It does not link to library anymore, but just includes Plumed.h file.
It thus could be compiled with different compilers and flags wrt plumed.

Notice that as of PLUMED 2.5 Plumed.h also contains the full implementation
of the dynamic loader, so it is sufficient to define the proper cpp
flags in order to recompile the loader and avoiding the need to link
plumedWrapper.a.

This basically allows the python wrapper to be selfcontained and installable
before having installed plumed.

Now we have explicit only used with C++11 and where it should be used.

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 changed Plumed::invalid() to Plumed::makeInvalid() and added a new function
Plumed::makeValid(). These names are more inline with stdlib names
(e.g. make_shared), though with our conventions for capitalization.

Hopefully there's no code yet using this (beta) interface.

In addition, I made it possible to use a macro to change the behavior
of the default constructor to makeInvalid(). This might be
useful in python wrappers to avoid opening the library twice
(python objects always use the "nullary" - default - constructor first).

I think python should use the C++ interface rather than the C one.
The reason is that the C++ interface included in PLUMED 2.5
rethrows exceptions and thus can be used to load
a shared library compiled with a different compiler or
linked against a different standard library.

In perspective, this will allow compiling PLUMED with
a different compiler/library than that used to compile
python itself.

now covered by the regtest better

It should prepend the libplumed.so library with prefix -Wl,
so as not to disturb NAMD makefile. (suggested by @jcphill)

Should have been removed with 1221e3e1

cc: @dvdesolve

See #407

As of PLUMED 2.4.1, an error is triggered when aligning using a pdb file
with zeros in the last column. I here fix the provided pdb file.

See this:
https://groups.google.com/d/msgid/plumed-users/4e2f69b8-1b2d-4bd3-a2e3-ecdfeef65d77%40googlegroups.com?utm_medium=email&utm_source=footer

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.