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[WIP] Handlers for DampedExp6810, AmoebaMultipoleForce, AxilrodTeller potentials #56

Merged
merged 59 commits into from
Oct 23, 2023
Merged

[WIP] Handlers for DampedExp6810, AmoebaMultipoleForce, AxilrodTeller potentials #56

merged 59 commits into from
Oct 23, 2023

Commits on Apr 16, 2023

  1. Initial handlers

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    aehogan committed Apr 16, 2023
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  2. Initial collections

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    aehogan committed Apr 16, 2023
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Commits on Apr 17, 2023

  1. Implement abstract methods, start building out tests

    @aehogan
    aehogan committed Apr 17, 2023
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  2. Stopping point

    @aehogan
    aehogan committed Apr 17, 2023
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  3. Continue building out tests

    @aehogan
    aehogan committed Apr 17, 2023
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  4. Doc

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    aehogan committed Apr 17, 2023
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  5. Fix small pydantic bugs

    @aehogan
    aehogan committed Apr 17, 2023
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  6. Continue filling out tests, ensure parameters are converted to OpenMM… 

    … units
    @aehogan
    aehogan committed Apr 17, 2023
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  7. Continue building tests

    @aehogan
    aehogan committed Apr 17, 2023
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  8. Initial amoebamultipoleforce creation logic

    @aehogan
    aehogan committed Apr 17, 2023
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Commits on Apr 19, 2023

  1. Polarity and partial charge assignment working in Multipole collection

    @aehogan
    aehogan committed Apr 19, 2023
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  2. Polarity assignment test passes

    @aehogan
    aehogan committed Apr 19, 2023
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Commits on Apr 20, 2023

  1. Use topology to generate exceptions (this is unique to AmoebaMultipol… 

    …eForce and a giant headache)
    @aehogan
    aehogan committed Apr 20, 2023
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  2. Implement axilrod teller collection functions

    @aehogan
    aehogan committed Apr 20, 2023
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  3. Test amoeba exceptions

    @aehogan
    aehogan committed Apr 20, 2023
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  4. Finish axilrod teller assignment test

    @aehogan
    aehogan committed Apr 20, 2023
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  5. Start de6810 energy test

    @aehogan
    aehogan committed Apr 20, 2023
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Commits on Apr 21, 2023

  1. de6810 and axilrod energy tests working

    @aehogan
    aehogan committed Apr 21, 2023
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  2. multipole energy test working

    @aehogan
    aehogan committed Apr 21, 2023
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  3. black / isort

    @aehogan
    aehogan committed Apr 21, 2023
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  4. lint unused imports

    @aehogan
    aehogan committed Apr 21, 2023
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Commits on Apr 22, 2023

  1. add test changing handler's options, change option names

    @aehogan
    aehogan committed Apr 22, 2023
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  2. noqa units giving lint problems

    @aehogan
    aehogan committed Apr 22, 2023
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  3. black

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    aehogan committed Apr 22, 2023
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  4. continuing the fight against lint

    @aehogan
    aehogan committed Apr 22, 2023
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Commits on Apr 23, 2023

  1. Add example of simulation running gas phase benzene, remove 1-5 inter… 

    …actions from multipole force or it will complain about exceptions
    @aehogan
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  2. set electrostatics 1-4 to zero to avoid double counting of energies

    @aehogan
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Commits on Apr 24, 2023

  1. Calculate de6810 test energies by hand

    @aehogan
    aehogan committed Apr 24, 2023
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  2. Calculate axilrod teller test energies by hand

    @aehogan
    aehogan committed Apr 24, 2023
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Commits on Apr 25, 2023

  1. Calculate multipole energies/dipoles test energies by hand

    @aehogan
    aehogan committed Apr 25, 2023
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  2. Optimize damped exp 6-8-10 energy expression

    @aehogan
    aehogan committed Apr 25, 2023
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Commits on Apr 26, 2023

  1. Add comments

    @aehogan
    aehogan committed Apr 26, 2023
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  2. Deleting benzene example because it didn't include bonded parameters … 

    …and the nonbonded parameters are unpublished at the moment.
    @aehogan
    aehogan committed Apr 26, 2023
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Commits on May 13, 2023

  1. Seem to be able to set 1-5 neighbors and OpenMM isn't complaining so … 

    …far, this is important for avoiding polarization catastrophe in small cyclic molecules
    @aehogan
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Commits on May 26, 2023

  1. Actually 1-5 interactions still don't work in production simulations

    @aehogan
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  2. Add exclusions to Axilrod Teller potential from either NonbondedForce… 

    … or CustomNonbondedForce, whatever is available
    @aehogan
    aehogan committed May 26, 2023
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  3. Small typo

    @aehogan
    aehogan committed May 26, 2023
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Commits on May 28, 2023

  1. Set the cutoff distance for Axilrod Teller

    @aehogan
    aehogan committed May 28, 2023
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  2. Fix tests

    @aehogan
    aehogan committed May 28, 2023
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  3. Lint

    @aehogan
    aehogan committed May 28, 2023
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Commits on May 30, 2023

  1. Axilrod Teller was potentially triple counting energies/forces

    @aehogan
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  2. Merge remote-tracking branch 'origin/6810_multipole_axilrod_handlers'… 

    … into 6810_multipole_axilrod_handlers

# Conflicts:
#	smirnoff_plugins/tests/handlers/test_nonbonded.py
    @aehogan
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  3. Fixed test

    @aehogan
    aehogan committed May 30, 2023
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Commits on Jun 6, 2023

  1. Add equilateral triangle to Axilrod-Teller energy tests, factor of 1/… 

    …3 not needed when permutation mode is correctly set to SinglePermutation
    @aehogan
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Commits on Jun 8, 2023

  1. Remove commented out code

    @aehogan
    aehogan committed Jun 8, 2023
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Commits on Jun 13, 2023

  1. Add check for custom bond force with Coulomb's law and zero the charg… 

    …es out there as well, AmoebaMultipoleForce will handle the scaling of 1-4 interactions itself
    @aehogan
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Commits on Jun 26, 2023

  1. Replace PolarizationCovalent11 that accidently got removed

    @aehogan
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Commits on Jun 27, 2023

  1. Update README.md

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Commits on Jul 25, 2023

  1. Merge remote-tracking branch 'origin/main' into 6810_multipole_axilro… 

    …d_handlers
    @aehogan
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Commits on Aug 24, 2023

  1. Merge remote-tracking branch 'origin/main' into 6810_multipole_axilro… 

    …d_handlers

# Conflicts:
#	smirnoff_plugins/collections/nonbonded.py
    @aehogan
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Commits on Aug 28, 2023

  1. Update custom collections to use periodic/nonperiodic method options

    @aehogan
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Commits on Aug 30, 2023

  1. Restrict no-cutoff to nonperiodic methods only

    @aehogan
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  2. Don't use periodic boundary conditions for 2 neon potential curve tes… 

    …t of DampedExp6810
    @aehogan
    aehogan committed Aug 30, 2023
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  3. lint

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    aehogan committed Aug 30, 2023
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Commits on Oct 10, 2023

  1. Merge pull request #63 from openforcefield/main 

    Bump actions/checkout from 3 to 4 (#62)
    @aehogan
    aehogan authored Oct 10, 2023
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  2. Fixed unit stripped warning in test_nonbonded.py

    @aehogan
    aehogan committed Oct 10, 2023
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  3. Fixed missing unit in test_nonbonded.py

    @aehogan
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Commits on Oct 23, 2023

  1. Merge pull request #65 from openforcefield/main 

    Update versioneer (#64)
    @aehogan
    aehogan authored Oct 23, 2023
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  2. Update .git-blame-ignore-revs

    @aehogan
    aehogan committed Oct 23, 2023
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