changes to the energy only consider the kinetic energy, so make that explicit in the augmented `fix dt/reset` docs

Allow limiting of the maximum energy change of an atom in
fix dt/reset in addition to the existing distance limit.
Useful especially for high-energy irradiation.

this introduces an optional keyword, so backward compatibility is preserved.
this closes #884

provide keyword/value option to compute ackland/atom for selecting legacy or current variant of implementation

changes to integrate USER-BOCS into LAMMPS and to closer follow the LAMMPS programming/documentation style

Primarily a list of small fixes, combined with cosmetic changes and cleanups
in several files.

6d0c917 2018-04-29 Fix missing deallocation of output stream object (reported by HanatoK) [Giacomo Fiorin]
c92d369 2018-04-17 Do not test for atom group size [Jérôme Hénin]
431e52a 2018-04-06 Allow scripted/custom colvars to be periodic [Jérôme Hénin]
81d391f 2018-04-05 Split colvarcomp constructor into POD constructor + init() function [Giacomo Fiorin]
9b85d5f 2018-03-13 Fix issue with out-of-order atom selections; clarify format for ref positions [Giacomo Fiorin]
0e0ed37 2018-03-07 Support triclinic unit cells in VMD, clean up PBC functions [Giacomo Fiorin]
eed97c9 2018-02-24 Obtain integer version number from version string [Giacomo Fiorin]
c17f3cd 2018-02-23 Write trajectory labels only when needed [Giacomo Fiorin]