Refactor virtual site interface
commit18f64ca4fe75f5a429215edbded173dbe9002d17
authorBerk Hess <hess@kth.se>
Tue, 12 May 2020 09:01:35 +0000 (12 09:01 +0000)
committerPaul Bauer <paul.bauer.q@gmail.com>
Tue, 12 May 2020 09:01:35 +0000 (12 09:01 +0000)
treea3e4204e29d1f919cf5d858f70ba0a104719fdfa
parent5cd8c68b2f0c8ff7ef421ed37029c72f43a525c8
Refactor virtual site interface

Replaced struct gmx_vsite_t by pimpled class VirtualSitesHandler.
Removed most arguments that stay the same from the construction
and spreading calls. Replaced rvec pointers by ArrayRefs.
This change is only refactoring and there are no functional changes
in the code using this, but the PBC and virial handling have been
simplified and the parameters reduced. Templating of the spreading
functions on virial handling should improve performance.
Added full doxygen documentation.
29 files changed:
src/gromacs/domdec/domdec.cpp
src/gromacs/domdec/domdec.h
src/gromacs/domdec/domdec_specatomcomm.cpp
src/gromacs/domdec/domdec_specatomcomm.h
src/gromacs/domdec/domdec_topology.cpp
src/gromacs/domdec/domdec_vsite.cpp
src/gromacs/domdec/mdsetup.cpp
src/gromacs/domdec/mdsetup.h
src/gromacs/domdec/partition.cpp
src/gromacs/domdec/partition.h
src/gromacs/gmxpreprocess/grompp.cpp
src/gromacs/mdlib/force.h
src/gromacs/mdlib/sim_util.cpp
src/gromacs/mdlib/vsite.cpp
src/gromacs/mdlib/vsite.h
src/gromacs/mdrun/isimulator.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/shellfc.cpp
src/gromacs/mdrun/shellfc.h
src/gromacs/modularsimulator/domdechelper.cpp
src/gromacs/modularsimulator/domdechelper.h
src/gromacs/modularsimulator/forceelement.cpp
src/gromacs/modularsimulator/forceelement.h
src/gromacs/modularsimulator/topologyholder.cpp
src/gromacs/modularsimulator/topologyholder.h