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===========================================================================
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tsscds. A computer program for finding reaction mechanisms and solving the
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kinetics.
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Copyright (C) 2018 Emilio Martinez-Nunez, Aurelio Rodriguez, Roberto
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Rodriguez-Fernandez, Saulo Vazquez-Rodriguez, George L. Barnes and
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James J. P. Stewart
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baaden |
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tsscds |
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This program is free software: you can redistribute it and/or modify
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it under the terms of the GNU General Public License as published by
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the Free Software Foundation, either version 3 of the License, or
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any later version.
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This program is distributed in the hope that it will be useful,
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but WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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GNU General Public License for more details.
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You should have received a copy of the GNU General Public License
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along with this program. If not, see <http://www.gnu.org/licenses/>.
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===========================================================================
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====================DESCRIPTION OF THE FILES/FOLDERS=======================
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The following files are needed or generated during configuration/installation
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steps and, therefore, they should not be edited:
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aclocal.m4
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ChangeLog
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config.log
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config.status
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configure
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configure.ac
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install-sh
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Makefile
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Makefile.am
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Makefile.in
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missing
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AUTHORS. This file contains a list of the authors of the program.
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docs. This folder contains tutorial.pdf, which should be printed out to consult
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instructions about the installation and execution of the program.
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examples. This folder contains several input files for testing purposes. The
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instructions are given in tutorial.pdf
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license.txt. GNU general public license.
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modules. This is a folder with the 2018 module that the user should load before
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the execution of the program as detailed in the tutorial.pdf.
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NEWS. A file with the news about the program.
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README. This file.
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scripts. This is a folder that contains all Bash and Python scripts for the specific
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tasks.
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share. This folder contains different (MOPAC/G09) template input files as well as
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other common files.
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src. The folder contains the fortran90 source files that need to be compiled.
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===========================================================================
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====================INSTALLATION INSTRUCTIONS==============================
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Untar and unzip the file tsscds-SOURCE-2018.tar.gz:
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tar xvfz tsscds-SOURCE-2018.tar.gz
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Before installing tsscds, be aware that the following packages are needed:
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bc, environment-modules, gawk, gcc, gfortran, parallel, python-numpy, python-scipy, sqlite3, zenity
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You can install the missing ones manually, or you can use install-required-packages-distro.sh (where distro=ubuntu-16.4lts, centos7 or sl7), which will do the work for you. The ubuntu-16.4lts script installs all dependencies, but for the RHEL derivatives (centos7 and sl7) you have to install parallel separately, and you have two choices:
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a) install-gnu-parallel-from-source.sh. This script installs parallel latest version from source thanks to Ole Tange (the author). Also it can fallback to a user private installation into $HOME/bin if you have not administrator permisions to install it globally.
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b) install-gnu-parallel-from-epel.sh. Enables the EPEL repository and installs parallel from it.
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To use any of the above scripts, first go to the tsscds-SOURCE-2018 folder:
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cd tsscds-SOURCE-2018
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The program runs using two levels of theory: semiempirical (or Low-Level LL) and ab initio/DFT (or High-Level HL). So far, the only program interfaced with tsscds to perform the ab initio/DFT calculations is G09. Therefore, if you want to perform the HL calculations G09 should be installed and should run like in this example: g09<inputfile>outputfile
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These packages might also be useful to analyze the results:
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gnuplot, molden, sqlitebrowser
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Once the above packages are installed, go to the tsscds-SOURCE-2018 folder (if you are not already there) to configure and install the package:
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cd tsscds-SOURCE-2018
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./configure
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This will install tsscds2018 in $HOME/tsscds-2018 by default. If you want to install it in a different directory, type:
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./configure --prefix=path_to_program
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Finally, complete the installation:
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make
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make install
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make clean
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The last command (make clean) is only necessary if you want to remove from the src directory the object files and executables created in the compilation process.
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For convenience, and once “Environment Modules” has been installed, you can add to your .bashrc file the following line to use the tsscds module:
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module use path_to_program/modules
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where path_to_program is the path where you installed tsscds (e.g., $HOME/tsscds-2018).
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THIS IS JUST FOR DEVELOPERS:
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-run 'autoreconf -i' after svn check out
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===========================================================================
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====================PROGRAM EXECUTION======================================
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To start using any of the scripts of the program, you have to load tsscds/2018 module:
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module load tsscds/2018
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Then, please follow the instructions given in the tutorial, which can be found in:
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tsscds-SOURCE-2018/docs/tutorial.pdf or
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path_to_program/doc/tutorial.pdf
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===========================================================================
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