Software
GNXAS
The GNXAS package is a computer code for EXAFS data analysis based on multiple-scattering (MS) calculations and a rigorous fitting procedure of the raw experimental data. The main characteristic of the software are: + atomic phase shifts calculations in the muffin-tin approximation based on atom self-consistent relativistic calculations. Account for the neighbors is taken. + Inclusion of inelastic losses through complex Hedin-Lundqvist potential. + Calculation of MS signals associated with two, three, and four atom configurations using advanced algorithms. Use of an advanced fitting procedure that allows: + to fit simultaneously any number of spectra containing any number of edges, + to use directly the raw data without any pre-analysis, + to account for complex background multi-electron excitation features, + to use various model peaks for the pair, triplet and quadruplet distribution functions, including non Gaussian models and extreme cases. In all cases absolute parameters can be fitted, - to treat liquid phase or disordered systems and extract reliable g(r) functions in the short range, - to perform a rigorous statistical error analysis and plot two-dimensional correlation maps, - to provide a flexible scientific tool for EXAFS data analysis where the user has access to every stage of the calculation. - full modularity that makes easy to interface parts of the GNXAS software with other available software.
Grasp
"GRASansP" is a MatlabTM script application designed for the graphical inspection, analysis and reduction of multi-detector data produced by the Small-Angle Neutron Scattering (SANS) instruments of the Institut Laue-Langevin (ILL). GRASansP deals with many of the diverse requirements for analysis and reduction of SANS data using a general set of tools and reduction algorithms. Data from the two ILL SANS instruments, D11 and D22, as well as SANS instruments at some other neutron sources, are currently catered for in the GRASansP package. In principle the architecture and coding of GRASansP combined with the matrix handling abilities, graphics and other advantages of the Matlab™ environment should allow continued development of this software and be able to provide more general aspects of multi-detector and complex data set handling. The drive for producing such a suite of software came from the overwhelming need for a modern, complete and general-purpose package to deal with typical procedures required for analysis of two-dimensional SANS multidetector data. By it’s very nature, two-dimensional data is often best appreciated in a graphical form. The birth of GRASansP came from the need for graphical inspection and ability to be able to quickly process and extract the scattered intensity, I(q), as a function of position on the multidetector (qx,qy) or as a function of sample environment conditions from a series of many measurement runs (e.g. temperature sweep, rocking curve etc.). This, combined with an interest in scientific software development and the abilities of the Matlab™ environment have brought GRASansP into it’s present state.
GROMACS
GROMACS (GROningen MAchine for Chemical Simulations) is a molecular dynamics and energy minimization package mainly designed to simulate the Newtonian equations of motion for systems with hundreds to millions of particles, typically of proteins, lipids and nucleic acids. GROMACS can run on CPUs and GPUs.
LAMP
LAMP (Large Array Manipulation Program) is designed for the treatment of data obtained from neutron scattering experiments at the Institut Laue-Langevin. However, LAMP is now a more general purpose application which can be seen as a GUI-laboratory for data analysis based on the IDL language.
MDANSE
MDANSE (Molecular Dynamics Analysis for Neutron Scattering Experiments) is a python application designed for computing properties that can be directly compared with neutron scattering experiments such as the coherent and incoherent intermediate scattering functions and their Fourier transforms, the elastic incoherent structure factor, the static coherent structure factor or the radial distribution function. Moreover, it can also compute quantities such as the mean-square displacement, the velocity autocorrelation function as well as its Fourier Transform (the so-called vibrational density of states) enlarging the scope of the program to a broader range of physico-chemical properties. Most of MDANSE calculations can be applied to the whole system or to arbitrary subsets that can be defined in the graphical interface while less common selections can be specified via the command-line interface. MDANSE is written in Python and currently works on Linux/debian, MacOS and Windows.
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.
nexdatas
Historically it is the job of the Control Client (CC) to write the data recorded during the experiment (this is true at least for low rate data-sources). However, with the appearance of complex data formats like Nexus the IO code becomes more complex. To cope with this complexity, NexDaTaS has been developed jointly by PNI-HDRI and PaNdata to provide an easy to use interface between the NeXus data integration and the control system. NexDaTaS is realized as a Tango server which allows to store NeXuS Data in H5 files. The server provides storing data from other Tango devices, various databases as well as passed by a user client via JSON strings.
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.
NRS
NRS is a fitting and simulation routine for nuclear resonant scattering, based on CONUSS (s. the related catalogue entry). It can fit and simulate both spectra in the time domain and in the energy domain. The program allows for three different scattering geometries: forward scattering, grazing incidence scattering, and a combination of both. In addition, it can be used to simulate electronic and nuclear reflectivity curves.
NSXTool
NSXTool is an application for reducing neutron single crystal data. It provides algorithms for indexing, refining UB matrix and instrument parameters, integrating Bragg peaks for future analyses using software such as FullProf or ShelX. It is made of a core crystallographic library written in C++ (standard 2011) with dependencies on boost, eigen, gsl standard libraries and of a graphical user interface written in Qt.
OCEAN
OCEAN is a versatile package for performing first-principles calculations of core edge spectroscopy. The many-body method is based on ground-state density-functional theory (DFT) and uses the Bethe-Salpeter equation. OCEAN utilizes the programs ABINIT or QuantumESPRESSO for ground-state DFT portion of the calculations. OCEAN is capable of producing various spectra including X-ray absorption near-edge spectra (XANES), X-ray emission spectra (XES), and non-resonant inelastic X-ray scatter (NRIXS or XRS). OCEAN is the result of collaboration between the Rehr group at the University of Washington and Eric Shirley at the National Institute of Standards and Technology (USA).
P
Combined EXAFS and XRPD data analysis with EXAFS full multiple scattering calculations and whole-spectrum fitting. A code designed to maximise the usefulness of the EXAFS technique in the investigation of crystalline materials which powder diffraction (PD) methods could not uniquely resolve. The program retains many of the features of EXCURVE (s. the related web pages) and provides most of the PD features of the program GSAS. For EXAFS this includes full multiple scattering calculations and whole-spectrum fitting, but at present it cannot deal with EXAFS polarisation dependence. PD calculations currently exclude calculation of the thermal diffuse scattering contribution, which is included in the background.
pni-libraries
The PNI libraries are a stack of related C++ libraries developed with the intention to simplify the development of scientific software in the field of Photon-, Neutron, and Ion-scattering.
Quantum Espresso
Quantum ESPRESSO (QE) is an integrated suite of Open-Source computer codes for ab initio quantum chemistry methods of electronic-structure calculations and materials modeling at the nanoscale. It is based on density functional theory, density functional perturbation theory, plane wave basisi sets, and pseudopotentials. The core plane wave DFT functions of QE are provided by the PWscf (Plane-Wave Self-Consistent Field) component,
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.
