Difference between revisions of "Software"

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* '''Multifitting''': Reflectivity calculations for multilayer systems
 
* '''Multifitting''': Reflectivity calculations for multilayer systems
 
** Citation: M. Svechnikov [http://scripts.iucr.org/cgi-bin/paper?te5051 Multifitting: software for the reflectometric reconstruction of multilayer nanofilms] ''J. Appl. Cryst.'' '''2019''' [https://doi.org/10.1107/S160057671901584X doi: 10.1107/S160057671901584X]
 
** Citation: M. Svechnikov [http://scripts.iucr.org/cgi-bin/paper?te5051 Multifitting: software for the reflectometric reconstruction of multilayer nanofilms] ''J. Appl. Cryst.'' '''2019''' [https://doi.org/10.1107/S160057671901584X doi: 10.1107/S160057671901584X]
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* '''MLReflect''': Machine-learning method for reflectivity curves
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** [https://mlreflect.readthedocs.io/en/latest/ Docs] and [https://github.com/schreiber-lab/mlreflect/tree/master code]
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** Citation: [https://arxiv.org/abs/2202.11609 arxiv]
  
 
===[[Crystallography]]===
 
===[[Crystallography]]===
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* '''τompas''': TEM online multi-purpose analyzing system
 
* '''τompas''': TEM online multi-purpose analyzing system
 
** Citation: R.-X. Xie and W.-Z. Zhang [http://scripts.iucr.org/cgi-bin/paper?ks5644 τompas: a free and integrated tool for online crystallographic analysis in transmission electron microscopy] ''J. Appl. Cryst.'' '''2020''', 53. [https://doi.org/10.1107/S1600576720000801 doi: 10.1107/S1600576720000801]
 
** Citation: R.-X. Xie and W.-Z. Zhang [http://scripts.iucr.org/cgi-bin/paper?ks5644 τompas: a free and integrated tool for online crystallographic analysis in transmission electron microscopy] ''J. Appl. Cryst.'' '''2020''', 53. [https://doi.org/10.1107/S1600576720000801 doi: 10.1107/S1600576720000801]
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* '''UnitCell Tools''': Determine unit-cell parameters from a single electron diffraction pattern.
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** Citation: Hong-Long Shi and Zi-An Li [https://journals.iucr.org/m/issues/2021/05/00/gq5014/index.html UnitCell Tools, a package to determine unit-cell parameters from a single electron diffraction pattern] ''IUCrJ'' '''2020''' [https://doi.org/10.1107/S2052252521007867 doi: 10.1107/S2052252521007867]
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===Wave/Matter interaction===
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====X-rays====
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These software packages directly simulation the propagation of an EM field, and/or the interaction between EM waves and material:
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* '''SRW''' (Synchrotron Radiation Workshop): Fast numerical simulation of near-field and far-field of radiation generated by electron beams traveling through magnetic fields. I.e. can be used to simulate x-ray emission from [[synchrotron]] sources (e.g. [[undulator]]).
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** [https://www.esrf.fr/Accelerators/Groups/InsertionDevices/Software/SRW Official site.]
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* '''Shadow''': X-ray optics simulation package for coherent x-ray wavefront propagation simulations​​.
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** Citation: Niccolo Canestrari, Oleg Chubar and Manuel Sanchez del Rio [https://iopscience.iop.org/article/10.1088/1742-6596/425/16/162007 Improved models for synchrotron radiation sources in SHADOW] ''J. Phys.: Conf. Ser.'' '''2013''', 425 162007. [http://dx.doi.org/10.1088/1742-6596/425/16/162007 doi: 10.1088/1742-6596/425/16/162007]
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* '''WPG''' (WavePropaGator): Software package for simulating coherent and partially coherent X-ray wavefront propagation, especially intended for simulating [[XFEL]]
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** [https://wpg.readthedocs.io/en/stable/wpg.html Docs.]
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** [https://github.com/samoylv/WPG Code.]
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====General EM field====
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* [https://github.com/flaport/fdtd Python 3D FDTD Simulator]
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* [https://github.com/kc-ml2/meent Meent]
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* [https://github.com/stefanmeili/FastFD FastFD]
  
 
==Computing [[Materials]] Properties==
 
==Computing [[Materials]] Properties==

Latest revision as of 08:40, 9 April 2024

A common question for new GISAXS users is: "What software can I use to analyze my data?" Unfortunately, there is no single package that will allow you to perform any possible analysis. This is in part due to the diversity of possible kinds of data analysis one might want to do on GISAXS or GIWAXS images. The following lists a variety of packages that are available.

Data Viewing, Reduction, and Simple Analysis

These packages provide ways to view data, and perform simple operations (linecuts, etc.).

Geared towards 2D data

Geared towards 1D data

Data Modeling and Fitting

These packages can predict scattering curves for various possible nano- or molecular- structures. Some of the packages allow fitting of experimental data.

SAXS

BioSAXS

GISAXS

Reflectivity

Crystallography

Wave/Matter interaction

X-rays

These software packages directly simulation the propagation of an EM field, and/or the interaction between EM waves and material:

  • SRW (Synchrotron Radiation Workshop): Fast numerical simulation of near-field and far-field of radiation generated by electron beams traveling through magnetic fields. I.e. can be used to simulate x-ray emission from synchrotron sources (e.g. undulator).
  • Shadow: X-ray optics simulation package for coherent x-ray wavefront propagation simulations​​.
  • WPG (WavePropaGator): Software package for simulating coherent and partially coherent X-ray wavefront propagation, especially intended for simulating XFEL

General EM field

Computing Materials Properties

Synchrotron

  • SILX: Data reading/writing for synchrotron data formats.
  • BlueSky: Instrument control, including data saving into a database and access via databroker.

General

  • SciStreams: Simple workflow/pipeline software (building on Dask and Streams), intended for asynchronous and distributed computations at a beamline.
  • ParaView: Generalized GUI for visualizing scientific data, such as 3D images (uses Python and QT).
  • Mantid: Framework for computing and visualizing materials science data.
    • Official site.
    • Citation: O. Arnold, et al., Mantid—Data analysis and visualization package for neutron scattering and μSR experiments, Nuclear Instruments and Methods in Physics Research Section A, Volume 764, 11 November 2014, Pages 156-166. doi: 10.1016/j.nima.2014.07.029
  • DAWN (Data Analysis WorkbeNch): An application (based on Eclipse) for general scientific data analysis. It is mainly developed by the Diamond Light Source and is well-optimized for analysis of x-ray data, including SAXS-specific features.

Custom

It is of course possible to code your own software for modeling or fitting scattering data. This is not as difficult as it may at first seem. The fundamental scattering equations are well-known (c.f. scattering, Fourier transform, Form Factor, Structure Factor, Lattice Factor), and can be brute-force solved numerically. Or, they can be solved (or simplified) analytically for a particular case. Many modern programming languages provide libraries for numerical integration, fitting, minimizing multi-dimensional parameter spaces, etc. (e.g. Python is particularly clean and powerful).

See Also

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