Merge pull request #34 from precice/main

Synchronization of `develop` branch with `main` branch

.github/issue_template.md

@@ -12,12 +12,12 @@ Please provide information about the operating system and relevant versions of
 the software.
 
 Example:
-Ubuntu 20.04 LTS, preCICE 2.3.0, DuMuX 3.4, DuMuX-preCICE 0.1
+Ubuntu 22.04 LTS, preCICE 3.0.0, DuMuX 3.7, DuMuX-preCICE 2.0.0
 --->
 
 ## Steps to reproduce
 
-<!-- Please describe the steps one has to execture to reproduce the problem. --->
+<!-- Please describe the steps one has to execute to reproduce the problem. --->
 
 ### Expected behavior
 

.github/workflows/build-and-test.yml

@@ -11,7 +11,7 @@ jobs:
     strategy:
       max-parallel: 2
       matrix:
-        dumux_version: [3.4, 3.5]
+        dumux_version: [3.7, 3.8]
         precice_version: [develop]
     container:
       image: precice/dumux-precice:${{ matrix.dumux_version }}-${{ matrix.precice_version }}

.github/workflows/build-docker-containers.yml

@@ -17,7 +17,7 @@ jobs:
         dockerhub_username: precice
     strategy:
       matrix:
-        dumux_version: [3.4, 3.5]
+        dumux_version: [3.7, 3.8]
         precice_version: [develop]
     steps:
       - name: Checkout Repository
@@ -37,8 +37,8 @@ jobs:
           file: "./dockerfile.slim"
           tags: ${{ env.dockerhub_username }}/dumux-precice:${{ matrix.dumux_version }}-${{ matrix.precice_version }}
           build-args: |
-            DUNEVERSION=2.8
-            PRECICEUBUNTU=focal
+            DUNEVERSION=2.9
+            PRECICEUBUNTU=jammy
             DUMUXVERSION=${{ matrix.dumux_version }}
             PRECICEVERSION=${{ matrix.precice_version }}
   build-dune-precice:
@@ -69,5 +69,5 @@ jobs:
           tags: ${{ env.dockerhub_username }}/dune-precice:${{ matrix.dune_version }}-${{ matrix.precice_version }}
           build-args: |
             DUNEVERSION=${{ matrix.dune_version }}
-            PRECICEUBUNTU=focal
+            PRECICEUBUNTU=jammy
             PRECICEVERSION=${{ matrix.precice_version }}

CHANGELOG.md

@@ -1,8 +1,8 @@
 # DuMuX-preCICE change log
 
-## Not released yet
+## v2.0.0
 
-- 2023-08-10: Updated the adapter to align with preCICE V3. Updated the examples accordingly.
+- 2023-08-10: Updated the adapter to be compatible with preCICE v3.0.0. Updated the examples too.
 
 ## v1.0.0
 

README.md

@@ -23,13 +23,13 @@ The DuMuX-preCICE adapter is a DUNE module named `dumux-precice` which can be bu
 
 ### Prerequisites
 
-- DuMuX **newer** than 3.2
+- DuMuX >= than 3.7
 
     - Builds using the current `master` branch of DuMuX might fail.
     - If you run into trouble with a new DuMuX release, please open an issue in the repository and add the error message that you receive.
     - Needs UMFPack (available via SuiteSparse) as solver for linear systems of equations. This is needed to run the examples included in the adapter. Otherwise you can skip UMFPack.
 
-- preCICE >=2.0.0
+- preCICE >=3.0.0
 
     - The adapter is build via the DUNE build system that is based on CMake. Thus, the CMake [link instructions for preCICE](https://precice.org/installation-linking.html#cmake) apply.
 
@@ -42,7 +42,7 @@ The DuMuX-preCICE adapter should build fine if DuMuX, preCICE and their dependen
 
 ### Detailed installation steps
 
-1. Install [DuMuX](https://dumux.org/) and the needed dependencies. The easiest way is to follow [DuMuX's installation instructions](https://dumux.org/installation/). The DuMuX project provides a script that installs and DuMuX and the DUNE modules required by DuMuX. This means, after installing DuMuX via the provided script you should be good to go to use the DuMuX-preCICE adapter.
+1. Install [DuMuX](https://dumux.org/) and the needed dependencies. The easiest way is to follow [DuMuX's installation instructions](https://dumux.org/docs/doxygen/master/installation.html). The DuMuX project provides a script that installs and DuMuX and the DUNE modules required by DuMuX. This means, after installing DuMuX via the provided script you should be good to go to use the DuMuX-preCICE adapter.
 
     After the installation you should have a root directory that contains the base DUNE modules, i.e. a  number of directories named like `dune-common`, `dune-geometry` etc., and a directory called `dumux`.
 
@@ -51,13 +51,13 @@ The DuMuX-preCICE adapter should build fine if DuMuX, preCICE and their dependen
 2. Download the DuMuX-preCICE adapter to the same directory as the DUNE modules and the `dumux` folder. It is recommended to use the latest release of the adapter, which can be found by checking out the relevant release tag.
 
     ```text
-    git clone -b v1.0.0 https://github.com/precice/dumux-adapter.git
+    git clone -b v2.0.0 https://github.com/precice/dumux-adapter.git
     ```
 
     You can also try to clone the repository via SSH:
 
     ```text
-    git clone -b v1.0.0 [email protected]:precice/dumux-adapter.git
+    git clone -b v2.0.0 [email protected]:precice/dumux-adapter.git
     ```
 
 3. Verify that the `dumux-adapter` folder is in the same directory as the DUNE module folders and the `dumux` folder.
@@ -68,7 +68,7 @@ The DuMuX-preCICE adapter should build fine if DuMuX, preCICE and their dependen
     ./dune-common/bin/dunecontrol --only=dumux-precice all
     ```
 
-    After the build and configure step a new directory `build-cmake` was created inside the `dumux-precice` directory.
+    After the build and configure step a new directory `build-cmake` was created inside the `dumux-adapter` directory.
 
     You can configure the build and configuration process using advanced options by manipulating CMake variables. `dunecontrol` allows to pass an options file for that
 
@@ -84,7 +84,7 @@ The DuMuX-preCICE adapter should build fine if DuMuX, preCICE and their dependen
 
     This provided `cmake-test.opts` file turns off some system-dependent optimizations such that the tests create comparable results on different computers.
 
-    For more ways do manipulate/adapt the build and configuration step, please consult the `dunecontrol` documentation.
+    For more ways to manipulate/adapt the build and configuration step, please consult the `dunecontrol` documentation.
 
 5. Optional, but recommended: Build all tests to verify the installation. For this navigate in the `build-cmake/` directory and build the `build_tests` target.
 

doc/user/docs/installation.md

@@ -4,7 +4,7 @@ The DuMuX-preCICE adapter is a DUNE module named `dumux-precice` which can be bu
 
 ## Prerequisites
 
-- DuMuX **newer** than 3.2
+- DuMuX >= 3.7
 
     - Builds using the current `master` branch of DuMuX might fail.
     - If you run into trouble with a new DuMuX release, please open an issue in the repository and add the error message that you receive.
@@ -46,7 +46,7 @@ The DuMuX-preCICE adapter should build fine if DuMuX, preCICE and their dependen
     dune-common/bin/dunecontrol --only=dumux-precice all
     ```
 
-    After the build and configure step a new directory `build-cmake` was created inside the `dumux-precice` directory.
+    After the build and configure step a new directory `build-cmake` was created inside the `dumux-adapter` directory.
 
     You can configure the build and configuration process using advanced options by manipulating CMake variables. `dunecontrol` allows to pass an options file for that
 
@@ -65,7 +65,7 @@ The DuMuX-preCICE adapter should build fine if DuMuX, preCICE and their dependen
     To use the adapter in a separate DUNE module, we recommend building the adapter as a shared library. To do so, use the CMake option `-DBUILD_SHARED_LIBS=ON` to build the adapter and upstream modules. The DuMux install script uses `dumux/cmake.opts`, which already sets this option.
     Note that to change this setting it may be required to clear the CMake caches in `build-cmake/CMakeCache.txt`.
 
-    For more ways do manipulate/adapt the build and configuration step, please consult the `dunecontrol` documentation.
+    For more ways to manipulate/adapt the build and configuration step, please consult the `dunecontrol` documentation.
 
 5. Optional, but recommended: Build all tests to verify the installation. For this navigate in the `build-cmake/` directory and build the `build_tests` target.
 

docker/README.md

@@ -19,15 +19,15 @@ For more details on what is installed, please check the `Dockerfile`.
 
 The versions of the main dependencies can be manipulated when building the Docker image via the arguments with given default values
 
-- `ARG DUNEVERSION=2.7`: DUNE version. Available in all recipes.
-- `ARG DUMUXVERSION=3.4`: DuMuX version. Available in all recipes.
-- `ARG PRECICEVERSION=2.2.1`: preCICE version. Available only in "large" and "slim" recipes.
-- `ARG PRECICEUBUNTU=focal`: preCICE target platform (here, Ubuntu Focal Fossa). Available only in "large" recipe.
+- `ARG DUNEVERSION=2.9`: DUNE version. Available in all recipes.
+- `ARG DUMUXVERSION=3.7`: DuMuX version. Available in all recipes.
+- `ARG PRECICEVERSION=3.0.0`: preCICE version. Available only in "large" and "slim" (use branch name e.g. "v3.0.0" or "develop") recipes.
+- `ARG PRECICEUBUNTU=jammy`: preCICE target platform (here, Ubuntu Jammy Jellyfish). Available only in "large" recipe.
 
-If one wants to build a "slim" image using DUNE 2.8, DuMuX from the current master branch and preCICE 2.4.0 one could call it with the following command:
+If one wants to build a "slim" image using DUNE 2.9, DuMuX from the current master branch and preCICE 3.0.0 one could call it with the following command:
 
 ```text
-sudo docker build --build-arg DUNEVERSION=2.8 --build-arg DUMUXVERSION=master --build-arg PRECICEVERSION=2.4.0 -t ajaust/dumux-precice:master-2.4.0 --file dockerfile.slim .
+sudo docker build --build-arg DUNEVERSION=2.9 --build-arg DUMUXVERSION=master --build-arg PRECICEVERSION=v3.0.0 -t precice/dumux-precice:master-v3.0.0 --file dockerfile.slim .
 ```
 
 The script `rebuild-docker-images.sh` can be used to rebuild the Docker images locally.

docker/dockerfile.base

@@ -1,4 +1,4 @@
-FROM ubuntu:20.04
+FROM ubuntu:22.04
 
 ENV DEBIAN_FRONTEND noninteractive
 
@@ -13,8 +13,8 @@ ARG DUMUXINSTALLPATH=/opt/DUMUX
 WORKDIR ${DUMUXINSTALLPATH}
 
 # Obtain DuMuX and Dune repositories
-ARG DUNEVERSION=2.8
-ARG DUMUXVERSION=3.5
+ARG DUNEVERSION=2.9
+ARG DUMUXVERSION=3.7
 COPY checkout_repositories.sh .
 RUN bash checkout_repositories.sh ${DUNEVERSION} ${DUMUXVERSION}
 

docker/dockerfile.large

@@ -1,4 +1,4 @@
-FROM ubuntu:20.04
+FROM ubuntu:22.04
 
 # Install DUNE and DuMuX in /home/dumux
 WORKDIR	${USER_HOME}
@@ -14,8 +14,8 @@ RUN apt-get install -y apt-utils vim htop git
 RUN apt-get install -y openmpi-bin libopenmpi-dev git gcc g++ wget cmake sudo libboost-all-dev pkg-config python3
 
 # Obtain DuMuX and Dune repositories
-ARG DUNEVERSION=2.7
-ARG DUMUXVERSION=3.4
+ARG DUNEVERSION=2.9
+ARG DUMUXVERSION=3.7
 COPY checkout_repositories.sh .
 RUN bash checkout_repositories.sh ${DUNEVERSION} ${DUMUXVERSION}
 
@@ -31,9 +31,9 @@ ENV DUNE_CONTROL_PATH=${USER_HOME}/dune-common/dune.module:${USER_HOME}/dune-geo
 ENV PYTHONPATH ${USER_HOME}/dumux/bin/testing:${PYTHONPATH}
 
 #Install preCICE
-ARG PRECICEVERSION=2.2.1
-ARG PRECICEUBUNTU=focal
-RUN wget https://github.com/precice/precice/releases/download/v${PRECICEVERSION}/libprecice2_${PRECICEVERSION}_${PRECICEUBUNTU}.deb -O libprecice${PRECICEVERSION}-${PRECICEUBUNTU}.deb \
+ARG PRECICEVERSION=3.0.0
+ARG PRECICEUBUNTU=jammy
+RUN wget https://github.com/precice/precice/releases/download/v${PRECICEVERSION}/libprecice3_${PRECICEVERSION}_${PRECICEUBUNTU}.deb -O libprecice${PRECICEVERSION}-${PRECICEUBUNTU}.deb \
 	&& apt install -y ./libprecice${PRECICEVERSION}-${PRECICEUBUNTU}.deb \
 	&& rm -f ./libprecice${PRECICEVERSION}-${PRECICEUBUNTU}.deb
 

docker/dockerfile.slim

@@ -1,4 +1,4 @@
-FROM ubuntu:20.04
+FROM ubuntu:22.04
 
 ENV DEBIAN_FRONTEND noninteractive
 
@@ -7,14 +7,14 @@ ADD 01_nodoc /etc/dpkg/dpkg.cfg.d/01_nodoc
 
 # Install dependencies from
 RUN apt-get update
-RUN apt-get install -y git gcc g++ gfortran cmake pkg-config libboost-log1.71.0 libboost-thread1.71.0 libboost-system1.71.0 libboost-filesystem1.71.0 libboost-program-options1.71.0 libboost-test1.71.0 libboost-container1.71.0 libeigen3-dev libxml2 libboost-log-dev libboost-thread-dev libboost-system-dev libboost-filesystem-dev libboost-program-options-dev libboost-test-dev libboost-container-dev libeigen3-dev libxml2-dev libsuitesparse-dev python3
+RUN apt-get install -y git gcc g++ gfortran cmake pkg-config libboost-log1.74.0 libboost-thread1.74.0 libboost-system1.74.0 libboost-filesystem1.74.0 libboost-program-options1.74.0 libboost-test1.74.0 libboost-container1.74.0 libeigen3-dev libxml2 libboost-log-dev libboost-thread-dev libboost-system-dev libboost-filesystem-dev libboost-program-options-dev libboost-test-dev libboost-container-dev libeigen3-dev libxml2-dev libsuitesparse-dev python3
 
 ARG DUMUXINSTALLPATH=/opt/DUMUX
 WORKDIR ${DUMUXINSTALLPATH}
 
 # Obtain DuMuX and Dune repositories
-ARG DUNEVERSION=2.8
-ARG DUMUXVERSION=3.5
+ARG DUNEVERSION=2.9
+ARG DUMUXVERSION=3.7
 COPY checkout_repositories.sh .
 RUN bash checkout_repositories.sh ${DUNEVERSION} ${DUMUXVERSION}
 
@@ -30,9 +30,8 @@ ENV DUNE_CONTROL_PATH=${DUMUXINSTALLPATH}/dune-common/dune.module:${DUMUXINSTALL
 ENV PYTHONPATH ${DUMUXINSTALLPATH}/dumux/bin/testing:${PYTHONPATH}
 
 # Compile minmum version of preCICE
-#ARG PRECICEVERSION=2.4.0
-ARG PRECICEVERSION=develop
-ARG PRECICEUBUNTU=focal
+ARG PRECICEVERSION=v3.0.0
+ARG PRECICEUBUNTU=jammy
 RUN git clone --depth 1 -b ${PRECICEVERSION} https://github.com/precice/precice.git precice-${PRECICEVERSION} && cd precice-${PRECICEVERSION} && mkdir build && cd build && cmake .. -DCMAKE_BUILD_TYPE=RelWithDebInfo -DPRECICE_FEATURE_MPI_COMMUNICATION=OFF -DPRECICE_FEATURE_PETSC_MAPPING=OFF -DPRECICE_FEATURE_PYTHON_ACTIONS=OFF -DCMAKE_INSTALL_PREFIX=/usr && make -j 4 && make test && make install && cd ../../ && rm -rf precice-${PRECICEVERSION}
 
 RUN apt-get purge -y libboost-log-dev libboost-thread-dev libboost-system-dev libboost-filesystem-dev libboost-program-options-dev libboost-test-dev libboost-container-dev libxml2-dev

docker/dockerfile_dune-precice.slim

@@ -1,4 +1,4 @@
-FROM ubuntu:20.04
+FROM ubuntu:22.04
 
 ENV DEBIAN_FRONTEND noninteractive
 
@@ -7,13 +7,13 @@ ADD 01_nodoc /etc/dpkg/dpkg.cfg.d/01_nodoc
 
 # Install dependencies from
 RUN apt-get update
-RUN apt-get install -y git gcc g++ gfortran cmake pkg-config libboost-log1.71.0 libboost-thread1.71.0 libboost-system1.71.0 libboost-filesystem1.71.0 libboost-program-options1.71.0 libboost-test1.71.0 libboost-container1.71.0 libeigen3-dev libxml2 libboost-log-dev libboost-thread-dev libboost-system-dev libboost-filesystem-dev libboost-program-options-dev libboost-test-dev libboost-container-dev libeigen3-dev libxml2-dev libsuitesparse-dev python3
+RUN apt-get install -y git gcc g++ gfortran cmake pkg-config libboost-log1.74.0 libboost-thread1.74.0 libboost-system1.74.0 libboost-filesystem1.74.0 libboost-program-options1.74.0 libboost-test1.74.0 libboost-container1.74.0 libeigen3-dev libxml2 libboost-log-dev libboost-thread-dev libboost-system-dev libboost-filesystem-dev libboost-program-options-dev libboost-test-dev libboost-container-dev libeigen3-dev libxml2-dev libsuitesparse-dev python3
 
 ARG DUMUXINSTALLPATH=/opt/DUMUX
 WORKDIR ${DUMUXINSTALLPATH}
 
 # Obtain DuMuX and Dune repositories
-ARG DUNEVERSION=2.8
+ARG DUNEVERSION=2.9
 COPY checkout_repositories.sh .
 RUN bash checkout_repositories.sh ${DUNEVERSION} none
 
@@ -27,9 +27,8 @@ RUN dunecontrol --opts=cmake-test.opts all
 ENV DUNE_CONTROL_PATH=${DUMUXINSTALLPATH}/dune-common/dune.module:${DUMUXINSTALLPATH}/dune-geometry/dune.module:${DUMUXINSTALLPATH}/dune-grid/dune.module:${DUMUXINSTALLPATH}/dune-localfunctions/dune.module:${DUMUXINSTALLPATH}/dune-istl/dune.module:${DUMUXINSTALLPATH}/dune-subgrid/dune.module
 
 # Compile minmum version of preCICE
-#ARG PRECICEVERSION=2.4.0
-ARG PRECICEVERSION=develop
-ARG PRECICEUBUNTU=focal
+ARG PRECICEVERSION=v3.0.0
+ARG PRECICEUBUNTU=jammy
 RUN git clone --depth 1 -b ${PRECICEVERSION} https://github.com/precice/precice.git precice-${PRECICEVERSION} && cd precice-${PRECICEVERSION} && mkdir build && cd build && cmake .. -DCMAKE_BUILD_TYPE=RelWithDebInfo -DPRECICE_FEATURE_MPI_COMMUNICATION=OFF -DPRECICE_FEATURE_PETSC_MAPPING=OFF -DPRECICE_FEATURE_PYTHON_ACTIONS=OFF -DCMAKE_INSTALL_PREFIX=/usr && make -j 4 && make test && make install && cd ../../ && rm -rf precice-${PRECICEVERSION}
 
 RUN apt-get purge -y libboost-log-dev libboost-thread-dev libboost-system-dev libboost-filesystem-dev libboost-program-options-dev libboost-test-dev libboost-container-dev libxml2-dev

docker/rebuild-docker-images.sh

@@ -1,7 +1,7 @@
 #!/usr/bin/env bash
 
-DUNE_VERSION="2.8"
-DUMUX_VERSIONS=("3.4" "3.5")
+DUNE_VERSION="2.9"
+DUMUX_VERSIONS=("3.7" "3.8")
 PRECICE_VERSIONS=("develop")
 
 for dumux_version in ${DUMUX_VERSIONS[@]}; do

dune.module

@@ -4,9 +4,9 @@
 
 #Name of the module
 Module: dumux-precice
-Version: 1.0.0
+Version: 2.0.0
 Maintainer: [email protected]
 # Required build dependencies
-Depends: dumux (>=3.2)
+Depends: dumux (>=3.7)
 # Optional build dependencies
 Suggests: dune-subgrid

examples/dummysolver/precice-dummy-solver-config.xml

@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 
-<precice-configuration >
+<precice-configuration>
 
   <log>
     <sink type="stream" output="stdout"  filter= "%Severity% > debug" format="preCICE:%ColorizedSeverity% %Message%" enabled="true" />

examples/ff-pm/flow-over-cube-3d/1pspatialparams.hh

@@ -24,11 +24,7 @@
 #ifndef DUMUX_1P_TEST_SPATIALPARAMS_HH
 #define DUMUX_1P_TEST_SPATIALPARAMS_HH
 
-#if DUMUX_VERSION_MAJOR >= 3 & DUMUX_VERSION_MINOR >= 5
 #include <dumux/porousmediumflow/fvspatialparams1p.hh>
-#else
-#include <dumux/material/spatialparams/fv1p.hh>
-#endif
 
 namespace Dumux
 {
@@ -39,30 +35,16 @@ namespace Dumux
  *        1p cc model
  */
 template<class FVGridGeometry, class Scalar>
-class OnePSpatialParams
-#if DUMUX_VERSION_MAJOR >= 3 & DUMUX_VERSION_MINOR >= 5
-    : public FVPorousMediumFlowSpatialParamsOneP<
-          FVGridGeometry,
-          Scalar,
-          OnePSpatialParams<FVGridGeometry, Scalar>>
-#else
-    : public FVSpatialParamsOneP<FVGridGeometry,
-                                 Scalar,
-                                 OnePSpatialParams<FVGridGeometry, Scalar>>
-#endif
+class OnePSpatialParams : public FVPorousMediumFlowSpatialParamsOneP<
+                              FVGridGeometry,
+                              Scalar,
+                              OnePSpatialParams<FVGridGeometry, Scalar>>
 {
     using GridView = typename FVGridGeometry::GridView;
-    using ParentType =
-#if DUMUX_VERSION_MAJOR >= 3 & DUMUX_VERSION_MINOR >= 5
-        FVPorousMediumFlowSpatialParamsOneP<
-            FVGridGeometry,
-            Scalar,
-            OnePSpatialParams<FVGridGeometry, Scalar>>;
-#else
-        FVSpatialParamsOneP<FVGridGeometry,
-                            Scalar,
-                            OnePSpatialParams<FVGridGeometry, Scalar>>;
-#endif
+    using ParentType = FVPorousMediumFlowSpatialParamsOneP<
+        FVGridGeometry,
+        Scalar,
+        OnePSpatialParams<FVGridGeometry, Scalar>>;
 
     using Element = typename GridView::template Codim<0>::Entity;
     using GlobalPosition = typename Element::Geometry::GlobalCoordinate;
@@ -108,7 +90,6 @@ public:
         return alphaBJ_;
     }
 
-#if DUMUX_VERSION_MAJOR >= 3 & DUMUX_VERSION_MINOR > 4
     /*!
      * \brief Return the temperature within the domain in [K].
      *
@@ -118,7 +99,6 @@ public:
     {
         return 273.15 + 10;  // 10°C
     }
-#endif
 
 private:
     Scalar permeability_;