Re: Calculating the PDFs from a crystal structure with PDFgui. The meaning of Qmax

[Pavol Juhas]

On Tue, May 28, 2013 at 01:35:22AM -0700, Ioana Sovago wrote:
> I was wondering why there is a Qmax option in the Calculating PDF from a
> structure in the PDFgui. Is it not the PDF calculated in real space in this
> case? If so why will the data be truncated?

Hi Ioana,

The Qmax option is there to simulate an experimental PDF that was
measured at a finite Qmax, but it is not required for the calculation
itself. When Qmax is set to 0 or to some large value, say 100, the
data truncation is not applied, and the PDF then equals a sum of
real-space Gaussians at the interatomic distances.

Hope this helps,

Pavol


--
Dr. Pavol Juhas
Condensed Matter Physics and Materials Science Department
building 510B
Brookhaven National Laboratory
P.O. Box 5000
Upton, NY 11973-5000

[Pavol Juhas]

Dear Ioana,

If you are trying to calculate PDF without any Qmax correction just set it to zero.  In such case the correction is not applied.  Equally, setting Qmax to pi/rstep=314 or above does the same, because r-sampling at rstep cannot capture frequencies beyond pi/rstep so there is nothing above Qmax to be cut off.

The thermal parameters should be all set to a nonzero value, otherwise there would be some peaks missing, because the peaks with a zero width are ignored.

Hope this helps,

Pavol

On Wed, May 29, 2013 at 7:17 AM, Ioana Sovago <ioana...@yahoo.com> wrote:

Dear Pavol,

Thanks for your reply.

What will be the minimum Qmax value at which I can still consider my data being calculated in real space.

Ive used Qmax 26. Looks identical with those from 0 or 100 apart from some straight smalls lines (at 0 or 100). This may arise for the fact that I have some thermal parameters set to zero or 0.05 as the data are from some polymorphic prediction results that do not contain adps. I was wondering if at Qmax 26 I can still consider my data as not being at an infinite range (not being truncated) so the PDFs still equals a sum of real-space Gaussians at the interatomic distances.

Thanks

Ioana

On Tuesday, May 28, 2013 10:35:22 AM UTC+2, Ioana Sovago wrote:

I was wondering why there is a Qmax option in the Calculating PDF from a structure in the PDFgui. Is it not the PDF calculated in real space in this case? If so why will the data be truncated?

Is it the PDFgui generating a powder pattern from the crystal structure and then calculating the PDF? Is there an 'ideal' value to be used for Qmax.

Thanks

Ioana Sovago

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--

    Dr. Pavol Juhas

    Condensed Matter Physics and Materials Science Department

    Brookhaven National Laboratory

    P.O. Box 5000

    Upton, NY  11973-5000

    tel: +1-631-344-3594

    fax: +1-631-344-2739

[Ioana Sovago]

Dear Pavol,

What about the Qmax in the pdfgetx3, is there a need to be set at the same value with the experimental or simulated powder data. For instance if I use Cu radiation 2thetamax = 40, so Qmax is 2.8, should I set up Omax 2.8 on the pdfgetx3.cfg file. I have tried Qmax 2.8 and 26 and I see no difference. Also what will be the appropriate qmaxinst to use for a simulated powder pattern from mercury, is it 26 (as shown in manual) ok? How can I calculate this value to be sure I am using the correct one.

Thanks,

Ioana

[Ioana Sovago]

If anyone can help with this I will highly appreciate.

 

[Pavol Juhas]

On Fri, Jun 07, 2013 at 01:58:18AM -0700, Ioana Sovago wrote:
> Dear Pavol,
>
> What about the Qmax in the pdfgetx3, is there a need to be set at the same
> value with the experimental or simulated powder data. For instance if I use
> Cu radiation 2thetamax = 40, so Qmax is 2.8, should I set up Omax 2.8 on
> the pdfgetx3.cfg file. I have tried Qmax 2.8 and 26 and I see no
> difference. Also what will be the appropriate qmaxinst to use for a
> simulated powder pattern from mercury, is it 26 (as shown in manual) ok?
> How can I calculate this value to be sure I am using the correct one.

Dear Ioana,

The qmax value used in the calculation is limited by the range of the
input data. There should be a warning notice about qmax if it is
outside the data range, but I just noticed it does not appear when both
qmaxinst and qmax are above the data limit. In your case, the actual
value applied was 2.8 regardless of the setting in the configuration file,
and that's why the results were the same.

For a good quality PDF it is better to use x-ray data from either
molybdenum or silver anode or ideally from a synchrotron source.
The r-resolution in the PDF signal is limited by pi/qmax which becomes
very low for Cu x-ray sources. The following paper has a nice
discussion of PDF resolution for various x-ray sources and Qmax
values http://slapper.apam.columbia.edu/bib/papers/dykhn_phmr11.pdf .

As for the powder pattern from mercury, you should use qmaxinst and
qmax equal to the upper bound in the simulated pattern. This will
happen automatically if you commented/removed the qmaxinst line from the
pdfgetx3.cfg file.

Hope this helps,

Pavol

--
Dr. Pavol Juhas
Condensed Matter Physics and Materials Science Department

building 510B