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

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.

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

Notice that this change required a bit of hacking.
setAveragingAction now takes a std::unique_ptr as an argument.

I think ownership is clearer now since it is explicitly declared.

I went through cppcheck warnings (style) and fixes those I understood.
Mostly issues related to scope of variables.

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

Regenerated after c40b96fe

This bug was pointed out by Jutta Rogal.  Also added regtest so
that bug stays fixed in future

After \par Examples there should be an empty line

[makedoc]

This fixes a problem in the way atoms are setup for calculations where you take an input
from a multicolvar filter as input to a new multicolvar if SPECIESA and SPECIESB are used.
For instance you might be calculating Q6 for those atoms that have a coordination number
greater than 4