<div dir="ltr"><div><div><div><div>Hello,<br><br></div>1. In the previous code to compute structure factors (sfactor.c) there 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 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></div>This loop is no more in the new code "scattering_factors.cpp". May I know why this loop is used in the previous code. Is this to introduce orientational averaging?<br><br></div>
2. I think sfactor.xml (input file for gmx waxsdebye) is still in the development stage?<br><br></div>Thanks in advance.<br><div><br><div><div><br></div></div></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">
On Fri, Aug 22, 2014 at 4:09 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:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="">On 2014-08-22 09:45, Anjaiah Nalaparaju wrote:<br>
</div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="">
Thank you very much for the response. I did the following.<br>
<br>
1. git clone git://<a href="http://git.gromacs.org/gromacs.git" target="_blank">git.gromacs.org/gromacs.<u></u>git</a><br></div>
<<a href="http://git.gromacs.org/gromacs.git" target="_blank">http://git.gromacs.org/<u></u>gromacs.git</a>> (to download the master branch)<div class=""><br>
<br>
2. git fetch <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 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 all the<br>
tools same as before and didn't see any new tool related to 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>
</div></blockquote>
gmx help commands<br>
should show the command to be<br>
gmx waxsdebye<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="">
Thanks in advance.<br>
<br>
<br>
<br>
On Fri, Aug 22, 2014 at 1:51 PM, David van der Spoel<br></div><div><div class="h5">
<<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 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 have two<br>
queries<br>
related to the this module and I have been suggested to 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 install<br>
this copy<br>
I still didn't get the gmx waxsdebye or g_waxdebye tool to use<br>
under bin<br>
folder. Could you please guide me how can we try and test this<br>
tool now.<br>
<br>
You download the latest master branch, then apply the patch to the<br>
source code, by copying the link on the gerrit web site and 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 g_sans has not<br>
been used in this module. I mean working in the real 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 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></div></div>
<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>
<br>
</blockquote><div class="HOEnZb"><div class="h5">
<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></div></div><span class="HOEnZb"><font color="#888888">
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