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Analysis Programs

The Computing for Science (CS) group supports ILL scientists, students and visitors in a number of activities including data analysis, instrument simulation and sample simulation.

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All Software

Analysis Programs for Small-Angle Scattering Data at the ILL

Index

assa

crysol

cryson

dammin

decon

gnom

itp

ito

mshell

multibody

nbcalc

Grasp

pdh

polymer

pyshell

rfit

sasgau

sasfit4

sasha

saspks

ssqfun

 

 

 

Introduction

The main programs maintained at the Institut Laue Langevin for small-angle scattering have been concerned primarily with correction of raw data, regrouping and simple plotting and inspection. It is impossible to meet the requirements of all experimenters for the analysis of their data as this necessarily varies according to the scientific problem. However some programs have been made available for common use by their authors and it seems useful to catalogue those that are presently available at the ILL.


No responsibility can be taken by the ILL for the operation of these programs or guarantee of correctness given. Indeed, in most cases the authors have made these programs available to other users on condition that they are not guaranteed or supported and that they are to be used only for non-profit purposes. It is expected that appropriate acknowledgment of the program and the authors would be made for any use.

The information presented here concerns only programs that are available for use on computers at the ILL. There are, of course, many other analysis programs that available elsewhere. Some further information can be found on the canSAS Homepage. Information about any other programs to be catalogued on this page would be very much appreciated. Please contact Adrian.Rennie(at)fysik.uu.se.

For simplicity the programs have been divided in to three broad categories that correspond to model and peak fitting, transform methods and visualisation and other utilities.

Model and Peak Fitting Programs

1. Assa

An interactive modelling program for solution scattering doing 3-D rendering and calculations for rigid bodies by M. Kozin and D. J. Svergun, EMBL Hamburg. svergun(at)EMBL-Hamburg.de. Local information about this program is available. The program has been installed at the ILL by Roland May. Email: may(at)ill.fr.

Follow the local instructions to use the program at the ILL. A manual for this and other programs by D. Svergun is available on the WWW at http://www.embl-hamburg.de/ExternalInfo/Research/Sax/software.html

2. cryson and crysol

Programs to calculate solution scattering for neutrons (cryson) from atomic co-ordinates by D. J. Svergun, EMBL Hamburg. svergun(at)EMBL-Hamburg.de and X-rays (crysol) written with C. Barberato. Local information about this program is available. The program has been installed at the ILL by Roland May. Email: may(at)ill.fr.

Follow the local instructions to use the programs at the ILL. A manual for these programs by D. J. Svergun is available on the WWW at http://www.embl-hamburg.de/ExternalInfo/Research/Sax/software.html

3. Grasp

This program performs data reduction, plotting and fitting operations on SANS data. It has been written by Charles Dewhurst, dewhurst(at)ill.fr and uses MatlabTM. Current versions (3.07) are installed on various PC's in the LSS group and on SG workstations.

There is a manual (available as PDF) and further information on the WWW.

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4. mshell

A program to fit simultaneously multiple data sets. The model comprises spherical particle with up to 4 concentric shells. The parameters for the different data sets can be linked or varied independently. Interactions between the particles can be included using the rescaled mean spherical approximation of Hayter and Penfold. Different data sets to be included in simultaneous fits might include series of contrast variation, different concentration or measurements in different instrument configurations at different resolution. The program uses a new modification of the FITFUN (https://www.ill.eu/computing/cs-software/all-software/clickfit/fitfun) library developed at the ILL by Ron Ghosh. Version 1.2 is under test at the ILL. The executable for SG is ~rennie/mfit/mshell.

Author: Adrian R. Rennie, Dept Physics, Box 530, 75121 Uppsala, Sweden
Email: Adrian.Rennie(at)fysik.uu.se

The calculation of interactions is described in papers and reports by J.B. Hayter and J. Penfold: 'SQHP: A Fortan Package to Calculate S(Q) for Macroion Solutions' ILL Report 80HA07S (1980), 'An Analytic Structure Factor for Macroion Solutions' Molecular Physics 42, 109-118 (1981) and 'Determination of Micelle Structure and Charge by neutron small-angle scattering' Colloid and Polymer Science 261, 1022-1030 (1983). Further mathematical detail is provided in papers by J-P. Hansen and J. B. Hayter: 'The Structure Factor of Charged Colloidal Dispersions at Any Density' ILL Report 82HA14T (1982), 'A Rescaled MSA Structure Factor for Dilute Charged Colloidal Dispersions' Molecular Physics 46, 651 (1981).

5. multibody

Program to calculate scattering curves and distance distribution functions from models made up of little spheres (or other bodies with known scattering function). The ILL version can read ATOM cards of the PDB (protein data base). The author of the program is Otto Glatter, University of Graz.

The version for Silicon Graphics is (OG) 1992. The last ILL update was May 1998 source code with Roland May. Email: may(at)ill.fr. The executable is ~sans/multib.

6. polymer

This fits simple models appropriate to polymers such as the Debye function, and adaptations for copolymers, polymer blends star polymers and polydisperse systems. It uses the FITFUN (https://www.ill.eu/computing/cs-software/all-software/clickfit/fitfun) library developed at the ILL by Ron Ghosh.
Author: Adrian R. Rennie, Dept Physics, Box 530, 75121 Uppsala, Sweden
Email: Adrian.Rennie(at)fysik.uu.se

Version 3.1 is available at the ILL on the SG Unix computers. Executable code is ~sans/polymer and the program requires the standard environment variables at the ILL for SANS analysis and PGPLOT. A version for DOS (& Windows 3.1, 9x & NT/2000/XP) is also available.

A short manual is available on the WWW at http://material.fysik.uu.se/Group_members/adrian/poly.htm that describes the models with literature references and how to use the program.

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7. pyshell

This fits a core-shell model for interacting, hard spherical colloidal particles. The interactions are calculated with the Ashcroft-Lekner model for hard spheres. It uses the FITFUN (https://www.ill.eu/computing/cs-software/all-software/clickfit/fitfun) library developed at the ILL by Ron Ghosh.
Author: Adrian R. Rennie, Dept Physics, Box 530, 75121 Uppsala, Sweden
Email: Adrian.Rennie(at)fysik.uu.se

Version 3.1 is available at the ILL on the SG Unix computers. Executable code is ~rennie/pyshell and the program requires the standard environment variables at the ILL for SANS analysis and PGPLOT. A version for DOS (Windows 3.1, 9x & NT) is also available.

A short manual is available on the WWW at http://material.fysik.uu.se/Group_members/adrian/pyshell.htm that describes the models with literature references and how to use the program.

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8. rfit

This fits models to SANS data and includes a parameterised instrument resolution function appropriate to pinhole cameras at fixed wavelength. Models include spheres, polymer coils, Gaussian peaks, Lorentzian broadening and other functions. Author: Adrian R. Rennie, Dept Physics, Box 530, 75121 Uppsala, Sweden Email: Adrian.Rennie(at)fysik.uu.se

Version 2.7 is available at the ILL on the SG Unix computers. Executable code is ~rennie/rfit and the program requires the standard environment variables at the ILL for SANS analysis and PGPLOT. Versions for DOS (Windows 9x & NT/2000) are also available.

A short manual is available on the WWW at http://material.fysik.uu.se/Group_members/adrian/rfit.htm

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9. sasgau and saspks

These use the FITFUN library to fit Gaussian and other peaks in regrouped SANS data. Author Ron Ghosh, ILL, 156X, F-38042 Grenoble Cedex France. Email: ron(at)ill.fr.

Versions are available for SG Unix at the ILL and the executable code is ~sans/sasgau and ~sans/saspks.

Documentation on the FITFUN library and how to use the FITFUN programs is available on the WWW at https://www.ill.eu/computing/cs-software/all-software/clickfit/fitfun

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10. sasfit4

This uses a development of the FITFUN library to fit up to 4 Gaussian, Lorentzian or pseudo-Voigt peaks to regrouped SANS data. A particular feature is the possibility of automatically fitting a sequence of spectra after an initial fit. Results can be output to a file or displayed as simple graphs. The author is Ron Ghosh, ILL, 156X, F-38042 Grenoble Cedex France. Email: ron(at)ill.fr.

Version 1.3 is available for SG Unix at the ILL and the executable code is ~sans/sasfit4. A version for W9x/NT/2000/XP is also available.

The use of this program is described in the following document: http://www.ill.fr/data_treat/sasfit4.html. General documentation on the FITFUN library and how to use the FITFUN programs is available on the WWW at https://www.ill.eu/computing/cs-software/all-software/clickfit/fitfun

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11. sasha

A program for generalised analysis of particle shape by D. J. Svergun, EMBL Hamburg & V. Volkov, Institute of Crystallography, Moscow. Svergun(at)EMBL-Hamburg.de.  The program has been installed at the ILL by Roland May.

Follow the local instructions to use the program at the ILL. A manual for this program is available on the WWW at http://www.embl-hamburg.de/ExternalInfo/Research/Sax/software.html

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12. ssqfun

This use the FITFUN library to fit a spherical core-shell model to regrouped SANS data. The original author was Martin Zulauf and the program has been updated and maintained by Ron Ghosh, ILL, 156X, F-38042 Grenoble Cedex France. Email: ron(at)ill.fr.

A version (3.1) is available for SG Unix at the ILL and the executable code is ~sans/ssqfun.

Documentation on the FITFUN library and how to use the FITFUN programs is available on the WWW at https://www.ill.eu/computing/cs-software/all-software/clickfit/fitfun

Go to: Top of Page, Index, Introduction, Fitting Programs, Transform Methods, Visualisation and Other Utilities,

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Transform Methods

1. dammin

Simulated annealing analysis of IFT results from gnom by D. J. Svergun, EMBL Hamburg. svergun(at)EMBL-Hamburg.de. The program has been installed at the ILL by Roland May.

Follow the local instructions to use the program at the ILL. A manual for this program is available on the WWW at http://www.embl-hamburg.de/ExternalInfo/Research/Sax/software.html

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2. gnom

An indirect Fourier transform program by D. J. Svergun, EMBL Hamburg and A. Semenyuk, Institute of Crystallography, Moscow. svergun(at)EMBL-Hamburg.de. This program automatically adjusts the regularisation parameters. The program has been installed at the ILL by Roland May.

Follow the local instructions to use the program at the ILL. A manual for this and other programs by D. Svergun is available on the WWW at http://www.embl-hamburg.de/ExternalInfo/Research/Sax/software.html

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3. itp and ito

itp is Otto Glatter's indirect Fourier transformation program. It has been adapted by Roland May for SGI machines, and a version compatible with HP stations will be prepared with Claudio Ferrero. ito is the output program for the optimal result. Email: may(at)ill.fr.

Version (OG) 1992, last ILL update was April 1998. The source code is with Roland May. The executable is ~sans/itp and ~sans/ito. The copyright is owned by the University of Graz. Otto Glatter has to give his permission prior to copying elsewhere. The Graz version (for PC) is complete; it requires Lahey FORTRAN compiler. ILL uses a few of Roland May's subroutines.

The program is described in various papers which are available from Roland May.

Visualisation and Other Utilities

1. decon

decon is Otto Glatter's DECON program for deconvoluting distance distribution functions in to radial density distribution functions. It has been adapted by Roland May for SG machines, and a version compatible with HP stations will be prepared with Claudio Ferrero (ESRF). Email: may(at)ill.fr .

Version (OG) 1992, last ILL update was January 1997. The source code is with Roland May. The executable for the Silicon graphics is ~sans/dec. The copyright is owned by the University of Graz. Otto Glatter has to give his permission prior to copying elsewhere. The Graz version (for PC) is complete; it requires Lahey FORTRAN compiler. The ILL version uses a few of Roland May's subroutines.

The program is described in various papers which are available from Roland May.

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2. nbcalc

nbcalc calculates scattering length densities from the chemical formula and information on the density provided by the user.

The program is written by R. Wilson

Email: rwilson(at)ill.fr.

A version is available for the SG unix system at the ILL. The executable code is ~rwilson/Programs/nbcalc.

3. pdh

pdh is Otto Glatter's primary data handling program. It has been adapted by Roland May for SGI machines, and a version compatible with HP stations will be prepared with Claudio Ferrero. Email: may(at)ill.fr .

Version (OG) 1992, last ILL update was April 1998. The source code is with Roland May. The executable for the Silicon graphics is ~sans/pdh. The copyright is owned by the University of Graz. Otto Glatter has to give his permission prior to copying elsewhere. The Graz version (for PC) is complete; it requires Lahey FORTRAN compiler. ILL uses a few of Roland May's subroutines.

The program is described in various papers which are available from Roland May. At the ILL, pdh is mainly required to read the output files of itp/ito, decon, etc, since they have extensions which are not compatible with the ILL conventions.

Go to: Top of Page, Index, Introduction, Fitting Programs, Transform Methods,

canSAS

A meeting was held in Grenoble in February 1998 to discuss data formats for small-angle X-ray and neutron scattering. The aim was to provide definitions of formats and interconversion routines between standard formats as an aid to users of facilities who might wish to share data treatment and analysis programs. Some information about conversion of data to other formats that may be useful in using other data treatment programs as well as links to documents describing data formats can be found on the canSAS Homepage. There are also links to some other descriptions of data analysis programs at other sites.


Please address any comments or report any errors to Dr Adrian R. Rennie at:

Dept Physics, Box 530, 75121 Uppsala, Sweden

Adrian.Rennie(at)fysik.uu.se


Go to: Introduction, Index, Fitting Programs, Transform Methods, Visualisation and Other Utilities, canSAS

Return to: Large Scale Structures Home Page, LSS Data Treatment



This page was last updated on 24th January 2006 (REG)

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