INCOMPATIBLE CHANGE TO CONFIG FILE:
change config file to use stepsPerPeriod and coolperiods/histperiods
(all based on trap frequency) rather than scaled time units directly;
this should allow us to do proper phase matchin by having an integer
number of steps per period.
Two frequency trap definition.
Working two frequency trap.
adjust time unit for cosine decay parameters
INCOMPATIBLE CHANGE TO CONFIG FILE:
change config file to use stepsPerPeriod and coolperiods/histperiods
(all based on trap frequency) rather than scaled time units directly;
this should allow us to do proper phase matchin by having an integer
number of steps per period.
Merge commit 'origin/retime^' into twoFreq

Conflicts:
	src/ccmd_sim.cpp
Now use Incompatible integrator params.

Save coordinates for povray.
Create default test configuration.
Add preliminary ion swapping for reactions.
4 Threads for Coulomb force.
Adds controllable multithreading to coulomb_force.

New parameters to set number of threads used in multithreading.
Code cleanup.

Remove BOOST_FOREACH.
Correct references passed in constructors.
Inhibit copying of some classes.
Blocked copy constructor for most classes.
Memory management cleanup.

Remove dependency on boost::shared_ptr.
Replaced most shared_ptr by references.
Remove some local variables.
Class name refactoring.
Changes to member variable names.
Replaced all boost dependency by stdlib.
Lots of tidying up.
Change stochastic heating to use C++11 random numbers engine.