2009-06-16 04:01
Submitted by:
John Chodera (jchodera)
Assigned to:
Nobody (None)
OpenMM API doxygen comments should include references to implemented algorithms, reproduce equations, and list all units

Detailed description
The OpenMM API doxygen comments should include a thorough description of the algorithm implemented, including a full set of references to the publications describing the algorithm implemented. In addition, the critical equations should be reproduced, especially those containing the variables provided in the API. It is also critical to list the units of ALL parameters, not just some parameters.

The current API documentation leaves too much confusion over what exactly is being implemented, and differences in convention leave question as to whether, for example, the Lennard-Jones sigma, radius, or diameter are expected. Some parameters are missing documentation of what units are expected as well, or explicitly declare that unitless parameters are unitless. Preconditions and allowed ranges should also be documented in the API, rather than just having the code throw an error when some parameter (like a radius) is set too small.

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Message  ↓
Date: 2009-08-21 23:43
Sender: Peter Eastman

Preview Release 4 includes a theory guide that contains all of this information.

Field Old Value Date By
status_idOpen2009-08-21 23:43peastman
close_date2009-08-21 23:432009-08-21 23:43peastman