Remove AdResS
authorMark Abraham <mark.j.abraham@gmail.com>
Tue, 10 Nov 2015 16:33:17 +0000 (17:33 +0100)
committerMark Abraham <mark.j.abraham@gmail.com>
Sun, 15 Nov 2015 19:18:09 +0000 (20:18 +0100)
commit85d918db94fde2ed1c9e84e8760c4e987e0f2a72
treef9bf1685fb46f3a7f802977c34459be830cd103f
parentf773382e93dcc3b78f268525bcb69d5420de2f33
Remove AdResS

This feature will disappear with the group scheme, so we might as well
get it out of the way first. Doing this removal on its own might help
re-implement some time, if someone was keen.

Removed bVir, bPress, bSurft fields of t_mdebin, because all MD
algorithms now support such calculations.

gmx grompp now issues a fatal error if the main adress .mdp option is
on, and otherwise ignores the obsolete fields (like we do with other
.mdp options we've removed).

mdrun can read old .tpr files, but issues a fatal error if AdResS was
active in them.

gmx dump and gmx compare ignore all AdResS related fields.

Other tools can still read such .tpr files for their other content.

Removed Sebastian Fritsch from GROMACS 2016 contributor list, since he
only worked on AdResS features. Christoph Junghans made other
contributions that are still useful, and so remains.

Removed obsolete literature references

Also fixed some incorrect doxygen of init_forcerec().

Part of #1852

Change-Id: I22fa0fe480148aeda0ace194646a5ec2f3d20a8c
41 files changed:
docs/manual/algorithms.tex
docs/manual/monster.bib
docs/manual/special.tex
docs/user-guide/cutoff-schemes.rst
docs/user-guide/mdp-options.rst
src/gromacs/fileio/copyrite.cpp
src/gromacs/fileio/tpxio.cpp
src/gromacs/fileio/txtdump.cpp
src/gromacs/gmxana/gmx_tune_pme.cpp
src/gromacs/gmxlib/names.cpp
src/gromacs/gmxlib/nonbonded/nb_generic_adress.cpp [deleted file]
src/gromacs/gmxlib/nonbonded/nb_generic_adress.h [deleted file]
src/gromacs/gmxlib/nonbonded/nb_kernel_adress_c/make_nb_kernel_adress_c.py [deleted file]
src/gromacs/gmxlib/nonbonded/nb_kernel_adress_c/nb_kernel_adress_template_c.pre [deleted file]
src/gromacs/gmxlib/nonbonded/nonbonded.cpp
src/gromacs/gmxlib/nrnb.cpp
src/gromacs/gmxpreprocess/grompp.cpp
src/gromacs/gmxpreprocess/readadress.cpp [deleted file]
src/gromacs/gmxpreprocess/readir.cpp
src/gromacs/gmxpreprocess/readir.h
src/gromacs/legacyheaders/names.h
src/gromacs/legacyheaders/types/enums.h
src/gromacs/legacyheaders/types/forcerec.h
src/gromacs/legacyheaders/types/mdatom.h
src/gromacs/legacyheaders/types/nrnb.h
src/gromacs/mdlib/adress.cpp [deleted file]
src/gromacs/mdlib/adress.h [deleted file]
src/gromacs/mdlib/broadcaststructs.cpp
src/gromacs/mdlib/forcerec.cpp
src/gromacs/mdlib/forcerec.h
src/gromacs/mdlib/mdatoms.cpp
src/gromacs/mdlib/mdebin.cpp
src/gromacs/mdlib/mdebin.h
src/gromacs/mdlib/ns.cpp
src/gromacs/mdlib/sim_util.cpp
src/gromacs/mdtypes/inputrec.h
src/gromacs/tables/forcetable.cpp
src/gromacs/tables/forcetable.h
src/gromacs/tools/compare.cpp
src/programs/mdrun/mdrun.cpp
src/programs/mdrun/runner.cpp