<br><br><div class="gmail_quote">On Fri, Jul 3, 2009 at 1:12 PM, Axel Kohlmeyer <span dir="ltr"><<a href="mailto:akohlmey@cmm.chem.upenn.edu" target="_blank">akohlmey@cmm.chem.upenn.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div>On Fri, 2009-07-03 at 12:58 -0400, Roland Schulz wrote:<br>
</div><br>
<div><br>
> Using the VMD plugin API would add 3 addiotional source files (hash.c,<br>
> molfile_plugin.h, vmdplugin.h).<br>
<br>
> Does this matter? Should I do this so that we can easily add further<br>
> vmd supported types in the future?<br>
<br>
</div>if you use the molfile API, you automatically add _all_ formats<br>
that the molfile plugins support. that would include for example<br>
native formats of LAMMPS, desmond, amber, amber/netcdf on top<br>
of .dcd without any extra coding effort from you.</blockquote><div><br>I'm not opposed to it. I just don't know what everyone things about adding so much additional source. <br><br>1) a few additional source files for the API<br>
2) the source for the different formats<br><br>which file formats should be included in the gromacs code? Which should be compiled in by default?<br><br>Or do we want to allow GROMACS to be compiled agains the vmd plugin? Then one would compile the vmd plugin directory and then could configure with : configure --with-vmd=$VMD_PATH<br>
<br>So I see 4 alternatives:<br>- Just add DCD (because it is most often used?)<br>- Add API and DCD and very few common used formats (which?)<br>- Add this "--with-vmd" option<br>- Add the whole vmd plugin code to GROMACS<br>
<br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
i'm not sure why you'd need hash.c. for writing an interface to<br>
the plugin API you should only need files from the include directory.</blockquote><div><br>I looked at the catdcd as an example. One needs to somehow have the register of the file formats. How do you do that register without hash? Is there a good example of the usage besides catdcd?<br>
<br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
i'd suggest you start from the latest (cvs) code, as VMD-1.8.7 is about<br>
to be released very, very soon and that would require vmdplugin.h,<br>
molfile_plugin.h and vmdconio.h.<br>
<br>
there have been some significant improvements. for example, the improved<br>
plugin API has support for reading angle, dihedral, improper<br>
definitions, or velocities (for file formats that support it).</blockquote><div><br>Thanks<br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
<br>
the main advantage is that you don't have to maintain the .dcd<br>
(or others format) readers yourself and keep it in sync with<br>
the VMD/molfile code base. there is already too much code<br>
replication already. for VMD i'm planning to adjust the gromacs<br>
support to use libxdrfile from the gromacs distribution, for example.</blockquote><div><br>I kept the changes very few (basically just removing the plugin api). But of course your solution is much better if one wants more than just DCD.<br>
<br>Roland<br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><br>
<br>
cheers,<br>
<font color="#888888"> axel.<br>
</font><div><div></div><div><br>
<br>
> Roland<br>
><br>
> On Fri, Jul 3, 2009 at 11:59 AM, Axel Kohlmeyer<br>
> <<a href="mailto:akohlmey@cmm.chem.upenn.edu" target="_blank">akohlmey@cmm.chem.upenn.edu</a>> wrote:<br>
> roland,<br>
><br>
> On Fri, Jul 3, 2009 at 6:44 AM, Roland Schulz<<a href="mailto:roland@utk.edu" target="_blank">roland@utk.edu</a>><br>
> wrote:<br>
> > Hi,<br>
> ><br>
> > what do you think about adding DCD read support to the<br>
> tools? Quite a few<br>
> > people in our group use the tools but (for a number of<br>
> reasons) do the<br>
> > simulation still with other MD packages. It is inconvenient<br>
> to have to<br>
> > convert the trajectories.<br>
><br>
><br>
> instead of adopting code to only read .dcd files,<br>
> why don't you write an interface to the VMD molfile API?<br>
> should be even less work and then you would interface<br>
> gromacs to a large number of file formats. also it would<br>
> avoid replicating and code (and problems with diverging<br>
> developments and missing bugfixes) and also you can add<br>
> new file formats or updated readers/writers<br>
> on the fly through the dynamic loading of plugins.<br>
><br>
> cheers,<br>
> axel.<br>
><br>
> p.s.: we're also in the process of gradually revising the<br>
> molfile API to make it more flexible and powerful and<br>
> particularly add support for "out-of-core" processing of<br>
> a collection of files (primarily for VMD but not limited to<br>
> it).<br>
> that might be interesting for gromacs tools just as well.<br>
><br>
><br>
> ><br>
> > Is it OK to add code which is under the University of<br>
> Illinois Open Source<br>
> > License? It is GPL compatible so does not cause license<br>
> conflicts<br>
> ><br>
> (<a href="http://en.wikipedia.org/wiki/University_of_Illinois/NCSA_Open_Source_License" target="_blank">http://en.wikipedia.org/wiki/University_of_Illinois/NCSA_Open_Source_License</a>).<br>
> ><br>
> > Roland<br>
> ><br>
> > --<br>
> > ORNL/UT Center for Molecular Biophysics <a href="http://cmb.ornl.gov" target="_blank">cmb.ornl.gov</a><br>
> > 865-241-1537, ORNL PO BOX 2008 MS6309<br>
> ><br>
><br>
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><br>
><br>
><br>
> --<br>
><br>
> =======================================================================<br>
> Axel Kohlmeyer <a href="mailto:akohlmey@cmm.chem.upenn.edu" target="_blank">akohlmey@cmm.chem.upenn.edu</a><br>
> <a href="http://www.cmm.upenn.edu" target="_blank">http://www.cmm.upenn.edu</a><br>
> Center for Molecular Modeling -- University of<br>
> Pennsylvania<br>
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA<br>
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> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel:<br>
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><br>
> --<br>
> ORNL/UT Center for Molecular Biophysics <a href="http://cmb.ornl.gov" target="_blank">cmb.ornl.gov</a><br>
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<br>
--<br>
=======================================================================<br>
Axel Kohlmeyer <a href="mailto:akohlmey@cmm.chem.upenn.edu" target="_blank">akohlmey@cmm.chem.upenn.edu</a> <a href="http://www.cmm.upenn.edu" target="_blank">http://www.cmm.upenn.edu</a><br>
Center for Molecular Modeling -- University of Pennsylvania<br>
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323<br>
tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425<br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>ORNL/UT Center for Molecular Biophysics <a href="http://cmb.ornl.gov" target="_blank">cmb.ornl.gov</a><br>865-241-1537, ORNL PO BOX 2008 MS6309<br>