Api version incremented for consistency, even though there was
no change in between v2.3 and v2.4

Fixes #236

* 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

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

In case of error with LOAD, the code was returning an error without
raising an exception.

This is done only in the cmd interpreter

This should make the code slightly fast.

fixes #211

[makedoc]

These are the files generated automatically with the cmd
dictionaries. I renamed them to inc which is a more standard
extension for include files.

that is used to flush all the actions
[ makedoc ]

Now works also when plumed has been installed with a different name

added local masses

No EOL at the end of the file is only tolerated in input file
(e.g. plumed.dat) and not in other files (including HILLS files).

Indeed, when using multiple walkers, it is possible that transiently
the HILLS file from other walkers have incomplete lines.
With this fix, those lines are ignored and read at the next iteration.

This fixes #190

this is usually not important, but for the case (like with
metainference) in which you have a bias that is applied on
a large number of arguments, then it was getting very slow

Now multi words commands are parsed like single word ones.
This will make it easy to automatize documentation.

Related to #182

this is usually not important, but for the case (like with
metainference) in which you have a bias that is applied on
a large number of arguments, then it was getting very slow

Since the pointer should be not null, the new name makes more sense

Defining a capitalized enum was useless in the end. I now use
cmd_string
as the name of the enum, where string is the string for the
cmd interpreter

map is now a global static object

Enum list and word map are now generated with a script.

To add a new command it is sufficient to add a case command as:

case PIPPO: // cmd pippo

It is related to #182, though I let the issue open since I think
we should automatize also the cmd documentation.

Allow for splitting of performCalc() into
performCalcNoUpdate() and update()

This makes it possible to call performCalc() multiple times per step

Before this fix, using cmd() with an erroneous string was triggering
no error. Now this is fixed.

Notice that this is an old bug (introduced in 0a46f15d).
It should be harmless when using MD codes with proper interfaces,
but could be very dangerous if there is a typo in a cmd string.

Before this fix, using cmd() with an erroneous string was triggering
no error. Now this is fixed.

Notice that this is an old bug (introduced in 0a46f15d).
It should be harmless when using MD codes with proper interfaces.