<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.<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><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 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 class="">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 class=""><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 class="">
<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 class="">
<<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 class=""><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 class=""><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 class="h5">
<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 class=""><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>
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<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>
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