phaseflow-dealii

The development of this code has just begun, starting from a copy of the author's convection-diffusion code at https://github.com/alexanderzimmerman/peclet

Phaseflow will solve the incompressible Navier-Stokes-Boussinesq equations coupled with an enthalpy-based energy equation allowing for melting and solidification of the phase-change material medium.

This is written in C++ and based on the deal.II finite element method library.

Author: Alexander G. Zimmerman alex.g.zimmerman@gmail.com

Doxygen generated HTML documentation: https://geo-fluid-dynamics.github.io/phaseflow-dealii/

(Continuous integration status; click the button to go to Travis-CI)

For users:

Run pre-built version on docker image

Get the free community edition of Docker here: https://www.docker.com/community-edition

Pull the image from https://hub.docker.com/r/zimmerman/phaseflow/ and run the container with docker

docker run -ti geo-fluid-dynamics/phaseflow-dealii:latest

Or run the container with access to a shared folder (shared between the host and the container)

docker run -ti -v $(pwd):/home/dealii/shared geo-fluid-dynamics/phaseflow-dealii:latest

If you plan to use this container repeatedly, then instead use this command to also give it a name

docker run -ti -v $(pwd):/home/dealii/shared --name phaseflow-dealii geo-fluid-dynamics/phaseflow-dealii:latest

After exiting the container, you can start it again with

docker start phaseflow-dealii

You can confirm that the container is running with

docker ps

or list all containers (running or not) with

docker ps -a

To enter a bash terminal inside of the running container

docker start phaseflow-dealii

docker exec -ti -u dealii phaseflow-dealii /bin/bash -l

For developers:

Build

git clone git@github.com:geo-fluid-dynamics/phaseflow-dealii.git

mkdir build

cd build

cmake ../phaseflow-dealii

make test

Design notes

The Phaseflow class is implemented entirely with header files. This reduces the structural complexity of the code and can increase programming productivity, but it leads to longer compile times. A header-only approach would be impractical for the deal.II library itself; but in this small project's experience, the header-only approach is more than adequate. Most notably, this simplifies working with C++ templates.

Documentation

The Doxygen generated HTML docs are hosted in the standard GitHub fashion on the gh-pages branch.

The procedure for keeping the HTML docs updated is rough. To initially create the gh-pages branch, we followed the outline in an issue from another repository, which uses the ideas from here and here. Since any of these links may break, in short the procedure was

cd phaseflow-dealii

mkdir doxygen_output

mkdir doxygen_output/html

cd doxygen_output/html

git clone git@github.com:geo-fluid-dynamics/phaseflow-dealii.git .

git checkout -b gh-pages

git branch -d master

git rm -r *

git commit "Removed everything from gh-pages branch"

cd ../..

git checkout master

doxygen

cd doxygen_output/html

git checkout gh-pages

git add *

git commit "Added all HTML documentation"

git push origin gh-pages

You can skip many of those steps for initial set up with your local clone. Simply make the target documents directory and clone the gh-pages branch inside of it.

cd phaseflow-dealii

mkdir doxygen_output

mkdir doxygen_output/html

cd doxygen_output/html

git clone git@github.com:geo-fluid-dynamics/phaseflow-dealii.git .

git checkout gh-pages

Then whenever commiting to the master branch, update the gh-pages branch as follows:

cd phaseflow

doxygen

cd doxygen_output/html

git add *

git commit -m "Refreshed HTML doc"

git push origin gh-pages