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transition state search using dynamics
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{{colorbox |text=<strong>Transition State Search Using Chemical Dynamics Simulations</strong> |color=silver |bordercolor=white }} 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\\ [mailto: 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 | http://forge.cesga.es/frs/?group_id=77&release_id=21]\\ Method described in these two publications: [1 | http://onlinelibrary.wiley.com/doi/10.1002/jcc.23790/abstract] [2 | http://pubs.rsc.org/en/content/articlelanding/2015/cp/c5cp02175h#!divAbstract] =========================================================================== 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 *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 ===========================================================================