Re: [sdpd] Re: Are restraints as good as observations ?

On 31/07/2013 03:07, Leonid Solovyov wrote: ... There is a widely scattered belief that restraints always improve not only the restrained values, but also the “unrestrained” part of structure such as intermolecular distances, orientations, planarity etc. Apart from your word "always", I certai

Re: [sdpd] Re: Are restraints as good as observations ?

On 31/07/2013 17:25, Leonid Solovyov wrote: One can make everything "OK" simply by choosing an "appropriate" weight of restraints. The uncertainty in the restraint's weight appropriateness makes every restrained refinement a "know how". Likelihood and/or the free R-factor offer routes to choose

Re: rocking curve

With a 2D detector you see spots for "grains" and smooth peaks for "texture". You can also observe a collection of grains which exhibit texture giving a non uniform spot density. Usually by "grains" people expect randomised changes in intensity with small orientation changes. For "texture" ther

Re: X-ray diffraction laboratory manager position

Did I click on the right link? The second point says: "Develop new experimental approaches and measurement routines as required by a growing user base." It doesn't sound so bad, unless the candidate can't think of any novel experimental techniques to invent. Jon On 05/12/2013 19:02, Cline,

Re: Dollase Paper

On 21/03/2014 10:59, Norberto Masciocchi wrote: ... > So, the question is: > Is there any way do get around this problem (without resorting to > spherical hamonics or to grind the specimen in a WC, SiC or BN mill)? High energy X-rays or neutrons in transmission geometry would seem to help? Best

Re: Stacking faults and antiphase boundary

On 06/04/2014 08:06, Leonid Solovyov wrote: The faulting model in DDM gives nearly perfect agreement with the experiment: http://sites.google.com/site/ddmsuite/home/Copper-DDM.png It looks a little bit reminiscent of this pattern for ice: http://www.science24.com/paper/15441 ...but the litt

Re: Polarization factor por Ge (111) monochromator

Jools, To get the value more directly I think you can also measure the scattering at two theta of 90 degrees in the horizontal versus vertical plane. We did this last week at the synchrotron in the course of making some detector correction files and there was a nice hole in the diffraction pa

Re: Thermal factor for magnetic phase?

Dear Jae-Ho The thermal parameters of the magnetic moments are identical to the thermal parameters of the nuclei which they are attached to (along with the x,y,z positions and occupancies). Normally they will refine much better from the nuclear intensities which should extend to higher Q. Be

Re: Statistics on semi-quantitative XRD data

Dear James, I'm not sure these are quite what you are after, but I'm suggesting them anyway. There were several papers from Gordon Barr about non-parametric methods: SNAP-1D: a computer program for qualitative and quantitative powder diffraction pattern analysis using the full pattern profi

Re: Intensity issue with synchrotron data

On 15/01/2015 12:15, Norberto Masciocchi wrote: Il 15/01/2015 11:46, Fauth Francois ha scritto: 1- the data format of the input file your are using for your refinement does not allow counts more than 10^6, This is typically the case with GSAS input file format Here at ALBA, as you suggeste

3D powder averaging...

On 2015-05-10 17:36, Alan Hewat wrote: Jon... nicely illustrated... by posting an interesting link... Thanks! Obviously I think these serial methods are a fantastic opportunity for this community. An IUCrJ commentary by me is here: "Serial crystallography for the masses": http://journals.iu

Re: Powder Diffraction Discussion Group on Facebook

Thanks Davide for this useful initiative, I have joined. I don't doubt the value of the Rietveld list but pictures are also useful. It was recently bought to my attention that funding may be related to "public perceptions" of research and for this reason we should pay attention to things like

bookmarks: Re: Powder Diffraction Discussion Group on Facebook

> > Powder Diffraction Discussion Group on facebook > > http://www.facebook.com/groups/1087352967946225/ So from what I gather we have: http://www.xrayforum.co.uk http://www.reddit.com/r/crystallography http://www.researchgate.net/topic/x-ray_diffraction There are many other places where c

Re: Anomalous scattering factor and Dispersion coefficients

Dear Xiaodong, Jeremy, Isn't it equation 3 here? http://www.nist.gov/srd/upload/jpcrd488.pdf f1/f2 are "dispersion" numbers and f'/f" are the "anomalous" ones. The relativisitic correction number for iron then shows up on page 221. Best, Jon === On 11/06/2015 17:27, Jeremy Karl Cockcroft

Re: source of diamond powder for internal standard

Hello In the reference below they say they purchased 2-4 micron grain size from Nilaco (perhaps it was: http://nilaco.jp/en/order.php?DIR=CHEMI&MENU=15&CODE=&FROM=14&ITEM1=Diamond_Powder&ITEM2=Powder). /J. Synchrotron Rad./(2014).*21*, 119-126[doi:10.1107/S1600577513028269

Re: R: Re: synchrotron beamline info

Dear Natale A good quality powder pattern starts with a good quality powder. Using a 2D area detector is probably easier than trying to align a small sample on a Gandolfi spinner, to increase grain statistics. Also a lower resolution instrument will have fewer problems for grain averaging. Wit

Re: structure solution terminology

On 16/12/2015 23:05, Lubomir Smrcok wrote: shuffles atoms or molecules around a cell and compares experimental and calculated patterns ? It could be well used also for single crystal data, I know, but it is not routinely done (yet ?). In protein crystallography one says "molecular replacement"

3D whole pattern fits for SFX data

3D whole pattern fitting has arrived: http://dx.doi.org/10.1107/S2052252516001238 ... and the samples are powders! ++ Please do NOT attach files to the whole list Send commands to eg: HELP as the subject with no body text The Rietv

Something to read...

Probably of interest to several readers here, a new paper on methodology: "Use of Bayesian Inference in Crystallographic Structure Refinement via Full Diffraction Profile Analysis" Chris M. Fancher, Zhen Han, Igor Levin, Katharine Page, Brian J. Reich, Ralph C. Smith, Alyson G. Wilson & Jacob

Re: Literature on Rietveld limitations in nano materials

Hello, I think it would be nice if I could cite some critical discussion, or There are a couple of comments in the current issue of J.Appl.Cryst that might be interesting for you: https://doi.org/10.1107/S1600576719006575 Best, Jon

Re: Software re-binned PD data

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 Hi Brian, your comment has triggered me it seems :-) For SAXS and PDF it could be better to under-sample the data (see end), but for profi

Postdoc openings at ESRF

Dear Friends and colleagues, The ESRF is currently recruiting postdoctoral fellows for various beamlines to coincide with the upgrade to the EBS light source. Details can be found at: https://esrf.gestmax.eu/ https://www.youtube.com/watch?v=btZlcuLDY5U It is unusual for there to be so many

Re: Computing code for hkl generation

Dear Martin, In addition to the other replies: I am currently looking for a Python xfab does this, see: https://github.com/FABLE-3DXRD/xfab/blob/fd3015dbd4145daf6a471765887c3aa139eb8bab/xfab/tools.py#L1039 or C/C++ module sginfo (https://github.com/rwgk/sginfo) offers a "simple_hkllist

Re: NIST SRM656 Analysis

Maybe a silly question: are you assuming you have the data on an absolute scale in order to do these calculations? Do things like surface roughness somehow not matter? Best Jon On 13/04/2022 11:56, Matthew Rowles wrote: Thanks Tony When I add the absorption edge correction to the silicon

Re: scattering factor for O2- ?

Hi Matthew, About the form factors : there is an active community doing "Quantum Crystallography" or charge density analysis with the IUCr. Some of them have been running a nice series of online lectures recently: https://qcrwebinar.chem.uw.edu.pl/ You can find many experts there, and there

FPSM : (was Re: [EXT] [External] Re: Step-like basline)

Hi Luca, Thanks for sharing the links to your method - I hope we can try it the next time we get stuck on identification. It is a shame to hear you were delayed for so long by J.Appl.Cryst. Did they ask you to cite some work from the Glasgow group as the commercial competitor? I have in min

Re: Misconduct

On 17/01/2024 09:40, Reinhard Kleeberg wrote: > "Automated mineralogy" Dear Colleagues, It sounds like there crisis for this community? I didn't see anyone mention the AI story that was also in the news: https://www.chemistryworld.com/news/new-analysis-raises-doubts-over-autonomous-labs-mater

Re: Rietveld ESD calc fortran code typo?

Dear Matthew That fortran snippet was corrected in Appendix 1 of Andreev's paper here: https://doi.org/10.1107/S002188989300891X It is a shame that implicit none was not part of fortran 77. The google search resul leading me to that was: https://www.researchgate.net/publication/359342753_Pro

Re: OMIT-map

It should be slightly different (https://doi.org/10.1107/S0021889887012755), see slide 9 here: https://brockhouse.lightsource.ca/media/uploads/xrd-school-2024/introduction_to_gsas-ii.pdf The calculation appears to be here: https://github.com/AdvancedPhotonSource/GSAS-II/blob/0b735da79488087ee5bc

Re: Neutron diffraction with boron

Armel wrote: >>And yes, the measurements have been done. >I would not call Science giving the MgB2 atomic >coordinates, already known. Was this meant to be serious? Checking for any subtle structural changes around Tc would be (has been?) a worthwhile investigation. Something easily worthy of t

Re: new GSAS

Bob, Ask and it shall appear! I'm very impressed by your speedy creation of the new GSAS windows version. I've not found any of these zero length files yet, so maybe that's platform specific? No file named expedt has turned up anywhere on my hard disks. Thinking back I remember there used to be a

Re: Neutron diffraction with boron

At 04:48 PM 3/29/01 +0200, you wrote: > >>You really think that MgB2 will give more ? Maybe... just routine to do so. > >Armel, it was you who asked if boron was possible with neutrons, and when >you are told that it is, you say that anyway it is borin' (excuse the pun :-) I hadn't realised ther

Update to PRODD rietveld software

Hi all, A new version [01_04_02] of the PRODD (windows) executable has just been deposited at ccp14. I think the link would be: http://www.ccp14.ac.uk/ccp/web-mirrors/prodd/~jpw22 Apart from a few bug fixes the main addition to this version, compared to the previous, is that it will do Lebail fi

Re: Hamilton's test

> The observations must be statistically independent, but need not be > independent in the sense of what they physically measure. It seems implicit from that sentence that the datapoints must be physically measuring some aspect of the model, is that the case? For example: Does a Hamilton test on

Re: Resolution in powder diffraction

Brian H. Toby wrote: > ... Besides, Q > is the Fourier conjugate of x (the coordinates); d-spaces have no > physical significance. D-spaces can mislead a novice into correlating > reciprocal space distances with real space distances. D-spacings are distances between lattice planes and provide m

RE: One GSAS question.

Better to work with a single phase and use the red and black symmetry operators, in my opinion. You might have to lower the symmetry for some magnetic structures and add contraints on the positions accordingly, but this saves a lot of headaches, even if it creates a few by making you think about t

Re: rietveld program (fwd)

At 05:51 PM 7/3/01 +0200, Luca Lutterotti wrote: > - only one type of peak is inside the program but the asymmetry is > handled in a much better way than in other programs (is a real > convolution as it should be) so I never found a pattern that I was not > able to fit very well with my functi

Re: x-ray scattering factors values for B-1

Asking purely as someone who once studied chemistry and has a selective memory about boron; what is the compound you're looking at? I remember things like (BH4)- and hearing about Wade's rules, but not isolated B- anions. Isn't boron even less electronegative than carbon? Could you get away with n

Re: Choosing origins

Bill, Thanks! Exactly what I was after and I'd never have guessed it from the title... Jon On Wed, 31 Mar 2004, David, WIF (Bill) wrote: > Hi Jon, > > A lot of what you'll need is in the back of the International Tables Vol. A > in Chapter 15 which goes under the snappy title of "Euclidean

Re: Magnetic Visualisation in GSAS

vrstplot, which is part of the GSAS package certainly used to plot the magnetic moments into a VRML file. You can view this with various tools, many of which are windows based, and they should allow you to fly around the structure as a 3D object. It also plots fourier maps in 3D. Good luck, Jon

Re: How to output correlation matrix in GSAS

Least matrix is in the .CMT, according to the manual. Alter the printing options in expedt to get it to print correlations on the normal list file. HTH, Jon On Tue, 30 Nov 2004, Sang-Heon Shim wrote: > Dear Experts, > > This might be an FAQ. Where (in which file) can I find correlation > ma

RE: Mean vs. Median to reduce bias in grainy intensities (was

> Of course, both are eventually linked, so the manner in which applying a > median filter to the 2-D image prior to producing a histogram affects > the whole procedure is what I was wondering about. Make a radial transform ("cake") BEFORE you apply any filters. > According to Jon's > comments,

Re: notes on rietveld method

On Mon, 27 Jun 2005, Vikrant Chauhan wrote: > Hello everyone, > I am a novice crystallographer ( so to say )..workingon XPERT PLUS..can > somebody tell me where to look for notes on rietveld method (online) ..coz > wherever I look its all about some other programs for rietveld fitting , > ana

Re: CIF format for powder work

The next file I have to make is from a Topas analysis as well. I'm not sure any other program could handle the constraints I constructed for that one (how's that for being controvertial?!). It might be very useful for any future reader of your cif file if you can paste the topas inp file in a

Re: R-Value SHELX/GSAS

Just had a look at an old refinement. Shelx came out with a much lower wR2 (few percent) than GSAS (12/14 %). I think I used hklf 5 and shelx should sum over peaks, not the contributing reflections as in Rietveld. Would have to investigate further, but I notice shelx had a gof (or chi^2) of 1 a

Re: Strange peaks from grainy Si (data re-attached)

... The problems bothering me are the measured peak is much wider than the simulation Peak widths should be 400 microns (your beamsize) divided by 3.5 cm (your distance) in radians, which is about 180*0.4/3.5/PI = 6.5 degrees. HTH, Jon

RE: Powder Diffraction In Q-Space

Klaus-Dieter was only proposing Q-scale plots for publishing results, Why this 2pi factor? Why not 1/d or sin(theta)/lambda. During a very brief look at SAXS it seemed at least a few authors disagree about the units, with "s" also appearing sometimes. It was confusing and there was a lot of s

Embedded plots, was Re: Powder Diffraction In Q-Space

From http://www.iucr.org/iucr-top/cif/faq/ # What is DDL3? DDL version 3 is the name given to some work in progress by Syd Hall and his colleagues at the University of Western Australia. It is intended to build on the greater consistency and data typing abilities of DDL2 without tying the d

Re: Fitting 2d image data

Phe, Have you investigated the "MFIT" menu in fit2d? It should fit a series of 1D rows of the image to 1D peak shape functions. Best, Jon On Wed, 4 Jul 2007, Phe Man Suherman wrote: Dear All, I have some ESRF data of diffraction from a single crystal thin film. The data was recorded o

Re: FullProf on Ubuntu 7.10

Hi there, Since I just got the graphics card working again after a similar upgrade, I'm feeling brave enough to try without wine (running). $ file fp2k ELF 32-bit LSB executable, Intel 80386, version 1, statically linked, corrupted section header size ... which shows up on google/ubuntu for

Re: question about PowPref, GSAS

Choice of space group origin will affect the computation of intensities but not which reflections are included in the pattern, so that is not the problem. The fact that the 222 reflection shows up in reflist makes it seem likely to me that you do not have the space group input correctly. H

Re: Neutron or X-ray?

Davide, Did you check for extinction and preferred orientation? Otherwise what does a combined fit give? The difference of about 10 sigma suggests a remaining systematic error. What is the impact of refining anisotropically? Good luck, Jon Davide Levy wrote: Dear All, I have a ”philosoph

Re: Preferred orientation?

Martin wrote: PS For anyone interested in an explanation of texture vs. PO, see: http://pd.chem.ucl.ac.uk/pdnn/inst1/texture1.htm http://pd.chem.ucl.ac.uk/pdnn/inst1/texture2.htm I disagree! The web page has confused "texture" with "granularity". See: http://en.wikipedia.org/wiki/Texture_(c

Re: atomic displacement parameters (ADPs)?

sisir ray wrote: How does the atomic displacement parameters (ADPs) works in TOPAS Academic? Typically "adp" is "anisotropic displacement parameter", and describes the rugby ball shapes atoms get in ortep pictures. Are / there any litrature on "unn /atomic displacement parameters" ? Thank you f

Re: Goodness of fit criterion

There can be some value in comparing S values for different models with the same data (eg ranking at least). A value much less than 1 (eg 1E-3) indicates that you lost an "esd" column (or scaling factor) somewhere in your data processing, and you should really try to find it again. Having S>>2

Re: PDF refinement pros and cons

Hi Alan, I also find it hard to understand the rationale behind this approach. G(r) can suffer from fourier truncation artifacts due to the finite q range of the data, but there seems to be no such limitation in a model. Isn't there a risk of fitting to truncation ripples with G(r)? As for c