From users at lists.sasview.org  Tue Mar  8 04:39:03 2022
From: users at lists.sasview.org (Anna Stephens via users)
Date: Tue, 8 Mar 2022 09:39:03 +0000
Subject: [SasView Users] need help with sasview on linux
Message-ID: <CAM-+FkQ_Lv4VqbvcBfhy_7mUZN8ep_qTCVg+axQEh_UYRySEjA@mail.gmail.com>

Hey,

I've downloaded version 5 of sas on my linux machine, when I go to load one
of my data .txt files I get the following error in the log explorer:

09:38:12 - ERROR: SasView threw exception: __init__() got an unexpected
keyword argument 'nonposx'
09:38:12 - ERROR: SasView threw exception: __init__() got an unexpected
keyword argument 'nonposy'

I'm not sure how to fix this, can you please help?

Thanks so much!

Anna
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From users at lists.sasview.org  Tue Mar  8 04:58:51 2022
From: users at lists.sasview.org (Stephen King - STFC UKRI via users)
Date: Tue, 8 Mar 2022 09:58:51 +0000
Subject: [SasView Users] [SasView Help] help with sasview
In-Reply-To: <CAM-+FkRfkVFQ8wD7-D_mAtbT+rt3qEP=YD0TwEvvyQYMpc9PEQ@mail.gmail.com>
References: <CAM-+FkRfkVFQ8wD7-D_mAtbT+rt3qEP=YD0TwEvvyQYMpc9PEQ@mail.gmail.com>
Message-ID: <CWLP265MB429711E95489948138FB8708B0099@CWLP265MB4297.GBRP265.PROD.OUTLOOK.COM>

Hello Anna,

Could you reply to help at sasview.org<mailto:help at sasview.org> attaching a failing data file and your SasView log file, please.

Also, if you try loading some of the test data shipped with the distribution, does that work?

Kind regards,
Steve King
On behalf of the developers

From: help <help-bounces at lists.sasview.org> On Behalf Of Anna Stephens via help
Sent: 08 March 2022 09:40
To: help at sasview.org
Subject: [SasView Help] help with sasview

Hey,

I've downloaded version 5 of sas on my linux machine, when I go to load one of my data .txt files I get the following error in the log explorer:

09:38:12 - ERROR: SasView threw exception: __init__() got an unexpected keyword argument 'nonposx'
09:38:12 - ERROR: SasView threw exception: __init__() got an unexpected keyword argument 'nonposy'

I'm not sure how to fix this, can you please help?

Thanks so much!

Anna

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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From users at lists.sasview.org  Thu Jun  9 09:56:26 2022
From: users at lists.sasview.org (Stephen King - STFC UKRI via users)
Date: Thu, 9 Jun 2022 13:56:26 +0000
Subject: [SasView Users] SasView News and a New Release (5.0.5)
Message-ID: <LO4P265MB42949282FF829DE5DA873C48B0A79@LO4P265MB4294.GBRP265.PROD.OUTLOOK.COM>

Dear Members of the SasView User List,

We hope this email finds you safe and well and once again pushing back the frontiers of your science as the restrictions of the pandemic continue to ease.

GENERAL NEWS
It is almost 6 months since we solicited your help in helping to test the first release candidate (rc1) of SasView 5.0.5, and we are now delighted to say that we have finally released it (see below for further details)! The testing threw up an assortment of issues that, with our limited resources, inevitably took time to rectify, but we have learnt some valuable lessons in the process.

Version 5.0.5 is still just short of achieving feature-parity with SasView 4.x, but we are now very close and can see the end of the road. So we would like to take this opportunity to encourage and remind any of you still using SasView 4.x to start actively making the transition to SasView 5.x. There is no active development of SasView 4.x, there has not been any for several years, and nor do we now envisage any in the future.

That said, moving to SasView 5.x will have consequences for some of you, particularly those of you using Mac's. In some instances the only way you will be able to run SasView 5.x will be to update your Mac OS or update your Mac. Unfortunately, the need for this is something that is simply beyond our control.

There is some good news for those of you that wish to use SasView on Linux. We recently learnt that Maksim Rakitin at the NSLS-II had been producing 64-bit conda packages of SasView for Linux and OSX. If these are of interest, please visit https://github.com/SasView/sasview/wiki/Conda-installation. And we remind you that for some years now, Stuart Prescott & Drew Parson have been maintaining a Debian implementation of SasView. You can find links to this on our Wiki at https://github.com/SasView/sasview/wiki/DevNotes_Projects_Debian.

The time spent finalising this new release has naturally impacted progress elsewhere in the collaboration, and so things like the paper on SasView are still not finished. However, there are also some positive developments to report:

-          We are very pleased to welcome a new developer to the collaboration. Lucas Wilkins is based in the new Research Software Engineering Team at ISIS and will spend up to 80% of his time working on SasView.


-          Annika Stellhorn at Lund University has put together an in-person Workshop<https://www.linxs.se/events/2022/6/13/linxs-workshop-magnetic-sans-data-analysis-and-software-prospects> in Lund later this month to explore what additional developments in SasView would be beneficial for the Magnetic-SANS community. This kind of community-led endeavour is something the Development Team is very pleased to see and encourage.


-          And the Magnetic-SANS Workshop will be followed by a 3-day 'new contributor event<https://indico.esss.lu.se/event/3009/>' for those who want to learn more about the structure of the SasView codebase and how to pursue their own developments.


-          We have also added a couple of new videos to our YouTube channel<https://www.youtube.com/channel/UCxvD3ysXJ05l6MgY7YKjEFQ> in the past year. Why not take a look!

NEW RELEASE
The Development Team is pleased to announce the release of SasView 5.0.5, available for download as usual through the website at www.sasview.org<http://www.sasview.org>.

This release fixes several issues:


  *   The long standing issue with the Levenberg-Marquardt optimiser not respecting parameter bounds has been resolved by the move to a later version of the Bumps package.



  *   A bug which prevented the radius_effective parameter from being updated in P(Q)*S(Q) models when the data were resolution smeared has been fixed.



  *   A bug that prevented the formation of composite mixture models with multiplicity (for example, models such as core_multi_shell * hardsphere + cylinder or core_multi_shell @ hardsphere + cylinder) has been fixed.



  *   The button to reset the selected Q-limits for fitting now works again!



  *   There has been a technical change to the point in the calculation at which the volume normalisation of P(Q)*S(Q) models is applied by the move to a later version of the Sasmodels package. This change was actually incorporated into v5.0.4 but due to an oversight was omitted from the release notes at the time, although a note was added to the web version after the release. In most instances this change will go un-noticed unless you happen to be plotting the individual contributions of P(Q) or S(Q) and comparing them with similar calculations performed in versions of SasView before v5.0.4, at which point the scaling of the functions will be seen to be different.



There are also some new features in this version. Most notably:



  *   The Generic Scattering Calculator Tool has been overhauled and its capabilities significantly expanded. In particular, it will now perform magnetic/polarised SANS computations. As part of this upgrade, coordinate data in some VTK formats are now also supported.



  *   The data loaders have also been improved. SasView will now read CanSAS1D XML data files with multiple <SASdata> blocks in a single <SASentry>. And, by popular demand, 1D data can now be saved in CSV format. SESANS data files with the extension .sesans are now also recognised.



  *   A Boucher-type interfacial profile function has been added to the spherical_sld model.



New Models

The following models have been added to the Model Marketplace<http://marketplace.sasview.org/> since v5.0.4 was released:



  *   Magnetic Whirl
  *   Maier-Saupe distribution
  *   Cyclic Gaussian distribution
  *   Superball Model - Neither Sphere nor Cube
  *   OrientedMagneticChains



Known Issues

The 'rpa' (Random Phase Approximation, for polymer scattering) model has been temporarily withdrawn. Some gremlins had crept into how the model parameters interacted with the Fit Page which meant you were not performing the calculation you thought you were. This is being investigated. Should you need it, a separate binary blend model (the most performed calculation) is available from the Model Marketplace<http://marketplace.sasview.org/> .

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 at sasview.org<mailto:help at sasview.org>.

FUTURE PLANS
It is likely that some of the Development Team will be present at SAS 2022 this September. If you are also heading there, please do take the opportunity to look us up and say 'Hello'!

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.

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From users at lists.sasview.org  Wed Jul 13 11:24:39 2022
From: users at lists.sasview.org (Mitchell Kennedy via users)
Date: Wed, 13 Jul 2022 11:24:39 -0400
Subject: [SasView Users] Question on adding structure factors to a custom
	model
Message-ID: <CADQdjzJ=_HBD_AH5cwrS0RiPnSbh8FGibfr9KkNYFxCyw4N0VA@mail.gmail.com>

Good Morning. I am examining a system that has a combination of interacting
spherical micelles, and a gel network. I am using the gel model and would
love to add a spherical model with a squarewell potential structure factor.
The only way I have found to do this is to add all three together as
separate models, but this is not working very well. My question is, is it
possible to add structure factors to custom models or to add a structure
factor onto the spherical portion of the model where the radius is
calculated using the sphere fitting parameters?

Thank you for any help
Mitchell Kennedy
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From users at lists.sasview.org  Fri Jul 15 12:47:47 2022
From: users at lists.sasview.org (Paul Butler via users)
Date: Fri, 15 Jul 2022 12:47:47 -0400
Subject: [SasView Users] Question on adding structure factors to a
	custom model
In-Reply-To: <CADQdjzJ=_HBD_AH5cwrS0RiPnSbh8FGibfr9KkNYFxCyw4N0VA@mail.gmail.com>
References: <CADQdjzJ=_HBD_AH5cwrS0RiPnSbh8FGibfr9KkNYFxCyw4N0VA@mail.gmail.com>
Message-ID: <CAMF-Q0W_TXom_HM5Gp910ZV+jx4QTNWcLX1a7gyxTVRvL9zaiw@mail.gmail.com>

Hi Mitchell,

So the answer to your basic question of combining several models in
different ways the answer is, I believe, yes (assuming I understand exactly
what you want to do).  Unfortunately there is a bug that prevents you from
using the Add/Multiply tool iteratively (and it does not allow combining
more than 2 models at once).  however you can use it to create for example
a sphere at squarewell and then use the Edit Custom Model to edit the file so
created.

Note the math has three (not just two) options: + which sums two models, *
which just multiplies two models and @ which multiplies assuming the the
second function is a structure factor (so provides some of the structure
factor features)

Doing so you will find several lines but the key one is this one:

model_info = load_model_info('sphere at hardsphere')

you can change this to be for example

model_info = load_model_info('powerlaw+sphere at hardsphere')

In principle you can do any number of these though you may want to be
careful about scale and background which are normally added outside the
parentheses.


That said, I'm not clear on your system. It sounds like you just have a
system of hard spheres that have formed a gel in which case I would
recommend either the Teixeira fractal, or, if you are looking at the liquid
glass transition from an attractive potential, maybe just spheres with the
Baxter potential? Of course if you have spheres in the "liquid" state in a
gel matrix (e.g. a polymer gel?) then I'm still not sure the solution you
sound like you are using is correct since the gel network would presumably
alter the effective interactions significantly?


Hope this helps


Stay safe

Paul





On Thu, Jul 14, 2022 at 10:00 AM Mitchell Kennedy via users <
users at lists.sasview.org> wrote:

> Good Morning. I am examining a system that has a combination of
> interacting spherical micelles, and a gel network. I am using the gel model
> and would love to add a spherical model with a squarewell potential
> structure factor. The only way I have found to do this is to add all three
> together as separate models, but this is not working very well. My question
> is, is it possible to add structure factors to custom models or to add a
> structure factor onto the spherical portion of the model where the radius
> is calculated using the sphere fitting parameters?
>
> Thank you for any help
> Mitchell Kennedy
> _______________________________________________
> users mailing list
> users at lists.sasview.org
> http://lists.sasview.org/cgi-bin/mailman/listinfo/users
>
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From users at lists.sasview.org  Fri Jul 15 12:47:47 2022
From: users at lists.sasview.org (Paul Butler via users)
Date: Fri, 15 Jul 2022 12:47:47 -0400
Subject: [SasView Users] Question on adding structure factors to a
	custom model
In-Reply-To: <CADQdjzJ=_HBD_AH5cwrS0RiPnSbh8FGibfr9KkNYFxCyw4N0VA@mail.gmail.com>
References: <CADQdjzJ=_HBD_AH5cwrS0RiPnSbh8FGibfr9KkNYFxCyw4N0VA@mail.gmail.com>
Message-ID: <CAMF-Q0W_TXom_HM5Gp910ZV+jx4QTNWcLX1a7gyxTVRvL9zaiw@mail.gmail.com>

Hi Mitchell,

So the answer to your basic question of combining several models in
different ways the answer is, I believe, yes (assuming I understand exactly
what you want to do).  Unfortunately there is a bug that prevents you from
using the Add/Multiply tool iteratively (and it does not allow combining
more than 2 models at once).  however you can use it to create for example
a sphere at squarewell and then use the Edit Custom Model to edit the file so
created.

Note the math has three (not just two) options: + which sums two models, *
which just multiplies two models and @ which multiplies assuming the the
second function is a structure factor (so provides some of the structure
factor features)

Doing so you will find several lines but the key one is this one:

model_info = load_model_info('sphere at hardsphere')

you can change this to be for example

model_info = load_model_info('powerlaw+sphere at hardsphere')

In principle you can do any number of these though you may want to be
careful about scale and background which are normally added outside the
parentheses.


That said, I'm not clear on your system. It sounds like you just have a
system of hard spheres that have formed a gel in which case I would
recommend either the Teixeira fractal, or, if you are looking at the liquid
glass transition from an attractive potential, maybe just spheres with the
Baxter potential? Of course if you have spheres in the "liquid" state in a
gel matrix (e.g. a polymer gel?) then I'm still not sure the solution you
sound like you are using is correct since the gel network would presumably
alter the effective interactions significantly?


Hope this helps


Stay safe

Paul





On Thu, Jul 14, 2022 at 10:00 AM Mitchell Kennedy via users <
users at lists.sasview.org> wrote:

> Good Morning. I am examining a system that has a combination of
> interacting spherical micelles, and a gel network. I am using the gel model
> and would love to add a spherical model with a squarewell potential
> structure factor. The only way I have found to do this is to add all three
> together as separate models, but this is not working very well. My question
> is, is it possible to add structure factors to custom models or to add a
> structure factor onto the spherical portion of the model where the radius
> is calculated using the sphere fitting parameters?
>
> Thank you for any help
> Mitchell Kennedy
> _______________________________________________
> users mailing list
> users at lists.sasview.org
> http://lists.sasview.org/cgi-bin/mailman/listinfo/users
>
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From users at lists.sasview.org  Fri Sep  2 11:44:26 2022
From: users at lists.sasview.org (Stephen King - STFC UKRI via users)
Date: Fri, 2 Sep 2022 15:44:26 +0000
Subject: [SasView Users] Issue fitting with a GPU in SasView 5.0.5
Message-ID: <CWLP265MB42975F9F3B864DDDE07DF807B07A9@CWLP265MB4297.GBRP265.PROD.OUTLOOK.COM>

Dear SasView Users,

We have become aware of an issue in the latest SasView 5.0.5 with the new Levenberg-Marquardt (LM) optimiser - the default optimiser - when you are fitting with a GPU enabled. Specifically, if the model you are fitting against contains C code, either embedded in the Python model file or in an ancillary C model file, then nothing happens when you click Fit! The parameters in the FitPage do not update and the fit to the data does not change. You must specifically enable GPU computations, if required, else they are performed on the CPU. So this is a very obvious bug and the chances that you have obtained incorrect results as a consequence are very low.

In contrast, if you are only using the CPU (the default condition), or if the model you are fitting is a pure Python model, then this new LM optimiser still works as expected. And if you are using an earlier version of SasView then the old LM optimiser works with a GPU.

But if you need to use a GPU for your fitting in SasView 5.0.5 then the workaround is simply to select a different optimiser from Fitting > Fit Algorithms. See https://www.sasview.org/docs/user/qtgui/Perspectives/Fitting/optimizer.html for more information.

For the technically-minded, this issue has arisen because we changed the source library for the LM optimiser from SciPy to MPFit. We did this because the SciPy version did not respect parameter bounds during fitting; something which several of you had complained about! Unfortunately, the fact that the MPFit version did not support parallelisation escaped our notice!

To tell if your model uses C code, go to https://github.com/SasView/sasmodels/tree/master/sasmodels/models. If there are .py and .c files with the same filename then the model will be affected by this bug. This is, unfortunately, the majority of the library models.


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.

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