Bump version after 4.6.3 release

Change-Id: I1d99c36e090b25ae70d7476715e97b972ae2778c
more pkg-config fixes

* fixed a typo from I57897609b9bbc558db01c237d3e24d78aa25a5ca
* fixed name of libmd in libmd.pc

Change-Id: I6be35d8f1c0d53d4e4298967f0dc63de2205a663
Fixed minor admin issues

- The installguide.xhtml file is intermediate output, and
  should not be versioned
- There is no need for HTML files to have date stamps to maintain
- Bumped some version numbers

Change-Id: I2783501f697ee1eae557fdbf365a7aaf5d640500
Fixed typos in #include guard #defines

Change-Id: Ifb366f7b10de3a23952ef427bd0e2cb7e282ccea
Fixed possible dereference of null pointer

getpwuid() can return null. For example, Shun Sakuruba reported that
on Cray XE6 compute nodes have passwd.h, but users will not have
passwd entries.

Fixes #1301

Change-Id: I66e8064438fc02591629b0d381bc00afd06795c0
Fixed pdb2gmx -vsite hydrogen -o conf.pdb

Generation of v-sites did not initialise the elem field of the t_atom
structs. Later when writing the output to PDB format, that elem is
used for the final column. Somehow, the memory in elem was
uninitialized at that point, despite the use of srenew. Oh for proper
constructors and copies!

I observed the problem with v-sites generated from a POPC lipid, but
presumably the underlying cause is common to all kinds of v-sites, so
I have filled the elem field for two other kinds of v-site
generation. I have no idea why not all of the aromatic v-site
generation schemes involve filling a new t_atom struct.

Change-Id: I69efee07d8fd51192808a85d5704d488a0d310be
Removed buggy -seppot output

ns() no longer computes forces, so the comment needs correcting.

dvdlambda was changed to an array at some point, but the output code
did not change in sync. So, that output has been broken in at least
4.6, and is always zero anyway. So the output code can go away.

A patch in master branch removes the useless parameters in the
neighbour-search code. When merging this patch into master branch,
eliminate the useless dvdlambda variable.

Fixes #1294

Change-Id: Iba48f549ee07f0ee1877035a9e506780439c8002
implemented plain-C SIMD macros for reference

This is mainly code reorganization.
Adds reference plain-C, slow, arbitrary width SIMD for testing.
Adds FMA for gmx_calc_rsq_pr.
Adds generic SIMD acceleration (also AVX or double) for pme solve.
Moved SIMD vector operations to gmx_simd_vec.h
The math functions invsqrt, inv, pmecorrF and pmecorrV have been
copied from the x86 specific single/double files to generic files
using the SIMD macros from gmx_simd_macros.h.
Moved all architecture specific nbnxn_kernel_simd_utils code to
separate files for each SIMD architecture and replaced all macros
by inline functions.
The SIMD reference nbnxn 2xnn kernels now support 16-wide SIMD.
Adds FMA for in nbnxn kernels for calc_rsq and Coulomb forces.

Refs #1173

Change-Id: Ieda78cc3bcb499e8c17ef8ef539c49cbc2d6d74d
Fixes #1312 uninitialized error in g_enemat.

Change-Id: Ia0ac6d095dd560f08576aad1b435c92b6de52b3b
Update management of linear algebra libraries

Management of detection and/or linking to BLAS and LAPACK libraries is
re-organized. The code has migrated to its own module. This will
help future extension and maintenance. This version communicates
things that are newsworthy and stays out of the way when nothing
is changing.

We no longer over-write the values specified by the user for
GMX_EXTERNAL_(BLAS|LAPACK). Previously, this was used to signal
whether detection succeeded, but that does not really get the job
done. Instead, the user is notified that detection failed (repeatedly,
if they deliberately set such an option on).

Correct usage and expected behaviour in all cases is documented both
in the code and the install guide.

The user interface is pretty much unchanged. We still don't offer full
configurability (e.g. MKL for FFTs must use MKL for linear algebra
unless GMX_*_USER is used, and the only way to get MKL for linear
algebra is to use it for FFTs). The size of any performance difference
is probably very small, and if the user really needs mdrun with
certain FFT and tools with certain linear algebra library, they can do
two configurations. Note that mdrun never calls any linear algebra
routines (tested empirically)!

Expanded the solution of #771 by testing that the user supplied
libraries that actually work. If not, we emit a warning and try to use
them anyway.

We also now check that MKL really does provide linear algebra
routines, and fall back to the default treatment if it does not.

Refs #771,#1186

Change-Id: Ife5c59694e29a3ce73fc55975e26f6c083317d9b
Find mkl.h on more icc versions

Refs #1110

Change-Id: I0b6bc2497fc2a504b6c29b0697ee9e354fe6cffd
Updated dlist.c to recognize more atom names.

Previously, g_chi basically only worked correctly for OPLS-AA and
Gromos96 force fields, based on C-terminal atom names.  This commit
adds atom names for AMBER and CHARMM force fields so that g_chi
calculates dihedral properties for all residues.

Change-Id: I48517fb55bd46e7d49941f7902f4f6531e443e62
cmake: Improve some error messages

Lessons learned from the Q-bio summer school

Change-Id: I521a08ba3a83566582137740a0d097c0637d7d3e
Properly finalize MPI on mdrun -version. Fixes #1313

Change-Id: I1ae5f342da96980df322770d134555e2dc9fe712
Refactored preparation of buffer for NBNxN table loads

The outer and inner kernels try to be hardware-agnostic, but some
architectures need a thread-local buffer for transferring computed
table indices to integer registers via memory. It is better to set up
this buffer using a helper function that is implemented in
hardware-specific files, because the compiler can help prevent some
bugs. In particular, you can no longer forget to make a function
definition on non-SSE2. This eliminates one of the special-case kernel

Change-Id: I1ebdd15afaf03ff4559365867970b88e9ce0ed5e
Fixing problem caused by overflow in expanded ensemble.

Basic problem: logic was failing for single precision because of round off errors.
Solution: convert some of the intermediate arrays into double.

Fixes redmine #1314

Change-Id: Id7e3771d257bbeebeed2f340593b817015a0cd4c
Fixed reference SIMD code to work with MSVC

Also noted minor issue with rounding to even. Using rint would be
preferable, but that's even harder to work around on MSVC.

Change-Id: I495cf2d43cf0b33cc0896958f15703ba8632c7e4
Reordered FFTW fatal error; avoids using unset variables

Now variables that are set in FFTW detection are only used when the
variable that reports FFTW has been found is set (i.e. there has not
been a fatal error). Not sure why we haven't seen problems with this
so far, but we do see them on Power7 with cmake 2.8.8 when FFTWF is
not available.

Change-Id: I1a3e84002dda7f29f90eb532ab14ce51dfca6e5c
fixed parallel normal modes with PME

When doing a normal mode calculation with PME and (thread-)MPI,
the PME forces were incorrect. Also fixed some EM/NM output layout.
Fixes #1308

Change-Id: Ia7862fa62e235336c546824afdcbe28f37b145c5
Fixed GMX_DD_DUMP_GRID

The pdb format string no longer matched the parameters it was given

Change-Id: I682154a0986fdbd73ae414264982a68fed164c87