* 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

Add extended adaptive biasing force or dynamic reference restraining method

Add extended adaptive biasing force or dynamic reference restraining method

Add extended adaptive biasing force or dynamic reference restraining method

the old one are still there for reference

The idea is that we can move towards defining the adjacency matrix using
some other measure of adjacency

The source code from crystallization allows you to calculate
Q4 and Q6 parameters.  You can also calculate local Q4 and local
Q6 parameters and you create compound collective variables based
on the relative orientations of internal vectors in adjacent molecules.

Regtests for this functionality are reasonably thorough.  Manual is
not so great as yet

Made .gitignore ignore regtests and src directories modules that are shipped separately to the plumed core

They are in a directory regtest.
See regtest/README file for some documentation.

Presently they just work with simplemd, but we should
at some point implement a driver and allow testing directly
from the driver