Verification of a distortion in the microstructure of GaN detected by EXAFS using ab initio density functional theory calculations.

X-ray absorption fine structure (XAFS) measurements on a series of epitaxially grown GaN samples have shown a distortion in the microstructure of GaN. More specifically the central N atom is 4-fold coordinated but the four Ga atoms are not equidistant. It has been shown that 2.9 to 3.5 of them (depending on the growth conditions) are found in the expected from XRD distance of 1.94 A and the remaining are at a distance longer by approximately 15%. Second derivative calculation of the conformation energy using the Density Functional Theory (DFT) is used to investigate if the symmetric GaN cluster as given by XRD is the most energetically favorable configuration and if not which distorted structure corresponds to the most energetically favorable one. A very good agreement between DFT results and experimental XAFS spectra has been found. Generalization this technique to other dislocated clusters is also discussed.

Chemical transferability of single- and multiple-scattering EXAFS Debye-Waller factors.

Single- and multiple-scattering EXAFS Debye-Waller factors are amplitude reduction parameters that appear in the EXAFS chi(k) equation accounting for the structural and thermal disorder of a given sample. These parameters must be known accurately in order to obtain quantitative agreement between theory and experiment. Since experimental data can only support a limited number of fitted parameters these factors must be known from another source. Although various approaches have been considered in the past with a variety of results, the self-consistent ab initio Density functional theory stands for the most accurate and reliable method regardless of molecular symmetry or other specific sample requirements. Since DFT scales as N3 where N is the number of atomic basis set, an ab initio calculation on a large structure is not feasible due to enormous CPU demand and in many cases due to hard energy/geometry convergence. In this paper we present two ways of overcoming this problem. Both they use the idea that by reducing the structure, the DWFs are still chemically transferable. In order to test this we use the Zn tetraimidazole. This molecule represents typical metalorganic ring samples that can be seen in active sites of metaloproteins. Results are compared to experimental EXAFS spectra.

APEX version 2.0: latest version of the cross-platform analysis program for EXAFS.

This report describes recent progress on APEX, a free, open source, cross platform set of EXAFS data analysis software. In a previous report we described APEX 1.0 (Dimakis, N. and Bunker, G., 1999), a free and open source code suite of basic X-Ray Absorption Fine Structure (XAFS) data analysis programs for classical data reduction and single scattering analysis. The first version of APEX was the only cross platform (linux/irix/windows/MacOS) EXAFS analysis program to our knowledge, but it lacked important features like multiple scattering fitting, generic format conversion from ASCII to University of Washington (UW) binary-type files, and user friendly interactive graphics. In the enhanced version described here we have added cross-platform interactive graphics based on the BLT package, which is an extension to TCL/TK. Some of the utilities have been rewritten in native TCL/TK, allowing for faster and more integrated functionality with the main package. The package also has been ported to SunOS. APEX 2.0 in its current form is suitable for routine data analysis and training. Addition of more advanced methods of data analysis are planned.