Welcome to the Wiki Page for: MDL - A Domain-Specific Language for Molecular Dynamics

Please post here any suggestions or comments to improve the language. It would also help to append the date, for the sake of organization.

These are suggestions per a meeting between Trevor and Dr. Izaguirre on 10-29-07:

1. Reorganization proposal, have everything within one level of directory structure: src/factories src/toplevel src/propagators -> example propagators data/ -> example physical systems (PDBs, PSFs, etc.) simulations/ -> example protocols lib/ -> shared object files (from SWIG)

REMAINING QUESTION: what about SWIG-wrapped Python modules? Like BBKIntegrator.py, should this go in lib/ or src/propagators?

2. Each object should override the Python methods for copying and deep copying.

3. Simplify the interface to ForceGroup. We have defaults for the switching function, cutoff, etc. but they are not currently adequate. OPEN DISCUSSION: what should these defaults be???

4. The reorganization described in step (1) will expose a great deal of low level functionality to the user (factories, etc.). Thus these need to be commented more fully.

5. Document the interface between linprotomol and MDL, in concordance with the long term goal of merging linprotomol and MDL as a single package.

6. Nowhere in MDL should there be a standalone function call. The module name to which a function belongs should always appear first.

7. Factories should be queryable, such that it is clear which propagators are available, for example.

8. Do not have propagate() return positions and velocities.

9. Long term goal, interface to GEMS.

***************************************************************************** 1. Cleanup the interface between linprotomol and MDL, such that if a new file is added (for example, an integrator) it is not necessary to modify two Makefiles. (10-17-07)

2. Eclipse produces warnings for unused variables. (10-17-07)

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