README.txt

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

# What is OOF2?

[OOF2](http://www.ctcms.nist.gov/oof/) 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)](http://www.python.org)
-   \[Swig (4.0 or 4.1)\] (https://www.swig.org)
-   [Magick++ (6.x, but not
    7.x)](http://www.imagemagick.org/Magick++/index.html)
-   [gtk3 (3.22 or later)](http://www.gtk.org/download/)
-   [pygobject (3.28 or later)](https://pypi.org/project/PyGObject/)
-   [cairomm (1.12 or later)](https://www.cairographics.org/cairomm/)
-   [pango (1.40 or later)](https://pango.gnome.org/)
-   [pangocairo (1.40 or
    later)](https://gnome.pages.gitlab.gnome.org/pango/PangoCairo/)
-   [OOFCanvas (1.1 or later)](http://www.ctcms.nist.gov/oof/oofcanvas)

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](http://www.ctcms.nist.gov/oof/oof2/prerequisites.html).

## 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](#disclaimerlink) at the end of this file
before proceeding.

### 1. Download

Download the latest OOF2 source distribution from the [OOF2
website](http://www.ctcms.nist.gov/oof/oof2/). 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.
-   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` wassn'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](http://www.ctcms.nist.gov/~langer/oof2man/) 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 {#disclaimerlink}

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.