Refactor gmx_group_t to SimulationAtomGroups
commitc8d88b1e4363ebabb52ed92fcd535d59f34c7d9c
authorPaul Bauer <paul.bauer.q@gmail.com>
Thu, 14 Mar 2019 11:21:55 +0000 (14 12:21 +0100)
committerMark Abraham <mark.j.abraham@gmail.com>
Tue, 2 Apr 2019 13:19:07 +0000 (2 15:19 +0200)
treef2dc83175ff81bc50336fc510f09800dbfa6cca7
parent2404693ffd11a3208a82433dd5b7dedc25b4bda6
Refactor gmx_group_t to SimulationAtomGroups

Change allocation on type to std::container, but did not touch to
underlying t_grps datastructure yet.

Change-Id: I3858e650a31764b3ab83090eaa0653fc579a8af1
45 files changed:
src/gromacs/fileio/enxio.cpp
src/gromacs/fileio/enxio.h
src/gromacs/fileio/tngio.cpp
src/gromacs/fileio/tpxio.cpp
src/gromacs/gmxpreprocess/grompp.cpp
src/gromacs/gmxpreprocess/readir.cpp
src/gromacs/gmxpreprocess/readir.h
src/gromacs/gmxpreprocess/topio.cpp
src/gromacs/listed_forces/orires.cpp
src/gromacs/mdlib/broadcaststructs.cpp
src/gromacs/mdlib/compute_io.cpp
src/gromacs/mdlib/compute_io.h
src/gromacs/mdlib/energyoutput.cpp
src/gromacs/mdlib/energyoutput.h
src/gromacs/mdlib/force.cpp
src/gromacs/mdlib/force.h
src/gromacs/mdlib/forcerec.cpp
src/gromacs/mdlib/mdatoms.cpp
src/gromacs/mdlib/mdoutf.cpp
src/gromacs/mdlib/membed.cpp
src/gromacs/mdlib/ns.cpp
src/gromacs/mdlib/ns.h
src/gromacs/mdlib/qmmm.cpp
src/gromacs/mdlib/shellfc.cpp
src/gromacs/mdlib/shellfc.h
src/gromacs/mdlib/sim_util.cpp
src/gromacs/mdlib/tgroup.cpp
src/gromacs/mdlib/update.cpp
src/gromacs/mdlib/vcm.cpp
src/gromacs/mdlib/vcm.h
src/gromacs/mdlib/wall.cpp
src/gromacs/mdlib/wall.h
src/gromacs/mdrun/md.cpp
src/gromacs/mdrun/mimic.cpp
src/gromacs/mdrun/minimize.cpp
src/gromacs/mdrun/rerun.cpp
src/gromacs/mdrun/runner.cpp
src/gromacs/mdrun/tpi.cpp
src/gromacs/mimic/utilities.cpp
src/gromacs/pulling/pull.cpp
src/gromacs/tools/dump.cpp
src/gromacs/topology/topology.cpp
src/gromacs/topology/topology.h
src/gromacs/utility/CMakeLists.txt
src/gromacs/utility/enumerationhelpers.h