Draft: Phonon thermostat

[Alexsp32]

Phonon thermostatting in NQCD

Implements MDEF + 2TM with Phonon coupling (https://github.com/NQCD/NQCDynamics.jl/issues/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 https://github.com/NQCD/NQCModels.jl/pull/39), applying a temperature to parts of a Simulation.

Combine with https://github.com/NQCD/NQCModels.jl/pull/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.