Update documentation of Molecular Dynamics
Update of the documentation of molecular dynamics, reflecting that two new algorithms have been added (Bussi dynamics and NoseHooverChainNVT dynamics).
- Add documentation of
NoseHooverChainNVT. (CC: @lan496) - Move documentation of
Bussito NVT section, tidy up doc string and use traditional name for kwargs parameter. - Add overview of algorithms for NVT and NPT ensembles, listing which algorithms work well.
- Add warning against my ancient NPT implementation.
For information, I have added tests to the Asap test suite testing all NVT algorithms (serial simulations only), to see if they can correctly reproduce the fluctuations in the canonical ensemble, and if they can thermalize a system where the initial temperature is wrong. The result is that only Langevin, Bussi and NoseHooverChainNVT do this correctly. They are therefore the recommended NVT algorithms in the documentation.
Checklist
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I am familiar with ASE's contribution guidelines. -
Doc strings in code changed in this MR are up to date. -
Unit tests have been added for new or changed code. -
Issue is resolved via "closes #XXXX" if applicable.