This could solve a problem arising when a specific c++ library is passed
in CXXFLAGS.

LDFLAGS were overwritten by mistake by CFLAGS when doing coverage

* Added Cosinus SwitchingFunction

* fixed astyle

* regtest cosinus switching function

* 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

* Better timing part2

* Fixed problems in Makefiles for regtests

* Fixed details from a resolved conflict

* Added Makefile for regtests

* Deleted tmp directories in regtests

* Revert "Deleted tmp directories in regtests"

This reverts commit 1fd981329f510c4a6384586a2e4a8eea9dc63353.

* Revert "Added Makefile for regtests"

This reverts commit 552cb527d4bfbca5e061a158ee7a9863c5cecd33.

* Reverted commit and Makefile added

* using the "serial" path for distance tests. This fixes the MPI errors in
regtests

* Fixed problems in regtests with debug flags for compiler

* PIV.cpp astyled