Software
MXAN
MXAN performs a quantitative analysis of the XANES energy range. This is based on a comparison between experimental data and many theoretical spectra that are calculated by varying selected structural parameters of an initial putative structure, i.e. a well defined initial geometrical configurations around the absorber. Hundreds of different geometrical configurations are needed to obtain the best fit of the experimental data. The calculations are performed in the energy space without involving any Fourier transform algorithm; polarized spectra can be easily analysed because the calculations are performed within the full multiple scattering approach. Recently, MXAN has been developed in the framework of the multiple scattering theory and successfully applied to the analysis of several system, both in solid and liquid state. The MXAN procedure,encompasses also the phenomenological broadening and the electronic charge fitting.
NAMD
NAMD is a parallel molecular dynamics code designed for high-performance simulations of large biomolecular systems.
NeXpy
NeXpy provides a high-level python interface to NeXus data contained within a simple GUI. It is designed to provide an intuitive interactive toolbox allowing users both to access existing NeXus files and to create new NeXus-conforming data structures without expert knowledge of the file format. The underlying Python API for reading and writing NeXus files is provided by the nexusformat package, which is also described here.
Nexus - Nuclear Elastic X-ray scattering Universal Software
The Nuclear Elastic X-ray scattering Universal Software (NEXUS) is a Python package for simulating and fitting of Moessbauer spectra, nuclear resonant scattering (NRS) data, pure electronic X-ray reflectivities (XRR), nuclear X-ray reflectivities, polarization dependent electronic scattering.
ORCA
ORCA is a modern electronic structure program package written by Frank Neese, with contributions from many current and former coworkers and several collaborating groups. The binaries of ORCA are available free of charge for academic users for a variety of platforms. ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects. Due to the user-friendly style, ORCA is considered to be a helpful tool not only for computational chemists, but also for chemists, physicists and biologists that are interested in developing the full information content of their experimental data with help of calculations.
PDFgetX3
PDFgetX3 is a command-line utility for converting X-ray powder diffraction data to atomic pair distribution functions (PDF) in automated batch processing. The interactive mode provides complete access to all parameters and intermediate results, as well as live-plotting feature for parameters tuning and visualization of their effects on the results. PDFgetX3 can be used either as a standalone application or as a Python library of PDF-processing functions.
Phenix
PHENIX is a software suite for automated macromolecular structure determination that can rapidly arrive at an initial partial model of a structure without significant human intervention, given moderate resolution and good quality data. This has been made possible by the development of novel algorithms for structure determination, maximum-likelihood molecular replacement (PHASER), heavy-atom search (HySS), template and pattern-based automated model-building (RESOLVE), automated macromolecular refinement (phenix.refine), and iterative model-building, density modification and refinement that can operate at moderate resolution (RESOLVE, AutoBuild). These algorithms are based on a set of crystallographic libraries that have been built and made available to the community.
Phonon
PHONON is a code to calculate lattice dynamics, mainly using input force constants from ab initio (DFT) codes like VASP. There are many kinds of output including spectroscopic scattering functions.
Pore3D
Pore3D is a software toolbox for quantitative analysis of three-dimensional images. The core of Pore3D consists in a set of state-of-the-art functions and procedures for performing filtering, segmentation, skeletonization and quantitative analysis of three-dimensional data. Although three-dimensional data can be produced by several techniques (for instance: magnetic resonance, x-ray scattering or confocal microscopy), the library was developed and optimized for micro-CT (Computed Tomography) data. Pore3D features are available through the high-level scripting environment IDL. Pore3D has been tested with IDL 64-bit from versions 6.4 to 8.5.
PtyPy
Framework for scientific ptychography including suitable classes for many concepts of ptychography
PyFAI
pyFAI is an azimuthal integration library that tries to be fast (as fast as C and even more using OpenCL and GPU). It is based on histogramming of the 2theta/Q positions of each (center of) pixel weighted by the intensity of each pixel, but parallel version uses a SparseMatrix-DenseVector multiplication
PyMca
X-ray Fluorescence Toolkit (visualization and analysis of energy-dispersive X-ray fluorescence data). . The program allows both interactive and batch processing of large data sets and is particularly well suited for X-ray imaging. Its implementation of a complete description of the M shell is particularly helpful for analysis of data collected at low energies. It features, among many other things, the fundamental parameters method
Quanty
Quanty is a script language which allows the user to program quantum mechanical problems in second quantization and when possible solve these. It can be used in quantum chemistry as post Hartree-Fock or in one of the LDA++ schemes. (self consistent field, configuration interaction, coupled cluster, restricted active space, ...) The idea of Quanty is that the user can focus on the model and its physical or chemical meaning. Quanty takes care of the mathematics.
REFTIM
The program REFTIM calculates and fits the time spectra of nuclear resonant reflectivity, delayed and prompt reflectivity curves and the corresponding conversion electron Mössbauer spectra (CEMS) for any multilayer structure containing 57Fe, 151Eu, 149Sm, 119Sn or other isotopes if they have M1 Mössbauer transition. The experimental details of the nuclear resonance scattering technique with synchrotron radiation are described in the ID18 beamline Web pages.
RFit2000
RFIT2000 fits X-ray and neutron reflectivity data. The search of global minima is done via successive descent from local minima. This method can be treated as a two stage loop repeated consequently. The first stage is the local minimization with the ?2 -like criterion and the second one is the descent from the most recent local minimum. Reflectivity curve is calculated with one of the methods: Kinematic, Parratt and Matrix. Matrix method works faster for films modeled with multiple repetion of one identcal structural units. Film structure is represented with the box model. Each box is characterized with the scattering density (Re and Im), thickness and roughness of the top interface.
