espressomd · RudolfWeeber · Aug 2, 2022 · Aug 3, 2022 · Aug 3, 2022 · Aug 3, 2022
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
@@ -80,6 +80,7 @@ default:
      myconfig: 'default'
      with_coverage: 'true'
      with_scafacos: 'true'
+     with_walberla: 'true'
      with_stokesian_dynamics: 'true'
      check_skip_long: 'true'
   script:
@@ -106,6 +107,24 @@ maxset:
     - docker
     - linux
 
+maxset-walberla:
+  <<: *global_job_definition
+  stage: build
+  variables:
+     with_cuda: 'false'
+     myconfig: 'maxset-walberla'
+     with_coverage: 'true'
+     with_walberla: 'true'
+     with_scafacos: 'false'
+     with_stokesian_dynamics: 'false'
+     check_skip_long: 'true'
+     check_procs: '4'
+  script:
+    - bash maintainer/CI/build_cmake.sh
+  tags:
+    - docker
+    - linux
+
 no_rotation:
   <<: *global_job_definition
   stage: build
@@ -281,11 +300,12 @@ tutorials-samples-maxset:
   variables:
      CC: 'gcc-8'
      CXX: 'g++-8'
-     myconfig: 'maxset'
+     myconfig: 'maxset-walberla'
      with_cuda: 'true'
      with_coverage: 'false'
      with_coverage_python: 'true'
      with_scafacos: 'true'
+     with_walberla: 'true'
      make_check_unit_tests: 'false'
      make_check_python: 'false'
      make_check_tutorials: 'true'
@@ -429,28 +449,29 @@ empty:
     - linux
     - cuda-kepler
 
-check_sphinx:
-  <<: *global_job_definition
-  stage: additional_checks
-  needs:
-    - cuda10-maxset
-  when: on_success
-  script:
-    - sed -i 's/ or "DISPLAY" in os.environ/ or True/' ${CI_PROJECT_DIR}/src/python/espressomd/visualization.pyx
-    - cd ${CI_PROJECT_DIR}/build
-    - make -t && rm src/python/espressomd/visualization.* && make sphinx
-    - make -j2 tutorials
-    - make check_utils
-    - bash ${CI_PROJECT_DIR}/maintainer/CI/doc_warnings.sh
-    - python3 ${CI_PROJECT_DIR}/maintainer/CI/jupyter_warnings.py
-  artifacts:
-    paths:
-    - build/doc/sphinx
-    expire_in: 1 week
-  tags:
-    - docker
-    - linux
-    - cuda-kepler
+# WALBERLA TODO
+#check_sphinx:
+#  <<: *global_job_definition
+#  stage: additional_checks
+#  needs:
+#    - cuda10-maxset
+#  when: on_success
+#  script:
+#    - sed -i 's/ or "DISPLAY" in os.environ/ or True/' ${CI_PROJECT_DIR}/src/python/espressomd/visualization.pyx
+#    - cd ${CI_PROJECT_DIR}/build
+#    - make -t && rm src/python/espressomd/visualization.* && make sphinx
+#    - make -j2 tutorials
+#    - make check_utils
+#    - bash ${CI_PROJECT_DIR}/maintainer/CI/doc_warnings.sh
+#    - python3 ${CI_PROJECT_DIR}/maintainer/CI/jupyter_warnings.py
+#  artifacts:
+#    paths:
+#    - build/doc/sphinx
+#    expire_in: 1 week
+#  tags:
+#    - docker
+#    - linux
+#    - cuda-kepler
 
 run_tutorials:
   <<: *global_job_definition
@@ -542,13 +563,15 @@ check_with_odd_no_of_processors:
     - linux
     - icp
 
-deploy_sphinx_documentation:
-  extends: .deploy_base
-  dependencies:
-    - check_sphinx
-  script:
-    - cd ${CI_PROJECT_DIR}/build/doc/sphinx/html &&
-      rsync -avz --delete -e "ssh -i ${HOME}/.ssh/espresso_rsa" ./ [email protected]:/home/espresso/public_html/html/doc
+# WALBERLA TODO
+#deploy_sphinx_documentation:
+#  extends: .deploy_base
+#  dependencies:
+#    - check_sphinx
+#  script:
+#    - cd ${CI_PROJECT_DIR}/build/doc/sphinx/html &&
+#      rsync -avz --delete -e "ssh -i ${HOME}/.ssh/espresso_rsa" ./ [email protected]:/home/espresso/public_html/html/doc
+#
 
 deploy_doxygen_documentation:
   extends: .deploy_base

diff --git a/.gitmodules b/.gitmodules
@@ -1,3 +1,4 @@
 [submodule "libs/h5xx"]
 	path = libs/h5xx
 	url = https://github.com/h5md/h5xx.git
+
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -20,13 +20,14 @@ repos:
         exclude: '\.pylintrc|.*.\.py\.in'
         args: ["--ignore=E266,E701,W291,W293", "--in-place", "--aggressive"]
 
-    -   id: cmake-format
-        name: cmake-format
-        entry: sh maintainer/format/cmake-format.sh
-        language: system
-        always_run: false
-        files: 'CMakeLists.txt'
-        args: ["-i"]
+# TODO WALBERLA
+#    -   id: cmake-format
+#        name: cmake-format
+#        entry: sh maintainer/format/cmake-format.sh
+#        language: system
+#        always_run: false
+#        files: 'CMakeLists.txt'
+#        args: ["-i"]
 
     -   id: ex-flags
         name: executable flags

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -78,6 +78,7 @@ option_if_available(WITH_STOKESIAN_DYNAMICS "Build with Stokesian Dynamics" ON)
 option(WITH_BENCHMARKS "Enable benchmarks" OFF)
 option(WITH_VALGRIND_INSTRUMENTATION
        "Build with valgrind instrumentation markers" OFF)
+option(WITH_WALBERLA "Build with WALBERLA Lattice-Boltzmann support" OFF)
 if(CMAKE_CXX_COMPILER_ID MATCHES "Clang")
   option(WITH_CLANG_TIDY "Run Clang-Tidy during compilation" OFF)
 endif()
@@ -490,6 +491,36 @@ if(WITH_BENCHMARKS)
   add_subdirectory(maintainer/benchmarks)
 endif(WITH_BENCHMARKS)
 
+
+# Walberla 
+if (WITH_WALBERLA)
+  cmake_minimum_required(VERSION 3.11)
+  include(FetchContent)
+  FetchContent_Declare(
+    walberla
+    GIT_REPOSITORY https://i10git.cs.fau.de/walberla/walberla
+    GIT_TAG        64a4d68
+    PATCH_COMMAND  patch -p0 --ignore-whitespace -i
+                   ${PROJECT_SOURCE_DIR}/cmake/waLBerlaFunctions.patch
+  )
+  FetchContent_Populate(walberla)
+  set(WALBERLA_BUILD_TESTS off CACHE BOOL "")
+  set(WALBERLA_BUILD_BENCHMARKS off CACHE BOOL "")
+  set(WALBERLA_BUILD_TOOLS off CACHE BOOL "")
+  set(WALBERLA_BUILD_TUTORIALS off CACHE BOOL "")
+  set(WALBERLA_BUILD_SHOWCASES off CACHE BOOL "")
+  set(WALBERLA_BUILD_DOC off CACHE BOOL "")
+  set(CMAKE_POSITION_INDEPENDENT_CODE on CACHE BOOL "")
+  add_subdirectory("${walberla_SOURCE_DIR}" "${walberla_BINARY_DIR}")
+  set(WALBERLA 1)
+  # TODO WALBERLA: remove -lmpi_cxx -lmpi (required to find symbol MPI::Datatype::Free() in VTK code) and -lstdc++fs
+  set(WALBERLA_LIBS walberla::core walberla::domain_decomposition walberla::blockforest walberla::boundary walberla::core walberla::domain_decomposition walberla::field walberla::lbm walberla::timeloop walberla::vtk)
+  if(NOT CMAKE_CXX_COMPILER_ID MATCHES "AppleClang")
+    set(WALBERLA_LIBS ${WALBERLA_LIBS} stdc++fs -lmpi_cxx -lmpi)
+  endif()
+endif(WITH_WALBERLA)
+
+#######################################################################
 #
 # Subdirectories
 #

diff --git a/cmake/FindwaLBerla.cmake b/cmake/FindwaLBerla.cmake
@@ -0,0 +1,20 @@
+set( WALBERLA_FOUND  OFF                     CACHE  BOOL  "waLBerla found" )
+set( WALBERLA_DIR    WALBERLA_DIR-NOTFOUND   CACHE  PATH  "waLBerla path"  )
+
+if(EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/walberla" )
+    # Subdirectory walberla exists
+    message( STATUS "Using walberla subfolder" )
+    add_subdirectory( walberla EXCLUDE_FROM_ALL )
+    waLBerla_import(NO_COMPILER_FLAGS)
+    set( WALBERLA_DIR   "${CMAKE_CURRENT_SOURCE_DIR}/walberla" CACHE  PATH  "waLBerla path"  FORCE )
+    set( WALBERLA_FOUND ON                                     CACHE  BOOL  "waLBerla found" FORCE )
+else()
+    # Search for a build directory elsewhere
+    find_package( waLBerla REQUIRED NO_MODULE ) 
+    message( STATUS "Found waLBerla source directory ${walberla_SOURCE_DIR}" )
+    message( STATUS "Found waLBerla binary directory ${walberla_BINARY_DIR}" )
+    add_subdirectory( ${walberla_SOURCE_DIR} ${walberla_BINARY_DIR} EXCLUDE_FROM_ALL )
+    waLBerla_import()
+    set( WALBERLA_DIR   "${walberla_BINARY_DIR}"  CACHE  PATH  "waLBerla path"  FORCE )
+    set( WALBERLA_FOUND ON                        CACHE  BOOL  "waLBerla found" FORCE )
+endif()
diff --git a/cmake/waLBerlaFunctions.patch b/cmake/waLBerlaFunctions.patch
@@ -0,0 +1,8 @@
+--- cmake/waLBerlaFunctions.cmake
++++ cmake/waLBerlaFunctions.cmake
+@@ -91,4 +91,5 @@ function ( waLBerla_add_module )
+     if ( hasSourceFiles )
+        add_library( ${moduleLibraryName} STATIC ${sourceFiles} ${otherFiles} )
++       add_library(walberla::${moduleLibraryName} ALIAS ${moduleLibraryName})
+  	else( )
+        add_custom_target( ${moduleLibraryName} SOURCES ${sourceFiles} ${otherFiles} )  # dummy IDE target
diff --git a/doc/sphinx/advanced_methods.rst b/doc/sphinx/advanced_methods.rst
@@ -523,7 +523,7 @@ or data files for further processing and analysis.
 Visualization in ParaView
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-For visualization we suggest the free software ParaView. All .vtk
+For visualization we suggest the free software ParaView [5]_. All .vtk
 files (boundaries, fluid, objects at all time steps) can be loaded at
 the same time. The loading is a two step process, because only after
 pressing the Apply button, are the files actually imported. Using the
@@ -1422,35 +1422,6 @@ Checkpointing in the EK works quite similar to checkpointing in the LB, because
 Output
 ~~~~~~
 
-.. _Fields:
-
-Fields
-^^^^^^
-
-::
-
-    ek.print_vtk_boundary(path)
-    ek.print_vtk_density(path)
-    ek.print_vtk_velocity(path)
-    ek.print_vtk_potential(path)
-
-A property of the fluid field can be exported into a
-file in one go. Currently supported
-are: density, velocity, potential and boundary, which give the LB fluid density, the LB fluid velocity,
-the electrostatic potential, and the location and type of the
-boundaries, respectively. The boundaries can only be printed when the
-``EK_BOUNDARIES`` is compiled in. The output is a vtk-file, which is readable by
-visualization software such as ParaView [5]_ and Mayavi2 [6]_.
-
-::
-
-    species.print_vtk_flux(path)
-    species.print_vtk_density(path)
-
-These commands are similar to the above. They enable the
-export of diffusive species properties, namely: ``density`` and ``flux``, which specify the
-number density and flux of species ``species``, respectively.
-
 .. _Local Quantities:
 
 Local Quantities
@@ -1475,8 +1446,6 @@ The local ``density`` and ``flux`` of a species can be obtained in the same fash
 
 .. [5]
    https://www.paraview.org/
-.. [6]
-   http://code.enthought.com/projects/mayavi/
 
 
 .. _Particle polarizability with thermalized cold Drude oscillators:

diff --git a/doc/sphinx/lb.rst b/doc/sphinx/lb.rst
@@ -216,41 +216,32 @@ drift. To remove the momentum in the fluid call::
 Output for visualization
 ------------------------
 
-|es| implements a number of commands to output fluid field data of the whole fluid into a file at once. ::
-
-    lb.print_vtk_velocity(path)
-    lb.print_vtk_boundary(path)
-    lb.print_velocity(path)
-    lb.print_boundary(path)
-
-Currently supported fluid properties are the velocity, and boundary flag in ASCII VTK as well as Gnuplot compatible ASCII output.
+|es| implements the :meth:`LBFluidWalberla.write_vtk()` command to output
+one or multiple fluid field data into a single file::
+
+
+    vtk_obs = ['density', 'velocity_vector']
+    # create a VTK callback that automatically writes every 10 LB steps
+    lb_vtk = lbf.add_vtk_writer('vtk_automatic', vtk_obs, delta_N=10)
+    self.system.integrator.run(100)
+    # can be deactivated
+    lb_vtk.disable()
+    self.system.integrator.run(10)
+    lb_vtk.enable()
+    # create a VTK callback that writes on demand
+    lb_vtk = lbf.add_vtk_writer('vtk_now', vtk_obs)
+    lb_vtk.write()
+
+Currently supported fluid properties are the density, velocity vector
+and pressure tensor. By default, the properties of the current state
+of the fluid are written to disk. To add a callback that writes to
+disk continuously, use the optional argument ``delta_N`` to indicate
+the level of subsampling. Such a callback can be deactivated.
 
 The VTK format is readable by visualization software such as ParaView [1]_
 or Mayavi2 [2]_. If you plan to use ParaView for visualization, note that also the particle
 positions can be exported using the VTK format (see :meth:`~espressomd.particle_data.ParticleList.writevtk`).
 
-The variant
-
-::
-
-   lb.print_vtk_velocity(path, bb1, bb2)
-
-allows you to only output part of the flow field by specifying an axis aligned
-bounding box through the coordinates ``bb1`` and ``bb1`` (lists of three ints) of two of its corners. This
-bounding box can be used to output a slice of the flow field. As an
-example, executing
-
-::
-
-    lb.print_vtk_velocity(path, [0, 0, 5], [10, 10, 5])
-
-will output the cross-section of the velocity field in a plane
-perpendicular to the :math:`z`-axis at :math:`z = 5` (assuming the box
-size is 10 in the :math:`x`- and :math:`y`-direction).
-
-.. If the bicomponent fluid is used, two filenames have to be supplied when exporting the density field, to save both components.
-
-
 .. _Choosing between the GPU and CPU implementations:
 
 Choosing between the GPU and CPU implementations

diff --git a/doc/tutorials/active_matter/active_matter.ipynb b/doc/tutorials/active_matter/active_matter.ipynb
@@ -218,7 +218,7 @@
     "by invoking\n",
     "\n",
     "```python\n",
-    "lbf = espressomd.lb.LBFluidGPU(agrid=1, dens=1.0, visc=1.0, tau=0.01)\n",
+    "lbf = espressomd.lb.LBFluidWalberla(agrid=1, dens=1.0, visc=1.0, tau=0.01)\n",
     "system.actors.add(lbf)\n",
     "system.thermostat.set_lb(LB_fluid=lbf, gamma=20.0, seed=42)\n",
     "```\n",
@@ -529,15 +529,15 @@
     "The first block of the script sets up the basic simulation parameters, with\n",
     "which you should be familiar – if you are struggling with this part, please\n",
     "consult the previous tutorials. The second block sets up the boundaries using\n",
-    "instances of <tt>LBBoundary</tt>, as was introduced in the LB tutorial.\n",
-    "Finally, in the third block the\n",
-    "code\n",
+    "instances of <tt>LBBoundary</tt>, as was introduced in the LB tutorial, and\n",
+    "fills the cavity with a fluid. Finally, in the third block, the code\n",
     "\n",
     "```python\n",
-    "lbf.print_vtk_boundary(\"{}/boundary.vtk\".format(outdir))\n",
+    "lb_vtk = lbf.add_vtk_writer(\"shape\", \"density\")\n",
+    "lb_vtk.write()\n",
     "```\n",
     "\n",
-    "ensures that the boundary data is exported to a <tt>.vtk</tt> file. This file\n",
+    "ensures that the fluid data is exported to a <tt>.vtu</tt> file. This file\n",
     "can be read in and visualized using the program ParaView, which should\n",
     "have been introduced in the LB and Electrostatics tutorials. Here, we briefly\n",
     "comment on how the geometry can be visualized. In the command prompt type\n",
@@ -546,13 +546,9 @@
     "paraview &\n",
     "```\n",
     "\n",
-    "to open ParaView. Open the relevant <tt>.vtk</tt> file (in our\n",
-    "case <tt>boundary.vtk</tt>). Click the green `Apply` button. Now add a\n",
-    "`Clip` from the ribbon just above the Pipeline Browser to the\n",
-    "highlighted <tt>boundary.vtk</tt> entry. Within the `Clip Properties` tab, select\n",
-    "`Scalar` in the `Clip Type` drop-down tab. Then set the value of the\n",
-    "scalar to 0.1 with the slide (or by typing in the field) and tick the\n",
-    "`Inside Out` box. Click `Apply`. Next do `Filter/Alphabetical/Extract Surface`\n",
+    "to open ParaView. Open the relevant <tt>.vtu</tt> file (in our\n",
+    "case <tt>vtk_out/shape/simulation_step_0.vtu</tt>). Click the green `Apply` button.\n",
+    "Next do `Filter/Alphabetical/Extract Surface` and click the green `Apply` button\n",
     "to create a surface mesh, then do `Filter/Alphabetical/Smooth` with 1000 in the\n",
     "`Number of iterations` field. Click `Apply`, then set the `Opacity` slide to\n",
     "0.25 to visualize the inside of the geometry that you have created. The result\n",