- users - SasView Mailing Lists

Help Needed with Scripting
by Daniel Rosenberg via users 28 Oct '21

28 Oct '21

Hello SASVIEW, I am a researcher at Berkeley Lab at the SIBYLS beamline at the ALS. I am trying to include triaxial fitting from sasmodels into a branch of our pipeline and am having trouble. I was hoping that I might be able to meet with someone in your group to talk it over if someone is available to do so. Thank you for your consideration. Kind Regards Daniel Rosenberg Advanced Light Source SIBYLS Beamline <http://sibyls.als.lbl.gov/> MBIB Division Lawrence Berkeley Lab <http://biosciences.lbl.gov/divisions/mbib/> Biophysics Department UC Berkeley <http://biophysics.berkeley.edu/>

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SasView is hiring!
by Stephen King - STFC UKRI via users 30 Sep '21

30 Sep '21

Thanks to support from the ISIS Pulsed Neutron & Muon Source, we now have a vacancy for a full-time research software engineer to work on SasView. The position will be part of a new Research Software Engineering Team based at ISIS. Full details can be found at: https://www.careersportal.co.uk/UKRI-careers/jobs/research-software-enginee… Interviews are being held on a rolling basis up to the closing date of October 31, 2021. PLEASE NOTE: Interested applicants must apply through the link above. Expressions of interest, resumes, CVs, etc, sent to any of the SasView mailing lists cannot be considered. This email and any attachments are intended solely for the use of the named recipients. If you are not the intended recipient you must not use, disclose, copy or distribute this email or any of its attachments and should notify the sender immediately and delete this email from your system. UK Research and Innovation (UKRI) has taken every reasonable precaution to minimise risk of this email or any attachments containing viruses or malware but the recipient should carry out its own virus and malware checks before opening the attachments. UKRI does not accept any liability for any losses or damages which the recipient may sustain due to presence of any viruses.

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SASVIEW SLD profiles
by Garvey, Christopher via users 21 Jul '21

21 Jul '21

Hi All, Some of the models can output nice SLD profiles of the model as a graphic. I’ve had a look if it’s possible to easily export this profile as a text file (distance vs SLD) but not yet. If someone else has looked at this problem, and perhaps even solved it, I’d be pleased to hear about it. Thanks for your consideration. Regards Chris

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Re-opening the fitting parameters on sasview
by Daniel Alexander Støvring Laima via users 23 Apr '21

23 Apr '21

Hi How do you re-open the fan with all the fitting parameters? I had fitted some data but then I had by accident closed the 'fit panel' fan before screen dumping them and now I can't find them again? Kindly Daniel

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News and a New Release (5.0.4)
by Stephen King - STFC UKRI via users 12 Apr '21

12 Apr '21

Dear Members of the SasView User List, We hope you are safe and well during these unusual times. GENERAL NEWS It is seven months since our last bulletin and in that time the Development Team has been working hard to bring SasView 5 to feature-parity with SasView 4. We are still not quite there, but some very good progress has been made as our latest release (see below) hopefully demonstrates. In the intervening months we have also held two virtual 'Hackathons'. The first, in October, saw the Development Team focus on writing a paper about SasView; something that has been on our to-do list for quite some time and which many of you have asked for ('Is there a reference for SasView?')! We now have a first draft, but it still needs some more work before we can send it off for publication. The second Hackathon, in January, focussed on usability issues in SasView and we believe that the new release has benefitted as a result. We also thought we would highlight what we see as a great contribution by some of YOU, the SasView user base. Since we released SasView 5 in May 2019, an astounding 24 new models have been added to the Model Marketplace. If you cannot find a model you need in the distributed model library, do remember to check the Marketplace. NEW RELEASE The Development Team is pleased to announce the release of SasView 5.0.4, available for download as usual through the website at www.sasview.org<http://www.sasview.org>. This release fixes several issues: - A bug that had been around since 4.2.2 and which prevented Batch Fitting from using any dI values in the data file has finally been fixed. The consequence of this bug was that Single Fits and Batch Fits on the same datasets could return different parameters. Now, where present, dI values will always be used by default in both cases. - The bug introduced in 5.0.3 which prevented the plotting of Batch Fit results has also been fixed. - An issue with the behaviour of the 1D pinhole resolution smearing routine in cases of large divergence has also been addressed. - There are a number of improvements to plotting and plot management. - Several usability issues in the P(r) Inversion and Invariant Analysis perspectives have been addressed. Improvements have also been made to the functioning of Project Save/Load. There are also some new features in SasView 5.0.4: - Though not strictly a new feature, the functionality and operation of parameter constraints has been significantly overhauled for this version. This was the excellent work of ILL intern, Nicholas Martinez, to whom we offer our grateful thanks. Nicolas has since moved on to a new position. - The slicer functionality has been significantly overhauled and made to work properly. - The slider bars on plots for selecting the q-range for fitting that featured in earlier versions of SasView have been re-introduced by popular request, although they do not yet work on linearized plots. - It is now possible to swap the dataset used to create an existing FitPage for a different dataset. This removes the need to re-generate a complex model (eg, featuring many parameters and/or constraints) many times over to use it to fit several datasets. - It is now also possible to assign custom names to loaded datasets, rather than just identifying the data by its filename. Right-click on a dataset in the Data Explorer to activate. Of course, as always, there remain many things that could be added, improved or, sadly, that need fixing. So please continue to provide feedback, bug reports (issues), and, when possible, fixes, either to the code or the documentation or tutorials, as GitHub pull requests, for those who can, or by simply emailing help(a)sasview.org<mailto:help@sasview.org>. FUTURE PLANS As we said last Autumn, it is our intention, as and when the pandemic allows, to engage the community more fully in the development process writ large, including the creation of tutorials, YouTube videos, documentation, and instructional materials, as well as code development. If any of you have thoughts on how to achieve these goals, or are simply interested in contributing in any capacity but aren't sure how, please feel free to email us on the help list. Thank you for your continued support! The SasView Development Team This email and any attachments are intended solely for the use of the named recipients. If you are not the intended recipient you must not use, disclose, copy or distribute this email or any of its attachments and should notify the sender immediately and delete this email from your system. UK Research and Innovation (UKRI) has taken every reasonable precaution to minimise risk of this email or any attachments containing viruses or malware but the recipient should carry out its own virus and malware checks before opening the attachments. UKRI does not accept any liability for any losses or damages which the recipient may sustain due to presence of any viruses. Opinions, conclusions or other information in this message and attachments that are not related directly to UKRI business are solely those of the author and do not represent the views of UKRI.

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Re: [SasView Users] SasView-5.0.2 and 4.2.2 Own Model on MaxOS
by Stephen King - UKRI STFC via users 28 May '20

28 May '20

Thanks. We'll take a look. From: Sebastian Lages <lages(a)chalmers.se> Sent: 28 May 2020 14:01 To: King, Stephen (STFC,RAL,ISIS) <stephen.king(a)stfc.ac.uk>; users(a)sasview.org Cc: Beatrice Swensson <beatrice.swensson(a)chalmers.se> Subject: Re: SasView-5.0.2 and 4.2.2 Own Model on MaxOS Dear Stephen, this is a quick reply! Thanks a lot! I feel obliged to return the favour of a quick answer and here it is. Please find the source code attached in a zip-file. Best regards from Sweden, Sebastian Materials Physics Department of Physics Chalmers University of Technology SE-412 96 Göteborg Sweden Homepage Liebi Group<https://www.chalmers.se/en/departments/physics/research/cmp/research/Liebi_…> ________________________________ From: Stephen King - UKRI STFC <stephen.king(a)stfc.ac.uk<mailto:stephen.king@stfc.ac.uk>> Sent: Thursday, May 28, 2020 2:56:03 PM To: Sebastian Lages; users(a)sasview.org<mailto:users@sasview.org> Cc: Beatrice Swensson Subject: RE: SasView-5.0.2 and 4.2.2 Own Model on MaxOS Dear Sebastian, Beatrice, Thank you for contacting us. Please could you resend the two attachments in a zip file. Mail clients are blocking plain source code attachments these days for security reasons. Thank you. Kind regards, Steve King On behalf of the Developers From: Sebastian Lages <lages(a)chalmers.se<mailto:lages@chalmers.se>> Sent: 28 May 2020 13:37 To: users(a)sasview.org<mailto:users@sasview.org> Cc: Beatrice Swensson <beatrice.swensson(a)chalmers.se<mailto:beatrice.swensson@chalmers.se>> Subject: SasView-5.0.2 and 4.2.2 Own Model on MaxOS Dear SasViewers, we wrote our own model, see attached files. It's based on in-build models and runs perfectly fine on my LinuxMint 18. The files live in "/home/sebastian/SasView/sasmodels/models/". Just like it said in the description for writing own models. However, on MacOS we cannot make it work. Not with SasView-4.2.2, not with SasView-5.0.2. Every time we choose the model from the FitPage's drop down menu, we get an error message. And there's more. The model "flexible_cylinder" stopped working as well. It stopped completely. Interestingly with the same error message we got for our own model. Only a fresh installation of SasView is able to correct this behaviour, restarting the software is not enough. How can we correct this? Best regards, Sebastian Materials Physics Department of Physics Chalmers University of Technology SE-412 96 Göteborg Sweden Homepage Liebi Group<https://www.chalmers.se/en/departments/physics/research/cmp/research/Liebi_…> This email and any attachments are intended solely for the use of the named recipients. If you are not the intended recipient you must not use, disclose, copy or distribute this email or any of its attachments and should notify the sender immediately and delete this email from your system. UK Research and Innovation (UKRI) has taken every reasonable precaution to minimise risk of this email or any attachments containing viruses or malware but the recipient should carry out its own virus and malware checks before opening the attachments. UKRI does not accept any liability for any losses or damages which the recipient may sustain due to presence of any viruses. Opinions, conclusions or other information in this message and attachments that are not related directly to UKRI business are solely those of the author and do not represent the views of UKRI.

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Re: [SasView Users] SasView-5.0.2 and 4.2.2 Own Model on MaxOS
by Stephen King - UKRI STFC via users 28 May '20

28 May '20

Dear Sebastian, Beatrice, Thank you for contacting us. Please could you resend the two attachments in a zip file. Mail clients are blocking plain source code attachments these days for security reasons. Thank you. Kind regards, Steve King On behalf of the Developers From: Sebastian Lages <lages(a)chalmers.se> Sent: 28 May 2020 13:37 To: users(a)sasview.org Cc: Beatrice Swensson <beatrice.swensson(a)chalmers.se> Subject: SasView-5.0.2 and 4.2.2 Own Model on MaxOS Dear SasViewers, we wrote our own model, see attached files. It's based on in-build models and runs perfectly fine on my LinuxMint 18. The files live in "/home/sebastian/SasView/sasmodels/models/". Just like it said in the description for writing own models. However, on MacOS we cannot make it work. Not with SasView-4.2.2, not with SasView-5.0.2. Every time we choose the model from the FitPage's drop down menu, we get an error message. And there's more. The model "flexible_cylinder" stopped working as well. It stopped completely. Interestingly with the same error message we got for our own model. Only a fresh installation of SasView is able to correct this behaviour, restarting the software is not enough. How can we correct this? Best regards, Sebastian Materials Physics Department of Physics Chalmers University of Technology SE-412 96 Göteborg Sweden Homepage Liebi Group<https://www.chalmers.se/en/departments/physics/research/cmp/research/Liebi_…> This email and any attachments are intended solely for the use of the named recipients. If you are not the intended recipient you must not use, disclose, copy or distribute this email or any of its attachments and should notify the sender immediately and delete this email from your system. UK Research and Innovation (UKRI) has taken every reasonable precaution to minimise risk of this email or any attachments containing viruses or malware but the recipient should carry out its own virus and malware checks before opening the attachments. UKRI does not accept any liability for any losses or damages which the recipient may sustain due to presence of any viruses. Opinions, conclusions or other information in this message and attachments that are not related directly to UKRI business are solely those of the author and do not represent the views of UKRI.

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Treatment of Self-Assembled Structures
by Grayson Johnson via users 08 May '20

08 May '20

Dear Users Forum, I’m new to the process of fitting SAXS data, and I am looking for guidance on what assumptions to make for my models. I have a set of small, probably spherical particles that assemble into micron length rectangular prism shaped structures. I have a known crystal structure from TEM images. Is it better to model the SAXS profile as a parallelepiped (and presumably miss out on the structure factor information that is present) or as spheres? If I do as spheres, is there a good way to use the crystal structure information to help the model along? When I perform a fit with spheres, I don’t seem to get the really low q behavior that I get with the parallelepiped. When I fit with the parallelepiped, the fit takes upwards of 30 minutes, and I haven’t quite been able to dial in on the parameters. The assemblies have a lot of variation in length, but not too much in width and height. Thanks for any help that you can provide, Grayson Johnson

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FW: theLightStuff online lecture series, lecture #3: Friday 17th, 15:30 UTC
by Stephen King - UKRI STFC via users 16 Apr '20

16 Apr '20

Dear colleagues and fellow scatterers, To help break the isolation between researchers stuck at home in these pandemic times, we have set up an international online short lecture series on scattering and diffraction. The lectures normally take place on Fridays via a Zoom webinar. Details on the current schedule are here: https://www.bam.de/thelightstuff With this lecture series we hope to highlight early-career researchers (ECRs) and their projects, with talks aimed at Ph.D. students, post-docs and other ECRs. With permission of the speakers, the talks are recorded and put online as well, to broaden the access to the talks. The first two of these talks have now appeared online: https://www.youtube.com/channel/UCrFK5hLLcuDcbKmWeuJvpTw The upcoming lecture is that of Dr. Lilo Pozzo talking about time-resolved neutron scattering to elucidate molecular transport mechanisms in oil emulsions. Details on this lecture, and how to join are here: https://www.bam.de/Content/EN/Events/2020/2020-04-17-the-light-stuff-online… See you there on Friday the 17th! Yours sincerely Brian R. Pauw — If you have received this email outside of working hours please be assured that there is no expectation that you will reply to it outside of your normal working pattern. Bundesanstalt für Materialforschung und -prüfung (BAM) Division 6.5 - Synthesis and Scattering of Nanostructured Materials Unter den Eichen 87 12205 Berlin Germany T: + 49 30 8104-3361 F: + 49 30 8104-1617 brian.pauw(a)bam.de<mailto:brian.pauw@bam.de><mailto:brian.pauw@bam.de> www.bam.de<http://www.bam.de> __________________________________________________ Die BAM ist eine Bundesoberbehörde im Geschäftsbereich des Bundesministeriums für Wirtschaft und Energie.

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Sum Multi Function Version 4.2.2
by Abitaev, Karina via users 07 Apr '20

07 Apr '20

Dear Sasview Team, I am using Sasview 4.2.2 to fit a colloidal crystal of polymer nanoparticles. Here I use a Form factor for spheres, where a polydispersity is included. Furthermore, I am using a hard sphere structure factor. I found the option to multiply the Spheres with hard spheres, so I can supply for each a radius and polydispersity. In this context I was wondering how the structure factor and form factor are combined (decoupling approximation, local monodisperse approx, ...) Thank you in advance for your help! Best wishes, Karina -- Karina Abitaev Institut für Physikalische Chemie Universität Stuttgart Pfaffenwaldring 55 70569 Stuttgart Germany karina.abitaev(a)ipc.uni-stuttgart.de Phone: +49 (0)711/685-64502 Fax: +49 (0)711/685-64443

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