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Add Einstein-Helfand viscosity implementation #25

Merged
merged 24 commits into from Aug 15, 2023
Merged

Add Einstein-Helfand viscosity implementation #25

merged 24 commits into from Aug 15, 2023

Commits on Aug 8, 2023

  1. Add Einstein-Helfand viscosity class skeleton 

    * Use class `VelocityAutocorr` as template
* Add items to `__init__()`
* Write `_prepare()` and `_single_frame()`
* Early work on `_conclude()`
    @xhgchen
    xhgchen committed Aug 8, 2023
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  2. Format viscosity.py with Black

    @xhgchen
    xhgchen committed Aug 8, 2023
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  3. Update docstrings in viscosity.py

    @xhgchen
    xhgchen committed Aug 8, 2023
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  4. Make variable names more readable 

    * Change `self.*_array` to simply `self.*`
* Fix `self._masses_rs`
    @xhgchen
    xhgchen committed Aug 8, 2023
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  5. Remove unnecessary type casting

    @xhgchen
    xhgchen committed Aug 8, 2023
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  6. Add initial volume handling 

    * Set up `self._volumes` in `_prepare()` and `_single_frame()`
    @xhgchen
    xhgchen committed Aug 8, 2023
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  7. Add remaining items to viscosity calculation 

    * Complete `_conclude()` with 2, Boltzman constant, average volume,
and average temp
    @xhgchen
    xhgchen committed Aug 8, 2023
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  8. Refactor _parse_dim_type() to static method

    @xhgchen
    xhgchen committed Aug 8, 2023
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  9. Write starter tests for Helfand viscosity class 

    * Check that AtomGroup is accepted
* Test some exceptions
* Functionality not yet tested here
    @xhgchen
    xhgchen committed Aug 8, 2023
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  10. Fix visc_by_particle division step 

    * Move `visc_by_particle` division step outside of for loop
    @xhgchen
    xhgchen committed Aug 8, 2023
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  11. Create full unit velocity trajectory for tests 

    * Contains mass, velocities, positions, and volume
    @xhgchen
    xhgchen committed Aug 8, 2023
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  12. Add characteristic polynomial for viscosity class 

    * Format `viscosity.py` with Black
    @xhgchen
    xhgchen committed Aug 8, 2023
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Commits on Aug 9, 2023

  1. Add basic test for Helfand viscosity 

    * Simplify `characteristic_poly_helfand()`
    @xhgchen
    xhgchen committed Aug 9, 2023
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  2. Use key "Boltzman_constant" until mda 2.6.0 

    * CI will not work otherwise
    @xhgchen
    xhgchen committed Aug 9, 2023
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  3. Fix Boltzmann KeyError 

    * use try except and update with mda 2.6.0 release
    @xhgchen
    xhgchen committed Aug 9, 2023
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Commits on Aug 11, 2023

  1. Vectorize basic Helfand viscosity test 

    * Improve accuracy and agreement with `ViscosityHelfand` class
* Improve performance
    @xhgchen
    xhgchen committed Aug 11, 2023
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  2. Add tests for start, stop, step

    @xhgchen
    xhgchen committed Aug 11, 2023
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  3. Store Boltzmann constant key instead of value

    @xhgchen
    xhgchen committed Aug 11, 2023
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  4. Update docstrings for clarity

    @xhgchen
    xhgchen committed Aug 11, 2023
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Commits on Aug 13, 2023

  1. Remove leftover comments/unused code

    @xhgchen
    xhgchen committed Aug 13, 2023
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  2. Get Boltzmann value instead of key

    @xhgchen
    xhgchen committed Aug 13, 2023
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  3. Use 5001 in place instead of fixture for tests

    @xhgchen
    xhgchen committed Aug 13, 2023
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  4. Comment Boltzmann issue from mdanalysis repo

    @xhgchen
    xhgchen committed Aug 13, 2023
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Commits on Aug 14, 2023

  1. Restore NSTEP and link issue number in tests

    @xhgchen
    xhgchen committed Aug 14, 2023
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