Merge branch 'sprint1' of https://git.scc.kit.edu/rtsn/rtsn into sprint1

code/include/common/globalconstants.h

@@ -103,6 +103,7 @@ enum SOLVER_NAME {
     CSD_SN_FOKKERPLANCK_SOLVER,
     CSD_SN_FOKKERPLANCK_TRAFO_SOLVER,
     CSD_SN_FOKKERPLANCK_TRAFO_SOLVER_2D,
+    CSD_SN_FOKKERPLANCK_TRAFO_SH_SOLVER_2D,
     PN_SOLVER,
     MN_SOLVER
 };
@@ -113,6 +114,7 @@ inline std::map<std::string, SOLVER_NAME> Solver_Map{ { "SN_SOLVER", SN_SOLVER }
                                                       { "CSD_SN_FOKKERPLANCK_SOLVER", CSD_SN_FOKKERPLANCK_SOLVER },
                                                       { "CSD_SN_FOKKERPLANCK_TRAFO_SOLVER", CSD_SN_FOKKERPLANCK_TRAFO_SOLVER },
                                                       { "CSD_SN_FOKKERPLANCK_TRAFO_SOLVER_2D", CSD_SN_FOKKERPLANCK_TRAFO_SOLVER_2D },
+                                                      { "CSD_SN_FOKKERPLANCK_TRAFO_SH_SOLVER_2D", CSD_SN_FOKKERPLANCK_TRAFO_SH_SOLVER_2D },
                                                       { "PN_SOLVER", PN_SOLVER },
                                                       { "MN_SOLVER", MN_SOLVER } };
 

code/include/solvers/csdsolvertrafofpsh2d.h

+#ifndef CSDSOLVERTRAFOFPSH2D_H
+#define CSDSOLVERTRAFOFPSH2D_H
+
+// externals
+#include "spdlog/spdlog.h"
+#include <mpi.h>
+
+#include "common/config.h"
+#include "common/io.h"
+#include "fluxes/numericalflux.h"
+#include "icru.h"
+#include "kernels/scatteringkernelbase.h"
+#include "problems/problembase.h"
+#include "quadratures/quadraturebase.h"
+#include "solvers/snsolver.h"
+#include "sphericalharmonics.h"
+
+class Physics;
+
+class CSDSolverTrafoFPSH2D : public SNSolver
+{
+  private:
+    std::vector<double> _dose; /*! @brief: TODO */
+
+    // Physics acess
+    Vector _energies; /*! @brief: energy levels for CSD, lenght = _nEnergies */
+    Vector _angle;    /*! @brief: angles for SN */
+
+    std::vector<Matrix> _sigmaSE; /*!  @brief scattering cross section for all energies*/
+    Vector _sigmaTE;              /*!  @brief total cross section for all energies*/
+
+    Matrix _L;  /*!  @brief Laplace Beltrami Matrix */
+    Matrix _IL; /*!  @brief Laplace Beltrami Matrix */
+
+    Matrix _O;
+    Matrix _S;
+    Matrix _M;
+
+    VectorVector _quadPoints;
+    VectorVector _quadPointsSphere;
+    Vector _weights;
+    Vector _mu;
+    Vector _phi;
+    Vector _wp;
+    Vector _wa;
+
+    double _alpha;
+    double _alpha2;
+    double _beta;
+
+    Vector _xi1;
+    Vector _xi2;
+    Matrix _xi;
+
+    unsigned _FPMethod;
+
+    bool _RT;
+
+    double _energyMin;
+    double _energyMax;
+
+    void GenerateEnergyGrid( bool refinement );
+
+  public:
+    /**
+     * @brief CSDSolverTrafoFP2D constructor
+     * @param settings stores all needed information
+     */
+    CSDSolverTrafoFPSH2D( Config* settings );
+    /**
+     * @brief Solve functions runs main time loop
+     */
+    virtual void Solve();
+    /**
+     * @brief Output solution to VTK file
+     */
+    virtual void Save() const;
+    virtual void Save( int currEnergy ) const;
+};
+
+#endif    // CSDSOLVERTRAFOFPSH2D_H

code/src/solvers/csdsolvertrafofpsh2d.cpp

+#include "solvers/csdsolvertrafofpsh2d.h"
+
+CSDSolverTrafoFPSH2D::CSDSolverTrafoFPSH2D( Config* settings ) : SNSolver( settings ) {
+    _dose = std::vector<double>( _settings->GetNCells(), 0.0 );
+
+    // Set angle and energies
+    _energies  = Vector( _nEnergies, 0.0 );    // equidistant
+    _energyMin = 1e-4 * 0.511;
+    _energyMax = 10e0;
+
+    // write equidistant energy grid (false) or refined grid (true)
+    GenerateEnergyGrid( false );
+
+    // create quadrature
+    unsigned order    = _quadrature->GetOrder();
+    unsigned nq       = _settings->GetNQuadPoints();
+    _quadPoints       = _quadrature->GetPoints();
+    _weights          = _quadrature->GetWeights();
+    _quadPointsSphere = _quadrature->GetPointsSphere();
+
+    // transform structured quadrature
+    _mu  = Vector( 2 * order );
+    _phi = Vector( 2 * order );
+    _wp  = Vector( 2 * order );
+    _wa  = Vector( 2 * order );
+
+    // create quadrature 1D to compute mu grid
+    QuadratureBase* quad1D = QuadratureBase::CreateQuadrature( QUAD_GaussLegendre1D, 2 * order );
+    Vector w               = quad1D->GetWeights();
+    VectorVector muVec     = quad1D->GetPoints();
+    for( unsigned k = 0; k < 2 * order; ++k ) {
+        _mu[k] = muVec[k][0];
+        _wp[k] = w[k];
+    }
+
+    for( unsigned i = 0; i < 2 * order; ++i ) {
+        _phi[i] = ( i + 0.5 ) * M_PI / order;
+        _wa[i]  = M_PI / order;
+    }
+
+    _FPMethod = 2;
+
+    double DMinus = 0.0;
+    double DPlus  = 0.0;
+
+    Vector gamma( 2 * order, 0.0 );
+    double dPlus;
+    double c, K;
+
+    double dMinus = 0.0;
+    DPlus         = DMinus - 2 * _mu[0] * w[0];
+    for( unsigned j = 0; j < 2 * order - 1; ++j ) {
+        DMinus   = DPlus;
+        DPlus    = DMinus - 2 * _mu[j] * w[j];
+        dPlus    = ( sqrt( 1 - _mu[j + 1] * _mu[j + 1] ) - sqrt( 1 - _mu[j] * _mu[j] ) ) / ( _mu[j + 1] - _mu[j] );
+        c        = ( DPlus * dPlus - DMinus * dMinus ) / _wp[j];
+        K        = 2 * ( 1 - _mu[j] * _mu[j] ) + c * sqrt( 1 - _mu[j] * _mu[j] );
+        gamma[j] = M_PI * M_PI * K / ( 2 * order * ( 1 - std::cos( M_PI / order ) ) );
+        dMinus   = dPlus;
+    }
+
+    // Heney-Greenstein parameter
+    double g = 0.8;
+
+    // determine momente of Heney-Greenstein
+    _xi1 = Vector( _nEnergies, 1.0 - g );    // paper Olbrant, Frank (11)
+    _xi2 = Vector( _nEnergies, 4.0 / 3.0 - 2.0 * g + 2.0 / 3.0 * g * g );
+    _xi  = Matrix( 4, _nEnergies );
+    for( unsigned n = 0; n < _nEnergies; ++n ) {
+        _xi( 1, n ) = 1.0 - g;
+        _xi( 2, n ) = 4.0 / 3.0 - 2.0 * g + 2.0 / 3.0 * g * g;
+    }
+
+    // initialize stopping power vector
+    _s = Vector( _nEnergies, 1.0 );
+
+    _RT = true;
+
+    // read in medical data if radiation therapy option selected
+    if( _RT ) {
+        ICRU database( _mu, _energies );
+        database.GetTransportCoefficients( _xi );
+        database.GetStoppingPower( _s );
+    }
+
+    _quadPointsSphere = _quadrature->GetPointsSphere();
+
+    SphericalHarmonics sph( _nq );
+    Matrix Y = blaze::zero<double>( ( _nq + 1 ) * ( _nq + 1 ), _nq );
+
+    for( unsigned q = 0; q < _nq; q++ ) {
+        blaze::column( Y, q ) = sph.ComputeSphericalBasis( _quadPointsSphere[q][0], _quadPointsSphere[q][1] );
+    }
+
+    _O = blaze::trans( Y );
+    _M = _O;
+
+    for( unsigned j = 0; j < _nq; ++j ) {
+        blaze::column( _M, j ) *= _weights;
+    }
+
+    _M.transpose();
+
+    _S               = Matrix( ( _nq + 1 ) * ( _nq + 1 ), ( _nq + 1 ) * ( _nq + 1 ), 0.0 );
+    unsigned counter = 0;
+    for( unsigned l = 0; l < _nq + 1; ++l ) {
+        for( int m = -static_cast<int>( l ); m <= static_cast<int>( l ); ++m ) {
+            if( !_RT ) {
+                _S( counter, counter ) = std::pow( g, l );
+            }
+            else
+                _S( counter, counter ) = -l * ( l + 1 );
+            counter++;
+        }
+    }
+
+    Vector v = ( _O * _S * _M ) * Vector( _nq, 1.0 );
+    for( unsigned q = 0; q < _nq; ++q ) {
+        blaze::column( _O, q ) /= v[q];
+    }
+
+    _density = std::vector<double>( _nCells, 1.0 );
+
+    _L = _O * _S * _M;
+}
+
+void CSDSolverTrafoFPSH2D::Solve() {
+    std::cout << "Solve SH" << std::endl;
+    auto log = spdlog::get( "event" );
+
+    // save original energy field for boundary conditions
+    auto energiesOrig = _energies;
+
+    // setup incoming BC on left
+    _sol = VectorVector( _density.size(), Vector( _settings->GetNQuadPoints(), 0.0 ) );    // hard coded IC, needs to be changed
+    for( unsigned k = 0; k < _nq; ++k ) {
+        if( _quadPoints[k][0] > 0 && !_RT ) _sol[0][k] = 1e5 * exp( -10.0 * pow( 1.0 - _quadPoints[k][0], 2 ) );
+    }
+    // hard coded boundary type for 1D testcases (otherwise cells will be NEUMANN)
+    _boundaryCells[0]           = BOUNDARY_TYPE::DIRICHLET;
+    _boundaryCells[_nCells - 1] = BOUNDARY_TYPE::DIRICHLET;
+
+    // setup identity matrix for FP scattering
+    Matrix identity( _nq, _nq, 0.0 );
+    for( unsigned k = 0; k < _nq; ++k ) identity( k, k ) = 1.0;
+
+    // angular flux at next time step
+    VectorVector psiNew( _nCells, Vector( _nq, 0.0 ) );
+    double dFlux = 1e10;
+    Vector fluxNew( _nCells, 0.0 );
+    Vector fluxOld( _nCells, 0.0 );
+    // for( unsigned j = 0; j < _nCells; ++j ) {
+    //    fluxOld[j] = dot( _sol[j], _weights );
+    //}
+
+    int rank;
+    MPI_Comm_rank( MPI_COMM_WORLD, &rank );
+    if( rank == 0 ) log->info( "{:10}   {:10}", "E", "dFlux" );
+
+    // do substitution from psi to psiTildeHat (cf. Dissertation Kerstion Kuepper, Eq. 1.23)
+    for( unsigned j = 0; j < _nCells; ++j ) {
+        for( unsigned k = 0; k < _nq; ++k ) {
+            _sol[j][k] = _sol[j][k] * _density[j] * _s[_nEnergies - 1];    // note that _s[_nEnergies - 1] is stopping power at highest energy
+        }
+    }
+
+    // store transformed energies ETilde instead of E in _energies vector (cf. Dissertation Kerstion Kuepper, Eq. 1.25)
+    double tmp   = 0.0;
+    _energies[0] = 0.0;
+    for( unsigned n = 1; n < _nEnergies; ++n ) {
+        tmp          = tmp + _dE * 0.5 * ( 1.0 / _s[n] + 1.0 / _s[n - 1] );
+        _energies[n] = tmp;
+    }
+
+    // store transformed energies ETildeTilde instead of ETilde in _energies vector (cf. Dissertation Kerstion Kuepper, Eq. 1.25)
+    for( unsigned n = 0; n < _nEnergies; ++n ) {
+        _energies[n] = _energies[_nEnergies - 1] - _energies[n];
+    }
+
+    // determine minimal density for CFL computation
+    double densityMin = _density[0];
+    for( unsigned j = 1; j < _nCells; ++j ) {
+        if( densityMin > _density[j] ) densityMin = _density[j];
+    }
+
+    // cross sections do not need to be transformed to ETilde energy grid since e.g. TildeSigmaT(ETilde) = SigmaT(E(ETilde))
+
+    // loop over energies (pseudo-time)
+    for( unsigned n = 0; n < _nEnergies - 1; ++n ) {
+        _dE = fabs( _energies[n + 1] - _energies[n] );    // is the sign correct here?
+
+        double xi1 = _xi( 1, _nEnergies - n - 1 );
+        double xi2 = _xi( 2, _nEnergies - n - 1 );
+        double xi3 = _xi( 3, _nEnergies - n - 1 );
+
+        // setup coefficients in FP step
+        if( _FPMethod == 1 ) {
+            _alpha  = 0.0;
+            _alpha2 = xi1 / 2.0;
+            _beta   = 0.0;
+        }
+        else if( _FPMethod == 2 ) {
+            _alpha  = xi1 / 2.0 + xi2 / 8.0;
+            _alpha2 = 0.0;
+            _beta   = xi2 / 8.0 / xi1;
+        }
+        else if( _FPMethod == 3 ) {
+            _alpha  = xi2 * ( 27.0 * xi2 * xi2 + 5.0 * xi3 * xi3 - 24.0 * xi2 * xi3 ) / ( 8.0 * xi3 * ( 3.0 * xi2 - 2.0 * xi3 ) );
+            _beta   = xi3 / ( 6.0 * ( 3.0 * xi2 - 2.0 * xi3 ) );
+            _alpha2 = xi1 / 2.0 - 9.0 / 8.0 * xi2 * xi2 / xi3 + 3.0 / 8.0 * xi2;
+        }
+
+        _IL = identity - _beta * _L;
+
+        // write BC for water phantom
+        if( _RT ) {
+            for( unsigned k = 0; k < _nq; ++k ) {
+                if( _quadPoints[k][0] > 0 ) {
+                    _sol[0][k] = 1e5 * exp( -200.0 * pow( 1.0 - _quadPoints[k][0], 2 ) ) *
+                                 exp( -50.0 * pow( _energyMax - energiesOrig[_nEnergies - n - 1], 2 ) ) * _density[0] * _s[_nEnergies - n - 1];
+                }
+            }
+        }
+
+        // add FP scattering term implicitly
+#pragma omp parallel for
+        for( unsigned j = 0; j < _nCells; ++j ) {
+            if( _boundaryCells[j] == BOUNDARY_TYPE::DIRICHLET ) continue;
+            //_sol[j] = blaze::solve( identity - _dE * _alpha2 * _L, psiNew[j] );
+            _sol[j] = _IL * blaze::solve( _IL - _dE * _alpha * _L, _sol[j] );
+        }
+
+// loop over all spatial cells
+#pragma omp parallel for
+        for( unsigned j = 0; j < _nCells; ++j ) {
+            if( _boundaryCells[j] == BOUNDARY_TYPE::DIRICHLET ) continue;
+            // loop over all ordinates
+            for( unsigned i = 0; i < _nq; ++i ) {
+                psiNew[j][i] = 0.0;
+                // loop over all neighbor cells (edges) of cell j and compute numerical fluxes
+                for( unsigned idx_neighbor = 0; idx_neighbor < _neighbors[j].size(); ++idx_neighbor ) {
+                    // store flux contribution on psiNew_sigmaS to save memory
+                    if( _boundaryCells[j] == BOUNDARY_TYPE::NEUMANN && _neighbors[j][idx_neighbor] == _nCells )
+                        continue;    // adiabatic wall, add nothing
+                    else
+                        psiNew[j][i] += _g->Flux( _quadPoints[i],
+                                                  _sol[j][i] / _density[j],
+                                                  _sol[_neighbors[j][idx_neighbor]][i] / _density[_neighbors[j][idx_neighbor]],
+                                                  _normals[j][idx_neighbor] ) /
+                                        _areas[j];
+                }
+                // time update angular flux with numerical flux and total scattering cross section
+                psiNew[j][i] = _sol[j][i] - _dE * psiNew[j][i];
+            }
+        }
+
+#pragma omp parallel for
+        for( unsigned j = 0; j < _nCells; ++j ) {
+            if( _boundaryCells[j] == BOUNDARY_TYPE::DIRICHLET ) continue;
+            _sol[j] = psiNew[j];
+        }
+
+        for( unsigned j = 0; j < _nCells; ++j ) {
+            fluxNew[j] = dot( _sol[j], _weights );
+            if( n > 0 ) {
+                _dose[j] += 0.5 * _dE * ( fluxNew[j] * _s[_nEnergies - n - 1] + fluxOld[j] * _s[_nEnergies - n] ) /
+                            _density[j];    // update dose with trapezoidal rule
+            }
+            else {
+                _dose[j] += _dE * fluxNew[j] * _s[_nEnergies - n - 1] / _density[j];
+            }
+            _solverOutput[j] = fluxNew[j];
+        }
+
+        // Save( n );
+        dFlux   = blaze::l2Norm( fluxNew - fluxOld );
+        fluxOld = fluxNew;
+        if( rank == 0 )
+            log->info( "{:03.8f}  {:03.8f}  {:01.5e}  {:01.5e}", energiesOrig[_nEnergies - n - 1], _energies[n], _dE / densityMin, dFlux );
+        if( std::isinf( dFlux ) || std::isnan( dFlux ) ) break;
+    }
+    Save( 1 );
+}
+
+void CSDSolverTrafoFPSH2D::Save() const {
+    std::vector<std::string> fieldNames{ "dose", "normalized dose" };
+    std::vector<std::vector<double>> dose( 1, _dose );
+    std::vector<std::vector<double>> normalizedDose( 1, _dose );
+    double maxDose = *std::max_element( _dose.begin(), _dose.end() );
+    for( unsigned i = 0; i < _dose.size(); ++i ) normalizedDose[0][i] /= maxDose;
+    std::vector<std::vector<std::vector<double>>> results{ dose, normalizedDose };
+    ExportVTK( _settings->GetOutputFile(), results, fieldNames, _mesh );
+}
+
+void CSDSolverTrafoFPSH2D::Save( int currEnergy ) const {
+    std::vector<std::string> fieldNames{ "flux" };
+    std::vector<std::vector<double>> scalarField( 1, _solverOutput );
+    std::vector<std::vector<std::vector<double>>> results{ scalarField };
+    ExportVTK( _settings->GetOutputFile() + "_" + std::to_string( currEnergy ), results, fieldNames, _mesh );
+}
+
+void CSDSolverTrafoFPSH2D::GenerateEnergyGrid( bool refinement ) {
+    _dE = ComputeTimeStep( _settings->GetCFL() );
+    if( !refinement ) {
+        _nEnergies = unsigned( ( _energyMax - _energyMin ) / _dE );
+        _energies.resize( _nEnergies );
+        for( unsigned n = 0; n < _nEnergies; ++n ) {
+            _energies[n] = _energyMin + ( _energyMax - _energyMin ) / ( _nEnergies - 1 ) * n;
+        }
+    }
+    else {
+        // hard-coded positions for energy-grid refinement
+        double energySwitch    = 0.58;
+        double energySwitchMin = 0.03;
+
+        // number of energies per intervals [E_min,energySwitchMin], [energySwitchMin,energySwitch], [energySwitch,E_Max]
+        unsigned nEnergies1 = unsigned( ( _energyMax - energySwitch ) / _dE );
+        unsigned nEnergies2 = unsigned( ( energySwitch - energySwitchMin ) / ( _dE / 2 ) );
+        unsigned nEnergies3 = unsigned( ( energySwitchMin - _energyMin ) / ( _dE / 3 ) );
+        _nEnergies          = nEnergies1 + nEnergies2 + nEnergies3 - 2;
+        _energies.resize( _nEnergies );
+
+        // write equidistant energy grid in each interval
+        for( unsigned n = 0; n < nEnergies3; ++n ) {
+            _energies[n] = _energyMin + ( energySwitchMin - _energyMin ) / ( nEnergies3 - 1 ) * n;
+        }
+        for( unsigned n = 1; n < nEnergies2; ++n ) {
+            _energies[n + nEnergies3 - 1] = energySwitchMin + ( energySwitch - energySwitchMin ) / ( nEnergies2 - 1 ) * n;
+        }
+        for( unsigned n = 1; n < nEnergies1; ++n ) {
+            _energies[n + nEnergies3 + nEnergies2 - 2] = energySwitch + ( _energyMax - energySwitch ) / ( nEnergies1 - 1 ) * n;
+        }
+    }
+}

code/src/solvers/solverbase.cpp

@@ -11,6 +11,7 @@
 #include "solvers/csdsnsolvernotrafo.h"
 #include "solvers/csdsolvertrafofp.h"
 #include "solvers/csdsolvertrafofp2d.h"
+#include "solvers/csdsolvertrafofpsh2d.h"
 #include "solvers/mnsolver.h"
 #include "solvers/pnsolver.h"
 #include "solvers/snsolver.h"
@@ -84,6 +85,7 @@ Solver* Solver::Create( Config* settings ) {
         case CSD_SN_FOKKERPLANCK_SOLVER: return new CSDSNSolverFP( settings );
         case CSD_SN_FOKKERPLANCK_TRAFO_SOLVER: return new CSDSolverTrafoFP( settings );
         case CSD_SN_FOKKERPLANCK_TRAFO_SOLVER_2D: return new CSDSolverTrafoFP2D( settings );
+        case CSD_SN_FOKKERPLANCK_TRAFO_SH_SOLVER_2D: return new CSDSolverTrafoFPSH2D( settings );
         case PN_SOLVER: return new PNSolver( settings );
         case MN_SOLVER: return new MNSolver( settings );
         default: return new SNSolver( settings );