Introduce ArrayRefWithPadding
commit93109ddfa51819c07677cfc1789ecc4eb220cf4e
authorMark Abraham <mark.j.abraham@gmail.com>
Thu, 18 Oct 2018 08:33:16 +0000 (18 10:33 +0200)
committerMark Abraham <mark.j.abraham@gmail.com>
Thu, 25 Oct 2018 09:02:29 +0000 (25 11:02 +0200)
treebfd8e1aacfa165a34ded88168273502800a50c16
parentaaa9dd89c53b1a6afd728b2dfa1a29e7838dcb94
Introduce ArrayRefWithPadding

Modules need to access views of memory with and without padding. This
class can be constructed from a PaddedVector, and provides the
capacity to hide the underlying padded container (and allocator),
while being able to obtain ArrayRef with and without padding.

Also updated wording of docs for ArrayRef, and attribution

Fixed issue with shell code using the same pointer for trial and
minimum configuration.

Fixes #2642
Fixes #2705

Change-Id: I45197215342ae011298abc310b877c34f8fab88b
18 files changed:
src/gromacs/math/CMakeLists.txt
src/gromacs/math/arrayrefwithpadding.h [new file with mode: 0644]
src/gromacs/math/paddedvector.h
src/gromacs/math/tests/CMakeLists.txt
src/gromacs/math/tests/arrayrefwithpadding.cpp [new file with mode: 0644]
src/gromacs/math/tests/paddedvector.cpp
src/gromacs/mdlib/force.h
src/gromacs/mdlib/shellfc.cpp
src/gromacs/mdlib/shellfc.h
src/gromacs/mdlib/sim_util.cpp
src/gromacs/mdlib/update.cpp
src/gromacs/mdlib/update.h
src/gromacs/mdrun/md.cpp
src/gromacs/mdrun/mimic.cpp
src/gromacs/mdrun/minimize.cpp
src/gromacs/mdrun/rerun.cpp
src/gromacs/mdrun/tpi.cpp
src/gromacs/utility/arrayref.h