Beamline Phone Number:
+44 (0) 1235 778711
Principal Beamline Scientist:
Alessandro Bombardi
Tel: +44 (0) 1235 778087
E-mail: [email protected]
Email: [email protected]
Tel: +44 (0) 1235 778056
The MaRS software is a simple web-based application that can be used to simulate the expected magnetic scattering in resonant and non-resonant conditions. The web-based form is accessible on the Diamond intranet, that we do hope to make soon available on the Internet.
Such a tool can be used to establish the feasibility of an experiment and also help in driving the data collection to maximize the users’ chances to distinguish between possible magnetic ordering solutions.
Rapidly viewing data from previous data collections has been improved significantly using a python based graphical interface tailored specifically to I16 called “I16_Data_Viewer”. This simple to use and robust software package performs routine analysis tasks such as data normalisation, profile fitting, generation of detector regions of interest and creation of publication quality plots. Commonly used metadata for each scan is displayed prominently and data from past beam times can be searched and viewed. This software has been developed by beamline staff and is open access and published online for user access.
Our fixed position area detectors – the Pilatus3-100K and the Quad Merlin now have their calibrated positions recorded in the scan metadata, allowing automated conversion of the full frame of each image to the sample reciprocal space. Such processing allows us to rapidly view diffraction data in a very natural way – not as a detector image but an object in reciprocal space. This capability makes simple the analysis of complex peak shapes to, for example, separate broadening due to strain from broadening due to crystallite degradation. Multiple scans can also be re-mapped together to produce high resolution reciprocal space maps over large areas of reciprocal space. The processing step works either from the GDA command line as a process run at the end of a scan, or it can be run offline. The reciprocal space map is produced in a nexus file and can be viewed using standard visualization libraries such as Dawn, Python and MATLAB.
The python package "Dans_Diffraction" provides a simple way to calculate structure factors, x-ray properties and scattering geometires for crystal structures defined by CIFs (e.g. "crystal.cif").
The software is available on the beamline and is open-source and will work in most python environments.
Users can easily simulate scattering conditions where multiple scattering is expected. Such a tool can be precious in establishing the feasibility of an experiment and we do hope to make it also soon available in a web-based interface to be accessed during the proposal submission if needed. It is currently available as part of the Dans_Diffraction python package.
Diffuse Multiple Scattering (DMS) has been central to two recent papers (Phys. Rev. Materials 5 2021, L120601, Adv. Mater. 2022, 34, 2106827 2022). This has been possible because of the in house development of a suit of DMS analysis tools. These include a numerical solver for triple intersections and a slider based tool to provide starting values for fitting DMS lines in images which can then be passed to numerous minimisers such as Nelder-Mead, Powell, basin hopping and genetic algorithms for precise lattice parameter determination.
Simulation package for the I16 6-circle kappa diffractometer at Diamond Light Source Ltd.
Implements diffcalc functionality in Blender and uses it to animate a model of the diffractometer.
If used for your research, please credit Aurys Silinga.
This is a list of software commonly used on the beamline, frequently used by beamline staff and users.
Name |
Author |
Description |
Link |
---|---|---|---|
GDA | Diamond | High level control and analysis of beamline systems through interactive console, plot live data | https://www.diamond.ac.uk/OpenGDA/ |
EPICS | - | Handles realtime control of all beamline systems | https://epics-controls.org/ |
Dawn | Diamond | View data files and plot data | https://dawnsci.org/ |
Name |
Author |
Description |
Environment |
Requirements |
Available From |
---|---|---|---|---|---|
Py16 | Dan Porter | Python Module for loading I16 data files (.dat), automatically making corrections, integrating and plotting. | ipython/ jupyter | Python 2/3, matplotlib, numpy, scipy, pil, h5py | https://github.com/DanPorter/Py16 |
I16_Data_Viewer | Dan Porter | Graphical front end for Py16 for quickly plotting and analysing I16 data | ipython | as above + tkinter (standard) | https://github.com/DanPorter/Py16 |
BabelScan | Dan Porter | BabelScan is a format independent data structure for holding different types of data from a scan file. | any python | Python 2/3, numpy, h5py, imageio | https://github.com/DanPorter/babelscan |
Dans_Diffraction | Dan Porter | Read cif+mcif files, edit crystal structure+create superstructure, calculate x-ray, neutron, magnetic, resonant structure factors, plot structures, powder patterns and diffraction patterns, write input files and analyse output files for FDMNES. | any python | python 2/3. matplotlib, numpy, scipy, tkinter |
https://github.com/DanPorter/Dans_Diffraction pip install dans-diffraction |
MaRS | Alessandro Bombardi | Web based simulation of non-resonant and resonant magnetic scattering | Web | None | |
dlstools | Steve Collins | Read nexus files, plot + fit data | python/ jupyter | ||
tensor-scattering-calculation-master | Steve Collins | Calculate scattering tensors | python/ jupyter | Python 2.7, | |
MXRS | Alessandro Bombardi | Calculate magnetic x-ray scattering | python/ jupyter | Python 3.4+, numpy, matplotlib, scipy | |
DMS_Code | Gareth Nisbet | Simulate diffuse multiple scattering | python/ dawn | cctbx | |
Crystal | Federica Fabrizi | Read cif files, simulate structure factors, resonant scattering | python | cctbx | |
samplerecord | Alessandro Bombardi | Web based database of samples in the dessicator cabinet | Web | Non | http://172.23.169.26/ |
i16sim | Aurys Silinga/ Dan Porter | Simulate the 6-axis diffractometer using DiffCalc in a Blender envrionment | Blender | Blender, Python, Diffcalc | https://github.com/DanPorter/i16sim |
Name |
Author |
Description |
Envrionment |
Requirements |
Available From |
---|---|---|---|---|---|
scisoftpy | Diamond | Implementation of numpy, including functions to load data, fitting and plotting in Dawn | Dawn, python/ jython | Unknown? | https://github.com/DawnScience/scisoft-core/tree/master/uk.ac.diamond.scisoft.python/src/scisoftpy |
Mapper | Peter Chang | Convert pilatus scans into 3D reciprocal space maps | Dawn (nightly?), jython | Not portable | Beamline computers? |
Dawn | Diamond | Load and plot data from different instruments. Good python editor. Display 3D recriprocal space maps. | Linux/ Windows/ Mac? | None | https://dawnsci.org/ |
Name |
Author |
Description |
Envrionment |
Requirements |
Available From |
---|---|---|---|---|---|
X-Ray Database | Element x-ray properties and data booklet | Web | Web | https://xdb.lbl.gov/Section1/Periodic_Table/X-ray_Elements.html | |
CXRO |
X-Ray Interactions With Matter |
Web | Web | https://henke.lbl.gov/optical_constants/ | |
ISOTROPY Software Suite | Harold T. Stokes, Dorian M. Hatch, Branton J. Campbell | Apply group theory to crystal systems and phase transitions | Web | Web | https://stokes.byu.edu/iso/isotropy |
Avisio | Pretty plots of 3D reciprocal space maps | Not portable | Beamline computers? | ||
FDMNES | Calculates electronic structure of a crystal structure and simulates the resonant scattering | Windows/ Linux? | None | https://fdmnes.neel.cnrs.fr/ | |
Vesta | Visualise 3D crystal structures including magnetic structures | Windows | None | http://jp-minerals.org/vesta/en/ | |
Jana | Refine crystal structures, including magnetic structures, super structures and subgroup analysis | Windows | None | http://www-xray.fzu.cz/jana/jana.html | |
GSAS II | Refine crystal structures (open source Python) | Python | Python2/3 | https://subversion.xray.aps.anl.gov/trac/pyGSAS | |
bonsu | M. Newton | Phase retrieval for coherent diffraction imaging (BCDI). Bonsu (Phase Retrieval) | Python | conda activate bonsu |
On the linux workstations additional software can be accessed using the module load system, accessed via the terminal, for example:
# Load the latest version of anaconda python: $ module load python/3 $ ipython
# Dawn $ module load dawn $ dawn
# Blender $ module load blender $ blender
# Search for software $ module avail python
# Install python packages without root privileges pip install --user Dans_Diffraction |
To request new software is installed, contact: [email protected]
Name |
Website |
Description |
---|---|---|
ISOTROPY Software (Isodistort) | http://stokes.byu.edu/iso/isotropy.php | Representation analysis, generation of distortions into symmetry groups, cif utilities |
Bilbao Crystallographic Server (MagMax) | http://www.cryst.ehu.es/cgi-bin/cryst/programs/msglist2.pl | Get possible magnetic spacegroups from parent SG + propagation vector |
Bilbao Crystallographic Server | http://www.cryst.ehu.es/#msgtop | Many useful magnetic symmetry applications |
MAGNDATA | http://webbdcrista1.ehu.es/magndata/ | Magnetic Cif files for many materials |
BasIreps (FullProf Suite) | https://www.ill.eu/sites/fullprof/ | Irreducible representations of space groups |
Mody | http://www.ftj.agh.edu.pl/~sikora/modyopis.htm | Representation analysis (appears to be defunct) |
SpinW | https://www.psi.ch/en/spinw | SpinW is a Matlab library that can plot and numerically simulate magnetic structures and excitations of given spin Hamiltonian. |
SARAh Representation Analysis | http://fermat.chem.ucl.ac.uk/spaces/willsgroup/software/sarah-magnetic-symmetry-calculations-magnetic-structure-analysis/ | Performs the calculations of Representational Analysis. |
If you have any comments, suggestions or corrections, please contact a member of the beamline staff.
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