Anisotropic rotational diffusion test #1622
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Maybe, it makes sense to have some tests (like this one) commented out or removed from the file |
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This is one of tests which validate both Velocity Verlet LD and future BD. Hence, it indirectly relates to #1360. |
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The mass and rinertia test reached a complexity so that I don't really understand it anymore. For rotation, only isotropic inertia tensors are tested. |
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@RudolfWeeber thanks for the feedback. I agree regarding the complexity, I already have the corresponding task #1905. The tests improvement here are tightly connected to the BD and LD results match comparison. I also need to backport the latest changes from the #1842.
Shortly, a relation is like this: [langevin_thermostat.py] + [Es. VV integrator] + statistical rules = [mass-and-rinertia_per_particle] If we are fully sure that the VV integrator is properly tested by other tests then, indeed, we could consider a removal of the test mass-and-rinertia_per_particle with a check that all test parameters are ported to the langevin_thermostat. |
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This PR depends on #2021. |
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For more durable runs I've detected the instability of the test. It could be either a technical or a conceptual issue. In the latter case extra theoretical/bibliography study is needed. Anyway, the present PR is not consistent anymore. I'll work on this separately (#2029).. Propose to close it. |
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. #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 #1622, #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
Description of changes:
mass-and-rinertia_per_particle.py. I've taken some measures to avoid a performance impact: limited loops for this specific calc and only 1 test case. Compare to overall bunch of python tests run, probably, there is not significant increase now: 17 minutes vs 15 minutes before. However, of course, up to the team to decide whether it is worth that. In my opinion: the rotational diffusion is a critically important physical process in Langevin Dynamics and its variance should be validated.PR Checklist