Fixed g_rmsdist NOE calculation

This fix solve a series of bugs in NOE calculations:
1) incorrect number of frames in the calculation of the average distance
2) wrong selection of equivalent atoms
3) -equiv was wrongly documented

Change-Id: Icc6bbed0e1ba65774ad470c3edbd7a6a96e63ee6
Fixed bug inverting compression precision.

In the TNG library the compression precision was modified to
suit GROMACS compression precision better (i.e. indicating
the multiplier applied to the compressed value). There was no
change in GROMACS to reflect this, meaning that compressed TNG
would have 0 coordinates for almost all atoms. That is fixed
in this commit.

Change-Id: Id906c710deb68d172a38acec34892aa4823c039d
Issue warnings for potential switch w/o defining switch regions.

If either older style switches or new potential-switch modifiers are
used, issue a warning if the PME regions is too long, resulting in
inaccurate energies. Also issue a warning if rvdw_switch is 0, which
occurs if no value is specified.

Discussion is in redmine #1463

Change-Id: I7a2c29f87ceb04712aab5076ac97f5f22f573671
Fix memory error in asc format IO

Found with cppcheck 1.64

Change-Id: I72e80cd2b11559be47d449d0a8d444857843979b
Fixed nbnxn FE list allocation issue

With free-energy calculations, the nbnxn search code could write
beyond the list bound, which could cause a segv.
Fixes #1474

Change-Id: I4c202fc14b04980f05ad1b3ea001732fdfaa9f00
More efficient TNG selection group creation

Do not create a TNG selection group if no selection is specified
explicitly, or if the selection contains all atoms in the system.

Change-Id: Ibe2a14e55aff829fdb74de074447f00f0e85f090
Made ORCA compile.

There are probably larger issues here with the QM/MM interface.
I made no effort to test the validity of any simulation done with
ORCA (since I don't have ORCA and I don't do QM/MM), so issues
definitely remain.

Change-Id: Ibd5dd83d05a3b42c641f0fc9def75c4641e3a7d4
Removed truncation of nrdf in v-rescale thermostat

The resampling function for the v-rescale thermostat expected an
integer value for nrdf, but a real was passed, which was truncated.
With a single coupling coupling group nrdf is analytically an int,
but could be off by a bit. The could lead to incorrect kinetic
energy fluctuations (averages were correct).
Now fractional nrdf's are properly handled for nrdf > 3.
For nrdf < 3 a check is added for integer values with a small margin
for rounding.
Fixes #1218

Change-Id: I4c60c337f9874d0bff51220ad09429140be2a056
Merge branch release-4-6 into release-5-0

Conflicts:
	src/gromacs/mdlib/coupling.c

Resolved in favour of release-4-6, except that the underlying
RNG calls are now made to the new cycle-based RNG.

Run uncrustify

Change-Id: I56286e19632ac28958a0d4ef60ff09b875aa3005
Fix usage of gmx_eof

gmx_eof has different behavior from gmx_eof and feof
should be used here.

Change-Id: I877c15d0edde64fe06ae2eedbda980f117509449
Fix incorrect limits in FloatOptionStorage

This typo didn't cause any problems in Gromacs, since currently, no code
path enters here.  But if user code would use FloatOption or RealOption,
it would trigger.  Found while taking this code into actual use in
master.

Change-Id: I712faf365359964f6f767991664da7981072e5bd
cmake: enable shared libraries by default on Hurd

Since the toolchain is mostly the same as used on e.g. GNU/Linux
(glibc, gcc, binutils, etc), they can be safely enabled.

Change-Id: Ic663c8c344b5dfa2910e9c30260588e1917038c1
Fix OpenMP unproteced update bug

Change-Id: Id881b3e2726fa9c9be7a37f7e909bb7b268e44a7
Fix OpenMP scope error

Change-Id: I5cea5df876a48e5868b5160170e8450e697f3b4b
Merge "Merge branch release-4-6 into release-5-0" into release-5-0
Fix comparison of array to NULL

Static char array is never NULL. Detected by clang 3.5. Also fixes
output of read_atype and print error for incorrect format.

Change-Id: I834fca2d8fdd49167a88dc15bc7a2e72f4d97269
Minor tweaks to the DD setup

Dynamic load balancing is now turned on when the total performance
loss is more than 2% (lower than that will not help).
The check for large prime factors should be done on the PP node
count when -npme is set by the user.

Change-Id: Ib81b56a7cb071540b143a4bfc98758788a8ac07d
Fix clang 3.5 warnings regarding *abs*

Fix abs() family functions type usage mismatch.

Change-Id: I85ed2931d681aa1ad024678b4209a524abc2cc61
Signed-off-by: Alexey Shvetsov <alexxy@omrb.pnpi.spb.ru>
Merge release-4-6 into release-5-0

Conflicts:
CMakeLists.txt (applied to cmake/gmxManageSharedLibraries.cmake)

Replaced gmx_llabs by llabs as mentioned in TODO.

Change-Id: I37e8cf5d6725cc9836e6dc29ca44e7ef915417c4
Merge release-5-0 into master

Change-Id: Ib309c33a5923d50757122b789df9430aaa1ee98d