<div dir="ltr"><div><div><div><div><div>Hello,<br><br></div>My question is related to the unmerged patch for module waxsdebye. <br><br>1. Can anybody tell the reference for the form factor coefficients(a1-a5,b1-b5,p1-p3) in file "sfactor_atom_nods_Fourier.xml" or all the new .xml files on sfactors. These number look very much different from the sfactor.dat which are cromer-mann coefficients.<br><br></div><div>2. If we use the following equation to calculate atomic form factors, at q=0 sum of co-eff a1 to a5 should be equal to the form factor value at q=0 given in the publication "Niebling, Björling and Westenhoff, J. Appl. Cryst. 47 (2014) 1190"<br><br></div><div><img style="display: inline;" class="" alt="View the MathML source" title="View the MathML source" src="http://ars.els-cdn.com.ezlibproxy1.ntu.edu.sg/content/image/1-s2.0-S0006349514006109-si41.gif" height="53" width="235"><br><br></div><div>But seems the coefficients in .xml files are not corresponding to this equation.<br></div><div><br></div>3. How can the coefficients after displaced volume correction can be a constant value ( sfactor_atom_ds_Fourier.xml), as the displaced volume correction term also function of "q". "Svergun, Barberato and Koch, J Appl. Cryst. 27 (1995) 768."<br><br></div>3. Where the form-factors with displaced volume corrections are calculated in the code. <br><br></div>Thank you for your time and help.<br><br></div>Best regards<br><div><div><br></div></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Aug 26, 2014 at 1:21 PM, Anjaiah Nalaparaju <span dir="ltr"><<a href="mailto:anjai.che@gmail.com" target="_blank">anjai.che@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"><div>Thank you.<br><br></div>I have noted the new code is completely different from old code. But I am still curious to know about the loop used in sfactor.c to compute the structure factors.<span class=""><br><br>/*<br>
* The big loop...<br>
* compute real and imaginary part of the structure factor for every<br>
* (kx,ky,kz))<br>
*/<br>
/*<br>
* compute the square modulus of the structure factor, averaging on<br>
the surface<br>
* kx*kx + ky*ky + kz*kz = krr*krr<br>
* note that this is correct only for a (on the macroscopic scale)<br>
* isotropic system.<br>
*/<br><br><br></span><div><div><div class="gmail_extra">Is there any reference discussing this approach. I want to know the rationale behind this implementation. <br><br></div><div class="gmail_extra">Thanks again for your time and help.<br>
</div><div><div class="h5"><div class="gmail_extra"><br><br><br> <br></div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Aug 25, 2014 at 7:08 PM, David van der Spoel <span dir="ltr"><<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div>On 2014-08-25 11:56, Anjaiah Nalaparaju wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
Hello,<br>
<br>
1. In the previous code to compute structure factors (sfactor.c) there<br>
is a loop<br>
/*<br>
* The big loop...<br>
* compute real and imaginary part of the structure factor for every<br>
* (kx,ky,kz))<br>
*/<br>
/*<br>
* compute the square modulus of the structure factor, averaging on<br>
the surface<br>
* kx*kx + ky*ky + kz*kz = krr*krr<br>
* note that this is correct only for a (on the macroscopic scale)<br>
* isotropic system.<br>
*/<br>
This loop is no more in the new code "scattering_factors.cpp". May I<br>
know why this loop is used in the previous code. Is this to introduce<br>
orientational averaging?<br>
</blockquote>
<br></div>
Note that there is no relation between the previous code and the new one, that is the new code is derived from scratch.<div><br>
<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<br>
2. I think sfactor.xml (input file for gmx waxsdebye) is still in the<br>
development stage?<br>
</blockquote></div>
Formally yes, we will implement some tests now to validate it.<br>
<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div>
<br>
Thanks in advance.<br>
<br>
<br>
<br>
<br>
On Fri, Aug 22, 2014 at 4:09 PM, David van der Spoel<br></div><div>
<<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <mailto:<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a>>> wrote:<br>
<br>
On 2014-08-22 09:45, Anjaiah Nalaparaju wrote:<br>
<br>
Thank you very much for the response. I did the following.<br>
<br></div>
1. git clone git://<a href="http://git.gromacs.org/gromacs.__git" target="_blank">git.gromacs.org/gromacs.<u></u>__git</a><br>
<<a href="http://git.gromacs.org/gromacs.git" target="_blank">http://git.gromacs.org/<u></u>gromacs.git</a>><br>
<<a href="http://git.gromacs.org/__gromacs.git" target="_blank">http://git.gromacs.org/__<u></u>gromacs.git</a><div><br>
<<a href="http://git.gromacs.org/gromacs.git" target="_blank">http://git.gromacs.org/<u></u>gromacs.git</a>>> (to download the master<br>
branch)<br>
<br>
<br></div>
2. git fetch <a href="https://gerrit.gromacs.org/__gromacs" target="_blank">https://gerrit.gromacs.org/__<u></u>gromacs</a><div><br>
<<a href="https://gerrit.gromacs.org/gromacs" target="_blank">https://gerrit.gromacs.org/<u></u>gromacs</a>> refs/changes/59/2659/84<br>
&& git format-patch -1 --stdout FETCH_HEAD (to apply patch to<br>
the source<br>
code)<br>
<br>
3. mkdir build and under the build folder $cmake .. -DGMX_MPI=ON<br>
-DGMX_GPU=OFF -DGMX_BUILD_OWN_FFTW=ON -DGMX_DEFAULT_SUFFIX=OFF<br>
-DGMX_BINARY_SUFFIX=_mpi -DGMX_LIBS_SUFFIX=_mpi<br>
<br>
4. Once the installation completed, under the bin folder I see<br>
all the<br>
tools same as before and didn't see any new tool related to<br>
waxsdebye.<br>
Version shows VERSION 5.1-dev-20140821-d9c0e41.<br>
<br>
May I know what is the name of new tool for WAXS/SAXS calculation.<br>
<br>
gmx help commands<br>
should show the command to be<br>
gmx waxsdebye<br>
<br>
Thanks in advance.<br>
<br>
<br>
<br>
On Fri, Aug 22, 2014 at 1:51 PM, David van der Spoel<br>
<<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <mailto:<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a>><br></div><div><div>
<mailto:<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <mailto:<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a>>><u></u>> wrote:<br>
<br>
On 2014-08-22 05:38, Anjaiah Nalaparaju wrote:<br>
<br>
Dear Dr. David van der Spoel,<br>
<br>
I am interested in the module you have been developing for<br>
WAXS/SAXS. I<br>
was introduced to this patch by Dr.Alexey Shvestov. I<br>
have two<br>
queries<br>
related to the this module and I have been suggested to<br>
contact<br>
you to<br>
get the accurate information on my queries.<br>
<br>
1. I have downloaded the latest code (patch 83), if I<br>
install<br>
this copy<br>
I still didn't get the gmx waxsdebye or g_waxdebye tool<br>
to use<br>
under bin<br>
folder. Could you please guide me how can we try and<br>
test this<br>
tool now.<br>
<br>
You download the latest master branch, then apply the patch<br>
to the<br>
source code, by copying the link on the gerrit web site and<br>
rebuild<br>
and install. This works for us. We are still doing a bit of<br>
development but it is almost finished.<br>
<br>
<br>
<br>
2. I am just curious to know why the same approach as<br>
g_sans has not<br>
been used in this module. I mean working in the real<br>
space was<br>
not chosen.<br>
<br>
In fact I don't know, Alexey has suggested the approaches are<br>
similar but I have not looked into it I must admit.<br>
<br>
<br>
Thanks in advance for your time and help. Sorry for<br>
sending mail<br>
to your<br>
personal email id.I have posted part of my queries in<br>
gmxdevelopers list<br>
but didnt get response.<br>
<br>
Sorry about that, but let's move the discussion back to the<br>
developers list so that others can join in as well. Please post<br>
further questions there in other words.<br>
<br>
<br>
Best regards,<br>
Anjaiah<br>
<br>
<br>
<br>
--<br>
David van der Spoel, Ph.D., Professor of Biology<br>
Dept. of Cell & Molec. Biol., Uppsala University.<br>
Box 596, 75124 Uppsala, Sweden. Phone: <a href="tel:%2B46184714205" value="+46184714205" target="_blank">+46184714205</a><br>
<tel:%2B46184714205><br>
<tel:%2B46184714205>.<br>
<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <mailto:<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a>><br></div></div>
<mailto:<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <mailto:<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a>>><div><br>
<a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a><br>
<br>
<br>
<br>
<br>
--<br>
David van der Spoel, Ph.D., Professor of Biology<br>
Dept. of Cell & Molec. Biol., Uppsala University.<br>
Box 596, 75124 Uppsala, Sweden. Phone: <a href="tel:%2B46184714205" value="+46184714205" target="_blank">+46184714205</a><br>
<tel:%2B46184714205>.<br>
<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <mailto:<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a>><br>
<a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a><br>
--<br></div><div>
Gromacs Developers mailing list<br>
<br>
* Please search the archive at<br></div>
<a href="http://www.gromacs.org/__Support/Mailing_Lists/GMX-__developers_List" target="_blank">http://www.gromacs.org/__<u></u>Support/Mailing_Lists/GMX-__<u></u>developers_List</a><br>
<<a href="http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List" target="_blank">http://www.gromacs.org/<u></u>Support/Mailing_Lists/GMX-<u></u>developers_List</a>><br>
before posting!<br>
<br>
* Can't post? Read <a href="http://www.gromacs.org/__Support/Mailing_Lists" target="_blank">http://www.gromacs.org/__<u></u>Support/Mailing_Lists</a><div><br>
<<a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/<u></u>Support/Mailing_Lists</a>><br>
<br>
* For (un)subscribe requests visit<br></div>
<a href="https://maillist.sys.kth.se/__mailman/listinfo/gromacs.org___gmx-developers" target="_blank">https://maillist.sys.kth.se/__<u></u>mailman/listinfo/gromacs.org__<u></u>_gmx-developers</a><br>
<<a href="https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers" target="_blank">https://maillist.sys.kth.se/<u></u>mailman/listinfo/gromacs.org_<u></u>gmx-developers</a>><br>
or send a mail to gmx-developers-request@__<a href="http://gromacs.org" target="_blank">groma<u></u>cs.org</a><br>
<mailto:<a href="mailto:gmx-developers-request@gromacs.org" target="_blank">gmx-developers-<u></u>request@gromacs.org</a>>.<br>
<br>
<br>
<br>
<br>
</blockquote><div><div>
<br>
<br>
-- <br>
David van der Spoel, Ph.D., Professor of Biology<br>
Dept. of Cell & Molec. Biol., Uppsala University.<br>
Box 596, 75124 Uppsala, Sweden. Phone: <a href="tel:%2B46184714205" value="+46184714205" target="_blank">+46184714205</a>.<br>
<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a><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/<u></u>Support/Mailing_Lists/GMX-<u></u>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/<u></u>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/<u></u>mailman/listinfo/gromacs.org_<u></u>gmx-developers</a> or send a mail to <a href="mailto:gmx-developers-request@gromacs.org" target="_blank">gmx-developers-request@<u></u>gromacs.org</a>.<br>
</div></div></blockquote></div><br></div></div></div></div></div></div>
</blockquote></div><br></div>