Correlation function calculations #4
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
Added a unit test for the correlation function calculation. Bindings were added in `bindings.cpp` for getting `c_ij` time series, as well as the time correlation function values.
`--no-build-isolation` doesn't seem to be needed.
Calculated the hydrogen bonds for the continuous bond definition. Does not otherwise change the effects of the unit test, since there is only one frame.
Use the continuous hydrogen bond definition by default.
Also changed value in `test_bonds.py` for the continuous bond definition.
Support for reading in all frames.
New bindings to the `time_correlation_function` which is templated on the type of the network (`UndirectedNetwork` or `DirectedNetwork`). Changed `test_correlation.py` to reflect this change.
Requires `spirit-extras` and `matplotlib` as dependencies.
Calculate the lifetime for time correlation function when using the continuous bond definition.
Removing B in lieu of 1-A gets rid of "bad" results (since B can be 0, and therefore tau2 could have huge/bad values, leading to a huge / nonsensical value of the lifetime) Co-authored-by: Moritz Sallermann <[email protected]>
Added some functionalities from ASE.
Functions from and similar to ASE functions now in a separate thirdparty folder with the license.
Now `io.py` is inside the `thirdparty/ase` directory.
Minor change in `io.py`
You can process a slice of frames in a trajectory.
TODO: add more checks to see that the positions are actually averaged.
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Outdated suggestions cannot be applied.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.
bindings.cppfor gettingc_ijtime series, as well as the time correlation function values.