[gmx-developers] grompp .mdp processing

[Roland Schulz]

On Mon, Feb 23, 2009 at 4:11 AM, David van der Spoel
<spoel at xray.bmc.uu.se>wrote:

>
>
> Over the last years we have discussed moving away from the current
> structure of gromacs, possibly using C++, or at least by using abstract data
> types in C, which are appearing in the code more and more now (see
> src/kernel/gmxcpp.h for an example). Abstract data types allow for a more
> clear separation of code and data, which is crucial for error checking and
> maintainability.


I very much agree with this. And I would add that, in my opinion, this could
also help new people (like me) to understand the code.


> Although Mark has a point that xml files can be complex, this does not need
> to be a problem if we provide an API (in different languages, but at least
> C, Perl) for editing the files that provides complete coverage of all the
> options. Think something like:


I think XML is great when read/written from a script. Because there a good
libraries for all languages. So speical routines might not even be
neccassary. If we provide a library to write the mdp file, the scripts are
independent of the file format.

Thus only editing by hand is influced by the format and my concern is that
XML makes it more difficult to edit by hand. Very few people use XML editors
for XML - most still use text editors. And I don't see what XML would add as
a benefit to the user. What does the user gain to have the abstract data
types in the code represented in the mdp file structure? I think the current
comments written in the mdout file structure the file for humans as well as
XML could do. In case we really think we need some markup language - I would
vote for something like YAML to make it best human readable/editable.

Roland



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ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
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