Installation instructions

Obtaining the source code

You can get a copy of the source code downloading Tsscds-SOURCE-2018.tar.gz. In this case you have to untar and unzip the file:

tar xvfz tsscds-SOURCE-2018.tar.gz

Alternatively you can create a local copy of the repository:

svn checkout --username anonsvn http://cvs.forge.cesga.es/svn/tsscds/tags/2018 tsscds

The password is 'anonsvn'. The local copy is stored in tsscds folder. Before installing the package, go there (cd tsscds) and run:

autoreconf --install

to prepare and create some missing scripts (e.g. configure) in the package source. The checkout has to be done only once. Then, everytime you run the command:

svn update

the local copy will be updated to the latest revision. In any of the two cases (download or checkout) you have to install the dependencies (2) and install tsscds (3).

Installing dependencies

Before installing tsscds for the first time, 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 (or tsscds if you employed checkout) 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

Installation

Once the above packages are installed, go to the tsscds-SOURCE-2018 folder (or tsscds if you employed checkout) to configure and install the package:

./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 should add the following line to your .bashrc file:

module use path_to_program/modules

where path_to_program is the path where you installed tsscds (e.g., $HOME/tsscds-2018).

Running the test

To run the formic acid test example (explained in the tutorial) for a few trajectories follow these steps:

1) Load the module:

module load tsscds/2018

2) Run the script:

run_test.sh

This will create a directory named test, where you can check the results (see the tutorial for details). The test may take a few minutes.

AutoMeKin