Simbody [![Travis][buildstatus_image_travis]][travisci] [![Appveyor][buildstatus_image_appveyor]][appveyorci] [![Codecov][buildstatus_image_codecov]][codecovci]
=======

Simbody is a high-performance, open-source toolkit for science- and
engineering-quality simulation of articulated mechanisms, including
biomechanical structures such as human and animal skeletons,
mechanical systems like robots, vehicles, and machines, and anything
else that can be described as a set of rigid bodies interconnected
by joints, influenced by forces and motions, and restricted by
constraints. Simbody includes a multibody dynamics library for
modeling motion in [generalized/internal coordinates in O(n) time][thy].
This is sometimes called a Featherstone-style physics engine.

Simbody provides a C++ API that is used to build domain-specific applications;
it is not a standalone application itself. For example, it is used by
biomechanists in [OpenSim](http://opensim.stanford.edu), by roboticists in
[Gazebo](http://gazebosim.org), and for biomolecular research in
[MacroMoleculeBuilder (MMB)](https://simtk.org/home/rnatoolbox). Here's an
artful simulation of several RNA molecules containing thousands of bodies,
performed with MMB by [Samuel Flores][flores]:

[![Sam Flores' Simbody RNA simulation][rna]][simbios]

Read more about Simbody at the [Simbody homepage](https://simtk.org/home/simbody).


Simple example: a double pendulum
---------------------------------
Here's some code to simulate and visualize a 2-link chain:

```cpp
#include "Simbody.h"
using namespace SimTK;
int main() {
    // Define the system.
    MultibodySystem system;
    SimbodyMatterSubsystem matter(system);
    GeneralForceSubsystem forces(system);
    Force::Gravity gravity(forces, matter, -YAxis, 9.8);

    // Describe mass and visualization properties for a generic body.
    Body::Rigid bodyInfo(MassProperties(1.0, Vec3(0), UnitInertia(1)));
    bodyInfo.addDecoration(Transform(), DecorativeSphere(0.1));

    // Create the moving (mobilized) bodies of the pendulum.
    MobilizedBody::Pin pendulum1(matter.Ground(), Transform(Vec3(0)),
            bodyInfo, Transform(Vec3(0, 1, 0)));
    MobilizedBody::Pin pendulum2(pendulum1, Transform(Vec3(0)),
            bodyInfo, Transform(Vec3(0, 1, 0)));

    // Set up visualization.
    Visualizer viz(system);
    system.addEventReporter(new Visualizer::Reporter(viz, 0.01));

    // Initialize the system and state.
    State state = system.realizeTopology();
    pendulum2.setRate(state, 5.0);

    // Simulate for 20 seconds.
    RungeKuttaMersonIntegrator integ(system);
    TimeStepper ts(system, integ);
    ts.initialize(state);
    ts.stepTo(20.0);
}
```

![Double-pendulum simulation in Simbody][doublePendulum]

See [Simbody's User Guide][user] for a step-by-step explanation of this
example.


Features
--------
- Wide variety of joint, constraint, and force types; easily user-extended.
- Forward, inverse, and mixed dynamics. Motion driven by forces or
  prescribed motion.
- Contact (Hertz, Hunt and Crossley models).
- Gradient descent, interior point, and global (CMA) optimizers.
- A variety of numerical integrators with error control.
- Visualizer, using OpenGL


You want to...
--------------
* **[install Simbody](#installing)**.
* [use Simbody in your own program][user].
* [view API documentation](https://simbody.github.io).
* [learn the theory behind Simbody](https://github.com/simbody/simbody/raw/master/Simbody/doc/SimbodyTheoryManual.pdf).
* [extend Simbody](https://github.com/simbody/simbody/raw/master/Simbody/doc/SimbodyAdvancedProgrammingGuide.pdf).
* [**get support** at the Simbody Forum](https://simtk.org/forums/viewforum.php?f=47).
* [report a bug or suggest a feature](https://github.com/simbody/simbody/issues/new).

---


Dependencies
------------

Simbody depends on the following:

* cross-platform building: [CMake](http://www.cmake.org/cmake/resources/software.html) 2.8.10 or later (3.1.3 or later for Visual Studio).
* compiler: [Visual Studio](http://www.visualstudio.com) 2015, 2017, or 2019 (Windows only), [gcc](http://gcc.gnu.org/) 4.9.0 or later (typically on Linux), [Clang](http://clang.llvm.org/) 3.4 or later, or Apple Clang (Xcode) 8 or later.
* linear algebra: [LAPACK](http://www.netlib.org/lapack/) 3.6.0 or later and [BLAS](http://www.netlib.org/blas/)
* visualization (optional): [FreeGLUT](http://freeglut.sourceforge.net/), [Xi and Xmu](http://www.x.org/wiki/)
* API documentation (optional): [Doxygen](http://www.stack.nl/~dimitri/doxygen/) 1.8.6 or later; we recommend at least 1.8.8.


Using Simbody
-------------

* **Creating your own Simbody-using project with CMake** To get started with
  your own Simbody-using project, check out the
  [cmake/SampleCMakeLists.txt](cmake/SampleCMakeLists.txt) file.


Installing
----------

Simbody works on Windows, Mac, and Linux. For each operating system, you can use a package manager or build from source. In this file, we provide instructions for 6 different ways of installing Simbody:

1. [**Windows**](#windows-using-visual-studio): build from source using Microsoft Visual Studio.
2. [**Linux or Mac (make)**](#linux-or-mac-using-make): build from source using gcc or Clang with make.
3. [**Mac (Homebrew)**](#mac-and-homebrew): automated build/install with Homebrew.
4. [**Ubuntu/Debian**](#ubuntu-and-apt-get): install pre-built binaries with apt-get.
5. [**FreeBSD**](#freebsd): install pre-built binaries with pkg.
6. [**Windows using MinGW**](#windows-using-mingw): build from source using MinGW.
7. [**Windows/Mac/Linux**](#windows-mac-and-linux-using-conda): install pre-built binaries with the Conda package manager.

If you use Linux, check [Repology](https://repology.org/project/simbody/versions) to see if your distribution provides a package for Simbody.

These are not the only ways to install Simbody, however. For example, on a Mac, you could use CMake and Xcode.

#### C++11 and gcc/Clang

Simbody 3.6 and later uses C++11 features (the `-std=c++11` flag). Simbody 3.3
and earlier use only C++03 features, and Simbody 3.4 and 3.5 can use either
C++03 or C++11; see the `SIMBODY_STANDARD_11` CMake variable in these versions.
Note that if you want to use the C++11 flag in your own project, Simbody must
have been compiled with the C++11 flag as well.


Windows using Visual Studio
---------------------------

#### Get the dependencies

All needed library dependencies are provided with the Simbody installation on Windows, including linear algebra and visualization dependencies.

1. Download and install [Microsoft Visual Studio](http://www.visualstudio.com), version [2015](https://www.visualstudio.com/vs/older-downloads/), 2017, or 2019. The Community edition is free and sufficient.
  * 2015: By default, Visual Studio 2015 does not provide C++ support; when installing, be sure to select *Custom*, and check *Programming Languages > Visual C++ > Common Tools for Visual C++ 2015*. If you have already installed Visual Studio without C++ support, simply re-run the installer and select *Modify*.
  * 2017 and later: In the installer, select the *Desktop development with C++* workload.
  * Any other C++ code you plan to use with Simbody should be compiled with the
    same compiler as used for Simbody.
2. Download and install [CMake](http://www.cmake.org/download), version 3.1.3 or higher.
3. (optional) If you want to build API documentation, download and install Doxygen, version 1.8.8 or higher.

#### Download the Simbody source code

* Method 1: Download the source code from https://github.com/simbody/simbody/releases. Look for the highest-numbered release, click on the .zip button, and unzip it on your computer. We'll assume you unzipped the source code into `C:/Simbody-source`.
* Method 2: Clone the git repository.
    1. Get git. There are many options:

       * [Git for Windows](http://gitforwindows.org/) (most advanced),
       * [TortoiseGit](https://tortoisegit.org/download/) (intermediate; good for TortoiseSVN users),
       * [GitHub Desktop](https://desktop.github.com/) (easiest).

    2. Clone the github repository into `C:/Simbody-source`. Run the following in a Git Bash / Git Shell, or find a way to run the equivalent commands in a GUI client:

            $ git clone https://github.com/simbody/simbody.git C:/Simbody-source
            $ git checkout Simbody-3.7

    3. In the last line above, we assumed you want to build a released version.
       Feel free to change the version you want to build.
       If you want to build the latest development version ("bleeding edge") of
       Simbody off the `master` branch, you can omit the `checkout` line.

       To see the set of releases and checkout a specific version, you can use
       the following commands:

            $ git tag
            $ git checkout Simbody-X.Y.Z

#### Configure and generate project files

1. Open CMake.
2. In the field **Where is the source code**, specify `C:/Simbody-source`.
3. In the field **Where to build the binaries**, specify something like `C:/Simbody-build`, just not inside your source directory. This is *not* where we will install Simbody; see below.
4. Click the **Configure** button.
    1. When prompted to select a *generator*, in the dropdown for *Optional platform for generator*, choose **x64** to build 64-bit binaries or leave blank to build 32-bit binaries. In older versions of CMake, select a generator ending with **Win64** to build 64-bit binaries (e.g., **Visual Studio 14 2015 Win64** or **Visual Studio 15 2017 Win64**), or select one *without* **Win64** to build 32-bit binaries (e.g., **Visual Studio 14 2015** or **Visual Studio 15 2017**).
    2. Click **Finish**.
5. Where do you want to install Simbody on your computer? Set this by changing the `CMAKE_INSTALL_PREFIX` variable. We'll assume you set it to `C:/Simbody`. If you choose a different installation location, make sure to use *yours* where we use `C:/Simbody` below.
6. Play around with the other build options:
    * `BUILD_EXAMPLES` to see what Simbody can do. On by default.
    * `BUILD_TESTING` to ensure your Simbody works correctly. On by default.
    * `BUILD_VISUALIZER` to be able to watch your system move about! If building remotely, you could turn this off. On by default.
    * `BUILD_DYNAMIC_LIBRARIES` builds the three libraries as dynamic libraries. On by default. Unless you know what you're doing, leave this one on.
    * `BUILD_STATIC_LIBRARIES` builds the three libraries as static libraries, whose names will end with `_static`. Off by default. You must activate either `BUILD_DYNAMIC_LIBRARIES`, `BUILD_STATIC_LIBRARIES`, or both.
    * `BUILD_TESTS_AND_EXAMPLES_STATIC` if static libraries, and tests or examples are being built, creates statically-linked tests/examples. Can take a while to build, and it is unlikely you'll use the statically-linked libraries.
    * `BUILD_TESTS_AND_EXAMPLES_SHARED` if tests or examples are being built, creates dynamically-linked tests/examples. Unless you know what you're doing, leave this one on.
7. Click the **Configure** button again. Then, click **Generate** to make Visual Studio project files.

#### Build and install

1. Open `C:/Simbody-build/Simbody.sln` in Visual Studio.
2. Select your desired *Solution configuration* from the drop-down at the top.
    * **Debug**: debugger symbols; no optimizations (more than 10x slower). Library and visualizer names end with `_d`.
    * **RelWithDebInfo**: debugger symbols; optimized. This is the configuration we recommend.
    * **Release**: no debugger symbols; optimized. Generated libraries and executables are smaller but not faster than RelWithDebInfo.
    * **MinSizeRel**: minimum size; optimized. May be slower than RelWithDebInfo or Release.

    You at least want optimized libraries (all configurations but Debug are optimized), but you
    can have Debug libraries coexist with them. To do this, go through the full
    installation process twice, once for each configuration.
3. Build the project **ALL_BUILD** by right-clicking it and selecting **Build**.
4. Run the tests by right-clicking **RUN_TESTS** and selecting **Build**. Make sure all tests pass. You can use **RUN_TESTS_PARALLEL** for a faster test run if you have multiple cores.
5. (Optional) Build the project **doxygen** to get API documentation generated from your Simbody source. You will get some warnings if your doxygen version is earlier than Doxygen 1.8.8; upgrade if you can.
6. Install Simbody by right-clicking **INSTALL** and selecting **Build**.

#### Play around with examples

Within your build in Visual Studio (not the installation):

1. Make sure your configuration is set to a release configuration (e.g., RelWithDebInfo).
2. Right click on one of the targets whose name begins with `Example -` and select **Select as Startup Project**.
3. Type **Ctrl-F5** to start the program.

#### Set environment variables and test the installation

If you are only building Simbody to use it with OpenSim, you can skip this section.

1. Allow executables to find Simbody libraries (.dll's) by adding the Simbody `bin/` directory to your `PATH` environment variable.
    1. In the Start menu (Windows 7 or 10) or screen (Windows 8), search `environment`.
    2. Select **Edit the system environment variables**.
    3. Click **Environment Variables...**.
    4. Under **System variables**, click **Path**, then click **Edit**.
    5. Add `C:/Simbody/bin;` to the front of the text field. Don't forget the semicolon!
2. Allow Simbody and other projects (e.g., OpenSim) to find Simbody. In the same Environment Variables window:
    1. Under **User variables for...**, click **New...**.
    2. For **Variable name**, type `SIMBODY_HOME`.
    3. For **Variable value**, type `C:/Simbody`.
3. Changes only take effect in newly-opened windows. Close any Windows Explorer or Command Prompt windows.
4. Test your installation by navigating to `C:/Simbody/examples/bin` and running `SimbodyInstallTest.exe` or `SimbodyInstallTestNoViz.exe`.

**Note**: Example binaries are *not* installed for Debug configurations. They are present in the build environment, however, so you can run them from there. They will run *very* slowly!

#### Layout of installation

How is your Simbody installation organized?

* `bin/` the visualizer and shared libraries (.dll's,  used at runtime).
* `doc/` a few manuals, as well as API docs (`SimbodyAPI.html`).
* `examples/`
    * `src/` the source code for the examples.
    * `bin/` the examples, compiled into executables; run them! (Not installed for Debug builds.)
* `include/` the header (.h) files; necessary for projects that use Simbody.
* `lib/` "import" libraries, used during linking.
* `cmake/` CMake files that are useful for projects that use Simbody.


Linux or Mac using make
-----------------------

These instructions are for building Simbody from source on either a Mac or on
Ubuntu.

#### Check the compiler version

Simbody uses recent C++ features, that require a modern compiler.
Before installing Simbody, check your compiler version with commands like that:

- `g++ --version`
- `clang++ --version`

In case your compiler is not supported, you can upgrade your compiler.

##### Upgrading GCC to 4.9 on Ubuntu 14.04

Here are some instructions to upgrade GCC on a Ubuntu 14.04 distribution.

    $ sudo add-apt-repository ppa:ubuntu-toolchain-r/test
    $ sudo apt-get update
    $ sudo apt-get install gcc-4.9 g++-4.9

If one wants to set `gcc-4.9` and `g++-4.9` as the default compilers, run the following command

    $ sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.9 60 --slave /usr/bin/g++ g++ /usr/bin/g++-4.9

Remember that when having several compilers, CMake flags
`CMAKE_C_COMPILER` and `CMAKE_CXX_COMPILER` can be used
to select the ones desired. For example, Simbody can be
configured with the following flags:

    $ cmake -DCMAKE_C_COMPILER=gcc-4.9 -DCMAKE_CXX_COMPILER=g++-4.9

#### Get dependencies

On a Mac, the Xcode developer package gives LAPACK and BLAS to you via the Accelerate
framework. Mac's come with the visualization dependencies.

On Ubuntu, we need to get the dependencies ourselves. Open a terminal and run the following commands.

1. Get the necessary dependencies: `$ sudo apt-get install cmake liblapack-dev`.
2. If you want to use the CMake GUI, install `cmake-qt-gui`.
3. For visualization (optional): `$ sudo apt-get install freeglut3-dev libxi-dev libxmu-dev`.
4. For API documentation (optional): `$ sudo apt-get install doxygen`.

LAPACK version 3.6.0 and higher may be required for some applications (OpenSim).
LAPACK can be downloaded from [http://www.netlib.org/lapack/](http://www.netlib.org/lapack/),
and compiled using the following method. It is sufficient to set `LD_LIBRARY_PATH` to your LAPACK install prefix
and build Simbody using the `-DBUILD_USING_OTHER_LAPACK:PATH=/path/to/liblapack.so` option in cmake.
```{bash}
cmake ../lapack-3.6.0 -DCMAKE_INSTALL_PREFIX=/path/to/new/lapack/ -DCMAKE_BUILD_TYPE=RELEASE -DBUILD_SHARED_LIBS=ON
make
make install
```

#### Get the Simbody source code

There are two ways to get the source code.

* Method 1: Download the source code from https://github.com/simbody/simbody/releases.
  Look for the highest-numbered release, click on the .zip button, and unzip it on your computer.
  We'll assume you unzipped the source code into `~/simbody-source`.
* Method 2: Clone the git repository.
    1. Get git.
        * Mac: You might have it already, especially if you have Xcode, which
          is free in the App Store. If not, one method is to install
          [Homebrew](http://brew.sh/) and run `brew install git` in a
          terminal.
        * Ubuntu: run `sudo apt-get install git` in a terminal.
    2. Clone the github repository into `~/simbody-source`.

            $ git clone https://github.com/simbody/simbody.git ~/simbody-source
            $ git checkout Simbody-3.7

    3. In the last line above, we assumed you want to build a released version.
       Feel free to change the version you want to build.
       If you want to build the latest development version ("bleeding edge") of
       Simbody off the `master` branch, you can omit the `checkout` line.

       To see the set of releases and checkout a specific version, you can use
       the following commands:

            $ git tag
            $ git checkout Simbody-X.Y.Z

#### Configure and generate Makefiles

1. Create a directory in which we'll build Simbody. We'll assume you choose `~/simbody-build`. Don't choose a location inside `~/simbody-source`.

        $ mkdir ~/simbody-build
        $ cd ~/simbody-build

2. Configure your Simbody build with CMake. We'll use the `cmake` command but you could also use the interactive tools `ccmake` or `cmake-gui`. You have a few configuration options to play with here.

    * If you don't want to fuss with any options, run:

            $ cmake ~/simbody-source

    * Where do you want to install Simbody? By default, it is installed to `/usr/local/`. That's a great default option, especially if you think you'll only use one version of Simbody at a time. You can change this via the `CMAKE_INSTALL_PREFIX` variable. Let's choose `~/simbody`:

            $ cmake ~/simbody-source -DCMAKE_INSTALL_PREFIX=~/simbody

    * Do you want the libraries to be optimized for speed, or to contain debugger symbols? You can change this via the `CMAKE_BUILD_TYPE` variable. There are 4 options:
        - **Debug**: debugger symbols; no optimizations (more than 10x slower). Library and visualizer names end with `_d`.
        - **RelWithDebInfo**: debugger symbols; optimized. This is the configuration we recommend.
        - **Release**: no debugger symbols; optimized. Generated libraries and executables are smaller but not faster than RelWithDebInfo.
        - **MinSizeRel**: minimum size; optimized. May be slower than RelWithDebInfo or Release.

        You at least want optimized libraries (all configurations but Debug are optimized),
        but you can have Debug libraries coexist with them. To do this, go through
        the full installation process twice, once for each configuration. It is
        typical to use a different build directory for each build type (e.g.,
        `~/simbody-build-debug` and `~/simbody-build-release`).

    * There are a few other variables you might want to play with:
        * `BUILD_EXAMPLES` to see what Simbody can do. On by default.
        * `BUILD_TESTING` to ensure your Simbody works
          correctly. On by default.
        * `BUILD_VISUALIZER` to be able to watch your system
          move about! If building on a cluster, you could turn this off. On by
          default.
        * `BUILD_DYNAMIC_LIBRARIES` builds the three libraries as dynamic libraries. On by default.
        * `BUILD_STATIC_LIBRARIES` builds the three libraries as static libraries, whose names will end with `_static`.
        * `BUILD_TESTS_AND_EXAMPLES_STATIC` if tests or examples are being built, creates statically-linked tests/examples. Can take a while to build, and it is unlikely you'll use the statically-linked libraries.
        * `BUILD_TESTS_AND_EXAMPLES_SHARED` if tests or examples are being built, creates dynamically-linked tests/examples. Unless you know what you're doing, leave this one on.

        You can combine all these options. Here's another example:

            $ cmake ~/simbody-source -DCMAKE_INSTALL_PREFIX=~/simbody -DCMAKE_BUILD_TYPE=RelWithDebInfo -DBUILD_VISUALIZER=off

#### Build and install

1. Build the API documentation. This is optional, and you can only do this if
   you have Doxygen. You will get warnings if your doxygen installation is a version older than Doxygen 1.8.8.

        $ make doxygen

2. Compile. Use the `-jn` flag to build using `n` processor cores. For example:

        $ make -j8

3. Run the tests.

        $ ctest -j8

4. Install. If you chose `CMAKE_INSTALL_PREFIX` to be a location which requires sudo access to write to (like `/usr/local/`, prepend this command with a `sudo `.

        $ make -j8 install

Just so you know, you can also uninstall (delete all files that CMake placed into `CMAKE_INSTALL_PREFIX`) if you're in `~/simbody-build`.

    $ make uninstall


#### Play around with examples

From your build directory, you can run Simbody's example programs. For instance, try:

        $ ./ExamplePendulum


#### Set environment variables and test the installation

If you are only building Simbody to use it with OpenSim, you can skip this section.

1. Allow executables to find Simbody libraries (.dylib's or so's) by adding the
   Simbody lib directory to your linker path. On Mac, most users can skip
   this step.
    * If your `CMAKE_INSTALL_PREFIX` is `/usr/local/`, run:

            $ sudo ldconfig

    * If your `CMAKE_INSTALL_PREFIX` is neither `/usr/` nor `/usr/local/` (e.g., `~/simbody`'):
        * Mac:

                $ echo 'export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:~/simbody/lib' >> ~/.bash_profile
        * Ubuntu:

                $ echo 'export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:~/simbody/lib/x86_64-linux-gnu' >> ~/.bashrc
        These commands add a line to a configuration file that is loaded every
        time you open a new terminal. If using Ubuntu, you may need to replace
        `x86_64-linux-gnu` with the appropriate directory on your computer.
2. Allow Simbody and other projects (e.g., OpenSim) to find Simbody. Make sure to replace `~/simbody` with your `CMAKE_INSTALL_PREFIX`.
    * Mac:

            $ echo 'export SIMBODY_HOME=~/simbody' >> ~/.bash_profile
    * Ubuntu:

            $ echo 'export SIMBODY_HOME=~/simbody' >> ~/.bashrc
3. Open a new terminal.
4. Test your installation:

        $ cd ~/simbody/share/doc/simbody/examples/bin
        $ ./SimbodyInstallTest # or ./SimbodyInstallTestNoViz

#### Layout of installation

The installation creates the following directories in `CMAKE_INSTALL_PREFIX`. The directory `[x86_64-linux-gnu]` only exists if you did NOT install to `/usr/local/` and varies by platform. Even in that case, the name of your directory may be different.

* `include/simbody/` the header (.h) files; necessary for projects that use Simbody.
* `lib/[x86_64-linux-gnu]/` shared libraries (.dylib's or .so's).
    * `cmake/simbody/` CMake files that are useful for projects that use Simbody.
    * `pkgconfig/` pkg-config files useful for projects that use Simbody.
    * `simbody/examples/` the examples, compiled into executables; run them! (Not installed for Debug builds.)
* `libexec/simbody/` the `simbody-visualizer` executable.
* `share/doc/simbody/` a few manuals, as well as API docs (`SimbodyAPI.html`).
    * `examples/src` source code for the examples.
    * `examples/bin` symbolic link to the runnable examples.


Mac and Homebrew
----------------

If using a Mac and Homebrew, the dependencies are taken care of for you.

#### Install

1. Install [Homebrew](http://brew.sh/).
2. Open a terminal.
3. Add the Open Source Robotics Foundation's list of repositories to Homebrew:
    ```
    $ brew tap osrf/simulation
    ```

2. Install the latest release of Simbody.
    ```
    $ brew install simbody
    ```
    To install from the master branch instead, append ` --HEAD` to the command above.

#### Where is Simbody installed?

Simbody is now installed to `/usr/local/Cellar/simbody/<version>/`,
where `<version>` is either the version number (e.g., `3.6.1`),
or `HEAD` if you specified `--HEAD` above.

Some directories are symlinked (symbolically linked) to `/usr/local/`, which is where your system typically expects to find executables, shared libraries (.dylib's), headers (.h's), etc. The following directories from the Simbody installation are symlinked:

* `include/simbody   -> /usr/local/include/simbody`
* `lib               -> /usr/local/lib`
* `share/doc/simbody -> /usr/local/share/doc/simbody`

#### Layout of installation

What's in the `/usr/local/Cellar/simbody/<version>/` directory?

* `include/simbody/` the header (.h) files; necessary for projects that use Simbody.
* `lib/` shared libraries (.dylib's), used at runtime.
    * `cmake/simbody/` CMake files that are useful for projects that use Simbody.
    * `pkgconfig/` pkg-config files useful for projects that use Simbody.
    * `simbody/examples/` the examples, compiled into executables; run them! (Not installed for Debug builds.)
* `libexec/simbody/` the `simbody-visualizer` executable.
* `share/doc/simbody/` a few manuals, as well as API docs (`SimbodyAPI.html`).
    * `examples/src` source code for the examples.
    * `examples/bin` symbolic link to executable examples.

Ubuntu and apt-get
------------------

Starting with Ubuntu 15.04, Simbody is available in the Ubuntu (and Debian) repositories. You can see a list of all simbody packages for all Ubuntu versions at the [Ubuntu Packages website](http://packages.ubuntu.com/search?keywords=simbody&searchon=names&suite=all&section=all). The latest version of Simbody is usually not available in the Ubuntu repositories; the process for getting a new version of Simbody into the Ubuntu repositories could take up to a year.

#### Install

1. Open a terminal and run the following command:

        $ sudo apt-get install libsimbody-dev simbody-doc

#### Layout of installation

Simbody is installed into the `usr/` directory.  The directory
`[x86_64-linux-gnu]` varies by platform.

* `usr/include/simbody/` the header (.h) files; necessary for projects that use Simbody.
* `usr/lib/[x86_64-linux-gnu]` shared libraries (.so's).
    * `cmake/simbody/` CMake files that are useful for projects that use Simbody.
    * `pkgconfig/` pkg-config files useful for projects that use Simbody.
* `usr/libexec/simbody/` the `simbody-visualizer` executable.
* `usr/share/doc/simbody/` a few manuals, as well as API docs (`SimbodyAPI.html`).
    * `examples/src` source code for the examples.
    * `examples/bin` symbolic link to executable examples.

FreeBSD and pkg
---------------

Simbody is available via the FreeBSD package repository.

#### Install

1. Open a terminal and run the following command:

        $ sudo pkg install simbody

Windows using MinGW
-------------------

Warning: The [MinGW](http://sourceforge.net/projects/mingw-w64/)
generation and build is experimental!

This build is still experimental, because of :

* the various MinGW versions available (Thread model, exception mechanism)
* the compiled libraries Simbody depends on (Blas, Lapack and optionnaly glut).

Below are three sections that gives a list of supported versions, command line
instructions, and reasons why is it not so obvious to use MinGW.

#### Supported MinGW versions

If you do not want to go into details, you need a MinGW version with :

* a Posix thread model and Dwarf exception mechanism on a 32 bit computer
* a Posix thread model and SJLJ exception mechanism on a 64 bit computer

Other versions are supported with additional configurations.

The table below lists the various versions of MinGW versions tested:

|   | OS      | Thread | Exception | Comment                                                             | URL                                           |
| - | ------- | ------ | --------- | ------------------------------------------------------------------- | --------------------------------------------- |
| 1 | 64 Bits | Posix  | SJLJ      | All features supported, all binary included (Recommended version)   | [MinGW64 GCC 5.2.0][mingw_520_64_posix_sjlj]  |
| 2 | 64 Bits | Posix  | SEH       | Needs to be linked against user's Blas and Lapack                   | [MinGW64 GCC 5.2.0][mingw_520_64_posix_seh]   |
| 3 | 32 Bits | Posix  | Dwarf     | No visualization, all binary included                               | [MinGW64 GCC 5.2.0][mingw_520_32_posix_dwarf] |
| 4 | 32 Bits | Posix  | SJLJ      | No visualization, needs to be linked against user's Blas and Lapack | [MinGW64 GCC 5.2.0][mingw_520_32_posix_sjlj]  |

We recommend to use the first configuration where all features are supported and
does not need additional libraries to compile and run.
The URL allows to download directly this version.
The second version needs to be linked against user's Blas and Lapack
(A CLI example is given below).
Blas and Lapack sources can be downloaded from
[netlib](http://www.netlib.org/lapack/lapack-3.5.0.tgz).
For the 3rd and 4th versions that run that target a 32 bit behaviour,
visualization is not possible for the time being.
(It is due to a compile and link problem with `glut`).
Moreover for the 4th one, one needs to provide Blas and Lapack libraries.

Please note that only Posix version of MinGW are supported.

If your version is not supported, CMake will detect it while configuring and stops.

#### Instructions

Below are some examples of command line instructions for various cases.
It is assumed you are running commands from a build directory, that can access Simbody source with a command `cd ..\simbody`.

It is recommended to specify with the installation directory with flag `CMAKE_INSTALL_PREFIX`
(e.g. `-DCMAKE_INSTALL_PREFIX="C:\Program Files\Simbody"`).
If not used, the installation directory will be `C:\Program Files (x86)\Simbody`
on a 64 bit computer. This might be confusing since it is the 32 bit installation location.

Example of instructions where one uses Blas and Lapack libraries provided (to be used in a Windows terminal, where MinGW is in the PATH):

    rem CMake configuration
    cmake ..\simbody -G "MinGW Makefiles" -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX="C:\Program Files\Simbody"
    rem Compilation
    mingw32-make
    rem Test
    mingw32-make test
    rem Installation
    mingw32-make install

Example of instructions where one uses Blas and Lapack libraries provided (to be used in a Windows terminal, where MinGW is NOT in the PATH):

    rem Variable and path definition
    set CMAKE="C:\Program Files\CMake\bin\cmake.exe"
    set MinGWDir=C:\Program Files\mingw-w64\i686-5.2.0-posix-sjlj-rt_v4-rev0\mingw32
    set PATH=%MinGWDir%\bin;%MinGWDir%\i686-w64-mingw32\lib
    rem CMake configuration
    %CMAKE% ..\simbody -G"MinGW Makefiles" -DCMAKE_BUILD_TYPE=Release ^
     -DCMAKE_INSTALL_PREFIX="C:\Program Files\Simbody" ^
     -DCMAKE_C_COMPILER:PATH="%MinGWDir%\bin\gcc.exe" ^
     -DCMAKE_CXX_COMPILER:PATH="%MinGWDir%\bin\g++.exe" ^
     -DCMAKE_MAKE_PROGRAM:PATH="%MinGWDir%\bin\mingw32-make.exe"
    rem Compilation
    mingw32-make
    rem Test
    mingw32-make test
    rem Installation
    mingw32-make install

Example of instructions where one uses Blas and Lapack libraries provided (to be used in a MSYS terminal with MinGW in the PATH):

    # CMake configuration
    cmake ../simbody -G "MSYS Makefiles" -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX="C:\Program Files\Simbody"
    # Compilation
    make
    # Test
    make test
    # Installation
    make install

Example of instructions where one provides our own Blas and Lapack libraries (to be used in a MSYS terminal with MinGW in the PATH):

    # CMake configuration
    cmake ../simbody -G"MSYS Makefiles" -DCMAKE_BUILD_TYPE=Release \
    -DCMAKE_INSTALL_PREFIX="C:\Program Files\Simbody" \
    -DCMAKE_C_COMPILER:PATH="C:\Program Files\mingw-w64\i686-5.2.0-posix-sjlj-rt_v4-rev0\mingw32\bin\gcc.exe" \
    -DCMAKE_CXX_COMPILER:PATH="C:\Program Files\mingw-w64\i686-5.2.0-posix-sjlj-rt_v4-rev0\mingw32\bin\g++.exe" \
    -DBUILD_USING_OTHER_LAPACK:PATH="C:\Program Files\lapack-3.5.0\bin\liblapack.dll;C:\Program Files\lapack-3.5.0\bin\libblas.dll"
    make
    # Test
    make test
    # Installation
    make install


#### MinGW details

This paragraph explains the reason why one can not use any MinGW version.

MinGW is available with two thread models :

* Win32 thread model
* Posix thread model

One has to use the Posix thread model, since all thread functionalities (e.g. `std:mutex`) are not implemented.

To ease building on Windows, Simbody provides compiled libraries for Blas and Lapack :

* On Windows 32 Bits, these were compiled with a Dwarf exception mechanism,
* On Windows 64 Bits, these were compiled with a SJLJ exception mechanism.

If one chooses a MinGW compilation, we need to respect this exception mechanism.
A program can not rely on both mechanisms.
This means that if we want to use the compiled libraries, our MinGW installation should
have the same exception mechanism.
Otherwise, we need to provide our own Blas and Lapack libraries.

To see which exception mechanism is used, user can look at dlls located in the `bin` directory of MinGW.
The name of mechanism is present in the file `libgcc_XXXX.dll`, where `XXXX` can be `dw`, `seh` or `sjlj`.
For some MinGW versions, this information is also available by looking at the result of `gcc --version`.

CMake will check the version of your MinGW, and if the exception mechanism is different,
then the configuration stops because of this difference.
If one provides Blas and Lapack libraries with the CMake variable `BUILD_USING_OTHER_LAPACK`,
compilation with MinGW is always possible.

Windows, Mac, and Linux Using Conda
-----------------------------------

[Conda](http://conda.pydata.org) is a cross platform package manager that can
be used to install Simbody on Windows, Mac, or Linux. To install Simbody using
Conda you must first install
[Miniconda](http://conda.pydata.org/miniconda.html) or
[Anaconda](https://www.continuum.io/downloads). Either of these will provide
the `conda` command which can be invoked at the command line to install Simbody
from the [Conda Forge](https://conda-forge.github.io/) channel as follows:

```
$ conda install -c conda-forge simbody
```

This command will install Simbody (both the libraries and headers) into
the Miniconda or Anaconda installation directory as per the standard layout for
each of the operating systems described above. The Conda Forge Simbody recipe
can be found in Conda Forge's [feedstock
repository](https://github.com/conda-forge/simbody-feedstock).

Acknowledgments
---------------
We are grateful for past and continuing support for Simbody's development in Stanford's Bioengineering department through the following grants:

- NIH U54 GM072970 (Simulation of Biological Structures)
- NIH U54 EB020405 (Mobilize Center)
- NIH R24 HD065690 (Simulation in Rehabilitation Research)
- OSRF subcontract 12-006 to DARPA HR0011-12-C-0111 (Robotics Challenge)

Prof. Scott Delp is the Principal Investigator on these grants and Simbody is used extensively in Scott's [Neuromuscular Biomechanics Lab](https://nmbl.stanford.edu) as the basis for the [OpenSim](http://opensim.stanford.edu) biomechanical simulation software application for medical research.



[buildstatus_image_travis]: https://travis-ci.org/simbody/simbody.svg?branch=master
[travisci]: https://travis-ci.org/simbody/simbody
[buildstatus_image_appveyor]: https://ci.appveyor.com/api/projects/status/2dua0qna2m85fts2/branch/master?svg=true
[appveyorci]: https://ci.appveyor.com/project/opensim-org/simbody/branch/master
[buildstatus_image_codecov]: https://codecov.io/gh/simbody/simbody/branch/master/graph/badge.svg
[codecovci]: https://codecov.io/gh/simbody/simbody
[user]: https://github.com/simbody/simbody/raw/master/Simbody/doc/SimbodyAndMolmodelUserGuide.pdf
[rna]: doc/images/simbios_11000_body_RNA.gif
[simbios]: http://simbios.stanford.edu/
[doublePendulum]: doc/images/doublePendulum.gif
[thy]: https://github.com/simbody/simbody/raw/master/Simbody/doc/SimbodyTheoryManual.pdf
[flores]: http://xray.bmc.uu.se/flores/Home.html
[buildwin]: https://github.com/simbody/simbody/raw/master/doc/HowToBuildSimbodyFromSource_Windows.pdf
[buildunix]: https://github.com/simbody/simbody/raw/master/doc/HowToBuildSimbodyFromSource_MacLinux.pdf
[mingw_520_64_posix_sjlj]: http://sourceforge.net/projects/mingw-w64/files/Toolchains%20targetting%20Win64/Personal%20Builds/mingw-builds/5.2.0/threads-posix/sjlj/x86_64-5.2.0-release-posix-sjlj-rt_v4-rev0.7z/download
[mingw_520_64_posix_seh]: http://sourceforge.net/projects/mingw-w64/files/Toolchains%20targetting%20Win64/Personal%20Builds/mingw-builds/5.2.0/threads-posix/seh/x86_64-5.2.0-release-posix-seh-rt_v4-rev0.7z/download
[mingw_520_32_posix_dwarf]: http://sourceforge.net/projects/mingw-w64/files/Toolchains%20targetting%20Win32/Personal%20Builds/mingw-builds/5.2.0/threads-posix/dwarf/i686-5.2.0-release-posix-dwarf-rt_v4-rev0.7z/download
[mingw_520_32_posix_sjlj]: http://sourceforge.net/projects/mingw-w64/files/Toolchains%20targetting%20Win32/Personal%20Builds/mingw-builds/5.2.0/threads-posix/sjlj/i686-5.2.0-release-posix-sjlj-rt_v4-rev0.7z/download