Re: Powder Diffraction In Q-Space
Simon, You left a couple of jackets at my house - they're on their way back to you. Did you see anything interesting with the realtor? Do let us know if you'll be coming back for another visit with your wife. Best, Peter ^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~^~ Peter W. Stephens Professor, Department of Physics and Astronomy Stony Brook University Stony Brook, NY 11794-3800 fax 631-632-8176
RE: Re: Embedded plots, was Re: Powder Diffraction In Q-Space
Worlton, Thomas G. said: > Do you have an electronic copy of lazy-pulverix that I could download? Tom, I will find the source for you tomorrow, but you can download The ICSD installation that contains Lazy PulverIx executables for various platforms from http://icsd.ill.fr/icsd/install/ Lazy P. still works fine, but it is a bit old now and consists of two separate programs - one to prepare the data and a second to run the calculation. that is why I was looking for a more modern implementation. It may indeed be better to separate the powder pattern calculation from the actual plotting (ICSD uses pgplot and exports PDF and postscript but a Java plotter back-end has some advantages). Alan. _ Dr Alan Hewat, ILL Grenoble, FRANCE <[EMAIL PROTECTED]>fax+33.476.20.76.48 +33.476.20.72.13 (.26 Mme Guillermet) http://www.ill.fr/dif/people/hewat/ _
RE: Re: Embedded plots, was Re: Powder Diffraction In Q-Space
Alan: Would lazy-pulverix be a good starting point for the program you propose? We have developed Java-based interactive graphics and might be interested in developing the utility you suggest. We have normally developed Java applications instead of Applets, but conversion to an Applet is pretty easy and the people at SNS are adapting our Java graphics for their web portal. Do you have an electronic copy of lazy-pulverix that I could download? I know we have some old versions laying around here, but I am not sure I can find them. Tom Worlton, Tel. 630-252-8755 Argonne National Laboratory http://www.pns.anl.gov/computing/ -Original Message- From: Alan Hewat [mailto:[EMAIL PROTECTED] Sent: Monday, February 26, 2007 7:38 AM To: rietveld_l@ill.fr Subject: Re: Embedded plots, was Re: Powder Diffraction In Q-Space At 11:54 22/02/2007, Alan Hewat wrote: >I would like to see a profile plotting package in Java or some other really portable language that would read in CIF files and plot calculated-observed patterns like Jmol now plots structures. At 21:40 22/02/2007, Luca Lutterotti wrote: >But with a little work a java applet can be put again to work >especially with the specific purpose of plotting CIF datafiles. First of all, why Java and not a browser helper based on a portable GUI language ? Because Java will work in most browsers on most platforms without the need for any user installation - completely automatic . I did a little test Saturday on a generic public access PC in a supermarket, and was able to display Jmol (Java) 3D crystal structures without installing anything manually. So what are the specs for a Java profile plotter ? 1) As simple as possible, with the GUI customised externally using Javascript, except that the mouse would be used for zooming, measuring etc... (cf Jmol). 2) Capable of plotting an experimental profile from powderCIF http://www.iucr.org/iucr-top/cif/pd/ 3) Capable of plotting a profile from (h,k,l,d-spacing,intensity) again from a powderCIF file. It should be possible to click on structures in a list and have an instant plot of the powder patterns. 4) Capable of calculating a profile using the crystal structure coordinates from a standard CIF file. 5) Capable of generating an Adobe PDF or postscript file for printing and archiving. In fact the profile calculations need not be done in Java, so it may be possible to simply take some standard Java plotting package, add some external code, to feed it the appropriate profile data, and some controls to adjust the parameters (wavelength, U,V,W etc - and of course the plot scale, even for Q-space :-) ) Alan. _ Dr Alan Hewat, ILL Grenoble, FRANCE<[EMAIL PROTECTED]>fax+33.476.20.76.48 +33.476.20.72.13 (.26 Mme Guillermet) http://www.ill.fr/dif/people/hewat/ _
Re: Embedded plots, was Re: Powder Diffraction In Q-Space
At 11:54 22/02/2007, Alan Hewat wrote: >I would like to see a profile plotting package in Java or some other really >portable language that would read in CIF files and plot calculated-observed >patterns like Jmol now plots structures. At 21:40 22/02/2007, Luca Lutterotti wrote: >But with a little work a java applet can be put again to work >especially with the specific purpose of plotting CIF datafiles. First of all, why Java and not a browser helper based on a portable GUI language ? Because Java will work in most browsers on most platforms without the need for any user installation - completely automatic . I did a little test Saturday on a generic public access PC in a supermarket, and was able to display Jmol (Java) 3D crystal structures without installing anything manually. So what are the specs for a Java profile plotter ? 1) As simple as possible, with the GUI customised externally using Javascript, except that the mouse would be used for zooming, measuring etc... (cf Jmol). 2) Capable of plotting an experimental profile from powderCIF http://www.iucr.org/iucr-top/cif/pd/ 3) Capable of plotting a profile from (h,k,l,d-spacing,intensity) again from a powderCIF file. It should be possible to click on structures in a list and have an instant plot of the powder patterns. 4) Capable of calculating a profile using the crystal structure coordinates from a standard CIF file. 5) Capable of generating an Adobe PDF or postscript file for printing and archiving. In fact the profile calculations need not be done in Java, so it may be possible to simply take some standard Java plotting package, add some external code, to feed it the appropriate profile data, and some controls to adjust the parameters (wavelength, U,V,W etc - and of course the plot scale, even for Q-space :-) ) Alan. _ Dr Alan Hewat, ILL Grenoble, FRANCE<[EMAIL PROTECTED]>fax+33.476.20.76.48 +33.476.20.72.13 (.26 Mme Guillermet) http://www.ill.fr/dif/people/hewat/ _
Re: Powder Diffraction In Q-Space
--- Olga Smirnova <[EMAIL PROTECTED]> wrote: > Isnt it much more natural to publish only atomic > coordinates in a direct space without inversion ? Publishing only the end result hides any errors that might have been made during the analysis: the reader of the paper should at least be able to see the fit of the calculated pattern to the experimental pattern to assess the quality of the structure determination and refinement, and this requires publication of the pattern. The pattern should also be available to allow the reader to reproduce the structure determination and refinement, or to allow comparison with other patterns or structures. Maybe there are impurity peaks present, or there is some interesting background, peak shape or preferred orientation. In short, a crystal structure does not contain the same amount of information as is contained in the experimental powder pattern, and this additional information would be lost if only the atomic coordinates were published. It could be argued that the same is true for single crystal determinations, but this is a Rietveld list, and for Rietveld refinement, it is certainly true. Ceterum censeo that single crystal structure detereminations should *also* show the powder pattern of the sample the crystal was taken from, to prove (or disprove!) phase purity. Best wishes, -- Dr Jacco van de Streek, Frankfurt University, Frankfurt am Main, Germany. ___ Copy addresses and emails from any email account to Yahoo! Mail - quick, easy and free. http://uk.docs.yahoo.com/trueswitch2.html
Re: Powder Diffraction In Q-Space
Dear all, Isnt it much more natural to publish only atomic coordinates in a direct space without inversion ? Therefore I propose, that publishing data in other units should be avoided. Sounds very tough. Best regards, -- Olga Smirnova Laboratoire de Cristallographie 24, quai Ernest-Ansermet CH-1211 Geneva 4, Switzerland Phone : [+[41] 22] 37 962 14, FAX : [+[41] 22] 37 961 08 On 2/21/07, Klaus-Dieter Liss <[EMAIL PROTECTED]> wrote: Dear Powder-Diffraction User, with the advancement of modern research infrastructure such as instruments, computing, complementary techniques, I like to raise again the necessity to present powder diffraction data in Q-space rather than in instrumental units. Other communities are already well ahead (single-xtal, SANS, SAXS, reflectometry etc) and to my view, only the powder diffractionist stick to their out-dated units (2-theta, TOF, d-spacing...). there is a poll I started a while ago under http://elpopo.ing.unitn.it:8064/maudFor/viewtopic.php?t=205 which, so far, is not very representative and I would encourage you to give your opinions. I suppose, all of us have learned the basics of crystallography somewhere during the career and the laws of Bragg diffraction. So, all of us are familiar with reciprocal space, where, for example, a reciprocal lattice can be constructed in order to represent the crystal symmetry in the natural space of diffraction. The Ewald construction and the Laue equation are examples which make most use of this. Further, reciprocal space is LINEAR, i.e. A second order reflection has double the distance from the origin than the fundamental reflection and a 110 reflection sqrt(2) times the distance than a 100 of a cubic system, etc. This alone would be a very good reason to plot all diffraction patterns as a function of reciprocal space coordinates Q. For Powder Diffraction, this means, patterns should NOT be plotted as a function of 2-theta, d, tof etc but Q which is the only natural unit! The relations are: Q = 4 * Pi * sin(theta) / lambda; or Q = 2 * Pi / d; The benefits of plotting and publishing data in this representation are obvious: * reciprocal space is the NATURAL space diffraction takes place; * reciprocal space is LINEAR and symmetries can be identified by eye; * the representation directly reflects crystal SYMMETRY; * the representation is INDEPENDENT of the instrument, type of radiation (electrons, neutrons, X-rays, light, atoms...) * the representation is INDEPENDENT of the wavelength used; * presentations and publications are directly COMPARABLE; * reciprocal space is WIDELY USED outside the powder diffraction community, such as single crystal diffraction SA(NX)S or reflectometry; Therefore I propose, that publishing data in other units should be avoided. _ Klaus-Dieter Liss -- Dr. Klaus-Dieter Liss Research Scientist, Bragg Institute Australian Nuclear Science and Technology Organisation PMB 1, Menai NSW 2234, Australia T: +61-2-9717+9479 F: +61-2-9717+3606 M: 0419 166 978 E: [EMAIL PROTECTED] http://www.ansto.gov.au/ansto/bragg/staff/s_liss.html see also: http://liss.freeshell.org
Re: Embedded plots, was Re: Powder Diffraction In Q-Space
On Feb 22, 2007, at 2:20 PM, Jonathan Wright wrote: 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 data model too closely to that of a relational database. A particular goal of DDL3 is to introduce methods into data dictionaries through a formal language known as dREL (Dictionary Regular Expression Language). I've not seen a DDL3 example, but many cases can probably be covered with what is in pdCIF already. The application which does the plotting doesn't need to end up inside the cif as part of the file, but the equation linking detector pixels to Q could be very useful. There has been a good deal of effort already in ImageCIF for single crystal experimental data. I understood Maud can read and plot cifs already, and is written in Java? Could there be a browser plugin version for this? Correct, it read data (datafiles and structures) in CIF format. It use the CIF sintax also for saving its own analysis files (with the addition of some extra non cif definitions missing in the formal cif but needed by the program and extra file substructures embedded as comments). In the past there was a browser/java applet version of Maud as well as a subsequent java webstart version, both are still in there and with the successive modifications I tried to keep the program compliant with them, with the idea to be able to activate them if needed. Only I have not used both of them recently so the first programmer rule states that what has not been tested does not work for sure. But with a little work a java applet can be put again to work especially with the specific purpose of plotting CIF datafiles. Well, in case someone is interested on it, he can just contact me with the idea/project and I may try to find out some spare time to do it. But I would prefer to have in case some specifications, files and what we need to just finalize and optimize it in the shortest time as possible. Best regards, Luca Lutterotti Best, Jon On Thu, 22 Feb 2007, Alan Hewat wrote: Now this sounds interesting. Certainly the raw data should be archived and people could then plot it as they wish. But are there examples of interactive plotting applications embedded in powderCIF files, and what language might they use ? I would like to see a profile plotting package in Java or some other really portable language that would read in CIF files and plot calculated-observed patterns like Jmol now plots structures. Alan. _ Dr Alan Hewat, ILL Grenoble, FRANCE<[EMAIL PROTECTED]>fax+33.476.20.76.48 +33.476.20.72.13 (.26 Mme Guillermet) http://www.ill.fr/dif/ people/hewat/ _
Re: Powder Diffraction In Q-Space: plotting CIFs
At 16:44 22/02/2007, Brian H. Toby wrote: >Alan, perhaps you might be able to figure out how to configure firefox to >launch pdCIFplot when it encounters a .CIF file on various platforms? Thanks Brian. I imagined that would be how it worked, since even if it could be done, embedding (the same) application in every CIF file would be overkill. Launching a helper application when Firefox (or even MSIE) encounters a file of a particular type is easy. Firefox will ask you what you want to do with the file - save it to disk, or open it with an application, and ask if you want to do that always. Actually it will use whatever is set as the default under Windows, so a trick is to just save a file to your desktop, double-click it, and select a default application if one is not already defined (right click if you want to change the default). Linux/OSX users, being more intelligent, will know how to do this with mime-types. Also look under Firefox/Tools/Options/Content/Manage. The only problem is that I already have enCIFer as my default CIF application :-) Tcl/Tk is good (and portable) but I would still like to see a Java version that could be embedded into WWW pages like Jmol, which is really impressive. BTW, thanks to Alex Renshaw I have been playing with Crystallographica's CSM search-match application, http://www.crystallographica.co.uk/searchmatch/ which generates a powder pattern "instantly" when you click on any structure in a long Powder Diffraction File list, and compares it with any other - very nice. (I am learning about search-match, something we don't do much with neutrons, but still have to figure out how to generate ASCII PDF-2 files that don't fail half the time for reasons that escape me). Alan. _ Dr Alan Hewat, ILL Grenoble, FRANCE<[EMAIL PROTECTED]>fax+33.476.20.76.48 +33.476.20.72.13 (.26 Mme Guillermet) http://www.ill.fr/dif/people/hewat/ _
RE: Powder Diffraction In Q-Space: plotting CIFs
I should add about cif is that there exists a number fundamental
incompatibilities between pdCIF & mmCIF. One main issue, as I understand
it, is that pdCIF naturally can describe multiple data sets (powder
patterns) used in a single structure analysis - mmCIF seems to forbid
this. This will cause trouble with the advent of multiple powder
patterns used in protein structure analyses. Atom naming conventions are
also different. The cif "factotum" committee must address this while
moving to new descriptions for cif (DDL3??).
R.B. Von Dreele
IPNS Division
Argonne National Laboratory
Argonne, IL 60439-4814
-Original Message-
From: Brian H. Toby [mailto:[EMAIL PROTECTED]
Sent: Thursday, February 22, 2007 9:44 AM
To: rietveld_l@ill.fr
Subject: Powder Diffraction In Q-Space: plotting CIFs
On Feb 22, 2007, at 4:54 AM, Alan Hewat wrote:
Now this sounds interesting. Certainly the raw data
should be archived and people could then plot it as they wish. But are
there examples of interactive plotting applications embedded in
powderCIF files, and what language might they use ? I would like to see
a profile plotting package in Java or some other really portable
language that would read in CIF files and plot calculated-observed
patterns like Jmol now plots structures.
Alan.
A large part of my motivation for the decade I invested in pdCIF
was that postage stamp size plots do not allow one to really understand
the quality of a Rietveld analysis fit. The pdCIFplot application will
plot in Q, provided the software has the information needed to convert
the supplied units (it does not know how to convert energy or
time-of-flight, but does fine with 2theta or d-space). It can be used to
plot intensity/s.u. -- although that is a rather clumsy thing to set up
in the "custom plot" menu. The source code (Tcl/Tk) is distributed, so
if anyone would like to add new features -- I'd love to get them. I
should also plug my work by noting that pdCIFplot also allows plotting
of Bill David's reduced chi squared or (obs-calc)/sigma and will show
the relationship between the intensity scale will also allow one to look
at the relationship between the reported intensity scale and the
equivalent value as "counts". (See www.ncnr.nist.gov/xtal or CCP14 for
ciftools downloads; N.B. the pdCIFplot paper is open access:
http://journals.iucr.org/j/issues/2003/05/00/aj0008/aj0008.pdf)
pdCIFplot is not an application embedded in a user's CIF (in
fact DDL3 embeds apps in the dictionary not in the files), nor is it
embedded in a web browser -- though I think that could be possible.
Alan, perhaps you might be able to figure out how to configure firefox
to launch pdCIFplot when it encounters a .CIF file on various platforms?
There is an open question of how pdCIF will get updated from
DDL1 to DDL3. The pdDMG needs a new chair willing to take pdCIF into the
next decade. I think I have paid my dues. I will not make any (more?)
enemies by suggesting suitable candidates.
Brian
Brian H. Toby, Ph.D.office:
630-252-5488
Materials Characterization Group Leader, Advanced Photon Source
9700 S. Cass Ave, Bldg. 433/D003 work cell:
630-327-8426
Argonne National Laboratory secretary (Marija):
630-252-5453
Argonne, IL 60439-4856 e-mail: brian dot toby at anl dot
gov
Powder Diffraction In Q-Space: plotting CIFs
On Feb 22, 2007, at 4:54 AM, Alan Hewat wrote: Now this sounds interesting. Certainly the raw data should be archived and people could then plot it as they wish. But are there examples of interactive plotting applications embedded in powderCIF files, and what language might they use ? I would like to see a profile plotting package in Java or some other really portable language that would read in CIF files and plot calculated-observed patterns like Jmol now plots structures. Alan. A large part of my motivation for the decade I invested in pdCIF was that postage stamp size plots do not allow one to really understand the quality of a Rietveld analysis fit. The pdCIFplot application will plot in Q, provided the software has the information needed to convert the supplied units (it does not know how to convert energy or time-of-flight, but does fine with 2theta or d-space). It can be used to plot intensity/s.u. -- although that is a rather clumsy thing to set up in the "custom plot" menu. The source code (Tcl/Tk) is distributed, so if anyone would like to add new features -- I'd love to get them. I should also plug my work by noting that pdCIFplot also allows plotting of Bill David's reduced chi squared or (obs-calc)/ sigma and will show the relationship between the intensity scale will also allow one to look at the relationship between the reported intensity scale and the equivalent value as "counts". (See www.ncnr.nist.gov/xtal or CCP14 for ciftools downloads; N.B. the pdCIFplot paper is open access: http://journals.iucr.org/j/issues/ 2003/05/00/aj0008/aj0008.pdf) pdCIFplot is not an application embedded in a user's CIF (in fact DDL3 embeds apps in the dictionary not in the files), nor is it embedded in a web browser -- though I think that could be possible. Alan, perhaps you might be able to figure out how to configure firefox to launch pdCIFplot when it encounters a .CIF file on various platforms? There is an open question of how pdCIF will get updated from DDL1 to DDL3. The pdDMG needs a new chair willing to take pdCIF into the next decade. I think I have paid my dues. I will not make any (more?) enemies by suggesting suitable candidates. Brian Brian H. Toby, Ph.D.office: 630-252-5488 Materials Characterization Group Leader, Advanced Photon Source 9700 S. Cass Ave, Bldg. 433/D003 work cell: 630-327-8426 Argonne National Laboratory secretary (Marija): 630-252-5453 Argonne, IL 60439-4856 e-mail: brian dot toby at anl dot gov
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 data model too closely to that of a relational database. A particular goal of DDL3 is to introduce methods into data dictionaries through a formal language known as dREL (Dictionary Regular Expression Language). I've not seen a DDL3 example, but many cases can probably be covered with what is in pdCIF already. The application which does the plotting doesn't need to end up inside the cif as part of the file, but the equation linking detector pixels to Q could be very useful. There has been a good deal of effort already in ImageCIF for single crystal experimental data. I understood Maud can read and plot cifs already, and is written in Java? Could there be a browser plugin version for this? Best, Jon On Thu, 22 Feb 2007, Alan Hewat wrote: Now this sounds interesting. Certainly the raw data should be archived and people could then plot it as they wish. But are there examples of interactive plotting applications embedded in powderCIF files, and what language might they use ? I would like to see a profile plotting package in Java or some other really portable language that would read in CIF files and plot calculated-observed patterns like Jmol now plots structures. Alan. _ Dr Alan Hewat, ILL Grenoble, FRANCE<[EMAIL PROTECTED]>fax+33.476.20.76.48 +33.476.20.72.13 (.26 Mme Guillermet) http://www.ill.fr/dif/people/hewat/ _
Re: Powder Diffraction In Q-Space
Dear Colleagues, I am happy to see, that the presentation of diffraction data is not just something neglected but that there a quite a lot of people with diferent thoughts and reasons and that is it a hot topic to find some ways to more modern and standard presentation. Nothing is really new, nor the Q-space of course. My initial intention for raising this topic was just the presentation of the data, since there are many ways to work with internal parameters, which is fully justified. I went quickly through the list mails and like to reply generally, since there are so many. and since it's late night, I resume from my mind, what I read during the day, not to be understood as a full report... Discssions were raised under the following topics: * display of results vs working units As I said above, it is fully justified to work in what parameter space is best for describing the data. To my opinion, there is needs to expand this with the new, unconventional scanning geometries. * many different units I was quitte surprised about the multitude of units which seems to be in use, suuch as 10E4/d. II believed so far, Astrophisicists hold the record. * 2Pi/d or 1/d It has been pointed out, that there is advantage for both! Me as a phhysicist, believe in 2Pi/d. c=1 ok, but that scales everything else, that means, other units become functions of c. 2Pi, howeve, designs the ratio of the circumference of a circle and its radius, and is never 1. how long did matematicians search for this number!!! so give us at least the options between 1 and 2Pi! As pointed out in the contibutions, much inelastic, SANS and reflectometry data is given including the 2Pi. * data acquisition in Q-space Interesting thoughts! certainly works well with a point detector. however, Q-space scans become quickly curved when using area detectors (cylindrical, flat, inclined...) * Cu-Kalpha problem Haven't thought about measuring with 2 wavenumbers (2Pi/lamda ;)) only. either used k- or angular dispersive with white or monochromatic beam so far. There was an interesting contribution, that the deconvoluted pattern should be presented. * intensity axis yes, I love sqrt(I) as well because of the statistics argument and found it quite nice, that it is used in some programs. * flat detector (ESRF) now to with what I fought: we used flat detectors with High-Energy X-Rays (doi:10.1080/07303300310001634952) which has a tangential depedence in 2-theta. So we need rebining of the data anyway. * cylindrical detectors QLD machines and powder diffractometers with quasi-2d detectors use quasi-cylindrical detectors. naturally none in in Q, 2-theta, TOF space. * individual solutions some colleagues brought up to read the output data from their rietveld software and then create their own plots. I tried half way for GSAS-output by myself. * programming needs In future, data spaces are much more parametric, as mentioned above in a few examples. it would be good, if rietveld programs (and any other) could handle parametric data and have a multitude of plotting or output functions for individual needs. I am sure, each point is a discussion point by itself... Best wishes, Klaus-Dieter. -- Dr. Klaus-Dieter Liss Research Scientist, Bragg Institute Australian Nuclear Science and Technology Organisation PMB 1, Menai NSW 2234, Australia T: +61-2-9717+9479 F: +61-2-9717+3606 M: 0419 166 978 E: [EMAIL PROTECTED] http://www.ansto.gov.au/ansto/bragg/staff/s_liss.html see also: http://liss.freeshell.org
Re: Powder Diffraction In Q-Space
>All of these problems of "what to plot" would go away if we all submitted >powderCIF files for our refinements. The "plot" could then be an interactive >application embedded in the electronic document and readers could select the >units they want. Now this sounds interesting. Certainly the raw data should be archived and people could then plot it as they wish. But are there examples of interactive plotting applications embedded in powderCIF files, and what language might they use ? I would like to see a profile plotting package in Java or some other really portable language that would read in CIF files and plot calculated-observed patterns like Jmol now plots structures. Alan. _ Dr Alan Hewat, ILL Grenoble, FRANCE<[EMAIL PROTECTED]>fax+33.476.20.76.48 +33.476.20.72.13 (.26 Mme Guillermet) http://www.ill.fr/dif/people/hewat/ _
Re: Powder Diffraction In Q-Space
Jacco, I/sigma_I is a good idea in principle. It just looks ugly if you get the sigmas right for certain instruments - there are meaningless steps all over the place. All of these problems of "what to plot" would go away if we all submitted powderCIF files for our refinements. The "plot" could then be an interactive application embedded in the electronic document and readers could select the units they want. They could also zoom in on it. It is hard to get away without a cif for a single crystal structure now - just make it so for powders too. Didn't a physicist already get caught faking results by leaving embedded plots in submitted documents? Is it just time to formalise that plots should embed the table of numbers they represent? When the next generation of CIF arrives (DDL3) I understood it will be possible to describe the equation linking 2theta to Q for example. This could keep Klaus happy, as well as the thousands of people using CuKa in the lab. Jon Jacco van de Streek wrote: --- "Von Dreele, Robert B." <[EMAIL PROTECTED]> wrote: Actually, I looked at Luca's little "show" & was sufficiently interested that GSAS will now plot sqrt(I) style plots. There is one "problem" - the value of "I" can be negative particularly after a background subtraction. These must be suppressed to zero for this plot to work - thus there is a small risk of something getting hidden. I think that that is because although it is called a SQRT plot, that is just because that is how it is usually implemented. What is meant is a more general principle, namely that of displaying the data points divided by their ESDs (where, of course, the ESDs must be calculated *from the raw number of counts*). I will try to explain why.
Re: Powder Diffraction In Q-Space
Jacco van de Streek a écrit : Example 1. Background subtraction. Measured: Iobs = 100 counts, so ESD = SQRT(100) = 10. The background at that point is determined to be, say, 102. The nett intensity at that point is then 100 - 102 = -2. However, the ESD of the point does not change as a result of the background subtraction, and is still 10. Plotting -2 / 10 gives the correct plot. Jacco, here you suppose that the uncertainty (s.u.) ESDbgr of the background is zero. That's usually not true. If your background Ibgr is determined with the s.u. ESDbgr and your total intensity Iobs with the s.u. ESDIobs, then the s.u. ESDnet of the net intensity Inet is not SQRT(Iobs) but ESDnet = SQRT(ESDIobs**2 + ESDbgr**2) = SQRT(Iobs + Ibgr) if we suppose the Poisson statistics for the background too. In your example ESDnet is not 10 but SQRT (100 + 102)~ 14 best regards Radovan -- Radovan Cerny Laboratoire de Cristallographie 24, quai Ernest-Ansermet CH-1211 Geneva 4, Switzerland Phone : [+[41] 22] 37 964 50, FAX : [+[41] 22] 37 961 08 mailto : [EMAIL PROTECTED] URL: http://www.unige.ch/sciences/crystal/cerny/rcerny.htm
Re: Powder Diffraction In Q-Space
Please see the following message from Apurva Mehta. If like him you receive messages but cannot post to the Rietveld list, it is not because you are being punished, but because your current "From" email address does not correspond exactly to your registered email address. In that case simply re-register by sending a message "SUBscribe Rietveld_L@ill.fr Your Name" to <[EMAIL PROTECTED]>. You may not be registered immediately because sometimes I am asleep. Glad to see so many people have strong feelings about plotting in Q-space :-) Alan. At 04:38 22/02/2007, Apurva wrote: >Dear Alan, > >I wanted to post the following message to the discussion of powder scan in Q >space, but the Rietveld list rejected the message. > >Will you please post it for me? Thanks. Apurva > > >This is an issue beyond just plotting of data. > >There is a distinct advantage in collecting powder data in constant Q steps >instead of const 2th space. > > (Peaks are broader at higher 2th and hence the resolution selected for > covering the low angle,sharper peaks is excessive for high angle peaks. >Collection in Q space levels out this discrepancy a little.) > >I do collect all my data in Q space. GSAS can read constant Q step data - >though it converts it to 2th for plotting and analysis. >My 2-cents worth >-- >*** >Apurva Mehta >SSRL/SLAC Stanford University >Bldg. 137, MS 69, 2575 Sand Hill Rd. >Menlo Park, CA 94025-7015 >(650) 926 4791, (650) 926 4100 - FAX >*** _ Dr Alan Hewat, ILL Grenoble, FRANCE<[EMAIL PROTECTED]>fax+33.476.20.76.48 +33.476.20.72.13 (.26 Mme Guillermet) http://www.ill.fr/dif/people/hewat/ _
RE: Powder Diffraction In Q-Space
At my opinion, the Q scale should not be used for the pattern data, but for representing the "extracted pattern" having refined natural peak widths, refined background etc. In an extracted pattern, there is no need for e.g. Kalpha1,2 doublets, they are stripped by refinement/deconvolution process. Regards Joerg Bergmann Am Mittwoch, den 21.02.2007, 13:58 -0600 schrieb Leopoldo Suescun: > Hi, > > As far as I am concerned, synchrotron x-rays and neutron data could be > represented in any x-axis unit without any problem other than the users > preference or a convention, but what about the kalpha 1,2 doublet for > filtered lab x-rays. > > I'd rather continue using 2theta as units for x-axis in my papers using lab > x-ray patterns just to keep the "true physical meaning" of all the peaks in > my pattern. At least until someone comes up with the program that converts a > 2-wavelength pattern collected in 2-theta into a correct pattern in Q, > 1/d.. I guess this should be like "time focusing" for TOF patterns isn't > it?, except that in lab x-rays both "channels" are merged in only one > signal. > > Maybe the day that detectors with energy discrimination becomes cheap and > accurate enough to only read the kalpha1 component of the lab x-rays this > discussion should be brougth up again. > > To me this specifical issue of representing the diffraction patterns is just > like calling the monoclinic angle beta or gamma, there are other issues like > the one Bob brought up, that are not just the way programmers wrote the > programs. > > Best regards. > Leo > > > > > > > Dr. Leopoldo Suescun > Postodoctoral Appointee > Materials Science Division - Bldg 223 - Rm D217 > Argonne National Laboratory > 9700 S. Cass Ave., Argonne, IL 60439 > Phone: 1 (630) 252 9760 > Fax: 1 (630) 252 > URL: http://www.msd.anl.gov/groups/nxrs/personnel/suescun/index.html > -Original Message- > From: Luca Lutterotti [mailto:[EMAIL PROTECTED] > Sent: Wednesday, February 21, 2007 11:30 AM > To: rietveld_l@ill.fr > Subject: Re: Powder Diffraction In Q-Space > > As we talk about plotting in Q-space (just for information in Maud is > available from few months thanks to Klaus-Dieter advocating for it), I would > advocate another "plot option" that I would rather see as a default way of > plotting. > > Looking at the other axis (the intensity) I am asking why we don't introduce > the practice to plot in a more useful scale as the root square of the > intensity (instead of the usual linear scale). This has several benefits: > - the plot will be at iso-error (I recall for who may have forgotten the > noise is proportional to the root square of the intensity), so in the > residuals you may better evaluate which are the peaks or part well fitted or > poor fitted. Otherwise with the linear scale you just see only the bad > residuals of the more intense peaks and you may think these are the peaks > poorly fitted. Instead most of the time in the true statistical meaning they > may be well fitted compare to other. In the square root intensity mode you > can evaluate them more unbiased > - you see also the small peaks and it is not necessary to enlarge the > intensity scale to check them > > In this regard some people are using the log10 scale plot (normally used for > reflectivity measurements). It may enhance more the small peaks but I don't > favor it as again you do not compare the fitting of different peak on an > equal statistical base. > > As an image is better than thousand words, as they say, I put together one > web page with the comparison of linear/sqrt/log10 scale, Q and 2theta so > everyone may take its own conclusion. > > http://www.ing.unitn.it/~maud/plotoptions/ > > I would encourage the list to propose a standard way (or advised way) to > plot, as it would be not too difficult for the different program to provide > a standard way to present the results for the benefit of comparisons. > > > Best regards, > > Luca Lutterotti >
RE: Re: Powder Diffraction In Q-Space
--- "Von Dreele, Robert B." <[EMAIL PROTECTED]> wrote: > Actually, I looked at Luca's little "show" & was > sufficiently interested > that GSAS will now plot sqrt(I) style plots. There > is one "problem" - > the value of "I" can be negative particularly after > a background > subtraction. These must be suppressed to zero for > this plot to work - > thus there is a small risk of something getting > hidden. I think that that is because although it is called a SQRT plot, that is just because that is how it is usually implemented. What is meant is a more general principle, namely that of displaying the data points divided by their ESDs (where, of course, the ESDs must be calculated *from the raw number of counts*). I will try to explain why. As mentioned elsewhere in this thread, the main error source in the raw number of counts is due to Poisson statistics, which means that if I measure Iobs counts for a given data point, then the ESD in that data point is SQRT(Iobs). If I divide Iobs by its ESD I get: Iobs / SQRT(Iobs) = SQRT(Iobs) It is the result, the SQRT(Iobs), that is generally implemented, but in cases where this gives problems, one should go back to the derivation, which allows the SQRT to be generalised: instead of taking SQRT(Iobs), one can divide by the ESD directly. For straigtforward cases, the results are the same, but for the more complicated cases, like background subtracted data, dividing by the ESD is the only way to get the correct result. Example 1. Background subtraction. Measured: Iobs = 100 counts, so ESD = SQRT(100) = 10. The background at that point is determined to be, say, 102. The nett intensity at that point is then 100 - 102 = -2. However, the ESD of the point does not change as a result of the background subtraction, and is still 10. Plotting -2 / 10 gives the correct plot. This suggests that simply plotting the SQRT is wrong not only for background subtracted data, but for *all* data where the raw number of counts has somehow been modified. The two main examples are variable count time (VCT) data where the separate ranges have been rescaled before they can be recombined, and synchrotron data that has been rescaled to correct for beam decay. The generalisation to plot each point divided by its ESD (calculated as the SQRT of the observed, unmodified number of counts) again provides the correct treatment: Example 2. VCT data. Measured: Iobs = 100 counts, so ESD = SQRT(100) = 10. Rescaling to counts per second to combine the ranges with different count times requires, say, rescaling by a factor of 2, giving 100 * 2 = 200. For the relative error to remain the same, the ESD must also be scaled with the same factor, i.e. ESD = 10 * 2 = 20. Plotting 200 / 20 now gives the correct plot. Note that simply plotting the SQRT would give a flattered plot, as the data obviously has not somehow become more accurate by multiplying everything by a constant (2 in this example). If it were possible to male experimental data more accurate that way, we could simply measure powder patterns in a fraction of a second and just multiply by a sufficiently big constant to achieve the desired accuracy, which is clearly absurd. Example 3. Synchrotron data, corrected for beam decay. Measured: Iobs = 100 counts, so ESD = SQRT(100) = 10. However, the intensity of the incoming beam is not constant, and the individual data points must therefore be rescaled before they can be combined. Let's say that a factor of 2 is required for this data point, then the rest of the argument is the same as for Example 2. This shows that it is very important to always keep track of the (rescaled) original ESDs during background subtraction etc. I hope this made some sense. Best wishes, -- Dr Jacco van de Streek Frankfurt University Frankfurt am Main, Germany ___ The all-new Yahoo! Mail goes wherever you go - free your email address from your Internet provider. http://uk.docs.yahoo.com/nowyoucan.html
RE: Powder Diffraction In Q-Space
I extract the data and plot all the curves myself in Origin:) You may find it's much easier to control in this way, and the file can be saved for later revise, although it takes time. Sincerely, Ling Yang -Original Message- From: Luca Lutterotti [mailto:[EMAIL PROTECTED] Sent: Wednesday, February 21, 2007 4:37 PM To: rietveld_l@ill.fr Subject: Re: Powder Diffraction In Q-Space Alan, I do not want to take the decision out of the author, but the contrary. When programs just only plot in one scale, than the author is forced to use that one. Can I plot in square root or in Q space with Topas if I like to do that? cheers, Luca On Feb 21, 2007, at 10:28 PM, AlanCoelho wrote: > > > I was not aware of Journals having rules stating that data must be > plotted > in square root scale and this is precisely the point. I certainly > do not > want an edict stating that authors must do so. It should be up to > the author > to choose whatever x-axis and y-axis scales that best shows up > features. > > If an author is writing a paper on an instrumet correction, say for > example > cylindrical or PSD correction, then it is sensible to use 2Th. > > Thus please do not take these decisions away from the author. > > And I was referring to the Fourier transform of the whole pattern > as is done > in PDF work not on a peak by peak basis for correcting aberrations. I > brought up the point because when people talk about Q space > especially for > comparison purposes there's typcally a conversion to Q space. A > quick visual > display opearting on a point by point basis is adequate in most > cases but > for analysis the conversion should be done properly; a point missed > by many. > > cheers > alan > > -Original Message- > From: Luca Lutterotti [mailto:[EMAIL PROTECTED] > Sent: Thursday, 22 February 2007 6:59 AM > To: rietveld_l@ill.fr > Subject: Re: Powder Diffraction In Q-Space > > Alan, > > if it is trivial to plot in the square root I presume it is already > available in Topas as well GSAS and Fullprof just to mention few. And > if it is so trivial and already available as a button options why no > one is using it. Why every time I look at a paper with a Rietveld > refinement I can only appreciate the big peaks and why the residuals > are so little meaningful at end? Every one can choose what he prefers > obviously, but why all (without exceptions) are using not exactly the > best way to just do a plot? Should not be trivial? > > Conversion from 2theta - d -1/d is trivial in MY OPINION. This is > really a problem of the programmer not of the users (in a Rietveld > list). Constant step or variable step? Why it should influence the > conversion except for the speed of the conversion. I am using fast > fourier transform in my program for computing peak profiles directly > from distribution of crystallites and microstrain; I don't assume any > constant step, but seems like I can do it. > > And this step or FT has really nothing to do with the original post > of Klaus-Dieter who was focusing on just asking people if we can try > to get used to a common way to plot data different from the > conventional one. There are obviously favorable points and cons. Why > we cannot discuss it. Seems like for the Rietveld users is not so > trivial. > > Oh, and no one is setting up web sites just to show > opinions.may be these were already there... > > Cheers, > Luca > > On Feb 21, 2007, at 8:11 PM, AlanCoelho wrote: > >> >> Whether a program has a button to display data as a function of 1/d >> or a >> button to take the square toor of intensities is trivial to the >> point of not >> being talked about much less setting up web sites to get opinions. >> >> The only point worth talking about is how a conversion from 2Th to >> 1/d is >> done in regards to takeing the fourier transform of a powder pattern. >> >> alan >> >> >> -Original Message- >> From: Joerg Bergmann [mailto:[EMAIL PROTECTED] >> Sent: Thursday, 22 February 2007 4:30 AM >> To: rietveld_l@ill.fr >> Subject: Re: Powder Diffraction In Q-Space >> >> It's a principle of software design not to presume any kind of >> equidistant data. Unfortunately, file formats for non-equidistant >> data are seldom. So I could not implement any in BGMN, until now. >> But, in principle, there is no restriction. >> >> Regards >> >> Joerg Bergmann >> >> >> > > >
Re: Powder Diffraction In Q-Space
Alan, I do not want to take the decision out of the author, but the contrary. When programs just only plot in one scale, than the author is forced to use that one. Can I plot in square root or in Q space with Topas if I like to do that? cheers, Luca On Feb 21, 2007, at 10:28 PM, AlanCoelho wrote: I was not aware of Journals having rules stating that data must be plotted in square root scale and this is precisely the point. I certainly do not want an edict stating that authors must do so. It should be up to the author to choose whatever x-axis and y-axis scales that best shows up features. If an author is writing a paper on an instrumet correction, say for example cylindrical or PSD correction, then it is sensible to use 2Th. Thus please do not take these decisions away from the author. And I was referring to the Fourier transform of the whole pattern as is done in PDF work not on a peak by peak basis for correcting aberrations. I brought up the point because when people talk about Q space especially for comparison purposes there's typcally a conversion to Q space. A quick visual display opearting on a point by point basis is adequate in most cases but for analysis the conversion should be done properly; a point missed by many. cheers alan -Original Message- From: Luca Lutterotti [mailto:[EMAIL PROTECTED] Sent: Thursday, 22 February 2007 6:59 AM To: rietveld_l@ill.fr Subject: Re: Powder Diffraction In Q-Space Alan, if it is trivial to plot in the square root I presume it is already available in Topas as well GSAS and Fullprof just to mention few. And if it is so trivial and already available as a button options why no one is using it. Why every time I look at a paper with a Rietveld refinement I can only appreciate the big peaks and why the residuals are so little meaningful at end? Every one can choose what he prefers obviously, but why all (without exceptions) are using not exactly the best way to just do a plot? Should not be trivial? Conversion from 2theta - d -1/d is trivial in MY OPINION. This is really a problem of the programmer not of the users (in a Rietveld list). Constant step or variable step? Why it should influence the conversion except for the speed of the conversion. I am using fast fourier transform in my program for computing peak profiles directly from distribution of crystallites and microstrain; I don't assume any constant step, but seems like I can do it. And this step or FT has really nothing to do with the original post of Klaus-Dieter who was focusing on just asking people if we can try to get used to a common way to plot data different from the conventional one. There are obviously favorable points and cons. Why we cannot discuss it. Seems like for the Rietveld users is not so trivial. Oh, and no one is setting up web sites just to show opinions.may be these were already there... Cheers, Luca On Feb 21, 2007, at 8:11 PM, AlanCoelho wrote: Whether a program has a button to display data as a function of 1/d or a button to take the square toor of intensities is trivial to the point of not being talked about much less setting up web sites to get opinions. The only point worth talking about is how a conversion from 2Th to 1/d is done in regards to takeing the fourier transform of a powder pattern. alan -Original Message- From: Joerg Bergmann [mailto:[EMAIL PROTECTED] Sent: Thursday, 22 February 2007 4:30 AM To: rietveld_l@ill.fr Subject: Re: Powder Diffraction In Q-Space It's a principle of software design not to presume any kind of equidistant data. Unfortunately, file formats for non-equidistant data are seldom. So I could not implement any in BGMN, until now. But, in principle, there is no restriction. Regards Joerg Bergmann
RE: Powder Diffraction In Q-Space
I was not aware of Journals having rules stating that data must be plotted in square root scale and this is precisely the point. I certainly do not want an edict stating that authors must do so. It should be up to the author to choose whatever x-axis and y-axis scales that best shows up features. If an author is writing a paper on an instrumet correction, say for example cylindrical or PSD correction, then it is sensible to use 2Th. Thus please do not take these decisions away from the author. And I was referring to the Fourier transform of the whole pattern as is done in PDF work not on a peak by peak basis for correcting aberrations. I brought up the point because when people talk about Q space especially for comparison purposes there's typcally a conversion to Q space. A quick visual display opearting on a point by point basis is adequate in most cases but for analysis the conversion should be done properly; a point missed by many. cheers alan -Original Message- From: Luca Lutterotti [mailto:[EMAIL PROTECTED] Sent: Thursday, 22 February 2007 6:59 AM To: rietveld_l@ill.fr Subject: Re: Powder Diffraction In Q-Space Alan, if it is trivial to plot in the square root I presume it is already available in Topas as well GSAS and Fullprof just to mention few. And if it is so trivial and already available as a button options why no one is using it. Why every time I look at a paper with a Rietveld refinement I can only appreciate the big peaks and why the residuals are so little meaningful at end? Every one can choose what he prefers obviously, but why all (without exceptions) are using not exactly the best way to just do a plot? Should not be trivial? Conversion from 2theta - d -1/d is trivial in MY OPINION. This is really a problem of the programmer not of the users (in a Rietveld list). Constant step or variable step? Why it should influence the conversion except for the speed of the conversion. I am using fast fourier transform in my program for computing peak profiles directly from distribution of crystallites and microstrain; I don't assume any constant step, but seems like I can do it. And this step or FT has really nothing to do with the original post of Klaus-Dieter who was focusing on just asking people if we can try to get used to a common way to plot data different from the conventional one. There are obviously favorable points and cons. Why we cannot discuss it. Seems like for the Rietveld users is not so trivial. Oh, and no one is setting up web sites just to show opinions.may be these were already there... Cheers, Luca On Feb 21, 2007, at 8:11 PM, AlanCoelho wrote: > > Whether a program has a button to display data as a function of 1/d > or a > button to take the square toor of intensities is trivial to the > point of not > being talked about much less setting up web sites to get opinions. > > The only point worth talking about is how a conversion from 2Th to > 1/d is > done in regards to takeing the fourier transform of a powder pattern. > > alan > > > -Original Message- > From: Joerg Bergmann [mailto:[EMAIL PROTECTED] > Sent: Thursday, 22 February 2007 4:30 AM > To: rietveld_l@ill.fr > Subject: Re: Powder Diffraction In Q-Space > > It's a principle of software design not to presume any kind of > equidistant data. Unfortunately, file formats for non-equidistant > data are seldom. So I could not implement any in BGMN, until now. > But, in principle, there is no restriction. > > Regards > > Joerg Bergmann > > >
Re: Powder Diffraction In Q-Space
Bob, for the negative points in case of a background subtraction I do a little trick. If the resulting data is negative I do the square root of the absolute value and I multiply by -1 (I retain the sign). So it plots in sqrt but remains negative. Luca On Feb 21, 2007, at 10:14 PM, Von Dreele, Robert B. wrote: Actually, I looked at Luca's little "show" & was sufficiently interested that GSAS will now plot sqrt(I) style plots. There is one "problem" - the value of "I" can be negative particularly after a background subtraction. These must be suppressed to zero for this plot to work - thus there is a small risk of something getting hidden. Anyway - the new version will be out in a day or two (after I make sure there are no bugs introduced by this!) R.B. Von Dreele IPNS Division Argonne National Laboratory Argonne, IL 60439-4814 -Original Message- From: Luca Lutterotti [mailto:[EMAIL PROTECTED] Sent: Wednesday, February 21, 2007 2:59 PM To: rietveld_l@ill.fr Subject: Re: Powder Diffraction In Q-Space Alan, if it is trivial to plot in the square root I presume it is already available in Topas as well GSAS and Fullprof just to mention few. And if it is so trivial and already available as a button options why no one is using it. Why every time I look at a paper with a Rietveld refinement I can only appreciate the big peaks and why the residuals are so little meaningful at end? Every one can choose what he prefers obviously, but why all (without exceptions) are using not exactly the best way to just do a plot? Should not be trivial? Conversion from 2theta - d -1/d is trivial in MY OPINION. This is really a problem of the programmer not of the users (in a Rietveld list). Constant step or variable step? Why it should influence the conversion except for the speed of the conversion. I am using fast fourier transform in my program for computing peak profiles directly from distribution of crystallites and microstrain; I don't assume any constant step, but seems like I can do it. And this step or FT has really nothing to do with the original post of Klaus-Dieter who was focusing on just asking people if we can try to get used to a common way to plot data different from the conventional one. There are obviously favorable points and cons. Why we cannot discuss it. Seems like for the Rietveld users is not so trivial. Oh, and no one is setting up web sites just to show opinions.may be these were already there... Cheers, Luca On Feb 21, 2007, at 8:11 PM, AlanCoelho wrote: Whether a program has a button to display data as a function of 1/d or a button to take the square toor of intensities is trivial to the point of not being talked about much less setting up web sites to get opinions. The only point worth talking about is how a conversion from 2Th to 1/d is done in regards to takeing the fourier transform of a powder pattern. alan -Original Message- From: Joerg Bergmann [mailto:[EMAIL PROTECTED] Sent: Thursday, 22 February 2007 4:30 AM To: rietveld_l@ill.fr Subject: Re: Powder Diffraction In Q-Space It's a principle of software design not to presume any kind of equidistant data. Unfortunately, file formats for non-equidistant data are seldom. So I could not implement any in BGMN, until now. But, in principle, there is no restriction. Regards Joerg Bergmann
RE: Re: Powder Diffraction In Q-Space
Actually, I looked at Luca's little "show" & was sufficiently interested that GSAS will now plot sqrt(I) style plots. There is one "problem" - the value of "I" can be negative particularly after a background subtraction. These must be suppressed to zero for this plot to work - thus there is a small risk of something getting hidden. Anyway - the new version will be out in a day or two (after I make sure there are no bugs introduced by this!) R.B. Von Dreele IPNS Division Argonne National Laboratory Argonne, IL 60439-4814 -Original Message- From: Luca Lutterotti [mailto:[EMAIL PROTECTED] Sent: Wednesday, February 21, 2007 2:59 PM To: rietveld_l@ill.fr Subject: Re: Powder Diffraction In Q-Space Alan, if it is trivial to plot in the square root I presume it is already available in Topas as well GSAS and Fullprof just to mention few. And if it is so trivial and already available as a button options why no one is using it. Why every time I look at a paper with a Rietveld refinement I can only appreciate the big peaks and why the residuals are so little meaningful at end? Every one can choose what he prefers obviously, but why all (without exceptions) are using not exactly the best way to just do a plot? Should not be trivial? Conversion from 2theta - d -1/d is trivial in MY OPINION. This is really a problem of the programmer not of the users (in a Rietveld list). Constant step or variable step? Why it should influence the conversion except for the speed of the conversion. I am using fast fourier transform in my program for computing peak profiles directly from distribution of crystallites and microstrain; I don't assume any constant step, but seems like I can do it. And this step or FT has really nothing to do with the original post of Klaus-Dieter who was focusing on just asking people if we can try to get used to a common way to plot data different from the conventional one. There are obviously favorable points and cons. Why we cannot discuss it. Seems like for the Rietveld users is not so trivial. Oh, and no one is setting up web sites just to show opinions.may be these were already there... Cheers, Luca On Feb 21, 2007, at 8:11 PM, AlanCoelho wrote: > > Whether a program has a button to display data as a function of 1/d > or a > button to take the square toor of intensities is trivial to the > point of not > being talked about much less setting up web sites to get opinions. > > The only point worth talking about is how a conversion from 2Th to > 1/d is > done in regards to takeing the fourier transform of a powder pattern. > > alan > > > -Original Message- > From: Joerg Bergmann [mailto:[EMAIL PROTECTED] > Sent: Thursday, 22 February 2007 4:30 AM > To: rietveld_l@ill.fr > Subject: Re: Powder Diffraction In Q-Space > > It's a principle of software design not to presume any kind of > equidistant data. Unfortunately, file formats for non-equidistant data > are seldom. So I could not implement any in BGMN, until now. But, in > principle, there is no restriction. > > Regards > > Joerg Bergmann > > >
Re: Powder Diffraction In Q-Space
Alan, if it is trivial to plot in the square root I presume it is already available in Topas as well GSAS and Fullprof just to mention few. And if it is so trivial and already available as a button options why no one is using it. Why every time I look at a paper with a Rietveld refinement I can only appreciate the big peaks and why the residuals are so little meaningful at end? Every one can choose what he prefers obviously, but why all (without exceptions) are using not exactly the best way to just do a plot? Should not be trivial? Conversion from 2theta - d -1/d is trivial in MY OPINION. This is really a problem of the programmer not of the users (in a Rietveld list). Constant step or variable step? Why it should influence the conversion except for the speed of the conversion. I am using fast fourier transform in my program for computing peak profiles directly from distribution of crystallites and microstrain; I don't assume any constant step, but seems like I can do it. And this step or FT has really nothing to do with the original post of Klaus-Dieter who was focusing on just asking people if we can try to get used to a common way to plot data different from the conventional one. There are obviously favorable points and cons. Why we cannot discuss it. Seems like for the Rietveld users is not so trivial. Oh, and no one is setting up web sites just to show opinions.may be these were already there... Cheers, Luca On Feb 21, 2007, at 8:11 PM, AlanCoelho wrote: Whether a program has a button to display data as a function of 1/d or a button to take the square toor of intensities is trivial to the point of not being talked about much less setting up web sites to get opinions. The only point worth talking about is how a conversion from 2Th to 1/d is done in regards to takeing the fourier transform of a powder pattern. alan -Original Message- From: Joerg Bergmann [mailto:[EMAIL PROTECTED] Sent: Thursday, 22 February 2007 4:30 AM To: rietveld_l@ill.fr Subject: Re: Powder Diffraction In Q-Space It's a principle of software design not to presume any kind of equidistant data. Unfortunately, file formats for non-equidistant data are seldom. So I could not implement any in BGMN, until now. But, in principle, there is no restriction. Regards Joerg Bergmann
RE: Powder Diffraction In Q-Space
Hi, As far as I am concerned, synchrotron x-rays and neutron data could be represented in any x-axis unit without any problem other than the users preference or a convention, but what about the kalpha 1,2 doublet for filtered lab x-rays. I'd rather continue using 2theta as units for x-axis in my papers using lab x-ray patterns just to keep the "true physical meaning" of all the peaks in my pattern. At least until someone comes up with the program that converts a 2-wavelength pattern collected in 2-theta into a correct pattern in Q, 1/d.. I guess this should be like "time focusing" for TOF patterns isn't it?, except that in lab x-rays both "channels" are merged in only one signal. Maybe the day that detectors with energy discrimination becomes cheap and accurate enough to only read the kalpha1 component of the lab x-rays this discussion should be brougth up again. To me this specifical issue of representing the diffraction patterns is just like calling the monoclinic angle beta or gamma, there are other issues like the one Bob brought up, that are not just the way programmers wrote the programs. Best regards. Leo Dr. Leopoldo Suescun Postodoctoral Appointee Materials Science Division - Bldg 223 - Rm D217 Argonne National Laboratory 9700 S. Cass Ave., Argonne, IL 60439 Phone: 1 (630) 252 9760 Fax: 1 (630) 252 URL: http://www.msd.anl.gov/groups/nxrs/personnel/suescun/index.html -Original Message- From: Luca Lutterotti [mailto:[EMAIL PROTECTED] Sent: Wednesday, February 21, 2007 11:30 AM To: rietveld_l@ill.fr Subject: Re: Powder Diffraction In Q-Space As we talk about plotting in Q-space (just for information in Maud is available from few months thanks to Klaus-Dieter advocating for it), I would advocate another "plot option" that I would rather see as a default way of plotting. Looking at the other axis (the intensity) I am asking why we don't introduce the practice to plot in a more useful scale as the root square of the intensity (instead of the usual linear scale). This has several benefits: - the plot will be at iso-error (I recall for who may have forgotten the noise is proportional to the root square of the intensity), so in the residuals you may better evaluate which are the peaks or part well fitted or poor fitted. Otherwise with the linear scale you just see only the bad residuals of the more intense peaks and you may think these are the peaks poorly fitted. Instead most of the time in the true statistical meaning they may be well fitted compare to other. In the square root intensity mode you can evaluate them more unbiased - you see also the small peaks and it is not necessary to enlarge the intensity scale to check them In this regard some people are using the log10 scale plot (normally used for reflectivity measurements). It may enhance more the small peaks but I don't favor it as again you do not compare the fitting of different peak on an equal statistical base. As an image is better than thousand words, as they say, I put together one web page with the comparison of linear/sqrt/log10 scale, Q and 2theta so everyone may take its own conclusion. http://www.ing.unitn.it/~maud/plotoptions/ I would encourage the list to propose a standard way (or advised way) to plot, as it would be not too difficult for the different program to provide a standard way to present the results for the benefit of comparisons. Best regards, Luca Lutterotti BEGIN:VCARD VERSION:2.1 N:Suescun;Leopoldo FN:Leopoldo Suescun ([EMAIL PROTECTED]) ORG:Argonne National Laboratory - Materials Science Division TITLE:Postdoctoral Appointee TEL;WORK;VOICE:+1 (630) 252-9760 TEL;HOME;VOICE:+1 (630) 910-1562 TEL;WORK;FAX:+1 (630) 252- ADR;WORK:;;9700 S. Cass Ave.;Argonne;Illinois;60439;USA LABEL;WORK;ENCODING=QUOTED-PRINTABLE:9700 S. Cass Ave.=0D=0AArgonne, Illinois 60439=0D=0AUSA URL;WORK:http://www.msd.anl.gov/groups/nxrs/people/suescun.html EMAIL;PREF;INTERNET:[EMAIL PROTECTED] REV:20050630T182807Z END:VCARD
RE: Powder Diffraction In Q-Space
Whether a program has a button to display data as a function of 1/d or a button to take the square toor of intensities is trivial to the point of not being talked about much less setting up web sites to get opinions. The only point worth talking about is how a conversion from 2Th to 1/d is done in regards to takeing the fourier transform of a powder pattern. alan -Original Message- From: Joerg Bergmann [mailto:[EMAIL PROTECTED] Sent: Thursday, 22 February 2007 4:30 AM To: rietveld_l@ill.fr Subject: Re: Powder Diffraction In Q-Space It's a principle of software design not to presume any kind of equidistant data. Unfortunately, file formats for non-equidistant data are seldom. So I could not implement any in BGMN, until now. But, in principle, there is no restriction. Regards Joerg Bergmann
Re: Powder Diffraction In Q-Space
It's a principle of software design not to presume any kind of equidistant data. Unfortunately, file formats for non-equidistant data are seldom. So I could not implement any in BGMN, until now. But, in principle, there is no restriction. Regards Joerg Bergmann AlanCoelho wrote: Representing data in Q space is fine for viewing etc... but the conversion from 2Th to Q needs a little thought. If unequal Q steps is not a problem then a straight conversion is ok. However if someone is going to use that Q data for further analysis then it is important to use the original data or at least know where it came from for reasons I gave in a previous reply to the mailing list which I have included again below. In other words if a diffractomer or some other instrument collect data in Q space at equal steps and this data is compared to data collected at 2Th then the match wont be 100% depending on how the conversion is done. Most importantly is that data from one or the other should not be thrown away. Thus to discuss the question of archiving data in Q space means understanding the data conversion principles. cheers alan
Re: Powder Diffraction In Q-Space
As we talk about plotting in Q-space (just for information in Maud is available from few months thanks to Klaus-Dieter advocating for it), I would advocate another "plot option" that I would rather see as a default way of plotting. Looking at the other axis (the intensity) I am asking why we don't introduce the practice to plot in a more useful scale as the root square of the intensity (instead of the usual linear scale). This has several benefits: - the plot will be at iso-error (I recall for who may have forgotten the noise is proportional to the root square of the intensity), so in the residuals you may better evaluate which are the peaks or part well fitted or poor fitted. Otherwise with the linear scale you just see only the bad residuals of the more intense peaks and you may think these are the peaks poorly fitted. Instead most of the time in the true statistical meaning they may be well fitted compare to other. In the square root intensity mode you can evaluate them more unbiased - you see also the small peaks and it is not necessary to enlarge the intensity scale to check them In this regard some people are using the log10 scale plot (normally used for reflectivity measurements). It may enhance more the small peaks but I don't favor it as again you do not compare the fitting of different peak on an equal statistical base. As an image is better than thousand words, as they say, I put together one web page with the comparison of linear/sqrt/log10 scale, Q and 2theta so everyone may take its own conclusion. http://www.ing.unitn.it/~maud/plotoptions/ I would encourage the list to propose a standard way (or advised way) to plot, as it would be not too difficult for the different program to provide a standard way to present the results for the benefit of comparisons. Best regards, Luca Lutterotti
RE: Powder Diffraction In Q-Space
Simon Billinge wrote: >We can resolve the problem by setting 2pi=1! What school did you go to; thanks for the info. This issue of plotting data is one of those's non-issues drummed up by groups familar with one format but not in another; I would suggest that everyone should be familar with both types of displays. If we had the case where only 1/d is plotted eclusively then a whole lot of useful information would be lost. For example, if I look at a fit of a 2Th plot then I can immediately ascertain the following by looking at the misfits: - Are the low angle peaks fitting properly; if not then something is wrong with either the axial or equitorial divergence corrections. - If the peaks are not fitting at 90 degrees then I know that sample penetration is not being accounted for proeprly. - If variable divergence slits are being used then I know the angle where spill over on a post monochromator takes occurs. You cannot make these deduction from 1/d plots. Bob's "Law of Unintended Consequences" cannot be ignored. Are we to teach crystalographers to ignore data collection - big mistake. Simon also mentioned Fourier transform; FFTs' work in equal data steps so be aware of data conversion. My guess is that most conversion programs do the wrong thing. alan -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Simon Billinge Sent: Thursday, 22 February 2007 2:52 AM To: rietveld_l@ill.fr Subject: Re: Powder Diffraction In Q-Space roughly speaking, historically, Q=2pi/d is used by physicists and S=1/d used by crystallographers and these communities define their reciprocal lattices and Fourier transforms accordingly. With the 2pi in there, Q is the momentum transfer. Without it in there the Laue Equations are much cleaner. Physicists are good at working in reduced units, like setting c=1. We can resolve the problem by setting 2pi=1! S On 2/21/07, Ray Osborn <[EMAIL PROTECTED]> wrote: > On 2007/02/21 9:06, "Jonathan Wright" <[EMAIL PROTECTED]> wrote: > > > 2pi/d just needs a better name than Q? > > I guess, to some extent, this debate depends on whether you are only > interested in talking to other powder diffraction specialists. As a > non-specialist, I would suggest that Q is a more widely used variable - > certainly in the inelastic scattering community, but also I believe in the > liquids and amorphous community, who might be interested in studying > crystallization processes, for example. > > If I want to check the elastic scattering contained within my inelastic > spectrum, it is certainly an inconvenience having to convert from two-theta, > even assuming I know the wavelength. I certainly hope you don't settle on > 10^4/d^2. > > Regards, > Ray > -- > Dr Ray OsbornTel: +1 (630) 252-9011 > Materials Science Division Fax: +1 (630) 252- > Argonne National Laboratory E-mail: [EMAIL PROTECTED] > Argonne, IL 60439-4845 > > > > -- Prof. Simon Billinge Department of Physics and Astronomy 4268 Biomed. Phys. Sciences Building Michigan State University East Lansing, MI 48824 tel: +1-517-355-9200 x2202 fax: +1-517-353-4500 email: [EMAIL PROTECTED] home: http://nirt.pa.msu.edu/
Re: Powder Diffraction In Q-Space
roughly speaking, historically, Q=2pi/d is used by physicists and S=1/d used by crystallographers and these communities define their reciprocal lattices and Fourier transforms accordingly. With the 2pi in there, Q is the momentum transfer. Without it in there the Laue Equations are much cleaner. Physicists are good at working in reduced units, like setting c=1. We can resolve the problem by setting 2pi=1! S On 2/21/07, Ray Osborn <[EMAIL PROTECTED]> wrote: On 2007/02/21 9:06, "Jonathan Wright" <[EMAIL PROTECTED]> wrote: > 2pi/d just needs a better name than Q? I guess, to some extent, this debate depends on whether you are only interested in talking to other powder diffraction specialists. As a non-specialist, I would suggest that Q is a more widely used variable - certainly in the inelastic scattering community, but also I believe in the liquids and amorphous community, who might be interested in studying crystallization processes, for example. If I want to check the elastic scattering contained within my inelastic spectrum, it is certainly an inconvenience having to convert from two-theta, even assuming I know the wavelength. I certainly hope you don't settle on 10^4/d^2. Regards, Ray -- Dr Ray OsbornTel: +1 (630) 252-9011 Materials Science Division Fax: +1 (630) 252- Argonne National Laboratory E-mail: [EMAIL PROTECTED] Argonne, IL 60439-4845 -- Prof. Simon Billinge Department of Physics and Astronomy 4268 Biomed. Phys. Sciences Building Michigan State University East Lansing, MI 48824 tel: +1-517-355-9200 x2202 fax: +1-517-353-4500 email: [EMAIL PROTECTED] home: http://nirt.pa.msu.edu/
Re: Powder Diffraction In Q-Space
I have always preferred to see data plotted in units of Q (though Q^2 or Q^3 makes sense from a perspective of spreading peaks.) Two-theta made sense only when everyone used CuK alpha (which was never true). Personally, I would be glad to never see another plot of intensity vs. d-space. On Feb 21, 2007, at 10:29 AM, Von Dreele, Robert B. wrote: OK, I did play about & display some Q-space (Q=2pi/d) plots in GSAS. It will be an option in the next release. It has been an option in LIVEPLOT (EXPGUI) for many years. (Sorry, could not resist.) LIVEPLOT output can be exported WYSIWYG to XMGRACE or as a .csv file. Brian Brian H. Toby, Ph.D.office: 630-252-5488 Materials Characterization Group Leader, Advanced Photon Source 9700 S. Cass Ave, Bldg. 433/D003 work cell: 630-327-8426 Argonne National Laboratory secretary (Marija): 630-252-5453 Argonne, IL 60439-4856 e-mail: brian dot toby at anl dot gov
RE: RE: Powder Diffraction In Q-Space
OK, I did play about & display some Q-space (Q=2pi/d) plots in GSAS. It will be an option in the next release. Pretty similar to conventional 2-theta plots - just a slight "squishing" of the scale at the upper end. Might not be really desirable for complex patterns. Some TOF data where data was collected to quite small TOF will need to have different limits picked by the user to see anything (plot dominated by large Q range). However, please don't be tempted to collect constant Q-step data; the programs/peak shape functions really do expect 2-theta/TOF scans. Alan Coelho's remark does raise an issue about such data & how it was really collected. Q-Step scans would probably just be an "oddly stepped" conventional step scan but slew scans split into constant Q steps would be a different matter. Beware of the Law of Unintended Consequences. Bob R.B. Von Dreele IPNS Division Argonne National Laboratory Argonne, IL 60439-4814 -Original Message- From: Alan Hewat [mailto:[EMAIL PROTECTED] Sent: Wednesday, February 21, 2007 9:45 AM To: rietveld_l@ill.fr Subject: RE: Powder Diffraction In Q-Space >Depends on the lattice? Cubic patterns look great in old "Q": >eg: "Tables of Q as a Function of 2theta" Acta Cryst 12, 421, (1959) >... where Q was 10^4/d^2. Yes, it does "en principe" depend on the lattice of course :-) but 10^4/d^2 still provides a better "constant peak density scale" than any other simple function I can think of. Certainly a lot better than a linear d-spacing scale. And yes, this is not a new idea. Alan. _ Dr Alan Hewat, ILL Grenoble, FRANCE<[EMAIL PROTECTED]>fax+33.476.20.76.48 +33.476.20.72.13 (.26 Mme Guillermet) +http://www.ill.fr/dif/people/hewat/ _
Re: Powder Diffraction In Q-Space
On 2007/02/21 9:06, "Jonathan Wright" <[EMAIL PROTECTED]> wrote: > 2pi/d just needs a better name than Q? I guess, to some extent, this debate depends on whether you are only interested in talking to other powder diffraction specialists. As a non-specialist, I would suggest that Q is a more widely used variable - certainly in the inelastic scattering community, but also I believe in the liquids and amorphous community, who might be interested in studying crystallization processes, for example. If I want to check the elastic scattering contained within my inelastic spectrum, it is certainly an inconvenience having to convert from two-theta, even assuming I know the wavelength. I certainly hope you don't settle on 10^4/d^2. Regards, Ray -- Dr Ray OsbornTel: +1 (630) 252-9011 Materials Science Division Fax: +1 (630) 252- Argonne National Laboratory E-mail: [EMAIL PROTECTED] Argonne, IL 60439-4845
RE: Powder Diffraction In Q-Space
Representing data in Q space is fine for viewing etc... but the conversion from 2Th to Q needs a little thought. If unequal Q steps is not a problem then a straight conversion is ok. However if someone is going to use that Q data for further analysis then it is important to use the original data or at least know where it came from for reasons I gave in a previous reply to the mailing list which I have included again below. In other words if a diffractomer or some other instrument collect data in Q space at equal steps and this data is compared to data collected at 2Th then the match wont be 100% depending on how the conversion is done. Most importantly is that data from one or the other should not be thrown away. Thus to discuss the question of archiving data in Q space means understanding the data conversion principles. cheers alan Von Dreele write: >However, the profile shape functions are not simple > functions of Q but are simple (Gaussian & > Lorentzian) functions of 2-theta. Case closed. == Previous reply on Q space conversion === Converting from one x-axis to another; you may want to consider the following Melinda when you do your conversion. For a particular data point in Q space the area of the space sampled is: Area(Q) = I(Q) del_Q For 2Th the area is: Area(2 Th) = I(2 Th) del_2Th where del_Q and del_2Th corresponds to the size of the receiving slit in the equitorial plane for Q and 2Th spaces respectively. We assume constant counting time at each data point. First transform point for point with equal areas at any particlar data point, or Area(Q) = Area(2 Th) or, I(2 Th) = I(Q) del_Q / del_2Th If both data sets were collected with fixed receiving slits then del_Q/del_2Th is a constant and can be ignored by setting it to 1. I(2 Th) at this stage would be at unequal x-axis steps as you pointed out. To convert to equal x-axis steps you need to sample I(2 Th) at equal 2Th steps, lets call the chosen step size 2Th_step_size. If you want the Sum of I(2 Th) to equal the Sum of I(Q) then you need to sample I(2 Th) with a receiving slit width that has a size equal to 2Th_step_step. Only when you do this do you use all of the observed data in the original I(Q) and use it only once. When it comes time to fitting the data you would then need to account for the chosen receiving slit, this can be done by a convolution. I dont know if GSAS does this but if it cant then I suggest you sample I(2 Th) at an infinitely small receiving slit and ignore any scaling constants. In this approach some of the original data may not be sampled. cheers alan
RE: Powder Diffraction In Q-Space
>Depends on the lattice? Cubic patterns look great in old "Q": >eg: "Tables of Q as a Function of 2theta" Acta Cryst 12, 421, (1959) >... where Q was 10^4/d^2. Yes, it does "en principe" depend on the lattice of course :-) but 10^4/d^2 still provides a better "constant peak density scale" than any other simple function I can think of. Certainly a lot better than a linear d-spacing scale. And yes, this is not a new idea. Alan. _ Dr Alan Hewat, ILL Grenoble, FRANCE<[EMAIL PROTECTED]>fax+33.476.20.76.48 +33.476.20.72.13 (.26 Mme Guillermet) http://www.ill.fr/dif/people/hewat/ _
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 swearing. it would indeed be useful for everyone to report on the same scale for comparison. I would personally prefer an (approx) constant density of peaks scale Depends on the lattice? Cubic patterns look great in old "Q": eg: Announcements 1959 "Tables of Q as a Function of 2theta (1959)" Acta Cryst 12, 421, (1959) ... where Q was 10^4/d^2. 2pi/d just needs a better name than Q? Best, Jon
RE: Powder Diffraction In Q-Space
>However, the profile shape functions are not simple functions of Q but are >simple (Gaussian & Lorentzian) functions of 2-theta. Case closed. OK, refinement is anyway done with different scales corresponding to the actual data collection - constant steps of 2theta or TOF. But Klaus-Dieter was only proposing Q-scale plots for publishing results, and it would indeed be useful for everyone to report on the same scale for comparison. I would personally prefer an (approx) constant density of peaks scale, but I doubt that we will get everyone to change :-) Alan. _ Dr Alan Hewat, ILL Grenoble, FRANCE<[EMAIL PROTECTED]>fax+33.476.20.76.48 +33.476.20.72.13 (.26 Mme Guillermet) http://www.ill.fr/dif/people/hewat/ _
RE: Powder Diffraction In Q-Space
One should handle each part of the pattern in it's natural scale: -Pattern representation (purely, without instrumental broadening) in Q -Geometric part of the instrumental function in an angular scale (e.g. radian) -Wavelength part of the instrumental function in the nm or k-scale (1/nm) for simple handling as done in BGMN plus related programs. Am Mittwoch, den 21.02.2007, 07:38 -0600 schrieb Von Dreele, Robert B.: > However, the profile shape functions are not simple functions of Q but are > simple (Gaussian & Lorentzian) functions of 2-theta. Case closed. > > > > From: Klaus-Dieter Liss [mailto:[EMAIL PROTECTED] > Sent: Wed 2/21/2007 4:03 AM > To: rietveld_l@ill.fr > Subject: Powder Diffraction In Q-Space > > > > Dear Powder-Diffraction User, > > with the advancement of modern research infrastructure such as > instruments, computing, complementary techniques, I like to raise again > the necessity to present powder diffraction data in Q-space rather than > in instrumental units. Other communities are already well ahead > (single-xtal, SANS, SAXS, reflectometry etc) and to my view, only the > powder diffractionist stick to their out-dated units (2-theta, TOF, > d-spacing...). > > there is a poll I started a while ago under > http://elpopo.ing.unitn.it:8064/maudFor/viewtopic.php?t=205 > which, so far, is not very representative and I would encourage you to > give your opinions. > > I suppose, all of us have learned the basics of crystallography > somewhere during the career and the laws of Bragg diffraction. So, all > of us are familiar with reciprocal space, where, for example, a > reciprocal lattice can be constructed in order to represent the crystal > symmetry in the natural space of diffraction. The Ewald construction and > the Laue equation are examples which make most use of this. > > Further, reciprocal space is LINEAR, i.e. A second order reflection has > double the distance from the origin than the fundamental reflection and > a 110 reflection sqrt(2) times the distance than a 100 of a cubic > system, etc. > > This alone would be a very good reason to plot all diffraction patterns > as a function of reciprocal space coordinates Q. For Powder Diffraction, > this means, patterns should NOT be plotted as a function of 2-theta, d, > tof etc but Q which is the only natural unit! > > The relations are: > > Q = 4 * Pi * sin(theta) / lambda; > > or > > Q = 2 * Pi / d; > > The benefits of plotting and publishing data in this representation are > obvious: > * reciprocal space is the NATURAL space diffraction takes place; > * reciprocal space is LINEAR and symmetries can be identified by eye; > * the representation directly reflects crystal SYMMETRY; > * the representation is INDEPENDENT of the instrument, type of radiation > (electrons, neutrons, X-rays, light, atoms...) > * the representation is INDEPENDENT of the wavelength used; > * presentations and publications are directly COMPARABLE; > * reciprocal space is WIDELY USED outside the powder diffraction > community, such as single crystal diffraction SA(NX)S or reflectometry; > > Therefore I propose, that publishing data in other units should be avoided. > _ > > Klaus-Dieter Liss > > -- > > Dr. Klaus-Dieter Liss > Research Scientist, Bragg Institute > Australian Nuclear Science and Technology Organisation > PMB 1, Menai NSW 2234, Australia > > T: +61-2-9717+9479 > F: +61-2-9717+3606 > M: 0419 166 978 > E: [EMAIL PROTECTED] > http://www.ansto.gov.au/ansto/bragg/staff/s_liss.html > see also: http://liss.freeshell.org <http://liss.freeshell.org/> > > > > -- Joerg Bergmann <[EMAIL PROTECTED]>
RE: Powder Diffraction In Q-Space
However, the profile shape functions are not simple functions of Q but are simple (Gaussian & Lorentzian) functions of 2-theta. Case closed. From: Klaus-Dieter Liss [mailto:[EMAIL PROTECTED] Sent: Wed 2/21/2007 4:03 AM To: rietveld_l@ill.fr Subject: Powder Diffraction In Q-Space Dear Powder-Diffraction User, with the advancement of modern research infrastructure such as instruments, computing, complementary techniques, I like to raise again the necessity to present powder diffraction data in Q-space rather than in instrumental units. Other communities are already well ahead (single-xtal, SANS, SAXS, reflectometry etc) and to my view, only the powder diffractionist stick to their out-dated units (2-theta, TOF, d-spacing...). there is a poll I started a while ago under http://elpopo.ing.unitn.it:8064/maudFor/viewtopic.php?t=205 which, so far, is not very representative and I would encourage you to give your opinions. I suppose, all of us have learned the basics of crystallography somewhere during the career and the laws of Bragg diffraction. So, all of us are familiar with reciprocal space, where, for example, a reciprocal lattice can be constructed in order to represent the crystal symmetry in the natural space of diffraction. The Ewald construction and the Laue equation are examples which make most use of this. Further, reciprocal space is LINEAR, i.e. A second order reflection has double the distance from the origin than the fundamental reflection and a 110 reflection sqrt(2) times the distance than a 100 of a cubic system, etc. This alone would be a very good reason to plot all diffraction patterns as a function of reciprocal space coordinates Q. For Powder Diffraction, this means, patterns should NOT be plotted as a function of 2-theta, d, tof etc but Q which is the only natural unit! The relations are: Q = 4 * Pi * sin(theta) / lambda; or Q = 2 * Pi / d; The benefits of plotting and publishing data in this representation are obvious: * reciprocal space is the NATURAL space diffraction takes place; * reciprocal space is LINEAR and symmetries can be identified by eye; * the representation directly reflects crystal SYMMETRY; * the representation is INDEPENDENT of the instrument, type of radiation (electrons, neutrons, X-rays, light, atoms...) * the representation is INDEPENDENT of the wavelength used; * presentations and publications are directly COMPARABLE; * reciprocal space is WIDELY USED outside the powder diffraction community, such as single crystal diffraction SA(NX)S or reflectometry; Therefore I propose, that publishing data in other units should be avoided. _ Klaus-Dieter Liss -- Dr. Klaus-Dieter Liss Research Scientist, Bragg Institute Australian Nuclear Science and Technology Organisation PMB 1, Menai NSW 2234, Australia T: +61-2-9717+9479 F: +61-2-9717+3606 M: 0419 166 978 E: [EMAIL PROTECTED] http://www.ansto.gov.au/ansto/bragg/staff/s_liss.html see also: http://liss.freeshell.org <http://liss.freeshell.org/>
Re: Powder Diffraction In Q-Space
Dear Klaus-Dieter Liss, just a comment: From the beginning, I have used Q-scale internally in my programs. Including e.g. BGMN. Plus, for complete compatibility to other sciences, I use 1/nm instead of 1/Angstroem as unit of Q. So, for example the BGMN *.par files contain data in this scale/unit. Regards Joerg Bergmann Am Mittwoch, den 21.02.2007, 21:03 +1100 schrieb Klaus-Dieter Liss: > Dear Powder-Diffraction User, > > with the advancement of modern research infrastructure such as > instruments, computing, complementary techniques, I like to raise again > the necessity to present powder diffraction data in Q-space rather than > in instrumental units. Other communities are already well ahead > (single-xtal, SANS, SAXS, reflectometry etc) and to my view, only the > powder diffractionist stick to their out-dated units (2-theta, TOF, > d-spacing...). > > there is a poll I started a while ago under > http://elpopo.ing.unitn.it:8064/maudFor/viewtopic.php?t=205 > which, so far, is not very representative and I would encourage you to > give your opinions. > > I suppose, all of us have learned the basics of crystallography > somewhere during the career and the laws of Bragg diffraction. So, all > of us are familiar with reciprocal space, where, for example, a > reciprocal lattice can be constructed in order to represent the crystal > symmetry in the natural space of diffraction. The Ewald construction and > the Laue equation are examples which make most use of this. > > Further, reciprocal space is LINEAR, i.e. A second order reflection has > double the distance from the origin than the fundamental reflection and > a 110 reflection sqrt(2) times the distance than a 100 of a cubic > system, etc. > > This alone would be a very good reason to plot all diffraction patterns > as a function of reciprocal space coordinates Q. For Powder Diffraction, > this means, patterns should NOT be plotted as a function of 2-theta, d, > tof etc but Q which is the only natural unit! > > The relations are: > > Q = 4 * Pi * sin(theta) / lambda; > > or > > Q = 2 * Pi / d; > > The benefits of plotting and publishing data in this representation are > obvious: > * reciprocal space is the NATURAL space diffraction takes place; > * reciprocal space is LINEAR and symmetries can be identified by eye; > * the representation directly reflects crystal SYMMETRY; > * the representation is INDEPENDENT of the instrument, type of radiation > (electrons, neutrons, X-rays, light, atoms...) > * the representation is INDEPENDENT of the wavelength used; > * presentations and publications are directly COMPARABLE; > * reciprocal space is WIDELY USED outside the powder diffraction > community, such as single crystal diffraction SA(NX)S or reflectometry; > > Therefore I propose, that publishing data in other units should be avoided. > _ > > Klaus-Dieter Liss >
Re: Powder Diffraction In Q-Space
Klaus-Dieter, I agree that anything scaling with sin(theta) / lambda is to be preferred over 2theta, TOF or d spacing. This is especially handy when comparing data from different sources, which we often do with lab X-ray, synchrotron and neutron data. Which factor k in the representation k * sin(theta) / lambda is ideal, however, is a matter of taste. Personally, I prefer k=2, i. e. to represent powder diffraction data as intensity vs. 1/d (= Q/2*pi). Physicist, who usually prefer Q, invariably tell me, that Q is the only natural choice because the momentum tranfer is Q*h_bar (= Q * h/2*pi). Well, usually I respond that h/d also gives the momentum tranfer, it is even simpler, since you use h instead of h_bar, and therefore it does not matter. Best regards -Holger *** Holger Kohlmann Fachrichtung 8.1 - Chemie Institut für Anorganische und Analytische Chemie und Radiochemie Postfach 151150 66041 Saarbruecken Germany [EMAIL PROTECTED] tel.: [+49] (681) 302 3378 fax [+49] (681) 302 4233 *** Zitat von Klaus-Dieter Liss <[EMAIL PROTECTED]>: Dear Powder-Diffraction User, with the advancement of modern research infrastructure such as instruments, computing, complementary techniques, I like to raise again the necessity to present powder diffraction data in Q-space rather than in instrumental units. Other communities are already well ahead (single-xtal, SANS, SAXS, reflectometry etc) and to my view, only the powder diffractionist stick to their out-dated units (2-theta, TOF, d-spacing...). there is a poll I started a while ago under http://elpopo.ing.unitn.it:8064/maudFor/viewtopic.php?t=205 which, so far, is not very representative and I would encourage you to give your opinions. I suppose, all of us have learned the basics of crystallography somewhere during the career and the laws of Bragg diffraction. So, all of us are familiar with reciprocal space, where, for example, a reciprocal lattice can be constructed in order to represent the crystal symmetry in the natural space of diffraction. The Ewald construction and the Laue equation are examples which make most use of this. Further, reciprocal space is LINEAR, i.e. A second order reflection has double the distance from the origin than the fundamental reflection and a 110 reflection sqrt(2) times the distance than a 100 of a cubic system, etc. This alone would be a very good reason to plot all diffraction patterns as a function of reciprocal space coordinates Q. For Powder Diffraction, this means, patterns should NOT be plotted as a function of 2-theta, d, tof etc but Q which is the only natural unit! The relations are: Q = 4 * Pi * sin(theta) / lambda; or Q = 2 * Pi / d; The benefits of plotting and publishing data in this representation are obvious: * reciprocal space is the NATURAL space diffraction takes place; * reciprocal space is LINEAR and symmetries can be identified by eye; * the representation directly reflects crystal SYMMETRY; * the representation is INDEPENDENT of the instrument, type of radiation (electrons, neutrons, X-rays, light, atoms...) * the representation is INDEPENDENT of the wavelength used; * presentations and publications are directly COMPARABLE; * reciprocal space is WIDELY USED outside the powder diffraction community, such as single crystal diffraction SA(NX)S or reflectometry; Therefore I propose, that publishing data in other units should be avoided. _ Klaus-Dieter Liss -- Dr. Klaus-Dieter Liss Research Scientist, Bragg Institute Australian Nuclear Science and Technology Organisation PMB 1, Menai NSW 2234, Australia T: +61-2-9717+9479 F: +61-2-9717+3606 M: 0419 166 978 E: [EMAIL PROTECTED] http://www.ansto.gov.au/ansto/bragg/staff/s_liss.html see also: http://liss.freeshell.org
Powder Diffraction In Q-Space
Dear Powder-Diffraction User, with the advancement of modern research infrastructure such as instruments, computing, complementary techniques, I like to raise again the necessity to present powder diffraction data in Q-space rather than in instrumental units. Other communities are already well ahead (single-xtal, SANS, SAXS, reflectometry etc) and to my view, only the powder diffractionist stick to their out-dated units (2-theta, TOF, d-spacing...). there is a poll I started a while ago under http://elpopo.ing.unitn.it:8064/maudFor/viewtopic.php?t=205 which, so far, is not very representative and I would encourage you to give your opinions. I suppose, all of us have learned the basics of crystallography somewhere during the career and the laws of Bragg diffraction. So, all of us are familiar with reciprocal space, where, for example, a reciprocal lattice can be constructed in order to represent the crystal symmetry in the natural space of diffraction. The Ewald construction and the Laue equation are examples which make most use of this. Further, reciprocal space is LINEAR, i.e. A second order reflection has double the distance from the origin than the fundamental reflection and a 110 reflection sqrt(2) times the distance than a 100 of a cubic system, etc. This alone would be a very good reason to plot all diffraction patterns as a function of reciprocal space coordinates Q. For Powder Diffraction, this means, patterns should NOT be plotted as a function of 2-theta, d, tof etc but Q which is the only natural unit! The relations are: Q = 4 * Pi * sin(theta) / lambda; or Q = 2 * Pi / d; The benefits of plotting and publishing data in this representation are obvious: * reciprocal space is the NATURAL space diffraction takes place; * reciprocal space is LINEAR and symmetries can be identified by eye; * the representation directly reflects crystal SYMMETRY; * the representation is INDEPENDENT of the instrument, type of radiation (electrons, neutrons, X-rays, light, atoms...) * the representation is INDEPENDENT of the wavelength used; * presentations and publications are directly COMPARABLE; * reciprocal space is WIDELY USED outside the powder diffraction community, such as single crystal diffraction SA(NX)S or reflectometry; Therefore I propose, that publishing data in other units should be avoided. _ Klaus-Dieter Liss -- Dr. Klaus-Dieter Liss Research Scientist, Bragg Institute Australian Nuclear Science and Technology Organisation PMB 1, Menai NSW 2234, Australia T: +61-2-9717+9479 F: +61-2-9717+3606 M: 0419 166 978 E: [EMAIL PROTECTED] http://www.ansto.gov.au/ansto/bragg/staff/s_liss.html see also: http://liss.freeshell.org
