README.md

Mechanica

Mechanica is an interactive, particle-based physics, chemistry and biology modeling and simulation environment. Mechanica provides the ability to create, simulate and explore models, simulations and virtual experiments of soft condensed matter physics at mulitple scales using a simple, intuitive interface. Mechanica is designed with an emphasis on problems in complex subcellular, cellular and tissue biophysics. Mechanica enables interactive work with simulations on heterogeneous computing architectures, where models and simulations can be built and interacted with in real-time during execution of a simulation, and computations can be selectively offloaded onto available GPUs on-the-fly. Mechanica is part of the Tellurium project.

Mechanica is a native compiled C++ shared library that's designed to be used for model and simulation specification in compiled C++ code. Mechanica includes an extensive Python API that's designed to be used for model and simulation specification in executable Python scripts, an IPython console and a Jupyter Notebook. Mechanica currently supports installations on 64-bit Windows, Linux and MacOS systems.

To get the latest version of Mechanica,

To run Mechanica online in JupyterLab,

Build Status

Binaries

The latest Mechanica developments are archived at the Mechanica Azure project.

Platform	Status
Linux
MacOS
Windows

Documentation

Mechanica documentation is available online,

Document	Link	Status
Mechanica Documentation	link
C++ API Documentation	link
Python API Documentation	link
C Library API Documentation	link

Installation

Pre-Built Binaries

Binary distributions of Mechanica are available via conda from the mechanica channel,

conda install -c mechanica mechanica

Pre-built binaries of the latest Mechanica developments are also archived at the Mechanica Azure project. Installing pre-built binaries requires Miniconda. Binaries on Linux require the Mesa packages libgl1-mesa-dev and libegl1-mesa-dev. Packages include a convenience script mx_install_env that installs the dependencies of the Mechanica installation on execution. After installing the dependencies environment, the Mechanica installation can be used after executing the following steps from a terminal with the root of the installation as the current directory.

On Windows

call etc/mx_vars
conda activate %MXENV%

On Linux and MacOS

source etc/mx_vars.sh
conda activate $MXENV

Launching the provided examples are then as simple as the following

python examples/cell_sorting.py

Likewise Mechanica can be imported in Python scripts and interactive consoles

import mechanica as mx

From Source

Supported installation from source uses Git and Miniconda for building and installing most dependencies. In addition to requiring Git and Miniconda, installation from source on Windows requires Visual Studio 2019 Build Tools, on Linux requires the Mesa packages libgl1-mesa-dev and libegl1-mesa-dev, and on MacOS requires Xcode with 10.9 SDK or greater.

To execute the standard installation, open a terminal in a directory to install Mechanica and clone this respository,

git clone --recurse-submodules https://github.com/tjsego/mechanica

From the directory containing the mechanica root directory, perform the following.

On Windows

call mechanica/package/local/mx_install

On Linux

bash mechanica/package/local/mx_install.sh

On MacOS, specify the installed MacOS SDK (e.g., for 10.9)

export MXOSX_SYSROOT=10.9
bash mechanica/package/local/mx_install.sh

The standard installation will create the directories mechanica_build and mechanica_install next to the mechanica root directory, the former containing the build files, and the latter containing the installed binaries and conda environment. The source and build directories can be safely deleted after installation. The conda environment will be installed in the subdirectory mx_env. To activate the conda environment with the Mechanica Python module, perform the following.

On Windows

call mechanica_install/etc/mx_vars
conda activate %MXENV%

On Linux and MacOS

source mechanica_install/etc/mx_vars.sh
conda activate $MXENV

Launching the provided examples are then as simple as the following

python mechanica/examples/cell_sorting.py

Likewise Mechanica can be imported in Python scripts and interactive consoles

import mechanica as mx

Customizing the Build

Certain aspects of the installation can be readily customized. The source directory mechanica/package/local contains subdirectories linux and win containing scripts mx_install_vars.sh and mx_install_vars.bat for Linux/MacOS and Windows, respectively, which declare default installation environment variables. These environment variables can be customized to specify where to find, build and install Mechanica, as well as the build configuration. For example, to install Mechanica from a source directory MYMXSRC, build Mechanica at path MYMXBUILD in debug mode and install into directory MYMXINSTALL, perform the following.

On Windows

call %MYMXSRC%/package/local/win/mx_install_vars
set MXBUILD_CONFIG=Debug
set MXSRCDIR=%MYMXSRC%
set MXBUILDDIR=%MYMXBUILD%
set MXINSTALLDIR=%MYMXINSTALL%
call %MXSRCDIR%/package/local/win/mx_install_env
conda activate %MXENV%
call %MXSRCDIR%/package/local/win/mx_install_all

On Linux

source $MYMXSRC/package/local/linux/mx_install_vars.sh
export MXBUILD_CONFIG=Debug
export MXSRCDIR=$MYMXSRC
export MXBUILDDIR=$MYMXBUILD
export MXINSTALLDIR=$MYMXINSTALL
bash ${MXSRCDIR}/package/local/linux/mx_install_env.sh
conda activate $MXENV
bash ${MXSRCDIR}/package/local/linux/mx_install_all.sh

On MacOS

source $MYMXSRC/package/local/osx/mx_install_vars.sh
export MXBUILD_CONFIG=Debug
export MXSRCDIR=$MYMXSRC
export MXBUILDDIR=$MYMXBUILD
export MXINSTALLDIR=$MYMXINSTALL
bash ${MXSRCDIR}/package/local/osx/mx_install_env.sh
conda activate $MXENV
bash ${MXSRCDIR}/package/local/osx/mx_install_all.sh

The default Python version of the installation is 3.7, though Mechanica has also been tested on Windows, Linux and MacOS for Python versions 3.8 and 3.9. To specify a different version of Python, simply add a call to update the conda environment in the previous commands before calling mx_install_all.

Enabling Interactive Mechanica

Mechanica supports interactive modeling and simulation specification in an IPython console and Jupyter Notebook. To enable interactive Mechanica in an IPython console, activate the installed environment as previously described and install the ipython package from the conda-forge channel,

conda install -c conda-forge ipython

To enable interactive Mechanica in a Jupyter Notebook, activate the installed environment as previously described and install the notebook, ipywidgets and ipyevents packages from the conda-forge channel,

conda install -c conda-forge notebook ipywidgets ipyevents