3.3.2. MacOS X InstallationΒΆ

There are a number of dependencies for RMG-Py. This page will guide you through installing them. You will need the Command Line Tools for XCode. If you are not using Anaconda to install RMG-Py, we highly recommend the Homebrew package manager. The following instructions assume that you have installed Homebrew and its requirements. We recommend using a Virtual Environment for your Python packages, but this is optional (without it you may need to add sudo before some commands to solve permission errors).

You will also need gfortran, Python, Numpy and Scipy. We typically install them using homebrew-python but other methods may work as well.

  • For example:

    brew tap homebrew/python
    brew install numpy
    brew install scipy
    brew install matplotlib --with-cairo --with-ghostscript --with-ticl-tk --with-pyqt --with-pygtk --withgtk3
    
  • Install git if you don’t already have it (you may also like some graphical interfaces like mxcl’s GitX or GitHub for Mac):

    brew update
    brew install git
    
  • Optional (but recommended for Nitrogen-chemistry nomenclature): install OpenBabel:

    brew install open-babel --with-python --HEAD
    
  • Install RDKit:

    brew tap rdkit/rdkit
    brew install rdkit --with-inchi
    brew link --overwrite rdkit
    

    You’ll need to set an environment variable to use it, eg. put this in your ~/.bash_profile file:

    export RDBASE=/usr/local/share/RDKit
    
  • Make a directory to put everything in:

    mkdir ~/Code
    
  • Get the RMG-Py source code and the RMG-database from GitHub:

    cd ~/Code
    git clone https://github.com/ReactionMechanismGenerator/RMG-database.git
    git clone https://github.com/ReactionMechanismGenerator/RMG-Py.git
    
  • Install the Python dependencies listed in the RMG-Py/requirements.txt file using pip (do easy_install pip if you don’t already have it):

    pip install -r RMG-Py/requirements.txt
    
  • Get and build PyDQED:

    cd ~/Code
    git clone https://github.com/ReactionMechanismGenerator/PyDQED.git
    cd PyDQED
    export LIBRARY_PATH=$(dirname $(gfortran -print-file-name=libgfortran.a))
    make
    make install
    
  • Get and build PyDAS:

    cd ~/Code
    git clone https://github.com/ReactionMechanismGenerator/PyDAS.git
    cd PyDAS
    export LIBRARY_PATH=$(dirname $(gfortran -print-file-name=libgfortran.a))
    make
    make install
    
  • Build RMG-Py:

    cd ~/Code/RMG-Py
    make -j4
    
  • Run an example:

    cd ~/Code/RMG-Py/
    python rmg.py examples/rmg/minimal/input.py
    

    Verify your installation by opening the resulting output.html file under the “examples/rmg/minimal” directory.

    You can also use the Makefile targets to test and run examples:

    cd ~/Code/RMG-Py/
    make test
    make eg1
    make eg2
    

To run with on-the-fly Quantum Mechanics calculations, you will also need to install MOPAC or Gaussian, then run make QM.