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OOF: Finite Element Analysis of Microstructures

This is the README file for OOF2, version 2.3.3 or later.

What is OOF2?

OOF2 is designed to help materials scientists calculate macroscopic properties from images of real or simulated microstructures. It reads an image, assigns material properties to features in the image, and conducts virtual experiments to determine the macroscopic properties of the microstructure.

The programs are written in C++ and Python and benefit from an object-oriented design. The underlying numerical solutions rely on finite element technology. Hence the name OOF, for object-oriented finite element analysis.

Installation

The executive summary of steps (to be typed in a terminal window) is:

mkdir oof2
cd oof2
tar -xzf /download_directory_name/oof2-<version>.tar.gz
mkdir build
cd build
cmake ../oof2-<version>
make
sudo make install

but please read the rest of this file before proceeding.

If something goes wrong, your system adminstrator may be able to help you, or you can contact the oof developers at oof_manager@nist.gov. It’s diagnostically useful to include all of the output from the installation commands.

OOF2 has been built and tested on Ubuntu Linux and macOS 13 (Ventura). It ought to work on other varieties of Linux.

Prerequisites

A computer running a variant of the Unix operating system, including Linux and Macintosh. OOF2 currently does not run on Microsoft Windows, but ought to run inside a Linux virtual machine on Windows.

The following external programs and libraries must be present before you can run OOF2. To compile OOF2 from sources, you will also require the header files (“includes”) associated with these programs and libraries. These are usually available as part of a “development” version of the library software.

• Python 3 (3.8 or later)
• [Swig (4.0 or 4.1)] (https://www.swig.org)
• Magick++ (6.x, but not 7.x)
• gtk3 (3.22 or later)
• pygobject (3.28 or later)
• cairomm (1.12 or later)
• pango (1.40 or later)
• pangocairo (1.40 or later)
• OOFCanvas (1.1 or later)

Please note that the words “or later” do not include later major versions. OOF2 will not work with gtk 4.x. It is recommended that you use a package manager to install the prerequisites, rather than compiling them yourself.

Macintosh users can install either native Quartz or X11 versions of gtk3, cairo, and pango. If using X11, they will have to also install an X11 server to run OOF2. But there seem to be some problems with gtk3 and X11 on Macs, so Quartz is recommended.

You should also have the ability to run lapack and the blas basic linear algebra subroutines. On macOS no special libraries are required. On Linux and commercial Unix systems, they may have to be installed, and you may require headers (sometimes provided as part of a “-dev” package).

Detailed instructions for installing the OOF2 prerequisites on a number of different operating systems can be found on the OOF2 Prerequisites page.

Installing OOF2

Commands in the following steps should be typed into a terminal window, after you have installed all the OOF2 prerequisites. In the commands below, type everything after the initial “%” into a terminal window.

0. Disclaimer

Please read the Disclaimer at the end of this file before proceeding.

1. Download

Download the latest OOF2 source distribution from the OOF2 website. That will create a file called something like oof2-2.3.0.tar.gz.

2. Create a working directory and move to it

In your home directory or some other convenient location, enter

% mkdir oof2
% cd oof2

3. Unpack

Unpack the .tar.gz file. The usual way is to run tar -xf on the file you want to unpack. If the file is in your Downloads directory, type

% tar -xf ~/Downloads/oof2-2.3.0.tar.gz

This will create a subdirectory named oof2-2.3.0 in the oof2 directory (if you followed the instructions in step 2).

4. Set PKG_CONFIG_PATH

The OOF2 installation process uses the pkg-config utility to gather information about its dependencies. The data for OOFCanvas needs to be in a spot where pkg-config can find it. Test it by running the command

% pkg-config --modversion oofcanvas

If pkg-config reports the correct OOFCanvas version number, nothing needs to be done. If it says it can’t find oofcanvas, set the environment variable PKG_CONFIG_PATH to the location of oofcanvas.pc. For example, if OOFCanvas was installed into your home directory, the file will be in ~/lib/pgkconfig, and after you run

% export PKG_CONFIG_PATH=~/lib/pkgconfig

pgk-config will be able to find it. (The syntax for setting environment variables depends on what shell you’re using.)

5. Configure

Create a build directory.

% mkdir build
% cd build

If you want to use the default settings, run cmake, pointing it to the unpacked source directory:

% cmake ../oof2-2.3.3

but beware that this will cause OOF2 to be installed in a system directory like /usr or /usr/local, where you might not have permission to create files. It’s better to use ccmake, which will let you edit settings:

% ccmake ../oof2-2.3.3

See https://cmake.org/cmake/help/latest/manual/ccmake.1.html for full instructions on how to use ccmake. At a minimum

• Type c to do the initial configuration
• Use the arrow keys to navigate to CMAKE_INSTALL_PREFIX, which is where OOF2 will be installed.
• Type <return>, edit the prefix, and type <return> again. Set the prefix to a directory where you can write files, such as your home directory. If you’re installing into an Anaconda environment named OOF2, set CMAKE_INSTALL_PREFIX to ~/Anaconda3/envs/OOF2.
• Similarly, change OOF2_PYTHON_VERSION to the version of python3 that you have installed, and OOF2_SWIG_VERSION to the version of swig4. Use the same values you used when installing OOFCanvas. Use <return> to cycle through the allowed values.
• If you are going to build OOF2 extension modules, set OOF2_DEV_INSTALL to ON. This will install the C++ headers and other useful files.
• Type c to update the configuration.
• Type g to generate the build scripts and exit.
• If g wasn’t an option at the bottom of the screen in the previous step and ccmake didn’t exit, the previous c probably added new variables. Check their values and type c again until the g appears, then type g.

6. Build and install

Run

% make install

If your computer’s version of make can run parallel jobs, you can build OOF2 faster by including the -j option

% make -j 10 install

Replace 10 by however many compilation processes you can run simultaneously.

If you don’t have permission to create files in the installation directory (possibly because you didn’t change CMAKE_INSTALL_PREFIX in step 3) you should run the build and installation steps separately so that you can use superuser privileges for installation:

% make -j 10
% sudo make -j 10 install

The installation procedure will create executable scripts called oof2, oof2-test, and oof2-guitest in <prefix>/bin, a bunch of shared libraries called liboof2*.so or liboof2*.dylib in <prefix>/lib, a directory called oof2 in <prefix>/lib/python3.x/site-packages (where 3.x is your python version number), and some example files in <prefix>/share/oof2/examples.

In addition, if OOF2_DEV_INSTALL was set, oof2-extension-setup will be installed in <prefix>/bin, the OOF2 C++ headers and swig files will be installed in <prefix>/include/oof2, and templates used by oof2-extension-setup will be installed in <prefix>/share/oof2/templates.

6. Set environment variables

If <prefix>/bin is not in your Unix command path, you’ll need to add it to the PATH environment variable, or create a symbolic link from a directory that is in your path (or start OOF2 the hard way by by typing <prefix>/bin/oof2). <prefix> is the value you gave to CMAKE_INSTALL_PREFIX in ccmake. (Typing echo $PATH will print the current value of your path. The method for setting environment variables depends on which Unix shell you’re using.)

On Linux, if <prefix>/lib is not in the list of directories that the dynamic linker searches for libraries, you’ll have to add it by setting the LD_LIBRARY_PATH environment variable. This should not be necessary on macOS.

7. Test

If you want to test the installation, run oof2-test and oof2-guitest.

oof2-test runs a variety of tests that don’t depend on the GUI. It can take a long time to complete. oof2-guitest runs GUI-dependent tests. It doesn’t takes as long but it can get confused if you accidentally click or type in one of its windows, so it’s best to just sit back and watch it run.

The test files are installed into <prefix>/lib/python3.x/site-packages/oof2/TEST and <prefix>/lib/python3.x/site-packages/oof2/TEST/GUI. Each of those directories has a README file that may be helpful.

In version 2.3.x there is something wrong with the GUI testing apparatus that makes a few of the tests fail erratically. If oof2-guitest fails, you can tell it to keep trying the tests (within reason) until they work, with

% oof2-guitest --retries=20

Uninstalling OOF2

Go to the build directory and run make uninstall. This deletes all the installed files but unfortunately leaves empty directories behind.

Running OOF2

At this point, you should have an executable file named oof2 in a bin directory in your execution path. You can now simply type oof2 at your shell prompt, and OOF2 will start up.

If you get a message like oof2: command not found, try opening a new terminal window – the old one doesn’t know that a new command has been added.

OOF2 also has many command line options, and you can get a summary of them by typing oof2 --help.

By default, OOF2 runs in graphics mode, opening a couple of windows to get you started. If you don’t want this, you can use the --text option to run it in command-line mode.

Be sure to read the OOF manual and to go through the tutorials provided in the OOF2 Help menu.

Reporting Bugs

If you encounter bugs in the program, please send e-mail to oof_bugs@nist.gov. Include as much information as possible – it is extremely difficult for us to fix a bug if we can’t reproduce it. In particular, include

• What version of OOF2 you’re using. Starting OOF with the -version flag will print the version number.

• What type of computer and what operating system you’re using.

• A complete description of the problem: what happened and what did you do to make it happen?

• If possible, an OOF2 script that reproduces the problem. A script can be saved from the File/Save/Python Log menu item in the main OOF2 window, or the Save button in the Quit dialog box.

  If OOF2 crashes before you get a chance to save a script, a script will be saved automatically in the your operating system’s temp directory, which is probably named tmp. Look for a file named oof2-abcdef.py where abcdef is a random string of characters. You can change the location of the temp directory by setting the OOFTMP environment variable.

• Be sure to include any files that the script requires, such as images or other scripts that it loads.

Contact Us

Other communications, including requests for help and suggestions for new features, can be sent to oof_manager@nist.gov.

Disclaimer

This software provided is provided by NIST as a public service. You may use, copy and distribute copies of the software in any medium, provided that you keep intact this entire notice. You may improve, modify and create derivative works of the software or any portion of the software, and you may copy and distribute such modifications or works. Modified works should carry a notice stating that you changed the software and should note the date and nature of any such change. Please explicitly acknowledge the National Institute of Standards and Technology as the source of the software. To facilitate maintenance we ask that before distributing modified versions of this software, you first contact the authors at oof_manager@nist.gov.

The software is expressly provided “AS IS”. NIST MAKES NO WARRANTY OF ANY KIND, EXPRESS, IMPLIED, IN FACT OR ARISING BY OPERATION OF LAW, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTY OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NON-INFRINGEMENT AND DATA ACCURACY. NIST NEITHER REPRESENTS NOR WARRANTS THAT THE OPERATION OF THE SOFTWARE WILL BE UNINTERRUPTED OR ERROR-FREE, OR THAT ANY DEFECTS WILL BE CORRECTED. NIST DOES NOT WARRANT OR MAKE ANY REPRESENTATIONS REGARDING THE USE OF THE SOFTWARE OR THE RESULTS THEREOF, INCLUDING BUT NOT LIMITED TO THE CORRECTNESS, ACCURACY, RELIABILITY, OR USEFULNESS OF THE SOFTWARE.

You are solely responsible for determining the appropriateness of using and distributing the software and you assume all risks associated with its use, including but not limited to the risks and costs of program errors, compliance with applicable laws, damage to or loss of data, programs or equipment, and the unavailability or interruption of operation. This software is not intended to be used in any situation where a failure could cause risk of injury or damage to property. The software was developed by NIST employees. NIST employee contributions are not subject to copyright protection within the United States.