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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
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
Method described in these two publications: 1 2
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/.
DESCRIPTION OF THE FILES/FOLDERS
The following files are needed or generated during configuration/installation steps and, therefore, they should not be edited:
aclocal.m4
ChangeLog
config.log
config.status
configure
configure.ac
install-sh
Makefile
Makefile.am
Makefile.in
missing
AUTHORS. This file contains a list of the authors of the program.
docs. This folder contains tutorial.pdf, which should be printed out to consult instructions about the installation and execution of the program.
examples. This folder contains several input files for testing purposes. The instructions are given in tutorial.pdf
license.txt. GNU general public license.
modules. This is a folder with the 2018 module that the user should load before the execution of the program as detailed in the tutorial.pdf.
NEWS. A file with the news about the program.
README. This file.
scripts. This is a folder that contains all Bash and Python scripts for the specific tasks.
share. This folder contains different (MOPAC/G09) template input files as well as other common files.
src. The folder contains the fortran90 source files that need to be compiled.
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
- 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)
THIS IS JUST FOR DEVELOPERS:
- run 'autoreconf -i' after svn check out
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, which can be found in: tsscds-SOURCE-2018/docs/tutorial.pdf or path_to_program/doc/tutorial.pdf