In typical applications of quantum chemistry, a single or a few calculations are usually not sufficient. Instead, more complicated workflows are needed, in which a series of interrelated computational tasks is performed. In particular multiscale simulations, which combine different levels of accuracy, require a large number of individual calculations that depend on each other.
To automate such workflows, we have developed PyADF, a scripting framework for quantum chemistry. It handles all steps necessary in a typical workflow in quantum chemistry and is easily extensible. PyADF is written in the Python programming language and is interfaced to a number of different program packages, most importantly ADF, Dalton, Dirac, and NWChem.
The calculation of vibrational spectra of large (bio-)molecules is not only demanding in terms of computational resources, but the resulting spectra are also difficult to analyze: Many close-lying normal modes contribute to each observed peak, and each of these normal modes is usually delocalized over the whole molecule.
To address this problem, we have developed an methodology for localizing normal modesand have shown how this makes an intuitive analysis of calculated vibrational spectra of polypeptides and proteins possible.
LocVib is a set of Python scripts for performing such an analysis in terms of localized vibrations.
Over the past years, we have contributed mainly to the implementation of the frozen-density embedding (FDE) scheme in ADF. The new implementation that became available in ADF2007, allows for a very flexible setup employing many fragments that can each be treated using different levels of accuracy.
In addition, we have developed implemented a scheme for embedding a wave-function theory (WFT) based description in a DFT environment. This WFT-in-DFT embedding implementation currently relies on ADF for the DFT part as well as for calculating the embedding potential.
Together with Andre Gomes (Lille) and Lucas Visscher (Amsterdam) we are working on the implementation of embedding schemes in DIRAC, that allow to include the effect of an environment described with density-functional theory in the very accurate relativistic calculations possible with DIRAC.