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Typing abstraction #9

Merged
merged 44 commits into from
Jun 9, 2020
Merged

Typing abstraction #9

merged 44 commits into from
Jun 9, 2020

Commits on May 12, 2020

  1. Add Potential class

    @mattwthompson
    mattwthompson committed May 12, 2020
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Commits on May 13, 2020

  1. Update Potential class

    @mattwthompson
    mattwthompson committed May 13, 2020
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Commits on May 15, 2020

  1. Make barebones system class

    @mattwthompson
    mattwthompson committed May 15, 2020
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Commits on May 18, 2020

  1. Merge branch 'master' into potential-1

    @mattwthompson
    mattwthompson committed May 18, 2020
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  2. Merge branch 'master' into potential-1

    @mattwthompson
    mattwthompson committed May 18, 2020
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  3. Update conda env

    @mattwthompson
    mattwthompson committed May 18, 2020
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Commits on May 21, 2020

  1. Update test structure

    @mattwthompson
    mattwthompson committed May 21, 2020
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  2. Make separate classes for parametrized and un-parametrized potentials

    @mattwthompson
    mattwthompson committed May 21, 2020
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  3. Store expressions as strings

    @mattwthompson
    mattwthompson committed May 21, 2020
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  4. Validate parameters with sympy and update tests

    @mattwthompson
    mattwthompson committed May 21, 2020
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  5. Let independent_variables be a string

    @mattwthompson
    mattwthompson committed May 21, 2020
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  6. Copy evaluator simtk->pint function from evaluator

    @mattwthompson
    mattwthompson committed May 21, 2020
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Commits on May 22, 2020

  1. Merge branch 'potential-1' into system-1

    @mattwthompson
    mattwthompson committed May 22, 2020
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Commits on May 27, 2020

  1. Add some templates for a class API

    @mattwthompson
    mattwthompson committed May 27, 2020
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  2. Merge remote-tracking branch 'origin/potential-1' into system-1

    @mattwthompson
    mattwthompson committed May 27, 2020
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  3. Add some basic classes

    @mattwthompson
    mattwthompson committed May 27, 2020
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Commits on May 29, 2020

  1. Add a prototype with example

    @mattwthompson
    mattwthompson committed May 29, 2020
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  2. Merge branch 'master' into system-1

    @mattwthompson
    mattwthompson committed May 29, 2020
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  3. More clearly distinguish between toolkit and system objects and add t… 

    …ests
    @mattwthompson
    mattwthompson committed May 29, 2020
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  4. Add toolkit dependency

    @mattwthompson
    mattwthompson committed May 29, 2020
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  5. Test constructing directly from toolkit objects

    @mattwthompson
    mattwthompson committed May 29, 2020
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Commits on Jun 1, 2020

  1. Don't assume toolkit >0.7.0

    @mattwthompson
    mattwthompson committed Jun 1, 2020
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  2. Directly use toolit atom

    @mattwthompson
    mattwthompson committed Jun 1, 2020
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Commits on Jun 2, 2020

  1. Add SMIRKS attribute

    @mattwthompson
    mattwthompson committed Jun 2, 2020
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  2. Move System ForceField to PotentialCollection

    @mattwthompson
    mattwthompson committed Jun 2, 2020
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  3. Merge branch 'master' into potential-1

    @mattwthompson
    mattwthompson committed Jun 2, 2020
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Commits on Jun 4, 2020

  1. Switch to directly using toolkit topology

    @mattwthompson
    mattwthompson committed Jun 4, 2020
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  2. Update gitignore

    @mattwthompson
    mattwthompson committed Jun 4, 2020
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  3. Rebrand System.forcefield to System.potential_collection

    @mattwthompson
    mattwthompson committed Jun 4, 2020
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  4. Start typing module

    @mattwthompson
    mattwthompson committed Jun 4, 2020
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  5. Remove un-used NumPy dependency

    @mattwthompson
    mattwthompson committed Jun 4, 2020
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  6. Remove classes that mimic toolkit objects

    @mattwthompson
    mattwthompson committed Jun 4, 2020
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  7. Move SMIRNOFF-specific things into its own submodule, subclassing thi… 

    …ngs in system/collections.py
    @mattwthompson
    mattwthompson committed Jun 4, 2020
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Commits on Jun 5, 2020

  1. Astract ForceField into ParameterCollection

    @mattwthompson
    mattwthompson committed Jun 5, 2020
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  2. Lint, fix imports

    @mattwthompson
    mattwthompson committed Jun 5, 2020
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  3. Rename and move around functions, fix tests

    @mattwthompson
    mattwthompson committed Jun 5, 2020
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  4. Add SMIRNOFF example

    @mattwthompson
    mattwthompson committed Jun 5, 2020
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  5. Use the right notebook

    @mattwthompson
    mattwthompson committed Jun 5, 2020
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  6. Merge branch 'potential-1' into typing-abstraction

    @mattwthompson
    mattwthompson committed Jun 5, 2020
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  7. Add bond parameter parsing and update examples

    @mattwthompson
    mattwthompson committed Jun 5, 2020
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  8. Merge branch 'master' into typing-abstraction

    @mattwthompson
    mattwthompson committed Jun 5, 2020
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  9. Initialize dicts to empty dicts, not None

    @mattwthompson
    mattwthompson committed Jun 5, 2020
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  10. Assorted fixes

    @mattwthompson
    mattwthompson committed Jun 5, 2020
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  11. Add ethanol example showing off loading Parsely and inspecting bond p… 

    …arameters
    @mattwthompson
    mattwthompson committed Jun 5, 2020
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