Merge branch 'develop' into spherical_harmonics_nn

KiT-RT · Nov 14, 2023 · fa9a8d7 · fa9a8d7
2 parents 17b9d0a + 22a5c21
commit fa9a8d7
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Showing 5 changed files with 25 additions and 20 deletions.
diff --git a/README.md b/README.md
@@ -140,13 +140,12 @@ ldconfig /usr/local/lib
 ```
 ## Cite
 ```
-@article{kitrt,
-  author = {Schotthöfer, Steffen and Kusch, Jonas and Stammer, Pia and Wolters, Jannick and Xiao, Tianbai },
-  title = {KiT-RT: Kinetic Transport for Radio Therapy Solver},
-  year = {2022},
-  publisher = {GitHub},
-  journal = {GitHub repository},
-  howpublished = {\url{https://github.com/CSMMLab/KiT-RT}},
-  commit = {b9943e1aae6a54c2c3d2033d168de1ab7912ae75}
+@misc{kitrt2022,
+      title={KiT-RT: An extendable framework for radiative transfer and therapy}, 
+      author={Jonas Kusch and Steffen Schotthöfer and Pia Stammer and Jannick Wolters and Tianbai Xiao},
+      year={2022},
+      eprint={2205.08417},
+      archivePrefix={arXiv},
+      primaryClass={physics.med-ph}
 }
 ```
diff --git a/examples/configs/DataGeneratorRegression2D.cfg b/examples/configs/DataGeneratorRegression2D.cfg
@@ -1,7 +1,7 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %  Data Generator for                  % 
 %   Neural Entropy Closure             %
-%  Author <Steffen Schotthöfer>		   %
+%  Author <Steffen Schotthöfer>		     %
 %  Date   17.12.2020                   %
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %
@@ -11,16 +11,22 @@ SAMPLER_NAME = REGRESSION_SAMPLER
 TRAINING_SET_SIZE = 10000
 SIZE_BY_DIMENSION = NO
 MAX_VALUE_FIRST_MOMENT = 1
-SPATIAL_DIM = 2
-MAX_MOMENT_SOLVER = 1
-REALIZABLE_SET_EPSILON_U1 = 0.08
-REALIZABLE_SET_EPSILON_U0 = 0.08
+
 NORMALIZED_SAMPLING = YES
 ALPHA_SAMPLING = YES
 UNIFORM_SAMPLING = NO
-ALPHA_SAMPLING_BOUND = 30
-MIN_EIGENVALUE_THRESHOLD = 1e-9
-REALIZABILITY_RECONSTRUCTION = NO
+
+
+%Configure the spatial dimension of the closure here
+SPATIAL_DIM = 2
+
+%Configure the maximum moment of the closure here
+MAX_MOMENT_SOLVER = 1
+
+% Determine, how close to the boundary you want to sample. Higher alpha inplies harder training
+ALPHA_SAMPLING_BOUND = 10
+% Higher eigenvalue treshold implies larger distance to the boundary
+MIN_EIGENVALUE_THRESHOLD = 1e-4
 
 %
 % ---- File specifications ----
@@ -31,7 +37,7 @@ OUTPUT_DIR = ../result
 OUTPUT_FILE = DataGenerator2D
 % Log directory
 LOG_DIR = ../result/logs
-LOG_FILE = dataGen2D
+LOG_FILE = Monomial_M1_2D_normal_gaussian
 
 %
 % --- Spherical Basis ----
@@ -42,6 +48,7 @@ SPHERICAL_BASIS = SPHERICAL_MONOMIALS
 % --- Entropy settings ----
 ENTROPY_FUNCTIONAL = MAXWELL_BOLTZMANN
 ENTROPY_OPTIMIZER = NEWTON
+REALIZABILITY_RECONSTRUCTION = NO
 %
 % ----- Newton Solver Specifications ----
 %

diff --git a/src/common/mesh.cpp b/src/common/mesh.cpp
@@ -17,7 +17,6 @@ Mesh::Mesh( std::vector<Vector> nodes,
     ComputeCellMidpoints();
     ComputeConnectivity();
     ComputeBounds();
-    // ComputeCellInterfaceMidpoints();
 }
 
 Mesh::~Mesh() {}

diff --git a/src/problems/starmapvalidation.cpp b/src/problems/starmapvalidation.cpp
@@ -88,7 +88,6 @@ StarMapValidation_Moment::StarMapValidation_Moment( Config* settings, Mesh* mesh
 StarMapValidation_Moment::~StarMapValidation_Moment() {}
 
 VectorVector StarMapValidation_Moment::SetupIC() {
-
     SphericalBase* tempBase  = SphericalBase::Create( _settings );
     unsigned ntotalEquations = tempBase->GetBasisSize();
     delete tempBase;
@@ -103,6 +102,7 @@ VectorVector StarMapValidation_Moment::SetupIC() {
         x                            = cellMidpoints[idx_cell][0];
         y                            = cellMidpoints[idx_cell][1];
         f                            = NormPDF( x, pos_beam[0], stddev ) * NormPDF( y, pos_beam[1], stddev );
+
         initialSolution[idx_cell][0] = f * StarMAPmoments[0];
         for( unsigned idx_sys = 1; idx_sys < ntotalEquations; idx_sys++ ) {
             initialSolution[idx_cell][idx_sys] = f * StarMAPmoments[idx_sys];    // must be VectorVector

diff --git a/src/solvers/csdmnsolver.cpp b/src/solvers/csdmnsolver.cpp
@@ -76,7 +76,7 @@ void CSDMNSolver::IterPreprocessing( unsigned idx_iter ) {
     _optimizer->SolveMultiCell( _alpha, _sol, _momentBasis, alpha_norm_dummy );
 
     // ------- Solution reconstruction step ----
-    //#pragma omp parallel for
+#pragma omp parallel for
     for( unsigned idx_cell = 0; idx_cell < _nCells; idx_cell++ ) {
         for( unsigned idx_quad = 0; idx_quad < _nq; idx_quad++ ) {
             // compute the kinetic density at all grid cells