This repository contains the code written for my master thesis.
The goal of my thesis is to simulate the movement of a microbubble in a capillary blood vein, using the Cut Finite Element Method (CutFEM). The project uses the finite element library deal.ii [1], in addition to code developed by Simon Sticko for the CutFEM spesific implementations.
The following solvers all use CutFEM, and hence solve the problems on an unfitted mesh.
- The Poisson Problem:
poisson - Stokes Equation:
stokes - Generalized Stokes Equation:
stokes_gen
- The Heat Equation:
heat_eqn - Time Dependent Stokes (Implicit Euler):
stokes_time - Time Dependent Stokes (BDF-2):
stokes_time2
- Heat equation
In addition, solvers for the Poisson problem and the Stokes Equations are also implemented on a fitted mesh, using Nitsches method for the Dirichlet boundary conditions.
The code written in this project depends upon a CutFEM library under development by Simon Sticko, and is therefore needed when compiling.
Endte med å måtte sette path til DealiiCutElements når jeg kjører cmake:
Create a folder build in the root of this project, then set the path to the project DealiiCutElements when running cmake, with the following command
build $ cmake -DCUTFEM_DIR=~/git/path/to/dealiicutelements/install ..
build $ make -j4Note that this only works for the code not using CutFEM, i.e. the solvers in the directory src/nitsche.
Get the Deal.II docker image from https://hub.docker.com/r/dealii/dealii/
$ docker pull dealii/dealii
Run an interactive shell in the container with this project as a volume in the container
$ docker run -itv ~/path/to/microbubble:/home/dealii/microbubble
dealii/dealii:<tag> If the project have already been compiled on the "outside" it may be necessary to delete all Cmake output before running the container.
Inside the container, compile by running
$ cd microbubble/
$ cmake .
$ make