Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Noise behavior of stokesian dynamics and other thermostats differ #3840

Closed
fweik opened this issue Jul 30, 2020 · 1 comment · Fixed by #3888 · May be fixed by #3884
Closed

Noise behavior of stokesian dynamics and other thermostats differ #3840

fweik opened this issue Jul 30, 2020 · 1 comment · Fixed by #3888 · May be fixed by #3884

Comments

@fweik
Copy link
Contributor

fweik commented Jul 30, 2020

SD seems to use a counter based noise source, as do the other thermostats. The counter value is derived from the simulation
time by calculating sim_time / time_step, which means that if the users resets the time, the noise is repeated. This differs from
the other thermostats, where the noise is derive from a monotonous counter which can not be reset. Also the SD version leads
to correlated noise if the time step is changed.
@jngrad
Copy link
Member

jngrad commented Jul 31, 2020

The long-term solution is for SD to use the same framework as the other thermostats, once the framework is refactored to use a single counter.

This was referenced Sep 3, 2020
Draft
Merged
@kodiakhq kodiakhq bot closed this as completed in #3888 Sep 18, 2020
kodiakhq bot added a commit that referenced this issue Sep 18, 2020
@kodiakhq
Refactor thermostat infrastructure (#3888)
4ccad28 
Description of changes:
- Remove RNG correlation stemming from seed offsets (fixes #3585)
    - seeds are now used as keys
    - a monotonically increasing counter is used in each thermostat
    - the only way to reset these counters is to create a new `System`
- Remove RNG correlation stemming from resetting `sim_time` or `time_step` during simulations with SD (fixes #3840)
    - the SD thermostat now uses the same RNG interface as other thermostats
- Accelerate RNG unit tests (fixes #3573)
    - they now take 2 seconds to run in coverage and sanitizer builds in CI
- Separate thermostats from integrators
    - better separation of concerns
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
2 participants
@fweik @jngrad