added uncertainty estimation on dump interval for jaxmd #312
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
|
also closes #309 |
for more information, see https://pre-commit.ci
|
pre-commit.ci autofix |
for more information, see https://pre-commit.ci
for more information, see https://pre-commit.ci
for more information, see https://pre-commit.ci
for more information, see https://pre-commit.ci
for more information, see https://pre-commit.ci
for more information, see https://pre-commit.ci
for more information, see https://pre-commit.ci
for more information, see https://pre-commit.ci
apax/md/simulate.py
Outdated
| def body_fn(i, state): | ||
| state, neighbor = state | ||
| state, outer_step, neighbor = state # neighbors |
There was a problem hiding this comment.
don't understand the comment
There was a problem hiding this comment.
The comment is superfluous and can be removed.
apax/md/simulate.py
Outdated
| if isinstance(state, simulate.NPTNoseHooverState): | ||
| box = state.box | ||
| apply_fn_kwargs = {} | ||
| else: | ||
| box = system.box | ||
| apply_fn_kwargs = {"box": box} | ||
| apply_fn_kwargs = {"box": box} # this might cause a bug |
There was a problem hiding this comment.
should we discuss this bevor merging?
There was a problem hiding this comment.
The comment was just a reminder for myself to look into this. it's all working as intended. I'll remove the comment
Tetracarbonylnickel
approved these changes
Aug 9, 2024
added temperature schedules
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
A full model is evaluated when a configuration is dumped.
Before we would evaluate an energy model at every time step but only collect the energy aver N steps, which was a bit redundant. Now we can save all model outputs.
closes #298