3.3.1. Installation by Source Using Anaconda Environment for Unix-based Systems: Linux and Mac OSX¶
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).
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/YourUsernamein 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.
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
sudo apt install git gcc g++ make
On Fedora and Red Hat derivatives (RHEL 8+) the package manager is
sudo dnf install git gcc gcc-c++ make
yumin the preceding for Red Hat 7 and lower.
On openSUSE the package manager is
sudo zypper install git gcc gcc-c++ make
On Manjaro or Arch Linux the package manager is
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.
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
git clone firstname.lastname@example.org:ReactionMechanismGenerator/RMG-Py.git git clone email@example.com:ReactionMechanismGenerator/RMG-database.git
It is still possible to clone the repositories using
httpsif you are unfamiliar with
git clone https://github.com/ReactionMechanismGenerator/RMG-Py.git git clone https://github.com/ReactionMechanismGenerator/RMG-database.git
For information on using
sshwith GitHub see the Connecting to GitHub with SSH
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
condacommand, 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
If on MacOS Catalina or later
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_envdue to underlying changes to standardize operation across different operating systems. However, a prerequisite to using the new syntax is having run the
conda initsetup routine, which can be done at the end of the install procedure if the user requests.
Compile RMG-Py after activating the conda environment
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.pyfrom 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
export PYTHONPATH=YourFolder/RMG-Py/:$PYTHONPATH export PATH=YourFolder/RMG-Py/:$PATH
NOTE: Make sure to change
YourFolderto the path leading to the
RMG-Pycode. Not doing so will lead to an error stating that python cannot find the module
Be sure to either close and reopen your terminal to refresh your environment variables (
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.
Finally, you can run RMG from any location by typing the following (given that you have prepared the input file as
input.pyin the current folder).
python-jl replace/with/path/to/rmg.py input.py
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
You may now use RMG-Py, Arkane, as well as any of the Standalone Modules included in the RMG-Py package.
184.108.40.206. 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.
Unit test suite: this will run all the unit tests in the
cd RMG-Py make test
Functional test suite: this will run all the functional tests in the
cd RMG-Py make test-functional
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
220.127.116.11. 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
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
cd RMG-Py make eg2
Liquid Phase Example: this will run a liquid phase RMG model. The results will be in the
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
cd RMG-Py make eg4