.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

@@ -4,45 +4,61 @@ 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-use-nodiscard,
+-modernize-macro-to-enum,
+-modernize-concat-nested-namespaces,
 
 mpi-*,
+-mpi-type-mismatch,
 
 openmp-*,
 -openmp-exception-escape,
 -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-control-flow,
 readability-redundant-declaration,
 readability-redundant-function-ptr-dereference,
@@ -53,11 +69,11 @@ readability-simplify-subscript-expr,
 readability-static-accessed-through-instance,
 readability-static-definition-in-anonymous-namespace,
 readability-string-compare,
-readability-uniqueptr-delete-release
+readability-uniqueptr-delete-release,
+readability-use-anyofallof
 
 '
 WarningsAsErrors: '*'
-HeaderFilterRegex: ''
-AnalyzeTemporaryDtors: false
+HeaderFilterRegex: '.*'
 ...
 

.editorconfig

 # See https://editorconfig.org/
-root = true # top-most .editorconfig-file
+# top-most .editorconfig-file
+root = true
 
 [*]
 tab_width = 3
@@ -7,4 +8,9 @@ indent_style = space
 indent_size = 3
 charset = utf-8
 trim_trailing_whitespace = true
-insert_final_newline = false
\ No newline at end of file
+insert_final_newline = false
+
+[*.py]
+tab_width = 4
+indent_size = 4
+insert_final_newline = true
\ No newline at end of file

.flake8

+[flake8]
+max-line-length=120
+exclude=apps/showcases/Mixer/GenerateModule.py, # contains only statements
+        apps/benchmarks/FieldCommunication/config.py # just a config file 
+        utilities/bashhelper/createShortcuts.py # contains a lot of really long strings
+ignore = W503 C901 E741

.github/workflows/basicTests.yml

+name: waLBerla Tests
+
+on: push
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: create build directory
+      run: mkdir build
+    - name: CMake
+      run: cmake -S . -B build -DWALBERLA_BUILD_WITH_MPI=OFF -DWALBERLA_BUILD_TESTS=ON -DWALBERLA_BUILD_WITH_OPENMP=ON
+    - name: make
+      run: cmake --build build -j 2
+    - name: ctest
+      run: cd build; ctest

.gitignore

@@ -8,6 +8,10 @@ qrc_*
 # macOS
 **/.DS_Store
 
+# CLion indexing
+*.uuid
+.fleet
+
 
 # Generated files
 *.out
@@ -26,10 +30,15 @@ qrc_*
 /CMakeSettings.json
 /.vs
 
+# Visual Studio Code
+/.vscode
+
+# Zed
+/.cache*
 
 # CLion
 *.idea
-
+*.clion*
 
 # QtCreator
 CMakeLists.txt.user.*
@@ -46,16 +55,21 @@ CMakeLists.txt.user.*
 logfile*.txt
 *TestLog_p*.txt
 
+# Python venv
+.venv
 
 # Compiled python
 *.pyc
 
+# Jupyter Notebook
+**/.ipynb_checkpoints
 
 # Blockforest saves
 *.sav
 
 
 # CMake
+CMakeUserPresets.json
 /CMakeLists.txt.user
 
 # CMake build files
@@ -68,5 +82,11 @@ cmake_install.cmake
 CMakeDefs.h
 /moduleStatistics.json
 /walberla-config.cmake
-/cmake-build-debug/
-/cmake-build-release/
+cmake-build-*
+
+
+# Virtual environments
+.venv/
+env/
+venv/
+ENV/

.isort.cfg

+[settings]
+line_length=100
+balanced_wrapping=True
+multi_line_output=4
+known_third_party=sympy

AUTHORS.txt

 List of contributors
 ====================
 
+Cameron Stewart
 Christian Feichtinger
 Christian Godenschwager
 Christoph Rettinger
@@ -12,22 +13,34 @@ Dominik Bartuschat
 Ehsan Fattahi
 Felix Winterhalter
 Florian Schornbaum
+Frederik Hennig
+Grigorii Drozdov
+Helen Schottenhamml
+Igor Ostanin
 Jan Götz
+Jan Hönig
+João Victor Tozatti Risso
 Johannes Habich
 Klaus Iglberger
 Kristina Pickl
 Lorenz Hufnagel
+Lukas Werner
+Markus Holzer
 Martin Bauer
 Matthias Markl
 Michael Kuron
+Nils Kohl
 Paulo Carvalho
+Philipp Suffa
 Regina Ammer
 Sagar Dolas
 Sebastian Eibl
 Silke Bergler
 Simon Bogner
 Stefan Donath
+Stephan Seitz
 Sunil Kontham
+Tobias Leemann
 Tobias Preclik
 Tobias Scharpff
 Tobias Schruff

CHANGELOG.md

 # Changelog
 
-## [Unreleased]
+## [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
+- Extend MESA-PD functionalities, including several molecular dynamics models
+- Fluid-particle coupling with MESA-PD: functionalities, tests, benchmark scenarios
+
+### Changed
+- Update to C++17
+- Update CUDA compiler support
+- Extend Clang-Tidy coverage
+- Add closer integration of code generation using pystencils and lbmpy
+- Python Coupling now build upon pybind11. Boost.Python is no longer supported
+  - lbm module dropped from python coupling due to deprecation for a long time
+  - geometry, postprocessing and timeloop dropped from python coupling due to its low usage
+  - PEP8-ification of Python API. This means all keyword arguments are now in snake_case and not in CamelCase as before.
+
+### Fixed
+- Guo force model for non-SRT, may change simulation results
 
 ## [4.1] - 2019-04-19
 ### Added
@@ -54,4 +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

apps/CMakeLists.txt

@@ -2,37 +2,26 @@
 # 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
 if ( WALBERLA_BUILD_WITH_PYTHON )
     add_subdirectory( pythonmodule )
-    # no else with "EXLUDE_FROM_ALL" here, since if WALBERLA_BUILD_WITH_PYTHON_MODULE is not activated
-    # waLBerla was build without -fPIC , so no linking into shared library is possible
 endif()
-

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 )