Add k_BT to HPMC integrator

[surajkannur]

Description

Previously, $kT$ was assumed to be 1. In this PR, $kT$ is implemented as a variant in the HPMC integrator.

Motivation and context

Assuming $kT = 1$ meant that the well depth of the potential had to be rescaled to simulate different temperatures in the case of patchy particles. It also made interpreting the $\beta P$ output of the SDF compute difficult. With this change,
the temperature can be user-defined.

How has this been tested?

• pytest set and get kT
• notebook to test
  • $\mu VT$,
  • cluster moves,
  • shape moves
• hoomd-validation tests

hoomd-validation:
LJ Fluid

LJ Union

Patchy Particle Pressure

MuVT simulation with octahedron particles initialized at $kT=1.0$ and $f=10$

Patchy particle simulation replicating results of the tutorial: 'Modelling Patchy Particles' with varying kT instead of the energy scale

TODO documentation

Change log

Add kT to HPMC integrator

Checklist:

• IntegratorHPMCMono.h
• $\mu VT$
• Cluster moves
• SDF pressure compute
• shape moves
• boxMC
• Change SDF input from betaP to P
• I have reviewed the Contributor Guidelines.
• I agree with the terms of the HOOMD-blue Contributor Agreement.
• My name is on the list of contributors (sphinx-doc/credits.rst) in the pull request source branch.

[github-actions]

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.

[surajkannur]

pre-commit.ci autofix

[joaander]

Thanks! I have made several suggestions to improve code style. I also found a bug in BoxMC (not your fault, the variable is named incorrectly).

As an added TODO item, we need to modify hpmc/compute.py.

• Add SDF.P which returns SDF.betaP * {the current kT}.

I also considered renaming betaP to P, but I now think we should keep betaP for backwards compatibility. betaP is also more natural for purely hard particle systems.