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

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

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

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.

update GMX2018.3 accordingly
- including API check

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

Actions are now shown in order also when they are more than 10.
Perhaps should be cleaned up a bit, but it works.

Changed so that start()/stop()/pause() return *this.
This allows things like
sw.start().stop()

Stopwatch can be initialized with the reference to a log. In this
case, it logs itself at destruction, provided the log is open.

Added Stopwatch::Handler class
It allows writing exception safe stopwatches which automatically
stop when an exception is caught.

Removed unnecessary start/stop in PlumedMain constructor.

Simplified interface: Use default arguments instead of multiple functions.

Moved __DATE__ and __TIME__ to config/Config.cpp

I added a try/catch block so that any error that arises within a
cmd() call is also reported on the log file (if open).

In principle, this should allow removing all the duplicate code where we
both write on the log and on the plumed_merror.

Notice that in order to satisfy astyle the whole content of PlumedMain::cmd()
has been indented so appears as changed in this commit. Actually, it is only
indented.

This commit closes #319

- added some info in the error message of the parser
- std::string everywhere

Using ...Args it is easy to forward any argument to the constructor.

This allows avoiding to explicitly put "new" statements when initializing
a ForwardDecl. In addition, all ForwardDecl that should be constructed
without arguments can be omitted from the initialization list, which
significantly simplifies the code.

Api version incremented for consistency, even though there was
no change in between v2.3 and v2.4

* Added first working python interface

* Tidied up python interface

* Further simplification of python

* Added example which should be deleted later

* Added functions for getting values from plumed to python

* Added regression test for python interface

* Added mechanism to return exceptions from plumed to python

* First commit of experimental stuff to catch exceptions in python correctly

* Got rid of unecessarily duplicated method in PlumedMain

* Fixed crazy MAC input encoding

* Oops, had also broken the script..

* Removed debug messages. Works on Ubuntu Linux

Linus rules. Apple sucks.

* Fixed PlumedMain passing of data from plumed to outside code

* Hard coded real precision for python interface - this should have been with the last commit

* Added first go at working makefile for python interface

* Added options to configure to build python interface from makefile

* Small changes to where loading of python interface is done

* Removed unecessary wrapper c++ function from python interface

* Made python install work in a way that is consistent with the rest of plumed

* Added pythonpath to travis.yml

* Added installation of Cython to travis.yml

* Added ifdef block to stop cppcheck throwing an error

* Using uniqu_ptr for DataFetching object in PlumedMain

* Added install command for numpy to travis

* Added string to tell me whether plumed+python is being built

* Small change in travis.yml file to see if I can get python compile working

* Compilers for cython are now specified from Makefile.conf

* Now printing stuff on environment to try to work out why linking doesn't work

* A new attempt to fix the travis-ci issues

* Got rid of troubling TRAVIS_PYTHON_FLAG

* Small change to see if we can get this to work on travis

* Now setting LDSHARED from LDSO in makefile

* Added something to print everything in the python path when we run the python test

* Fixed python path in travis.yml

* Removed stuff for debugging configuration on travis

* Customized conda install (for python) in travis.yml so that osx version is installed for osx and linux version is installed for linux

* Set TMPDIR in .travis.yml to hopefully get osx to compile PLUMED + Python

* Made it so that python interface is rebuilt when user does make install so that correct paths are used

* Made it so that python interface is rebuilt in staging area during install procedure

* Corrected regtest script so that python tests are dealt with the same as everything else

This change required some small fixes here and there.

In particular, the code accessing elements of ActionSet thinking it was
a pointer now need a .get() in order to access the pointer (e.g. for
a dynamic_cast)

I changed all the forward references to unique_ptr
using an auxiliary class (ForwardDecl).

Notice that in this manner the order of destructors
is exactly the reverse of the order of constructors.
This forces me to move a variable up in the layout
of PlumedMain to avoid a segfault.

This change is necessary to make plumed exception-safe.

This change is necessary to make plumed exception-safe

Fixes #236

* speed up of sharing and applying in plumed core
the main differences are:
- new member of class atoms to track unique local atoms (i.e. all the atoms needed by plumed action in a domain)
- positions are retrieved only for unique local atoms
- forces are zeroed only for unique local aotms
- forces are applied only for unique local atoms
in a system of 200K atoms on 4 mpi rank with plumed using only 4 atoms the
sharing and applyign time improves by 2 order of magnitudes

* removed leftover printf

* core: make it a bit faster also without domain decomposition

* astyle

* fix-241: unique atoms are update only if:
- particle decomposition has been updated
- domain decomposition has been updated
- replica-exchange step
- neighbour lists have been updated
overall this should make the sharing code even faster

* actionAtomistic have now a list of local atoms that is updated on:
- neighbour list step
- update of the pd/dd list
this allow to simplify the loop for the generation of global local list of unique atoms

* atoms: small tweaks

* fix: reallocate memory less often

* fix: for the scalar case there is no need to generate the list of unique atoms

* style

* few comments

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