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

Implemented syntax to allow simpler syntax with multiple replicas
using an almost identical input file.

Closes #221

[makedoc]

now METAD and PBMETAD can write grid files upon checkpointing
related to #37 and #125

this is usually not important, but for the case (like with
metainference) in which you have a bias that is applied on
a large number of arguments, then it was getting very slow

this is usually not important, but for the case (like with
metainference) in which you have a bias that is applied on
a large number of arguments, then it was getting very slow

of a usefull error message

This change makes it possible to calculate the average x component
of a the vector defining the orientation of a molecule by using something like
MOLECULES MOL1=1,2 MOL2=3,4 MEAN={COMPONENT=2}

Only add to the manual RESTART UPDATE_FROM and UPDATE_UNTIL
in the actions for which this makes sense

Allow individual action to set restart, using RESTART=YES or
RESTART=NO. By default, RESTART=AUTO, that means that global
restart settings are used.

Notice that this required to change the way OFile knows about
restart. Indeed, if the file is linked to an action,
it should use Action::getRestart instead of PlumedMain::getRestart.

I found out how to remove UPDATE_UNTIL/FROM from the manual of setup
actions without breaking the code.

At least one of the two extremes should be inclusive. I decided to have
UPDATE_FROM inclusive (and let UPDATE_UNTIL exclusive)

When specified, the update() method is only invoked
within this time range. This allows to perform some tasks
in a single simulation, e.g.:
Equilibration + Metadynamics + umbrella sampling refinement
with analysis of the last part only.

Currently this is an optional flag for all the actions.
I am not sure this is a good idea (currently update() method
is only used in some ActionPilot), since this will make
the keyword appear in every manual page.
However, since the update method is in principle available on all
the actions I preferred to add these keywords everywhere.

Fixes #65

This makes it such the order in which dependencies are activated
is deterministic. It is related to a bug (#51) which was already fixed
by changing the way prepare() works in multicolvar. Anyway, I commit
this change because I think it is clearer if, in a multiple proc simulation,
all the procs prepare all the actions in the very same order.

MultiColvarFunction allows you to calculate thing like the average coordination
number for the atoms an sphere centred on a particular atom.  If crystallization
is installed you can also use it to calculate things like the local q4 parameter.

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

This allows citing without explicitly including PlumedMain

Now the code crashes in the following cases:
1. An exchange is attempted on a step where neighbor list for COORDINATION
(or DHENERGY) are not updated
2. An exchange is attempted and neighbor list for PATHMSD or PROPERTYMAP are enabled.

The second should be fixed better to allow using strides for lists which are
divisor of the stride between steps. The better thing will likely come later, at least
the code is safe now.

Gromacs patch has been fixed (this is compulsory for big Endian machine)

If you want to but a plumed_assert in a loop you should now use
plumed_dbg_assert / plumed_dbg_massert.  This will not be included
in the code if you compile with -DNDEBUG

I used cppcheck --enable=all.

Detected by cppcheck

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