improve setup of multiple tf tables

* buffer string was not initialized
* put tf table info in log instead of on the screen

Change-Id: I11ecdcd8c9a18a8931dbccef528ff02a74959ee1
use legacy CUDA non-bonded kernels only on Fermi

This solves a remainig todo as well as clarifies some variable naming
and documentation.

Change-Id: Ifad80cb7e740d1329a9c84df992d899400efeca2
Fixed the MPI recognition string in g_tune_pme

Since the identifying string "NNODES="is not printed any more by MPI-enabled
mdrun, we now use the "MPI library:" string instead.

Change-Id: Ibbcc0678a7c89057743129aa664fad8bb68f1941
Fix and add Verlet kernel error messages

Handles default cases better

Change-Id: I45d8ebd73184630180e6ed87d54c3a8fc3cbef73
More descriptive Verlet kernel macro parameter names

Also more consistent with SIMD kernel usage

Change-Id: Ia8dd723075b5c289d0171e3d34ecd51a0fc152f4
Fix code bug with thread-MPI on PowerPC with xlc

Change-Id: I8254ae915fdd24e02cf8f07789c69c3d4b35525e
Unwinds flag dependencies in g_order.

A feature added a while back to g_order had a flag dependency
(-calcdist forced -radial). This patch attempts to unwind that
dependency and allow -calcdist independent of -radial.

Fixed help message for -calcdist

Change-Id: I8c368f9109ee305d79a3c0c1b6838439598a4e89
Minor fixes to Verlet kernels

* clarified some comments
* documented use of nbfp_s4 better

Change-Id: I0848f2e570daef881368a45d4a429a3f80fde81b
Fixed an initialization issue in gmx_dipoles.

This fixes a warning in gcc 4.7

Change-Id: Ief8a057dff24c9a61c20301215a7009c2a16e74a
Use explicit kernel pointer typecasts

Some compilers don't like implicit casts from function pointers
to void*, so if we're going to be dirty, dirty people, we may
as well come clean about it.

Change-Id: Ia071c6a10a4ec20b83ddb13e4f0cd2a7b139264f
bugfix for md-vv + nose-hoover + (nstcalcenergy > nsttcouple)

Need global communication the step befre nsttcouple
in order to get the kinetic energy right, because
of the offsets velocity verlet from leapfrog.

Fixes redmine #1129

Change-Id: Ia6157db8304cc4fb8cccbda0ac3b949e800efeb5
Issue errors/warnings for ICC before 12.0.0

ICC 11.1 with SSE4.1 gives incorrect results, so CMake will
refuse to build with that minor version. Given that we
currently don't know anything specific and 11 is old, we
warn with any version older than 12.0.0. If more information
is available later, this warning can be made more specific.

Fixes #1126

Change-Id: I3c37844c69ce34769187f288c43cd8aef4086c53
Fix CMake namespace pollution

When gmxManageMPI finds MPI and CMake version is less than 2.8.10,
the variable file_cmd ends up in the non-advanced CMake namespace.
Made it advanced in those cases.

Change-Id: I79fd46e1b66d6c5ab008973e654092939eeae4dc
Made g_tune_pme work with 4.6 if user sets "-p" command line option

Added "-p" (performance statistics log file) to the list of files that
must not appear on the mdrun command line at launch time. (This would lead
mdrun to refuse to launch due to an unknown command line option.)

Change-Id: I268bbf6513709866b9a6a8d81c97706ccc832988
fixed GPU particle gridding performance issue

The scaling factor for the grid binning for the GPU pair search
was set incorrectly, which made the binning 50% slower.

Change-Id: I146592c37094a3d81a7ae50b3903fcc615e748d5
fixed issues with FEP soft-core and cut-off's

Now the cut-off is applied to the PME mesh correction for perturbed
pairs with soft-core. Now the cut-off is applied to VdW with soft-core.
Fixes possible NaN in free energy kernel with r close to 0.
Replaced a confusing grompp warning with PME and soft-core by a note.
Removed an invalid grompp warning about soft-core and twin-range.
Fixes #1146

Change-Id: I79a06b20158df2bce575808b6e31e660163bd307
Bump shared object version to 8

libs are not compatible with the ones from Gromacs 4.5.x, which had so
version 6 through 4.5.6, and now so version 7 for 4.5.7.

Fixes #1147

Change-Id: If96fd044b00a99eb4ba8376ffa0a2ecbea37894a
added mdrun check for Verlet+perturbed atoms

Currently the Verlet scheme does not support perturbed atoms.
This will be implemented soon.

Change-Id: Id8656aa680b6581882f5371514cdbd85f429c418
fix imcompatibility with tpr vers<64 with free energy option

should fix to redmine #1156

Change-Id: I6e60f1efbb03bf460009b8bc59f80f2e0e15bf44
Uncrustify template.cpp and selection.cpp.

template.cpp was missed in the original reformatting, and selection.cpp
got rebased past the uncrustify commit and got missed in reformatting
that I did for such changes.

Part of #845.

Change-Id: I9753e6add8aed894b10e829b63dc729f0d3d9b4b