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tsscds. 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.
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====================INSTALLATION INSTRUCTIONS==============================
Untar and unzip the file tsscds-SOURCE-2018.tar.gz:

	tar xvfz tsscds-SOURCE-2018.tar.gz

Before installing tsscds, be aware that the following packages are needed:

bc, environment-modules, gawk, gcc, gfortran, parallel, python-numpy, python-scipy, sqlite3, zenity

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:

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.
b) install-gnu-parallel-from-epel.sh. Enables the EPEL repository and installs parallel from it.

To use any of the above scripts, first go to the tsscds-SOURCE-2018 folder:

       cd tsscds-SOURCE-2018

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
These packages might also be useful to analyze the results:

gnuplot, molden, sqlitebrowser

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:

	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, type:

./configure --prefix=path_to_program

Finally, complete the installation:

	make
	make install
	make clean

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.

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
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====================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

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