<div dir="ltr"><div class="gmail_extra"><br><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">
Date: Mon, 13 Oct 2014 22:03:50 +0800<br>
From: Anjaiah Nalaparaju <<a href="mailto:anjai.che@gmail.com">anjai.che@gmail.com</a>><br>
To: Discussion list for GROMACS development<br>
<<a href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a>><br>
Subject: Re: [gmx-developers] Regarding commit Implementation of<br>
WAXS/SAXS refinement in MD!<br>
Message-ID:<br>
<CANEpNGj+Rdy9o+zV7e-vmBMoM11u8go1iR9Y-xH_WzpYT=<a href="mailto:TNSQ@mail.gmail.com">TNSQ@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Thank you for providing a detailed explanation.<br>
<br>
Actually I should focus only on asking about all atom form factors table<br>
which is " sfactor_atom_nods_Fourier.xml ". In this there is no solvent<br>
displaced correction so we no need to use any polynomial correction. I<br>
suppose the coefficients in these table should be close to the cromer-mann<br>
coefficients (from quantum calculations) or to be in a form to use in the<br>
following equation to calculate atomic form factor.<br>
[image: Inline image 1]<br>
<br>
As I can see the coefficients given in the .xml file are very different I<br>
would like to know what is the equation used to calculate atomic form<br>
factor. In principle, whatever the method or coefficients we use the atomic<br>
factor at q=0 will be equal to atom number. I am not clear how this is<br>
satisfied from your coefficients given in " sfactor_atom_nods_Fourier.xml<br>
". For example for atom "Carbon" I expect sum of a1 to a5 should be equal<br>
to 6. </blockquote><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<br>
Please correct me if I have mistaken any concept in your implementation.<br></blockquote><div><br>Again, the numbers in the xml files are _not_ Cromer-Mann parameters. The numeric scattering factors are calculated for the appropriate q-grid in scattering_factors.cpp.<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>
Thanks for your time and kind help.<br>
Best regards<br>
<br>
<br>
<br>
<br>
On Mon, Oct 13, 2014 at 6:26 PM, Alexander Bj?rling <<a href="mailto:alex.bjorling@gmail.com">alex.bjorling@gmail.com</a><br>
> wrote:<br>
<br>
><br>
> From: Anjaiah Nalaparaju <<a href="mailto:anjai.che@gmail.com">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>
>><br>
> There is no reference (yet). The numbers are different because it's a<br>
> different parametrization. Since solvent-corrected form factors have a more<br>
> complex shape, we've used a short Fourier sum plus a polynomial, instead of<br>
> gaussians. The form factor is calculated from these parameters in<br>
> src/gromacs/waxsdebye/scattering_factors.cpp.<br>
><br>
><br>
>><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<br>
>> q=0<br>
>> given in the publication "Niebling, Bj?rling and Westenhoff, J. Appl.<br>
>> Cryst. 47 (2014) 1190"<br>
>><br>
> No they shouldn't, there's also a polynomial there. Again, see<br>
> scattering_factors.cpp. Have that code print out the scattering factors if<br>
> you would like to test them.<br>
><br>
><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<br>
>> Appl.<br>
>> Cryst. 27 (1995) 768."<br>
>><br>
> I'm not sure what you mean by "constant value".<br>
><br>
><br>
>><br>
>> 3. Where the form-factors with displaced volume corrections are<br>
>> calculated<br>
>> in the code.<br>
>><br>
> The displaced volume corrections are not done in the code. The scattering<br>
> factors with or without the correction (depending on which xml file is<br>
> used) are calculated in scattering_factors.cpp.<br>
><br>
><br>
> --<br>
> Gromacs Developers mailing list<br>
><br>
> * Please search the archive at<br>
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> posting!<br>
><br>
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<br>
Message: 2<br>
Date: Tue, 14 Oct 2014 12:38:22 +0800<br>
From: Anjaiah Nalaparaju <<a href="mailto:anjai.che@gmail.com">anjai.che@gmail.com</a>><br>
To: Discussion list for GROMACS development<br>
<<a href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a>><br>
Subject: Re: [gmx-developers] Regarding commit Implementation of<br>
WAXS/SAXS refinement in MD!<br>
Message-ID:<br>
<<a href="mailto:CANEpNGiqX9wCH4zDuVQduWUSVJh9ed4rShadgd_XUOHQW39fWQ@mail.gmail.com">CANEpNGiqX9wCH4zDuVQduWUSVJh9ed4rShadgd_XUOHQW39fWQ@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi,<br>
<br>
I understood the coefficients in .xml file. There is a coefficient "a0",<br>
this is taking care of formfactor value at q=0.<br>
<br>
Best regards<br>
<br>
On Mon, Oct 13, 2014 at 10:03 PM, Anjaiah Nalaparaju <<a href="mailto:anjai.che@gmail.com">anjai.che@gmail.com</a>><br>
wrote:<br>
<br>
> Thank you for providing a detailed explanation.<br>
><br>
> Actually I should focus only on asking about all atom form factors table<br>
> which is " sfactor_atom_nods_Fourier.xml ". In this there is no solvent<br>
> displaced correction so we no need to use any polynomial correction. I<br>
> suppose the coefficients in these table should be close to the cromer-mann<br>
> coefficients (from quantum calculations) or to be in a form to use in the<br>
> following equation to calculate atomic form factor.<br>
> [image: Inline image 1]<br>
><br>
> As I can see the coefficients given in the .xml file are very different I<br>
> would like to know what is the equation used to calculate atomic form<br>
> factor. In principle, whatever the method or coefficients we use the atomic<br>
> factor at q=0 will be equal to atom number. I am not clear how this is<br>
> satisfied from your coefficients given in " sfactor_atom_nods_Fourier.xml<br>
> ". For example for atom "Carbon" I expect sum of a1 to a5 should be equal<br>
> to 6.<br>
><br>
> Please correct me if I have mistaken any concept in your implementation.<br>
><br>
> Thanks for your time and kind help.<br>
> Best regards<br>
><br>
><br>
><br>
><br>
> On Mon, Oct 13, 2014 at 6:26 PM, Alexander Bj?rling <<br>
> <a href="mailto:alex.bjorling@gmail.com">alex.bjorling@gmail.com</a>> wrote:<br>
><br>
>><br>
>> From: Anjaiah Nalaparaju <<a href="mailto:anjai.che@gmail.com">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"<br>
>>> 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>
>>><br>
>> There is no reference (yet). The numbers are different because it's a<br>
>> different parametrization. Since solvent-corrected form factors have a more<br>
>> complex shape, we've used a short Fourier sum plus a polynomial, instead of<br>
>> gaussians. The form factor is calculated from these parameters in<br>
>> src/gromacs/waxsdebye/scattering_factors.cpp.<br>
>><br>
>><br>
>>><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<br>
>>> q=0<br>
>>> given in the publication "Niebling, Bj?rling and Westenhoff, J. Appl.<br>
>>> Cryst. 47 (2014) 1190"<br>
>>><br>
>> No they shouldn't, there's also a polynomial there. Again, see<br>
>> scattering_factors.cpp. Have that code print out the scattering factors if<br>
>> you would like to test them.<br>
>><br>
>><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<br>
>>> Appl.<br>
>>> Cryst. 27 (1995) 768."<br>
>>><br>
>> I'm not sure what you mean by "constant value".<br>
>><br>
>><br>
>>><br>
>>> 3. Where the form-factors with displaced volume corrections are<br>
>>> calculated<br>
>>> in the code.<br>
>>><br>
>> The displaced volume corrections are not done in the code. The scattering<br>
>> factors with or without the correction (depending on which xml file is<br>
>> used) are calculated in scattering_factors.cpp.<br>
>><br>
>><br>
>> --<br>
>> Gromacs Developers mailing list<br>
>><br>
>> * Please search the archive at<br>
>> <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<br>
>> 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>
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