in variableNames)
{
var space = trainingSet.Variables.TryFind(variableName).Value;
var rv = new RandomVariable(variableName, space);
bn.AddVariable(rv);
}
// Store in task so that task can send updates to its listeners.
learningTask.BayesianNetwork = bn;
learningTask.LearningState = ComputationState.Computing;
// Build Dirichlet parameters
IDictionary<string, DirichletDistribution> priors = new Dictionary<string, DirichletDistribution>();
foreach (var variableName in variableNames)
{
var space = trainingSet.Variables.TryFind(variableName).Value;
DirichletDistribution prior;
if (options.DistributionDirichletAlpha > 0)
{
prior = new DirichletDistribution();
foreach (var value in space.Values)
{
prior.SetParameter(value, options.DistributionDirichletAlpha);
}
priors[variableName] = prior;
}
}
// Initialize a sufficient statistics.
SufficientStatistics sufficientStatistics
= new SufficientStatistics(trainingSet, Utils.Some(priors));
// Learn structure.
switch (options.Structure)
{
case LearningOptions.StructureEnum.DisconnectedStructure:
break;
case LearningOptions.StructureEnum.RandomStructure:
bn.GenerateStructure(
StructureClass.Random,
Utils.Some(options.StructureSeed),
Utils.Some(options.StructureParentLimit));
break;
case LearningOptions.StructureEnum.TreeStructure:
bn.LearnStructure(
sufficientStatistics,
StructureClass.Tree,
Utils.None<int>(),
Utils.None<int>());
break;
case LearningOptions.StructureEnum.GeneralStructure:
bn.LearnStructure(
sufficientStatistics,
StructureClass.General,
Utils.None<int>(),
Utils.Some(options.StructureParentLimit));
break;
}
// Learn distributions.
bn.LearnDistributions(sufficientStatistics);
// Done.
learningTask.LearningState = ComputationState.Done;
}
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));
}
protected void DoLearning(LearningTask learningTask)
{
if (learningTask.LearningState == ComputationState.Done)
{
return;
}
// Grab options.
var options = learningTask.Options;
// Grab training set.
var trainingSet = learningTask.TrainingSet;
// Grab variable names.
var firstObservation = learningTask.TrainingSet.First();
var variableNames = firstObservation.VariableNames;
// Build a starter Bayesian network.
var bn = new BayesianNetwork(learningTask.TrainingSet.Name);
// Build variables for each variable in the training set.
foreach (var variableName in variableNames)
{
var space = trainingSet.Variables.TryFind(variableName).Value;
var rv = new RandomVariable(variableName, space);
bn.AddVariable(rv);
}
// Store in task so that task can send updates to its listeners.
learningTask.BayesianNetwork = bn;
learningTask.LearningState = ComputationState.Computing;
// Build Dirichlet parameters
IDictionary <string, DirichletDistribution> priors = new Dictionary <string, DirichletDistribution>();
foreach (var variableName in variableNames)
{
var space = trainingSet.Variables.TryFind(variableName).Value;
DirichletDistribution prior;
if (options.DistributionDirichletAlpha > 0)
{
prior = new DirichletDistribution();
foreach (var value in space.Values)
{
prior.SetParameter(value, options.DistributionDirichletAlpha);
}
priors[variableName] = prior;
}
}
// Initialize a sufficient statistics.
SufficientStatistics sufficientStatistics
= new SufficientStatistics(trainingSet, Utils.Some(priors));
// Learn structure.
switch (options.Structure)
{
case LearningOptions.StructureEnum.DisconnectedStructure:
break;
case LearningOptions.StructureEnum.RandomStructure:
bn.GenerateStructure(
StructureClass.Random,
Utils.Some(options.StructureSeed),
Utils.Some(options.StructureParentLimit));
break;
case LearningOptions.StructureEnum.TreeStructure:
bn.LearnStructure(
sufficientStatistics,
StructureClass.Tree,
Utils.None <int>(),
Utils.None <int>());
break;
case LearningOptions.StructureEnum.GeneralStructure:
bn.LearnStructure(
sufficientStatistics,
StructureClass.General,
Utils.None <int>(),
Utils.Some(options.StructureParentLimit));
break;
}
// Learn distributions.
bn.LearnDistributions(sufficientStatistics);
// Done.
learningTask.LearningState = ComputationState.Done;
}
