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Wang frenkel #1970

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@MartinGirard MartinGirard commented Dec 15, 2024

Description

This draft PR would add the Wang-Frenkel potential to hoomd (equation (2) in Wang & Frenkel, https://pubs.rsc.org/en/content/articlelanding/2020/cp/c9cp05445f).

Motivation and context

This is largely motivated by coarse-grained IDP models, specifically by MPIPI (https://www.nature.com/articles/s43588-021-00155-3), which uses this type of potential.

How has this been tested?

This is work in progress, unit tests will be added to hoomd. At the time of writing this draft PR, I would want some feedback on the implementation. Specifically, in eq (2) of Wang et al, the cutoff radius appears in the potential. I have chosen to change "r_c" there by an adjustable parameter, and remove "alpha".

This is driven by performance considerations. Using the cutoff value at runtime would require computing an extra power, which is usually expansive (log + exp).

An alternative is to enforce exponents to be half integers (>= 1/2), which suits my needs and considerably simplify calculations. The other available implementation (lammps) uses a similar restriction.

Checklist:

  • 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.
  • I have summarized these changes in CHANGELOG.rst following the established format.

dependabot bot and others added 13 commits December 1, 2024 12:43
Bumps the actions-version group with 2 updates: [mamba-org/setup-micromamba](https://github.com/mamba-org/setup-micromamba) and [softprops/action-gh-release](https://github.com/softprops/action-gh-release).


Updates `mamba-org/setup-micromamba` from 2.0.0 to 2.0.2
- [Release notes](https://github.com/mamba-org/setup-micromamba/releases)
- [Commits](mamba-org/setup-micromamba@617811f...06375d8)

Updates `softprops/action-gh-release` from 2.0.9 to 2.1.0
- [Release notes](https://github.com/softprops/action-gh-release/releases)
- [Changelog](https://github.com/softprops/action-gh-release/blob/master/CHANGELOG.md)
- [Commits](softprops/action-gh-release@e7a8f85...01570a1)

---
updated-dependencies:
- dependency-name: mamba-org/setup-micromamba
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: actions-version
- dependency-name: softprops/action-gh-release
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: actions-version
...

Signed-off-by: dependabot[bot] <[email protected]>
Bumps the pip-version group with 2 updates: [ipython](https://github.com/ipython/ipython) and [numpy](https://github.com/numpy/numpy).


Updates `ipython` from 8.29.0 to 8.30.0
- [Release notes](https://github.com/ipython/ipython/releases)
- [Commits](ipython/ipython@8.29.0...8.30.0)

Updates `numpy` from 2.1.2 to 2.1.3
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](numpy/numpy@v2.1.2...v2.1.3)

---
updated-dependencies:
- dependency-name: ipython
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip-version
- dependency-name: numpy
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: pip-version
...

Signed-off-by: dependabot[bot] <[email protected]>
…actions-trunk-patch-actions-version-bfa42ab09b

Bump the actions-version group with 2 updates
…nk-patch-pip-version-d90aa5e57e

Bump the pip-version group with 2 updates
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2 participants