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

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/>.
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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 the scripts located 
in tsscds-SOURCE-2018 and called 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.

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

To run the low-level calculations use:

nohup llcalcs.sh molecule.dat ntasks niter runningtasks >llcalcs.log 2>&1 &

where:
molecule is the name of your molecule
ntasks is the number of tasks
niter is the number of iterations
runningtasks is the number of simultaneous tasks

To run the high-level calculations use:

nohup hlcalcs.sh molecule.dat runningtasks >hlcalcs.log 2>&1 &

For more details, follow the instructions given in the tutorial, which is located here:
path_to_program/doc/tutorial.pdf
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