Background material
The StoBe-deMon (StockholmBerlin) DFT code has been developed by Lars G.M.
Pettersson (Stockholm University) and Klaus Hermann (FHI, Berlin) from the
original deMon program with special emphasis on large clusters and inner-shell
spectroscopies.
StoBe web pages and distribution (including manual):
http://w3.rzberlin.mpg.de/~hermann/StoBe/index.html
A very simple StoBe tutorial:
http://www.physto.se/~xes/PDF/Lecture7.pdf
(The rest of the lectures on inner-shell spectroscopies and Surface Chemical Physics
given by Anders Nilsson, Lars G.M. Pettersson and Michael Odelius at Stockholm
University in 2006 can be found here: http://www.physto.se/~xes/surfchemphys.html
(scroll down to Lecture plan)
Nilsson and Pettersson, Surface Science Report 55, 49-167 (2004)
An extensive review of x-ray emission spectroscopy (XES) applied experimentally
and computationally to analyze surface chemical bonding. Chemical Bonding on
Surfaces.pdf
Nilsson, Pettersson and Nørskov (Editors): Chemical Bonding at Surfaces
and Interfaces (Elsevier, Amsterdam, 2008).
Summarizes the report above in a more chemical context as part of an in-depth
introduction to surface chemistry and heterogeneous catalysis.
Chapters by:
1. D.P. Woodruff: Surface Structure
2. A. Nilsson; L.G.M. Pettersson: Adsorbate structure and bonding
3. A.C. Luntz: Dynamics of making and breaking bonds at surfaces
4. T. Bligaard; J.K. Nørskov: Heterogeneous catalysis
5. S. F. Bent: Semiconductor surface chemistry
6. P. Strasser; H. Ogasawara: Surface electrochemistry
7. G.E. Brown, Jr; T.P. Trainor; A.M. Chaka: Geochemistry
(Click here or figure for link).
The GPAW spectroscopy implementation
The GPAW code is a DFT code based on real space grids and the PAW (Projector
Augmented Wave) method. Both periodic and non-periodic boundary conditions can
be imposed. The code is written mostly in Python with the most time consuming
routines written in C.
The implementation of XAS is based on the transition potential method: first one
creates a PAW setup (very similar to a pseudo-potential) from an atomic calculation
with a core hole (full or half) then a DFT calculation is carried out using this PAW
setup on the atom one is looking at. The XAS spectrum can then be obtained in either
of two ways: in the first the transition dipoles between the core orbital and the
unoccupied states are calculated, in the second a recursion method is used to calculate
the cross section without the need for unoccupied states. The latter method is
preferred if the density of states is very high (a large unit cell) and when one wants
the spectrum for high energies.
Unbound states have the characteristics of plane waves and can be very well
described on real space grids. Also, the density of states can be much increased by
using k-point sampling in periodic systems. Both basis set and density of states can
thus be very well converged. For additional information on the GPAW Project, see
https://wiki.fysik.dtu.dk/gpaw/
Some StoBe related publications from the Stockholm group:
1. L. Triguero, L.G.M. Pettersson and H. Ågren, Calculations of Near-Edge X-ray
Absorption Spectra of Gas Phase and Chemisorbed Molecules by means of
Density Functional and Transition Potential Theory, Phys. Rev. B 58, 8097
(1998). (PDF)
2. L.G.M. Pettersson, T. Hatsui, and N. Kosugi, Ni 2p-3d photoabsorption and
strong charge transfer satellites in divalent Ni complexes with molecular ligands.
Evaluation of -backdonation based on the DFT approach, Chem. Phys. Letters,
311, 299 (1999). (PDF)
3. A. Föhlisch, P. Bennich, J. Hasselström, O. Karis, A. Nilsson, L. Triguero, M.
Nyberg and L.G.M Pettersson, The Ground State Picture of X-Ray Emission
Spectroscopy on Adsorbates: CO adsorbed on Cu(100), Phys. Rev. B 61, 16229
(2000). (PDF)
4. C. Kolczewski, R. Püttner, O. Plashkevych, H. Ågren, V. Staemmler, M. Martins,
G. Snell, M. Sant'anna, G. Kaindl and L.G.M. Pettersson, Detailed Study of
pyridine at the C 1s and N 1s ionization thresholds: The influence of the
vibrational fine structure, J. Chem. Phys. 115, 6426-6437 (2001). (PDF)
5. M. Cavalleri, H. Ogasawara, L. G. M. Pettersson and A.Nilsson, The
interpretation of X-ray absorption spectra in water and ice, Chem. Phys. Letters
364, 363-370 (2002). (PDF)
6. O. Takahashi and L.G.M. Pettersson, Functional Dependence of Core-Excitation
Energies, J. Chem. Phys. 121, 10339-10345 (2004). (PDF)
7. M. Odelius, H. Ogasawara, D. Nordlund, O. Fuchs, L. Weinhardt, F. Maier, E.
Umbach, C. Heske, Y. Zubavicus, M. Grunze, J. Denlinger, L.G.M. Pettersson
and A. Nilsson, Ultrafast dissociation dynamics in water probed by x-ray
emission spectroscopy, Phys. Rev. Letters 94, 227401 (2005). (PDF)
8. M. Cavalleri, D. Nordlund, M. Odelius, A. Nilsson, and L.G.M. Pettersson, Half
or full core-hole in Density Functional Theory X-ray absorption spectrum
calculations of water?, Phys. Chem. Chem. Phys. 7, 2854 – 2858 (2005). (PDF)
9. M. Odelius, M. Cavalleri, A. Nilsson and L.G.M. Pettersson, The X-ray
Absorption Spectrum of Liquid Water from Molecular Dynamics Simulations:
Asymmetric Model, Phys. Rev. B. 73, 024205 (2006). (PDF)
10. H. Öström, H. Ogasawara, L.-Å Näslund, L.G.M. Pettersson and A. Nilsson,
Physisorption-induced C-H bond elongation in methane, Phys. Rev. Letters 96,
146104 (2006). (PDF)
11. Emiliana Damian Risberg, Lars Eriksson, János Mink, Lars G. M. Pettersson,
Mikhail Yu. Skripkin and Magnus Sandström, Sulfur X-ray absorption and
vibrational spectroscopic study of sulfite, sulfur dioxide and sulfonate solutions
and the substituted sulfonate ions X3CSO3 - (X=H, Cl, F), Inorg. Chem.46, 83328348 (2007). (PDF)
Personal webpages:
Lars G.M. Pettersson: http://www.physto.se/~xes/
Klaus Hermann:
http://www.fhi-berlin.mpg.de/th/cms/index.php?option=com_wrapper&Itemid=176