Large-Scale Automated Mechanism Modeling
Intallation of Auto-Mech dependencies
We recommend building our own pre-set Auto-Mech dependency environment, which includes MESS. This environment can be created and activated with the commands:
conda env create auto-mech/amech-deps
conda activate amech-deps
If your Conda commands are not functioning, you may need to iniliatize Conda via the command
. /path/to/conda.sh
which places Conda executables in your PATH. The specific location of conda.sh depends on the Conda install. If you do not have Conda, it can be installed using the shell script debug/install-conda.sh.
Direct install of Auto-Mech codes
We are currently working on re-setting up the AutoMech codes for direct conda install. For now, please clone the dev versions of each of the AutoMech repositories from GitHub.
git clone --branch dev [email protected]:Auto-Mech/autoio.git
git clone --branch dev [email protected]:Auto-Mech/autofile.git
git clone --branch dev [email protected]:Auto-Mech/autochem.git
git clone --branch dev [email protected]:Auto-Mech/mechanalyzer.git
git clone --branch dev [email protected]:Auto-Mech/mechdriver.git
And put them in your python path by running the following fake-install.sh bash script with
. ./fake-install.sh
Next up:
Individual Installation using Conda
To add invidual AutoMech packages to an existing conda environment through the conda package manager
(1) activate an environment in you wish to use to install MESS, and
(2) run the install command:
conda install -c auto-mech mess
If you do not have a preferred Conda environment set up, an empty environment with no packages can be created and activated with the following commands
conda create --name myenv
conda activate myenv
where myenv should be replaced with your preferred name for the environment.
Available packages:
Building from source using Conda environment for dependencies
To build the code from source for development or debugging purposes, first create a conda environment with the necessary dependencies as follows:
conda env create -f environment.yml
which will create the mess-env environment. You can then activate the environment and build the code as follows:
conda activate mess-env
bash debug/build.sh
To put the MESS executables in your PATH, you can then run
. debug/fake-install.sh
Note that the above command does not permanently alter your PATH, it only affects PATH for the current login session.
Building from source without Conda
This is not the advised way to install, since the user will have to deal with their specific system setup. Each package will have its own dependencies that are given in the README. These will need to be installed.
bash build.sh
Note that the results of the make install command in build.sh will depend on your system setup.
©2022, Sarah N Elliott |