Software


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.

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.

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.

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.

Ptychography Alignment Tools

This project provides a PyQtGraph-based GUI to assist users on the alignment of Ptychography scans. The tool has the following features: -Load set of images (tiff files supported) -Select pairs of images for alignment -Import/Export probe positions (npy array) -Image controls: levels, contrast, look up tables, zooming, translation -Preview the global picture by combining all positions

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

PyHST2

Hybrid distributed code for high speed tomographic reconstruction with iterative reconstruction and a priori knowledge capabilities. PyHST2 (formerly known as PyHST) has been engineered to sustain the high data flow typical of the third generation synchrotron facilities (10 terabytes per experiment) by adopting a distributed and pipelined architecture. The code implements, beside a default filtered backprojection reconstruction, iterative reconstruction techniques with a-priori knowledge. The latter are used to improve the reconstruction quality or in order to reduce the required data volume and reach a given quality goal. The implemented a-priori knowledge techniques are based on the total variation penalisation and a new recently found convex functional which is based on overlapping patches.

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

PyNX

Python toolkit for accelerated Nano-structures Crystallography and Coherent X-ray Imaging techniques. The software included in this package can be used for: 1. the computing of X-ray scattering using graphical processing units 2. X-ray wavefield propagation (from near to far field) 3. simulation and GPU-accelerated analysis of experiments using the ptychography and coherent diffraction imaging techniques See the full documentation at: http://ftp.esrf.fr/pub/scisoft/PyNX/doc/

QENS library

This library provides different building blocks that users can combine, convolute and plug in different frameworks for visualizing or fitting Quasi Elastic Neutron Scattering (QENS) data S(Q, omega). It was developed as part of SINE2020 Workpackage 10 on Data Treatment to develop an exhaustive library of dynamical models in order to increase interoperability and modularity for a rapid prototyping. The models are written in Python for easy integration in workflows. In order to help users, a few examples of data analyses using different standard fitting engines (lmfit, scipy, bumps) are provided as Jupyter notebooks5. Tools are also provided to help those interested in contributing to the project by adding models or sharing examples of data treatment. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 654000.

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,

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.