Brownian Dynamics within the existing VV loop

[bogdan-tanygin]

Fixes #1360, also it contains the integrated changes from PRs #1622, #1757 which were required to validate both existing Langevin- (LD) and new Brownian Dynamics (BD) viscous and fluctuation dynamics including the rotational one.

Description of changes:

• Generally, this is a conventional simplest BD [schlick2010].
• Corresponding Sphinx documentation section is populated with the required details to reveal the concept.
• A velocity, even though it is optional for a simplest implementation of the BD, has been added for a consistency with the existing VV loop (c.f. Do we need a Brownian Dynamics (BD) integrator ? #1360 (comment)) and all the existing tests and new tests. It does not impact the positional mechanics though which is natural for the BD [schlick2010].
• The velocity and position random walk has been added according to the classical diffusion equations [schlick2010,Pottier2014].
• Rotational motion BD is implemented analogously. Existing quaternion approach has been reused where possible.
• New test brownian_thermostat.py is based on the existing langevin_thermostat.py. It contains some commented out fragments which are inconsistent for the simplest BD cause ones correspond to more fine dynamical structure compare to the BD temporal relation time_step >> mass / gamma. The Maxwell distribution test is passing well and the Gaussian noise type is crucial for this which has been done in the thermostat.hpp.
• The mass-and-rinertia_per_particle.py contains changes described within the PRs Anisotropic rotational diffusion test #1622, Drag terminal velocity tests #1757. Probably, it is of interest for both the LD and BD independently. This is why I've opened that PRs in advance.
• Existing automatic tests execution timeline is minimized.
• Additional "heavy" test has been added without an automatic run: mass-and-rinertia_per_particle_rotdiff-longrun.py. It requires ~2 hours of a run and provides the intensive validation of the existing LD and new BD dynamics in the same way.

PR Checklist

• Tests?
  • Interface
  • Core
• Docs?

References
schlick2010: https://link.springer.com/book/10.1007%2F978-1-4419-6351-2
Pottier2014: https://link.springer.com/article/10.1007/s10955-010-0114-6

[jngrad]

@RudolfWeeber Let me know if ede6e7e is what you had in mind. Don't forget to add #define BROWNIAN_PER_PARTICLE in your myconfig.hpp.

[RudolfWeeber]

@jngrad, yes. Could you please gather all the Brownian-dynamics related globals in a sinlge struct? Then, it's ready, I think.

[jngrad]

The Brownian globals are now in a struct.

In jngrad/therm-refactor I also moved the Langevin and NPT globals in structs and moved the Langevin code to integrators/langevin_inline.hpp for consistency with integrators/brownian_inline.hpp. Feel free to do git merge --ff-only. If you consider it's out of scope, I'll open a dedicated PR once this one is merged.

[RudolfWeeber]

@hmenke, from my side, this PR is ready. Please check your open review for things not addressed. If there aren't any, please approve the PR.

[KaiSzuttor]

still missing a check for virtual particles here and probably at other places too

[RudolfWeeber]

@KaiSzuttor, the virtual sites are excluded for translational degrees in
void brownian_dynamics_propagator(const ParticleRange &particles)

For rotational degrees, VS are not excluded, which is correct. If the virtual sites have_quanterion feature is used, the virtual sites update will assign the correc orientation after the propagation step.

[espresso-ci]

this was the last unresolved remark of @hmenke. so this PR can be merged

…

Am 23.01.2020 um 12:53 schrieb RudolfWeeber ***@***.***>:  @KaiSzuttor, the virtual sites are excluded for translational degrees in void brownian_dynamics_propagator(const ParticleRange &particles) For rotational degrees, VS are not excluded, which is correct. If the virtual sites have_quanterion feature is used, the virtual sites update will assign the correc orientation after the propagation step. — You are receiving this because you commented. Reply to this email directly, view it on GitHub, or unsubscribe.

[RudolfWeeber]

I found a different but related issue. The testcase for checking thermo_virtual with Brownian dynamics was incorrect (copy/paste error from the Langevin test).
Fixing the test revealed that thermo_virtual=True was ignored by the virtual sites guards. Pushing the fix now.

outdated

[fweik]

@jngrad I think we should merge this now, or you should push your tests onto this branch.