Differences

This shows you the differences between two versions of the page.

--- fenicsx [2023/03/24 14:35] – bdatta1
+++ fenicsx [2024/04/18 10:33] (current) – [Learning FEniCSx] bdatta1
@@ Line 1: / Line 1: @@
-===== What is FEniCSx =====
+===== FEniCSx =====
-FEniCSx is an open source multi-platform computing environment to solve partial differential equations using finite element method. FEniCSx supports parallel computing with Python and C++ interface. FEniCSx is comprised of the libraries UFL, Basix, FFCx and DOLFINx which are the build blocks of it. To learn more about FEniCSx: https://fenicsproject.org.
+FEniCSx is an open-source multi-platform computing environment to solve partial differential equations using the finite element method. FEniCSx supports parallel computing with Python and C++ interface. FEniCSx is comprised of the libraries UFL, Basix, FFCx, and DOLFINx which are the build blocks of it. To learn more about FEniCSx: [[https://fenicsproject.org]].
-The FEniCS project originally started in 2003 and was known as FEniCS. In 2020, the developers released a new version of the library and renamed FEniCS as FEniCSx. The latest stable version of legacy FEniCS was released on April 2019 and its barely updated. But many tutorials and legacy codes are perhaps written in legacy FEniCS. So you may want to install a version of it. We will demonstrate installing both versions on multiple different platforms here.
+The FEniCS project originally started in 2003 and was known as FEniCS. In 2020, the developers released a new version of the library and renamed FEniCS as FEniCSx. The latest stable version of legacy FEniCS was released in April 2019 and it's barely updated. But many tutorials and legacy codes are perhaps written in legacy FEniCS. So you may want to install a version of it. We will demonstrate installing both versions on multiple different platforms here.
-Both FEniCSx and FEniCS are available on Linux, macOS, and Windows. You can download and install it in different ways. Check out the options here for FEniCSx: https://github.com/FEniCS/dolfinx and here for legacy FEniCS: https://fenicsproject.org/download/archive/. For both versions, our preferred approach is to install them via Anaconda.
+Both FEniCSx and FEniCS are available on Linux, macOS, and Windows. You can download and install it in different ways. Check out the options here for FEniCSx: [[https://github.com/FEniCS/dolfinx]] and here for legacy FEniCS: [[https://fenicsproject.org/download/archive/]]. For both versions, our preferred approach is to install them via Anaconda.
-===== Installation on Windows =====
+==== Installation on Windows =====
 This step in only applicable if you are using Windows. You will have to set up Windows Subsystem for Linux (WSL) to use Anaconda based installation of FEniCSx and legacy FEniCS. WSL is a virtual Linux environment within Windows which allows you to use Linux command line tools and GUI applications (GUI is natively supported on Windows 11). If you are on macOS or Linux, you can skip this step. If you are on Windows and already have installed WSL, it still might be interesting to download the recommended applications/ tools, such as VS Code.
-===== Get your tools ready first =====
+==== Get your tools ready first =====
 ==== PowerShell 7 ====
@@ Line 25: / Line 26: @@
 Windows Terminal is a command line tool, available on **Microsoft Store** (https://apps.microsoft.com/store/apps). You can manage multiple command line environments such as Windows PowerShell 5.1, PowerShell 7.X.Y, CMD, WSL, etc. using a single application. Check out more about it here: https://learn.microsoft.com/en-us/windows/terminal/install. You can customize your command line applications using Terminal.
-===== Windows Subsystem for Linux (WSL) =====
+==== Windows Subsystem for Linux (WSL) =====
 The current stable version for Windows Subsystem for Linux is WSL2 and this is the default installation.
-  - Open PowerShell 7.X.Y (your current installation version) as **administrator** \\ \\
+  - Open PowerShell 7.X.Y (your current installation version) as **administrator** using the Terminal app from the Windows Start menu and then type the following command: <code>
-  - using the Terminal app from the Windows Start menu and then type the following command: <code>
+$ wsl --list --online </code> This command will show you currently available Linux distributions on Windows.
-  $ wsl --list --online </code> This command will show you currently available Linux distributions on Windows.
   - Install the latest LTS version of Ubuntu which is Ubuntu 22.04.02 LTS. <code>$ wsl --install -d Ubuntu </code> It will ask you to create an user account and set a password. The installation process is fast and straightforward. Once Ubuntu in WSL is installed, you can use it similar to a regular Ubuntu distribution. To run Ubuntu, open it from the Terminal application option. If this is your first time using Linux, you can familiarize yourself with some commands and operations from here: https://ubuntu.com/tutorials/command-line-for-beginners.
   - We will now update the Ubuntu distribution and install two packages for WSL virtual display settings. <code>
@@ Line 38: / Line 38: @@
   - You can open the WSL home directory and browse, copy, and move files like Windows. Once you have installed Ubuntu in WSL and VS Code, you can follow these tutorials to get yourself more familiarized with the VS Code environments and capabilities in WSL: https://learn.microsoft.com/en-us/windows/wsl/tutorials/wsl-vscode and https://code.visualstudio.com/docs/remote/wsl-tutorial. \\ To use packages and libraries install in WSL, start VS Code from Ubuntu terminal.
-===== Anaconda on Linux (WSL) and macOS =====
+==== Anaconda on Linux (WSL) and macOS =====
 If this is the first time you are using Python, then seat back, it is going to get confusing like this xkcd comic. Even if you are experienced in Python, you might find this interesting (https://xkcd.com/1987/).
@@ Line 44: / Line 44: @@
 Most of the Python based libraries and packages often depend on other libraries and packages (called dependencies). Installing the right version of those packages and maintaining them is often a complex task even for experienced developers. So, we will use a popular Python distribution, Anaconda, to manage all the Python based libraries and relevant dependencies. Anaconda uses conda package manager and works well with pip (Python’s default package manager). Installation of Anaconda comes with popular Python packages such as NumPy, SciPy, Matplotlib, and <//insert hundred other packages here//>. It also comes with Jupyter Notebook and Spyder IDE. Anaconda also has a minimalist version, called Miniconda, which is light weight because it only includes the conda manager and a few packages. We strongly recommend installing Anaconda
-  - This step is only for macOS. We will install ''%%xcode%%'' command line tools to enable basic development libraries and features. On macOS terminal, type: <code> (base) $ xcode-select --install </code>
+  - This step is only for macOS. We will install ''%%xcode%%'' command line tools to enable basic development libraries and features. On macOS terminal, type: <code>
-  - Download Anaconda from here based on your operating system and architecture: https://www.anaconda.com/products/distribution. On macOS, you can download the graphical installer and install it like every other software by following the on-screen instructions. Details of the installation procedure is available here: https://docs.anaconda.com/anaconda/install/mac-os/. Alternatively, you can download the installation script and using command line to install Anaconda like Linux.
+(base) $ xcode-select --install </code>
-  - For WSL, you will download the installation script. Open Ubuntu terminal and use the following command to copy this script from your Windows Downloads folder to WSL home directory: <code>$ wget https://repo.anaconda.com/archive/Anaconda3-2023.03-Linux-x86_64.sh </code>
+  - Download Anaconda from here based on your operating system and architecture: https://www.anaconda.com/products/distribution. On macOS, you can download the graphical installer and install it like every other software by following the on-screen instructions. Details of the installation procedure is available here: https://docs.anaconda.com/anaconda/install/mac-os/. Alternatively, you can download the installation script and using command line to install Anaconda like Linux. \\ \\
-  - ''%%Anaconda3-2023.03-Linux-x86_644%%'' is the latest version of Anaconda available at the time this guide is being written. Check the available versions here: https://repo.anaconda.com/archive. Replace it wish the version you downloaded for installation. Once it is copied in the home directory, you can run the following command on Ubuntu terminal for installation: <code>$ bash Anaconda3-2022.10-Linux-x86_64.sh </code>
+  - For WSL, you will download the installation script. Open Ubuntu terminal and use the following command to copy this script from your Windows Downloads folder to WSL home directory: <code>$ wget https://repo.anaconda.com/archive/Anaconda3-2023.03-Linux-x86_64.sh </code> ''%%Anaconda3-2023.03-Linux-x86_644%%'' is the latest version of Anaconda available at the time this guide is being written. Check the available versions here: https://repo.anaconda.com/archive. Replace it wish the version you downloaded for installation.
-  - Please make sure to use the version you downloaded. It will ask you to read the license agreement and your permission for installation. Proceed as needed. Close the Ubuntu terminal and open it back, you will see the base environment for Anaconda is now available. This is how your terminal is going to look like: <code> (base) $  </code>
+  - Once it is downloaded to the home directory, you can run the following command on Ubuntu terminal for installation: <code>$ bash Anaconda3-2022.10-Linux-x86_64.sh </code>
+  - Please make sure to use the version you downloaded. It will ask you to read the license agreement and your permission for installation. Proceed as needed. Close the Ubuntu terminal and open it back, you will see the base environment for Anaconda is now available. This is how your terminal is going to look like: <code>
+(base) $  </code>
   - Check out these operations and commands for using Conda: https://docs.conda.io/projects/conda/en/4.6.0/_downloads/52a95608c49671267e40c689e0bc00ca/conda-cheatsheet.pdf
-===== FEniCSx on Linux and macOS =====
+==== FEniCSx on Linux and macOS =====
 As of March 2023, the latest stable release of ''%%dolfinx%%'' available via Anaconda is 0.6. If you build FEniCSx from the source, you can perhaps install 0.7.
-  - Once Anaconda is properly installed, create an environment for FEniCSx. In addition to the ''%%dolfinx%%'' library, we will install ''%%mpich%%'', ''%%pyvista%%'', ''%%matplotlib%%'', and ''%%cycler%%'',. ''%%mpich%%'' allows parallel processing of different operations within FEniCSx and the other three packages are used for quick visualization. Standard installation of Anaconda already comes with these three packages but we will still need to install them inside the FEniCSx environment. <code>
+  - Once Anaconda is properly installed, create an environment for FEniCSx. In addition to the ''%%dolfinx%%'' library, we will install ''%%mpich%%'', ''%%pyvista%%'', ''%%matplotlib%%'', and ''%%cycler%%''. Parallel processing library ''%%mpich%%'' allows different multi-processor operations within FEniCSx and the other three packages are used for quick visualization. Standard installation of Anaconda already comes with these three packages but we will still need to install them inside the FEniCSx environment. <code>
 (base)    $ conda create -n fenicsx
 (base)    $ conda activate fenicsx
@@ Line 64: / Line 66: @@
 (base)    $ conda clean --all </code> It will ask your permission; proceed as needed. FEniCSx should be completely uninstalled now.
-===== Legacy FEniCS on Linux and macOS (optional) =====
+==== Legacy FEniCS on Linux and macOS (optional) =====
 A lots of the tutorials, examples, and published codes are still written in legacy FEniCS. So, you may want to install the legacy version in case you want to run codes written in legacy FEniCS.
@@ Line 77: / Line 79: @@
 (base)   $ conda clean --all </code>
-===== An alternative way to install on Ubuntu (not recommended) =====
+==== An alternative way to install on Ubuntu (not recommended) =====
   - On Ubuntu, we can also install FEniCSx using ''%%apt%%'' package manager. Albeit the installation process being simple and lightweight, FEniCSx version available via ''%%apt%%'' is often not the latest version. So, we do not recommend installing this way. <code>
@@ Line 89: / Line 91: @@
 $ sudo apt purge --auto-remove fenicsx </code> Legacy FEniCS can be installed using this approach as well. Please make sure to use ''%%fenics%%'' instead of ''%%fenicsx%%'' in the command line for installing and uninstalling legacy FEniCS.
-===== Visual Studio Code (optional but recommended) =====
+==== Visual Studio Code (optional but recommended) =====
 Visual Studio Code is a cross-platform code editor from Microsoft. You can install different extensions within VS Code to enable features for code development such as remote SSH, debugging, compiling, etc. If you have another favorite IDE (e.g., Spyder or PyCharm) or code editor (e.g., Sublime text, Atom, Notepad++) you like to use, you can configure it yourself.
@@ Line 98: / Line 100: @@
   - Once installed, add the extension packs for Python, Remote Development, and Jupyter, from Microsoft. These packages will be necessary for smooth operation. Do Google search to find out a few more extension packs of your liking. You can also install ''%%Vim%%'' extension pack as well but exit at your own risk.
-===== Test your FEniCSx installation =====
+==== Test your FEniCSx installation =====
 We will now demonstrate how to run a simple FEniCSx example code here using VS Code. If you open Ubuntu or macOS terminal now, you will see the ''%%(base)%%'' environment is active.
@@ Line 199: / Line 201: @@
 </code>
   - Now run the python code from the Ubuntu terminal: <code>(fenicsx) $ python3 poisson.py </code>
-  - This should save ''%%.h5%%'' and ''%%.xdmf%%'' files with the results and save the mesh and contour plot of the primary variable ''%%.pdf%%'' files in the working directory.
+  - This should return the calculated error of the finite element solution and save ''%%.h5%%'' and ''%%.xdmf%%'' files with the results and save the mesh and contour plot of the primary variable ''%%.pdf%%'' files in the working directory.
-===== A few more settings =====
+==== A few more settings =====
 If this is the first time you are setting up Python and Anaconda on macOS or WSL, you may need to follow a few more steps for smooth operation. If you have done used Anaconda + VS Code combination before, you might find some of these steps redundant.
@@ Line 229: / Line 231: @@
   - This will return the following on your terminal: <code> (base) $ </code>
-===== Known issues with PyVista =====
+==== Known issues with PyVista =====
   - PyVista plot window needs to be closed before proceeding to the next action (saving the file or plotting another image). To take screenshot on Windows (or WSL), use ''%%q%%'' to exit the plot window instead of clicking on ''%%X%%'' icon. \\ \\
   - WSL on Windows 10 lacks native X-11 forwarding support. When the code is run from the terminal or a Python file from VS Code, plotting through ''%%PyVista%%'' will not show the plot unless X-11 server is configured somehow. It can save the plot as ''%%.pdf, .eps, .svg, .tex, .ps%%'' file using ''%%save_graphic()%%'' function or as ''%%.png%%'' file as ''%%plotter.screenshot()%%'' function. This might not be an issue on Windows 11 as WSL natively supports X-11 forwarding (not tested yet). \\ \\
   - If you are running the Python code interactively from VS Code on WSL, it can show the interactive plot within the Jupyter notebook environment but it has trouble saving the screenshot as ''%%.png%%'' file with ''%%show_edges=True%%'' option. Best is to use the ''%%save_graphic()%%'' function and save it ''%%.pdf, .eps, .svg, .tex, .ps%%'' file. \\ \\
-  - PyVista has trouble rendering higher order ($p \ge 2$) Quadrilateral and Hexahedron elements. For 2nd order Hexahedron element, it renders Tetrahedron. Visualization in ParaView works properly.
+  - PyVista has trouble rendering higher order (2nd order or higher) Quadrilateral and Hexahedron elements. For 2nd order Hexahedron element, it renders Tetrahedron. Visualization in ParaView works properly.
+==== Learning FEniCSx ====
+Since FEniCSx was released very recently, there aren't many tutorial or resources available based on FEniCSx. Please check the first two web resources which demonstrates some wonderful problems using FEniCSx. On the other hand, legacy FEniCS has numerous hands-on tutorials, books, and lecture series available. Fortunately, most of the concepts and APIs are similar between FEniCS and FEniCSx, so it shouldn't be hard to use those resources. In addition, FEniCSx developers are active in responding questions and concerns.
+  - The FEniCx tutorial: https://jsdokken.com/dolfinx-tutorial/
+  - Numerical tours of computational mechanics with FEniCSx: https://bleyerj.github.io/comet-fenicsx/index.html
+  - FEniCSx demos on the official site: https://docs.fenicsproject.org/dolfinx/main/python/demos.html
+  - Legacy FEniCS demos on the official site: https://fenicsproject.org/olddocs/dolfin/1.3.0/python/demo/index.html
+  - Logg, Anders, Kent-Andre Mardal, and Garth Wells, eds. Automated solution of differential equations by the finite element method: The FEniCS book. Vol. 84. Springer Science & Business Media, 2012. (https://doi.org/10.1007/978-3-642-23099-8)
+  - Langtangen, Hans Petter, and Anders Logg. Solving PDEs in python: the FEniCS tutorial I. Springer Nature, 2017. (https://doi.org/10.1007/978-3-319-52462-7)
+  - Courses offered using FEniCS: https://fenicsproject.org/pub/course/lectures/