Description

This python utility offers simultaneus PES scan of intrinsic coordinates. It is not to be mistaken with the
multidimensinal PES scanning provided by opt(modred) keyword of Gaussian 09. The scan goes along only 1 dimension.
Technically a sequence of two-step scans are performed advancing by all given coordinates maintaining the others.
The program creates an xyz file including the geometries and SCF energies (in kcal/mol) for each complete step.

Dependencies

The program uses python3 environment and some of its packages, as well as cclib package version 1.4.
https://cclib.github.io/
Obviously, in order to perform the calculation one must have access to Gaussian (09) suite.
http://gaussian.com/

Help for dependencies

Python3
Download the latest python environment (3.x.x)
extract tarball:
tar xf Python-3.*.tar.xz
configure python:
cd Python-3.*.tar.xz ./configure --prefix=$HOME
compile:
make
make test
make install
define pythonpath: NOTE: local can be .local instead
echo "export PYTHONPATH="${PYTHONPATH}:/home/berta/local/lib/python3.*/site-packages"" >> $HOME/.bashrc
. $HOME/.bashrc
Now you have easy_install-3.*
cclib 1.4(!)
easy_install-3.* --prefix=$HOME/local cclib-1.4

Installation and configuration

Download the script from https://github.com/bertadenes/g09_mcs.
You might have to specify the permissions:
chmod +x multi_coord_scan.py
Place the file in your bin, add to your PATH or create a symlink.
A command for gaussian submission must be given. Note that the script expect the gaussian outputs in the same directory
where the input was submitted, with same filename and .out extension. The code will fail or malfunction otherwise.
The option can be set in the beginning of the script.
Note also that depending on your submission code the program may display output on the same shall where it was executed.

Usage

multi_coord_scan.py <gaussian input>.gjf
The input structure should identical to gaussian scan calculations (opt=modred), however, the modred section after the
geometry must start with "multicoord" keyword. Then the list of coordinates to be scanned are expected in same syntax
to gaussian. Note that step numbers must be identical. Check the example if in doubt.
CURRENTLY ONLY BONDS ARE IMPLEMENTED

Further notes

The program will create a subdirectory "scan" where gaussian jobs are run. Their names resemble the step and the index
of the actually changing coordinate. The xyz file is created here at the end of calculation.
There will be a file "logfile" in the parent directory containing useful information, as the PID of the background
python process and the termination of gaussian jobs.
In case of unexpected job failure the calculation can be relaunched as started. The normally terminated jobs will be
skipped and reused.

Feel free to check out the provided example at the github repository, and address questions to berta.denes@ttk.mta.hu.