Phonon thermostat

[Alexsp32]

Phonon thermostatting in NQCD

Implements MDEF + 2TM with Phonon coupling (#73) by changing Simulations to allow the use of different temperatures (either a constant value or function) for each atom by using Thermostats, which behave like a Subsystem (see NQCD/NQCModels.jl#39), applying a temperature to parts of a Simulation.

Combine with NQCD/NQCModels.jl#39, which introduces Subsystems, which apply a Model exclusively to certain atoms in a Simulation. These can be combined arbitrarily for Model types implementing potential, derivative or friction to generate a combined friction matrix for electronic and phononic friction.

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ToDo

• Update documentation for new additions.
• Demonstrate usage with harmonic oscillator model used to validate implementation.
• Turn validation examples into unit tests.