Honoring Bob Von Dreele on his 80th

2023-09-21 Thread Toby, Brian H. 
Hi everyone,

  This December we will celebrate Bob Von Dreele’s 80th birthday with a set of 
talks and remembrances. This will be held at NIST in Gaithersburg, MD (USA) on 
Monday, December 4. We welcome talks on Bob’s contributions to science and data 
analysis, talks on work done cooperatively with Bob and talks where 
participants share how Bob’s work has impacted their own science or scientific 
careers. We recognize that not everyone who wants to contribute will be able to 
get to the Washington DC area for this. Short (<5 min) recorded presentations 
to be shared are also welcomed. We are investigating the possibility of live 
streaming or placing recordings of presentations on the web after the event.

   If you are interested in speaking, attending or wish to contribute a 
recording, please contact us.

   Details will be placed here as they become available: 
https://subversion.xray.aps.anl.gov/trac/pyGSAS/wiki/VonDreeleFest

Brian Toby (brian.t...@anl.gov)
Jim Cline (james.cl...@nist.gov)
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Re: Rietveld condamnation considered as established by some more people

2023-08-17 Thread Toby, Brian H. 
My personal feelings are that regardless of the origin of the idea, Hugo did 
the work that made crystallographic full pattern fitting possible. That 
implementation was not just a “programming task” as the minimal capabilities of 
computers of the day required significant innovation for memory and 
computational efficiency. The reasons why “Rietveld Analysis” is my preferred 
name for this technique are spelled out in chapter 4.7 of Volume H of the 
International Tables and I will not repeat them here, but I also like to draw 
additional attention to his minimally-credited method for intensity extraction, 
which was later cleverly extended into the LeBail technique. His solo 1967 
paper outlined the groundwork needed to fit all peaks in a pattern.

I was not active in the days when this work was done, and only spoke with Hugo 
twice, though we also exchanged a few e-mails, but I did have the chance to 
speak with many people who were active in CW neutron diffraction in those days. 
All were very supportive of the name "Rietveld Analysis”; none ever commented 
about to giving too much credit to Hugo. Those people included Ted Prince, who 
himself proved the statistical superiority of Rietveld Analysis over other 
approaches.

One minor update on what is below. Hugo’s original code, as published solo in 
1969, was written in Algol, but to make the technique more accessible, he 
rewrote his program in Fortran and he circulated that widely (unpublished). 
After Alan, his Fortran code went through many hands (including mine) with new 
features added from each; this is also discussed in ITH 4.7. However, GSAS was 
an all-new program in its day and did not use any of Hugo’s code.

Brian

On Aug 17, 2023, at 2:28 PM, Alan W Hewat  wrote:

Concerning the code, many, including the first versions of GSAS (and FullProf?) 
were based on the original Rietveld code that I 
modified
 at Harwell in 1972 and distributed at ILL

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Re: scattering factor for O2- ?

2023-02-21 Thread Toby, Brian H. 
I am going to make the comment that (A) neutral atom form factors are probably 
closer to the actual electron distribution in most materials where there is 
significant covalent bonding (~= almost everything) and (B) even if that were 
not true, the difference between O, O1- and O2- is probably pretty minor for 
powder diffraction, so the choice does not matter. Except at very low angle, 
the form factor curves are just about the same for ionized atoms as neutral 
ones. (This is understandable since ionization only affects the outer shell 
electrons.) So, other than a small change in the first reflection or two, 
easily swamped by experimental artifacts, one just does not see any difference.

I personally use only neutral atom form factors.

Brian


On Feb 21, 2023, at 4:10 AM, Matthew Rowles 
mailto:rowle...@gmail.com>> wrote:

Thanks all

It looks like fat fingers all around!

W&K doesn't contain O2-, does contain O-
RR&G _does_ contain O2-, doesn't contain O- (every version of the waasameir 
data I've found online has this typo, so I'm pretty sure they're all the same 
file.)

Now just to cross-check the data to see if they're the same (and actually 
_read_ the papers)

I'll also check out the other papers, and start looking for some N3-.

Thanks


Matthew








On Tue, 21 Feb 2023 at 17:44, Kern, Arnt 
mailto:arnt.k...@bruker.com>> wrote:
Hello Daniel, hello all!

Daniel, you are right. I just obtained the Hovestreydt paper, he actually 
published a 9 coefficients representation.

My apologies!

Cheers,

Arnt


-Bruker Confidential-
Von: rietveld_l-requ...@ill.fr 
mailto:rietveld_l-requ...@ill.fr>> Im Auftrag von 
Többens, Daniel
Gesendet: Dienstag, 21. Februar 2023 09:58
An: rietveld_l@ill.fr
Betreff: Re: scattering factor for O2- ?

Hello Arnt,

I believe you are probably mistaken. The file at GitHub cites at the source of 
most of its scattering factors either the paper of Waasmaier & Kirfel ("New 
Analytical Scattering Factor Functions for Free Atoms and Ions", D. Waasmaier & 
A. Kirfel, Acta Cryst. A 95) or the International Tables, with the sole 
exception of "Fit for O1- based on the tabulated values of Table 2 (D. Rez, P. 
Rez & I.Grant, Acta Cryst. (1994), A50, 481-497)."

This is most certainly a typing error, as neither of the former two contains 
values for O2-, while the paper of Rez does not contains values for O2-, but 
not for O1-. I would be very surprised if the values there were not fitted to 
the table of Rez.

Just for the sake of completeness, there are at least two more papers with 
scattering factors for O2-:

Schmidt, P.C., K.D. Sen, and A. Weiss, The Spherical Crystal-Potential and 
Physical-Properties of Ions in Crystals - a Hf-Calculation for the 10,18, and 
36-Electron Closed Shell Ions of X-Ray-Scattering Factors, Diamagnetic 
Susceptibilities, and Dipole Polarizabilities. Berichte Der Bunsen-Gesellschaft 
- Physical Chemistry Chemical Physics, 1980. 84(12): p. 1240-1251.

Azavant, P. and A. Lichanot, X-Ray-Scattering Factors of Oxygen and Sulfur Ions 
- an Ab initio Hartree-Fock Calculation. Acta Crystallographica Section A, 
1993. 49: p. 91-97.

Good Luck to everyone out there,
Daniel Többens
Am 21.02.2023 um 07:52 schrieb Kern, Arnt:
Hi Matthew,

I am pretty sure, this is

“On the atomic scattering factor for O2-“
E. Hovestreydt

Acta Cryst. (1983). A39, 268-269
https://doi.org/10.1107/S0108767383000550

I don’t have the paper at hand, unfortunately.

Cheers,

Arnt



-Bruker Confidential-
Von: rietveld_l-requ...@ill.fr 
 Im Auftrag von 
Matthew Rowles
Gesendet: Dienstag, 21. Februar 2023 01:38
An: RIETVELD_L Distribution List 
Betreff: scattering factor for O2- ?

**EXTERNAL EMAIL**
Hi all

I've been looking at atomic scattering factors recently, and in particular, the 
11-coefficient parameterisation by Waasmaier and Kirfel [1].

In their paper, they give a parameterisation for O and O-, but in tables I can 
find online (eg libdiffpy/f0_WaasKirf.dat at master · diffpy/libdiffpy 
(github.com)),
 there is also an entry for O2-.

Does anybody know where this came from?

Thanks

Matthew


[1] D. Waasmaier & A. Kirfel, New Analytical Scattering Factor Functions for 
Free Atoms and Ions for Free Atoms and Ions,  Acta Cryst. (1995). A51, 416-413



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Re: ITO source code

2021-08-08 Thread Toby, Brian H. 
https://subversion.xray.aps.anl.gov/CMPR/trunk/src/ito15/

On Aug 8, 2021, at 6:58 AM, Peter Stephens  
wrote:

Does anybody know where I can find the source code of the powder indexing 
software ITO?

All the best,
Peter

**
Peter W. Stephens
SUNY Distinguished Professor Emeritus
Department of Physics and Astronomy
Stony Brook University


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Re: Computing code for hkl generation

2021-07-18 Thread Toby, Brian H. 
Sure.

This can be done in GSAS-II from the GUI (see 
https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/Simulation/SimTutorial.htm,
 just export a HKL file rather than a simulated pattern) or from a Python 
script (see 
https://gsas-ii.readthedocs.io/en/latest/GSASIIscriptable.html#pattern-simulation,
 note this example writes both reflections and a simulated pattern.)

Those examples use a CIF as input, but if all that is wanted would be 
reflections, it is possible to define a phase using a space group (which can be 
a non-standard setting), unit cell dimensions and a single dummy atom position 
as input.

Brian

On Jul 18, 2021, at 3:13 PM, Gallington, Leighanne C. 
mailto:galling...@anl.gov>> wrote:

I would think GSAS-II might also have something.  Maybe Brian Toby can chime in?

Get Outlook for Android


From: rietveld_l-requ...@ill.fr 
mailto:rietveld_l-requ...@ill.fr>> on behalf of 
Simon Billinge mailto:sb2...@columbia.edu>>
Sent: Sunday, July 18, 2021, 3:01 PM
To: JR
Cc: Etter, Martin; Rietveld
Subject: Re: Computing code for hkl generation

FOX can do this (http://fox.vincefn.net/Manual/Powder) and ObjCryst, which is 
the engine beyond FOX, has python bindings (look for pyobjcryst).

I am not sure if there is an example of how to use pyobjcryst to do this, or if 
it is even possible, but it seems as if it would be a good thing to look into. 
Vincent Favre-Nicolin would know if he is monitoring this list...

S

On Sun, Jul 18, 2021 at 3:45 PM JR mailto:rohli...@fzu.cz>> 
wrote:
Dear Martin,

try CCTBX, https://cci.lbl.gov/cctbx_docs/

Jan

Dne 18. 7. 2021 18:03 napsal uživatel "Etter, Martin" 
mailto:martin.et...@desy.de>>:

Dear Colleagues,

I am currently looking for a Python or C/C++ module or function which generates 
hkl reflections with the correct systematic absences by giving the space group 
number or symbol to it. Is anybody aware, if there are open source modules 
exisiting already, before I start to write it by myself?
If not I would appreciate also, if there are hints on optimized code for this 
problem, as I would like to write a time-saving algorithm.

With kind regards from Hamburg,

Martin Etter

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--
Simon Billinge
Professor, Columbia University
Physicist, Brookhaven National Laboratory


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Re: GSAS-II - indexing TOF data

2020-04-13 Thread Toby, Brian H. 
Alex,

We do not have a routine that will merge peaks from multiple histograms, but 
you can use “Save peaks” on each histogram to obtain the files for each. Them 
manually edit them to create a composite file which can be read in and then 
used for indexing.

Brian

On Apr 13, 2020, at 1:24 PM, Alexandros Lappas 
mailto:lap...@iesl.forth.gr>> wrote:

Dear colleagues,

We are working on some neutron time-of-flight (TOF) data and attempt to index 
them within GSAS-II.

As the low-angle detector banks contain information that is not resolved by the 
higher angle banks, data indexing is not thorough.

Could you please advise whether it is possible to combine “Peak List” 
information from individual detector banks with the purpose to create an “Index 
Peak List” that contains a more exhaustive set of reflections for indexing 
purposes within GSAS-II?

If this is not possible within GSAS-II, could you please suggest an alternative 
‘auto-indexing’ suite that may be able to handle TOF neutron data?

Thank you.
Alex Lappas

--
Dr. Alexandros Lappas,
Research Director,
Institute of Electronic Structure and Laser (IESL),
Foundation for Research and Technology - Hellas (FORTH),
P.O. Box 1385, Vassilika Vouton,
711 10 Heraklion, Crete,
GREECE

Tel   +30 2810 391344
Fax   +30 2810 391305
Quantum Materials & Magnetism 
Lab
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Re: Software re-binned PD data

2019-09-26 Thread Toby, Brian H. 
Tony,

These days many if not most powder instruments (~100% of those at 
synchrotron and neutron sources) do some sort of data processing to take raw 
measurements and convert them to diffractograms that are used in Rietveld. The 
key for how to know if this is done properly is to ask if any experimental 
measurement ends up in being used in more than one bin in the final 
diffractogram. If this rule is broken, such as the mode in FIT2D that smooths 
patterns by pixel-splitting) then one introduces correlation between points in 
the pattern and the statistically expected R becomes overestimated (and reduced 
chi-squared values can drop below 1). That could be handled in theory (using a 
weight matrix in construction of the Hessian), but no Rietveld code does.

Brian



On Sep 25, 2019, at 10:40 PM, iangie mailto:ian...@126.com>> 
wrote:

Dear Rietvelder,

I hope you are doing well.
It is generally acknolwdged that Rietveld refinement should be performed on raw 
data, without any data processing.
One of our diffractometer/PSD  scans data at its minimal step size (users can 
see that the step size during scan is much smaller than what was set), and upon 
finishing, the measurement software re-bin the counts to the step size what 
users set (so the data also looks smoother, after re-bin).
My I ask is this re-bined data from the measurement software considered as "raw 
data" or "treated data"? And can we apply Rietveld refinement on this data?

Any comments are welcome. :)

--
Dr. Xiaodong (Tony) Wang
Research Infrastructure Specialist (XRD)
Central Analytical Research Facility (CARF)   |   Institute for Future 
Environments
Queensland University of Technology
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Re:

2018-08-13 Thread Toby, Brian H. 
Dear Henk,

   I am not sure if this is what was intended in your commentary and e-mail, 
but I read from it the point that have heard often over the years, which is 
that someone is less than fully deserving of scientific credit because “s/he 
only developed the software” and in particular the term "the Rietveld Method” 
neglects the range of contributions from others in the scientific process. I 
think this needs a response.

   There is no doubt that pattern fitting for extracting peak intensities 
predates the 1967 and 1969 papers from Hugo Rietveld, even though back then 
peak areas were most commonly estimated with a planimeter 
(https://en.wikipedia.org/wiki/Planimeter — I can remember my father around 
then using one for chromatography) or cutting and weighing. Likewise many 
people worked on developing the parameterization that allowed quantitative 
modeling of CW neutron diffraction peaks (though notably my understanding is 
that the well-known Cagliotti equation is a reformulation that Hugo first 
published, but credited to Cagliotti.) Van Laar sometime later contributed 
greatly to our understanding of low-angle asymmetric peak broadening (but 
again, fairly or not, most credit goes to Finger, Cox and Jephcoat who first 
released a general purpose program, even though Eddy and David first showed 
that it could be coded). I would guess that many people discussed the idea of 
determining crystallographic parameters by directly fitting to a diffractogram, 
but Hugo first developed an Algol code that actually implemented that concept, 
in a time when tackling such a large problem with the tiny computers available 
those days was an incredible achievement. If that was not enough, since Algol 
was not widely used, he then rewrote his code in Fortran to make his method 
more available.

His Fortran code offered quite sophisticated crystallographic models, 
including magnetic scattering, and allowed complex groupings of parameters. 
Taking the idea of full pattern fitting from a concept to a method required 
considerable innovation. As one example, Hugo invented an intensity extraction 
algorithm that, as far as I am aware, is in every current program powder 
fitting in current use. Hugo’s extraction method was later incorporated into 
the LeBail method, when Armel came up with his smart idea to recycle those 
intensities.

One measure of how far ahead of the curve Hugo’s work had been is to look 
at how long it took to see widespread acceptance. Around 1985, when I was first 
exposed to it, it was only just becoming be used outside of a few choice labs. 
Incidentally, what I used then was a code that had been passed through several 
hands and modified in each, but was based on Hugo’s original Fortran 
implementation. My understanding is that just about every Rietveld code that 
was available through to the 1990’s, with the one exception of GSAS, contained 
some of Hugo’s code.

Hugo was one of many, many people who contributed to modern powder 
diffraction practice, but his solo work handed the world a tool which invented 
my field — powder diffraction crystallography — and I am most respectful of 
that. I cannot speak for others, but I personally will continue to use the term 
Rietveld analysis to honor an accomplishment that was well ahead of its time. 
It did not occur in a vacuum — little in science does, including the work of 
both Newton and Einstein — but still was an incredible step forward.

Brian

On Aug 9, 2018, at 5:32 AM, h.sch...@uva.nl wrote:

Bob van Laar and I wrote an article about the development of the powder Profile 
Refinement at the Reactor Centre Netherlands. This method is later called 
Rietveld refinement. We show that there were three persons involved in this 
enterprise, Bert Loopstra for the idea, Bob van Laar for the mathematical 
treatment and Hugo Rietveld for the computer program, rather than one. For all 
users of the method it will be interesting to read.

The article (Acta Cryst. (2018). A74, 88-92) is Open Access and can be 
downloaded from: http://journals.iucr.org/a/issues/2018/02/00/ib5058/ib5058.pdf

At the moment it is the most read article of Acta Cryst. A of the last 6 
months: http://178.33.252.149/a/services/mostread.html

Kind greetings,
Henk Schenk
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Re: Si Zero-Background Holder Pattern subtraction in GSASII

2018-02-02 Thread Toby, Brian H. 
Have you looked at this: 
https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/BkgFit/FitBkgTut.htm, but 
why is your zero-background plate giving you peaks? It should be off-cut so 
that there is no Bragg diffraction.

Brian

On Feb 2, 2018, at 10:09 AM, Muir, Caelin Frederick 
mailto:cfm...@sandia.gov>> wrote:

Hi all,
I am performing refinement in GSASII on a pattern that was taken with a Si 
zero-background holder. I am unable to figure out how to subtract/ignore the 
peaks associated with the zero-background holder. Any advice is appreciated, 
thanks in advance.

Best,
Caelin
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Re: 2-theta shift due to sample displacement in parallel beam

2017-02-02 Thread Toby, Brian H. 
Shay,

I have to disagree with much of the previous discussion. Yes, there are 
aberrations in two-theta with sample displacement in a pseudo-parallel beam 
instrument and they are different for displacement along the beam direction and 
for displacement perpendicular to the beam (but in the detection plane). 
Typically you can only see the first correction when data are collected over a 
very wide angular range (>150 degrees) so this is almost never noticed with 
x-rays. The functional form for the corrections is coded into GSAS-II, so if 
you want read through the source code you can see what they are or you can do 
some simulations to see the effect. The functional form for these corrections 
are completely different from those for Bragg-Brentato geometry, which is 
extremely sensitive to the sample height and in some cases sample transparency.

   The Debye-Sherrer geometry corrections are typically very minor. When only 
the second term is needed, the correction can be replaced with small shifts in 
the two-theta zero correction and lattice constants. This is why in practice 
with synchrotrons and CW neutrons one does not see the problems with sample 
placement that leads to large peak shifts in a Bragg-Brentano geometry, making 
it much easier to index patterns from synchrotron data, but it is not true that 
there are no corrections.

Brian


On Feb 2, 2017, at 9:14 AM, Shay Tirosh 
mailto:stiro...@gmail.com>> wrote:

Dear Rietvelders

Does the 2-teta shift due to sample displacement in parallel beam is similar to 
Bragg Brentano mode?
If not then what is the mathematical expression in parallel beam?

Thanks

Shay
--
_

Dr. Shay Tirosh
Institute for Nanotechnology & Advanced Materials
Bar Ilan University
Ramat Gan, 52900
Israel
Phone: +972-(0)30-531-7320
Mobile: +972-(0)54-8834533
Email: stiro...@gmail.com
_
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APS Powder Diffraction Educational Content, APS 100 Years of Powder Diffraction Minisymposium

2016-12-19 Thread Toby, Brian H. 
Due to the wonders of web page management, our web content on powder 
diffraction, which includes quite a few on-line lectures, has moved to a new 
location: 
https://www1.aps.anl.gov/Education/Powder-Diffraction-Educational-Materials. 
This URL is hard to find at present, so this is worthwhile to bookmark.

This page contains some new content that may be of interest: On November 11, 
2016 we held a half-day symposium on historical developments in powder 
diffraction as well as contemporary APS work to commemorate the 100th 
anniversary of powder diffraction. Speakers were: David Cox (Brookhaven 
National Laboratory, retired), Tim Fawcett (International Centre for 
Diffraction Data) Pete Chupas (APS), Andrey Yakovenko (APS), Saul Lapidus 
(APS), Olaf J. Borkiewicz (APS) and Robert B. Von Dreele (APS). Recorded 
versions (slides/audio) of all lectures are now available on-line here: 
https://www1.aps.anl.gov/Education/Powder-Diffraction-Century-Symposium.

Brian++
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Re: Help for analysis strain using GSAS？

2016-12-19 Thread Toby, Brian H. 
I am not an expert on strain analysis, but can offer a few comments. The first 
is that GSAS-II is way better for this than GSAS/EXPGUI for the simple reason 
that it decouples the instrumental broadening (which should be determined from 
a standard) from the sample-depended terms (size/microstrain) and offers a 
three-level approach to the model 
(isotropic/uniaxial/full-blown-Stephens-expansion) which is also nice. The 
values for these broadenings are expressed as a function of the peak widths 
(delta d/d or equivalently delta Q/Q, no units).

As to what one can do with a lab instrument: usually one wants to separate size 
broadening from strain broadening (unless the former can be ruled out); this 
requires data over a wide angular range. This depends on the scattering from 
the sample as well as the instrument. Likewise, it is very hard to discern 
small broadening values affecting peaks that are already broad from a low 
resolution instrument — so it depends on your project and is very hard to say 
much on a general basis.

Brian


On Dec 19, 2016, at 6:45 AM, Daxu Liu 
mailto:daxu...@yahoo.com>> wrote:

Hi, everyone,

Someone can supply some information on analyzing strain using GSAS?  Because 
one of the reviewers asked me to determine the stain of biogenic calcite, 
however I don't know how to analyze the refinement data to obtain the strain. I 
wonder whether the resolution of conventional Bragg-Brentano X-ray 
diffratometer is able to determine the strain. I know GSAS does describe the 
strain using some functions for conventional XRPD data. How to output the 
corresponding data to calculate the strain.


Best regrads, Daxu
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open access: Powder Diffraction journal Special Software Issue

2015-01-04 Thread Toby, Brian H. 
I would like to announce that the ICDD and Cambridge Journals have released a 
special issue of Powder Diffraction (Volume 29 Issue 
S2)
 as open access for all of 2015. This issue contains eight articles related to 
powder diffraction software on topics including powder diffraction indexing, 
software for the ICDD and CSD databases, 3-D printing, and that describe 
aspects of software packages including MSTRUC, HighScore and GSAS-II. There is 
also an educational article on the Python programming language.

I think this is the first toe that has been placed in the open-access river, at 
least within our field of expertise, so I would encourage readers of this to 
look at what is of interest to them, which may help demonstrate the level of 
interest in this type of community service.

The Journal can also be accessed from this URL: 
http://journals.cambridge.org/action/displayJournal?jid=PDJ, but click on 
“Latest Issue” and then “Next Issue” until Supplement S2 - December 2014 is 
seen. You should be able read every article for free for the remainder of the 
calendar year.

Brian
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Travel fellowship for US-based based scientists

2014-03-25 Thread Toby, Brian H. 
I would like to pass on word that there are fellowships available for younger 
scientists based at US institutions (recipients need not be a US citizen) for 
the IUCr Congress in Montreal this August. Awardees must present their work – 
either as a poster or talk – at the Congress, and will be expected to attend a 
few special mentoring events as well. The application deadline is soon: April 
10. Eligibility and application details are in the flyer: 
http://tinyurl.com/ka7vypu.

If you are only young at heart (or not even that), please help pass on the word 
of this great opportunity.

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