[ESPResSo-devel] [bug #35952] Improve virtual sites and topology handling

[Christoph Junghans]

URL:
  <http://savannah.nongnu.org/bugs/?35952>

                 Summary: Improve virtual sites and topology handling
                 Project: ESPResSo
            Submitted by: junghans
            Submitted on: Thu 22 Mar 2012 05:02:32 PM GMT
                Category: Simulation core
                Severity: 1 - Wish
                  Status: None
             Assigned to: None
             Open/Closed: Open
         Discussion Lock: Any
                 Release: None
           Fixed Release: None

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Details:

VIRTUAL_SITES_RELATIVE and VIRTUAL_SITES_COM are implemented in opposite
ways.
VIRTUAL_SITES_RELATIVE uses particle properties, while VIRTUAL_SITES_COM uses
the topology data.
The first approach seems easy to generalize, however for many molecule the
second one save memory as every molecule data is only stores once.
Also the setup is very different VIRTUAL_SITES_RELATIVE uses the part command,
while VIRTUAL_SITES_COM uses the "analyze set" command.
The first one is more obvious to use as there is no documentation for the
second one ("analyze set chain" is documented, but this is something else).

The suggestion would be to make both accessible via the part command under a
"vs" sub-command:
part ... vs relative ...
part ... vs relative_auto ...
part ... vs com ...

With this we can disallow the direct setting of the virtual property via  the
"part .. virtual {0|1}" command.

Additionally the "analyze set" could be reworked into a topology command:
topology create mol_id parts id id id type int excl {0|1}
topology delete mol_id
topology create mol_id chain ....

With this we can disallow the direct setting of the mol_id  property via  the
"part .. mol_id id" command.




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