Set DOI strings.
Updated regressiontest hash.

Change-Id: If7c04fbd26756275daea1c252ef977a367669b42

When a GPU is a exclusive or prohibited mode, early detection calls can
fail and as a result an mdrun run abort with an error, even if all GPU
offload is explicitly disabled by the user.
This change adds a status code to handle the case of devices being
unavailable.

Additionally, other errors may be encountered during the dummy kernel
sanity check (e.g. out of memory), but since the change that switches
to using launchGpuKernel() wrapper did not handle the exception in the
sanity checking, this can also abort a run even if the GPU in question
is not selected to be used.
This change adds code to catch the exception this and report the error
and avoid abort the run.

Fixes #3178 #3399

Change-Id: I0cdedbc02769084c172e4a42fe5c1af192007cec

This at least temporarily fixes #3400.

Change-Id: I04d67d9bb3edbd66049573de71940e4bb7fa1ad4

The gmx disre program used the labels in the distance restraint entries
(see manual) as an index in internal arrays. This might lead to either
memory errors or the program stopping due to uninitialized variables.

Fixes #3384

Change-Id: Ic2d77c3fd81547e030bf7ce21860a71e3adbb2b3

Fixes #3375

Change-Id: I0f64b386477b9a72f18c95fd977ac8cf5dbeeccd

PME would incorrectly ignore the mesh forces on perturbed atoms when
no charges or LJ atom types were actually perturbed.
This is because the "fix" in commit 12f01f79 incorrectly changed the
lambda value used for the PME forces from the actual lambda value
to 1 instead of to 0 as it should have been.

Fixes #2640
Fixes #3359

Change-Id: Ib19565bf017ddbd2fddc66c52be0ff9efc7e707c

Change-Id: I34f4215f2112579b1a92c87aca28b270b4aca09e

Reset doi strings

Change-Id: I38fa39c52cde5d967525770ec2a6381b7fcee33a

Added doi strings
Updated regressiontest hash.

Change-Id: If6c34638caf40f562fd8a744af767be4941ff73b

This reverts commit 1ebc7b0b.

Reason for revert: The parallel running of tests doesn't work the way we want here and the effort for fixing things in a soon to be critical fixes only branch is not worth it in my opinion

Change-Id: I59fb6f9daf7019592de7e8db202ccd050c133610

It could happen that the calculation of the standard deviation
for angles caused a divide by zero error for empty populations.
Because this standard deviation of per frame averages over all
frames was anyhow meaningless, it has been removed.

Refs #3206

Change-Id: Icf541a8b3bef502da9a22b55a8e8154b2d4fc8f8

Fix originally proposed by Boris Timofeev.

Refs #3225

Change-Id: Ie742f2c751473d17fc8f69e9ed79faacdd6fc56c

Added the flag that triggers ctest to use the flags that will produce
multiple ranks in both thread-MPI and real MPI cases.

Change-Id: I4ef3af4fd1750ab7cc231a29191fc4042385c309

WIth 1 PP + 1 PME rank the GpuBonded constructor gets passed the
non-local nonbonded stream which is nullptr and as a result the bonded
kernel launch happens in the default stream blocking concurrent
kernel execution.
This change makes sure that only when there is PP domain decomposition
is the GpuBonded constructor passed the nonlocal stream.

Fixes #3241

Change-Id: I858401b78c620adc3bea176e40e6fa179e583483

Fix originally contributed by Boris Timofeev.

Fixes #3225

Change-Id: I4862679e4aeae514736df53f0eff44bf3b85f928

Also add assertion in the code to prevent errors from linking
against the wrong library while running.

Fixes #3200

Change-Id: Ib2f2861702e111f67c38b0c9d65ccbe4c81a0ccd

Fixes #2722

Change-Id: Ic697f596285acdb5c7728b7ebc995ea44c82f3ac

Users were confused by the "a.u." label in the RMSD distance
distribution output. This patch changes the label to "counts"
to better state that this is the number of events captured in the
histogram column.

Change-Id: I6c082147ae9f1647ec743275af6b72564401de8d

When not using the initial stage in AWH, we should not check
for coverage and histogram anomalies at step 0.

Fixes #3217

Change-Id: Iee19c4740c02ce56c0b43ad89efb6e37f4ad1a0d

Removed fatal error with AWH with periodic pull-geometry 'direction'
when the distance was within 2% of half the box size.
Changed an assertion failure when the AWH interval was larger than
the box size to a fatal error.
Clarified the documentation for pull geometry 'direction-periodic'.

Refs #2946

Change-Id: I447a9a490a5883139afc268fd367b8b249591fbc

When adding connect records in pdb files, it was not checked if records
already existed and were thus duplicated in output. This patch fixes
this behavior.

Fix originally provided by Boris Timofeev.

refs #3206

Change-Id: I5850f4b6279b37df07282acc4416f433099d90c8

The links for atoms with intermolecular interactions would use
incorrect atom indices. This meant that mdrun could exit with
a missing interactions errors when using domain decompostion
with intermolecular interactions at distance larger than the cutoff.

Fixes #3204

Change-Id: I0c78810204f116f028b18c83bc6b51859ed7245a

Contrary to the format specification in the manual, the box components
in the .gro file were not separated by whitespace when components
(except for the first one) were >= 1000 or <= -100. Now a space is
always printed. This might not match the original GROMOS format,
but most codes reading .gro file assume space separation.
Note formatting of boxes that did have spacing is not changed.

Fixes #3176

Change-Id: I8cfcde98b46550b16b9f6bc299dc0b67454b2437

The Xcode compiler in Mac OS Catalina checks and enforces
stack alignment by default, but embarrasingly enough the
C library provided by Apple fails to adhere to the
aligned stack for AVX despite bug reports being filed during
their beta cycle. We work around this sloppiness by removing
the check, since AVX does not require the alignment.

Fixes #3199.

Change-Id: I9c16b156cc5b3a5d9fc542335cbf63a6caf6fb1b

With free-energy calculations not using lambda states, an output
buffer would be accessed one element beyond it's allocated size.

Note that this code should be completely refactored, but not
in a release branch.

Fixes #3173

Change-Id: I677e602ba96c9f64fbf79a626e43c9e590c18bea

This is needed because of larger differences when running
this test on multiple ranks.

Change-Id: I3056ae5933800e30e274791e8d27e2b8e79f6e04

Change-Id: I77e014ec2005e5289a0bd13ec608c73641928b54

The GPU atom data init timer was read conditionally on the timing
of the local pairlist transfer. But the local pairlist transfer
is not timed with an empty list, leading to an inconsistent timer
state.

Change-Id: Ifc2a63c7273ae65ae66708c6a8b0fb526041ee38

Missing zero initialization of never computed LJ PME energy and virial
terms with PME on the GPU could lead to random energy, virial and
pressure numbers.

The effect of this bug was that the potential and total energy could
be off (not the Coulomb mesh energy). This didn't affect sampling.
The pressure could be off, which would affect sampling when pressure
coupling is used, but likely the simulation would explode after
a few steps.

Fixes #3120

Change-Id: I309dde958f1b73e7f71f87f4f5ad016d16f8d16b

The doxygen manual seems to have been relocated from
http://www.stack.nl/~dimitri/doxygen/manual/index.html
to http://www.doxygen.nl/manual/

Change-Id: I321072065576c52a104a119abb5e05dc90eece3a

Reset DOI strings

Change-Id: I259bcc910b6676a9443090197f9209a399061a4b

Set DOI strings.
Updated regressiontest hash

Change-Id: Ic63b9942083b122a3d5ce509da51a29a65aa89a6

The tool was still using the oldest possible way to read in structure
files, leading to issues with the chain IDs being overwritten and
replaced with the default id.

Fixes #3070
Refs #3113

Change-Id: I25112103a043d0266fe64c7619fe8e4abc56ffa5

When the last step did not coincide with an energy calculation step,
the kinetic energy and temperature written to the energy and log
file were incorrect when using the leap frog integrator.

Fixes #2950

Change-Id: I9a0bc2280235f233a37cd3b2cd03d9d5067bd4f9

A previous fix for converting the force constant in gmx wham
for angle and dihedral geometry applied an incorrect conversion
factor.

Fixes #2609 and #3094

Change-Id: I0aa9b848c7fa62306ccf15b327a650b1ad88e03f

The bug was found with editconf, but the issue was present in writing
of any gro file for which index groups were used (not just index
groups supplied by the user).

Fixes #3107

Change-Id: I3fc586c69066a354b3210d9616125ef666f1ce26

Changed the Zen flag in gmx_hw_info_t to a Zen1 flag, so Zen 2,
and newer, is treated as a generic x86 AVX2 architecture.

Change-Id: I5a0fd73973416bbd8cd46422a6f22f1ad95d9924

MPI_C_COMPILE_FLAGS is a list instead of a string
see: https://gitlab.kitware.com/cmake/cmake/issues/18349
We mainly want to workaround this issue as RHEL 8 triggers it:
https://bugzilla.redhat.com/show_bug.cgi?id=1749463

This issue is fixed in cmake-3.12.3

Change-Id: I14c1c0a4f33f26b128d55baa1b0455f8a463a999

The shift force indices were inverted for the second and third
atom in the CMAP term, leading to incorrect virial and pressure
contributions when these atoms resided in different periodic images.

Fixes #2845 and #2867

Change-Id: I1946a1d375d6c62e4e6d23ee25b92b42a3d4a6f7

With recent versions of cmake on Mac, the CPU detection
program failed to compile since it was very fragile (buggy)
with respect to how compiler flags were defined - and that
in turn will mean losing all SIMD support.
This will fix the build, and it also adds a more vocal warning
if the CPU detection code cannot be compiled at all.

Change-Id: Idcdc8b59a4252b3faf8572311d2ca63a4d2a1bc0