<div dir="ltr"><div><div><div><div><div>Thank you for providing a detailed explanation.<br><br></div>Actually I should focus only on asking about all atom form factors table which is " sfactor_atom_nods_Fourier.xml ". In this there is no solvent displaced correction so we no need to use any polynomial correction. I suppose the coefficients in these table should be close to the cromer-mann coefficients (from quantum calculations) or to be in a form to use in the following equation to calculate atomic form factor.<br><img alt="Inline image 1" src="cid:ii_14909c9ce9cd626d" height="81" width="235"><br><br></div>As I can see the coefficients given in the .xml file are very different I would like to know what is the equation used to calculate atomic form factor. In principle, whatever the method or coefficients we use the atomic factor at q=0 will be equal to atom number. I am not clear how this is satisfied from your coefficients given in " sfactor_atom_nods_Fourier.xml ". For example for atom "Carbon" I expect sum of a1 to a5 should be equal to 6.<br><br></div>Please correct me if I have mistaken any concept in your implementation.<br><br></div>Thanks for your time and kind help.<br></div>Best regards<br><div><div><div><div><br><br><br></div></div></div></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Oct 13, 2014 at 6:26 PM, Alexander Björling <span dir="ltr"><<a href="mailto:alex.bjorling@gmail.com" target="_blank">alex.bjorling@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><br><div class="gmail_extra"><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
From: Anjaiah Nalaparaju <<a href="mailto:anjai.che@gmail.com" target="_blank">anjai.che@gmail.com</a>><br>
<br>
My question is related to the unmerged patch for module waxsdebye.<br>
<br>
1. Can anybody tell the reference for the form factor<br>
coefficients(a1-a5,b1-b5,p1-p3) in file "sfactor_atom_nods_Fourier.xml" or<br>
all the new .xml files on sfactors. These number look very much different<br>
from the sfactor.dat which are cromer-mann coefficients.<br></blockquote><div>There is no reference (yet). The numbers are different because it's a different parametrization. Since solvent-corrected form factors have a more complex shape, we've used a short Fourier sum plus a polynomial, instead of gaussians. The form factor is calculated from these parameters in src/gromacs/waxsdebye/scattering_factors.cpp.<br></div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<br>
2. If we use the following equation to calculate atomic form factors, at<br>
q=0 sum of co-eff a1 to a5 should be equal to the form factor value at q=0<br>
given in the publication "Niebling, Bj?rling and Westenhoff, J. Appl.<br>
Cryst. 47 (2014) 1190"<br></blockquote><div>No they shouldn't, there's also a polynomial there. Again, see scattering_factors.cpp. Have that code print out the scattering factors if you would like to test them.<br><br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<br>
[image: View the MathML source]<br>
<br>
But seems the coefficients in .xml files are not corresponding to this<br>
equation.<br>
<br>
3. How can the coefficients after displaced volume correction can be a<br>
constant value ( sfactor_atom_ds_Fourier.xml), as the displaced volume<br>
correction term also function of "q". "Svergun, Barberato and Koch, J Appl.<br>
Cryst. 27 (1995) 768."<br></blockquote><div>I'm not sure what you mean by "constant value". <br></div><div> <br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<br>
3. Where the form-factors with displaced volume corrections are calculated <br>
in the code.<br></blockquote><div>The displaced volume corrections are not done in the code. The scattering factors with or without the correction (depending on which xml file is used) are calculated in scattering_factors.cpp.</div><div> <br></div></div></div></div>
<br>--<br>
Gromacs Developers mailing list<br>
<br>
* Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List</a> before posting!<br>
<br>
* Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
<br>
* For (un)subscribe requests visit<br>
<a href="https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers" target="_blank">https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers</a> or send a mail to <a href="mailto:gmx-developers-request@gromacs.org">gmx-developers-request@gromacs.org</a>.<br></blockquote></div><br></div>