- Added macros to simplify addition of new functions
- Added all trigonometric functions that were present in libmatheval
- Added atan2

- Added many points to rt-lepton test
- Added nandelta() function
- Made definitions of delta(0) and step(0) equal to matheval

Works both with and without ASMJIT

Makes it easier to compare regtets on different machines.

fixed a few typos

Atomic units

Piv merge

cc @silviopipolo

See #370

cc @silviopipolo

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

----

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

cc: @silviopipolo

cc @silviopipolo

Lepton constants are now placed in lepton. They can be
accessed with a function lepton::Constants() so as to
avoid initialization problems.

cc: @valsson

cc: @gtribello

Some of the optimizations done in 5d0ff6aa
would break multithread calculations. In particular one should not use
non-const static variables. I made these fixes:

- for variables fd, C, and D, I use a std::array of fixed (exaggerated) size
- for other variables, unfortunately I just had to remove the static specifier

In case this slows down the code significantly, we should work out some alternate
solution. Maybe this would require changing the interfaces to some method so
that they accept e.g. a pointer rather than a vector. I have a tentative implementation
but did not have time to really test it so I prefer not to merge it.

Plumedbot pull request

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