Matrix: removed warnings

and openMP

(this function should be rewritten from scratch)

[makedoc]

[makedoc]

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.

This regtest was located in the wrong directory

This regtest is failing on travis from time to time, in an
irreproducible way. I took note of the problem at issue #183

I temporarily change this regtest by:
1. moving COLVAR.reference to COLVAR.reference.dontcheck
2. adding HILLS.reference so that at least one file is checked.

Notice that this is not a solution of the problem, just a way
to avoid random failures on travis.

As soon as someone is willing to fix this, just put COLVAR.reference
back in place and push it to travis

[makedoc]

[makedoc]

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.

(actually, this was to test citations but the log file
is not checked)

Allows to feed plumed with a single input line directly
from the MD code.