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

  1. Download and install Anaconda Individual Edition <https://www.anaconda.com/products/individual#Downloads>.

    The download will be a .sh file with a name like Anaconda3-2021.05-Linux-x86_64.sh. Open a terminal in the same directory as this file, and type the following to install Anaconda (replace the name of your .sh file below).

    bash Anaconda3-2021.05-Linux-x86_64.sh

    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). When prompted, you do not need to install Microsoft VSCode (but feel free to if you are looking for a lightweight IDE).

    Note that you should restart your terminal in order for the changes to take effect, as the installer will tell you.

  2. There are a few system-level dependencies which are required and should not be installed via Anaconda. These include Git for version control, GNU Make, and the C and C++ compilers from the GNU Compiler Collection (GCC) for compiling RMG.

    For Linux users, you can check whether these are already installed by simply calling them via the command line, which will let you know if they are missing. To install any missing packages, you should use the appropriate package manager for your system.

    On Ubuntu and Debian the package manager is apt

    sudo apt install git gcc g++ make

    On Fedora and Red Hat derivatives (RHEL 8+) the package manager is dnf

    sudo dnf install git gcc gcc-c++ make

    Replace dnf with yum in the preceding for Red Hat 7 and lower.

    On openSUSE the package manager is zypper:

    sudo zypper install git gcc gcc-c++ make

    On Manjaro or Arch Linux the package manager is pacman

    sudo pacman -S git gcc make

    For MacOS users, the above packages will not come preinstalled, but can be easily obtained by installing the XCode Command Line Tools. These are a set of packages relevant for software development which have been bundled together by Apple. The easiest way to install this is to simply run one of the commands in the terminal, e.g. git. The terminal will then prompt you on whether or not you would like to install the Command Line Tools.

    For MacOS users only, download and install the latest macOS julia from here: <https://julialang.org/downloads/>. Then add julia to PATH by running the following command replacing 1.6 with the first two numbers in the Julia version designation (ex: 1.6.2->1.6, 1.1.1->1.1)

    echo 'export PATH="/Applications/Julia-1.6.app/Contents/Resources/julia/bin:$PATH"' >> ~/.bash_profile
    export PATH="/Applications/Julia-1.6.app/Contents/Resources/julia/bin:$PATH"

    Note that this julia install will not respect conda environmental boundaries this means only one conda environment can be linked to it at a time. For linux users julia will be installed automatically.

  3. 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. Github has deprecated password authentication from the command line, so it is preferred to clone the repositories using ssh:

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

    It is still possible to clone the repositories using https if you are unfamiliar with ssh:

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

    For information on using ssh with GitHub see the Connecting to GitHub with SSH

  4. Now create the conda environment for RMG-Py

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

    If the command returns an error due to being unable to find the conda command, try to either close and reopen your terminal to refresh your environment variables or type the following command.

    If on Linux or pre-Catalina MacOS

    source ~/.bashrc

    If on MacOS Catalina or later

    source ~/.zshrc
  5. Activate conda environment

    conda activate rmg_env

    Note regarding differences between conda versions: Prior to Anaconda 4.4, the command to activate an environment was source activate rmg_env. It has since been changed to conda activate rmg_env due to underlying changes to standardize operation across different operating systems. However, a prerequisite to using the new syntax is having run the conda init setup routine, which can be done at the end of the install procedure if the user requests.

  6. Compile RMG-Py after activating the conda environment

  7. Modify environment variables. Add RMG-Py to the PYTHONPATH to ensure that you can access RMG modules from any folder. Also, add your RMG-Py folder to PATH to launch rmg.py from any folder.

    In general, these commands should be placed in the appropriate shell initialization file. For Linux users using bash (the default on distributions mentioned here), these should be placed in ~/.bashrc. For MacOS users using bash (default before MacOS Catalina), these should be placed in ~/.bash_profile, which you should create if it doesn’t exist. For MacOS users using zsh (default beginning in MacOS Catalina), these should be placed in ~/.zshrc.

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

    NOTE: Make sure to change YourFolder to the path leading to the RMG-Py code. Not doing so will lead to an error stating that python cannot find the module rmgpy.

    Be sure to either close and reopen your terminal to refresh your environment variables (source ~/.bashrc or source ~/.zshrc).

  8. Install and Link Julia dependencies

    python -c "import julia; julia.install(); import diffeqpy; diffeqpy.install()"
    julia -e 'using Pkg; Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="main")); using ReactionMechanismSimulator;'

    Note that this links your python to python-jl enabling calls to Julia through pyjulia. Occasionally programs will interact with python-jl differently than the default python. If this occurs for you we recommend doing that operation in a different conda environment. However, if convenient you can undo this linking by replacing python-jl with python3 in the second command above. Just make sure to rerun the linking command once you are done.

  9. Finally, you can run RMG from any location by typing the following (given that you have prepared the input file as input.py in the current folder).

    python-jl replace/with/path/to/rmg.py input.py
  10. 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, Arkane, as well as any of the Standalone Modules included in the RMG-Py package. 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. Make sure that the environment is active before running the tests: conda activate rmg_env.

  1. Unit test suite: this will run all the unit tests in the rmgpy and arkane packages

    cd RMG-Py
    make test
  2. Functional test suite: this will run all the functional tests in the rmgpy and arkane packages

    cd RMG-Py
    make test-functional
  3. 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 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.

  1. 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
  2. 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
  3. 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
  4. 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