now an option to avoid clearDependecies.
This allows to have in a single class actionAtomistic and actionWithArguments
and actually use them together

this is used in Action build on MetainferenceBase where requestAtomst(atoms, false)

I think this is more robust. If an MD code uses a negative value with a
specific meaning (e.g. -1 to imply some choice) casting to unsigned
will translate -1 to 4294967295, which is positive

This fixes #446

Requires adding a cpp-suppress

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

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

Notice that I had to change to interface of a couple of functions
ActionSet:getLabelList() and getLabelVector()
adding a template parameter.
Should be harmless since these functions were used in a few places only.

make the error more informative

Now every exception thrown within PLUMED is remapped in the wrapper.

In particular:
- All standard C++ exceptions are remapped to equivalent ones.
- PLUMED exceptions and lepton exceptions are remapped to ad hoc classes.
- Any other exception derived from std::exception is mapped to std::exception.
- Any other exception is rethrown after printing a warning.

I added a plumed_cmd_nothrow function to the interface, that is used from
C++. This allows better support for mixed compilers (e.g. MD code and PLUMED
compiled with different compilers or linked against different std libraries).

Notice that I tried in the past to achieve the same using cmd("setErrorHandler"),
but this does not work correctly with some combination of compilers.
In addition, it implies throwing from a extern "C" function, which is not standard
and might lead to portability issues.

The plumed_cmd_nothrow implementation catches any exception raised within plumed,
converts it to an error code, and rethrows it within the MD code. This approach
should be more robust.

update GMX2018.3 accordingly
- including API check

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

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.

Using auto when creating a unique_ptr

Using c++11 to initialize the map instead of calling a function everytime

This is to avoid potential clashes.

all -> allatoms
physical -> mdatoms
virtual removed

See https://github.com/plumed/plumed2/pull/372

@ all (all atoms)
@ physical (all physical atoms)
@ virtual (all virtual atoms)

see #195

I removed many allocation/deallocation using arrays or even simple objects
when possible. I also added a custom destructor to properly free the regexp
in case of an exception.