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Script for automated workflow #78

Merged
merged 44 commits into from
Jul 30, 2024
Merged

Script for automated workflow #78

merged 44 commits into from
Jul 30, 2024

Commits on Jun 11, 2024

  1. Minimal script

    @Misty-W
    Misty-W committed Jun 11, 2024
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  2. Move register and settings files to analog dir.

    @Misty-W
    Misty-W committed Jun 11, 2024
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  3. Basic flow with example input file

    @Misty-W
    Misty-W committed Jun 11, 2024
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  4. Merge branch 'main' into 75-script-for-automated-workflow

    @Misty-W
    Misty-W committed Jun 11, 2024
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Commits on Jun 17, 2024

  1. use lattice to calculate register pos and coeffs

    @Misty-W
    Misty-W committed Jun 17, 2024
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  2. Add Gaussian-Laplacian filtering

    @Misty-W
    Misty-W committed Jun 17, 2024
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Commits on Jun 18, 2024

  1. Make filtering configurable, more lattice options

    @Misty-W
    Misty-W committed Jun 18, 2024
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  2. Remove unused variables and imports

    @Misty-W
    Misty-W committed Jun 18, 2024
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  3. Add transformation back to 3D-RISM coords

    @Misty-W
    Misty-W committed Jun 18, 2024
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  4. Create automated_analog_script_guide.md 

    Create automated_analog_script_guide.md
Clean up readability in `automated_flow.py`
    @Misty-W
    Misty-W committed Jun 18, 2024
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  5. Revert some file structure changes

    @Misty-W
    Misty-W committed Jun 18, 2024
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  6. Wordsmith, format automated_analog_script_guide.md

    @Misty-W
    Misty-W committed Jun 18, 2024
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Commits on Jun 19, 2024

  1. Revert pulse param dict to fix warning

    @Misty-W
    Misty-W committed Jun 19, 2024
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Commits on Jun 21, 2024

  1. Add dockerfile tested with real script

    @Misty-W
    Misty-W committed Jun 21, 2024
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Commits on Jun 24, 2024

  1. Refine location to 3D-RISM mapping

    @Misty-W
    Misty-W committed Jun 24, 2024
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Commits on Jun 25, 2024

  1. Scale the grid from the slice i.s.o 3D-RISM info

    @Misty-W
    Misty-W committed Jun 25, 2024
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  2. Update locations.txt

    @Misty-W
    Misty-W committed Jun 25, 2024
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Commits on Jun 26, 2024

  1. Generalize midplane point calculation 

    Update locations.txt after midplane update
    @Misty-W
    Misty-W committed Jun 26, 2024
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  2. Revert scaling change

    @Misty-W
    Misty-W committed Jun 26, 2024
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  3. Clarify guide for analog flow

    @Misty-W
    Misty-W committed Jun 26, 2024
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Commits on Jul 5, 2024

  1. Solve slicing point reading issue 

    Solve slicing point reading issue and update example with the failing case
    @Misty-W
    Misty-W committed Jul 5, 2024
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Commits on Jul 6, 2024

  1. Sort slicing planes by distance from origin 

    Fixes empty slice error
    @Misty-W
    Misty-W committed Jul 6, 2024
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Commits on Jul 9, 2024

  1. Use consistent density shape for poisson lattice

    @Misty-W
    Misty-W committed Jul 9, 2024
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  2. Update counter if try burned when creating lattice 

    Update counter if try burned when creating poisson lattice
Add cropping back into example settings now that it's no longer stuck
    @Misty-W
    Misty-W committed Jul 9, 2024
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  3. Merge branch 'main' into 75-script-for-automated-workflow

    @Misty-W
    Misty-W committed Jul 9, 2024
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  4. Crop to slice bounds if crop window out of slice bounds

    @Misty-W
    Misty-W committed Jul 9, 2024
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Commits on Jul 11, 2024

  1. Consistent mapping back to 3D-RISM coordinates

    @Misty-W
    Misty-W committed Jul 11, 2024
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  2. Initialize threshold_distances w/ defaultdict 

    Initialize `threshold_distances` in `calculate_detunings` w/ `defaultdict` to handle the case where `threshold_distances` is empty
    @Misty-W
    Misty-W committed Jul 11, 2024
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Commits on Jul 12, 2024

  1. Cropping from 3D-RISM coordinates

    @Misty-W
    Misty-W committed Jul 12, 2024
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Commits on Jul 15, 2024

  1. Use slice coordinates for density canvas lengths

    @Misty-W
    Misty-W committed Jul 15, 2024
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  2. Merge branch 'md/bugfix' into 75-script-for-automated-workflow

    @Misty-W
    Misty-W committed Jul 15, 2024
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  3. Ensure center of cropping box on canvas plane 

    Make test cases distinct settings files
    @Misty-W
    Misty-W committed Jul 15, 2024
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Commits on Jul 16, 2024

  1. added a getter function for lattice, with argument for minimal distance 

    changed default, fixed typo
    @Misty-W
    Mauro d'Arcangelo authored and Misty-W committed Jul 16, 2024
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  2. Updates to script for lattice scaling 

    Also modify settings to generate a useful lattice
    @Misty-W
    Misty-W committed Jul 16, 2024
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  3. Additional settings and results

    @Misty-W
    Misty-W committed Jul 16, 2024
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  4. Merge branch 'main' into 75-script-for-automated-workflow

    @Misty-W
    Misty-W committed Jul 16, 2024
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  5. Update analog_settings_example2

    @Misty-W
    Misty-W committed Jul 16, 2024
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Commits on Jul 18, 2024

  1. Avoid oblong slice geometry

    @Misty-W
    Misty-W committed Jul 18, 2024
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Commits on Jul 19, 2024

  1. Fix remaining crop issue

    @Misty-W
    Misty-W committed Jul 19, 2024
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  2. Update original test case to run faster

    @Misty-W
    Misty-W committed Jul 19, 2024
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Commits on Jul 26, 2024

  1. Fix filepath issues

    @Misty-W
    Misty-W committed Jul 26, 2024
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  2. Make slicing demo nb work w/ updated analog flow

    @Misty-W
    Misty-W committed Jul 26, 2024
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Commits on Jul 29, 2024

  1. Update automated_flow.py

    @Misty-W
    Misty-W committed Jul 29, 2024
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Commits on Jul 30, 2024

  1. Working combination for script and notebooks

    @Misty-W
    Misty-W committed Jul 30, 2024
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