Add wood simulation container files

woodSim_Container/Containerfile

+FROM ubuntu:22.04
+LABEL maintainer="klaus.boehnlein@tu-dresden.de"
+
+ARG DEBIAN_FRONTEND=noninteractive
+
+RUN apt-get update && apt-get install -y ssh rsh-client && apt-get install -y libibverbs-dev ibverbs-utils && apt-get install -y \
+    gcc \
+    g++ \
+    make \
+    doxygen \
+    slurm-client \
+    wget \
+    build-essential \
+    cmake \
+    coinor-libipopt-dev \
+    libdune-common-dev \
+    libdune-grid-dev \
+    libdune-istl-dev \
+    libdune-localfunctions-dev \
+    libdune-typetree-dev \
+    libdune-uggrid-dev \
+    gdb \
+    gfortran \
+    git \
+    libadolc-dev \
+    libmetis-dev \
+    libopenblas-base \
+    libparmetis-dev \
+    libsuitesparse-dev \
+    libsuperlu-dev \
+    libsuperlu-dist-dev \
+    libtinyxml2-dev \
+    ninja-build \
+    pkg-config \
+    python2.7 \
+    python2.7-dev \
+    python3 \
+    python3-dev \
+    python3-pip \
+    python3-venv \
+    python3-prettytable\
+    python3-numpy \
+    python3-matplotlib \
+    python3-seaborn \
+    python3-tabulate \
+    valgrind \
+    vim \
+    && apt-get autoremove && apt-get clean
+
+
+WORKDIR /dune
+
+
+RUN \
+     git clone https://gitlab.dune-project.org/core/dune-common.git \
+  && git clone https://gitlab.dune-project.org/core/dune-geometry.git \
+  && git clone https://gitlab.dune-project.org/core/dune-grid.git \
+  && git clone https://gitlab.dune-project.org/core/dune-istl.git \
+  && git clone https://gitlab.dune-project.org/core/dune-localfunctions.git \
+  && git clone https://gitlab.dune-project.org/staging/dune-functions.git      \
+  && git clone https://gitlab.dune-project.org/staging/dune-uggrid.git         \
+  && git clone https://gitlab.dune-project.org/staging/dune-typetree.git       \
+  && git clone https://git.imp.fu-berlin.de/agnumpde/dune-matrix-vector.git \
+  && git clone https://git.imp.fu-berlin.de/agnumpde/dune-fufem.git  \
+  && git clone https://git.imp.fu-berlin.de/agnumpde/dune-solvers.git \
+  && git clone https://gitlab.mn.tu-dresden.de/iwr/dune-gmsh4.git \
+  && git clone https://gitlab.mn.tu-dresden.de/s7603593/dune-microstructure.git
+
+# For the sake of reproducibility:
+# Set HEAD to particular commits wherever we are not using release branches.
+RUN cd dune-common             && git checkout releases/2.9
+RUN cd dune-geometry           && git checkout releases/2.9
+RUN cd dune-grid               && git checkout releases/2.9
+RUN cd dune-istl               && git checkout releases/2.9
+RUN cd dune-localfunctions     && git checkout releases/2.9
+RUN cd dune-functions          && git checkout releases/2.9
+RUN cd dune-uggrid             && git checkout releases/2.9
+RUN cd dune-typetree           && git checkout releases/2.9
+RUN cd dune-matrix-vector      && git checkout releases/2.9
+RUN cd dune-fufem              && git checkout releases/2.9
+RUN cd dune-solvers            && git checkout releases/2.9
+RUN cd dune-gmsh4              && git checkout releases/2.9
+RUN cd dune-microstructure     && git checkout 9298cbd07a99c23f55e245bae19199eee34aa289  
+
+# Build the non-packaged modules from source
+COPY dune-sequential.opts  /dune/
+RUN dunecontrol --opts=dune-sequential.opts all
+
+
+# ENTRYPOINT ["/bin/bash", "--login", "--rcfile", "/dune/dune-startup", "-i"]
+
+# LABEL run podman run --interactive --tty --rm IMAGE

woodSim_Container/Simulation-Readme.md

+# In order to run the simulations, an installation of docker is required (see https://docs.docker.com/engine/install/ ).
+# The simulations as well as the creation of figures is done in the following steps:
+
+@RUN THE SIMULATIONS
+
+# 1.  Build the docker Container image (named 'woodsim_image') from 'Containerfile':
+
+docker build --no-cache=true -t woodsim_image -f Containerfile .
+
+# 2.  Start the computation of Correctors and effective quantities.
+# create container woodsim_container from the image 'woodsim_image' and run the command 'python3 ...'
+# *input arguments: 1: Container-Flag(True if script is used inside container) 2: first experiment number 3: last experiment number.
+# e.g. "1 0 3" ~ computations inside the container from experiment 0 to experiment 3
+
+docker run  --name woodsim_container woodsim_image python3 /dune/dune-microstructure/experiment/compWood/runWoodSimulations.py 1 0 3
+
+
+@CREATE THE FIGURES
+
+# 1. Copy files/results (/compWood - folder) from the container to a $LOCALPATH on the Host machine: 
+docker cp woodsim_container:/dune/dune-microstructure/experiment/compWood $LOCALPATH
+
+# 2. Run python-script 'createFigures.py' to generate the paper figures. 
+($LOCALPATH)  python3 createFigures.py 
+
+

woodSim_Container/dune-sequential.opts

+# set flags for CMake:
+CMAKE_FLAGS="-DCMAKE_CXX_FLAGS='-g -fdiagnostics-color=always -Wall -fmax-errors=2 -DHAVE_CSTDDEF' -DCMAKE_DISABLE_FIND_PACKAGE_MPI=TRUE -DUG_ENABLE_PARALLEL=false -DCMAKE_BUILD_TYPE=Release" 

woodSim_Container/runSimulations.sh

+# build with "chmod +x runSimulations.sh"
+# run via "./runSimulations.sh"
+
+# Define your local path for simulation results and figures
+echo "Define output path on your host machine: " 
+# LOCALPATH='/home/klaus/Desktop/test'
+read LOCALPATH
+
+docker build --no-cache=true -t woodsim_image -f Containerfile .
+
+docker rm woodsim_container
+
+image_id=$(docker images --quiet | head -1)
+
+echo "image ID used: $image_id"
+
+docker run  --name woodsim_container $image_id python3 /dune/dune-microstructure/experiment/compWood/runWoodSimulations.py 1 0 3
+
+docker cp woodsim_container:/dune/dune-microstructure/experiment/compWood $LOCALPATH
+
+cd $LOCALPATH 
+
+python3 $LOCALPATH/compWood/createFigures.py 
+