announce deprecations in GROMACS 2019 - Redmine #2569
Suggestions for functionality to announce as deprecated, either to remove or replace at some later time.
Several of these are intended to clarify what combinations of things are actually supported in mdrun, simplifying its documentation challenge. Many things have custom input and output files, and we are a long way from all-works-with-all support. Many of the current decisions date from the time when we did not want to increase our install footprint of 80+ tools.
- aromatic vsite construction in pdb2gmx
gmx mdrun -rerun(replace with
gmx tpi; see also #1868)
gmx mdrun -membed(replace with
gmx membed; we had the old
g_membed, whose implementation we fixed, but the distinct tool is useful)
- non-integrators in the integrator .mdp option (replace with
gmx emalong with an mdp option to choose an EM flavour;
gmx mdrun -gcom(need freedom to refactor integrators, and hopefully remove the motivation for this option; see also #1925)
- Benchmarking functionality
gmx mdrun -nsteps n -resetstep x -resethwayare not something normal mdrun users should use, and creates questions about
gmx mdrun -c confout.groand checkpointing; whereas
gmx benchmarkhas a clear use and more options for implementations)
- Aspects of
trjcatthat belong as separate tools (e.g.
gmx do_dssp(at some point we will want to reimplement this natively)
We should also have a docs page for all features that are deprecated, along with the version in which they got that status. Release notes will record when they were removed.
(from redmine: issue id 2569, created on 2018-07-11 by mark.j.abraham, closed on 2018-12-17)
- Revision cf2d8336 by Mark Abraham on 2018-10-13T19:53:48Z:
Deprecate various functionality in GROMACS 2019 Published a deprecation policy. Updated the release notes to refer also to previously deprecated features. Announced intent to change some functionality: * gmx mdrun -membed options (but not feature) * gmx mdrun -rerun option (but not feature) * integrator .mdp field will contain only integrators * gmx do_dssp to be replaced by gmx dssp * gmx trjconv and friends to be split and rewritten List of newly deprecated functionality: * conversion of aromatic rings to virtual sites * gmx mdrun -table options (but not feature) * gmx mdrun -gcom option and feature * gmx mdrun -nsteps option and feature * gmx mdrun -nsteps -resetstep -resethway moved to a gmx benchmark tool * gmx mdrun -confout removed Also updated release notes for functionality removed in GROMACS 2019. Refs #2495, #1781 Fixes #2569, #1925 Change-Id: I1d00859d0f15409a472984f5a65347a50c71ad17
- Revision 21f509ef by Paul Bauer on 2018-11-05T13:28:15Z:
Make QM/MM code always compile Brought all the old interfaces back to a state where they can always compile regardless of the build configuration, and give fatal errors if used from a configuration that didn't support the method. When configured, this should work as before, but we have no ability to test that in Jenkins. Added some necessary const correctness. Did QM/MM preparation all in the same place, to simplify runner.cpp Added deprecation status to release notes. Refs #2706, #2569 Change-Id: I4a6566c60bfbf27a7b1916be1874b36987fb7da5