* 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

In case of error with LOAD, the code was returning an error without
raising an exception.

This is done only in the cmd interpreter

This should make the code slightly fast.

fixes #211

[makedoc]

These are the files generated automatically with the cmd
dictionaries. I renamed them to inc which is a more standard
extension for include files.

that is used to flush all the actions
[ makedoc ]

Now works also when plumed has been installed with a different name

added local masses

No EOL at the end of the file is only tolerated in input file
(e.g. plumed.dat) and not in other files (including HILLS files).

Indeed, when using multiple walkers, it is possible that transiently
the HILLS file from other walkers have incomplete lines.
With this fix, those lines are ignored and read at the next iteration.

This fixes #190

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

Now multi words commands are parsed like single word ones.
This will make it easy to automatize documentation.

Related to #182

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

Since the pointer should be not null, the new name makes more sense

Defining a capitalized enum was useless in the end. I now use
cmd_string
as the name of the enum, where string is the string for the
cmd interpreter

map is now a global static object

Enum list and word map are now generated with a script.

To add a new command it is sufficient to add a case command as:

case PIPPO: // cmd pippo

It is related to #182, though I let the issue open since I think
we should automatize also the cmd documentation.

Allow for splitting of performCalc() into
performCalcNoUpdate() and update()

This makes it possible to call performCalc() multiple times per step