This commit contains changes automatically generated by plumedbot on Travis-ci.

Added possibility to specify kt in driver

* speed up of sharing and applying in plumed core
the main differences are:
- new member of class atoms to track unique local atoms (i.e. all the atoms needed by plumed action in a domain)
- positions are retrieved only for unique local atoms
- forces are zeroed only for unique local aotms
- forces are applied only for unique local atoms
in a system of 200K atoms on 4 mpi rank with plumed using only 4 atoms the
sharing and applyign time improves by 2 order of magnitudes

* removed leftover printf

* core: make it a bit faster also without domain decomposition

* astyle

* fix-241: unique atoms are update only if:
- particle decomposition has been updated
- domain decomposition has been updated
- replica-exchange step
- neighbour lists have been updated
overall this should make the sharing code even faster

* actionAtomistic have now a list of local atoms that is updated on:
- neighbour list step
- update of the pd/dd list
this allow to simplify the loop for the generation of global local list of unique atoms

* atoms: small tweaks

* fix: reallocate memory less often

* fix: for the scalar case there is no need to generate the list of unique atoms

* style

* few comments

There was a bug in driver with --debug-pd when, unluckily, the
last domain had by chance zero atoms

(cherry picked from commit d669afb2)

There was a bug in driver with --debug-pd when, unluckily, the
last domain had by chance zero atoms

added a two regtests
close #243

[makedoc]

Allow passing a single trajectory to driver --multi.
The same logic is implemented as in IFile tool, that is:
- look for file.##.ext
- if it does not exist, look for file.ext

Here ## is the replica index and .ext the extension of the file

Fixed #228

This is a huge commit, applying indentation to the whole
code. Notice that this commit is made on master branch
after having merged with -s ours from branch v2.3

See #215

This is a huge commit, applying indentation to the whole
code.

See #215

addresses #213

[makedoc]

Fix #209

driver-float was not documented

Added option in driver to evaluate forces due to a bias numerically so that they can be compared with the analytical forces evaluated by plumed

When using driver with --trajectory-stride 0
the number of the step is read from the xtc/trr file.

Notice that this only works when reading with xdr library
(--ixtc or --itrr) and not with the molfile plugins

I added the possibility to personalize charge and mass units
in the same way as length, energy, and time units were treated so far.

Notice that since two new cmd() strings have been added to set
units from an MD code, it is necessary to increase the API version
to 4.

I also added the appropriate developer documentation.

Fixes #179

This change makes the driver less error prone

It requires a lot of regtests to be fixed,
mostly adding an mc file when required or replacing
COM with CENTER

This makes these options consistent with others.

THIS REQUIRES ./configure AGAIN!!