Correlation function calculations #4
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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 <moritzsallermann@gmail.com>
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.
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bindings.cppfor gettingc_ijtime series, as well as the time correlation function values.