Initial Commit

.gitignore

+# gitignore file
+# this file lists files not to be tracked by git.
+# keine Kommentare in die gleiche Zeile, sonst wird die Zeile ignoriert
+
+# LaTeX files not to be tracked
+*.aux
+*.bbl
+*.blg
+*.log
+*.backup
+*.bak
+*.kilepr
+*.toc
+*.dvi
+*.tdo
+*.figlist
+*.bcf
+*.auxlock
+*.dpth
+*.pdf
+
+#Beamer
+*.acn
+*.glo
+*.nav
+*.out
+*.snm
+*.syg
+*.vrb
+*.brf
+
+# Ignoriere temp files von gaengigen Texteditoren
+*~
+
+
+# MATLAB Numerische Experimente
+*.mat
+
+# Archive
+*.tar
+*.gz
+*.tar.gz
+*.zip
+
+# Ignoriere files vom Typ
+*.pdf
+*.ps
+*.doc
+*.docx
+*.odt
+*.ods
+*.xml
+*.svg
+*.fig
+*.md5
+
+# Ignoriere Bilder und Graphiken sowie Videos und Musik
+#*.png
+#*.jpg
+#*.jpeg
+#*.eps
+*.svg
+*.pgf
+#*.gif
+#*.avi
+#*.mp4
+#*.mp3
+#*.xcf
+
+# always consider files containing source code regardless of their name
+!*.cc
+!*.hh
+!*.c
+!*.h
+!*.sh
+!*.py
+
+
+# Directories
+

Anleitungen/doNix.manual.md

+# Using FeMuX in Docker
+
+
+## Build the docker image:
+
+
+    docker build -t femux .
+
+## Run docker container with graphical display, share folder `pwd`:
+
+    docker run -it --env HOST_UID=$(id -u $USER) --env HOST_GID=$(id -g $USER) --env 
+DISPLAY=unix$DISPLAY --device /dev/dri --volume /tmp/.X11-unix:/tmp/.X11-unix:rw --volume 
+$(pwd):/home/fenics/shared --name femux femux /bin/bash
+
+If you want the container do be automatically deleted after exiting add `--rm` option.
+
+If you have trouble with internet connection inside the container use
+
+        --dns=YOUR_DNS_SERVER
+
+
+## Step into the container:
+
+    docker start femux & docker exec -ti -u fenics femux /bin/bash -l
+
+
+## Install NSAC and dumux-fenics:
+    ./install_femux.sh
+
+## Usefull docker commands:
+
+List all docker container
+
+    docker ps -a
+
+Remove container
+
+    docker rm $container
+
+Remove all stopped container
+
+    docker container prune
+
+List all images
+
+    docker images
+
+Remove image
+
+    docker rmi $image
+
+
+
+
+# Troubleshooting:
+
+**Problem**
+1. I can't install packages via `apt-get install` inside the  container
+
+**Solution**
+
+1. If the package is not found first `apt-get update` and then try again. If there is no connection 
+check your dns settings.
+
+
+
+# Navier-Stokes-Allen-Cahn Framework
+## Installation for anaconda.
+### Tested with [minconda3 v4.3.31](https://conda.io/miniconda.html)
+--------------------------------------------------------------------
+```
+conda create -n NSAC -c mikaem/label/docker-conda-gcc hdf5-parallel
+source activate NSAC
+conda install -c mikaem/label/docker-conda-gcc h5py-parallel
+conda install -c mikaem/label/docker-conda-gcc fenics
+conda install -c mikaem/label/docker-conda-gcc mshr
+pip install -r requirements.txt
+```
+
+
+[fenicstools](https://github.com/mikaem/fenicstools) for postprocessing
+```
+git clone https://github.com/mikaem/fenicstools.git fenicstools
+python fenicstools/setup.py install;
+```
+
+--------------------------------------------------------------------
+## Installation for [Docker](https://www.docker.com/).
+
+Install Docker following https://docs.docker.com/engine/getstarted/step_one/
+
+Pull the latest fenics Docker image
+```
+docker pull quay.io/fenicsproject/stable:latest;
+```
+Run Docker with the dns option for the uni-network
+```
+docker run --dns=129.69.252.252 -ti -v $(pwd):/home/fenics/shared --name NSAC 
+quay.io/fenicsproject/stable:latest;
+echo "export PYTHONPATH=/home/fenics/shared/" >> fenics.env.conf
+source fenics.env.conf
+```
+Clone this git repo and install dependencies
+```
+git clone https://gitlab.mathematik.uni-stuttgart.de/ostrowls/NSAC.git shared/NSAC
+pip3 install --user -r NSAC/requirements.txt;
+```
+Install fenicstools for postprocessing (might not be possible without sudo)
+```
+git clone https://github.com/mikaem/fenicstools.git fenicstools;
+cd fenicstools;
+sudo python3 setup.py install;
+cd ..
+rm -rvf fenicstools;
+```
+
+Start/stop the Container with
+```
+docker start/stop NSAC
+```
+After starting enter the container with
+```
+docker exec -ti -u fenics LDD-scheme /bin/bash -l
+```
+Exit the container with
+```
+exit
+```
+
+
+docker run --dns=129.69.252.252 -it --env HOST_UID=$(id -u $USER) --env HOST_GID=$(id -g $USER) --env DISPLAY=unix$DISPLAY --device /dev/dri --volume /tmp/.X11-unix:/tmp/.X11-unix:rw --volume $(pwd):/home/fenics/shared --name LDD-TPR quay.io/fenicsproject/stable:latest /bin/bash 

README.md

+# Numerical experiments for LDD-TPR
+## Manual on using latest fenix image in Docker
+Pull the latest fenics Docker image
+```
+	docker pull quay.io/fenicsproject/stable:latest;
+
+## Create docker container named LDD-TPR with graphical display, share folder `pwd`:
+
+    docker run --dns=129.69.252.252 -it --env HOST_UID=$(id -u $USER) --env HOST_GID=$(id -g $USER) --env DISPLAY=unix$DISPLAY --device /dev/dri --volume /tmp/.X11-unix:/tmp/.X11-unix:rw --volume $(pwd):/home/fenics/shared --name LDD-TPR quay.io/fenicsproject/stable:latest /bin/bash 
+
+If you want the container do be automatically deleted after exiting add `--rm` option.
+
+
+If you have trouble with internet connection inside the container use
+
+        --dns=YOUR_DNS_SERVER
+
+
+## Start LDD-TPR container and step into the container:
+
+    docker start LDD-TPR & docker exec -ti -u fenics LDD-TPR /bin/bash -l
+
+
+## Usefull docker commands:
+
+List all docker container
+
+    docker ps -a
+
+Remove container
+
+    docker rm $container
+
+Remove all stopped container
+
+    docker container prune
+
+List all images
+
+    docker images
+
+Remove image
+
+    docker rmi $image
+
+
+# Troubleshooting:
+
+**Problem**
+1. I can't install packages via `apt-get install` inside the  container
+
+2. I cannot create files or folders (no write permissions)
+
+**Solution**
+
+1. If the package is not found first `apt-get update` and then try again. If there is no connection 
+check your dns settings.
+
+2. In the container, execute once the script `Rechtesetup/setpermissions.sh` to gain write access in `/home/fenics/shared`
+	
+	cd /home/fenics/shared/Rechtesetup & sudo ./setpermissions.sh
+

Rechtesetup/setpermissions.sh

+#!/bin/bash
+# The user can pass the user and group id by passing
+# --env HOST_UID=$(id -u $USER) --env HOST_GID=$(id -g $USER)
+# with the UID on the host to the container. Should work for Linux, Mac and Windows.
+# Allows to manage the writes for shared volumes.
+if [ "$HOST_UID" ]; then
+    usermod -u $HOST_UID fenics
+fi
+if [ "$HOST_GID" ]; then
+    groupmod -g $HOST_GID fenics
+fi
+# Make sure that everything in /dumux is accessible by the dumux user
+# sed "1d" removes first line which is the folder itself
+# exclude the shared folder using grep. This folder should be accessible by setting the UID/GID.
+# chown transfers ownership to group dumux user dumux
+# the OR true trick avoids the script exiting due to use of set -e
+# find /dumux -maxdepth 1 | sed "1d" | grep -v "/dumux/shared" | xargs chown -R dumux:dumux 2> /dev/null || true
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