.clang-format

@@ -61,48 +61,54 @@ IncludeCategories:
     Priority:        3
   - Regex:           '^"core/'
     Priority:        4
-  - Regex:           '^"cuda/'
-    Priority:        5
   - Regex:           '^"domain_decomposition/'
-    Priority:        6
+    Priority:        5
   - Regex:           '^"executiontree/'
-    Priority:        7
+    Priority:        6
   - Regex:           '^"fft/'
-    Priority:        8
+    Priority:        7
   - Regex:           '^"field/'
-    Priority:        9
+    Priority:        8
   - Regex:           '^"gather/'
-    Priority:        10
+    Priority:        9
   - Regex:           '^"geometry/'
+    Priority:        10
+  - Regex:           '^"gpu/'
     Priority:        11
-  - Regex:           '^"gui/'
+  - Regex:           '^"gpu/'
     Priority:        12
   - Regex:           '^"lbm/'
     Priority:        13
-  - Regex:           '^"mesh/'
+  - Regex:           '^"lbm_mesapd_coupling/'
     Priority:        14
-  - Regex:           '^"pde/'
+  - Regex:           '^"mesh/'
     Priority:        15
-  - Regex:           '^"pe/'
+  - Regex:           '^"mesa_pd/'
     Priority:        16
-  - Regex:           '^"pe_coupling/'
+  - Regex:           '^"pde/'
     Priority:        17
-  - Regex:           '^"postprocessing/'
+  - Regex:           '^"pe/'
     Priority:        18
-  - Regex:           '^"python_coupling/'
+  - Regex:           '^"pe_coupling/'
     Priority:        19
-  - Regex:           '^"simd/'
+  - Regex:           '^"postprocessing/'
     Priority:        20
-  - Regex:           '^"stencil/'
+  - Regex:           '^"python_coupling/'
     Priority:        21
-  - Regex:           '^"timeloop/'
+  - Regex:           '^"simd/'
     Priority:        22
-  - Regex:           '^"vtk/'
+  - Regex:           '^"sqlite/'
     Priority:        23
-  - Regex:           '^<boost/'
+  - Regex:           '^"stencil/'
     Priority:        24
-  - Regex:           '^<'
+  - Regex:           '^"timeloop/'
     Priority:        25
+  - Regex:           '^"vtk/'
+    Priority:        26
+  - Regex:           '^<boost/'
+    Priority:        27
+  - Regex:           '^<'
+    Priority:        28
 IndentCaseLabels: false
 IndentPPDirectives: AfterHash
 IndentWidth: 3

.clang-tidy

@@ -4,30 +4,39 @@ Checks:          '
 -*,
 
 boost-*,
+-boost-use-ranges,
 
 bugprone-*,
 -bugprone-branch-clone,
 -bugprone-exception-escape,
+-bugprone-easily-swappable-parameters,
+-bugprone-crtp-constructor-accessibility,
+-bugprone-implicit-widening-of-multiplication-result,
+-bugprone-macro-parentheses,
+-bugprone-narrowing-conversions,
+-bugprone-switch-missing-default-case,
+-bugprone-assignment-in-if-condition,
+-bugprone-reserved-identifier,
 
 misc-*,
--misc-misplaced-const,
 -misc-no-recursion,
 -misc-non-private-member-variables-in-classes,
+-misc-include-cleaner,
+-misc-header-include-cycle,
+-misc-use-internal-linkage,
+-misc-use-anonymous-namespace,
+-misc-const-correctness,
+-misc-misplaced-const
 
 modernize-*,
 -modernize-use-auto,
--modernize-loop-convert,
 -modernize-pass-by-value,
 -modernize-raw-string-literal,
--modernize-use-using,
--modernize-avoid-bind,
--modernize-return-braced-init-list,
 -modernize-use-transparent-functors,
--modernize-redundant-void-arg,
 -modernize-use-trailing-return-type,
--modernize-avoid-c-arrays,
--modernize-concat-nested-namespaces,
 -modernize-use-nodiscard,
+-modernize-macro-to-enum,
+-modernize-concat-nested-namespaces,
 
 mpi-*,
 -mpi-type-mismatch,
@@ -37,25 +46,25 @@ openmp-*,
 -openmp-use-default-none,
 
 performance-*,
+-performance-enum-size,
+-performance-noexcept-swap,
+-performance-unnecessary-value-param,
+-performance-avoid-endl,
+-performance-no-int-to-ptr,
 
 portability-*,
 
-readability-const-return-type,
 readability-container-size-empty,
 readability-delete-null-pointer,
 readability-deleted-default,
-readability-isolate-declaration,
-readability-misleading-indentation,
 readability-misplaced-array-index,
 readability-non-const-parameter,
-readability-redundant-access-specifiers,
 readability-redundant-control-flow,
 readability-redundant-declaration,
 readability-redundant-function-ptr-dereference,
 readability-redundant-preprocessor,
 readability-redundant-smartptr-get,
 readability-redundant-string-cstr,
-readability-simplify-boolean-expr,
 readability-simplify-subscript-expr,
 readability-static-accessed-through-instance,
 readability-static-definition-in-anonymous-namespace,

.editorconfig

 # See https://editorconfig.org/
-root = true # top-most .editorconfig-file
+# top-most .editorconfig-file
+root = true
 
 [*]
 tab_width = 3
@@ -12,4 +13,4 @@ insert_final_newline = false
 [*.py]
 tab_width = 4
 indent_size = 4
-insert_final_newline = true
+insert_final_newline = true
\ No newline at end of file

.gitignore

@@ -8,6 +8,10 @@ qrc_*
 # macOS
 **/.DS_Store
 
+# CLion indexing
+*.uuid
+.fleet
+
 
 # Generated files
 *.out
@@ -29,9 +33,12 @@ qrc_*
 # Visual Studio Code
 /.vscode
 
+# Zed
+/.cache*
+
 # CLion
 *.idea
-
+*.clion*
 
 # QtCreator
 CMakeLists.txt.user.*
@@ -48,6 +55,8 @@ CMakeLists.txt.user.*
 logfile*.txt
 *TestLog_p*.txt
 
+# Python venv
+.venv
 
 # Compiled python
 *.pyc
@@ -60,6 +69,7 @@ logfile*.txt
 
 
 # CMake
+CMakeUserPresets.json
 /CMakeLists.txt.user
 
 # CMake build files
@@ -72,6 +82,11 @@ cmake_install.cmake
 CMakeDefs.h
 /moduleStatistics.json
 /walberla-config.cmake
-/cmake-build-debug/
-/cmake-build-release/
-/cmake-build-debug-remote/
+cmake-build-*
+
+
+# Virtual environments
+.venv/
+env/
+venv/
+ENV/

.gitmodules

-[submodule "extern/pybind11"]
-	path = extern/pybind11
-	url = https://github.com/pybind/pybind11.git

AUTHORS.txt

@@ -31,6 +31,7 @@ Matthias Markl
 Michael Kuron
 Nils Kohl
 Paulo Carvalho
+Philipp Suffa
 Regina Ammer
 Sagar Dolas
 Sebastian Eibl

CHANGELOG.md

 # Changelog
 
+## [6.1] - 2022-07-25
+### Added
+- Free-surface LBM extension:
+  - Add implementation
+  - Add several showcases
+  - Add several tests
+- LBM - MESA_PD coupling:
+  - Add partially saturated cells method (PSM)
+  - Add fluidized bed showcase
+  - Add virtual mass stabilization technique for light particles
+  - Add support for more shapes, e.g., convex polyhedron
+- MESA_PD:
+   - Add extensive application for dense particle packing generation
+- AMD - HIP support
+  - Support of the ROCm Toolchain and thus AMD HIP as second GPU language
+  - All CUDA related files, namespaces, folders etc are renamed to gpu.
+  - Include "GPUWrapper.h" to use general GPU functions cudaMalloc -> gpuMalloc
+  - WALBERLA_BUILD_WITH_HIP and WALBERLA_BUILD_WITH_GPU_SUPPORT as new CMake variables introduced
+
+### Changed
+- Update and extend phase-field LBM showcases
+- Allow access to PDF centering information (for being used in generated LBM kernels)
+- Adapt code generation backend to be compatible with pystencils 1.0 and lbmpy 1.0
+- Required minimum dependencies:
+  - C++17-compliant compiler
+  - CMake 3.14
+  - pybind 2.6.2
+  - lbmpy 1.0
+  - pystencils 1.0
+
+### Deprecated
+- GUI
+
 ## [5.1] - 2020-04-09
 ### Added
 - Add new tutorials and showcases
@@ -71,4 +104,3 @@
 
 ### Deprecated
 - all dynamic level-wise balance functions (use the more general ones, without "level-wise")
-

CMakePresets.json

+{
+    "version": 6,
+    "cmakeMinimumRequired": {
+      "major": 3,
+      "minor": 23,
+      "patch": 0
+    },
+    "configurePresets": [
+      {
+        "name": "clang-tidy",
+        "generator": "Unix Makefiles",
+        "binaryDir": "${sourceDir}/build/clang-tidy",
+        "cacheVariables": {
+          "CMAKE_EXPORT_COMPILE_COMMANDS": true,
+          "WALBERLA_BUFFER_DEBUG": true,
+          "WALBERLA_BUILD_TESTS": true,
+          "WALBERLA_BUILD_BENCHMARKS": true,
+          "WALBERLA_BUILD_TUTORIALS": true,
+          "WALBERLA_BUILD_TOOLS": true,
+          "WALBERLA_BUILD_WITH_MPI": true,
+          "WALBERLA_BUILD_WITH_OPENMP": true,
+          "CMAKE_BUILD_TYPE": "Debug",
+          "WALBERLA_BUILD_WITH_METIS": true,
+          "WALBERLA_BUILD_WITH_PARMETIS": true,
+          "WALBERLA_BUILD_WITH_OPENMESH": true,
+          "WALBERLA_DOUBLE_ACCURACY": true,
+          "WALBERLA_LOGLEVEL": "DETAIL"
+        }
+      }
+    ]
+  }
+  
\ No newline at end of file

README.md

@@ -80,7 +80,7 @@ Many thanks go to waLBerla's [contributors](AUTHORS.txt)
 If you use waLBerla in a publication, please cite the following articles:
 
 Overview:
-- M. Bauer et al, *waLBerla: A block-structured high-performance framework for
+- M. Bauer et al., *waLBerla: A block-structured high-performance framework for
   multiphysics simulations*. Computers & Mathematics with Applications, 2020.
   https://doi.org/10.1016/j.camwa.2020.01.007.
 
@@ -94,13 +94,23 @@ LBM - Particle Coupling:
   fully resolved lattice Boltzmann simulations*. Computers & Fluids, 2017.
   https://doi.org/10.1016/j.compfluid.2017.05.033
 
+Free-surface LBM:
+- C. Schwarzmeier et al., *Comparison of free-surface and conservative Allen-Cahn phase-field
+  lattice Boltzmann method*. Journal of Computational Physics, 2023.
+  https://doi.org/10.1016/j.jcp.2022.111753
+
+Allen-Cahn phase-field LBM
+- M. Holzer et al., *Highly efficient lattice Boltzmann multiphase simulations of immiscible
+  fluids at high-density ratios on CPUs and GPUs through code generation*. The International Journal of High Performance Computing Applications, 2021.
+  https://doi.org/10.1177/10943420211016525
+
 MESA-PD:
 - S. Eibl and U. Rüde, *A Modular and Extensible Software Architecture for Particle Dynamics*.
   Proceedings Of The 8Th International Conference On Discrete Element Methods.
   https://mercurylab.co.uk/dem8/full-papers/#page-content
 
 Carbon Nanotubes:
-- G. Drozdov et al, *Densification of single-walled carbon nanotube films:
+- G. Drozdov et al., *Densification of single-walled carbon nanotube films:
   Mesoscopic distinct element method simulations and experimental validation*.
   Journal of Applied Physics, 2020. https://doi.org/10.1063/5.0025505
 

apps/CMakeLists.txt

@@ -2,31 +2,23 @@
 # Benchmarks
 if ( WALBERLA_BUILD_BENCHMARKS )
     add_subdirectory ( benchmarks )
-else ()
-    add_subdirectory ( benchmarks EXCLUDE_FROM_ALL )
 endif()
 
 
 # Tools
 if ( WALBERLA_BUILD_TOOLS )
     add_subdirectory ( tools )
-else ()
-    add_subdirectory ( tools EXCLUDE_FROM_ALL )
 endif()
 
 
 # Tutorials
 if ( WALBERLA_BUILD_TUTORIALS )
     add_subdirectory ( tutorials )
-else ()
-    add_subdirectory ( tutorials EXCLUDE_FROM_ALL )
 endif()
 
 # Showcases
 if ( WALBERLA_BUILD_SHOWCASES )
     add_subdirectory ( showcases )
-else ()
-    add_subdirectory ( showcases EXCLUDE_FROM_ALL )
 endif()
 
 # Python module

apps/benchmarks/AdaptiveMeshRefinementFluidParticleCoupling/AMRSedimentSettling.cpp

@@ -20,8 +20,14 @@
 //======================================================================================================================
 
 #include "blockforest/Initialization.h"
-#include "blockforest/communication/UniformBufferedScheme.h"
-#include "blockforest/loadbalancing/all.h"
+#include "blockforest/loadbalancing/InfoCollection.h"
+#include "blockforest/loadbalancing/DynamicCurve.h"
+#include "blockforest/loadbalancing/DynamicDiffusive.h"
+#include "blockforest/loadbalancing/DynamicParMetis.h"
+#include "blockforest/loadbalancing/StaticCurve.h"
+#include "blockforest/loadbalancing/StaticParMetis.h"
+#include "blockforest/loadbalancing/weight_assignment/MetisAssignmentFunctor.h"
+#include "blockforest/loadbalancing/weight_assignment/WeightAssignmentFunctor.h"
 #include "blockforest/AABBRefinementSelection.h"
 
 #include "boundary/all.h"
@@ -35,7 +41,6 @@
 #include "core/timing/RemainingTimeLogger.h"
 #include "core/mpi/Broadcast.h"
 
-#include "domain_decomposition/SharedSweep.h"
 #include "domain_decomposition/BlockSweepWrapper.h"
 
 #include "field/AddToStorage.h"
@@ -43,26 +48,21 @@
 #include "field/communication/PackInfo.h"
 
 #include "lbm/boundary/all.h"
-#include "lbm/communication/PdfFieldPackInfo.h"
 #include "lbm/field/AddToStorage.h"
 #include "lbm/field/PdfField.h"
 #include "lbm/field/VelocityFieldWriter.h"
 #include "lbm/lattice_model/D3Q19.h"
 #include "lbm/refinement/all.h"
 #include "lbm/sweeps/CellwiseSweep.h"
-#include "lbm/sweeps/SweepWrappers.h"
 
 #include "pe/basic.h"
 #include "pe/Types.h"
 #include "pe/fcd/GJKEPACollideFunctor.h"
-#include "pe/vtk/BodyVtkOutput.h"
 #include "pe/vtk/SphereVtkOutput.h"
 #include "pe/vtk/EllipsoidVtkOutput.h"
 #include "pe/cr/ICR.h"
 #include "pe/synchronization/ClearSynchronization.h"
 #include "pe/amr/InfoCollection.h"
-#include "pe/amr/weight_assignment/WeightAssignmentFunctor.h"
-#include "pe/amr/weight_assignment/MetisAssignmentFunctor.h"
 
 #include "pe_coupling/amr/all.h"
 #include "pe_coupling/mapping/all.h"
@@ -165,9 +165,9 @@ template< typename LatticeModel_T, typename Filter_T >
 void VectorGradientRefinement< LatticeModel_T, Filter_T >::operator()( std::vector< std::pair< const Block *, uint_t > > & minTargetLevels,
                                                                        std::vector< const Block * > &, const BlockForest & )
 {
-   for( auto it = minTargetLevels.begin(); it != minTargetLevels.end(); ++it )
+   for(auto & minTargetLevel : minTargetLevels)
    {
-      const Block * const block = it->first;
+      const Block * const block = minTargetLevel.first;
 
       const uint_t currentLevelOfBlock = block->getLevel();
 
@@ -175,7 +175,7 @@ void VectorGradientRefinement< LatticeModel_T, Filter_T >::operator()( std::vect
 
       if( uField == nullptr )
       {
-         it->second = uint_t(0);
+         minTargetLevel.second = uint_t(0);
          continue;
       }
 
@@ -253,12 +253,12 @@ void VectorGradientRefinement< LatticeModel_T, Filter_T >::operator()( std::vect
       if( refine && currentLevelOfBlock < maxLevel_ )
       {
          WALBERLA_ASSERT( !coarsen );
-         it->second = currentLevelOfBlock + uint_t(1);
+         minTargetLevel.second = currentLevelOfBlock + uint_t(1);
       }
       if( coarsen && currentLevelOfBlock > uint_t(0) )
       {
          WALBERLA_ASSERT( !refine );
-         it->second = currentLevelOfBlock - uint_t(1);
+         minTargetLevel.second = currentLevelOfBlock - uint_t(1);
       }
    }
 }
@@ -500,7 +500,7 @@ static shared_ptr< StructuredBlockForest > createBlockStructure( const AABB & do
 
    MPIManager::instance()->useWorldComm();
 
-   sforest.addRefinementSelectionFunction( std::bind( refinementSelection, std::placeholders::_1, numberOfLevels, refinementBox ) );
+   sforest.addRefinementSelectionFunction( [numberOfLevels, refinementBox](auto && PH1) { refinementSelection(std::forward<decltype(PH1)>(PH1), numberOfLevels, refinementBox); } );
    sforest.addWorkloadMemorySUIDAssignmentFunction( workloadAndMemoryAssignment );
 
    Vector3<bool> periodicity( true, true, false);
@@ -1375,7 +1375,7 @@ int main( int argc, char **argv )
    cr.setRelaxationModel( pe::cr::HardContactSemiImplicitTimesteppingSolvers::ApproximateInelasticCoulombContactByDecoupling );
 
    // set up synchronization procedure
-   std::function<void(void)> syncCall = std::bind( pe::syncNextNeighbors<BodyTypeTuple>, std::ref(blocks->getBlockForest()), bodyStorageID, &(*timingTreePE), overlap, false );
+   std::function<void(void)> syncCall = [&capture0 = blocks->getBlockForest(), bodyStorageID, capture1 = &(*timingTreePE), overlap] { pe::syncNextNeighbors<BodyTypeTuple>(capture0, bodyStorageID, capture1, overlap, false); };
 
    // create pe bodies
 
@@ -1492,17 +1492,17 @@ int main( int argc, char **argv )
    LatticeModel_T latticeModel = LatticeModel_T( lbm::collision_model::TRT::constructWithMagicNumber( omega, lbm::collision_model::TRT::threeSixteenth, finestLevel ) );
 
    // add PDF field
-   BlockDataID pdfFieldID = lbm::addPdfFieldToStorage< LatticeModel_T >( blocks, "pdf field (zyxf)", latticeModel,
+   BlockDataID pdfFieldID = lbm::addPdfFieldToStorage< LatticeModel_T >( blocks, "pdf field (fzyx)", latticeModel,
                                                                          Vector3< real_t >( real_t(0) ), real_t(1),
-                                                                         FieldGhostLayers, field::zyxf );
+                                                                         FieldGhostLayers, field::fzyx );
    // add flag field
    BlockDataID flagFieldID = field::addFlagFieldToStorage<FlagField_T>( blocks, "flag field", FieldGhostLayers );
 
    // add body field
-   BlockDataID bodyFieldID = field::addToStorage<BodyField_T>( blocks, "body field", nullptr, field::zyxf, FieldGhostLayers );
+   BlockDataID bodyFieldID = field::addToStorage<BodyField_T>( blocks, "body field", nullptr, field::fzyx, FieldGhostLayers );
 
    // add velocity field and utility
-   BlockDataID velocityFieldID = field::addToStorage<VelocityField_T>( blocks, "velocity field", Vector3<real_t>(real_t(0)), field::zyxf, uint_t(2) );
+   BlockDataID velocityFieldID = field::addToStorage<VelocityField_T>( blocks, "velocity field", Vector3<real_t>(real_t(0)), field::fzyx, uint_t(2) );
 
    using VelocityFieldWriter_T = lbm::VelocityFieldWriter<PdfField_T, VelocityField_T>;
    BlockSweepWrapper< VelocityFieldWriter_T > velocityFieldWriter( blocks, VelocityFieldWriter_T( pdfFieldID, velocityFieldID ) );
@@ -1525,14 +1525,14 @@ int main( int argc, char **argv )
 
    // force averaging functionality
    shared_ptr<pe_coupling::BodiesForceTorqueContainer> bodiesFTContainer1 = make_shared<pe_coupling::BodiesForceTorqueContainer>(blocks, bodyStorageID);
-   std::function<void(void)> storeForceTorqueInCont1 = std::bind(&pe_coupling::BodiesForceTorqueContainer::store, bodiesFTContainer1);
+   std::function<void(void)> storeForceTorqueInCont1 = [bodiesFTContainer1] { bodiesFTContainer1->store(); };
 
    shared_ptr<pe_coupling::BodiesForceTorqueContainer> bodiesFTContainer2 = make_shared<pe_coupling::BodiesForceTorqueContainer>(blocks, bodyStorageID);
-   std::function<void(void)> setForceTorqueOnBodiesFromCont2 = std::bind(&pe_coupling::BodiesForceTorqueContainer::setOnBodies, bodiesFTContainer2);
+   std::function<void(void)> setForceTorqueOnBodiesFromCont2 = [bodiesFTContainer2] { bodiesFTContainer2->setOnBodies(); };
 
    shared_ptr<pe_coupling::ForceTorqueOnBodiesScaler> forceScaler = make_shared<pe_coupling::ForceTorqueOnBodiesScaler>(blocks, bodyStorageID, real_t(0.5));
-   std::function<void(void)> setForceScalingFactorToOne = std::bind(&pe_coupling::ForceTorqueOnBodiesScaler::resetScalingFactor,forceScaler,real_t(1));
-   std::function<void(void)> setForceScalingFactorToHalf = std::bind(&pe_coupling::ForceTorqueOnBodiesScaler::resetScalingFactor,forceScaler,real_t(0.5));
+   std::function<void(void)> setForceScalingFactorToOne = [forceScaler] { forceScaler->resetScalingFactor(real_t(1)); };
+   std::function<void(void)> setForceScalingFactorToHalf = [forceScaler] { forceScaler->resetScalingFactor(real_t(0.5)); };
 
    if( averageForceTorqueOverTwoTimSteps ) {
       bodiesFTContainer2->store();
@@ -1616,7 +1616,7 @@ int main( int argc, char **argv )
       }
       else if( loadEvaluationStrategy == "PE" )
       {
-         pe::amr::WeightAssignmentFunctor weightAssignmentFunctor(peInfoCollection, peBlockBaseWeight );
+         blockforest::WeightAssignmentFunctor weightAssignmentFunctor(peInfoCollection, peBlockBaseWeight );
          blockforest.setRefreshPhantomBlockDataAssignmentFunction(weightAssignmentFunctor);
       }
       else if( loadEvaluationStrategy == "LBM" )
@@ -1700,7 +1700,7 @@ int main( int argc, char **argv )
       }
       else if( loadEvaluationStrategy == "PE" )
       {
-         pe::amr::MetisAssignmentFunctor weightAssignmentFunctor(peInfoCollection, peBlockBaseWeight );
+         blockforest::MetisAssignmentFunctor weightAssignmentFunctor(peInfoCollection, peBlockBaseWeight );
          blockforest.setRefreshPhantomBlockDataAssignmentFunction(weightAssignmentFunctor);
       }
       else if( loadEvaluationStrategy == "LBM" )
@@ -1743,7 +1743,7 @@ int main( int argc, char **argv )
       }
       else if( loadEvaluationStrategy == "PE" )
       {
-         pe::amr::WeightAssignmentFunctor weightAssignmentFunctor(peInfoCollection, peBlockBaseWeight );
+         blockforest::WeightAssignmentFunctor weightAssignmentFunctor(peInfoCollection, peBlockBaseWeight );
          blockforest.setRefreshPhantomBlockDataAssignmentFunction(weightAssignmentFunctor);
       }
       else if( loadEvaluationStrategy == "LBM" )
@@ -2244,4 +2244,4 @@ int main( int argc, char **argv )
 
 int main( int argc, char **argv ){
    amr_sediment_settling::main(argc, argv);
-}
+}
\ No newline at end of file

apps/benchmarks/AdaptiveMeshRefinementFluidParticleCoupling/AMRSettlingSphere.cpp

@@ -158,9 +158,9 @@ template< typename LatticeModel_T, typename Filter_T >
 void VectorGradientRefinement< LatticeModel_T, Filter_T >::operator()( std::vector< std::pair< const Block *, uint_t > > & minTargetLevels,
                                                                        std::vector< const Block * > &, const BlockForest & )
 {
-   for( auto it = minTargetLevels.begin(); it != minTargetLevels.end(); ++it )
+   for(auto & minTargetLevel : minTargetLevels)
    {
-      const Block * const block = it->first;
+      const Block * const block = minTargetLevel.first;
 
       const uint_t currentLevelOfBlock = block->getLevel();
 
@@ -168,7 +168,7 @@ void VectorGradientRefinement< LatticeModel_T, Filter_T >::operator()( std::vect
 
       if( uField == nullptr )
       {
-         it->second = uint_t(0);
+         minTargetLevel.second = uint_t(0);
          continue;
       }
 
@@ -246,12 +246,12 @@ void VectorGradientRefinement< LatticeModel_T, Filter_T >::operator()( std::vect
       if( refine && currentLevelOfBlock < maxLevel_ )
       {
          WALBERLA_ASSERT( !coarsen );
-         it->second = currentLevelOfBlock + uint_t(1);
+         minTargetLevel.second = currentLevelOfBlock + uint_t(1);
       }
       if( coarsen && currentLevelOfBlock > uint_t(0) )
       {
          WALBERLA_ASSERT( !refine );
-         it->second = currentLevelOfBlock - uint_t(1);
+         minTargetLevel.second = currentLevelOfBlock - uint_t(1);
       }
    }
 }
@@ -307,28 +307,28 @@ private:
 static void refinementSelection( SetupBlockForest& forest, uint_t levels, const AABB & refinementBox )
 {
    real_t dx = real_t(1); // dx on finest level
-   for( auto block = forest.begin(); block != forest.end(); ++block )
+   for(auto & block : forest)
    {
-      uint_t blockLevel = block->getLevel();
+      uint_t blockLevel = block.getLevel();
       uint_t levelScalingFactor = ( uint_t(1) << (levels - uint_t(1) - blockLevel) );
       real_t dxOnLevel = dx * real_c(levelScalingFactor);
-      AABB blockAABB = block->getAABB();
+      AABB blockAABB = block.getAABB();
 
       // extend block AABB by ghostlayers
       AABB extendedBlockAABB = blockAABB.getExtended( dxOnLevel * real_c(FieldGhostLayers) );
 
       if( extendedBlockAABB.intersects( refinementBox ) )
          if( blockLevel < ( levels - uint_t(1) ) )
-            block->setMarker( true );
+            block.setMarker( true );
    }
 }
 
 static void workloadAndMemoryAssignment( SetupBlockForest& forest )
 {
-   for( auto block = forest.begin(); block != forest.end(); ++block )
+   for(auto & block : forest)
    {
-      block->setWorkload( numeric_cast< workload_t >( uint_t(1) << block->getLevel() ) );
-      block->setMemory( numeric_cast< memory_t >(1) );
+      block.setWorkload( numeric_cast< workload_t >( uint_t(1) << block.getLevel() ) );
+      block.setMemory( numeric_cast< memory_t >(1) );
    }
 }
 
@@ -378,7 +378,7 @@ static shared_ptr< StructuredBlockForest > createBlockStructure( const AABB & do
 
    WALBERLA_LOG_INFO_ON_ROOT(" - refinement box: " << refinementBox);
 
-   sforest.addRefinementSelectionFunction( std::bind( refinementSelection, std::placeholders::_1, numberOfLevels, refinementBox ) );
+   sforest.addRefinementSelectionFunction( [numberOfLevels, refinementBox](auto && PH1) { refinementSelection(std::forward<decltype(PH1)>(PH1), numberOfLevels, refinementBox); } );
    sforest.addWorkloadMemorySUIDAssignmentFunction( workloadAndMemoryAssignment );
 
    sforest.init( domainAABB, numberOfCoarseBlocksPerDirection[0], numberOfCoarseBlocksPerDirection[1], numberOfCoarseBlocksPerDirection[2], true, true, true );
@@ -498,13 +498,8 @@ public:
 
       WALBERLA_MPI_SECTION()
       {
-         mpi::allReduceInplace( pos[0], mpi::SUM );
-         mpi::allReduceInplace( pos[1], mpi::SUM );
-         mpi::allReduceInplace( pos[2], mpi::SUM );
-
-         mpi::allReduceInplace( transVel[0], mpi::SUM );
-         mpi::allReduceInplace( transVel[1], mpi::SUM );
-         mpi::allReduceInplace( transVel[2], mpi::SUM );
+         mpi::allReduceInplace( pos, mpi::SUM );
+         mpi::allReduceInplace( transVel, mpi::SUM );
       }
 
       position_ = pos[2];
@@ -625,9 +620,9 @@ public:
       for( uint_t level = 0; level < numberOfLevels_; ++level)
       {
          real_t timeOnLevelProcessLocal = real_t(0);
-         for( auto timerIt = timerOnEachLevel_.begin(); timerIt != timerOnEachLevel_.end(); ++timerIt )
+         for(auto const & timerIt : timerOnEachLevel_)
          {
-            std::string timerName = *timerIt + " (" + std::to_string(level) + ")";
+            std::string timerName = timerIt + " (" + std::to_string(level) + ")";
             timeOnLevelProcessLocal += real_c((*levelwiseTimingPool_)[timerName].total());
          }
 
@@ -635,15 +630,14 @@ public:
          {
             // evaluate more timers on finest level
 
-            for( auto timerIt = timerOnFinestLevel_.begin(); timerIt != timerOnFinestLevel_.end(); ++timerIt )
+            for(auto const & timerIt : timerOnFinestLevel_)
             {
-               std::string timerName = *timerIt + " (" + std::to_string(level) + ")";
+               std::string timerName = timerIt + " (" + std::to_string(level) + ")";
                timeOnLevelProcessLocal += real_c((*levelwiseTimingPool_)[timerName].total());
             }
-            for( auto timerIt = timerInPE_.begin(); timerIt != timerInPE_.end(); ++timerIt )
+            for(auto const & timerName : timerInPE_)
             {
-               std::string timerName = *timerIt;
-               timeOnLevelProcessLocal += real_c((*peTimingTree_)[timerName].total());
+                timeOnLevelProcessLocal += real_c((*peTimingTree_)[timerName].total());
             }
          }
 
@@ -955,7 +949,7 @@ int main( int argc, char **argv )
    pe::cr::DEM cr(globalBodyStorage, blocks->getBlockStoragePointer(), bodyStorageID, ccdID, fcdID, &(*timingTreePE));
 
    // set up synchronization procedure
-   std::function<void(void)> syncCall = std::bind( pe::syncShadowOwners<BodyTypeTuple>, std::ref(blocks->getBlockForest()), bodyStorageID, &(*timingTreePE), overlap, false );
+   std::function<void(void)> syncCall = [&capture0 = blocks->getBlockForest(), bodyStorageID, capture1 = &(*timingTreePE), overlap] { pe::syncShadowOwners<BodyTypeTuple>(capture0, bodyStorageID, capture1, overlap, false); };
 
    // create pe bodies
 
@@ -982,17 +976,17 @@ int main( int argc, char **argv )
    LatticeModel_T latticeModel = LatticeModel_T( lbm::collision_model::TRT::constructWithMagicNumber( omega, lbm::collision_model::TRT::threeSixteenth, finestLevel ) );
 
    // add PDF field
-   BlockDataID pdfFieldID = lbm::addPdfFieldToStorage< LatticeModel_T >( blocks, "pdf field (zyxf)", latticeModel,
+   BlockDataID pdfFieldID = lbm::addPdfFieldToStorage< LatticeModel_T >( blocks, "pdf field (fzyx)", latticeModel,
                                                                          Vector3< real_t >( real_t(0) ), real_t(1),
-                                                                         FieldGhostLayers, field::zyxf );
+                                                                         FieldGhostLayers, field::fzyx );
    // add flag field
    BlockDataID flagFieldID = field::addFlagFieldToStorage<FlagField_T>( blocks, "flag field", FieldGhostLayers );
 
    // add body field
-   BlockDataID bodyFieldID = field::addToStorage<BodyField_T>( blocks, "body field", nullptr, field::zyxf, FieldGhostLayers );
+   BlockDataID bodyFieldID = field::addToStorage<BodyField_T>( blocks, "body field", nullptr, field::fzyx, FieldGhostLayers );
 
    // add velocity field and utility
-   BlockDataID velocityFieldID = field::addToStorage<VelocityField_T>( blocks, "velocity field", Vector3<real_t>(real_t(0)), field::zyxf, uint_t(2) );
+   BlockDataID velocityFieldID = field::addToStorage<VelocityField_T>( blocks, "velocity field", Vector3<real_t>(real_t(0)), field::fzyx, uint_t(2) );
 
    using VelocityFieldWriter_T = lbm::VelocityFieldWriter<PdfField_T, VelocityField_T>;
    BlockSweepWrapper< VelocityFieldWriter_T > velocityFieldWriter( blocks, VelocityFieldWriter_T( pdfFieldID, velocityFieldID ) );
@@ -1014,12 +1008,12 @@ int main( int argc, char **argv )
 
    // force averaging functionality
    shared_ptr<pe_coupling::BodiesForceTorqueContainer> bodiesFTContainer1 = make_shared<pe_coupling::BodiesForceTorqueContainer>(blocks, bodyStorageID);
-   std::function<void(void)> storeForceTorqueInCont1 = std::bind(&pe_coupling::BodiesForceTorqueContainer::store, bodiesFTContainer1);
+   std::function<void(void)> storeForceTorqueInCont1 = [bodiesFTContainer1] { bodiesFTContainer1->store(); };
    shared_ptr<pe_coupling::BodiesForceTorqueContainer> bodiesFTContainer2 = make_shared<pe_coupling::BodiesForceTorqueContainer>(blocks, bodyStorageID);
-   std::function<void(void)> setForceTorqueOnBodiesFromCont2 = std::bind(&pe_coupling::BodiesForceTorqueContainer::setOnBodies, bodiesFTContainer2);
+   std::function<void(void)> setForceTorqueOnBodiesFromCont2 = [bodiesFTContainer2] { bodiesFTContainer2->setOnBodies(); };
    shared_ptr<pe_coupling::ForceTorqueOnBodiesScaler> forceScaler = make_shared<pe_coupling::ForceTorqueOnBodiesScaler>(blocks, bodyStorageID, real_t(0.5));
-   std::function<void(void)> setForceScalingFactorToOne = std::bind(&pe_coupling::ForceTorqueOnBodiesScaler::resetScalingFactor,forceScaler,real_t(1));
-   std::function<void(void)> setForceScalingFactorToHalf = std::bind(&pe_coupling::ForceTorqueOnBodiesScaler::resetScalingFactor,forceScaler,real_t(0.5));
+   std::function<void(void)> setForceScalingFactorToOne = [forceScaler] { forceScaler->resetScalingFactor(real_t(1)); };
+   std::function<void(void)> setForceScalingFactorToHalf = [forceScaler] { forceScaler->resetScalingFactor(real_t(0.5)); };
 
    if( averageForceTorqueOverTwoTimSteps ) {
       bodiesFTContainer2->store();
@@ -1336,4 +1330,4 @@ int main( int argc, char **argv )
 
 int main( int argc, char **argv ){
    amr_settling_sphere::main(argc, argv);
-}
+}
\ No newline at end of file

apps/benchmarks/AdaptiveMeshRefinementFluidParticleCoupling/CMakeLists.txt

-waLBerla_add_executable( NAME WorkloadEvaluation FILES WorkloadEvaluation.cpp DEPENDS blockforest boundary core field lbm pe pe_coupling postprocessing stencil timeloop vtk )
+waLBerla_add_executable( NAME WorkloadEvaluation FILES WorkloadEvaluation.cpp DEPENDS walberla::blockforest walberla::boundary walberla::core walberla::field walberla::lbm walberla::pe walberla::pe_coupling walberla::postprocessing walberla::stencil walberla::timeloop walberla::vtk )
 
-waLBerla_add_executable( NAME AMRSedimentSettling FILES AMRSedimentSettling.cpp DEPENDS blockforest boundary core field lbm pe pe_coupling postprocessing stencil timeloop vtk )
+waLBerla_add_executable( NAME AMRSedimentSettling FILES AMRSedimentSettling.cpp DEPENDS walberla::blockforest walberla::boundary walberla::core walberla::field walberla::lbm walberla::pe walberla::pe_coupling walberla::postprocessing walberla::stencil walberla::timeloop walberla::vtk )
 
-waLBerla_add_executable( NAME AMRSettlingSphere FILES AMRSettlingSphere.cpp DEPENDS blockforest boundary core field lbm pe pe_coupling postprocessing stencil timeloop vtk )
+waLBerla_add_executable( NAME AMRSettlingSphere FILES AMRSettlingSphere.cpp DEPENDS walberla::blockforest walberla::boundary walberla::core walberla::field walberla::lbm walberla::pe walberla::pe_coupling walberla::postprocessing walberla::stencil walberla::timeloop walberla::vtk )

apps/benchmarks/AdaptiveMeshRefinementFluidParticleCoupling/WorkloadEvaluation.cpp

@@ -540,7 +540,7 @@ int main( int argc, char **argv )
    // connect to pe
    const real_t overlap = real_c( 1.5 ) * dx;
 
-   std::function<void(void)> syncCall = std::bind( pe::syncNextNeighbors<BodyTypeTuple>, std::ref(blocks->getBlockForest()), bodyStorageID, &timingTreePE, overlap, false );
+   std::function<void(void)> syncCall = [&capture0 = blocks->getBlockForest(), bodyStorageID, capture1 = &timingTreePE, overlap] { pe::syncNextNeighbors<BodyTypeTuple>(capture0, bodyStorageID, capture1, overlap, false); };
 
    auto generationDomain = AABB( real_t(0), real_t(0), real_t(0), real_c(XCells), real_c(YCells), real_c(ZCells) - topWallOffset);
    auto peMaterial = pe::createMaterial( "mat", densityRatio, real_t(1), real_t(0.25), real_t(0.25), real_t(0), real_t(200), real_t(100), real_t(100), real_t(100) );
@@ -682,15 +682,15 @@ int main( int argc, char **argv )
    LatticeModel_T latticeModel = LatticeModel_T( lbm::collision_model::TRT::constructWithMagicNumber( omega ) );
 
    // add PDF field
-   BlockDataID pdfFieldID = lbm::addPdfFieldToStorage< LatticeModel_T >( blocks, "pdf field (zyxf)", latticeModel,
+   BlockDataID pdfFieldID = lbm::addPdfFieldToStorage< LatticeModel_T >( blocks, "pdf field (fzyx)", latticeModel,
                                                                          Vector3< real_t >( real_t(0) ), real_t(1),
-                                                                         uint_t(1), field::zyxf );
+                                                                         uint_t(1), field::fzyx );
 
    // add flag field
    BlockDataID flagFieldID = field::addFlagFieldToStorage<FlagField_T>( blocks, "flag field" );
 
    // add body field
-   BlockDataID bodyFieldID = field::addToStorage<BodyField_T>( blocks, "body field", nullptr, field::zyxf );
+   BlockDataID bodyFieldID = field::addToStorage<BodyField_T>( blocks, "body field", nullptr, field::fzyx );
 
    // add boundary handling & initialize outer domain boundaries
    BlockDataID boundaryHandlingID = blocks->addStructuredBlockData< BoundaryHandling_T >(
@@ -761,11 +761,11 @@ int main( int argc, char **argv )
                          ( blocks, pdfFieldID, boundaryHandlingID, bodyStorageID, globalBodyStorage, bodyFieldID, reconstructor, FormerMO_Flag, Fluid_Flag, pe_coupling::selectRegularBodies, optimizeForSmallObstacleFraction ), "PDF Restore" );
 
    shared_ptr<pe_coupling::BodiesForceTorqueContainer> bodiesFTContainer1 = make_shared<pe_coupling::BodiesForceTorqueContainer>(blocks, bodyStorageID);
-   std::function<void(void)> storeForceTorqueInCont1 = std::bind(&pe_coupling::BodiesForceTorqueContainer::store, bodiesFTContainer1);
+   std::function<void(void)> storeForceTorqueInCont1 = [bodiesFTContainer1] { bodiesFTContainer1->store(); };
    shared_ptr<pe_coupling::BodiesForceTorqueContainer> bodiesFTContainer2 = make_shared<pe_coupling::BodiesForceTorqueContainer>(blocks, bodyStorageID);
-   std::function<void(void)> setForceTorqueOnBodiesFromCont2 = std::bind(&pe_coupling::BodiesForceTorqueContainer::setOnBodies, bodiesFTContainer2);
+   std::function<void(void)> setForceTorqueOnBodiesFromCont2 = [bodiesFTContainer2] { bodiesFTContainer2->setOnBodies(); };
    shared_ptr<pe_coupling::ForceTorqueOnBodiesScaler> forceScaler = make_shared<pe_coupling::ForceTorqueOnBodiesScaler>(blocks, bodyStorageID, real_t(1));
-   std::function<void(void)> setForceScalingFactorToHalf = std::bind(&pe_coupling::ForceTorqueOnBodiesScaler::resetScalingFactor,forceScaler,real_t(0.5));
+   std::function<void(void)> setForceScalingFactorToHalf = [forceScaler] { forceScaler->resetScalingFactor(real_t(0.5)); };
 
    if( averageForceTorqueOverTwoTimSteps ) {
       bodiesFTContainer2->store();
@@ -981,4 +981,4 @@ int main( int argc, char **argv )
 
 int main( int argc, char **argv ){
    workload_evaluation::main(argc, argv);
-}
+}
\ No newline at end of file

apps/benchmarks/CMakeLists.txt

@@ -4,9 +4,12 @@ add_subdirectory( ComplexGeometry )
 add_subdirectory( DEM )
 add_subdirectory( MeshDistance )
 add_subdirectory( CouetteFlow )
+add_subdirectory( FreeSurfaceAdvection )
+add_subdirectory( FluidizedBed )
 add_subdirectory( FluidParticleCoupling )
 add_subdirectory( FluidParticleCouplingWithLoadBalancing )
 add_subdirectory( ForcesOnSphereNearPlaneInShearFlow )
+add_subdirectory(Percolation)
 add_subdirectory( GranularGas )
 add_subdirectory( IntegratorAccuracy )
 add_subdirectory( LennardJones )
@@ -21,13 +24,15 @@ if ( WALBERLA_BUILD_WITH_PYTHON )
    add_subdirectory( FieldCommunication )
 
    if ( WALBERLA_BUILD_WITH_CODEGEN )
-      add_subdirectory( FlowAroundSphereCodeGen )
       add_subdirectory( UniformGridCPU )
       add_subdirectory( PhaseFieldAllenCahn )
+      add_subdirectory( NonUniformGridCPU )
+      add_subdirectory( TurbulentChannel )
    endif()
 
-   if ( WALBERLA_BUILD_WITH_CODEGEN AND WALBERLA_BUILD_WITH_CUDA )
+   if ( WALBERLA_BUILD_WITH_CODEGEN AND WALBERLA_BUILD_WITH_GPU_SUPPORT )
       add_subdirectory( UniformGridGPU )
+      add_subdirectory( NonUniformGridGPU )
    endif()
 
 endif()

apps/benchmarks/CNT/CMakeLists.txt

@@ -7,4 +7,4 @@ waLBerla_add_executable( NAME 01_cnt_film
         InitializeCNTs.cpp
         SQLProperties.cpp
         Statistics.cpp
-   DEPENDS blockforest core mesa_pd sqlite vtk )
+      DEPENDS walberla::blockforest walberla::core walberla::mesa_pd walberla::sqlite walberla::vtk )

apps/benchmarks/ComplexGeometry/CMakeLists.txt

 if ( WALBERLA_BUILD_WITH_OPENMESH )
+   
+	waLBerla_link_geometry_to_builddir( "*.obj" )             
+	waLBerla_link_files_to_builddir( "*.conf" )  
 
-	waLBerla_link_files_to_builddir( "*.obj" )                 
-   waLBerla_link_files_to_builddir( "*.conf" )  
-                                  
-	waLBerla_add_executable( NAME ComplexGeometry FILES ComplexGeometry.cpp DEPENDS boundary core lbm mesh vtk )
+   waLBerla_add_executable( NAME ComplexGeometry FILES ComplexGeometry.cpp DEPENDS walberla::boundary walberla::core walberla::lbm walberla::mesh walberla::vtk )
 
 	##############
 	# Some tests #