solver according to Mevenkamp thesis added

code/include/common/globalconstants.h

@@ -89,10 +89,10 @@ enum KERNEL_NAME { KERNEL_Isotropic, KERNEL_Isotropic1D };
 inline std::map<std::string, KERNEL_NAME> Kernel_Map{ { "ISOTROPIC", KERNEL_Isotropic }, { "ISOTROPIC_1D", KERNEL_Isotropic1D } };
 
 // Solver name
-enum SOLVER_NAME { SN_SOLVER, CSD_SN_SOLVER, PN_SOLVER, MN_SOLVER };
+enum SOLVER_NAME { SN_SOLVER, CSD_SN_SOLVER, CSD_SN_NOTRAFO_SOLVER, PN_SOLVER, MN_SOLVER };
 
 inline std::map<std::string, SOLVER_NAME> Solver_Map{
-    { "SN_SOLVER", SN_SOLVER }, { "CSD_SN_SOLVER", CSD_SN_SOLVER }, { "PN_SOLVER", PN_SOLVER }, { "MN_SOLVER", MN_SOLVER } };
+    { "SN_SOLVER", SN_SOLVER }, { "CSD_SN_SOLVER", CSD_SN_SOLVER },{ "CSD_SN_NOTRAFO_SOLVER", CSD_SN_NOTRAFO_SOLVER }, { "PN_SOLVER", PN_SOLVER }, { "MN_SOLVER", MN_SOLVER } };
 
 // Entropy functional
 enum ENTROPY_NAME { QUADRATIC, MAXWELL_BOLZMANN, BOSE_EINSTEIN, FERMI_DIRAC };

code/include/solvers/csdsnsolvernotrafo.h

+#ifndef CSDSNSOLVERNOTRAFO_H
+#define CSDSNSOLVERNOTRAFO_H
+
+#include "solvers/snsolver.h"
+
+class Physics;
+
+class CSDSNSolverNoTrafo : 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 */
+    Vector _density;  /*! @brief: patient density for each grid cell */
+
+    std::vector<Matrix> _sigmaSE; /*!  @brief scattering cross section for all energies*/
+    Vector _sigmaTE;              /*!  @brief total cross section for all energies*/
+
+  public:
+    /**
+     * @brief CSDSNSolverNoTrafo constructor
+     * @param settings stores all needed information
+     */
+    CSDSNSolverNoTrafo( 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 // CSDSNSOLVERNOTRAFO_H

code/input/example_csd_1d.cfg

@@ -3,12 +3,12 @@ OUTPUT_FILE = example_csd_1d
 LOG_DIR = ../result/logs
 MESH_FILE = 1DMesh.su2
 PROBLEM = WATERPHANTOM
-SOLVER = CSD_SN_SOLVER
+SOLVER = CSD_SN_NOTRAFO_SOLVER
 CONTINUOUS_SLOWING_DOWN = YES
 HYDROGEN_FILE = ENDL_H.txt
 OXYGEN_FILE = ENDL_O.txt
 KERNEL = ISOTROPIC_1D
-CFL_NUMBER = 0.001
+CFL_NUMBER = 0.01
 TIME_FINAL = 1.0
 CLEAN_FLUX_MATRICES = NO
 

code/src/solvers/csdsnsolvernotrafo.cpp

+#include "solvers/csdsnsolvernotrafo.h"
+#include "common/config.h"
+#include "common/io.h"
+#include "fluxes/numericalflux.h"
+#include "kernels/scatteringkernelbase.h"
+#include "problems/problembase.h"
+
+// externals
+#include "spdlog/spdlog.h"
+#include <mpi.h>
+
+CSDSNSolverNoTrafo::CSDSNSolverNoTrafo( Config* settings ) : SNSolver( settings ) {
+    _dose = std::vector<double>( _settings->GetNCells(), 0.0 );
+
+    // Set angle and energies
+    _angle           = Vector( _settings->GetNQuadPoints(), 0.0 );    // my
+    _energies        = Vector( _nEnergies, 0.0 );                     // equidistant
+    double energyMin = 1e-1;
+    double energyMax = 5e0;
+    // write equidistant energy grid
+
+    _dE        = ComputeTimeStep( settings->GetCFL() );
+    _nEnergies = unsigned( ( energyMax - energyMin ) / _dE );
+    _energies.resize( _nEnergies );
+    for( unsigned n = 0; n < _nEnergies; ++n ) {
+        _energies[n] = energyMin + ( energyMax - energyMin ) / ( _nEnergies - 1 ) * n;
+    }
+    // write mu grid
+    Matrix muMatrix( _settings->GetNQuadPoints(), _settings->GetNQuadPoints() );
+    for( unsigned l = 0; l < _settings->GetNQuadPoints(); ++l ) {
+        for( unsigned k = 0; k < _settings->GetNQuadPoints(); ++k ) {
+            double inner = 0.0;
+            for( unsigned j = 0; j < 3; ++j ) {
+                inner += _quadPoints[l][j] * _quadPoints[k][j];    // compute mu at Omega_l*Omega_k
+            }
+            muMatrix( l, k ) = inner;
+        }
+    }
+
+    _sigmaSE = _problem->GetScatteringXSE( _energies, muMatrix );
+    _sigmaTE = _problem->GetTotalXSE( _energies );    // M_PI * 1e19 *
+    // compute scaling s.t. scattering kernel integrates to one for chosen quadrature
+    for( unsigned n = 0; n < _nEnergies; ++n ) {
+        for( unsigned p = 0; p < _nq; ++p ) {
+            double cp = 0.0;
+            for( unsigned q = 0; q < _nq; ++q ) {
+                cp += _weights[q] * _sigmaSE[n]( p, q );
+            }
+            for( unsigned q = 0; q < _nq; ++q ) {
+                _sigmaSE[n]( p, q ) = _sigmaTE[n] / cp * _sigmaSE[n]( p, q );
+            }
+        }
+    }
+
+    _s = _problem->GetStoppingPower( _energies );
+    _Q = _problem->GetExternalSource( _energies );
+
+    // recompute scattering kernel. TODO: add this to kernel function
+    for( unsigned p = 0; p < _nq; ++p ) {
+        for( unsigned q = 0; q < _nq; ++q ) {
+            _scatteringKernel( p, q ) = 0.0;
+        }
+        _scatteringKernel( p, p ) = _weights[p];
+    }
+    // Get patient density
+    _density = Vector( _nCells, 1.0 );
+}
+
+void CSDSNSolverNoTrafo::Solve() {
+    std::cout << "Solve" << std::endl;
+    auto log = spdlog::get( "event" );
+
+    // angular flux at next time step (maybe store angular flux at all time steps, since time becomes energy?)
+    VectorVector psiNew( _nCells, Vector( _nq, 0.0 ) );
+    double dFlux = 1e10;
+    Vector fluxNew( _nCells, 0.0 );
+    Vector fluxOld( _nCells, 0.0 );
+
+    int rank;
+    MPI_Comm_rank( MPI_COMM_WORLD, &rank );
+    if( rank == 0 ) log->info( "{:10}   {:10}", "E", "dFlux" );
+
+    // revert energies and stopping power
+    Vector sSave = _s;
+    for( unsigned n = 0; n < _nEnergies; ++n ) {
+        _energies[n] = _energies[_nEnergies - 1] - _energies[n];
+        _s[n] = sSave[_nEnergies-1-n];
+    }
+
+    for( unsigned j = 0; j < _nCells; ++j ) {
+        for( unsigned k = 0; k<_nq; ++k){
+            fluxOld[j] += _weights[k]*_sol[j][k]*_s[0];
+        }
+    }
+
+    // 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?
+        // loop over all spatial cells
+        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],
+                                                  _sol[_neighbors[j][idx_neighbor]][i],
+                                                  _normals[j][idx_neighbor] ) /
+                                        _areas[j]/(_density[j]*_s[n+1]);
+                }
+                // time update angular flux with numerical flux and total scattering cross section
+                psiNew[j][i] = _sol[j][i] - _dE * psiNew[j][i] - _dE * _sigmaTE[_nEnergies - n - 1] * _sol[j][i]/(_density[j]*_s[n+1]) + (_s[n]/_s[n+1]-1)*_sol[j][i];
+            }
+            // compute scattering effects (_scatteringKernel is simply multiplication with quad weights)
+            psiNew[j] += _dE * ( _sigmaSE[_nEnergies - n - 1] * _scatteringKernel * _sol[j] )/(_density[j]*_s[n+1]);    // multiply scattering matrix with psi
+            // TODO: Check if _sigmaS^T*psi is correct
+
+            // TODO: figure out a more elegant way
+            // add external source contribution
+            /*
+            if( _Q.size() == 1u ) {            // constant source for all energies
+                if( _Q[0][j].size() == 1u )    // isotropic source
+                    psiNew[j] += _dE * _Q[0][j][0] * _s[_nEnergies - n - 1];
+                else
+                    psiNew[j] += _dE * _Q[0][j] * _s[_nEnergies - n - 1];
+            }
+            else {
+                if( _Q[0][j].size() == 1u )    // isotropic source
+                    psiNew[j] += _dE * _Q[n][j][0] * _s[_nEnergies - n - 1];
+                else
+                    psiNew[j] += _dE * _Q[n][j] * _s[_nEnergies - n - 1];
+            }
+            */
+        }
+        _sol = psiNew;
+
+        for( unsigned j = 0; j < _nCells; ++j ) {
+            fluxNew[j] = 0.0;
+            for( unsigned k = 0; k<_nq; ++k){
+                fluxNew[j] += _weights[k]*_sol[j][k]*_s[n+1];
+            }
+            _dose[j] += 0.5 * _dE * ( fluxNew[j] + fluxOld[j] );    // update dose with trapezoidal rule
+            _solverOutput[j] = fluxNew[j];
+        }
+
+        // Save( n );
+        dFlux   = blaze::l2Norm( fluxNew - fluxOld );
+        fluxOld = fluxNew;
+        std::cout << _energies[n] << " " << dFlux << std::endl;
+        if( rank == 0 ) log->info( "{:03.8f}  {:01.5e}  {:01.5e}", _energies[n], _dE / densityMin, dFlux );
+        if( std::isinf( dFlux ) || std::isnan( dFlux ) ) break;
+    }
+}
+
+void CSDSNSolverNoTrafo::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 CSDSNSolverNoTrafo::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 );
+}

code/src/solvers/solverbase.cpp

@@ -10,6 +10,7 @@
 #include "solvers/mnsolver.h"
 #include "solvers/pnsolver.h"
 #include "solvers/snsolver.h"
+#include "solvers/csdsnsolvernotrafo.h"
 
 Solver::Solver( Config* settings ) : _settings( settings ) {
     // @TODO save parameters from settings class
@@ -72,6 +73,7 @@ Solver* Solver::Create( Config* settings ) {
     switch( settings->GetSolverName() ) {
         case SN_SOLVER: return new SNSolver( settings );
         case CSD_SN_SOLVER: return new CSDSNSolver( settings );
+        case CSD_SN_NOTRAFO_SOLVER: return new CSDSNSolverNoTrafo( settings );
         case PN_SOLVER: return new PNSolver( settings );
         case MN_SOLVER: return new MNSolver( settings );
         default: return new SNSolver( settings );