Merge release-5-0 into master
authorRoland Schulz <roland@utk.edu>
Sat, 28 Jun 2014 05:12:35 +0000 (01:12 -0400)
committerRoland Schulz <roland@utk.edu>
Sat, 28 Jun 2014 06:06:41 +0000 (02:06 -0400)
commit899ac8c074216c14a5047987219278b2d038d3d7
tree67a2900f59802248d2fc0b0dd0b1490495eaf683
parenta7251dfa1d0e1c4ebd321c2ac0a806b96d5bec24
parent73006fec155234f1fb74460233eff330acec509c
Merge release-5-0 into master

Conflicts:
src/contrib/pmetest.c
src/gromacs/gmxpreprocess/pdb2top.cpp
src/programs/mdrun/repl_ex.cpp

Fixed minor issues in:
src/gromacs/gmxana/gmx_principal.c
src/gromacs/gmxlib/checkpoint.cpp
src/gromacs/gmxlib/nonbonded/nb_free_energy.c
src/gromacs/mdlib/shellfc.c

Change-Id: Idbd2ef28223f8a868ca313f9702c8e6890e6ddc1
69 files changed:
CMakeLists.txt
cmake/gmxCFlags.cmake
manual/monster.bib
src/gromacs/CMakeLists.txt
src/gromacs/fileio/libxdrf.c
src/gromacs/fileio/pdbio.c
src/gromacs/fileio/pdbio.h
src/gromacs/fileio/tngio.cpp
src/gromacs/fileio/tpxio.c
src/gromacs/fileio/trx.h
src/gromacs/fileio/trxio.c
src/gromacs/gmxana/anadih.c
src/gromacs/gmxana/gmx_anaeig.c
src/gromacs/gmxana/gmx_analyze.c
src/gromacs/gmxana/gmx_angle.c
src/gromacs/gmxana/gmx_chi.c
src/gromacs/gmxana/gmx_cluster.c
src/gromacs/gmxana/gmx_density.c
src/gromacs/gmxana/gmx_dos.c
src/gromacs/gmxana/gmx_editconf.c
src/gromacs/gmxana/gmx_enemat.c
src/gromacs/gmxana/gmx_energy.c
src/gromacs/gmxana/gmx_genpr.c
src/gromacs/gmxana/gmx_mdmat.c
src/gromacs/gmxana/gmx_mindist.c
src/gromacs/gmxana/gmx_polystat.c
src/gromacs/gmxana/gmx_principal.c
src/gromacs/gmxana/gmx_rama.c
src/gromacs/gmxana/gmx_rms.c
src/gromacs/gmxana/gmx_tcaf.c
src/gromacs/gmxana/gmx_traj.c
src/gromacs/gmxana/gmx_trjconv.c
src/gromacs/gmxana/gmx_vanhove.c
src/gromacs/gmxana/gmx_wham.cpp
src/gromacs/gmxlib/bondfree.c
src/gromacs/gmxlib/checkpoint.cpp
src/gromacs/gmxlib/nonbonded/nb_free_energy.c
src/gromacs/gmxlib/nonbonded/nb_generic.c
src/gromacs/gmxlib/nonbonded/nonbonded.c
src/gromacs/gmxlib/txtdump.c
src/gromacs/gmxpreprocess/addconf.c
src/gromacs/gmxpreprocess/grompp.c
src/gromacs/gmxpreprocess/hackblock.c
src/gromacs/gmxpreprocess/pdb2gmx.c
src/gromacs/gmxpreprocess/pdb2top.cpp
src/gromacs/gmxpreprocess/readir.c
src/gromacs/gmxpreprocess/readpull.c
src/gromacs/gmxpreprocess/topio.c
src/gromacs/gmxpreprocess/toppush.c
src/gromacs/gmxpreprocess/xlate.c
src/gromacs/legacyheaders/nonbonded.h
src/gromacs/legacyheaders/shellfc.h
src/gromacs/legacyheaders/types/inputrec.h
src/gromacs/mdlib/constr.c
src/gromacs/mdlib/domdec.c
src/gromacs/mdlib/forcerec.c
src/gromacs/mdlib/ns.c
src/gromacs/mdlib/pme.c
src/gromacs/mdlib/shellfc.c
src/gromacs/mdlib/sim_util.c
src/gromacs/mdlib/tables.c
src/gromacs/mdlib/update.c
src/gromacs/mdlib/wall.c
src/gromacs/pulling/pull.c
src/gromacs/tools/compare.c
src/programs/mdrun/md.cpp
src/programs/mdrun/mdrun.cpp
src/programs/mdrun/repl_ex.cpp
src/programs/mdrun/runner.cpp