Fixes #582

Clarify that the energy CV is actually the potential energy

Make sure that output files are written out at the final step. Should fix issues with restarting reported by @PabloPiaggi

cc: @gtribello

I think this has been here since the beginning, the effect is measurable

Solves a bug with METAD + TARGET + GRID_SPARSE
See also #467

I verified it, I will then modified a regtest so to keep checking for this

See #435

[makedoc]

(cherry picked from commit 781e5677)

Can be found with the following python snippet

import re
plumedDictionary={}
with open("/opt/local/lib/plumed/vim/syntax/plumed.vim") as fin:
    for line in fin:
        if re.match("^let b:plumedDictionary\[.*$",line):
            line=re.sub("^let b:","",line)
            exec(line,{'__builtins__': None},{'plumedDictionary':plumedDictionary})
for key in plumedDictionary.keys():
    diction={}
    for opt in plumedDictionary[key]:
        if(opt['word'] in diction):
            print(key,opt['word'])
        diction[opt['word']]=1

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

I tried to interpret and fix the code and for me it works nicely with 1 to 3 CVs.
Here a brief description: the index i spans through the whole reweghting-grid (according to the mpi rank in case of mpi).
rewf_grid_ contains the size on each dimension of the reweghting-grid. t_index is the array containing the coordinates of i in each dimension of the grid. The indexes had to be changed from i to j in line 1967, which indeed spans correctly the dimensions of the grid. In 1968 in order to get the correct index, we need to subtract the former index (ncv-2 -- instead of "ncv-1" which is yet not assigned -- from what is left of kk).

I didn't attempt any further test.

Please let me know if I had misinterpreted the code.

Fixes #399

cc: @valsson

cc: @carlocamilloni

Notice that I had to change to interface of a couple of functions
ActionSet:getLabelList() and getLabelVector()
adding a template parameter.
Should be harmless since these functions were used in a few places only.

and improved regtests

See #416