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	revision 269, Fri Apr 27 17:48:47 2018 UTC	revision 271, Fri Apr 27 22:16:02 2018 UTC
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19	along with this program.  If not, see <http://www.gnu.org/licenses/>.	along with this program.  If not, see <http://www.gnu.org/licenses/>.
20	===========================================================================	===========================================================================
21
	====================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.
	===========================================================================
22	====================INSTALLATION INSTRUCTIONS==============================	====================INSTALLATION INSTRUCTIONS==============================
23	Untar and unzip the file tsscds-SOURCE-2018.tar.gz:	Untar and unzip the file tsscds-SOURCE-2018.tar.gz:
24
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26
27	Before installing tsscds, be aware that the following packages are needed:	Before installing tsscds, be aware that the following packages are needed:
28
29	bc, environment-modules, gawk, gcc, gfortran, parallel, python-numpy, python-scipy, sqlite3, zenity	bc, environment-modules, gawk, gcc, gfortran, parallel, python-numpy,
30		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:
31
32	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.	You can install the missing ones manually, or you can use the scripts located
33	b) install-gnu-parallel-from-epel.sh. Enables the EPEL repository and installs parallel from it.	in tsscds-SOURCE-2018 and called install-required-packages-distro.sh (where
34		distro=ubuntu-16.4lts, centos7 or sl7), which will do the work for you. The
35	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.	ubuntu-16.4lts script installs all dependencies, but for the RHEL derivatives
36		(centos7 and sl7) you have to install parallel separately, and you have two choices:
37
38		a) install-gnu-parallel-from-source.sh. This script installs parallel latest
39		version from source thanks to Ole Tange (the author). Also it can fallback to
40		a user private installation into $HOME/bin if you have not administrator permisions
41		to install it globally.
42
43		b) install-gnu-parallel-from-epel.sh. Enables the EPEL repository and installs
44		parallel from it.
45
46		The program runs using two levels of theory: semiempirical (or Low-Level LL) and
47		ab initio/DFT (or High-Level HL). So far, the only program interfaced with tsscds
48		to perform the ab initio/DFT calculations is G09. Therefore, if you want to perform
49		the HL calculations G09 should be installed and should run like in this example:
50		g09<inputfile>outputfile.
51
52	These packages might also be useful to analyze the results:	These packages might also be useful to analyze the results:
53
54	gnuplot, molden, sqlitebrowser	gnuplot, molden, sqlitebrowser
55
56	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:	Once the above packages are installed, go to the tsscds-SOURCE-2018 folder
57		(if you are not already there) to configure and install the package:
58
59	cd tsscds-SOURCE-2018	cd tsscds-SOURCE-2018
60
61	./configure	./configure
62
63	This will install tsscds2018 in $HOME/tsscds-2018 by default. If you want to install it in a different directory, type:	This will install tsscds2018 in $HOME/tsscds-2018 by default. If you want to install
64		it in a different directory, type:
65
66	./configure --prefix=path_to_program	./configure --prefix=path_to_program
67
#	Line 97	Line 71
71	make install	make install
72	make clean	make clean
73
74	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.	The last command (make clean) is only necessary if you want to remove from the src
75		directory the object files and executables created in the compilation process.
76
77	For convenience, and once “Environment Modules” has been installed, you can add to your .bashrc file the following line to use the tsscds module:	For convenience, and once “Environment Modules” has been installed, you can add to
78		your .bashrc file the following line to use the tsscds module:
79
80	module use path_to_program/modules	module use path_to_program/modules
81
#	Line 110	Line 86
86	-run 'autoreconf -i' after svn check out	-run 'autoreconf -i' after svn check out
87	===========================================================================	===========================================================================
88
89	====================PROGRAM EXECUTION======================================	====================PROGRAM EXECUTION======================================
90	To start using any of the scripts of the program, you have to load tsscds/2018 module:	To start using any of the scripts of the program, you have to load tsscds/2018 module:
91
92	module load tsscds/2018	module load tsscds/2018
93
94	Then, please follow the instructions given in the tutorial, which can be found in:	To run the low-level calculations use:
	tsscds-SOURCE-2018/docs/tutorial.pdf  or
	path_to_program/doc/tutorial.pdf
95
96		nohup llcalcs.sh molecule.dat ntasks niter runningtasks >llcalcs.log 2>&1 &
97
98		where:
99		molecule is the name of your molecule
100		ntasks is the number of tasks
101		niter is the number of iterations
102		runningtasks is the number of simultaneous tasks
103
104		To run the high-level calculations use:
105
106		nohup hlcalcs.sh molecule.dat runningtasks >hlcalcs.log 2>&1 &
107
108		For more details, follow the instructions given in the tutorial, which is located here:
109		path_to_program/doc/tutorial.pdf
110	===========================================================================	===========================================================================

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