[gmx-developers] Gromacs API development and example scripts

[Peter Kasson]

In response to Joe's question, we have a three-phase support model planned.

Phase 0.  Mapping arguments to gmx command-line syntax is somewhat klunky
but will allow us to support most gmx operations out of the box without
substantial refactoring of core Gromacs code.
Phase 1.  In conjunction with planned refactoring of option parsing, we
plan a more sophisticated and pythonic way to pass arguments to gmx
command-line operations.
Phase 2.  Ultimately, we'd like to offer more modular access to high-level
Gromacs operations that might not be the current monolithic gmx
command-line operations.  This obviously requires more design work and more
core code refactoring.

We have a similar three-phase model planned for things that are currently
file input/output also.
Phase 0.  Statically named files
Phase 1.  Files that are managed by the API (you see some examples of this)
Phase 2.  Data objects that are managed by the API and might or might not
correspond to files on disk.

Our 6-month development timescale focuses on Phase 0 for command-line
syntax (maybe stretch goal of Phase 1) and Phases 0/1 for files.  But I've
outlined our slightly longer-term vision here.  Thanks for the comments!

--Peter
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