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

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

Notice that almost all files were updated with the astyle commit
2813d759

Year in header is here updated to 2017

This is a huge commit, applying indentation to the whole
code. Notice that this commit is made on master branch
after having merged with -s ours from branch v2.3

See #215

This is a huge commit, applying indentation to the whole
code.

See #215

In all STL implementations std::valarray are equivalent to
std::vector. No need to really use them.

All commits listed above, with the execption of the "while" stuff on pbc

commit 3708ff55d9987803182a7703874d2bbb1d1a3e3e
Merge: fc5ca30 9cab511f
Author: Michele Ceriotti <michele.ceriott@epfl.ch>
Date:   Fri Mar 13 16:45:04 2015 +0100

    Merge branch 'master' into fccubic

commit 9cab511f
Merge: c77549c7 76abc96b
Author: Michele Ceriotti <michele.ceriott@epfl.ch>
Date:   Fri Mar 13 16:43:29 2015 +0100

    Merge branch 'master' of github.com:plumed/plumed2

    Conflicts:
    	src/core/Atoms.cpp
    	src/core/Atoms.h

commit c77549c7
Author: Michele Ceriotti <michele.ceriott@epfl.ch>
Date:   Fri Mar 13 16:27:39 2015 +0100

    Gareth fix for LAMMPS

commit fc5ca30d2b0dd2bed2ead4866317503576e46cd6
Author: Michele Ceriotti <michele.ceriotti@gmail.com>
Date:   Sat Feb 7 18:19:58 2015 +0100

    S**t wrong sign of displacement vector!!

commit 02fa9e6439eb33ac98c26bc46b7950583b3abaa5
Merge: 96c1481 100b3efd
Author: Michele Ceriotti <michele.ceriotti@gmail.com>
Date:   Sat Feb 7 17:17:10 2015 +0100

    Merge branch 'master' into fccubic

    Conflicts:
    	src/crystallization/Fccubic.cpp

commit 96c1481f410516ca7c019033d3c880fc5a5dc9c3
Author: Michele Ceriotti <michele.ceriotti@gmail.com>
Date:   Sat Feb 7 16:44:15 2015 +0100

    Finished messing around with optimizations.

commit aa772a4dde348459a9b61d7d23fa22527541abf2
Merge: b371043 52ed4a59
Author: Michele Ceriotti <michele.ceriotti@gmail.com>
Date:   Sat Feb 7 15:02:30 2015 +0100

    Further speedups...

    Merge branch 'master' into fccubic

    Conflicts:
    	src/multicolvar/BridgedMultiColvarFunction.cpp
    	src/tools/SwitchingFunction.cpp

commit b37104386b57c4e9291c63ee21149352c18792f9
Author: Michele Ceriotti <michele.ceriotti@gmail.com>
Date:   Sat Feb 7 14:01:41 2015 +0100

    Tried to shave off some time from the PBC evaluation

commit cfc2f9491261154cddf7cc0fdde5807f7b01199d
Author: BingqingCheng <tonicbq@gmail.com>
Date:   Tue Jan 6 18:43:55 2015 +0100

    Ouch...

commit 43f7df5c9f5c237002c5a325765947753340a13b
Author: BingqingCheng <tonicbq@gmail.com>
Date:   Tue Jan 6 18:11:35 2015 +0100

    Another mistake

commit 4980c617a8bfd1cff0840d296517c6255d505d92
Author: BingqingCheng <tonicbq@gmail.com>
Date:   Tue Jan 6 17:54:44 2015 +0100

    Made a mistake in the derivative

commit 7eaa00302a4432c5a2ad5bc8bbde77495c48283b
Author: BingqingCheng <tonicbq@gmail.com>
Date:   Tue Jan 6 17:35:09 2015 +0100

    Add orientation specification in FCCUBIC

commit 441bc44a5d901f076170c53d69081ba072b6863a
Author: BingqingCheng <tonicbq@gmail.com>
Date:   Fri Dec 5 13:55:08 2014 +0100

    add alpha to modify the fcc harmonic function

commit 0de35e6edfa8e8306d602154eefb8c573a43c5b8
Author: BingqingCheng <tonicbq@gmail.com>
Date:   Tue Nov 25 16:59:26 2014 +0100

    Modified FCCubic

It requires macro PBC_WHILE to be defined

This reverts commit b46d0793.

This commit break several regtests. Most of the problems are harmless
numerical derivatives. However, the regtests on pbc hangs forever.
I have to further inspect this.

Taken from the fccubic branch of @ceriottm

The "while" implementation for orthorombic cells is slighlty faster,
so I decided to enable it by default.

The "while" implementation for Tools::pbc is either slower
or equivalent, so I did not include it.

I think the reason is that in the first case one can avoid a couple
of multiplications, whereas in the second this is more difficult
since images are implemented in scaled coordinates and require
anyway two matrix*vector multiplications.

I set it to 2 instead of 2.0, so that it will not be necessary
to update it

I took advantage of the fact that we have the reduced cell. This
allows to avoid the comparison of different shifts for
many values of the scaled coordinates, as well as using the
sign of the scaled coordinates to check which shifts should
be attempted. The average number of shift vector to be evaluated
is approximately 1 (plus the "null-shift")

There is also a Pbc::test() function which I used during debugging.
I leave it there for future reference.

I replaced all the "using namespace PLMD" statements with explicit
namespace PLMD{ …… }. This is more clear and simplify the syntax for
defining operators

All the source code have been moved into subdirectories of src/
Some of these subdirectories are treated in a special manner:
src/wrapper contains the wrappers for MD codes
src/main contains the main.cpp file
src/config contains files generated without compilation,
  just based on configuration info
src/lib is the place where executables and libraries are put
  at the end
src/cltools contains the command line tools
src/tools contains plumed tools (reusable classes)
src/basic contains PlumedMain, Action hierarchy and other basic stuff
src/multicolvar contains MultiColvar stuff
src/imd is the interactive MD (still not totally portable).

Notice that, to allow easy inclusion of .h files from other modules,
I link all the directories in src/ into module directory. In this
way it is possible e.g. to write #include "config/PlumedConfig.h"

See src/README and src/basic/Makefile to understand how inter-module
dependencies are set