packages.mccode.org repository

Welcome !

This experimental software repository provides a simple way to install scientific software for the neutron scattering community.

Note: we only support 64 bits, mostly Debian-based distributions.
Debain 8-9-10 Jessie/Buster, Mint 16-19 Ubuntu 14.04, 16.04, 18.04 are supported.
RedHat distributions support is limited (see below)

  1. Configuration for Debian distributions (Ubuntu, Mint, ...)
  2. Configuration for RedHat distributions (RedHat, CentOS, Fedora, ...)
  3. List of available Debian packages

Configuration for Debian distributions (Ubuntu, Mint, ...)

Software SourcesTo use this repository, open the Software Sources settings (from e.g. Synaptic, Ubuntu Software Center or System Settings) and select the Other Software tab, then press the 'Add...' button and enter 'deb http://packages.mccode.org/debian stable main'

You can also open a terminal and type:
for a Debian Jessie (8)/Ubuntu trusty (14.04) system:
% cd /etc/apt/sources.list.d
% sudo wget http://packages.mccode.org/debian/mccode.list
% sudo apt-get update
for a Ubuntu/xenial (16.04)/Mint 16-17 system:
% cd /etc/apt/sources.list.d
% sudo wget http://packages.mccode.org/debian/mccode-xenial.list
% sudo apt-get update
for a Ubuntu/bionic (18.04)/Debian Buster/Sid (9-10)/Mint 18-19 system:
% cd /etc/apt/sources.list.d
% sudo wget http://packages.mccode.org/debian/mccode-bionic.list
% sudo apt-get update
All packages from the software repository are then available from e.g. Synaptic, Aptitude, Ubuntu Software Center, and basically all 'apt' clients.

To install a package from the command line, use
% sudo apt-get install <package_name>
Alternatively, you can also download manually each Debian package from:
http://packages.mccode.org/debian/dists/stable/main/
http://packages.mccode.org/debian/dists/trusty/main/binary-amd64
http://packages.mccode.org/debian/dists/xenial/main/binary-amd64
http://packages.mccode.org/debian/dists/bionic/main/binary-amd64
Some packages rely on others, and you might need to resolve all dependencies yourself. This is automatically done by Apt-clients and GDebi.

To install a single package, use:
# sudo dpkg -i <package_name-version.deb>
or
# gksudo gdebi-gtk <package_name-version.deb>
# sudo gdebi <package_name-version.deb>
NOTE: Many Debian packages have been created with the excellent Debreate.

Configuration for RedHat distributions (RedHat, CentOS, Fedora, ...)

RPM-based distributions may use alien for package conversion. However, we provide a few RPM packages.

Add the McCode repo to your system 
cd /etc/yum.repos.d
sudo wget http://packages.mccode.org/rpm/mccode.repo
sudo yum update
Our RPM repository URL is

Add the EPEL extensions to your system 
sudo yum install epel-release
sudo yum update

Add the MAX IV RedHat repository, where other X-ray oriented packages can be found:
cd /etc/yum.repos.d
sudo nano maxiv.repo
Type in the following content
[maxiv]
name = Max IV CentOS - $basearch
baseurl = http://pubrepo.maxiv.lu.se/rpm/el7/$basearch
enabled = 1
skip_if_unavailable=1
gpgcheck=0
sslverify=0

Then type a 'yum update' and install packages.

The MAX IV RPM repository URL are at:

Other repositories may be added, such as GhettoForge (GF), IUS.

List of available Debian packages

Package Name
 		In short
 		Description
abinit
[ 7.10.5 amd64 trusty ]
[ 8.2.3 amd64 trusty ]
[ 8.2.3 amd64 xenial ]
abinit-psp
[ 2 all ]
abinit-psp-jth (pawxml)
[ 1.0 all ]
abinit-psp-gbrv (paw)
[ 1.5 all ]
 ABINIT and pseudo potentials

Abinit

http://www.abinit.org/

 ABINIT package for electronic structure calculations.
Compiled with OpenMPI, OpenMP, and msym = 10368 to allow 6x6x6 supercells.
This psp package contains a full set of pseudopotentials, as gathered by ASE.

The installation location of pseudo potentials is in /usr/share/abinit/psp

X. Gonze et al, Computer Physics Communications 180, 2582-2615 (2009).

We recommend that you install the abinit-psp-jth, abinit-psp-gbrv and abinit-psp pseudo potentials.
adxv
[ 1.9.14 amd64 ]
 A program to display X-Ray diffraction images

https://www.scripps.edu/tainer/arvai/adxv.html
 Adxv can be used to display and analyze 2-D area detector data. It is optimized to display X-Ray crystallography diffraction images. The data may be displayed as a 1-D cross section, 2-D image or 3-D surface. Sequential images may be displayed as an animation. The magnification, contrast and color mapping are adjustable. Displayed data may be saved in a variety of formats including ASCII, SMV/IMG, TIFF, JPEG and Postscript.
Many common detector and data formats are recognized, including: ADSC Mar ccd Mar image plate (old and new format) Raxis II & IV Crystallographic Binary Format (CBF) XDS .pck files European Data Format (EDF) Numerical Python (NUMPY) Hierarchical Data Format (HDF5) Tagged Image File Format (TIFF) Raw binary integer and floating point data
Adxv is freely available to everyone. There is no registration, license or fee required to use it.
bigdft
[ 1.8.0 amd64 trusty ]
 BigDFT is a DFT massively parallel electronic structure code
bigdft
http://bigdft.org/

 BigDFT is a DFT massively parallel electronic structure code (GPL license) using a wavelet basis set. Wavelets form a real space basis set distributed on an adaptive mesh (two levels of resolution in our implementation). GTH or HGH pseudopotentials are used to remove the core electrons. Thanks to our Poisson solver based on a Green function formalism, periodic systems, surfaces and isolated systems can be simulated with the proper boundary conditions.
Pseudo potentials are included in the package. Tutorials and Manuals are in /usr/share/doc/bigdft.
On a multicore machine (SMP) you do not need MPI, as OpenMP will use available CPU's. Just launch 'bigdft', not 'mpirun -np N bigdft'.

L. Genovese et al, J. Chem Phys 129 014109 (2008)

This package is built with OpenMPI and OpenMP support.
bornagain
 [ 0.9.1 amd64 ]
[ 1.3.0 amd64 ] 		BornAgain - Simulate and fit neutron and x-ray scattering at grazing incidence (GISANS and GISAXS)

BornAgain

http://apps.jcns.fz-juelich.de/BornAgain

by C. Durniak, G. Pospelov, W. Van Herck, J. Wuttke

License: GPL3
 BornAgain is a free software package to simulate and fit small-angle scattering at grazing incidence (GISAS). It supports analysis of both X-ray (GISAXS) and neutron (GISANS) data. Its name, BornAgain, indicates the central role of the distorted-wave Born approximation (DWBA) in the physical description of the scattering process. The software provides a generic framework for modeling multilayer samples with smooth or rough interfaces and with various types of embedded nanoparticles.

The installation location is /usr/local/BornAgain
chimera
[ 1.15 amd64 ]
 Molecular Modeler

https://www.cgl.ucsf.edu/chimera/

License: UCSF

UCSF Chimera is a program for the interactive visualization and analysis of molecular structures and related data, including density maps, trajectories, and sequence alignments. It is available free of charge for noncommercial use.

Install location is /opt/UCSF

We encourage Chimera users to try ChimeraX for much better performance with large structures, as well as other major advantages and completely new features. Chimera is no longer under active development.
cif2hkl
[ 1.2_amd64 ]
 Convert crystallographic CIF/CFL/SHX/PCR to HKL F2 for McStas/McXtrace

by E. Farhi

License: EUPL
 Read a CIF/CFL/SHX/PCR crystallographic description and generates a HKL F^2 reflection list. Such files can then be used by e.g. the Mcstas components PowderN, Single_crystal and isotropic_Sqw.
* CrysFML by Juan Rodriguez-Carvajal and Javier Gonzalez-Platas, ILL and ULL, Tenerife, Spain (LGPL 3.0)
* Commission on Crystallographic Computing, IUCr Newsletter No.1, pp 50-58,
January 2003
* McStas: K. Lefmann and K. Nielsen, Neutron News 10, 20, (1999) ; P. Willendrup, E. Farhi and K. Lefmann, Physica B, 350 (2004) 735.

To use the software, launch 'cif2hkl' from a Terminal. Installation is in /usr/local/cif2hkl

A web service also exists at <http://barns.ill.fr/cif2hkl.html>
cp2k
[ 4.1 amd64 trusty xenial ]

Warning: We recommend you also upgrade the cp2k-data with the release 4.1 from here.		 Ab Initio Molecular Dynamics

cp2k

by CP2K developers group

https://www.cp2k.org/

License: GPL 2
 CP2K is a quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems. CP2K provides a general framework for different modeling methods such as DFT using the mixed Gaussian and plane waves approaches GPW and GAPW. Supported theory levels include DFTB, LDA, GGA, MP2, RPA, semi-empirical methods (AM1, PM3, PM6, RM1, MNDO, …), and classical force fields (AMBER, CHARMM, …). CP2K can do simulations of molecular dynamics, metadynamics, Monte Carlo, Ehrenfest dynamics, vibrational analysis, core level spectroscopy, energy minimization, and transition state optimization using NEB or dimer method.

https://www.cp2k.org/

This debian distribution is built with Scalapack, Blacs, openMPI.
dacapo
[ 2.7 amd64 ]
pseudo-potentials
[ 2 all ]
 Plane-wave ultra-soft pseudopotential code.

Dacapo

by DTU Fysik, Copenhagen

License: GPL2

https://wiki.fysik.dtu.dk/dacapo/
 Dacapo is a total energy program based on density functional theory. It uses a plane wave basis for the valence electronic states and describes the core-electron interactions with Vanderbilt ultrasoft pseudo-potentials.

To use the software, use dacapo_serial.run or through ASE (apt://python-ase).

B. Hammer et al, Phys.Rev. B 59, 7413 (1999).
dave
[ 2.3 amd64 ] 		DAVE - Data Analysis and Visualization Environment (neutron scattering)

Dave

http://www.ncnr.nist.gov/dave/

by Richard Azuah, NIST

License: NIST
 DAVE is an integrated environment for the reduction, visualization and analysis of inelastic neutron scattering data. It is built using IDL (Interactive Data Language) from ITT Visual Information Solutions,* which is a cross-platform application development tool with built-in graphics. All efforts have been made to ensure that DAVE is supported on Linux, Windows and MacOS X. It is available at no cost to users in two forms. The first is as a binary executable with an embedded IDL runtime license which can be used by anyone running on any of the three supported operating systems. In addition, for those who have an IDL development license, the complete source code for DAVE is also available.

 The main objective of DAVE is to provide a user friendly tool for scientists involved in neutron scattering research to quickly reduce, visualize and interpret their data. Currently, much progress has been made towards achieving this goal even though a lot still remains to be done. Support for several neutron scattering spectrometers at NCNR and PSI is included.

 DAVE: A comprehensive software suite for the reduction, visualization, and analysis of low energy neutron spectroscopic data, R.T. Azuah, L.R. Kneller, Y. Qiu, P.L.W. Tregenna-Piggott, C.M. Brown, J.R.D. Copley, and R.M. Dimeo, J. Res. Natl. Inst. Stan. Technol. 114, 341 (2009).

 The installation location is /usr/local/dave
dlpoly
[ 1.10 amd64 xenial ]
 General purpose (parallel and serial) molecular dynamics simulation package

https://www.scd.stfc.ac.uk/Pages/DL_POLY.aspx

by W. Smith, T.R. Forester and I.T. Todorov

License: STFC
 DL_POLY_Classic is a general purpose (parallel and serial) molecular dynamics simulation package derived from the package formerly known as DL_POLY_2 (Version 20) which was originally written by W. Smith and T.R. Forester at Daresbury Laboratory to support the CCP5 project `Computer Simulation of Condensed Phases'.

Users of the package are referred to the User Manual supplied.

This is the OpenMPI version. The 'gopoly' command will launch DL_POLY with 4 cores, or use 'mpirun -np NP DL_POLY.X'.
The dl-gui command will launch a GUI.

Data files (examples) are in /usr/share/dlpoly/data and documentation in /usr/share/doc/dlpoly
eiger2cbf
[ 160415 amd64 ]
 Converts HDF5 files from EIGER detectors to miniCBF format, with Bitshuffle-LZ4 compression

https://github.com/biochem-fan/eiger2cbf
 eiger2cbf is a simple program that converts diffraction images from EIGER in the HDF5 format to the miniCBF format. This program is intended to be used with MOSFLM. You do not need this program to process images with DIALS; DIALS can process HDF5 images directly (DIALS 1.2.0, which comes with CCP4 7.0.13).
elk-lapw
[ 4.3.6 amd64 trusty ]
[ 4.3.6 amd64 xenial
[ 6.2.8 bionic ]
 		All-Electron Density-Functional Electronic Structure Code

ELK

http://elk.sourceforge.net/

License: GPL3

WARNING: the efficiency is good with either OpenMP OR OpenMPI, not both. Use commands:
  • with MPI: OMP_NUM_THREADS=1 mpirun -n 8 elk-lapw ...
  • with OpenMP: elk-lapw ...
 All-Electron Density-Functional Electronic Structure Code
Elk is an all-electron full-potential linearised augmented-plane wave (FP-LAPW) code. By not including pseudo-potentials, Elk can provide very reliable high-precision results and works for every chemical element. Features include:
* FP-LAPW basis with local-orbitals
* APW radial derivative matching to arbitrary orders at muffin-tin surface (super-LAPW, etc.)
* Arbitrary number of local-orbitals allowed (all core states can be made valence for example)
* Total energies resolved into components
* LSDA and GGA functionals available
* Isolated molecules or periodic systems
* Core states treated with the radial Dirac equation
Elk is parallelized via OpenMP and MPI. Using OpenBLAS.

This version has been compiled with elk/src/modmain.f90:289 maxsymcrys=10368 to handle 6x6x6 supercells.
flatcone
[ 13.11 amd64 ]
Flatcone data treatment for neutron scattering triple-axis spectrometers
Flat Cone
http://www.ill.fr/tas

by Paul Steffens <steffens@ill.eu>

License: GPL3
 This application handles flat-cone data from IN20/IN14 TAS spectrometers at the ILL.
 To start the flatcone, type 'plotmultiple file' at the prompt.
 Any Matlab expression/command can, also be entered.
 
 The installation location is /usr/local/flatcone, which contains 'doc' and 'examples'
 The main command for using FlatCone is 'plotmultiple'.
 
 To use this software, you need to install the Matlab Compiler Runtime in /opt/MATLAB,
 so that you should have a directory /opt/MATLAB/MATLAB_Compiler_Runtime/v713/.
 If you install the MCR in an other location, assign the MCRROOT env variable to
 its location.
 
 Refer to <http://www.ill.fr/tas> for on-line documentation.
 Matlab is a registered trademark of The Mathworks Inc.
frida
[ 2.1.8 amd64 ]
 		Frida - Fast reliable interactive data analysis (neutron scattering)

Frida

http://apps.jcns.fz-juelich.de/doku/frida/start

by Joachim Wuttke <j.wuttke@fz-juelich.de>

License: GPL3
 Frida (Fast reliable interactive data analysis) is a versatile data analysis program with special routines for inelastic neutron scattering.

 It has been written for the analysis of inelastic neutron scattering data, and it contains highly specialized routines for this purpose. Its data model, however, is abstract and generic so that Frida can be applied to whatever data of the form y(x,z0,z1,...).

 Frida's main capabilities are:

    Import/export tabular data from/to various formats.
    Reorganize, bin, sort, clone data.
    Perform mathematical operations on the data.
    Automatically document all data manipulations.
    Fit the data with user-defined functions.
    Plot data and functions, generating publication-grade PostScript graphics.

 Besides, Frida is also a powerful pocket calculator.

 Frida is operated through a command-line interface. Commands are cryptic. Everything is designed to offer a maximum of computational power and flexibility for a minimum of typing. Learning Frida is not easy, but rewarding.

 Some example data files and documentation is available in /usr/local/share/frida
fullprof
[ 13.10 amd64 ]

FullProf - Crystallographic tools for Rietveld, profile matching and integrated intensity refinements of X-ray and/or neutron data (neutron diffraction)

FullProf

https://www.ill.eu/sites/fullprof/

by Juan Rodriguez-Carvajal <fullprof@ill.fr>

License: Unspecified (ILL,LLB) 		The FullProf Suite (for Windows and Linux) is formed by a set of crystallographic programs (FullProf, WinPLOTR, EdPCR, GFourier, etc...) mainly developed for Rietveld analysis (structure profile refinement) of neutron (constant wavelength, time of flight, nuclear and magnetic scattering) or X-ray powder diffraction data collected at constant or variable step in scattering angle 2theta.

 The different programs can be run either in stand alone form (from a console window or clicking directly in a shortcut) or from the interfaces WinPLOTR and/or EdPCR.

 The programs within the FullProf Suite are distributed in the hope that they will be useful, but WITHOUT ANY WARRANTY of being free of internal errors. In no event will the authors (or their institutions) be liable to you for damages, including any general, special, incidental or consequential damages arising out of the use or inability to use the programs (including but not limited to loss of data or data being rendered inaccurate or losses sustained by you or third parties or a failure of the program to operate with any other programs). The authors are not responsible for erroneous results obtained with the programs.

 The installation location is /usr/local/fullprof
 To start the FullProf toolbar, use 'tfp'
geant4
[ 10.05 amd64 bionic ]
[ 10.05 amd64 xenial ] 		Geant4 is a toolkit for the simulation of the passage of particles through matter.

g4

https://geant4.web.cern.ch/

License: Geant4 Software License
 Geant4 is a toolkit for the simulation of the passage of particles through matter. Its areas of application include high energy, nuclear and accelerator physics, as well as studies in medical and space science.

Installation location in /usr/local/geant4.10.05
Start with;
- cd /tmp; mkdir B1-test; cd B1-test/
- cmake /usr/local/geant4.10.05/share/Geant4-10.5.1/examples/basic/B1/
- make
- ./exampleB1
genx
[ 2.4.1 amd64 ]  		GenX is a versatile program for fitting X-ray and neutron reflectivity data (scattering)

GenX

http://genx.sourceforge.net/

by Matts Bjorck <Matts.Bjorck@gmail.com>

License: GPL3
 GenX is a versatile program using the differential evolution algorithm for fitting, primarily, X-ray and neutron reflectivity data, lately also surface x-ray diffraction data. The differential evolution algorithm is a robust optimization method which avoids local minima but at same is a highly effective. GenX is written in python and uses the wxpython package for the Graphical User Interface (GUI) Screenshot. A model to fit is defined either through a GUI plug-in or via a python script. The possibility to script everything makes it easy to develop completely new fitting model. Clearly, GenX is extremely modular, making it possible to extend the program with models and plug-ins for most fitting problems. At the present GenX is shipped with models for x-ray and neutron specular reflectivity, off-specular x-ray reflectivity and surface x-ray diffraction. A detailed description, of a older version, has been published in J. Appl. Cryst. 40, 1174 (2007).

 The installation location is /usr/local/genx
gpaw
[ 0.10.0 amd64 trusty 1.2 amd64 trusty 1.2_amd64_xenial ]
gpaw-setups
[ 0.9 all ]
 Grid-based projector-augmented wave method

GPAW

https://wiki.fysik.dtu.dk/gpaw/
 GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) method and the atomic simulation environment (ASE). It uses real-space uniform grids and multigrid methods, atom-centered basis-functions or plane-waves.

J. J. Mortensen et al, Phys Rev B, Vol. 71, 035109 (2005).
grasp
[ 6.87 amd64 ]
 		GRASP - graphical inspection, analysis and reduction of multi-detector data produced by the Small-Angle Neutron Scattering (SANS) instruments

Grasp

https://www.ill.eu/users/support-labs-infrastructure/software-scientific-tools/grasp/

by Charles Dewhurst <dewhurst@ill.fr>

License: Unspecified (ILL)
 GRASansP" is a Matlab 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.
 
 The installation location is /usr/local/grasp, which contains documentation.
 Examples can be found at http://www.ill.eu/instruments-support/instruments-groups/groups/lss/grasp/example-data
 
 To use this software, you need to install the Matlab Compiler Runtime in /opt/MATLAB,  so that you should have a directory /opt/MATLAB/MATLAB_Compiler_Runtime/v713/.
 If you install the MCR in an other location, assign the MCRROOT env variable to its location.
gsas
[ 1.1188 amd64 ]
 		GSAS - General Structure Analysis System (neutron/x-ray diffraction)

GSASEXPGUI

http://www.ncnr.nist.gov/xtal/software/gsas.html

by Allen C. Larson and Robert B. Von Dreele, B. H. Toby

License: NIST

 GSAS (General Structure Analysis System) is a comprehensive system for the refinement of structural models to both x-ray and neutron diffraction data. The GSAS package can be used with both single-crystal and powder diffraction data (Rietveld analysis), even both simultaneously. Neutron data can be either from single-wavelength instruments, or for those a bit more masochistic, time-of-flight instrumentation. Up to 99 different sets of data can be modeled using mixtures of up to 9 different phases.
 
 GSAS has been created by Allen C. Larson and Robert B. Von Dreele of Los Alamos National Laboratory. Executable versions of GSAS are distributed more-or-less freely (see the friendly message from the Regents of the University of California, below), but the source code is not distributed (don't complain to me on this one, I agree with you).
 
 The installation location is /usr/local/gsas
hdfview
[ 3.1.0 amd64 ]
 Java HDF Object viewer

License: HDF Group

https://www.hdfgroup.org/downloads/hdfview/

The official Debian package (2.9) can not read recent HDF files.

 HDFView software consists of the HDFView utility and the Java HDF Object Package.

HDFView is a visual tool written in Java for browsing and editing HDF (HDF5 and HDF4) files. Using HDFView, you can:

View a file hierarchy in a tree structure
Create new files, add or delete groups and datasets
View and modify the content of a dataset
Add, delete and modify attributes
HDFView uses the Java HDF Object Package, which implements HDF4 and HDF5 data objects in an object-oriented form.
horace
[ 2.13.11 amd64 ]
 		Horace - Visualisation and analysis  of large datasets from time-of-flight neutron inelastic scattering spectrometers.

Horace

http://horace.isis.rl.ac.uk/Main_Page

by Toby Perring <toby.perring@stfc.ac.uk>

License: ISIS
 Horace is a suite of programs for the visualisation and analysis
 of large datasets from time-of-flight neutron inelastic scattering spectrometers.
 
 To start Horace, use: horace
 Example files are included in the software, and can be used with e.g. 'demo_script'
 The installation location is /usr/local/horace
 
 To use this software, you need to install the Matlab Compiler Runtime in /opt/MATLAB,  so that you should have a directory /opt/MATLAB/MATLAB_Compiler_Runtime/v713/.
 If you install the MCR in an other location, assign the MCRROOT env variable to its location.
 
 Refer to <http://horace.isis.rl.ac.uk> for on-line documentation.
 Matlab is a registered trademark of The Mathworks Inc.
idl2matlab [ 1.6.1 amd64 ]
 IDL to Matlab/Scilab translato

http://idl2matlab.sourceforge.net/
Coordinators: Didier Richard <richard(at)ill.eu> and Emmanuel Farhi <farhi(at)ill.fr>

License: GPL2

An automatic translator from IDL to Matlab and Scilab.
The translation performs an IDL syntax check, and reports possible warnings and errors into a Log.
This library is quite big, and covers the most useful IDL/Matlab functions, particularly mathematical functions, basic plotting functions, widgets/uicontrols

Refer to http://idl2matlab.sourceforge.net/

A web service also exists at <http://barns.ill.fr/idl2matlab.html>

ifit
[ 1.10 amd64 ]
[ 2.0 amd64 ]
[ 2.0.2 amd64 ]
 		iFit generic data analysis and fitting to models

iFitResLibCal

http://ifit.mccode.org

by Emmanuel Farhi <farhi@ill.fr>

License: EUPL (GPL)
 Simple methods to be used for complex data analysis
 
 The iFit program provides a set of methods to load, analyze, plot, fit and optimize models, and export results. iFit is based on Matlab, but stand-alone version does not require a Matlab license to run. Any text file can be imported straight away, and a set of binary files are supported. Any data dimensionality can be handled, including event based data sets.
 
 The spirit of the software is to include simple object definitions for Data sets and Models, with  a set of methods that provide all the means to perform the usual data analysis procedures.
 - iData objects to hold data sets ; Import with:          iData('filename')
 - iFunc objects to hold models ;    Create new ones with: iFunc('expression')
 - fit model to data with: fits(data, model)
 - documentation is available in /usr/local/share/doc/ifit

 You can not define new Matlab functions in this stand-alone release, but can define new iFunc objects to hold your function body.

 Main functionalities are: [ iData Load Plot Math Fit Save Optimization iFunc Models ]

Contains special hooks with McStas, and computation of Phonons as well as ResLibCal.

 To use this software, you need to install the Matlab Compiler Runtime in /opt/MATLAB,  so that you should have a directory /opt/MATLAB/MATLAB_Compiler_Runtime/v713/.  If you install the MCR in an other location, assign the MCRROOT env variable to its location. This step can be automated by selecting the MCRInstaller package.

 To start iFit, use: ifit

 Refer to <ifit.mccode.org> for on-line documentation.
 Matlab is a registered trademark of The Mathworks Inc.

E. Farhi, Y. Debab and P. Willendrup, J. Neut. Res., 17 (2013) 5. DOI: 10.3233/JNR-130001
ifit-phonons
[ 1.10_amd64 ]
 iFit with Ab-initio packages to compute phonon dispersions.
SqwPhonons-logo
 A selection of ab-initio packages to be launched by iFit and ASE.

Includes: openmpi-bin, libxc1, libnetcdf-dev, phon, quantum-espresso-sssp, quantum-espresso, abinit-psp, abinit-psp, abinit-doc, abinit, python-matplotlib, gpaw-setups, gpaw, elk-lapw, ifit

To use this tool, start iFit, then type: help sqw_phonons
ifit-web-services
[ 1.9 all ]
[ 2.0.0 all ]
 		iFit services through the Web
 A selection of services provided by iFit. Converters, Computations. Includes sqw_phonons.
Once installed, access these services from a web browser at e.g. http://localhost/ifit-web-services
isaw
[ 1.9.1.18 amd64 ]
 		ISAW - Integrated Spectral Analysis Workbench (neutron scattering)

Isaw

http://ftp.sns.gov/ISAW/

by Dennis Mikkelson <mikkelsond@uwstout.edu>

License: GPL2

 The Integrated Spectral Analysis Workbench software project (ISAW) is a Platform-Independent system Data Reduction/Visualization. ISAW can be used to read, manipulate, view, and save neutron scattering data. It reads data from IPNS run files or NeXus files and can merge and sort data from separate measurements.
 
 Reference: J. Tao et al, NIMA 422 (2006) 562
 
 The installation location is /usr/local/isaw
lamp
[ 15.02 amd64 ]
[ 18.05 amd64 ]
 		LAMP (Large Array Manipulation Program)

LAMP

https://www.ill.eu/users/support-labs-infrastructure/software-scientific-tools/lamp/

by Didier Richard <lamp@ill.fr>

License: ILL
 LAMP (Large Array Manipulation Program) is designed for the treatment of data obtained from neutron scattering experiments at the Institut Laue-Langevin.
 LAMP provides a predictable and intuitive graphical user interface which integrates scientific visualisation with an enhanced data language. Many high level modules are predefined to enable interactive data analysis and visualisation of 2D , 3D data and atomistic representations.
 
  LAMP also provides:
 
    Input and output of various data-type files with CUSTOMIZED MODULES.
    Expansion and simplification of data with USER-MACROS in Interactive Data Language IDL.
    General fitting interfaces for 2D and SIMULTANEOUS FITS with CONSTRAINTS.
    Visualisation of calculated PHONONS and molecular VIBRATIONS.
    Cristal and Magnetic STRUCTURES with propagation vectors EDITOR.
    Miller planes in the CRYSTALLOGRAPHIC CELL easily animated to help visualise local structure.
    RECIPROCAL SPACE densities calculated from multiple instrument acquisition scans.
    Automatic ELECTRONIC LOG BOOKS updated in html format by a right click on images.
    Lamp , Nxml , NeXuS FILE BROWSER with snapshot images.
    Direct link to a powerful IMAGE-MANIPULATION module, Scan.
    The live control of an experiment with GEORGE.
    The same behaviour on Unix Motif platforms, MS_windows, MacIntosh.
    A distribution package for the scientific community with a FREE embedded IDL license.
    A LIVE-UPDATE feature to keep your application always up-to-date.
 
  Reference: D. Richard, M. Ferrand and G.J. Kearley, J. Neutron Research 4, 33-39, 1996.
 
  The installation location is /usr/local/lamp, which contains documentation.
looktxt
[ 1.4 amd64 ]
 a numeric data importer from text files
 E. Farhi

<http://looktxt.sourceforge.net/>
mcrinstaller
[ 7.13 amd64 ]
 		Matlab Compiler Runtime (free)

http://www.mathworks.com

 This is the Matlab Compiler Runtime installed in /opt/MATLAB,
 This package is needed to execute any Matlab compiled application (stand-alone) such as iFit <ifit.mccode.org>, grasp, flatcone, ...
 Matlab is a registered trademark of The Mathworks Inc.

Packaged by E. Farhi, ILL.
mcstas-suite
[ 2.2 amd64 ]
[ 2.3-py amd64 ]
[ 2.3-perl amd64 ]
 McStas is a general tool for simulating neutron scattering instruments and experiments

McStas

http://mcstas.org/

by P. Willendrup, E. Knudsen, K. Lefmann, E. Farhi, U. Filges <mcstas-users@mcstas.org>

License: GPL

McStas is based on a compiler that reads a high-level specification language defining the instrument to be simulated and produces C code that performs the Monte Carlo Simulation. The system is very fast in use, both when setting up the instrument definition and when doing calculations. Typical figures are 500000 neutron histories per second on a fast PC.

McStas supports triple-axis,  time-of-flight instruments, and polarised neutrons. It comes with a comprehensive manual and a library of well-tested components that include most standard elements of neutron scattering instruments, including steady-state and pulsed sources, monochromators/analysers, guides, collimators, vanadium and powder samples, velocity selectors and choppers, and a variety of detectors.

  • K. Lefmann and K. Nielsen, Neutron News 10, 20, (1999).
  • P. Willendrup, E. Farhi and K. Lefmann, Physica B, 350 (2004) 735.
mcxtrace-suite
[ 1.2 amd64 ] 		McXtrace is a general tool for simulating x-ray scattering instruments and experiments.

McXtrace

http://mcxtrace.org/

by E. Knudsen <mcxtrace-users@mcxtrace.org>

License: GPL
 McXtrace is a general Monte Carlo ray-tracing software for simulation X-ray beamlines and experiments, distributed under the open source license of GPL.

It is a collaborative effort between DTU Physics, European Synchrotron radiation Facility, Niels Bohr Insitute. Initial funding came from a grant under the NaBiIT program of the Danish Strategic Research Council DSF and from SAXSLAB ApS, in addition to the above parties.

It is built upon the code base of the proven and succesful neutron ray-tracing package McStas and today McXtrace and McStas share a central code repository.

A substantial amount of work has gone into creating this software package. If you enjoy it, and use it for your work please use this reference:

  • E Bergback Knudsen, Andrea Prodi, Jana Baltser, Maria Thomsen, P Kjer Willendrup, M Sanchez del Rio, Claudio Ferrero, Emmanuel Farhi, Kristoffer Haldrup, Anette Vickery, et al. Mcxtrace: a monte carlo software package for simulating x-ray optics, beamlines and experiments. Journal of Applied Crystallography, 46(3):679-696, 2013.
MDANSE
[ 1.2 amd64 trusty ]
[ 1.2 amd64 xenial ]
[ 1.3 amd64 trusty/xenial/bionic ]

 MDANSE - Molecular Dynamics Analysis for Neutron Scattering Experiments.

mdanse

https://mdanse.org/

License: CeCILL

code at https://code.ill.fr/scientific-software/mdanse
 MDANSE is an interactive analysis program for Molecular Dynamics simulations. It is especially designed for the computation and decomposition of neutron scattering spectra, but also computes other quantities.
This distribution includes the Molecular Modelling Toolkit (MMTK), a library which contains a wide range of algorithms that are used in molecular simulations and modelling. It is particularly useful for data analysis and visualization, but also contains standard techniques such as energy minimization and Molecular Dynamics.

The installation location is /usr/local/mdanse. Example files are in /usr/share/doc/mdanse.

Packaged by E. Pellegrini, ILL.

cite: J. Chem. Inf. Model. 2017, 57, 1−5 - DOI: 10.1021/acs.jcim.6b00571
mfit
[ 4.3.3 amd64 ]

Warning: deprecated. We recommend you rather use ifit instead (see above). 		MFit/MView/Rescal - Matlab based data analysis for fitting (neutron scattering)

MFit

http://www.ill.eu/instruments-support/computing-for-science/cs-software/all-software/matlab-ill/

by Emmanuel Farhi <farhi@ill.fr> and others

License: GPL
 Mfit (now v4.3.3, Aug 23rd 2005) - refer to iFit for a more recent software
 provides an attractive and easy to use point-and-click interface. Most operations (including guessing starting parameters for fits) can be performed via the mouse. The main object is to fit any type of (x,y) data with any fit function (even combinaisons), with various efficient algorithms. Many options are also available. A full manual is available at <http://www.ill.eu/instruments-support/computing-for-science/cs-software/all-software/matlab-ill/mfit/home/>
 
 Mview (now v4.2.2,  Aug 22nd 2005) - refer to iFit for a more recent implementation
 is designed in order to manipulate and display up to 20 data files. As Mfit, it is also a point-and-click application. A link with MFit permits to fit each data set.
 
 Rescal (now v5.1) - refer to ResLibCal for a more recent software
 is a specific application to compute 4D resolution ellipsoid for inelastic scattering instruments (neutrons... Popovici's and Cooper Nathan's methods). It is then possible to use it through a 4D convolution in a fit function (see "trix", which is included in archives).(note : this program is not based on "Rescal" famous code). A full manual is available at <http://www.ill.eu/instruments-support/computing-for-science/cs-software/all-software/matlab-ill/rescal-for-matlab>
 
 The installation location is /usr/local/mfit_mview

Warning: deprecated. We recommend you rather use ifit instead (see above).
neutron-encyclopedia
[ 1.0.1 amd64 ]
 NeutronEncyclopedia is an encyclopedia (2004/2005) which explains neutrons and the unique properties that make them so useful to science and industry.

neutrons4science

https://www.ill.eu/neutronencyclopedia/

by A. Filhol <filhol@ill.fr>

License: Artistic
 NeutronEncyclopedia is a standalone version of the encyclopedia “Exploring matter with neutrons” published in 2004/2005 by iMediaSoft (out of business) and now public domain. This encyclopedia explains neutrons and the unique properties that make them so useful to science and industry. The experimental instruments and the large array of neutron applications in the most advanced fields of physics, chemistry, biology, and materials science are described in an interactive manner. The encyclopedia is destined for students, teachers, research institutes, industry and the general public interested in these topics. The multiple-entry points permit each and every visitor to explore the CD-ROM according to their own knowledge and curiosity. Both 2D and 3D animations, and virtual reconstruction with computer-generated images are used to guide visitors through this scientific and technical world, helping to make it both understandable and exciting.
However, it is important to note that the project was never finished and iMediaSoft published a version that lacks many corrections.
Topics from the content: Science:
* The neutron, Neutrons and states of matter; Internal motions of matter; Magnetism; Nuclear physics; Materials. Neutron Sources:
* Natural sources; Transportable sources; High flux sources; Sources of the future; Miscellaneous. Tools for neutron science: Neutron activation; Transmission imaging; Diffraction; Small-angle scattering; Reflectometry; Inelastic scattering; Quasielastic scattering; Spin echo; Isotopic substitution; Neutron holography; Recoil and gamma spectrometry; neutrons optics; Neutron detection; Sample environment Applications
The multimedia encyclopedia "Exploring matter with neutrons" was created by Alain FILHOL (main author, Institut Laue-Langevin) and Dan BOG (developer and editor through iMediaSoft & Nanopolis). Today the "Exploring matter with Neutrons" encyclopedia is reproduced here with permission of Alain FILHOL and Dan BOG.

Installation location is /opt/ILL/NEUTRON-ENCYCLOPEDIA
neutrons4science
[ 2.6.1 amd64 ]
 		Neutrons4Science offers a set of multiplatform and interactive 3D animations for the education (neutron scattering)

neutrons4science

https://www.ill.eu/neutrons4science/

by Alain Filhol <filhol@ill.fr>

License: ILL, Ipter
 Enter the world of neutrons! They are a powerful and highly acclaimed tool not only for the study of condensed matter (the world we live in) but also for confirming our current understanding of physics. What's more, you don't even need to be a scientist to use Neutrons4Science. Just be curious!
 
 Neutrons and protons are elementary particles constituting the nucleus of atoms. The neutron has no electric charge but has a spin and a magnetic moment. Neutron beams - like beams of X-rays, electrons or muons - are valuable tools for studying the multitude of materials that surround us in our daily lives (alloys, magnets, superconductors, polymers, colloids, proteins, biological systems, ...). However, the way neutrons interact with matter is quite unique and, as a result, it can often reveal to us what is normally hidden. With Neutrons4Science you can discover one of the many types of neutron spectroscopy.
 The neutron also answers questions on the very foundations of physics, helping us to solve some of the great mysteries of the universe (Is the Grand Unified Theory valid? Is there a fifth fundamental force? ...) As an example, Neutrons4Science gives you insights to a brand new method of neutron spectroscopy that takes advantage of the quantum states of this light neutral particle.
 
 Neutrons4Science lets you experience neutron science through three interactive 3D animations:
 * ThALES: Use a neutron spectrometer (ThALES) as if you were performing a real experiment.
 * Magnons: Discover the spin waves that exist inside magnetic materials and understand how ThALES can observe them.
 * GRANIT: Discover an innovative gravitational spectrometer (GRANIT) based on neutron quantum states in a gravitational field."
 
 These three educational animations were developed with the help of scientists at the "Institut Laue-Langevin", one of the world's flagship facilities for neutron science.
 
 The installation location is /usr/local/neutrons4science
nmoldyn
[ 3.0.9 amd64 ]

Obsolete: use MDANSE package. Does not run under modern systems.
 nMoldyn - Computation and decomposition of neutron scattering intensities from Molecular Dynamics trajectories (ILL)

nMoldyn

https://forge.epn-campus.eu/projects/nmoldyn

by K. Hinsen, M.R. Johnson, G. Kneller,E. Pellegrini <pellegrini@ill.fr>

Obsolete: use MDANSE package
 nMOLDYN is an interactive analysis program for Molecular Dynamics simulations. It is especially designed for the computation and decomposition of neutron scattering spectra, but also computes other quantities.

 This distribution includes the Molecular Modelling Toolkit (MMTK), a library which contains a wide range of algorithms that are used in molecular simulations and modelling. It is particularly useful for data analysis and visualization, but also contains standard techniques such as energy minimization and Molecular Dynamics.

 The installation location is /usr/local/nmoldyn.
 
This project has been renamed MDANSE (see above)
octopus
[ 7.1 trusty xenial ]
 DFT ab-initio code

http://octopus-code.org/wiki/Main_Page

License: LGPL3, GPL2, ...
 Octopus is a scientific program aimed at the ab initio virtual experimentation on a hopefully ever-increasing range of system types. Electrons are described quantum-mechanically within density-functional theory (DFT), in its time-dependent form (TDDFT) when doing simulations in time. Nuclei are described classically as point particles. Electron-nucleus interaction is described within the pseudopotential approximation.

Pseudo-potentials are provided in /usr/share/octopus
orange3-quasar
[ 0.5.0 amd64 ]
 Extends Orange Workflow to handle spectral and hyperspectral analysis.

Orange3

https://github.com/Quasars/orange-spectroscopy

https://quasar.codes/

License: BSD-like
 Quasar is an open source project, a collection of data analysis toolboxes extending the Orange suite. We empower researchers from a variety of fields to gain better insight to their data through interactive data visualization, powerful machine learning methods and combining different datasets in easy to understand visual workflows.
Freely build visual data analysis workflows that help answer your scientific questions. Combine widgets that share input and output types. There are infinite possibilities!
A whole is always more than the sum of parts. Although our journey started with (hyper)spectral data through the Orange Spectroscopy toolbox, Quasar intends to add file readers, processing tools, and visualizations for multiple measurement techniques. This will allow the discovery of new scientific insights through multimodal data analysis.
Orange is a general purpose machine learning and visualization platform which can be extended. Quasar is a variant of Orange and includes pre-installed toolboxes for scientific data analysis. Another member of the Orange family is Single Cell Orange, specializing in genomics data.
This package provides Orange3 with Quasar/Spectroscopy.

Launch: Quasar from the Dash/Search or 'quasar' command.
orange3-oasys
[ 1.2.7 amd64 ]
 Extends Orange Workflow to model synchrotron X-ray optics.

oasys

https://github.com/oasys-kit/OASYS1
https://www.aps.anl.gov/Science/Scientific-Software/OASYS
M. S. del-Rio and L. Rebuffi. License: MIT
 OASYS (OrAnge SYnchrotron Suite) is a graphical environment
for optic simulation software used in synchrotron facilities,
based on Orange 3.

This package provides Shadow/XRayLib/SRW in a simplified Orange3 environment. All python libraries are included (virtual env).
Installation is in /usr/local/oasys1env and examples are in /usr/share/doc/orange3-oasys. launch 'oasys' or search for it as an App.
phon
[ 1.40 amd64 ]
[ 1.41 amd64 ]
 PHON - A program to calculate phonons using the small displacement method

http://www.homepages.ucl.ac.uk/~ucfbdxa/phon/

by Dario Alfe
 The program PHON calculates force constant matrices and phonon frequencies in crystals. From the frequencies it also calculates various thermodynamic quantities, like the Helmholtz free energy, the entropy, the specific heat and the internal energy of the harmonic crystal. The procedure is based on the small displacement method, and can be used in combination with any program capable to calculate forces on the atoms of the crystal.

Computer Physics Communications 180, 2622-2633 (2009)
python-pyne
[ 0.5 amd64 ]

Xenial 16.04: also install libhdf5-7
 PYNE - The Nuclear Engineering Toolkit

pyne

http://pyne.io/

pyne-dev@googlegroups.com
 PyNE is a suite of tools to aid in computational nuclear science & engineering. PyNE seeks to provide native implementations of common nuclear algorithms, as well as Python bindings and I/O support for other industry standard nuclear codes.

Includes MOAB <https://bitbucket.org/fathomteam/moab> and PyTAPS <https://pythonhosted.org/PyTAPS/index.html>.


python-ase
[ 3.9.1 all 3.14.0 all ]
python-ase-qe-spglib
[ 0.1.16 amd64 ]
 Atomic Simulation Environment

https://wiki.fysik.dtu.dk/ase/index.html
 ASE is an Atomic Simulation Environment written in the Python programming language with the aim of setting up, stearing, and analyzing atomic simulations.
ASE is part of CAMPOS, the CAMP Open Source project.
ASE contains Python interfaces to several different electronic structure codes including Abinit, Asap, Dacapo, Elk, GPAW and SIESTA.
This package provides the Python 2 modules.

The ASE-QE package provides an ASE-QuantumEspresso interface. We also recommend to install the abinit-psp abinit-psp-jth abinit-psp-gbrv and quantum-espresso-sssp packages.
python-hdf5storage
[ 0.1.13 all ]
 hdf5storage

https://pythonhosted.org/hdf5storage/
 This package is made available for trusty/jessie.
python3-pyhst2
[ 2019a amd64 (MPI) ]
[ 2019b amd64 (MPI/CUDA) ]
 Python High Speed Tomography

https://gitlab.esrf.fr/mirone/pyhst2

A. Mirone ESRF. License GPL2
 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.

Launch:
  • pyhst_2_2019b input.par `hostname`,0 (to use 1st GPU)
  • pyhst_2_2019b input.par (to use only MPI)
The CUDA version is built with NVIDIA Cuda support (requires an NVIDIA GPU). It also comes with a set of test files in /usr/share/doc/python3-pyhst2-cuda

Test the installation with e.g.:
  • cd /usr/share/doc/python3-pyhst2-cuda
  • python3 nonregression.py
When no GPU is specified, a pure MPI computation is used. In addition, you may install the ASTRA Toolbox to make use of the SIRT filter.
python3-pynx
[ 2019.2.6 amd64 ]
 Python toolkit for accelerated Nano-structures Crystallography and Coherent X-ray Imaging techniques.

http://ftp.esrf.fr/pub/scisoft/PyNX/

V. Favre-Nicolin ESRF
License: CeCILL-B

 The PyNX 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

* J. Appl. Cryst. 44 (2011), 635-640 Fast computation of scattering maps of nanostructures using graphical processing units

Installation resides in:
-  /usr/local/lib/python3.6/dist-packages/PyNX-2019.2.6-py3.6.egg/

Test with command:
- pynx-test.py opencl live_plot

A few example Python Notebooks reside with the documentation and some data set in:
- /usr/share/doc/python3-pynx
python-phonopy
[ 1.11.10 all ]
 PHONOPY open source package for phonon calculations at harmonic and quasi-harmonic levels.

https://atztogo.github.io/phonopy/

togo.atsushi.f40@kyoto-u.jp
 Phonopy is an open source package for phonon calculations at harmonic and quasi-harmonic levels.

Selected features Phonon band structure, phonon DOS and partial-DOS Phonon thermal properties: Free energy, heat capacity (Cv), and entropy Phonon group velocity Thermal ellipsoids / Mean square displacements Irreducible representations of normal modes Quasi-harmonic approximation: Thermal expansion, heat capacity at constant pressure (Cp), Mode Grüneisen parameters Non-analytical-term correction: LO-TO splitting (Born effective charges and dielectric constant are required.) Interfaces to calculators: VASP, VASP DFPT, Abinit, Pwscf, Siesta, Elk, FHI-aims, Wien2k, CRYSTAL Python APIs

Phonon database: A collection of first principles phonon calculations is available as open data at http://phonondb.mtl.kyoto-u.ac.jp/ , where the raw data of phonopy & VASP results are downloaded.
quantum-espresso-sssp
[ 0.7 all ]

you should remove the quantum_espresso-data package, which may conflict and lead simulations to produce strange results.
 Electronic-Structure and Ab-Initio Molecular Dynamics Suite (pseudo-potentials)

qe

http://www.quantum-espresso.org/
 Quantum ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving, ultrasoft, and PAW).

This package contains a full set of pseudo-potentials PAW/US/NC from the SSSP library accuracy set, version 0.7. DeltaCodes=0.31 meV.

Test calculations have been performed with
kpoints=6; ecut=1500 [eV]; smearing=0.27 [eV]
but the actual values depend on the elements and crystal structure. Suggested settings are specified at http://materialscloud.org/.


P. Giannozzi, et al J.Phys.:Condens.Matter, 21, 395502 (2009).
Pseudo potentials from http://materialscloud.org/ by Ivano E. Castelli
To be used within ASE, we recommend to install the python-ase-qe-spglib package.
rescal
[ 15.08 amd64 ]
 ResCal - legacy Neutron TAS resolution calculation The legacy RESCAL TAS resolution calculation (source code and executable)
reslibcal
[ iFit 1.10 amd64 ]
[ iFit 2.0 amd64 ] 		ResLibCal - Neutron TAS resolution calculation

ResLibCal

http://ifit.mccode.org/Applications/ResLibCal/doc/ResLibCal.html

by Emmanuel Farhi <farhi@ill.fr> and others

License: EUPL
 The ResLibCal application gathers a set of analytical computation methods to estimate the resolution function of a triple-axis neutron spectrometer (TAS), with Cooper-Nathans, Popovici and full Monte-Carlo (McStas) methods.

This is part of iFit <http://ifit.mccode.org>.
restrax
[ 5.2.4 amd64 ]
 ResTrax - Monte Carlo data analysis for three-axis neutron spectrometers

ResTrax

http://neutron.ujf.cas.cz/restrax/

by Jan Saroun <saroun@ujf.cas.cz> and Jiri Kulda

License: GPL2
 The software package RESTRAX has been developed in the last decade into an efficient tool for neutron ray-tracing simulations of neutron scattering instruments, useful for instrument design, optimization of experimental conditions and analysis of experimental data.
 
 The installation location is /usr/local/restrax.
 Java VM must be installed to run this software.
root
[ 6.18.00 amd64 (bionic) ]
[ 6.18.00 amd64 (xenial) ]
 ROOT is a modular scientific software toolkit.

root

https://root.cern.ch/
 A modular scientific software toolkit. It provides all the functionalities needed to deal with big data processing, statistical analysis, visualisation and storage. It is mainly written in C++ but integrated with other languages such as Python and R.

Installation goes in /usr/local/root
To start it, search for ROOT as an App.
sasfit
[ 0.93.5 amd64 ]
 SASfit - Software package for fitting small-angle scattering curves (neutron scattering)

SASfit

https://kur.web.psi.ch/sans1/SANSSoft/sasfit.html

by Joachim Kohlbrecher <joachim.kohlbrecher at psi.ch>

License: GLP3
 SASfit has been written for analyzing and plotting small angle scattering data. It can calculate integral structural parameters like radius of gyration, scattering invariant, Porod constant. Furthermore it can fit size distributions together with several form factors including different structure factors. Additionally an algorithm has been implemented, which allows to simultaneously fit several scattering curves with a common set of (global) parameters. This last option is especially important in contrast variation experiments or measurements with polarised neutrons. The global fit helps to determine fit parameters unambiguously which by analyzing a single curve would be otherwise strongly correlated. The program has been written to fulfill the needs at the small angle neutron scattering facility at PSI (kur.web.psi.ch). The numerical routines have been written in C whereas the menu interface has been written in tcl/tk and the plotting routine with the extension blt.
 
 The installation location is /usr/local/sasfit
sasview
[ 2.2.1 amd64 (old) ]
 SASView - Software package for fitting small-angle scattering curves (neutron scattering)

SANSView

http://www.sasview.org/

by Mathieu Doucet <doucetm@ornl.gov>

License: GPL3
 SasView/SANSView is a Small Angle Scattering Analysis Software Package, originally developed as part of the NSF DANSE project under the name SansView, now managed by an international collaboration of facilities. Feedback and contributions are welcome and encouraged.

 The installation location is /usr/local/lib/python2.7/dist-packages/sasview
siesta
[4.0.1 trusty xenial ]
 siesta
SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids.

https://departments.icmab.es/leem/siesta/

License: GPL 3
 SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. SIESTA's efficiency stems from the use of strictly localized basis sets and from the implementation of linear-scaling algorithms which can be applied to suitable systems. A very important feature of the code is that its accuracy and cost can be tuned in a wide range, from quick exploratory calculations to highly accurate simulations matching the quality of other approaches, such as plane-wave and all-electron methods.
The possibility of treating large systems with some first-principles electronic-structure methods has opened up new opportunities in many disciplines. The SIESTA program is distributed freely to academics and has become quite popular, being increasingly used by researchers in geosciences, biology, and engineering (apart from those in its natural habitat of materials physics and chemistry). Currently there are several thousand users all over the world, and the paper describing the method (J. Phys. Cond. Matt. 14, 2745 (2002)) has received more than 6000 citations so far.

pseudo potentials (TM and FHI) are provided in /usr/share/siesta
simres
[ 6.1.2 amd64 ]
 SimRes - Monte Carlo simulations for three-axis neutron spectrometers

simres

http://neutron.ujf.cas.cz/restrax/

by Jan Saroun <saroun@ujf.cas.cz>

License: GPL2
 The software package RESTRAX has been developed in the last decade into an efficient tool for neutron ray-tracing simulations of neutron scattering instruments, useful for instrument design, optimization of experimental conditions and analysis of experimental data.
 
 The installation location is /usr/local/simres
spinwave
[ 1-2011 amd64 ]

 SpinWave - An easy-to-use and versatile software to calculate spin waves in any arbitrary magnetic lattice

http://www-llb.cea.fr/logicielsllb/SpinWave/SW.html

Sylvain Petit, LLB CEA/Saclay


 An easy-to-use and versatile software to calculate spin waves in any arbitrary magnetic lattice

Since the 1950’s, spin wave theory has been of fundamental importance in condensed matter physics. Spin waves are obtained from the linearization of the equation of motion, and can be seen as precession modes of the magnetically ordered structure, with typical energies of a few meV (or THz). Spin wave dispersions are routinely measured by neutron spectroscopy, and provide information about the coupling between spins and magnetic anisotropy parameters.

A spin wave calculating code, SpinWave, has been developed at the Laboratoire Léon Brillouin and is now freely available.

Examples in /usr/share/doc/spinwave
Executable is 'spinwave'
vDiffraction
[ 1.0.2 amd64 ]
 vDiffraction - This game is a fun way to discover the world of crystals and their symmetries through diffraction.

vdiffraction

https://www.ill.eu/vdiffraction

Alain Filhol <vdiffraction@ill.eu>

License: GPL2
 Crystals are characterised by the fact that their constituents are arranged in a highly ordered structure. This internal order and its symmetry is clearly visible in the diffraction patterns produced by any crystal. It is this symmetry which is also gives crystals their often amazing shapes, making them highly prized by rockhounds. Whether you are a senior scientist, a student, or just curious about science, vDiffraction is a serious game that will let you try your hand at crystal diffraction so that you can begin to understand how scientists identify the symmetry characteristics of a crystal. This is the first, crucial step towards understanding the atomic and molecular structure of a crystalline material, in other words what type of atoms and molecules make up the crystal and how they are organised.


vitess
[ 3.3 amd64 ]		 VITESS - Virtual Instrumentation Tool for Neutron Scattering at Pulsed and Continuous Sources (neutron scattering)

Vitess

http://www.helmholtz-berlin.de/forschung/grossgeraete/neutronenstreuung/projekte/vitess/index_en.html

by Klaus Lieutenant <vitess@helmholtz-berlin.d>

License: GPL
 VITESS is a tool for simulation of neutron scattering instruments for neutron scattering at pulsed and continuous sources. Using VITESS, you can simulate a large variety of instruments at all major current and future neutron sources, including the European Spallation Source (www.esss.se), which is currently being designed. VITESS is supported by a graphical user interface (GUI), making it simple for you to compose your instrument and run simulations. You can use VITESS on a Windows, Linux or Macintosh computer. Simply choose the appropriate download file on the right and install VITESS on your computer. The VITESS installation includes some example instruments to demonstrate the main features of the program. You can also use the examples as an initial aid for your own instruments.
 
 The installation location is /usr/local/vitess
vtas
[ 0.6 amd64 ]
 vTAS - A Virtual Three Axis Spectrometer (neutron scattering)

vTAS

https://www.ill.eu/users/support-labs-infrastructure/software-scientific-tools/vtas/

by Y. Raoul, A. Filhol, A. Bouvet

License: EUPL
 Using a Three Axis Spectrometer (TAS) is not easy since one has constantly translate parameters from real space to reciprocal space and vice versa
 The goal of vTAS is to provide an interactive and graphical display of both the instrument configuration and the corresponding measured space thus making easier the understanding of the behavior of the instrument and its limits.
 vTAS supports both the classical TAS geometry and the multiplexed geometry of FLATCONE. Other geometries are available through the vTAS suite described below.
 
 Simulation mode: vTAS allows experimentation with sample parameters, for example the Miller indices of the unit cell, whilst maintaining a representation of the instruments physical state, for example the location of the walls around the instrument, and its angular limits.
 The instrument resolution function is computed using the Cooper Nathan's method. A yet untested McStas like Monte Carlo approach is also available but for the bundled version only.
 
 Data viewer mode: vTAS is capable of reading ILL TAS data files. It displays both the data and the corresponding instrument configuration.
 
 Ref.: "The vTAS suite: a simulator for classical and multiplexed three-axis neutron spectrometers"
       M. Boehm, A. Filhol, Y. Raoul, J. Kulda, W. Schmidt, K. Schmalzl,
       Nuclear Inst. and Methods in Physics Research, A (2013) 697, 40-44.
 
 The installation location is /usr/local/vtas
 There are 3 interfaces: vTAS, vUFO and vIMPS
wcs2kml
[ 0.2.1 trusty/xenial ]
[ 0.2.1 bionic ]
wcs2kml - Converts astrophysical images into a Sky in Google Earth friendly format

https://code.google.com/archive/p/wcs2kml/

License: Apache 2
 Professional astronomers typically store their imaging data in a binary format called FITS that has internal headers known as a WCS (World Coordinate System) that specify the location of the image on the sky.

This project consists of an API and several tools for converting FITS images with WCS information into imagery that can be viewed directly in Sky in Google Earth.

The conversion involves warping the input image from its native spherical coordinate system to the lat-long coordinate system and writing out an accompanying KML document describing the location of the image on the sky.

This was compiled from the original wcs2kml source code, with a few patches to adapt to libpng16. Source code is included as well as Makefile in /usr/share/doc/wcs2kml


Last update: March 2020 by E. Farhi <emmanuel.farhi@synchrotron-soleil.fr> - mccode.org