[gmx-developers] libxml2

Erik Lindahl erik.lindahl at scilifelab.se
Mon Nov 11 14:23:03 CET 2013


On 11 Nov 2013, at 05:12, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> Another drawback with a monster XML file is that it would move us away 
> from modularity again: having sfactor reading and writing completely 
> modular encapsulated in the waxsdebye module also means that if I break 
> that code everything else will not be affected.

Ah, although I haven’t tried it yet, but I _think_ that’s going to be the beauty. Since it is a separate namespace, we can make the structurefactor module  entirely responsible for reading and writing that part of the file!

XML now also supports includes, so in most cases we would not use a single file, but just like now have a number of files in the present (or library) directory that are read when the components need them. These files will not even be aware of the higest-level Gromacs namespace - we only use that in the case where you absolutely want to merge all data into a single file (which will be rare, at least for now, although it would be great for archival storage).

So, for structure factors we would only need to decide:

1) We probably don’t want a completely separate namespace just for structure factors, so we should invent a reasonable name and internal layout for a namespace that deals with chemical data (or whatever we call it).

2) To avoid shooting ourselves in the foot, it is probably a good idea to have a reasonably good idea where we see this namespace fitting in relative to all others. If nothing else, this might help with naming…



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