Fix the setup-dumux.sh script in two-scale-heat-conduction (#518)

* [two-scale-heat-conduction] adapt to micro-manager-v0.4.0

* [two-scale-heat-conduction] use dumux install script from release 3.7

* [two-scale-heat-conduction] make setup-dumux.sh more robust

* Add comment about running setup-dumux.sh in the README

* [two-scale-heat-conduction] suppress DUNE_CONTROL_PATH in setup

---------

Co-authored-by: Ishaan Desai <[email protected]>

Author: mathiskelm

two-scale-heat-conduction/README.md

@@ -30,7 +30,12 @@ preCICE configuration (image generated using the [precice-config-visualizer](htt
 * Both the macro and micro simulations can be solved using the finite element library [Nutils](https://nutils.org/install.html) v7 or the simulation framework [DuMu<sup>x</sup>](https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/).
 * While using Nutils, the macro simulation is written in Python, so it requires the [Python bindings of preCICE](https://precice.org/installation-bindings-python.html).
 * The [Micro Manager](https://precice.org/tooling-micro-manager-installation.html) controls all micro-simulations and facilitates coupling via preCICE. Use the [develop](https://github.com/precice/micro-manager/tree/develop) branch of the Micro Manager.
-* To solve either the macro or micro simulations with the DuMu<sup>x</sup> framework, the necessary DUNE modules need to be downloaded and set up. Run `sh setup-dumux.sh` in the tutorial folder to set up the DUNE modules.
+
+### DuMu<sup>x</sup> setup
+
+To solve either the macro or micro simulations with the DuMu<sup>x</sup> framework, the necessary DUNE modules need to be downloaded and set up. This is done by running `sh setup-dumux.sh` in the tutorial folder.
+
+Note that if an existing installation of DUNE modules is detected in a default location, this may lead to problems in running the `setup-dumux.sh` script. The environment variable `DUNE_CONTROL_PATH` is suppressed by the script.
 
 ## Running the simulation
 

two-scale-heat-conduction/micro-dumux/appl/micro_sim.cpp

@@ -311,7 +311,7 @@ PYBIND11_MODULE(micro_sim, m)
   m.doc() = "pybind11 example plugin"; // optional module docstring
 
   py::class_<MicroSimulation>(m, "MicroSimulation")
-      .def(py::init())
+      .def(py::init<int>())
       .def("initialize", &MicroSimulation::initialize)
       .def("solve", &MicroSimulation::solve)
       //.def("save_checkpoint", &MicroSimulation::save_checkpoint)
@@ -328,7 +328,7 @@ PYBIND11_MODULE(micro_sim, m)
               throw std::runtime_error("Invalid state!");
 
             /* Create a new C++ instance */
-            MicroSimulation ms;
+            MicroSimulation ms(0);
             ms.initialize();
             ms.setState(t);
 

two-scale-heat-conduction/setup-dumux.sh

@@ -9,8 +9,13 @@ rm -rfv dune-*/
 rm -rfv install*
 
 # Get the DuMuX install script and install it
-wget https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/raw/master/bin/installdumux.py
-python3 installdumux.py
+wget https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/raw/releases/3.7/bin/installdumux.py
+DUNE_CONTROL_PATH=. python3 installdumux.py
+# clear build directories
+cd dumux
+rm -r dune-common/build-cmake/dune-env/lib/dunecontrol || true
+DUNE_CONTROL_PATH=. ./dune-common/bin/dunecontrol exec rm -r build-cmake
+cd ..
 
 # Take out all the module folders from the dumux/ folder and remove the dumux/ folder
 mv dumux dumux-install
@@ -23,11 +28,10 @@ git clone https://github.com/precice/dumux-adapter.git
 # DuMux phasefield implementation
 git clone -b cell_problems https://git.iws.uni-stuttgart.de/dumux-appl/dumux-phasefield.git
 # DUNE SPGrid for periodic boundary conditions
-python3 dumux/bin/installexternal.py spgrid
+DUNE_CONTROL_PATH=. python3 dumux/bin/installexternal.py spgrid
 
-# Clear CMake caches and re-build environment
-./dune-common/bin/dunecontrol bexec rm -r CMakeFiles CMakeCache.txt
-./dune-common/bin/dunecontrol --opts=./dumux/cmake.opts all
+# Re-build environment
+DUNE_CONTROL_PATH=. ./dune-common/bin/dunecontrol --opts=./dumux/cmake.opts all
 
 # Compile and move macro-dumux and micro-dumux executables to the participant folder level
 ./compile-dumux-cases.sh