GenLocDip
GenLocDip is a program for calculating and visualizing local dipole moments of molecular subsystems. It currently uses the Atoms-In-Molecules (AIM) partitioning scheme [1] and employs a modified version of Bader’s and Laidig’s approach [2,3] for achieving origin-independence of local dipoles by referring to internal reference points such as bond critical points.
Citation:
Groß, L., GenLocDip – A program to calculate and visualize local electric dipole moments via Atoms-In-Molecules analysis, University of Hamburg, 2014-2015.Download:
Source code ('tar -jxvf genlocdip.tar.bz2' to extract)
The manual is available here and may also be found in the 'doc' directory of distribution.
Key features of GenLocDip v0.4:
- It interfaces grid-based AIM codes where the critical point search is bypassed in order to improve the computational efficiency. In particular, this offers the advantage of investigating extended non-covalently bonded systems on surfaces using plane-wave based electronic structure packages, such as Quantum Espresso [4]
- It is open source and interfaces only AIM programs that are readily available
- It requires only minimal user input
- It prints out a POV-Ray [5] format file visualizing the data in three dimensions
A few examples are provided in the 'examples' directory of the distribution:
- Methanol
- Water dimer
- Benzene stacked with pyridine
Currently supported programs for AIM analysis:
References:
[1] Bader, R. F. W., Atoms in Molecules: A Quantum Theory, Oxford University Press:Oxford, U.K., 1990.
[2] Laidig, K. E. and Bader, R. F. W., J. Chem. Phys., 1990, 93(10), 7213–7224.
[3] Bader, R. F. W.; Keith, T. A.; Gough, K. M. and Laidig, K. E., Mol. Phys., 1992,75(5), 1167–1189.
[4] Giannozzi, P.; Baroni, S.; Bonini, N.; Calandra, M.; Car, R.; Cavazzoni, C.; Ceresoli, D.; Chiarotti, G. L.; Cococcioni, M.; Dabo, I.; Dal Corso, A.; de Gironcoli, S.; Fabris, S.; Fratesi, G.; Gebauer, R.; Gerstmann, U.; Gougoussis, C.; Kokalj, A.; Lazzeri, M.; Martin-Samos, L.; Marzari, N.; Mauri, F.; Mazzarello, R.; Paolini, S.; Pasquarello, A.; Paulatto, L.; Sbraccia, C.; Scandolo, S.; Sclauzero, G.; Seitsonen, A. P.; Smogunov, A.; Umari, P. and Wentzcovitch, R. M., J. Phys.:Condens. Matter, 2009, 21(39), 395502.
[5] Buck, D. K. and Collins, A. A., POV-Ray - The Persistence of Vision Raytracer.
[6] Keith, T. A., AIMAll (version 14.11.23), TK Gristmill Software, Overland Park KS, USA, 2014 (aim.tkgristmill.com).
[7] Lu, T. and Chen, F., J. Comp. Chem., 2011, 33(5), 580–592.
[8] Henkelman, G.; Arnaldsson, A. and Jónsson, H., Comp. Mater. Sci., 2006, 36(3), 354–360.
[9] Sanville, E.; Kenny, S. D.; Smith, R. and Henkelman, G., J. Comp. Chem., 2007, 28(5), 899–908.
[10] Tang, W.; Sanville, E. and Henkelman, G., J. Phys. Condens. Matter, 2009, 21(8), 084204.