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Transition State Search Using Chemical Dynamics Simulations

This program discovers reaction mechanisms and solves the kinetics in an automated fashion. TS guess structures are obtained from accelerated trajectory simulations, and minima/products from the IRC. Finally, the kinetics is solved using KMC

AUTHORS

Main developer:
Emilio Martínez-Núñez
Departamento de Química Física, Facultade de Química
Avda. das Ciencias s/n
15782 Santiago de Compostela, SPAIN
emilio.nunez@usc.es

With contributions from:
George L. Barnes
Aurelio Rodríguez
Roberto Rodríguez-Fernández
James J. P. Stewart
Saulo A. Vázquez

Download code & tutorial

Method described in these two publications: 1 2

LICENSE

A computer program for finding reaction mechanisms and solving the kinetics.
Copyright (C) 2018 Emilio Martinez-Nunez, Aurelio Rodriguez, Roberto Rodriguez-Fernandez, Saulo Vazquez-Rodriguez, George L. Barnes and James J. P. Stewart

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.

INSTALLATION INSTRUCTIONS

Before installing tsscds, be aware that the program makes use of the following packages that need to be installed in your linux distribution:

Environment Modules
G09
GNU parallel
Python2 (with Numpy and Scipy libraries)
SQLite3
Zenity3

Note: If you do not have G09, you will not be able to use the scripts for the high-level calculations, but you still will be able to use the low-level ones.

Once the above packages are installed, go to the tsscds-SOURCE-2018 folder and install the package

cd tsscds-SOURCE-2018

./configure

This will install tsscds2018 in $HOME/tsscds-2018 by default.

If you want to install it in a different directory, use

./configure --prefix=path_to_program

Finally, complete the installation

make

make install

For convenience, and once "Environment Modules" has been installed, you can add to your .bashrc file the following line to use the tsscds module:

module use path_to_program/modules

where path_to_program is the path where you installed tsscds (e.g., $HOME/tsscds-2018)

PROGRAM EXECUTION

To start using any of the scripts of the program, you have to load tsscds/2018 module

module load tsscds/2018

Then, please follow the instructions given in the tutorial