.clang-format

+Language:        Cpp
+AccessModifierOffset: -2
+AlignAfterOpenBracket: Align
+AlignConsecutiveAssignments: true
+AlignConsecutiveDeclarations: false
+AlignEscapedNewlines: DontAlign
+AlignOperands:   true
+AlignTrailingComments: true
+AllowAllParametersOfDeclarationOnNextLine: false
+AllowShortBlocksOnASingleLine: true
+AllowShortCaseLabelsOnASingleLine: false
+AllowShortFunctionsOnASingleLine: All
+AllowShortIfStatementsOnASingleLine: true
+AllowShortLoopsOnASingleLine: false
+AlwaysBreakAfterReturnType: None
+AlwaysBreakBeforeMultilineStrings: false
+AlwaysBreakTemplateDeclarations: true
+BinPackArguments: true
+BinPackParameters: true
+BraceWrapping:   
+  AfterClass:      true
+  AfterControlStatement: true
+  AfterEnum:       false
+  AfterFunction:   true
+  AfterNamespace:  true
+  AfterObjCDeclaration: false
+  AfterStruct:     true
+  AfterUnion:      true
+  AfterExternBlock: true
+  BeforeCatch:     false
+  BeforeElse:      true
+  IndentBraces:    false
+  SplitEmptyFunction: false
+  SplitEmptyRecord: false
+  SplitEmptyNamespace: false
+BreakBeforeBinaryOperators: None
+BreakBeforeBraces: Custom
+BreakBeforeInheritanceComma: false
+BreakBeforeTernaryOperators: false
+BreakConstructorInitializers: BeforeColon
+BreakStringLiterals: true
+ColumnLimit:     120
+CommentPragmas:  '^ IWYU pragma:'
+CompactNamespaces: false
+ConstructorInitializerAllOnOneLineOrOnePerLine: false
+ConstructorInitializerIndentWidth: 3
+ContinuationIndentWidth: 3
+Cpp11BracedListStyle: false
+DerivePointerAlignment: false
+DisableFormat:   false
+ExperimentalAutoDetectBinPacking: false
+FixNamespaceComments: true
+ForEachMacros:   [ foreach, Q_FOREACH, BOOST_FOREACH ]
+IncludeBlocks: Regroup
+IncludeCategories: 
+  - Regex:           '^"blockforest/'
+    Priority:        1
+  - Regex:           '^"boundary/'
+    Priority:        2
+  - Regex:           '^"communication/'
+    Priority:        3
+  - Regex:           '^"core/'
+    Priority:        4
+  - Regex:           '^"domain_decomposition/'
+    Priority:        5
+  - Regex:           '^"executiontree/'
+    Priority:        6
+  - Regex:           '^"fft/'
+    Priority:        7
+  - Regex:           '^"field/'
+    Priority:        8
+  - Regex:           '^"gather/'
+    Priority:        9
+  - Regex:           '^"geometry/'
+    Priority:        10
+  - Regex:           '^"gpu/'
+    Priority:        11
+  - Regex:           '^"gpu/'
+    Priority:        12
+  - Regex:           '^"lbm/'
+    Priority:        13
+  - Regex:           '^"lbm_mesapd_coupling/'
+    Priority:        14
+  - Regex:           '^"mesh/'
+    Priority:        15
+  - Regex:           '^"mesa_pd/'
+    Priority:        16
+  - Regex:           '^"pde/'
+    Priority:        17
+  - Regex:           '^"pe/'
+    Priority:        18
+  - Regex:           '^"pe_coupling/'
+    Priority:        19
+  - Regex:           '^"postprocessing/'
+    Priority:        20
+  - Regex:           '^"python_coupling/'
+    Priority:        21
+  - Regex:           '^"simd/'
+    Priority:        22
+  - Regex:           '^"sqlite/'
+    Priority:        23
+  - Regex:           '^"stencil/'
+    Priority:        24
+  - Regex:           '^"timeloop/'
+    Priority:        25
+  - Regex:           '^"vtk/'
+    Priority:        26
+  - Regex:           '^<boost/'
+    Priority:        27
+  - Regex:           '^<'
+    Priority:        28
+IndentCaseLabels: false
+IndentPPDirectives: AfterHash
+IndentWidth: 3
+IndentWrappedFunctionNames: true
+KeepEmptyLinesAtTheStartOfBlocks: false
+MacroBlockBegin: ''
+MacroBlockEnd:   ''
+MaxEmptyLinesToKeep: 1
+NamespaceIndentation: None
+ObjCBlockIndentWidth: 2
+ObjCSpaceAfterProperty: false
+ObjCSpaceBeforeProtocolList: true
+PenaltyBreakAssignment: 2
+PenaltyBreakBeforeFirstCallParameter: 19
+PenaltyBreakComment: 300
+PenaltyBreakFirstLessLess: 120
+PenaltyBreakString: 1000
+PenaltyExcessCharacter: 1000000
+PenaltyReturnTypeOnItsOwnLine: 60
+PointerAlignment: Left
+ReflowComments:  true
+SortIncludes:    true
+SortUsingDeclarations: true
+SpaceAfterCStyleCast: true
+SpaceAfterTemplateKeyword: false
+SpaceBeforeAssignmentOperators: true
+SpaceBeforeParens: ControlStatements
+SpaceInEmptyParentheses: false
+SpacesBeforeTrailingComments: 1
+SpacesInAngles:  true
+SpacesInContainerLiterals: true
+SpacesInCStyleCastParentheses: false
+SpacesInParentheses: false
+SpacesInSquareBrackets: false
+Standard:        Cpp11
+TabWidth:        3
+UseTab:          Never
\ No newline at end of file

.clang-tidy

+---
+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-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-pass-by-value,
+-modernize-raw-string-literal,
+-modernize-use-transparent-functors,
+-modernize-use-trailing-return-type,
+-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-container-size-empty,
+readability-delete-null-pointer,
+readability-deleted-default,
+readability-misplaced-array-index,
+readability-non-const-parameter,
+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-subscript-expr,
+readability-static-accessed-through-instance,
+readability-static-definition-in-anonymous-namespace,
+readability-string-compare,
+readability-uniqueptr-delete-release,
+readability-use-anyofallof
+
+'
+WarningsAsErrors: '*'
+HeaderFilterRegex: '.*'
+...
+

.editorconfig

+# See https://editorconfig.org/
+# top-most .editorconfig-file
+root = true
+
+[*]
+tab_width = 3
+indent_style = space
+indent_size = 3
+charset = utf-8
+trim_trailing_whitespace = true
+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

@@ -4,48 +4,72 @@ ui_*
 qrc_*
 *~
 
-# Backup files of kate/kwrite
+
+# macOS
+**/.DS_Store
+
+# CLion indexing
+*.uuid
+.fleet
+
 
 # Generated files
 *.out
 /src/waLBerlaDefinitions.h
 /src/core/waLBerlaBuildInfo.cpp
 
+
 # Eclipse
 /.cproject
 /.project
 /.pydevproject
 /.settings
 
+
 # Visual Studio
 /CMakeSettings.json
 /.vs
 
+# Visual Studio Code
+/.vscode
+
+# Zed
+/.cache*
+
+# CLion
+*.idea
+*.clion*
+
+# QtCreator
+CMakeLists.txt.user.*
+
+
 # Binary Files
 /bin/
 /lib/
 *.a
-/build
+/build*
 
 
 # Logfiles
 logfile*.txt
 *TestLog_p*.txt
 
+# Python venv
+.venv
 
 # Compiled python
 *.pyc
 
+# Jupyter Notebook
+**/.ipynb_checkpoints
+
 # Blockforest saves
 *.sav
 
 
-/utilities/.idea
-/utilities/py_waLBerla/.idea
-/python/.idea
-
-/src/stencil/.idea
-
+# CMake
+CMakeUserPresets.json
 /CMakeLists.txt.user
 
 # CMake build files
@@ -58,3 +82,11 @@ cmake_install.cmake
 CMakeDefs.h
 /moduleStatistics.json
 /walberla-config.cmake
+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
+Christoph Schwarzmeier
 Daniel Ritter
 Daniela Anderl
 David Staubach
@@ -11,22 +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
+
+## [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
+- Galerkin coarsening for Multigrid
+- LBM-PE-Coupling:
+  - new coupling approach for unresolved particle interactions (discrete particle method)
+  - adaptive grid refinement for coupled simulations
+  - load balancing functionalities for coupled simulations
+  - module description
+- integrated *pystencils* and *lbmpy* code generation for kernels and pack infos
+- new GPU communication, including support for GPUDirect
+- load balancing functionality for the pe
+- implemented IProbe communication as an alternative to two message communication for unknown size communication
+- new creation helpers for BlockForest
+- Minor:
+   - dynamic load balancing now possible with levels ignored
+   - `ExtendedBoundaryHandlingFactory` now uses `ParserUBB` instead of `UBB` so that velocity profiles can be specified as an equation in a parameter file
+   - Enabled the body selection functions for PSM coupling method
+   - grid_generators now allow range based for loops
+
+### Changed
+- A compiler with full C++14 support is now required
+- All Boost usage has been replaced with the corresponding standard library functionality, except for Boost.Python (used for the `python_coupling` module), Boost.PropertyTree (used in `config::configToBoostPropertyTree`) and Boost.Graph (used by `math::EquationSystem`). This usually means you need to replace `boost::` with `std::` in your code and change some `#include`s.
+- API changes in blockforest::PhantomBlockForest, blockforest::loadbalancing, pe::amr::weight_assignment
+- API change for vtk::VTKOutput::getFilenames
+- made SendBuffer memory access more high level
+- PE coupling:
+   - changed body mapping functions: removed most of them, added mapping-decider function, accomodated changes to test cases, added new mapping test case
+   - changed pe coupling mapping functions interfaces, added new mapping functions, adapted test cases and benchmarks
+   - change in lubrication correction functionality to not require the lattice model but use the dynamic viscosity directly
+- PE:
+   - rebased Union on BodyStorage
+   - `pe::Union`, `boundary::BoundaryHandling` and `boundary::BoundaryHandlingCollection` are now variadic templates instead of taking a tuple of bodies/boundaries/handlers. This means that you need to replace `std::tuple<A,B>` with `A,B` in these cases.
+   - using smart pointers for all memory management
+   - made setMass protected
+   - extended DEM collision model with dt
+   - pe::createBlockForest changed to support a variable number of processes
+   - changed BodyStatistics to use shared_ptr instead of reference
+
+### Removed
+- Remove dependency resolution from Singleton
+- from PE
+   - Node
+   - PtrVector
+   - contacts from RigidBody
+   - attached bodies
+   - attachables
+
+### Fixed
+- Fix implict/explict naming in pe::cr
+
+### Deprecated
+- all dynamic level-wise balance functions (use the more general ones, without "level-wise")