Add patchy pair potential

[cbkerr]

Description

Clean and publish code to simulate patchy particles, including janus particles, based on that used in Phase behavior of Janus colloids determined by sedimentation equilibrium.

Using templates, the code can "modulate" any isotropic pair potential by an "envelope" that is created based on an angle dependence factor.

TODOS remaining

• [x] Add support for patches not aligned with particle orientation.
• [x] Add tests in a new file
• [x] Check casting, line 112 of GeneralEnvelope.h
• [x] Confirm a negative sign relating to dot products, line 78 of JanusFactor.h
• [x] Confirm math in PairModulator.h, line 218
• [x] Add type_shapes in aniso.py.

Motivation and context

How has this been tested?

I wrote expressions in Mathematica and had it do the math to check the values used in the potential. That notebook will be attached to this PR.

Old nomenclature lookup table

Use this to translate when comparing old and new versions of the code.

Kind of Entity	in Old Plugin	in New Code
thing created from template	JanusDirectionalEvaluator	JanusEnvelope
Header file	EvaluatorPairIsoModulated.h	PairModulator.h
template typename	isoEval	pairEvaluator
variable	iParam (“isotropic”)	pairParam
variable	iP (for “isotropic parameter”), _iP	pairP, _pairP
template typename	dirEval	directionalEnvelope
variable ?	dParam	envelopeParam
variable	dP, _dP	envelP, _envelP
protected variable	iEv (“isotropic (pair) evaluator”)	pairEval
protected variable	dEv (“directional (pair) evaluator”)	envelEval
variable in PairModulator	isoModulator	envelope
Header file	DirectionalEvaluatorPairSphere.h	GeneralEnvelope.h
old header file with bugs	DirectionalEvaluatorPair
returned name	deps	genenv
template typename	AngularModulator	AngleDependence
Header file	ModulatorJanus(“Sphere” in code).h	JanusFactor.h
Header file	AllAnisoPairPotentialsExt.h	Linking done in “module.cc” and “module-md.cc”
exported name	PotentialPairJanusLJ	PotentialPairJanusLJ
	AnisoPotentialPair	[already exists]
Header file	EvaluatorPairAnisoModulated.h	?

Change log

Checklist:

• [x] I have reviewed the Contributor Guidelines.
• [x] I agree with the terms of the HOOMD-blue Contributor Agreement.
• [x] My name is on the list of contributors (sphinx-doc/credits.rst) in the pull request source branch.

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[github-actions[bot]]

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This pull request has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs.

[github-actions[bot]]

This pull request has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs.

[github-actions[bot]]

This pull request has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs.

[github-actions[bot]]

This pull request has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs.

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[joaander]

@cbkerr continues to work on this pull request.

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[cbkerr]

I'm still working on validating the potential

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[joaander]

Not stale.

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This pull request has been automatically closed because it has not had recent activity.