Task #1781: re-design benchmarking functionality
replace -noconfout with mdp option
At https://gerrit.gromacs.org/#/c/7451 Berk suggested, and Erik and I agreed, that we replace
mdrun -noconfout with an mdp option, which is on by default so that normal behaviour that normal users see stays the same. This option can be turned off when it is useful, e.g. in an .mdp file for benchmark tpr.
Deprecate various functionality in GROMACS 2019
Published a deprecation policy.
Updated the release notes to refer also to previously deprecated
- 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
- 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.
Having the benchmark tool removes the (short term) need for an mdp option for confout.gro.
But the confout.gro file is an awkward construct for all its current uses. For capturing the state of the system for transfer between EM and MD tng would be a better option. For transfer between MD and MD a checkpoint works, although I'm not sure what happens when you change coupling algorithms etc.
And indeed we need a proper way of signaling that a simulation has finished successfully.