Squashed all commits from PIV.

See #370

cc @silviopipolo

Logs are below. Commits affecting the core have been squashed separately.
In addition, I fixed namespace name (should be `piv`).

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PIV metric coupled with PathCV and added input example for doxygen.

Line CRYST1 of a PDB file is read and box vectors, axis and angles are
computed. Functions are added to get box parameters.

Added function getClosePairAtomNumber to get pairs in AtomNumber format
for piv construction.

Added function set_r0 to set the R_0 value from piv class once the
scaling factor has been defined.

piv module added

Added piv module regtests on distance and derivatives/virial

PIV.cpp Astyled

Files astyled using plumed astyle

solved Travis warnings on non-initialized member variables

Solved the R_0 issue without adding any new function in
SwitchingFunction.cpp, but by substituting its value in the string read as
in PIV.cpp.

Fixed format in reading box parmaters (CRYST1) in pdb.cpp

Changed the construction of the box vectors from length and angle
parameters in pdb.cpp

fixed update_piv

astyle PIV

pic