Optimize grids removing many push_back
RANDOM_EXCHANGES now appears in manual

Still we should write some doc. Also, there is not regtest for this...
Updated version number
Fixed missing include
moved include and changed to C++ (cmath instead of math.h)
Merge branch 'optimize-grid' into v2.0

After Max validation I feel I can merge on release branch
Tested and added doc

This closes #5
Merge branch 'fixing-random-exchanges' into v2.0
Fixed virial when biasing ENERGY

Virial was not scaled together with forces. The contribution is not
negligible, and I verified it is correct by testing with gromacs
a box of water in NPT and biasing the energy, then comparing the
-kt*log(histogram) biased and unbiased. It seems after this fix agreement
is much better
Fixed time units in quantum espresso

In PW, they use Ry units instead of Ha units, which leads
to a factor 2 in time. I realized it looking at the output of
espresso, where time is written also in ps. Now colvar and
output are consistent.
Fixed detection of MD codes

Currently the .diff file is compulsory, the .config is not. So, the list
of MD codes should be built looking at .diff files
Passing virial back to quantum espresso (fixes #3)

I had to change the place plugin_forces is called in espresso.
This is because in the original implementation plugin_forces
was called *before* stress calculation.
I did some qualitative test, but I am not able to run a proper
thermostated variable cell simulation with QE. Probably will
require some extra validation by QE guys.

I also updated qe version to 5.0.2
Updated gmx 4.6 patches

Old patches have been remove.
COMBINE documentation:

added the keyword PERIODIC=NO in the example
Fixes #22
Added possibility to give format for files output by HISTOGRAM
Merge branch 'v2.0' of github.com:plumed/plumed2 into v2.0
Same sequence of Gaussian numbers with different compilers

This fixes #23
Notice that it slows down (with icpc) generation of Gaussian numbers
by a factor 2.5. I think it is better now to have reproducible regtests.
Fixed simplemd to write output file

It was a longstanding (unknown) bug!
I added reference output files for all the simpledmd
regtest. This will allow to distinguish bugs in plumed
from Lyapunov effects in trajectories.
Fixed calculation of neighbors index with pbc

I think the way pbc were applied was not correct (Fix #19).