* 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

Not used yet, but we can use it to throw different exception types.

this makes the link visible also when browsing with a mobile

Not used now, but might be used in the future to better
translate exceptions.

When using the C++ interface, this change remaps exception within plumed
to a class that inherits from std::runtime_error.
This allows them to be catched also from an MD code linked to
a different C++ library.

I also removed some cpp options, I think it is better to enforce
exceptions to be managed in this way.

Returned argument should be last.

* flying Gaussian added

* Update MetaD.cpp

Making plumedcheck happy

* Update MetaD.cpp

Making plumedcheck happy again

* Update MetaD.cpp

Making plumedcheck finally happy

* regtest for flying Gaussian

* Update MetaD.cpp

Adding flying Gaussian with parallel tempering.

* Update MetaD.cpp

* Flying Gaussian with Parallel tempering

* Added PT to FG

* PT for FG

* PT for FG

* PT for FG

* pokus

* Making patch to know from plumed.dat

* Make patch know from plumed.dat

* Make patch know from plumed.dat

* Make patch to know from plumed.dat

* Update GREX.cpp

* Update GREX.cpp

* Update PlumedMain.h

* Update GREX.cpp

* Update GREX.cpp

* Update GREX.cpp

* Update repl_ex.cpp

* PTFG

* oprava

* blbost

* blbost2

* flying gaussian with parallel tempering

* PTFG

* just Flying Gaussian without PT

* just Flying Gaussian without PT 2

- expand some macros
- order methods

New Plumed.h file, with more features (see #385)

Closes #354

Should be more robust when combining different libraries.