3.2.1. Installation by Source Using Anaconda Environment for Unix-based Systems: Linux and Mac OSX

  • Download and install the Anaconda Python Platform for Python 2.7 (make sure not to install Python 3.0+, which is incompatible with RMG). When prompted to append Anaconda to your PATH, select or type Yes. Install the Anaconda folder inside your home directory (typically /home/YourUsername/ in Linux and /Users/YourUsername in Mac).

  • Install Git, the open source version control package through the Terminal. For Mac OS X: Git is already packages with OS X 10.9 or later, but requires installation of Xcode’s Command Line Tools. Skip the git installation and run it through the terminal, where you will be prompted to install the Command Line Tools if they are not already installed.

    sudo apt-get install git

  • Install the latest versions of RMG and RMG-database through cloning the source code via Git. Make sure to start in an appropriate local directory where you want both RMG-Py and RMG-database folders to exist.

    git clone https://github.com/ReactionMechanismGenerator/RMG-Py.git
git clone https://github.com/ReactionMechanismGenerator/RMG-database.git

  • Now create the anaconda environment for RMG-Py

    For Linux users:

    cd RMG-Py
conda env create -f environment_linux.yml

    For Mac users:

    cd RMG-Py
conda env create -f environment_mac.yml

  • Compile RMG-Py after activating the anaconda environment

    source activate rmg_env
make

  • Modify environment variables. Add RMG-Py to the PYTHONPATH to ensure that you can access RMG modules from any python prompt. Modify your ~/.bashrc file by adding the following line

    export PYTHONPATH=$PYTHONPATH:YourFolder/RMG-Py/

  • If you wish to always be able to run RMG-Py, you can modify the anaconda path to point to the RMG environment. Modify the following line in your ~/.bashrc file

    export PATH=~/anaconda/bin:$PATH

    by changing it to the following line

    export PATH=~/anaconda/envs/rmg_env/bin:$PATH

    be sure to either close and reopen your terminal to refresh your environment variables, or type the following command

    source ~/.bashrc

  • Optional: If you wish to use the QMTP interface with MOPAC to run quantum mechanical calculations for improved thermochemistry estimates of cyclic species, please obtain a legal license through the MOPAC License Request Form. Once you have it, type the following into your Terminal

    mopac password_string_here

You may now use RMG-Py, CanTherm, as well as any of the Standalone Modules included in the RMG-Py package.

3.2.1.1. Test Suite

There are a number of basic tests you can run on the newly installed RMG. It is recommended to run them regularly to ensure the code and databases are behaving normally.

  • Unit test suite: this will run all the unit tests in the rmgpy package

    cd RMG-Py
make test

  • Database test suite: this will run the database unit tests to ensure that groups, rate rules, and libraries are well formed

    cd RMG-Py
make test-database

3.2.1.2. Running Examples

A number of basic examples can be run immediately. Additional example input files can be found in the RMG-Py/examples folder. Please read more on Example Input Files in the documentation.

  • Minimal Example: this will run an Ethane pyrolysis model. It should take less than a minute to complete. The results will be in the RMG-Py/testing/minimal folder:

    cd RMG-Py
make eg1

  • Hexadiene Example: this will run a Hexadiene model with pressure dependence and QMTP. Note that you must have MOPAC installed for this to run. The results will be in the RMG-Py/testing/hexadiene folder:

    cd RMG-Py
make eg2

  • Liquid Phase Example: this will run a liquid phase RMG model. The results will be in the RMG-Py/testing/liquid_phase folder

    cd RMG-Py
make eg3

  • ThermoEstimator Example: this will run the Thermo Estimation Module on a few molecules. Note that you must have MOPAC installed for this to run completely. The results will be in the RMG-Py/testing/thermoEstimator folder

    cd RMG-Py
make eg4