Give MDModules responsibility for option handling
commit7c27d02fa1b8a35242e818222487e083ae0690a4
authorMark Abraham <mark.j.abraham@gmail.com>
Mon, 30 Jan 2017 14:29:37 +0000 (30 15:29 +0100)
committerMark Abraham <mark.j.abraham@gmail.com>
Wed, 8 Feb 2017 15:09:15 +0000 (8 16:09 +0100)
treeaaeff38dca91e904334786b99024f434d265aa94
parentd1950dc6d7bfb0b067cdac3608958ae13b5f52ac
Give MDModules responsibility for option handling

Centralized responsibility for option handling to avoid repetitious
code. This includes the (temporary) need to convert old-style mdp
options to key-value paths during the transition period, and the
ongoing need to integrate the default values declared by modules for
their options with the user's input (which will eventually be given in
key-value form).

Eliminated init_ir, after one of its responsibilities disappeared.

Noted TODOs for future changes.

Change-Id: Ifd763e050944055c1d51a416fa0f9f3a7682ec5d
src/gromacs/applied-forces/tests/electricfield.cpp
src/gromacs/gmxpreprocess/grompp.cpp
src/gromacs/gmxpreprocess/readir.cpp
src/gromacs/gmxpreprocess/readir.h
src/gromacs/mdrunutility/mdmodules.cpp
src/gromacs/mdrunutility/mdmodules.h
src/gromacs/mdtypes/inputrec.h