AKIRA - the Mode-Tracking program for the purpose-driven calculation of pre-selected molecular vibrations
by J. Neugebauer, C. Herrmann, K. Kiewisch, S. Luber, S. Schenk and M. Reiher
The standard quantum chemical calculation of vibrational spectra involves the calculation of the complete Hessian matrix, which becomes the more time-consuming the larger the molecule and/or the more elaborate the quantum chemical electronic structure method is. We have developed a conceptually new and efficient method (Mode-Tracking) for the exact calculation of only those normal modes, which are important for the physics and chemistry of the system, thus circumventing the calculation of the full Hessian matrix. Detailed studies on convergence characteristics of the Mode-Tracking principle for selectively targeting molecular properties (in particular, for calculating pre-selected molecular vibrations) have been carried out and shows the behavior of the algorithm with respect to
- numerical accuracy and stability,
- choice of the guess vibration(s),
- implicit restriction to a symmetry species,
- near degeneracy effects,
- intermolecular vibrations,
- convergence to the complete spectrum as the limiting case, and
- convergence to the lowest mode for the characterization of stationary points.
Mode-Tracking is well suited in cases of
- very large molecules for which a complete calculation of the spectrum is not feasible,
- standard systems if only limited computer time is available so that a complete calculation cannot be carried out, and
- smaller systems in combination with highly accurate ab initio calculations.
Cite this work as:
Currently supported program packages for calculation of primary data:
The program package AKIRA has been developed to implement the Mode-Tracking idea. Selected vibrations (normal modes and wavenumbers) can be obtained using the harmonic approximation. The vibrational frequencies are determined using numerical differentiation of analytic gradients of the total electronic energy with respect to collective Cartesian nuclear coordinates.
AKIRA requires single-point calculations with either DALTON or TURBOMOLE or ADF or GAUSSIAN, which can be performed using coarse-grained parallelization (PVM and MPI) with automatic load-balancing. Note that you need to possess an official licence for any of these quantum chemistry packages!! AKIRA does not intermingle with any of these programs but only scans the output of them in order to extract all relevant raw data for the Mode-Tracking protocol. AKIRA will automatically start DALTON, TURBOMOLE, ADF, or GAUSSIAN single-point jobs on slave nodes (if no PC cluster is available it is possible to run AKIRA in a single-processor mode).
For the easy set up and handling of the calculations you may start the set-up tool AKIRADEFINE.
Normal modes may be tracked for any electronic structure method implemented in DALTON, TURBOMOLE, ADF, or GAUSSIAN for which analytic energy gradients are available.
To install Akira, you need the following steps:
- unpack: tar -xvjf akira-3.4.0.tar.bz2
- change to subdirectory: cd akira-3.4.0
- read help: less INSTALL
- configure package: ./configure --with-pvm --with-scp
- compile package: make -j2
If you encounter any problems with the installation: you might install the SNF package first in order to make sure that the PVM or MPI libraries, resp., work properly! If SNF is running on your system, AKIRA also will!
The Mode-Tracking algorithm has been systematically studied with respect to:
- Convergence M. Reiher, J. Neugebauer, Phys. Chem. Chem. Phys. 6 (2004), 4621.
- QM/MM environments C. Herrmann, J. Neugebauer, M. Reiher, J. Comput. Chem. 29 (2008), 2460.
- adsorbates on surfaces C. Herrmann, M. Reiher, Surf. Science 600 (2006), 1891.
- for a general review see C. Herrmann, J. Neugebauer, M. Reiher, New J. Chem. 31 (2007), 818.
Updates to come
Our recently developed Intensity-Tracking protocols for converging only those normal modes that carry most of the intensity will be made available soon:
for Resonance Raman spectroscopy:
K. Kiewisch, J. Neugebauer, M. Reiher, J. Chem. Phys., 129 (2008), 204103.
for IR spectroscopy:
S. Luber, J. Neugebauer, M. Reiher, J. Chem. Phys., 130 (2009), 069105.
For Raman and ROA spectroscopy:
S. Luber, M. Reiher, ChemPhysChem, 10 (2009), 2049-2057.
© by Laboratorium für Physikalische Chemie, ETH Zürich, 2009.
© by Laboratory of Physical Chemistry, ETH Zurich, 2009.