Software


McXtrace

Monte Carlo Xray Tracing. Allows simulation of X-ray beam lines, as well as sample simulations in so-called virtual experiments.

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.

MOLDY

Moldy is a C program for performing molecular-dynamics simulations of solids and liquids using periodic boundary conditions. The model system is completely specified in a run-time input file and may contain atoms, molecules or ions in any mixture. Molecules or molecular ions are treated in the rigid-molecule approximation and their rotational motion is modeled using quaternion methods. The equations of motion are integrated using a modified form of the Beeman algorithm. Simulations may be performed in the usual NVE ensemble or in isobaric and/or isothermal ensembles. Potential functions of the Lennard–Jones, 6-exp and MCY forms are supported and the code is structured to give an straightforward interface to add a new functional form. The Ewald method is used to calculate long-ranged electrostatic forces.

MOSFLM

Mosflm can process diffraction images from a wide range of detectors and produces, as output, an MTZ file of reflection indices with their intensities and standard deviations (and other parameters). This MTZ file is passed onto other programs of the CCP4 program suite (SORTMTZ, SCALA, TRUNCATE) for further data reduction.

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.

nanoMAD

NanoMAD stands for Multiwavelength Anomalous Diffraction for Nano-structures: it is a command-line tool to analyze x-ray diffraction data collected at several wavelengths around one element's absorption edge, and extract the partial structure factor for the resonant atom.

nanomax-analysis-utils

A set of Python tools and widgets for handling and visualizing scanning imaging data at the NanoMAX (MAX IV) beamline.

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.

OASYS

OASYS (OrAnge SYnchrotron Suite) is an open-source Graphical Environment for optic simulation software packages used in synchrotron facilities, based on [Orange 3](http://orange.biolab.si/orange3/). It includes SHADOWOUI, a port to the [SHADOW](https://github.com/srio/shadow3) ray-tracing code and XOPPY (the Python version of [XOP](http://www.esrf.eu/Instrumentation/software/data-analysis/xop2.4)

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).

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.