Hi
I am using GSAS to process some synchotron data with high background from the sample holder. I am trying to hone in on some key regions by excluing the rest but it seems like only one region can be excluded at a time. I just updated to the latest version but this is still an issue. I'm not sure if I am doing anything wrong or if this is a bug. Thanks for looking into it. Attached is my GSAS project with the 3 excluded regions.
gsas_exclusionbug.zip

Good day,

I cannot constrain the phase fraction by constraint equation. The error is as follows in the image.

Thank you for the help!

When a structure is reported in a non-standard setting, it is possible that the reported setting may not match the one that GSAS-II will generate from the space group name. One possible solution to this would be to use Bilbao to xform the structure into a standard setting on import.

As an example, this entry:

_database_code_ICSD 420002
_chemical_name_common 'Iron oxide hydroxide - epsilon'

in

_space_group_name_H-M_alt 'P 21 n m'
_space_group_IT_number 31

is not set correctly. This could be offered as an import option: https://www.cryst.ehu.es/cryst/cif2standard.html when non-standard settings are encountered.

From "Konjeti, Vineeth" [email protected]:

Hey, I finally can get around to explaining the process of what I did to get this bug.

All work done on Windows 11.
I am using a similar GSAS-II project to the base.gpx file except this time, I have the Shelx HKLF 4 data attached and have already done a refinement cycle.

I click CSV file option or the Text File option under Export > "Single Crystal data as"

it asks me to give the file a name as usual

when I open the file up, it comes up empty

refinement.gpx.zip

The LANL Cinema: Debye-Scherrer visualization package looks nice. What would be needed to allow GSAS-II to generate files that could be used in that?

wxpython offers a html viewer that may be better that the current webbrowser import for use with help & possibly tutorials. Maybe access to external codes (SUBGROUPS & ISODISTORT?).

Code outline:

import wx
import wx.html2

class Frame(wx.Frame):
    def __init__(self, *args, **kwargs):
        super().__init__(*args, **kwargs)
        
        self.browser = wx.html2.WebView.New(self)

        self.Bind(wx.html2.EVT_WEBVIEW_NAVIGATING,
                  lambda v: self.SetTitle(v.URL))

if __name__ == "__main__":
    app = wx.App()
    frm = Frame(None)
    frm.browser.LoadURL("https://www.office.com/?auth=1") # Microsoft 365
    frm.Show()
    app.MainLoop()

FabIO reads lots of image types that GSAS-II does not. An importer could call FabIO. This requires matching FabIO metadata reporting to the GSAS-II input needs.

When attempting to calibrate data from a Ni standard, GSASIIplot.py flags a TypeError: Ellipse.__init__() takes 4 positional arguments but 5 were given when trying to call Plot.add_artist() on line 8985.

This issue seems to be due to a redefinition of matplotlib.patches.Ellipse where angle is no longer a positional argument but a keyword argument (at least, it appears after * and must now be called as a keyword). I have verified that updating line 8985 of GSASIIplot.py with:

Plot.add_artist(Ellipse([cent[0],cent[1]],2*width,2*height,angle=phi,ec=col,fc='none'))

corrects the issue.

For completeness, here is the GSAS-II configuration:

Python/module versions loaded:
  Python:     3.11.9  from /Users/niklas/opt/gsas2full/GSAS-II/GSAS-II.app/Contents/MacOS/GSAS-II. 
  wx:         4.2.1  
  matplotlib: 3.8.4  
  numpy:      1.26.4  
  scipy:      1.13.0  
  OpenGL:     3.1.6  
  Image:      10.3.0 (PIL or Pillow)
  Platform:   darwin 64bit arm64
  GSAS-II:    b26156 from 20-May-2024 14:49 (0.1 days old). Version: last tag #5788
MIDAS_Zarr Reader skipped because zarr module is not installed

Request from Wenqian: superimpose ring positions for a new or expected phase onto an image.

The GSASIIfiles.LoadImportRoutines is called multiple times on startup (from GSASIIdataGUI.py). This could be streamlined so that the imports are done only once and then the objects are scanned only on later calls.

Alternately, perhaps error messages can be displayed once.

Rigid body parameters determine the uncertainties on atom coordinates for atoms in those groups. Likewise for Uiso and Uaniso values from TLS fits, etc. At present these s.u. values are not computed, but should be (from the rigid body derivatives and the covariance matrix). Report these in the CIF export.

The plot shown during fitting can be in TOF or 2theta, but not Q. If the plotting mode has been set to Q, it would be nice if it stayed in Q.

Requested by Yishu Wang (UTk) so that she can do single-crystal scripting

04102024

Agenda

• Documentation needed for the k-vector search functionality -> howto?

• How are those ARM32 binaries built? Do we have dedicated machines or virtual machines with the specific architecture?

• I created a branch called develop from the main master branch and added in our new implementation of the k-vector search functionality. I tested it out, fixed several little bugs and I am now confident that the functionality is working robustly. This also includes the change of the k-vector search routine itself, which does need a bit of attention as detailed below.

• Through testing against artificially generated data (for which we know exactly the ground truth k-vector), we found that we have to go with a fine k-grid for the k-vector searching. This proposes the need for fast calculation. Concerning the speedup, we introduced a combination of two types of solutions -- using multiprocessing together with Cython.

• Question for @briantoby -- are we currently using any Cython in GSAS-II? Basically, a Cython file is something pretty much like Python code but can be compiled as C library to be imported into Python routine, which can significantly boost up the calculation. So I implemented multiprocessing in Cython and considering the two layers of speedup, we can now perform a heavy calculation with relatively acceptable amount of time (but still on the level of several hours).

• Testing routine needed for internal people to test out the implementation before releasing to public. I will work on creating a script for people to easily test out the new implementation, with the develop branch.

Minutes

• Add the Cython compiling stuff into the local build scripts

  Create new files for the new implementation

  Refer to those files that are not starting with G2 here

• GSAS-II Web Documentation (here) contains general introduction to GSAS-II, meaning it is NOT the place to host the technical details.

  Refer to the source codes here for building the documentation with sphinx.

• The repo here is for building up the tutorial website. We need to manually populate HTML files for new tutorials (by creating its own directory or putting into existing ones). If a new directory is created to host the new tutorials, we need to follow the instructions here to worry about getting the new directory into the website structure.

• The GSAS-II development documentation (see here) is built from source RST files together with the docstring in GSAS-II source codes. The source RST files can be found here. To populate the docstring in GSAS-II python source codes into the rendered documentation, we only need to follow the source code structure and refer to certain classes/methods inside the RST file. The place to search for the source Python files for the doc building purpose is defined here.

  Concerning the documentation for the k-vector search, we want to put the reference to the k-vector search docstring into GSASIIutil.rst file which can be found here.

• For creating the tutorials, relevant exercise files should go into the data subdirectory under certain directory for the specific tutorial. There is an index.htm file inside the data subdirectory -- we don't need to worry about it as it will be automatically generated based on the files we have in the data subdirectory.

• Do a local build for sphinx to make sure the documentation is rendered as expected before pushing to the repo.

• Refer to the GSASIImapvars.py and GSASIIscriptable.rst files for nitty-gritties of using reStructuredText.

04032024

Agenda

• See the todo list in k_vector_search.py.

• Easy way to have a local test version for beamline scientists to test out, e.g., the k-vector search functionality?

• When clicking on different items in the tree, the menu options will be updated. How?

Minutes

• Finish up the k-vector search new implementation.

• Create a branch for hosting the new implementation of k-vector and we will work out a way for people to do the testing.

• Brian walked through the implementation of the menu bar items => see notebook for more information.

  https://yr.iris-home.net/gsasiimenunotes

Allow grouping of histograms in sequential fitting: combined fits or for TOF instruments that produce multiple histograms.

Needs a tool (in controls) to select groups histograms into groups and save them (nested list?). Then in sequential fit, iterate over groups of histograms. Need to think how to display results in sequential fit table.

Bob objects to the three "not available" messages during a git update:

Press any key to continue . . . git repo opened
Updating to latest GSAS-II version
git: updated to latest version
Restart GSAS-II without a project file
pypowder is not available - profile calcs. not allowed
pydiffax is not available for this platform
pypowder is not available - profile calcs. not allowed
exiting update process

This probably can be fixed without too much work.

To facilitate testing of branches, it would be useful to have a menu command (available only in debug mode) that allows one to switch to a remote branch (and back to master)

Steps needed:

• confirm there are no local changes etc.
• find remote branches (is there anything better than?
  brList = [i.split()[1] for i in g2repo.git.ls_remote('--heads').split('\n')])
• fetch the remote branch (how?)
• switch to that branch
• restart GSAS-II

See PR AdvancedPhotonSource/GSAS-II-buildtools#7

The logging code, mostly commented out at present, would provide a useful track of what has been done in a refinement if placed into the GSAS-II notebook. Perhaps a filter on the notebook would also be useful to pick out only some types of entries there.

MIDAS provides an integrated HS pipeline for 2D data treatment, but for non-HEDM analysis, it is desired that MIDAS should transfer powder diffraction patterns (aka lineouts in 1D-speak) directly to GSAS-II. The MIDAS export mechanism has been established as Zarr, but the MIDAS Zarr importer needs more work.

From APS CAT member & GSAS-II user "Would it be possible to put the Goniometer radius in the instrument parameter file? It would be useful to make this instrument specific."

Likewise, the other stuff in the .samprm ('Type', 'Gonio. radius', 'InstrName') also makes sense in a .instprm file.

Thoughts: add to existing file; could somehow combine reading/writing the two.

Scripting needs a way to generate a status message that shows version #'s. This works:

from GSASIIdataGUI import ShowVersions
ShowVersions()

but only if wx etc is present. Need something with only script-needed packages.

The contribution of each histogram and restraints to overall fit could be shown better

When a change is made to the config, for example, when saving a "previous file" after a "save as", this change is not retained when the final version of the file is saved when the program exists.

Note comments below from 2/12/24 email "GSAS-II CIF requests"

Hi, Brian and Bob:
A committee of the Commission on Powder Diffraction and IUCr staff in Chester have been working on making checkCIF and the publication process more powder diffraction friendly. Some progress has been made in eliminating irrelevant alerts, but a few things would be better fixed from your end.

1. Could GSAS-II add
   the weighting scheme
   the excluded regions
   H-atom treatment
   the number of restraints
   to the CIF it writes? Or do we make the author add these?
2. I gave them a CIF where the radiation was Mo. _diffrn_radiation_type was just K\a1,2. The Mo had to be added. Is this a glitch?
3. There is the matter of the maximum shift/esd. If the refinement has converged, could this value be set to the convergence criterion, or could you just do the one more cycle suggested?
   Are these things doable?

They have fixed the problem of senseless esds on bond distances and angles involving non-refined H (!). They are also working on recognizing wavelengths and residuals which are art of loops.

Reply 2/15/24

I have to say that writing code to create CIFs is one of my least
favorite tasks, but I am certainly willing to work on improving the
CIFs that GSAS-II creates. What would make this task a lot easier
would be examples showing what GSAS-II produces and what would be
better. I’ll include some comments and questions below.

On Feb 12, 2024, at 2:56 PM, [email protected] wrote:

1. Could GSAS-II add
   the weighting scheme

As far as I am aware, Rietveld is always weighted by experimental
uncertainties (which depends on the data provider getting that right),
except that we provide the possibility for changing the relative
importance of different data sets. How would all this be indicated in
CIF?

the excluded regions

This information is there, in that weights are set to zero for
excluded points, but I could specify the actual regions. I’m not sure
this was in pdCIF when I wrote the exporter or maybe I was just lazy.

H-atom treatment

What is being sought? How were the positions generated? Or how were
they refined? The former is going to need to be put in by the user,
but could go into the template for each phase. As for refinement, I
don’t think we offer a riding mode, but people can create their own
restraints and constraints so that could be messy.

the number of restraints

Is this number really worth anything? What about constraints? What
about the relative contributions of restraints to the total chi
squared? All of this can be produced.

2. I gave them a CIF where the radiation was Mo.
   _diffrn_radiation_type was just K\a1,2. The Mo had to be added. Is
   this a glitch?

I’m not sure if we store the anode or perhaps just the wavelengths.
This will need some investigation and might be a no-can-do.

3. There is the matter of the maximum shift/esd. If the refinement
   has converged, could this value be set to the convergence criterion,
   or could you just do the one more cycle suggested?

I’m not sure if I understand this. Are you saying to have the
refinement engine run for one more cycle after convergence is
detected? Or run a cycle of refinement just before creating the CIF
(I’d be reluctant to do that). What do you want reported for this?

I think most of this is doable. Maybe all.

Brian

cynarine_5.cif.gz
cynarine_5.gpx.gz
cynarine_H2O_R1.cif.gz
vege083.gpx.gz
vege083E_GSAS.cif.gz
vege083E.cif.gz

Provide users with a mechanism to supply an arbitrary equation into GSAS-II that derives a value from the fitted parameters. The derivatives for that equation can then be determined numerically and the uncertainty for that parameter can then be evaluated.

Hi, I'm doing a Rietveld refinement of lab XRD data which includes large background peaks at high angles.
I set up histogram excluded regions in a project using the GUI.
Excluded regions were [64.58, 65.58] and [77.84, 78.84].
When I open this project in the scripting interface I can inspect the excluded regions I set up:

In:  hist.get('Limits')  
Out: [(10.0, 80.0), [10.0, 80.0], [64.58, 65.58], [77.84, 78.84]]

In a new project (starting without any excluded regions) my attempt to add exclusions to hist parameters via the scripting interface is as follows:

limits = hist.get('Limits')
exclusions = [[64.58, 65.58], [77.84, 78.84]]
limits.extend(exclusions)
hist.set_refinements({"Limits": limits,
                          "Background": {"no. coeffs": coeffs, "refine": True},
                          "Sample Parameters": ["Scale"]})

Returns the error:

hist.set_refinements({"Limits": limits,

  File ~\gsas2full\GSASII\GSASIIscriptable.py:3444 in set_refinements
    old_limits[0], old_limits[1] = new_limits

ValueError: too many values to unpack (expected 2)

Any help, pointers, code most welcome and appreciated!

Cheers,
Operandos

I tried to install GSAS-II via the self-installer downloads at https://github.com/AdvancedPhotonSource/GSAS-II-buildtools/releases/tag/v1.0.1, but the install failed (see commands below). I think the installer is looking for an exe file that I likely don't have (MacOS 14.4, Intel Core i7)

PS - The installer implies the version is 4446, but the download page implies 5773. Which is correct?

PSS - Do you want installer questions here, or in build tools (https://github.com/AdvancedPhotonSource/GSAS-II-buildtools/). The new webpage guidance only directs here (https://advancedphotonsource.github.io/GSAS-II-tutorials/bug.html)

cd Downloads/
./gsas2full-4446-MacOSX-x86_64.sh 

Welcome to gsas2full 4446

In order to continue the installation process, please review the license
agreement.
Please, press ENTER to continue

Do you accept the license terms? [yes|no]
[no] >>> yes

gsas2full will now be installed into this location:
/Users/**********/gsas2full

  - Press ENTER to confirm the location
  - Press CTRL-C to abort the installation
  - Or specify a different location below

[/Users/**********/gsas2full] >>> /Users/**********/gsas2full-5773  
PREFIX=/Users/**********/gsas2full-5773
Unpacking payload ...
/Users/**********/gsas2full-5773/conda.exe: line 1: =============================================: command not found
/Users/**********/gsas2full-5773/conda.exe: line 2: syntax error near unexpected token `c'
/Users/**********/gsas2full-5773/conda.exe: line 2: ` Copyright (c) 2016, Continuum Analytics, Inc.'
ERROR: could not extract tar starting at offset 000000000000015246+9490254+2

• (bug) NiO with space group R-3m and k=(0,0,3/2) with respect to the conventional cell (hexagonal axes). This one doesn't seem to work correctly: when searching high symmetry points, (0,0,3/2) doesn't appear in the list of potential solutions, which suggests there's a bug in either the conventional/primitive cell conversion or the d-spacing calculation.

• The "HighSymPts & HighSymPaths" option actually searches only HighSymPaths. So we should change the label.

• replacing the tolerance box with a "List top N results" box, that defaults to show the top 10 results (if there are more than 10, and all results otherwise).

• isodistort implementation

• List Avg. \delta(d) and Max. \delta(d) in the table, as well as Avg. \delta(d)/d.

Review and add new tutorial from Adam Phelan