/// <summary>
/// Set Mus in nodes
/// </summary>
/// <param name="us">mus </param>
/// <param name="smesh">spatial mesh</param>
/// <param name="input">simulation input</param>
public static void SetMus(ref double[][][] us, SpatialMesh[] smesh, SimulationInput input)
{
int j, k, l;
int nt = smesh[input.MeshDataInput.SMeshLevel].Nt;
var tissueInput = ((MultiEllipsoidTissueInput)input.TissueInput);
int nLayerRegions = tissueInput.LayerRegions.Length;
int nInclusionRegions = tissueInput.EllipsoidRegions.Length;
int sMeshLevel = input.MeshDataInput.SMeshLevel;
us[sMeshLevel] = new double[nt][];
for (j = 0; j < nt; j++)
{
us[sMeshLevel][j] = new double[3];
for (k = 0; k < 3; k++)
{
for (l = 0; l < nLayerRegions - 2; l++)
{
if (smesh[sMeshLevel].Region[smesh[sMeshLevel].T[j][0]] == l)
{
us[sMeshLevel][j][k] = tissueInput.LayerRegions[l + 1].RegionOP.Mus;
}
}
for (l = 0; l < nInclusionRegions; l++)
{
if (smesh[sMeshLevel].Region[smesh[sMeshLevel].T[j][0]] == l + nLayerRegions - 2)
{
us[sMeshLevel][j][k] = tissueInput.EllipsoidRegions[l].RegionOP.Mus;
}
}
}
}
}
/// <summary>
/// FEM Simulation Input Data View Model
/// </summary>
/// <param name="input"></param>
public FemSimulationInputDataViewModel(Vts.FemModeling.MGRTE._2D.SimulationInput input)
{
_simulationInput = input;
TissueTypeVM = new OptionViewModel <string>("Tissue Type:", true, _simulationInput.TissueInput.TissueType);
_tissueTypeViewModel.PropertyChanged += (sender, args) =>
{
switch (_tissueTypeViewModel.SelectedValue)
{
case "MultiLayer":
_simulationInput.TissueInput = new MultiLayerTissueInput();
break;
throw new ArgumentOutOfRangeException();
}
UpdateTissueTypeVM(_simulationInput.TissueInput.TissueType);
};
UpdateTissueInputVM(_simulationInput.TissueInput);
}
/// <summary>
/// Execute MG RTE solver
/// </summary>
/// <param name="input">Simulation inputs</param>
/// <returns>measurements</returns>
public static Measurement ExecuteMGRTE(SimulationInput input)
{
int nMismatch;
int i, j, k, m, n;
int level;
double res = 0, res0 = 1, rho = 1.0;
int ds = input.MeshDataInput.SMeshLevel - input.SimulationOptionsInput.StartingSmeshLevel;
int da = input.MeshDataInput.AMeshLevel - input.SimulationOptionsInput.StartingAmeshLevel;
/* Read the initial time. */
DateTime startTime1 = DateTime.Now;
ILogger logger = LoggerFactoryLocator.GetDefaultNLogFactory().Create(typeof(SolverMGRTE));
// step 1: compute "level"
// level: the indicator of mesh levels in multigrid
switch (input.SimulationOptionsInput.MethodMg)
{
case 1:
level = da;
break;
case 2: //SMG:
level = ds;
break;
case 3: //MG1:
level = Math.Max(da, ds);
break;
case 4: //MG2:
level = ds + da;
break;
case 5: //MG3:
level = ds + da;
break;
case 6: //MG4_a:
level = ds + da;
break;
case 7: //MG4_s:
level = ds + da;
break;
default:
level = -1;
break;
}
//Create Dynamic arrays based on above values
var amesh = new AngularMesh[input.MeshDataInput.AMeshLevel + 1];
var smesh = new SpatialMesh[input.MeshDataInput.SMeshLevel + 1];
var b = new BoundaryCoupling[level + 1];
var noflevel = new int[level + 1][];
var ua = new double[input.MeshDataInput.SMeshLevel + 1][][];
var us = new double[input.MeshDataInput.SMeshLevel + 1][][];
var rhs = new double[level + 1][][][];
var d = new double[level + 1][][][];
var flux = new double[level + 1][][][];
var q = new double[level + 1][][][];
var mgrid = new MultiGridCycle();
var rteout = new OutputCalculation();
var tissueInput = (MultiEllipsoidTissueInput)input.TissueInput;
int incRegions = tissueInput.EllipsoidRegions.Length;
int tisRegions = tissueInput.LayerRegions.Length;
double depth = 0.0;
for (i = 1; i < tissueInput.LayerRegions.Length - 1; i++)
{
depth += ((LayerTissueRegion)(tissueInput.LayerRegions[i])).ZRange.Stop - ((LayerTissueRegion)(tissueInput.LayerRegions[i])).ZRange.Start;
}
input.MeshDataInput.SideLength = depth;
int totRegions = incRegions + tisRegions;
// MG-RTE does not converge when g = 1.0;
for (i = 0; i < totRegions; i++)
{
if (input.TissueInput.Regions[i].RegionOP.G >= 1.0)
{
input.TissueInput.Regions[i].RegionOP.G = 1.0 - 1e-5;
}
}
// Check refractive index mismatch
if (Math.Abs(input.TissueInput.Regions[0].RegionOP.N - input.TissueInput.Regions[1].RegionOP.N)
/ input.TissueInput.Regions[0].RegionOP.N < 0.01) // refraction index mismatch at the boundary
{
nMismatch = 1;
}
else
{
nMismatch = 0;
}
//Create spatial and angular mesh
MathFunctions.CreateSquareMesh(ref smesh, input.MeshDataInput.SMeshLevel, depth);
MathFunctions.AssignRegions(ref smesh, input.MeshDataInput.SMeshLevel, tissueInput);
MathFunctions.CreateAnglularMesh(ref amesh, input.MeshDataInput.AMeshLevel, tissueInput);
MathFunctions.SweepOrdering(ref smesh, amesh, input.MeshDataInput.SMeshLevel, input.MeshDataInput.AMeshLevel);
MathFunctions.SetMus(ref us, smesh, input);
MathFunctions.SetMua(ref ua, smesh, input);
// load optical property, angular mesh, and spatial mesh files
Initialization.Initial(
ref amesh, ref smesh, ref flux, ref d,
ref rhs, ref q, ref noflevel, ref b,
level, input.SimulationOptionsInput.MethodMg, nMismatch, input.SimulationOptionsInput.NExternal,
input.SimulationOptionsInput.NExternal, input.MeshDataInput.AMeshLevel, input.SimulationOptionsInput.StartingAmeshLevel,
input.MeshDataInput.SMeshLevel, input.SimulationOptionsInput.StartingSmeshLevel, ua, us, mgrid);
//Assign external source if available
if (input.ExtSourceInput != null)
{
IExtSource extsource = FemSourceFactory.GetExtSource(input.ExtSourceInput);
extsource.AssignMeshForExtSource(amesh, input.MeshDataInput.AMeshLevel, smesh, input.MeshDataInput.SMeshLevel, level, q);
}
//Assign internal source if available
if (input.IntSourceInput != null)
{
//Assign an internal source
IIntSource intsource = FemSourceFactory.GetIntSource(input.IntSourceInput);
intsource.AssignMeshForIntSource(amesh, input.MeshDataInput.AMeshLevel, smesh, input.MeshDataInput.SMeshLevel, level, rhs);
}
/* Read the end time. */
DateTime stopTime1 = DateTime.Now;
/* Compute and print the duration of this first task. */
TimeSpan duration1 = stopTime1 - startTime1;
logger.Info(() => "Initlalization for RTE_2D takes " + duration1.TotalSeconds + " seconds\n");
//step 2: RTE solver
DateTime startTime2 = DateTime.Now;
int ns = amesh[input.MeshDataInput.AMeshLevel].Ns;
if (input.SimulationOptionsInput.FullMg == 1)
{
int nt1, ns1;
int nt2 = smesh[noflevel[level][0]].Nt;
int ns2 = amesh[noflevel[level][1]].Ns;
for (n = level - 1; n >= 0; n--)
{
nt1 = smesh[noflevel[n][0]].Nt;
ns1 = amesh[noflevel[n][1]].Ns;
if (nt1 == nt2)
{
mgrid.FtoC_a(nt1, ns1, rhs[n + 1], rhs[n]);
}
else
{
if (ns1 == ns2)
{
mgrid.FtoC_s(nt1, ns1, rhs[n + 1], rhs[n], smesh[noflevel[n][0] + 1].Smap, smesh[noflevel[n][0] + 1].Fc);
}
else
{
mgrid.FtoC(nt1, ns1, rhs[n + 1], rhs[n], smesh[noflevel[n][0] + 1].Smap, smesh[noflevel[n][0] + 1].Fc);
}
}
nt2 = nt1; ns2 = ns1;
}
nt1 = smesh[noflevel[0][0]].Nt;
ns1 = amesh[noflevel[0][1]].Ns;
for (n = 0; n < level; n++)
{
if (input.SimulationOptionsInput.MethodMg == 6)
{
if (((level - n) % 2) == 0)
{
for (i = 0; i < input.SimulationOptionsInput.NCycle; i++)
{
res = mgrid.MgCycle(amesh, smesh, b, q, rhs, ua, us, flux, d, input.SimulationOptionsInput.NPreIterations, input.SimulationOptionsInput.NPostIterations,
noflevel[n][1], input.SimulationOptionsInput.StartingAmeshLevel, noflevel[n][0], input.SimulationOptionsInput.StartingSmeshLevel, ns, nMismatch, 6);
}
}
else
{
for (i = 0; i < input.SimulationOptionsInput.NCycle; i++)
{
mgrid.MgCycle(amesh, smesh, b, q, rhs, ua, us, flux, d, input.SimulationOptionsInput.NPreIterations, input.SimulationOptionsInput.NPostIterations,
noflevel[n][1], input.SimulationOptionsInput.StartingAmeshLevel, noflevel[n][0], input.SimulationOptionsInput.StartingSmeshLevel, ns, nMismatch, 7);
}
}
}
else
{
if (input.SimulationOptionsInput.MethodMg == 7)
{
if (((level - n) % 2) == 0)
{
for (i = 0; i < input.SimulationOptionsInput.NCycle; i++)
{
mgrid.MgCycle(amesh, smesh, b, q, rhs, ua, us, flux, d, input.SimulationOptionsInput.NPreIterations, input.SimulationOptionsInput.NPostIterations,
noflevel[n][1], input.SimulationOptionsInput.StartingAmeshLevel, noflevel[n][0], input.SimulationOptionsInput.StartingSmeshLevel, ns, nMismatch, 7);
}
}
else
{
for (i = 0; i < input.SimulationOptionsInput.NCycle; i++)
{
mgrid.MgCycle(amesh, smesh, b, q, rhs, ua, us, flux, d, input.SimulationOptionsInput.NPreIterations, input.SimulationOptionsInput.NPostIterations,
noflevel[n][1], input.SimulationOptionsInput.StartingAmeshLevel, noflevel[n][0], input.SimulationOptionsInput.StartingSmeshLevel, ns, nMismatch, 6);
}
}
}
else
{
for (i = 0; i < input.SimulationOptionsInput.NCycle; i++)
{
mgrid.MgCycle(amesh, smesh, b, q, rhs, ua, us, flux, d, input.SimulationOptionsInput.NPreIterations, input.SimulationOptionsInput.NPostIterations,
noflevel[n][1], input.SimulationOptionsInput.StartingAmeshLevel, noflevel[n][0], input.SimulationOptionsInput.StartingSmeshLevel, ns, nMismatch,
input.SimulationOptionsInput.MethodMg);
}
}
}
nt2 = smesh[noflevel[n + 1][0]].Nt;
ns2 = amesh[noflevel[n + 1][1]].Ns;
if (nt1 == nt2)
{
mgrid.CtoF_a(nt1, ns1, flux[n + 1], flux[n]);
}
else
{
if (ns1 == ns2)
{
mgrid.CtoF_s(nt1, ns1, flux[n + 1], flux[n], smesh[noflevel[n][0] + 1].Smap, smesh[noflevel[n][0] + 1].Cf);
}
else
{
mgrid.CtoF(nt1, ns1, flux[n + 1], flux[n], smesh[noflevel[n][0] + 1].Smap, smesh[noflevel[n][0] + 1].Cf);
}
}
nt1 = nt2; ns1 = ns2;
for (m = 0; m <= n; m++)
{
for (i = 0; i < amesh[noflevel[m][1]].Ns; i++)
{
for (j = 0; j < smesh[noflevel[m][0]].Nt; j++)
{
for (k = 0; k < 3; k++)
{
flux[m][i][j][k] = 0;
}
}
}
}
}
}
// 2.2. multigrid solver on the finest mesh
n = 0;
while (n < input.SimulationOptionsInput.NIterations)
{
n++;
res = mgrid.MgCycle(amesh, smesh, b, q, rhs, ua, us, flux, d, input.SimulationOptionsInput.NPreIterations, input.SimulationOptionsInput.NPostIterations, input.MeshDataInput.AMeshLevel,
input.SimulationOptionsInput.StartingAmeshLevel, input.MeshDataInput.SMeshLevel, input.SimulationOptionsInput.StartingSmeshLevel, ns, nMismatch, input.SimulationOptionsInput.MethodMg);
for (m = 0; m < level; m++)
{
for (i = 0; i < amesh[noflevel[m][1]].Ns; i++)
{
for (j = 0; j < smesh[noflevel[m][0]].Nt; j++)
{
for (k = 0; k < 3; k++)
{
flux[m][i][j][k] = 0;
}
}
}
}
if (n > 1)
{
rho *= res / res0;
logger.Info(() => "Iteration: " + n + ", Current tolerance: " + res + "\n");
if (res < input.SimulationOptionsInput.ConvTolerance)
{
rho = Math.Pow(rho, 1.0 / (n - 1));
n = input.SimulationOptionsInput.NIterations;
}
}
else
{
logger.Info(() => "Iteration: " + n + ", Current tolerance: " + res + "\n");
res0 = res;
if (res < input.SimulationOptionsInput.ConvTolerance)
{
n = input.SimulationOptionsInput.NIterations;
}
}
}
// 2.3. compute the residual
//Mgrid.Defect(amesh[para.AMeshLevel], smesh[para.SMeshLevel], ns, RHS[level], ua[para.SMeshLevel], us[para.SMeshLevel],
// flux[level], b[level], q[level], d[level], vacuum);
//res = Mgrid.Residual(smesh[para.SMeshLevel].nt, amesh[para.AMeshLevel].ns, d[level], smesh[para.SMeshLevel].a);
/* Read the start time. */
DateTime stopTime2 = DateTime.Now;
TimeSpan duration2 = stopTime2 - startTime2;
TimeSpan duration3 = stopTime2 - startTime1;
logger.Info(() => "Iteration time: " + duration2.TotalSeconds + "seconds\n");
logger.Info(() => "Total time: " + duration3.TotalSeconds + "seconds, Final residual: " + res + "\n");
// step 3: postprocessing
// 3.1. output
Measurement measurement = rteout.RteOutput(flux[level], q[level], amesh[input.MeshDataInput.AMeshLevel], smesh[input.MeshDataInput.SMeshLevel], b[level], nMismatch);
return(measurement);
}