Activity tutorial by kmjens · Pull Request #205 · glotzerlab/hoomd-examples

kmjens · 2026-02-04T18:10:40Z

Description

Resolves issue #86

Add activity tutorial to hoomd-examples repo.
This includes:

an introduction to active particles (defines ABPs, MIPS, Pe etc..)
Active Brownian Particles (adding an active force to a 2D system)
MIPS (demonstrating MIPs in 2D)
Active Torque on Rigid Bodies (example of activity on rigid bodies. Explains that this shares mots of the same principles for adding linear active forces to rigid bodies)

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 authors.

Add Kate and Philipp to authors list

…D MIPS.

modifying overdamped viscous dynamics section

…les into activity-tutorial Fixed wording section 4

* rewrite of introduction section of active matter tutorial * Revise content on Active Brownian Particles and MIPS Updated descriptions of Active Brownian Particles and Motility-Induced Phase Separation. Revised section on applying active forces to rigid bodies w/ focus on rigid bodies instead of torque * Fix link formatting in MIPS section * Update repository in test workflow from hoomd-blue to hoomd-examples Issue making a pull request to merge into activity-tutorial because the CI workflow checks out glotzerlab/hoomd-blue using the PR branch name (activity-tutorial*) instead of hoomd-examples --------- Co-authored-by: kmjens <[email protected]>

undo previous change to workflow file as it did not fix the test approval

* Fix text formatting in simulation setup description * Simplify simulation setup description for 2D Removed mention of constraining particle motion to the z-direction for clarity. * Remove 'exclusions' parameter from Cell initialization * Refine MIPS tutorial and clarify simulation details Updated the tutorial to clarify the simulation setup and parameters for MIPS, including changes to the integrator and explanations of key concepts like the Péclet number. Improved language for clarity and conciseness throughout the notebook. * Fix formatting issues in MIPS documentation * Fix LaTeX formatting and clarify parameters in notebook * Fix formatting of LaTex to fix notebook unreadable error * Fix formatting of markdown * collapse fresnel code --------- Co-authored-by: Jared-Shi <[email protected]>

review-notebook-app · 2026-02-04T18:10:45Z

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…cells and collapse fresnel

* Update conda lockfiles (#153) Co-authored-by: joaander <[email protected]> * Bump actions/cache from 4.2.0 to 4.2.2 in the actions-version group (#154) Bumps the actions-version group with 1 update: [actions/cache](https://github.com/actions/cache). Updates `actions/cache` from 4.2.0 to 4.2.2 - [Release notes](https://github.com/actions/cache/releases) - [Changelog](https://github.com/actions/cache/blob/main/RELEASES.md) - [Commits](actions/cache@1bd1e32...d4323d4) --- updated-dependencies: - dependency-name: actions/cache dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions-version ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump actions/cache from 4.2.2 to 4.2.3 in the actions-version group (#156) Bumps the actions-version group with 1 update: [actions/cache](https://github.com/actions/cache). Updates `actions/cache` from 4.2.2 to 4.2.3 - [Release notes](https://github.com/actions/cache/releases) - [Changelog](https://github.com/actions/cache/blob/main/RELEASES.md) - [Commits](actions/cache@d4323d4...5a3ec84) --- updated-dependencies: - dependency-name: actions/cache dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions-version ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Update conda lockfiles (#157) Co-authored-by: joaander <[email protected]> * [pre-commit.ci] pre-commit autoupdate (#158) updates: - [github.com/astral-sh/ruff-pre-commit: v0.8.6 → v0.11.4](astral-sh/ruff-pre-commit@v0.8.6...v0.11.4) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Update conda lockfiles (#159) Co-authored-by: joaander <[email protected]> * Mesh tutorial (#155) * Initial draft of Flexicle Tutorial Docs * Update AUTHORS.md Add Kate and Philipp to authors list * rename tutorial * add new tutorial branch and set up index * update README * first draft of creating meshes * finish mesh creation tutorial * add tutorial 10-1 and 10-2 * finished version of 01- and 02- * fix triangulation image * remove third example * update imported libraries * update execution_count * fix my name * remove id in 00-index * fix ids * spell check * fully comment out pyvista cell * np -> numpy * pre-commit * improve tutorial according to Josh's suggestions * fix precommit * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Switch to a uniform figure style. * Tweaks * Spellcheck * Truncate long output * Hide the fresnel code * Make section titles consistent. * pre-commit --------- Co-authored-by: Kate Jensen <[email protected]> Co-authored-by: kmjens <[email protected]> Co-authored-by: SchoeniPhlippsn <[email protected]> Co-authored-by: Joshua A. Anderson <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Use **row** in the organizing and executing simulations tutorial (#160) * First draft of row tutorial. * Remove unused project file. * ruff format * Fix link. * Test with python 3.13 * pre-commit * Fix cache key. * Grammar pass. * pre-commit * Grammar and consistency. * More tweaks. * Run dependabot quarterly. * More tweaks to dependabot config. * Update uv and conda lockfiles quarterly. * Fix cron. * Switch back to fugit syntanx. Dependabot fails with the POSIX syntax. * Update conda lockfiles (#161) Co-authored-by: joaander <[email protected]> * Bump the actions-version group with 2 updates (#162) Bumps the actions-version group with 2 updates: [mamba-org/setup-micromamba](https://github.com/mamba-org/setup-micromamba) and [glotzerlab/workflows](https://github.com/glotzerlab/workflows). Updates `mamba-org/setup-micromamba` from 2.0.4 to 2.0.5 - [Release notes](https://github.com/mamba-org/setup-micromamba/releases) - [Commits](mamba-org/setup-micromamba@0dea637...b09ef9b) Updates `glotzerlab/workflows` from 0.6.0 to 0.7.0 - [Release notes](https://github.com/glotzerlab/workflows/releases) - [Commits](glotzerlab/workflows@a36a971...1855eec) --- updated-dependencies: - dependency-name: mamba-org/setup-micromamba dependency-version: 2.0.5 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions-version - dependency-name: glotzerlab/workflows dependency-version: 0.7.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions-version ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Close files instead of calling flush. (#163) Fully close gsd and h5 files to promote best practices and better match typical use cases where scripts complete and exit, implicitly closing open files. With the new auto_flush feature in 5.3.0, we do not need to encourage users to call flush. Closing the file is a final act, so users will be more considerate about it -- they cannot continue writing to a closed file. * [pre-commit.ci] pre-commit autoupdate (#164) updates: - [github.com/astral-sh/ruff-pre-commit: v0.11.4 → v0.12.2](astral-sh/ruff-pre-commit@v0.11.4...v0.12.2) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Configure Renovate (#166) * Add renovate.json * Use pixi * Use prek. * prek autoupdate * Use correct pixi.toml. * Add openmpi. * Remove use of deprecated mode argument. --------- Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Joshua A. Anderson <[email protected]> * Update actions/cache action to v4.2.4 (#167) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Update actions/checkout action to v4.3.0 (#168) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Update actions/checkout action to v5 (#171) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Update glotzerlab/workflows action to v0.10.0 (#170) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Lock file maintenance (#172) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Update actions/cache action to v4.3.0 (#173) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Lock file maintenance (#174) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Lock file maintenance (#175) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Update dependency python to 3.14.* (#176) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Lock file maintenance (#177) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Lock file maintenance (#178) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Update prefix-dev/setup-pixi action to v0.9.2 (#179) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Lock file maintenance (#180) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Lock file maintenance (#181) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Update prefix-dev/setup-pixi action to v0.9.3 (#182) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Lock file maintenance (#183) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Lock file maintenance (#184) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Update actions/checkout action to v5.0.1 (#185) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Lock file maintenance (#186) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Fix the HPMC wall potential example. (#187) * Update actions/checkout action to v6 (#188) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Update glotzerlab/workflows action to v0.11.0 (#189) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Lock file maintenance (#190) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * 6.0 fixes (#193) * Rerender missing images. * Attempt to format code as code in alerts. * Use HOOMD 6.0 parameter assignment. * Update actions/checkout action to v6.0.1 (#191) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Lock file maintenance (#192) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Update actions/cache action to v5 (#194) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Update actions/cache action to v5.0.1 (#195) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Lock file maintenance (#196) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Lock file maintenance (#197) * Lock file maintenance * Execute correctly with matplotlib 3.10 --------- Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Joshua A. Anderson <[email protected]> * Lock file maintenance (#198) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Lock file maintenance (#199) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Update actions/cache action to v5.0.2 (#200) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Copyright year. * Lock file maintenance (#201) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Update actions/checkout action to v6.0.2 (#202) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Fix particle position assignment in simulation frame * Fix position_3D assignment in notebook * Remove flush call from simulation run * Refine explanation of active self-propelled particles --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: pull-request-submitter[bot] <82944014+pull-request-submitter[bot]@users.noreply.github.com> Co-authored-by: joaander <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: SchoeniPhlippsn <[email protected]> Co-authored-by: Kate Jensen <[email protected]> Co-authored-by: kmjens <[email protected]> Co-authored-by: SchoeniPhlippsn <[email protected]> Co-authored-by: Joshua A. Anderson <[email protected]> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>

kmjens · 2026-02-04T20:05:34Z

prek told me there was no files available to act on, yet fails the style check here.

joaander

It would be great to complete this!

…P introduction

kmjens · 2026-07-27T20:39:38Z

@joaander @SchoeniPhlippsn @zoecruse @bws212 @Jared-Shi Would love a final look.

Changed the torque notebook to a rigid body tutorial as requested. Implemented all suggested changes in my notes and in the review comments above.

I believe this should be a near final iteration.

…ve variables which are not used

kmjens and others added 23 commits February 13, 2025 18:28

Initial draft of Flexicle Tutorial Docs

88bfea9

Update AUTHORS.md

63dd200

Add Kate and Philipp to authors list

rename active particle tutorial

260dbe9

reorganize turoial files

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tester

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tester part 2

2c0f581

Uploading Active Torque Tutorial

070c3a0

quick edit clean up

a08538f

update activity tutorials to slightly more coherent state. Complete 2…

e9dcb9d

…D MIPS.

Commit quick changes from colloids review from meeting.

9825b72

implement 1st round of edits for activity tutorial

1223fad

make tutorials 2D, add beginner info on Pe number

848e91c

last changes editting text

096f1eb

remove Run and Tumble, small tweaks

8bf8159

Update 02-Active-Brownian-Particles.ipynb

bc1ed17

modifying overdamped viscous dynamics section

Update 02-Active-Brownian-Particles.ipynb

f6f6d4a

edits to rigid body and torque

5f96c75

Update AUTHORS.md

bf40549

Merge branch 'activity-tutorial' of github.com:glotzerlab/hoomd-examp…

ffeaf3c

…les into activity-tutorial Fixed wording section 4

Update repository reference in test workflow

d6696d2

undo previous change to workflow file as it did not fix the test approval

Add Zoe Cruse and Jared Shi to AUTHORS.md

7be23f0

Move Pe definition to section 01. Final read through and edit. Rerun …

464cf7c

…cells and collapse fresnel

kmjens force-pushed the activity-tutorial branch from 8624aea to 464cf7c Compare February 4, 2026 18:38

Jared-Shi and others added 2 commits February 4, 2026 15:03

Merge branch 'trunk' into activity-tutorial

c0f5df3

kmjens requested review from SchoeniPhlippsn and joaander February 4, 2026 20:04

kmjens requested review from Jared-Shi, bws212 and zoecruse February 4, 2026 20:04

kmjens marked this pull request as ready for review February 4, 2026 20:06

kmjens added 4 commits February 4, 2026 15:53

precommit and ruff

6b241e8

retry prek

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manually add prek checks

ec009df

new prek checks

e2c3ad2

SchoeniPhlippsn reviewed Feb 13, 2026

View reviewed changes

First round of review comments adressed; one more set left to address

03edd29

joaander reviewed Jul 22, 2026

View reviewed changes

kmjens added 3 commits July 27, 2026 16:27

resolve comments and suggestions about rigid bodies and clarifying AB…

dda79eb

…P introduction

first round of ruff and prek

8fdf7bf

rename Active torque --> active forces on rigid bodies

ea4ed29

kmjens requested review from SchoeniPhlippsn and joaander July 27, 2026 20:39

kmjens added 2 commits August 12, 2026 12:02

typos and rearrangement of sections. Remove repeat explanations. remo…

ed49e6c

…ve variables which are not used

prek check

b74e305

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Activity tutorial - #205

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