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.

[reinimaurer1]

I left lots of minor comments, mostly related to docs. There is one bit I don't quite understand, but we can discuss offline at some point.

[Alexsp32]

Thermostat is pretty self explanatory, is it not? What about other ensembles? E.g. barostats?

Yes, however the Integrator chosen as part of the DynamicsMethod decides the implementation of the thermostat, while these structs just store a temperature and which parts of the system experience it.

[Alexsp32]

@reinimaurer1 ready for re-review

[reinimaurer1]

thanks for the changes. all good