MESS

Master Equation System Solver

The primary purpose of the program is to calculate temperature and pressure dependent rate coefficients for complex-forming reactions via solution of the one-dimensional master equation. Ancillary calculations of various quantities (e.g., stabilization probabilities for microcanonical initial distributions, microcanonical rate constants, partition functions, and related thermochemical information, time dependent propagation of species populations, etc.) are also available.

Requirements

To build MESS, the following libraries are required:
BLAS
LAPACK
SLATEC https://github.com/Auto-Mech/SLATEC
MPACK https://github.com/Auto-Mech/MPACK

Direct Installation using Conda

The most direct way to install the code is through the conda package manager. If you have conda installed,
(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.

Alternatively, we also recommend building our own pre-set Auto-Mech environment, which includes MESS and all its dependencies. This environment can be created and activated with the commands:

conda env create auto-mech/amech-env
conda activate amech-env

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.

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.

Download SLATEC and MPACK from GitHub, and install them in a location that your system can find them.

With SLATEC and MPACK installed, run build.sh, which uses cmake to compile MESS.

bash build.sh

Note that the results of the make install command in build.sh will depend on your system setup.

Reference

See Y. Georgievskii, J. A. Miller, M. P. Burke, and S. J. Klippenstein, Reformulation and Solution of the Master Equation for Multiple-Well Chemical Reactions, J. Phys. Chem. A, 117, 12146-12154 (2013).

Acknowledgment

This work was supported by the U.S. Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences under DOE Contract Number DE-AC02-06CH11357 as well as the Exascale Computing Project (ECP), Project Number: 17-SC-20-SC. The ECP is a collaborative effort of two DOE organizations, the Office of Science and the National Nuclear Security Administration, responsible for the planning and preparation of a capable exascale ecosystem including software, applications, hardware, advanced system engineering, and early test bed platforms to support the nation's exascale computing imperative.

Notice

Copyright (c) 2018 Yuri Georgievski (ygeorgi@anl.gov), Stephen J. Klippenstein (sjk@anl.gov), and Argonne National Laboratory.

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.