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

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Oct 23, 2023
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26a9223
Initial handlers
aehogan Apr 16, 2023
d45ee05
Initial collections
aehogan Apr 16, 2023
369a220
Implement abstract methods, start building out tests
aehogan Apr 17, 2023
575f99b
Stopping point
aehogan Apr 17, 2023
b04a61a
Continue building out tests
aehogan Apr 17, 2023
686df92
Doc
aehogan Apr 17, 2023
9f6b120
Fix small pydantic bugs
aehogan Apr 17, 2023
f95a5b9
Continue filling out tests, ensure parameters are converted to OpenMM…
aehogan Apr 17, 2023
ce9eb34
Continue building tests
aehogan Apr 17, 2023
7d2b13c
Initial amoebamultipoleforce creation logic
aehogan Apr 17, 2023
ab85166
Polarity and partial charge assignment working in Multipole collection
aehogan Apr 19, 2023
b9e6d5d
Polarity assignment test passes
aehogan Apr 19, 2023
e49f9f4
Use topology to generate exceptions (this is unique to AmoebaMultipol…
aehogan Apr 20, 2023
a16f4b4
Implement axilrod teller collection functions
aehogan Apr 20, 2023
98b9c34
Test amoeba exceptions
aehogan Apr 20, 2023
4c4e3f2
Finish axilrod teller assignment test
aehogan Apr 20, 2023
5bde066
Start de6810 energy test
aehogan Apr 20, 2023
a5e238b
de6810 and axilrod energy tests working
aehogan Apr 21, 2023
7aa78fb
multipole energy test working
aehogan Apr 21, 2023
6ebb7cd
black / isort
aehogan Apr 21, 2023
2e4b121
lint unused imports
aehogan Apr 21, 2023
3b5f15c
add test changing handler's options, change option names
aehogan Apr 22, 2023
1ca3109
noqa units giving lint problems
aehogan Apr 22, 2023
dcb9936
black
aehogan Apr 22, 2023
67e34d1
continuing the fight against lint
aehogan Apr 22, 2023
363ad37
Add example of simulation running gas phase benzene, remove 1-5 inter…
aehogan Apr 23, 2023
5a6b986
set electrostatics 1-4 to zero to avoid double counting of energies
aehogan Apr 23, 2023
d5d55eb
Calculate de6810 test energies by hand
aehogan Apr 24, 2023
78950f0
Calculate axilrod teller test energies by hand
aehogan Apr 24, 2023
216fba1
Calculate multipole energies/dipoles test energies by hand
aehogan Apr 25, 2023
965b02d
Optimize damped exp 6-8-10 energy expression
aehogan Apr 25, 2023
91fc633
Add comments
aehogan Apr 26, 2023
2cebe83
Deleting benzene example because it didn't include bonded parameters …
aehogan Apr 26, 2023
f3406dc
Seem to be able to set 1-5 neighbors and OpenMM isn't complaining so …
aehogan May 13, 2023
c9dd4cd
Actually 1-5 interactions still don't work in production simulations
aehogan May 26, 2023
7d2ab45
Add exclusions to Axilrod Teller potential from either NonbondedForce…
aehogan May 26, 2023
0caebd9
Small typo
aehogan May 26, 2023
62a9b22
Set the cutoff distance for Axilrod Teller
aehogan May 28, 2023
11257bc
Fix tests
aehogan May 28, 2023
2136598
Lint
aehogan May 28, 2023
6e09ef5
Axilrod Teller was potentially triple counting energies/forces
aehogan May 30, 2023
3811c8f
Merge remote-tracking branch 'origin/6810_multipole_axilrod_handlers'…
aehogan May 30, 2023
1b74a8b
Fixed test
aehogan May 30, 2023
7dea090
Add equilateral triangle to Axilrod-Teller energy tests, factor of 1/…
aehogan Jun 6, 2023
f311c27
Remove commented out code
aehogan Jun 8, 2023
0aa2bbe
Add check for custom bond force with Coulomb's law and zero the charg…
aehogan Jun 13, 2023
8e2e311
Replace PolarizationCovalent11 that accidently got removed
aehogan Jun 26, 2023
2ea90d9
Update README.md
aehogan Jun 27, 2023
1156cc6
Merge remote-tracking branch 'origin/main' into 6810_multipole_axilro…
aehogan Jul 25, 2023
f870e16
Merge remote-tracking branch 'origin/main' into 6810_multipole_axilro…
aehogan Aug 24, 2023
e1aa569
Update custom collections to use periodic/nonperiodic method options
aehogan Aug 28, 2023
0bffc3e
Restrict no-cutoff to nonperiodic methods only
aehogan Aug 30, 2023
044ad58
Don't use periodic boundary conditions for 2 neon potential curve tes…
aehogan Aug 30, 2023
9d16428
lint
aehogan Aug 30, 2023
3cd5f46
Merge pull request #63 from openforcefield/main
aehogan Oct 10, 2023
36ca81c
Fixed unit stripped warning in test_nonbonded.py
aehogan Oct 10, 2023
94b1279
Fixed missing unit in test_nonbonded.py
aehogan Oct 10, 2023
f889cdf
Merge pull request #65 from openforcefield/main
aehogan Oct 23, 2023
be86922
Update .git-blame-ignore-revs
aehogan Oct 23, 2023
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3 changes: 3 additions & 0 deletions .git-blame-ignore-revs
Original file line number Diff line number Diff line change
@@ -1,2 +1,5 @@
# Some linting
a597529128b11fd0e2a88e5ec1880409db7fa26d

# Versioneer auto-generated
94a0ae93bc06fa2e1cef137eec3f7fdefc0f9c01
3 changes: 3 additions & 0 deletions README.md
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Expand Up @@ -11,6 +11,9 @@ Currently, these include:

* `DampedBuckingham68` - a damped version of the 6-8 buckingham potential proposed by [Tang and Toennies](https://aip.scitation.org/doi/10.1063/1.447150).
* `DoubleExponential` - a double exponential van der Waals potential proposed by [Man et al](https://doi.org/10.1021/acs.jctc.0c01267)
* `DampedExp6810` - a damped version of the 6-8-10 exponential repulsion proposed by [Tang and Toennies](https://aip.scitation.org/doi/10.1063/1.447150) with mixing rules from [Smith](https://doi.org/10.1103/PhysRevA.5.1708)
* `Multipole` - an induced dipole polarizability potential implemented with the AmoebaMultipoleForce in OpenMM
* `AxilrodTeller` - a three-body dispersion potential proposed by [Axilrod and Teller](https://doi.org/10.1063%2F1.1723844)

## Installation

Expand Down
6 changes: 6 additions & 0 deletions setup.py
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Expand Up @@ -40,10 +40,16 @@
"openff.toolkit.plugins.handlers": [
"DampedBuckingham68Handler = smirnoff_plugins.handlers.nonbonded:DampedBuckingham68Handler",
"DoubleExponentialHandler = smirnoff_plugins.handlers.nonbonded:DoubleExponentialHandler",
"DampedExp6810Handler = smirnoff_plugins.handlers.nonbonded:DampedExp6810Handler",
"AxilrodTellerHandler = smirnoff_plugins.handlers.nonbonded:AxilrodTellerHandler",
"MultipoleHandler = smirnoff_plugins.handlers.nonbonded:MultipoleHandler",
],
"openff.interchange.plugins.collections": [
"SMIRNOFFDampedBuckingham68Collection = smirnoff_plugins.collections.nonbonded:SMIRNOFFDampedBuckingham68Collection",
"DoubleExponentialCollection = smirnoff_plugins.collections.nonbonded:SMIRNOFFDoubleExponentialCollection",
"SMIRNOFFDampedExp6810Collection = smirnoff_plugins.collections.nonbonded:SMIRNOFFDampedExp6810Collection",
"SMIRNOFFAxilrodTellerCollection = smirnoff_plugins.collections.nonbonded:SMIRNOFFAxilrodTellerCollection",
"SMIRNOFFMultipoleCollection = smirnoff_plugins.collections.nonbonded:SMIRNOFFMultipoleCollection",
],
},
)
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