It looks like there were many incorrect simd statements. In particular:
- In all cases where a double was reduced, I added a reduction clause
- In all cases where a Vector was reduced, I just removed the pragma

This error lead to many failures in regtests when compiling with
intel -O3. It looks we have to make sure a compiler with simd support
is tested on travis-ci

Here I fix something I think might be wrong. In particular, if
safe==false && alEqDis
it looks like dist was initialized to the correct value but then not used.

From the current code coverage it looks this path was never tried.
Anyway, I am pretty sure the old code does not make sense.

With some compiler it is undefined. Notice that it is not in the c++
standard.

Builds are faster on travis. Notice that all developers
recompile the code without this option, so in order to check if the
dependency options are fine we really do not need travis-ci.

with 315e6746

This tests for 31adcd34

Strings like "x(abc)" where erroneously considered as equivalent to "(abc)"

Code results unchanged

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.