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Updated AdvancedMH.jl wrapper and fixed compatibility issue. #322

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wants to merge 26 commits into from
Closed

Updated AdvancedMH.jl wrapper and fixed compatibility issue. #322

wants to merge 26 commits into from

Commits on Aug 25, 2023

  1. Correct for periodicity in quantise_diatomic

    @Alexsp32 @jamesgardner1421
    Alexsp32 authored and jamesgardner1421 committed Aug 25, 2023
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  2. Split velocity array into slab & molecule as well

    @Alexsp32 @jamesgardner1421
    Alexsp32 authored and jamesgardner1421 committed Aug 25, 2023
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  3. Checking for PeriodicCell now type invariant

    @Alexsp32 @jamesgardner1421
    Alexsp32 authored and jamesgardner1421 committed Aug 25, 2023
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  4. Partial fix for #292

    @Alexsp32 @jamesgardner1421
    Alexsp32 authored and jamesgardner1421 committed Aug 25, 2023
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  5. Add debug info

    @Alexsp32 @jamesgardner1421
    Alexsp32 authored and jamesgardner1421 committed Aug 25, 2023
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  6. More debug info

    @Alexsp32 @jamesgardner1421
    Alexsp32 authored and jamesgardner1421 committed Aug 25, 2023
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  7. Possibly translating in the wrong direction

    @Alexsp32 @jamesgardner1421
    Alexsp32 authored and jamesgardner1421 committed Aug 25, 2023
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  8. More debug outputs

    @Alexsp32 @jamesgardner1421
    Alexsp32 authored and jamesgardner1421 committed Aug 25, 2023
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  9. Fix unrelated typo

    @Alexsp32 @jamesgardner1421
    Alexsp32 authored and jamesgardner1421 committed Aug 25, 2023
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  10. Improve accuracy of equilibrium bond length

    @jamesgardner1421
    jamesgardner1421 committed Aug 25, 2023
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  11. Fix missing import

    @jamesgardner1421
    jamesgardner1421 committed Aug 25, 2023
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  12. Add vectorised version of quantise_diatomic 

    `quantise_diatomic` is now able to process a single configuration
or a vector of multiple configurations.
This improves performance for multiple configurations,
as only one potential-specific binding curve is
generated to analyse all configurations.
    @Alexsp32 @jamesgardner1421
    Alexsp32 authored and jamesgardner1421 committed Aug 25, 2023
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  13. Delay rounding of J values until return

    @jamesgardner1421
    jamesgardner1421 committed Aug 25, 2023
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  14. Fix type definition

    @jamesgardner1421
    jamesgardner1421 committed Aug 25, 2023
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Commits on Sep 14, 2023

  1. Add energy_distribution_from_quantisation 

    Added functions to calculate classical translational, rotational and vibrational energies
from the ro-vibrational quantum numbers from quantise_diatomic.
    @Alexsp32
    Alexsp32 committed Sep 14, 2023
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  2. Calculate force constant differently

    @Alexsp32
    Alexsp32 committed Sep 14, 2023
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  3. Mistake in energy expression

    @Alexsp32
    Alexsp32 committed Sep 14, 2023
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Commits on Sep 29, 2023

  1. Use implemented method for force constant

    @Alexsp32
    Alexsp32 committed Sep 29, 2023
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  2. Made E_delta more meaningful

    @Alexsp32
    Alexsp32 committed Sep 29, 2023
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Commits on Nov 7, 2023

  1. Merge branch 'main' into AS_dev

    @Alexsp32
    Alexsp32 committed Nov 7, 2023
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Commits on Dec 4, 2023

  1. Attempted fix for #320 

    AdvancedMH or one of its dependencies may have updated a keyword from "initial_config" to "initial_params".
This caused NQCD to not deliver initial positions to the sampling chain correctly.
    @Alexsp32
    Alexsp32 committed Dec 4, 2023
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  2. Initial test for #321

    @Alexsp32
    Alexsp32 committed Dec 4, 2023
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Commits on Dec 5, 2023

  1. Modify AdvancedMH.jl keyword handling #321 

    - Update ThermalMonteCarlo.jl with new keywords movement_ratio and stop_ratio, where movement_ratio=1-stop_ratio
- Add warning for deprecated kwargs.
- Update documentation with information about new keywords
    @Alexsp32
    Alexsp32 committed Dec 5, 2023
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  2. Drop compat for AdvancedMH.jl<0.8 for #320,#321

    @Alexsp32
    Alexsp32 committed Dec 5, 2023
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  3. Diagnosis attempt for failing workflow

    @Alexsp32
    Alexsp32 committed Dec 5, 2023
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  4. Found the culprit, it's a new MKL build

    @Alexsp32
    Alexsp32 committed Dec 5, 2023
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