.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

.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
@@ -72,5 +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

@@ -13,7 +13,10 @@ Dominik Bartuschat
 Ehsan Fattahi
 Felix Winterhalter
 Florian Schornbaum
+Frederik Hennig
+Grigorii Drozdov
 Helen Schottenhamml
+Igor Ostanin
 Jan Götz
 Jan Hönig
 João Victor Tozatti Risso
@@ -28,6 +31,7 @@ Matthias Markl
 Michael Kuron
 Nils Kohl
 Paulo Carvalho
+Philipp Suffa
 Regina Ammer
 Sagar Dolas
 Sebastian Eibl

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

README.md

 # waLBerla
 
-waLBerla (widely applicable Lattice Boltzmann from Erlangen) is a massively 
-parallel framework for multi physics applications. Besides its original 
-objective, Lattice Boltzmann solvers for hydrodynamics, it now contains 
-modules for other applications like Multigrid and rigid body dynamics 
-as well. Great emphasis is placed on the interoperability between the modules 
-in particular the fluid-particle coupling. 
-It scales from laptops to current and future supercomputers while maintaining 
+waLBerla (widely applicable Lattice Boltzmann from Erlangen) is a massively
+parallel framework for multi physics applications. Besides its original
+objective, Lattice Boltzmann solvers for hydrodynamics, it now contains
+modules for other applications like Multigrid and rigid body dynamics
+as well. Great emphasis is placed on the interoperability between the modules
+in particular the fluid-particle coupling.
+It scales from laptops to current and future supercomputers while maintaining
 near-perfect efficiency.
 
 See https://www.walberla.net/ for more information and a showcase of applications.
@@ -19,13 +19,45 @@ is documented in [Sphinx](http://walberla.net/sphinx/index.html).
 
 ## Getting started
 
-The minimum requirements are a C++14-compliant compiler (e.g. GCC or Clang),
-the [Boost](http://www.boost.org) library and the [CMake](http://www.cmake.org)
+The minimum requirements are a C++17-compliant compiler (e.g. GCC or Clang)
+and the [CMake](http://www.cmake.org)
 build system. Furthermore, you need an MPI library (like
 [Open MPI](http://www.open-mpi.org)) if you want to make use of parallel
 processing capabilities. All of these dependencies are typically available in
 your operating system's package manager.
 
+### CMake
+
+The typical steps, assuming your are in the waLBerla source directory, are:
+
+- `mkdir build; cd build` create a build directory and change into it
+- `cmake ..` call CMake with the waLBerla source directory as an argument
+- `make` build waLBerla
+
+To specify a CMake option you need to use `-D(Option)=(Value)`. For example to set the C++ compiler one can use:
+`cmake -DCMAKE_CXX_COMILER=clang++`
+
+To list and modify the CMake options the `ccmake` tool can be used. Just call `ccmake .` in your **build** directory to see and change the
+CMake options and variables.
+
+Some important CMake variables:
+
+- `WALBERLA_BUILD_WITH_CODEGEN` Enable pystencils code generation"
+- `Python_ROOT_DIR` Specify the directory of the `python` executable. e.g. `~/miniconda/bin/`
+- `MPI_HOME` Specify the base directory of the MPI installation.
+- `WALBERLA_BUILD_WITH_PYTHON` Support for embedding Python
+- `WALBERLA_BUILD_WITH_CUDA` Enable CUDA support
+
+For a full list of CMake Option see the [CMakeLists.txt](CMakeLists.txt) file or use `ccmake` as described above.
+
+### Codegen and Python
+
+To use the `lbmpy`/`pystencils` code generation please install the packages with e.g. `pip3 install lbmpy` and specify the correct python
+environment when calling CMake.
+
+In previous versions of CMake one could use `PYTHON_EXECUTABLE` or `PYTHON_ROOT_DIR` (all upper case) to specify the python executable or
+the directory. This does **NOT** work anymore. Please use `Python_ROOT_DIR`.
+
 ## Get involved
 
 ### Contributing
@@ -47,15 +79,40 @@ Many thanks go to waLBerla's [contributors](AUTHORS.txt)
 
 If you use waLBerla in a publication, please cite the following articles:
 
-- C. Godenschwager, F. Schornbaum, M. Bauer, H. Köstler, and U. Rüde. A
-framework for hybrid parallel flow simulations with a trillion cells in complex
-geometries. In: Proceedings of the International Conference on High Performance
-Computing, Networking, Storage and Analysis, page 35. ACM, 2013.
-- M. Bauer, S. Eibl, C. Godenschwager, N. Kohl, M. Kuron, C. Rettinger,
-F. Schornbaum, C. Schwarzmeier, D. Thönnes, H. Köstler, and U. Rüde. waLBerla:
-A block-structured high-performance framework for multiphysics simulations. In:
-Computers & Mathematics with Applications, doi:10.1016/j.camwa.2020.01.007.
-Elsevier, 2020.
+Overview:
+- 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.
+
+Grid Refinement:
+- F. Schornbaum and U. Rüde, *Massively parallel algorithms for the lattice boltzmann
+  method on nonuniform grids*. SIAM Journal on Scientific Computing, 2016.
+  https://doi.org/10.1137/15M1035240
+
+LBM - Particle Coupling:
+- C. Rettinger and U. Rüde, *A comparative study of fluid-particle coupling methods for
+  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:
+  Mesoscopic distinct element method simulations and experimental validation*.
+  Journal of Applied Physics, 2020. https://doi.org/10.1063/5.0025505
 
 ## License