Add DuMuX as a participant to the two-scale-heat-conduction tutorial (#…

…376)

* port two-scale-heat-conduction case with DuMuX-DuMuX

* Initial folder restructuring for setting up a DUNE modules environment and running the DuMuX-DuMuX case

* Removing unnecessary CMake files

* [two-scale-heat-conduction] add dune module wrapper

* [two-scale-heat-conduction] macro-dumux as dune module

* [two-scale-heat-conduction] update macro-dumux to preCICE 3.0 and DuMux 3.8

* [two-scale-heat-conduction] remove dumux subdirectory

* Remove dune-wrapper folder and restructure macro-dumux

* [two-scale-heat-conduction] revert setup script to rebuild modules in working directory

* [two-scale-heat-conduction][tmp] change branch in dumux-adapter

* [two-scale-heat-conduction] fix macro participant

* Construct mesh name macro-mesh of 10 characters

* [two-scale-heat-conduction] fixes macro-dumux

* Formatting

* Formatting and use string literals

* PEP8 formatting

* Go back to cloning the develop branch of dumux-adapter in setup-dumux.sh

* Formatting

* Remove dumux-dumux because all the code in it is now ported

* Add appropriate run scripts

* Adding correct cleaning scripts and cleaning functions

* Remove unnecessary cleaning script

* Remove all references to clean-example.sh

* [two-scale-heat-conduction] update micro-dumux for DuMux 3.7

* restructured micro-dumux, added run.sh for macro-dumux

* repair communication of concentration

* add shebang for cleaning script

* customize cleaning file in micro-dumux

* modify cleaning file to delete log file

* add dumux-dumux method in README

* Make the execution level of Nutils and DuMuX participants consistent

* Add DuMuX information to README

* Minor edit in README

* Add cleaning script to micro-dumux and add DuMuX cleaning in the tools

* add image of results for dumux-dumux simulation

* Add information on which participants can be run in parallel

* Fix linting docs

* image modified

* image resized

* [two-scale-heat-conduction] cleanup

* [two-scale-heat-conduction] add compile-dumux-cases.sh

* Swapping maintainers of macro-dumux and micro-dumux

---------

Co-authored-by: Jun Chen <[email protected]>
Co-authored-by: Ishaan Desai <[email protected]>
Co-authored-by: Mathis Kelm <[email protected]>

tools/cleaning-tools.sh

@@ -141,3 +141,15 @@ clean_dune() {
         clean_precice_logs .
     )
 }
+
+clean_dumux() {
+   (
+        set -e -u
+	cd "$1"
+	echo "--- Cleaning up DuMuX case in $(pwd)"
+	rm -fv ./*.vtu
+	rm -fv ./*.pvd
+	clean_precice_logs .
+   )
+
+}

two-scale-heat-conduction/.gitignore

@@ -0,0 +1,6 @@
+dumux/
+dumux-phasefield/
+dumux-adapter/
+dune-*
+*/build-cmake/
+install*

two-scale-heat-conduction/README.md

@@ -1,7 +1,7 @@
 ---
 title: Two-scale heat conduction
 permalink: tutorials-two-scale-heat-conduction.html
-keywords: Macro-micro, Micro Manager, Nutils, Heat conduction
+keywords: Macro-micro, Micro Manager, Nutils, DuMuX, Heat conduction
 summary: We solve a two-scale heat conduction problem with a predefined micro structure of two materials. One macro simulation is coupled to several micro simulations using the Micro Manager.
 ---
 
@@ -21,27 +21,34 @@ At each Gauss point of the macro domain there exists a micro simulation. The mac
 
 ## Available solvers and dependencies
 
-* Both the macro and micro simulations are solved using the finite element library [Nutils](https://nutils.org/install.html) v7.
-* The macro simulation is written in Python, so it requires the [Python bindings of preCICE](https://precice.org/installation-bindings-python.html)
+* 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.
 
 ## Running the simulation
 
+You can find the corresponding `run.sh`script for running the case in the folders corresponding to the solvers you want to use.
+
 Run the macro problem:
 
 ```bash
 cd macro-nutils
 ./run.sh
 ```
 
-Check the Micro Manager [configuration](https://precice.org/tooling-micro-manager-configuration.html) and [running](https://precice.org/tooling-micro-manager-running.html) documentation to understand how to set it up and launch it. There is a Python script `run-micro-problems.py` in the tutorial directory to directly run the Micro Manager. This script imports the Micro Manager, and calls its `initialize()` and `solve()` methods. The Micro Manager can be run via this script in serial or parallel. Run it in serial:
+Check the Micro Manager [configuration](https://precice.org/tooling-micro-manager-configuration.html) and [running](https://precice.org/tooling-micro-manager-running.html) documentation to understand how to set it up and launch it. There is a Python script `run-micro-problems.py` in the tutorial directory to directly run the Micro Manager. This script imports the Micro Manager, and calls its `solve()` method. The Micro Manager can be run via this script in serial or parallel. Run it in serial:
 
 ```bash
 cd micro-nutils
 ./run.sh -s
 ```
 
-Run it in parallel:
+If you want to use DuMu<sup>x</sup>, use `cd macro-dumux` instead of `cd macro-nutils` and/or `cd micro-dumux` instead of `cd micro-nutils`.
+
+## Running the simulation in parallel
+
+Only the `micro-nutils` participant can be run in parallel. To run it in parallel, run:
 
 ```bash
 cd micro-nutils
@@ -50,14 +57,24 @@ cd micro-nutils
 
 The `num_procs` needs to fit the decomposition specified in the `micro-manager-config.json` (default: two ranks).
 
-Even though the case setup and involved physics is simple, each micro simulation is an instance of Nutils, which usually has a moderately high computation time. If the Micro Manager is run on 2 processors, the total runtime is approximately 25-30 minutes. Do not run the Micro Manager in serial, because the runtime will be several hours.
+**NOTE**: When running `micro-nutils`, even though the case setup and involved physics is simple, each micro simulation is an instance of Nutils, which usually has a moderately high computation time. If the Micro Manager is run on 2 processors, the total runtime is approximately 25-30 minutes. Do not run the Micro Manager in serial, because the runtime will be several hours.
+
+Running `micro-dumux` is much faster. A serial simulation takes approximately 2 minutes to finish.
 
 ## Post-processing
 
-![Results of two-scale-heat-conduction case](images/tutorials-two-scale-heat-conduction-results.png)
+Here are the results from Nutils-Nutils and DuMu<sup>x</sup>-DuMu<sup>x</sup> combination:
+
+<img src="images/tutorials-two-scale-heat-conduction-results.png" alt="Macro and micro data of macro-nutils - micro-nutils simulation" width=50% height=30%>
+
+<img src="images/tutorials-two-scale-heat-conduction-results-du-du.png" alt="Macro and micro data of macro-nutils - micro-nutils simulation" width=50% height=30%>
+
+The differences of the fields are mainly introduced in by the different numerical schemes in the two solvers.
 
 The participant `macro-nutils` outputs `macro-*.vtk` files which can be viewed in ParaView to see the macro concentration field. The Micro Manager uses the [export functionality](https://precice.org/configuration-export.html#enabling-exporters) of preCICE to output micro simulation data and [adaptivity related data](https://precice.org/tooling-micro-manager-configuration.html#adding-adaptivity-in-the-precice-xml-configuration) to VTU files which can be viewed in ParaView. To view the data on each micro simulation, create a Glyph on the Micro Manager VTU data. In the figure above, micro-scale porosity is shown. For a lower concentration value, the porosity increases (in the lower left corner).
 
-![Evolving micro simulations](images/tutorials-two-scale-heat-conduction-evolving-micro-simulations.png)
+<img src="images/tutorials-two-scale-heat-conduction-evolving-micro-simulations.png" alt="Adaptive mesh refinement in the micro simulation" width=50% height=30%>
 
 The micro simulations themselves have a circular micro structure which is resolved in every time step. To output VTK files for each micro simulation, uncomment the `output()` function in the file `micro-nutils/micro.py`. The figure above shows the changing phase field used to represent the circular micro structure and the diffuse interface width.
+
+Similar to the output data files from simulation with Nutils, the `VTU` files from macro and micro solvers, that are written in DuMu<sup>x</sup>, could also be rendered and inspected with ParaView with the mentioned method.

two-scale-heat-conduction/compile-dumux-cases.sh

@@ -0,0 +1,12 @@
+#!/bin/sh
+set -e -u
+
+cd macro-dumux/build-cmake/appl
+make macro_dumux
+cd ../../../micro-dumux/build-cmake/appl
+make
+cd ../../../
+
+# Move macro-dumux and micro-dumux executables to the participant folder level
+mv macro-dumux/build-cmake/appl/macro_dumux macro-dumux/
+mv micro-dumux/build-cmake/appl/micro_sim.cpython-310-x86_64-linux-gnu.so micro-dumux/

two-scale-heat-conduction/macro-dumux/CMakeLists.txt

@@ -0,0 +1,28 @@
+cmake_minimum_required(VERSION 3.13)
+project(macro-dumux CXX)
+
+if(NOT (dune-common_DIR OR dune-common_ROOT OR
+      "${CMAKE_PREFIX_PATH}" MATCHES ".*dune-common.*"))
+    string(REPLACE  ${PROJECT_NAME} dune-common dune-common_DIR
+      ${PROJECT_BINARY_DIR})
+endif()
+
+#find dune-common and set the module path
+find_package(dune-common REQUIRED)
+list(APPEND CMAKE_MODULE_PATH "${PROJECT_SOURCE_DIR}/cmake/modules"
+  ${dune-common_MODULE_PATH})
+
+#include the dune macros
+include(DuneMacros)
+
+# start a dune project with information from dune.module
+dune_project()
+
+dune_enable_all_packages()
+
+add_subdirectory(doc)
+add_subdirectory(cmake/modules)
+add_subdirectory(appl)
+
+# finalize the dune project, e.g. generating config.h etc.
+finalize_dune_project(GENERATE_CONFIG_H_CMAKE)

two-scale-heat-conduction/macro-dumux/appl/CMakeLists.txt

@@ -0,0 +1,7 @@
+add_executable(macro_dumux main.cc)
+target_compile_definitions(macro_dumux PUBLIC "ENABLEMONOLITHIC=0")
+target_link_libraries(macro_dumux PRIVATE dumux-precice)
+target_compile_definitions(macro_dumux PUBLIC TYPETAG=OnePNIConductionCCTpfa)
+
+# add a symlink for each input file
+add_input_file_links()