IshaanDesai / HK-macro-micro

Two-scale heat conduction with DuMu^x and preCICE

This repository showcases two-scale coupling of DuMu^x simulations with preCICE, using a two-scale coupled heat conduction problem in 2D as an example. The DuMu^x simulations can also be coupled with their respective counterparts in Nutils.

Setup

Being an example, this repository is sensitive to versioning, so make sure to get the correct versions of the involved software packages. TLDRs might be sufficient for quick setup, but they ignore all dependencies and will almost certainly fail or create conflicts for any system without previous configuration. Consulting the full setup instructions for each software component is very much recommended.

After following the steps below, your repository structure should look like this:

|-- dumux
    |-- dumux
        |-- dumux-adapter
            |--examples
               |--macro-micro
               ...
        |-- dumux-phasefield
        |-- dune-common
        |-- dune-geometry
        |-- dune-grid
        |-- dune-istl
        |-- dune-localfunctions
        |-- dune-spgrid

Dependencies

Apart from DuMu^x and preCICE, this project relies on three other software components: the DuMu^x-preCICE adapter, the Micro Manager and the (currently still private) DuMuX module dumux-phasefield.

Micro Manager

Version: develop branch

Follow the installation instructions for the Micro Manager. This also lists the necessary dependencies such as preCICE.

Note: Currently (at the time of precice-micro-manager v.0.2.1), this code relies on the develop branch, so make sure to follow the steps for manual installation and use the develop branch.

TLDR:

git clone -b develop https://github.com/precice/micro-manager
cd micro-manager
pip install --user .

DuMu^x

Version: DuMu^x 3.6, DUNE 2.8

Follow the installation instructions for DuMuX. Using the install script is recommended, but check that it contains the correct versions. This creates the following directory structure:

|-- dumux
    |-- dumux
    |-- dune-common
    |-- dune-geometry
    |-- dune-grid
    |-- dune-istl
    |-- dune-localfunctions

In the following, dumux always refers to the outer dumux folder.

TLDR:

Download the install script and run it with python installdumux.py.

DuMu^x-preCICE adapter

Version: precice/dumux-adapter v.1.0.0

Follow the installation instructions for the DuMu^x adapter.

TLDR:

cd dumux
git clone -b v1.0.0 https://github.com/precice/dumux-adapter.git
./dune-common/bin/dunecontrol --only=dumux-adapter/dumux-precice all

Additional DuMu^x Modules

Version: dune-spgrid 2.6, dumux-phasefield cell_problems branch

Steps to download and build the modules:

1. Clone dumux-phasefield and dune-spgrid into the dumux folder.

cd dumux
git clone -b cell_problems https://git.iws.uni-stuttgart.de/dumux-appl/dumux-phasefield/
python3 dumux/bin/installexternal.py spgrid

Note: dumux-phasefield is still private!

2. Clean the CMake cache.

./dune-common/bin/dunecontrol bexec rm -r CMakeFiles CMakeCache.txt

3. Reconfigure and build DuMu^x via dunecontrol.

./dune-common/bin/dunecontrol --opts=./dumux/cmake.opts all

Setup of the macro-micro example

Version: macro-micro main branch , pybind11 v2.10

1. Navigate into dumux-adapter/examples/ and clone this repo.

cd dumux/dumux-adapter/examples/
git clone https://github.com/HelenaKschidock/macro-micro

2. Add the line add_subdirectory(macro-micro) to dumux-adapter/examples/CMakeLists.txt. This integrates the example into the overall cmake build structure.

3. Add dumux-phasefield to dumux-adapter/dune.module as a required build dependency. The line should then look like this:

# Required build dependencies
Depends: dumux (>=3.2) dumux-phasefield

4. Navigate into the micro-heat directory and clone and build pybind11 there. For more information, see also https://github.com/pybind/cmake_example.

cd macro-micro/micro-heat
git clone -b v2.10 https://github.com/pybind/pybind11
cd pybind11 
pip install --user .

5. Rebuild the DuMu^x-preCICE adapter.

cd dumux
./dune-common/bin/dunecontrol --only=dumux-precice all

Building the macro and micro executables

To build the macro and micro executables, simply rebuild the dumux-adapter using dunecontrol:

cd dumux 
./dune-common/bin/dunecontrol --only=dumux-precice all

The executables are built into dumux/dumux-adapter/build-cmake/examples/macro-micro.

In case you want to rebuild only the macro executable, this can also be done directly via:

cd dumux/dumux-adapter/build-cmake/examples/macro-micro/macro-heat
make test_macro_heat

Running The Coupled Simulation

0. Open two terminals.

1. In one of them, run the macro simulation via

cd dumux/dumux-adapter/build-cmake/examples/macro-micro/macro-heat 
./test_macro_heat

2. In the other shell, run the micro simulation via

cd dumux/dumux-adapter/build-cmake/examples/macro-micro/micro-heat
python3 run_micro_manager.py 

To run the micro code in parallel, use mpirun -n <NThreads> python3 run-micro-manager.py instead. (not tested yet)

Coupling with Nutils

For the same problem, similar macro and micro simulations have also been implemented in Nutils, which can be coupled with their DuMu^x counterparts. To do so:

Setup the Nutils macro and micro case files

1. Install Nutils.

2. Clone the coupled-heat-conduction git into your macro-micro directory.

cd dumux-adapter/examples/macro-micro
git clone https://github.com/IshaanDesai/coupled-heat-conduction

3. Add the line add_subdirectory(coupled-heat-conduction) to macro-micro/CMakeLists.txt to link it to CMake.

4. To make the coupled-heat-conduction code available in your build directory, create a new empty CMakeLists.txt file within your source coupled-heat-conduction directory and add the following code:

add_custom_target(copy_nutils_all ALL
    COMMAND ${CMAKE_COMMAND} -E copy_directory ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_BINARY_DIR})

This simply copies it to the build directory and time you execute the copy_nutils_all command or anytime you rebuild the entire dumux-precice module.

5. Modify the coupled-heat-conduction/precice-config.xml file such that it reads

 <m2n:sockets from="Micro-Manager" to="Macro-heat" network="lo" exchange-directory="../"/>

This allows the macro and micro simulations to find each other.

6. Rebuild the adapter.

dunecontrol --only=dumux-precice all

Coupling the Nutils simulations

You can couple the Nutils simulations with each other or with their counterpart in DuMu^x, as long as one participant is the macro simulation and the other the micro simulation/micro manager. To do so, simply execute your chosen participants in separate shells.

• Run the Nutils macro simulation via

cd build-cmake/examples/macro-micro/coupled-heat-conduction
python3 macro-heat.py

• Run the micro simulation via

cd build-cmake/examples/macro-micro/coupled-heat-conduction
python3 run-micro-manager.py

or in parallel via

mpirun -n <num_procs> python3 run-micro-manager.py

TBC

Note about the Macro parameters

In order to modify the simulation parameters, modify params.input. The parameters are currently tuned to the dimensionless micro-simulation. When modifying these, note the following:

• The domain is defined by its LowerLeft and UpperRight corners and split into [nx ny] Cells.
• Set RunWithCoupling to false to run the macro simulation independently or to true to run the coupled simulation. The independent simulation uses SolidThermalConductivity and DefaultPorosity, respectively, as its conductivity tensor and porosity.
• Set BcTypeLeft/Right/Top/Bottom to dirichlet or neumann, and the corresponding value in BcLeft/Right/Top/Bottom. Note that Neumann boundary conditions are currently hardcoded to 0.0.
• To run the hardcoded asymmetric case with a heat source in the bottom left, set UseHeatSourceBottomLeft to true, else to false. The corresponding value can be set via HeatSourceBottomLeft.