Merge branch 'fixDoxygenModules' into 'develop'

Move doxygen documentation for classes and functions to actual classes and functions

See merge request !391

Fixes #187

src/gpu/GridGenerator/grid/MultipleGridBuilderFacade.h

@@ -30,8 +30,6 @@
 //! \ingroup gpu_GridGenerator GridGenerator
 //! \{
 //! \author Anna Wellmann
-//! \brief A class that makes the setup of simulations on multiple gpus easier
-//! \details Using this class is optional.
 
 //=======================================================================================
 
@@ -58,8 +56,9 @@ class FileCollection;
 
 //! \class MultipleGridBuilderFacade
 //! \brief Simplifies the creation of the grids for a multi-gpu simulation
+//! \details Using this class is optional.
 //!
-//! \details Steps to set up the grids:
+//! Steps to set up the grids:
 //!
 //! - 1. initialize class with a MultipleGridBuilder and the dimensions of the entire domain
 //!

src/gpu/core/DataStructureInitializer/GridReaderGenerator/IndexRearrangementForStreams.cpp

@@ -30,7 +30,6 @@
 //! \ingroup gpu_core core
 //! \{
 //! \author Anna Wellmann
-//! \details See [master thesis of Anna Wellmann]
 //=======================================================================================
 #include "IndexRearrangementForStreams.h"
 

src/gpu/core/DataStructureInitializer/GridReaderGenerator/IndexRearrangementForStreams.h

@@ -30,7 +30,6 @@
 //! \ingroup gpu_core core
 //! \{
 //! \author Anna Wellmann
-//! \details See [master thesis of Anna Wellmann]
 //=======================================================================================
 #ifndef IndexRearrangementForStreams_H
 #define IndexRearrangementForStreams_H
@@ -47,10 +46,14 @@ namespace vf::parallel
 class Communicator;
 }
 
+//! \brief class that is used to rearrange the arrays of node indices for communication between gpus. The rearrangement is
+//! needed for communication hiding with cuda streams
+//! \details This class changes the order of the node indices that are needed for communication between gpus. The indices are
+//! reordered so that they can be split into two groups: nodes that are part if the interpolation between grid levels, and
+//! nodes that are not. These groups are needed for communication hiding. For details see [master thesis of Anna Wellmann]
 class IndexRearrangementForStreams
 {
 public:
-    //! \brief Construct IndexRearrangementForStreams object
     IndexRearrangementForStreams(std::shared_ptr<Parameter> para, std::shared_ptr<GridBuilder> builder, vf::parallel::Communicator& communicator);
 
     virtual ~IndexRearrangementForStreams() = default;

src/gpu/core/DataStructureInitializer/GridReaderGenerator/IndexRearrangementForStreamsTest.cpp

@@ -30,7 +30,6 @@
 //! \ingroup gpu_core_tests core
 //! \{
 //! \author Anna Wellmann
-//! \details See [master thesis of Anna Wellmann]
 //=======================================================================================
 #include <gmock/gmock.h>
 

src/gpu/core/DataStructureInitializer/GridReaderGenerator/InterpolationCellGrouper.cpp

@@ -30,7 +30,6 @@
 //! \ingroup gpu_core core
 //! \{
 //! \author Anna Wellmann
-//! \details See [master thesis of Anna Wellmann]
 //=======================================================================================
 #include "InterpolationCellGrouper.h"
 

src/gpu/core/DataStructureInitializer/GridReaderGenerator/InterpolationCellGrouper.h

@@ -30,7 +30,6 @@
 //! \ingroup gpu_core core
 //! \{
 //! \author Anna Wellmann
-//! \details See [master thesis of Anna Wellmann]
 //=======================================================================================
 
 #ifndef InterpolationCellGrouper_H
@@ -46,9 +45,11 @@ class GridBuilder;
 
 using LBMSimulationParameters = std::vector<std::shared_ptr<LBMSimulationParameter>>;
 
+//! \brief Split the interpolation cells into two groups: cells which are at the border between gpus and therefore involved
+//! in the communication between gpus, and cells which are not directly related to the communication between gpus.
+//! \details See [master thesis of Anna Wellmann]
 class InterpolationCellGrouper {
 public:
-    //! \brief Construct InterpolationCellGrouper object
     InterpolationCellGrouper(const LBMSimulationParameters &parHs, const LBMSimulationParameters &parDs,
                              SPtr<GridBuilder> builder);
 

src/gpu/core/DataStructureInitializer/GridReaderGenerator/InterpolationCellGrouperTest.cpp

@@ -30,7 +30,6 @@
 //! \ingroup gpu_core_tests core
 //! \{
 //! \author Anna Wellmann
-//! \details See [master thesis of Anna Wellmann]
 //=======================================================================================
 #include <gmock/gmock.h>
 #include "Utilities/testUtilitiesGPU.h"

src/gpu/core/Output/DistributionDebugInspector.h

@@ -31,12 +31,6 @@
 //! \{
 //! \author Henrik Asmuth
 //! \date 13/012/2022
-//! \brief Basic debugging class to print out f's in a certain area of the domain
-//!
-//! Basic debugging class. Needs to be directly added in UpdateGrid (could potentially also be added as a proper Probe in the
-//! future) How to use: Define a part of the domain via min/max x, y, and z. The DistributionDebugInspector will print out
-//! all f's in that area.
-//!
 //=======================================================================================
 
 #ifndef DISTRIBUTION_INSPECTOR_H
@@ -46,6 +40,11 @@
 
 class Parameter;
 
+//! \brief Basic debugging class to print out f's in a certain area of the domain
+//!
+//! Basic debugging class. Needs to be directly added in UpdateGrid (could potentially also be added as a proper Probe in the
+//! future) How to use: Define a part of the domain via min/max x, y, and z. The DistributionDebugInspector will print out
+//! all f's in that area.
 class DistributionDebugInspector
 {
 public:

src/gpu/core/Parameter/EdgeNodeFinder.cpp

@@ -29,10 +29,6 @@
 //! \addtogroup gpu_Parameter Parameter
 //! \ingroup gpu_core core
 //! \{
-//! \author Anna Wellmann
-//! \brief Functions for finding edge nodes in the multi-gpu implementation
-//! \details Edge nodes are nodes, which are part of the communication in multiple directions
-//! \ref master thesis of Anna Wellmann (p. 54-57)
 //=======================================================================================
 #include <vector>
 #include <optional>

src/gpu/core/Parameter/EdgeNodeFinder.h

@@ -30,9 +30,6 @@
 //! \ingroup gpu_core core
 //! \{
 //! \author Anna Wellmann
-//! \brief Functions for finding edge nodes in the multi-gpu implementation
-//! \details Edge nodes are nodes, which are part of the communication in multiple directions
-//! \ref master thesis of Anna Wellmann (p. 54-57)
 //=======================================================================================
 #ifndef GPU_EDGENODES_H
 #define GPU_EDGENODES_H
@@ -43,7 +40,9 @@ class Parameter;
 
 namespace vf::gpu
 {
-//! \brief Find nodes which are part of communication in multiple coordinate directions
+//! \brief Function for finding edge nodes in the multi-gpu implementation
+//! \details Edge nodes are nodes, which are part of the communication in multiple directions
+//! \ref master thesis of Anna Wellmann (p. 54-57)
 void findEdgeNodesCommMultiGPU(Parameter& parameter);
 } // namespace vf::gpu
 

src/gpu/core/Parameter/EdgeNodeFinderTest.cpp

@@ -29,10 +29,6 @@
 //! \addtogroup gpu_Parameter_tests Parameter
 //! \ingroup gpu_core_tests core
 //! \{
-//! \author Anna Wellmann
-//! \brief Functions for finding edge nodes in the multi-gpu implementation
-//! \details Edge nodes are nodes, which are part of the communication in multiple directions
-//! \ref master thesis of Anna Wellmann (p. 54-57)
 //=======================================================================================
 #include <gmock/gmock.h>
 

src/gpu/core/PostProcessor/DragLift.cpp

@@ -30,8 +30,6 @@
 //! \ingroup gpu_core core
 //! \{
 //! \author Martin Schoenherr
-//! \brief note, that the drag/lift calculations are build for being used with 
-//! \brief geometry boundary nodes and the related area has to be defined here
 //=======================================================================================
 
 #include "DragLift.h"
@@ -49,6 +47,8 @@
 
 using namespace std;
 
+//! \brief Calculate drag and lift for a geometry
+//! \details note, that the drag/lift calculations are build for being used with geometry boundary nodes and the related area has to be defined here
 void calcDragLift(Parameter* para, CudaMemoryManager* cudaMemoryManager, int lev)
 {
     //////////////////////////////////////////////////////////////////////////

src/gpu/core/PreCollisionInteractor/PrecursorWriter.h

@@ -31,10 +31,6 @@
 //! \{
 //! \author Henry Korb, Henrik Asmuth
 //! \date 05/12/2022
-//! \brief Probe writing planes of data to be used as inflow data in successor simulation using PrecursorBC
-//!
-//! The probe writes out yz-planes at a specific x position ( \param xPos ) of either velocity or distributions 
-//! that can be read by PrecursorBC as inflow data.
 //=======================================================================================
 
 
@@ -87,6 +83,11 @@ struct PrecursorStruct
     cudaStream_t stream;
 };
 
+//! \brief Probe writing planes of data to be used as inflow data in successor simulation using PrecursorBC
+//!
+//! The probe writes out yz-planes at a specific x position ( \param xPos ) of either velocity or distributions 
+//! that can be read by PrecursorBC as inflow data.
+//!
 class PrecursorWriter : public PreCollisionInteractor
 {
 public:

src/gpu/core/PreCollisionInteractor/Probes/PlanarAverageProbe.h

@@ -31,11 +31,6 @@
 //! \{
 //! \author Henrik Asmuth
 //! \date 13/05/2022
-//! \brief Probe computing statistics across planes spanning the entire domain
-//!
-//! Computes spatial statistics across x, y or z-normal planes defined by planeNormal. 
-//! The planes include all points of the domain at each respective position along that normal direction.
-//! The spatial statistics can additionally be averaged in time.
 //!
 //=======================================================================================
 
@@ -50,6 +45,11 @@ __global__ void moveIndicesInPosNormalDir( uint* pointIndices, uint nPoints, uin
 
 ///////////////////////////////////////////////////////////////////////////////////
 
+//! \brief Probe computing statistics across planes spanning the entire domain
+//!
+//! Computes spatial statistics across x, y or z-normal planes defined by planeNormal. 
+//! The planes include all points of the domain at each respective position along that normal direction.
+//! The spatial statistics can additionally be averaged in time.
 class PlanarAverageProbe : public Probe
 {
 public:

src/gpu/core/PreCollisionInteractor/Probes/PlaneProbe.h

@@ -31,11 +31,6 @@
 //! \{
 //! \author Henry Korb, Henrik Asmuth
 //! \date 13/05/2022
-//! \brief Probe computing point-wise statistics for a set of points across a plane
-//!
-//! The set of points can be defined by providing a list or on an x-normal plane.
-//! All statistics are temporal.
-//!
 //=======================================================================================
 
 #ifndef PlaneProbe_H
@@ -45,6 +40,11 @@
 
 #include "Probe.h"
 
+//! \brief Probe computing point-wise statistics for a set of points across a plane
+//!
+//! The set of points can be defined by providing a list or on an x-normal plane.
+//! All statistics are temporal.
+//!
 class PlaneProbe : public Probe
 {
 public: 

src/gpu/core/PreCollisionInteractor/Probes/PointProbe.h

@@ -31,11 +31,6 @@
 //! \{
 //! \author Henry Korb, Henrik Asmuth
 //! \date 13/05/2022
-//! \brief Probe computing statistics for a set of points in space
-//!
-//! The set of points can be defined by providing a list or on an x-normal plane (the latter being somewhat redundant with PlaneProbe)
-//! All statistics are temporal.
-//!
 //=======================================================================================
 
 #ifndef PointProbe_H
@@ -43,6 +38,11 @@
 
 #include "Probe.h"
 
+//! \brief Probe computing statistics for a set of points in space
+//!
+//! The set of points can be defined by providing a list or on an x-normal plane (the latter being somewhat redundant with PlaneProbe)
+//! All statistics are temporal.
+//!
 class PointProbe: public Probe
 {
 public:

src/gpu/core/PreCollisionInteractor/Probes/Probe.h

@@ -31,15 +31,6 @@
 //! \{
 //! \author Henry Korb, Henrik Asmuth
 //! \date 13/05/2022
-//! \brief Base class for probes called in UpdateGrid27
-//!
-//! Any probe should be initiated in the app and added via para->addProbe( someProbe )
-//! Note, that all probes generally require that macroscopic variables have been updated in the 
-//! time step they are called in. Most collision kernels (atm, all except K17CompressibleNavierStokes)
-//! don't do this and would require an explicit call of calcMacroscopicQuantities. It does seem quite 
-//! inexpensive though to simply save vx, vy, etc., directly in the collider.
-//!
-//! \todo might have to adapt conversionFactors when using grid refinement
 //=======================================================================================
 
 #ifndef Probe_H
@@ -137,6 +128,15 @@ __global__ void interpAndCalcQuantitiesKernel(   uint* pointIndices,
 
 uint calcOldTimestep(uint currentTimestep, uint lastTimestepInOldSeries);
 
+//! \brief Base class for probes called in UpdateGrid27
+//!
+//! Any probe should be initiated in the app and added via para->addProbe( someProbe )
+//! Note, that all probes generally require that macroscopic variables have been updated in the 
+//! time step they are called in. Most collision kernels (atm, all except K17CompressibleNavierStokes)
+//! don't do this and would require an explicit call of calcMacroscopicQuantities. It does seem quite 
+//! inexpensive though to simply save vx, vy, etc., directly in the collider.
+//!
+//! \todo might have to adapt conversionFactors when using grid refinement
 class Probe : public PreCollisionInteractor 
 {
 public:

src/gpu/core/PreCollisionInteractor/Probes/WallModelProbe.h

@@ -31,11 +31,6 @@
 //! \{
 //! \author Henrik Asmuth
 //! \date 13/05/2022
-//! \brief Probe computing statistics of all relevant wall model quantities used in the StressBC kernels
-//!
-//! Computes spatial statistics for all grid points of the StressBC 
-//! The spatial statistics can additionally be averaged in time.
-//!
 //=======================================================================================
 
 #ifndef WallModelProbe_H
@@ -47,6 +42,11 @@
 
 ///////////////////////////////////////////////////////////////////////////////////
 
+//! \brief Probe computing statistics of all relevant wall model quantities used in the StressBC kernels
+//!
+//! Computes spatial statistics for all grid points of the StressBC 
+//! The spatial statistics can additionally be averaged in time.
+//!
 class WallModelProbe : public Probe
 {
 public: 

src/lbm/collision/K17CompressibleNavierStokes.h

@@ -29,19 +29,8 @@
 //! \addtogroup collision
 //! \ingroup lbm
 //! \{
-//! \author Anna Wellmann, Martin Schönherr, Henry Korb, Henrik Asmuth
+//! \author Martin Schönherr, Anna Wellmann, Henry Korb, Henrik Asmuth
 //! \date 05/12/2022
-//! \brief Kernel for CumulantK17 including different turbulence models and options for local body forces and writing
-//! macroscopic variables
-//!
-//! CumulantK17 kernel using chimera transformations and quartic limiters as present in Geier et al. (2017). Additional
-//! options are three different eddy-viscosity turbulence models (Smagorinsky, AMD, QR) that can be set via the template
-//! parameter turbulenceModel (with default TurbulenceModel::None). The kernel is executed separately for each subset of
-//! fluid node indices with a different tag CollisionTemplate. For each subset, only the locally required options are
-//! switched on ( \param writeMacroscopicVariables and/or \param applyBodyForce) in order to minimize memory accesses. The
-//! default refers to the plain cumlant kernel (CollisionTemplate::Default). Nodes are added to subsets (taggedFluidNodes) in
-//! Simulation::init using a corresponding tag with different values of CollisionTemplate. These subsets are provided by the
-//! utilized PostCollisionInteractiors depending on they specific requirements (e.g. writeMacroscopicVariables for probes).
 
 //=======================================================================================
 #include <basics/constants/NumericConstants.h>
@@ -77,7 +66,20 @@ namespace vf::lbm
 {
 
 //////////////////////////////////////////////////////////////////////////
-//! Cumulant K17 Kernel is based on \ref
+//! \brief Kernel for CumulantK17 including different turbulence models and options for local body forces and writing
+//! macroscopic variables
+//!
+//! \details
+//! CumulantK17 kernel using chimera transformations and quartic limiters as present in Geier et al. (2017). Additional
+//! options are three different eddy-viscosity turbulence models (Smagorinsky, AMD, QR) that can be set via the template
+//! parameter turbulenceModel (with default TurbulenceModel::None). The kernel is executed separately for each subset of
+//! fluid node indices with a different tag CollisionTemplate. For each subset, only the locally required options are
+//! switched on ( \param writeMacroscopicVariables and/or \param applyBodyForce) in order to minimize memory accesses. The
+//! default refers to the plain cumlant kernel (CollisionTemplate::Default). Nodes are added to subsets (taggedFluidNodes) in
+//! Simulation::init using a corresponding tag with different values of CollisionTemplate. These subsets are provided by the
+//! utilized PostCollisionInteractiors depending on they specific requirements (e.g. writeMacroscopicVariables for probes).
+//!
+//! The CumulantK17 Kernel is based on \ref
 //! <a href="https://doi.org/10.1016/j.jcp.2017.05.040"><b>[ M. Geier et al. (2017), DOI:10.1016/j.jcp.2017.05.040
 //! ]</b></a> and \ref <a href="https://doi.org/10.1016/j.jcp.2017.07.004"><b>[ M. Geier et al. (2017),
 //! DOI:10.1016/j.jcp.2017.07.004 ]</b></a>