| 1 : |
tsscds |
210 |
===========================================================================
|
| 2 : |
tsscds |
233 |
tsscds. A computer program for finding reaction mechanisms and solving the
|
| 3 : |
|
|
kinetics.
|
| 4 : |
|
|
Copyright (C) 2018 Emilio Martinez-Nunez, Aurelio Rodriguez, Roberto
|
| 5 : |
|
|
Rodriguez-Fernandez, Saulo Vazquez-Rodriguez, George L. Barnes and
|
| 6 : |
|
|
James J. P. Stewart
|
| 7 : |
baaden |
3 |
|
| 8 : |
tsscds |
210 |
This program is free software: you can redistribute it and/or modify
|
| 9 : |
|
|
it under the terms of the GNU General Public License as published by
|
| 10 : |
|
|
the Free Software Foundation, either version 3 of the License, or
|
| 11 : |
|
|
any later version.
|
| 12 : |
|
|
|
| 13 : |
|
|
This program is distributed in the hope that it will be useful,
|
| 14 : |
|
|
but WITHOUT ANY WARRANTY; without even the implied warranty of
|
| 15 : |
|
|
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
| 16 : |
|
|
GNU General Public License for more details.
|
| 17 : |
|
|
|
| 18 : |
|
|
You should have received a copy of the GNU General Public License
|
| 19 : |
|
|
along with this program. If not, see <http://www.gnu.org/licenses/>.
|
| 20 : |
|
|
===========================================================================
|
| 21 : |
|
|
|
| 22 : |
tsscds |
233 |
====================DESCRIPTION OF THE FILES/FOLDERS=======================
|
| 23 : |
|
|
The following files are needed or generated during configuration/installation
|
| 24 : |
|
|
steps and, therefore, they should not be edited:
|
| 25 : |
tsscds |
96 |
|
| 26 : |
tsscds |
233 |
aclocal.m4
|
| 27 : |
|
|
ChangeLog
|
| 28 : |
|
|
config.log
|
| 29 : |
|
|
config.status
|
| 30 : |
|
|
configure
|
| 31 : |
|
|
configure.ac
|
| 32 : |
|
|
install-sh
|
| 33 : |
|
|
Makefile
|
| 34 : |
|
|
Makefile.am
|
| 35 : |
|
|
Makefile.in
|
| 36 : |
|
|
missing
|
| 37 : |
tsscds |
132 |
|
| 38 : |
tsscds |
233 |
AUTHORS. This file contains a list of the authors of the program.
|
| 39 : |
tsscds |
132 |
|
| 40 : |
tsscds |
233 |
docs. This folder contains tutorial.pdf, which should be printed out to consult
|
| 41 : |
|
|
instructions about the installation and execution of the program.
|
| 42 : |
tsscds |
132 |
|
| 43 : |
tsscds |
233 |
examples. This folder contains several input files for testing purposes. The
|
| 44 : |
|
|
instructions are given in tutorial.pdf
|
| 45 : |
tsscds |
132 |
|
| 46 : |
tsscds |
233 |
license.txt. GNU general public license.
|
| 47 : |
tsscds |
132 |
|
| 48 : |
tsscds |
233 |
modules. This is a folder with the 2018 module that the user should load before
|
| 49 : |
|
|
the execution of the program as detailed in the tutorial.pdf.
|
| 50 : |
tsscds |
96 |
|
| 51 : |
tsscds |
233 |
NEWS. A file with the news about the program.
|
| 52 : |
tsscds |
96 |
|
| 53 : |
tsscds |
233 |
README. This file.
|
| 54 : |
tsscds |
96 |
|
| 55 : |
tsscds |
233 |
scripts. This is a folder that contains all Bash and Python scripts for the specific
|
| 56 : |
|
|
tasks.
|
| 57 : |
tsscds |
96 |
|
| 58 : |
tsscds |
233 |
share. This folder contains different (MOPAC/G09) template input files as well as
|
| 59 : |
|
|
other common files.
|
| 60 : |
baaden |
3 |
|
| 61 : |
tsscds |
233 |
src. The folder contains the fortran90 source files that need to be compiled.
|
| 62 : |
|
|
===========================================================================
|
| 63 : |
tsscds |
92 |
|
| 64 : |
tsscds |
233 |
====================INSTALLATION INSTRUCTIONS==============================
|
| 65 : |
tsscds |
262 |
Untar and unzip the file tsscds-SOURCE-2018.tar.gz:
|
| 66 : |
tsscds |
92 |
|
| 67 : |
tsscds |
262 |
tar xvfz tsscds-SOURCE-2018.tar.gz
|
| 68 : |
|
|
|
| 69 : |
|
|
Before installing tsscds, be aware that the following packages are needed:
|
| 70 : |
|
|
|
| 71 : |
tsscds |
255 |
bc, environment-modules, gawk, gcc, gfortran, parallel, python-numpy, python-scipy, sqlite3, zenity
|
| 72 : |
tsscds |
233 |
|
| 73 : |
tsscds |
269 |
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:
|
| 74 : |
tsscds |
233 |
|
| 75 : |
tsscds |
266 |
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.
|
| 76 : |
tsscds |
265 |
b) install-gnu-parallel-from-epel.sh. Enables the EPEL repository and installs parallel from it.
|
| 77 : |
tsscds |
255 |
|
| 78 : |
tsscds |
269 |
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.
|
| 79 : |
tsscds |
265 |
|
| 80 : |
tsscds |
262 |
These packages might also be useful to analyze the results:
|
| 81 : |
tsscds |
255 |
|
| 82 : |
tsscds |
262 |
gnuplot, molden, sqlitebrowser
|
| 83 : |
tsscds |
233 |
|
| 84 : |
tsscds |
262 |
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:
|
| 85 : |
tsscds |
257 |
|
| 86 : |
tsscds |
233 |
cd tsscds-SOURCE-2018
|
| 87 : |
|
|
|
| 88 : |
|
|
./configure
|
| 89 : |
|
|
|
| 90 : |
tsscds |
262 |
This will install tsscds2018 in $HOME/tsscds-2018 by default. If you want to install it in a different directory, type:
|
| 91 : |
tsscds |
233 |
|
| 92 : |
tsscds |
262 |
./configure --prefix=path_to_program
|
| 93 : |
tsscds |
233 |
|
| 94 : |
|
|
Finally, complete the installation:
|
| 95 : |
|
|
|
| 96 : |
|
|
make
|
| 97 : |
|
|
make install
|
| 98 : |
tsscds |
262 |
make clean
|
| 99 : |
tsscds |
233 |
|
| 100 : |
tsscds |
262 |
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.
|
| 101 : |
tsscds |
233 |
|
| 102 : |
tsscds |
262 |
For convenience, and once “Environment Modules” has been installed, you can add to your .bashrc file the following line to use the tsscds module:
|
| 103 : |
|
|
|
| 104 : |
tsscds |
233 |
module use path_to_program/modules
|
| 105 : |
|
|
|
| 106 : |
tsscds |
262 |
where path_to_program is the path where you installed tsscds (e.g., $HOME/tsscds-2018).
|
| 107 : |
tsscds |
233 |
|
| 108 : |
|
|
|
| 109 : |
|
|
THIS IS JUST FOR DEVELOPERS:
|
| 110 : |
|
|
-run 'autoreconf -i' after svn check out
|
| 111 : |
|
|
===========================================================================
|
| 112 : |
|
|
|
| 113 : |
|
|
|
| 114 : |
|
|
====================PROGRAM EXECUTION======================================
|
| 115 : |
|
|
To start using any of the scripts of the program, you have to load tsscds/2018 module:
|
| 116 : |
|
|
|
| 117 : |
|
|
module load tsscds/2018
|
| 118 : |
|
|
|
| 119 : |
|
|
Then, please follow the instructions given in the tutorial, which can be found in:
|
| 120 : |
|
|
tsscds-SOURCE-2018/docs/tutorial.pdf or
|
| 121 : |
|
|
path_to_program/doc/tutorial.pdf
|
| 122 : |
|
|
|
| 123 : |
|
|
===========================================================================
|
Parent Directory
Revision Log