mBuild 2.0 polymer and simulation improvements: Introduce `Path` class, `Polymer.build_from_path()` and add new HOOMD-Blue simulation methods.#1261

Merged

chrisjonesBSU merged 184 commits intomosdef-hub:developfrom

chrisjonesBSU:path-class

Oct 31, 2025

Commits on Nov 22, 2024

add random walk util, new methods to Polymer()
chrisjonesBSU
committed
add straighten method
chrisjonesBSU
committed

Commits on Nov 26, 2024

rename file to conformaitons, add lamellae method
chrisjonesBSU
committed
pass in seed param, fix import
chrisjonesBSU
committed
clean up lamellar func
chrisjonesBSU
committed

Commits on Nov 28, 2024

move polymer.py out of recipes
chrisjonesBSU
committed
remove Polymer from entry points in setup
chrisjonesBSU
committed
clean up random walk
chrisjonesBSU
committed

Commits on Dec 5, 2024

remove Rg method from polymer class for now
chrisjonesBSU
committed

Commits on Jan 19, 2025

change file location
chrisjonesBSU
committed

Commits on Feb 14, 2025

merge with upstream
chrisjonesBSU
committed
remove polymer from plugins during install
chrisjonesBSU
committed

Commits on Feb 19, 2025

add new build methods
chrisjonesBSU
committed

Commits on Feb 20, 2025

remove build_straight
chrisjonesBSU
committed

Commits on Feb 27, 2025

Merge branch 'main' of github.com:mosdef-hub/mbuild into polymer-config
chrisjonesBSU
committed

Commits on Mar 11, 2025

Merge branch 'main' of github.com:mosdef-hub/mbuild into polymer-config
chrisjonesBSU
committed
Merge branch 'main' of github.com:mosdef-hub/mbuild into polymer-config
chrisjonesBSU
committed
Merge branch 'main' of github.com:mosdef-hub/mbuild into polymer-config
chrisjonesBSU
committed
update imports in tests
chrisjonesBSU
committed

Commits on Mar 12, 2025

update doc strings
chrisjonesBSU
committed
Merge branch 'main' of github.com:mosdef-hub/mbuild into polymer-config
chrisjonesBSU
committed

Commits on Mar 13, 2025

move all energy minimization stuff to its own file, move polymer, update tests
chrisjonesBSU
committed

Commits on Mar 19, 2025

Merge branch 'main' of github.com:mosdef-hub/mbuild into polymer-config
chrisjonesBSU
committed

Commits on Mar 25, 2025

Merge branch 'main' of github.com:mosdef-hub/mbuild into polymer-config
chrisjonesBSU
committed

Commits on Mar 26, 2025

move chunk of bounding box code to utils, add Path classes
chrisjonesBSU
committed
add build_from_path method
chrisjonesBSU
committed
update doc strings
chrisjonesBSU
committed
add notes to doc strings
chrisjonesBSU
committed

Commits on Mar 28, 2025

begin adding lamellar Path
chrisjonesBSU
committed

Commits on Apr 10, 2025

add Lamellar path/template class
chrisjonesBSU
committed

Commits on May 8, 2025

Merge branch 'main' of github.com:mosdef-hub/mbuild into path-class
chrisjonesBSU
committed

Commits on May 29, 2025

remove build random method
chrisjonesBSU
committed

Commits on Jun 6, 2025

remove if statement from random walk initial step
chrisjonesBSU
committed

Commits on Jun 13, 2025

merge with upstream, fix conflicts
chrisjonesBSU
committed

Commits on Jun 17, 2025

Add update_bond_graph method to Compound
chrisjonesBSU
committed
Merge branch 'set-bond-graph' into path-class
chrisjonesBSU
committed
remove conformations.py, add cls method to Path, make bond_graph a parameter
chrisjonesBSU
committed

Commits on Jun 18, 2025

add some basic tests
chrisjonesBSU
committed
Merge branch 'main' of github.com:mosdef-hub/mbuild into reformat
chrisjonesBSU
committed
start framework for hoomd emin methods
chrisjonesBSU
committed

Commits on Jun 19, 2025

more work on hoomd sim methods
chrisjonesBSU
committed
update doc strings
chrisjonesBSU
committed
Merge branch 'set-bond-graph' into path-class
chrisjonesBSU
committed

Commits on Jun 20, 2025

Save progress with remove overlaps
chrisjonesBSU
committed
add more parameters
chrisjonesBSU
committed

Commits on Jun 22, 2025

move parameters around
chrisjonesBSU
committed

Commits on Jun 23, 2025

Commits on Jun 24, 2025

Commits on Jun 25, 2025

Merge branch 'main' of github.com:mosdef-hub/mbuild into path-class
chrisjonesBSU
committed
add bond graph to lamellar path, create class for straight path
chrisjonesBSU
committed
Save self.add for end of build, add head first, all monomers, then tail, to maintain expected order of polymer chain children
chrisjonesBSU
committed

Commits on Jun 26, 2025

add parameter to bond head and tail monomers without having to create a periodic bond, useful for cyclic polymers
chrisjonesBSU
committed
Add CyclicPath class
chrisjonesBSU
committed
use numpy 2.0 in env files, and update tests
chrisjonesBSU
committed
fix numpy version
chrisjonesBSU
committed
add upper bound for rdkit
chrisjonesBSU
committed
add doc strings
chrisjonesBSU
committed
add conditional install of openbabel to CI
chrisjonesBSU
committed
update environment-dev file to match gmso
chrisjonesBSU
committed

Commits on Jun 27, 2025

use py313 in arch test
chrisjonesBSU
committed
fix str
chrisjonesBSU
committed
Use newer version of setup-wsl action
chrisjonesBSU
committed
update environment.yml
chrisjonesBSU
committed
Add Knot class to path.py
chrisjonesBSU
committed

Commits on Jun 30, 2025

update python version in pyproject.toml
chrisjonesBSU
committed
update python version in pyproject.toml
chrisjonesBSU
committed
Add note about openbabel and python 3.13
chrisjonesBSU
committed
Merge pull request #1252 from chrisjonesBSU/numpy2
chrisjonesBSU
authored
[pre-commit.ci] pre-commit autoupdate
pre-commit-ci[bot]
authored

Commits on Jul 1, 2025

Merge pull request #1253 from mosdef-hub/pre-commit-ci-update-config
chrisjonesBSU
authored

Commits on Jul 2, 2025

Merge branch 'main' of github.com:mosdef-hub/mbuild into path-class
chrisjonesBSU
committed

Commits on Jul 3, 2025

Add zig-zag, add 3rd dimension to lamellar class
chrisjonesBSU
committed

Commits on Jul 7, 2025

[pre-commit.ci] pre-commit autoupdate
pre-commit-ci[bot]
authored

Commits on Jul 8, 2025

Merge pull request #1254 from mosdef-hub/pre-commit-ci-update-config
chrisjonesBSU
authored
Merge branch 'main' of github.com:mosdef-hub/mbuild into path-class
chrisjonesBSU
committed
Add EmbedMolecule when loading SMILES from rdkit
chrisjonesBSU
committed

Commits on Jul 9, 2025

add embed option for to_rdkit, add volume method
chrisjonesBSU
committed

Commits on Jul 11, 2025

merge simulation/emin changes
chrisjonesBSU
committed
rework hoomd sim funcs
chrisjonesBSU
committed

Commits on Jul 21, 2025

[pre-commit.ci] pre-commit autoupdate
pre-commit-ci[bot]
authored

Commits on Jul 22, 2025

add Monomer class
chrisjonesBSU
committed
use more reasonable lengths for sidemax test
chrisjonesBSU
committed
use smaller sidemax values in test
chrisjonesBSU
committed

Commits on Jul 23, 2025

make hoomd sim class for better flexibility in designing sim methods
chrisjonesBSU
committed

Commits on Jul 25, 2025

Add logic to start RW from another Path Object
chrisjonesBSU
committed

Commits on Jul 28, 2025

Bump to version 1.2.1
chrisjonesBSU
committed
precommit fix for setup.cfg
chrisjonesBSU
committed
[pre-commit.ci] pre-commit autoupdate
pre-commit-ci[bot]
authored

Commits on Jul 29, 2025

Commits on Aug 1, 2025

set dtype based on tolerance
chrisjonesBSU
committed
use numpy for pair dist calculations instead of freud
chrisjonesBSU
committed

Commits on Aug 2, 2025

use trial batch approach for initial pos from another path
chrisjonesBSU
committed
Add numba methods
chrisjonesBSU
committed
A couple of fixes
chrisjonesBSU
committed

Commits on Aug 3, 2025

update doc stirngs, remove unused class methods
chrisjonesBSU
committed

Commits on Aug 4, 2025

update doc strings in path
chrisjonesBSU
committed
Add abilityto set only one part of sim data dict
chrisjonesBSU
committed
[pre-commit.ci] pre-commit autoupdate
pre-commit-ci[bot]
authored

Commits on Aug 5, 2025

Commits on Aug 6, 2025

fix introduced bug when adding compounds from a list
chrisjonesBSU
committed
Add some code comments
chrisjonesBSU
committed

Commits on Aug 7, 2025

Add numba to env files
chrisjonesBSU
committed
clear _hoomd_data when cloning a compound
chrisjonesBSU
committed

Commits on Aug 8, 2025

update version for codeql runners
chrisjonesBSU
committed
Change RNG for use with numba, use numba methods only in random walk, add basic tests
chrisjonesBSU
committed
Add a couple more tests, code comments and doc strings
chrisjonesBSU
committed
Try making numba methods more vectorized
chrisjonesBSU
committed
Add constraint classes, implement in random walk
chrisjonesBSU
committed

Commits on Aug 9, 2025

Add unit test, CylinderConstraint class
chrisjonesBSU
committed
start method for choosing initial point
chrisjonesBSU
committed

Commits on Aug 11, 2025

Commits on Aug 12, 2025

Merge pull request #1260 from mosdef-hub/pre-commit-ci-update-config
chrisjonesBSU
authored
add doc strings
chrisjonesBSU
committed
Merge branch 'main' of github.com:mosdef-hub/mbuild into path-class
chrisjonesBSU
committed

Commits on Aug 13, 2025

Lots of doc string and code comments added
chrisjonesBSU
committed

Commits on Aug 14, 2025

Use particle hashes instead of coordinates in get_child_indices, update doc strings, and failing tests
chrisjonesBSU
committed
Remove changes in load from rdkit smiles that broke unit tests
chrisjonesBSU
committed
Add develop branch to CI trigger
chrisjonesBSU
committed
Add more doc strings and code comments
chrisjonesBSU
committed
Transition to logging instead of warnings module
CalCraven
committed

Commits on Aug 17, 2025

Commits on Aug 18, 2025

Add dihedral and ignore params in gmso.apply
chrisjonesBSU
committed
[pre-commit.ci] pre-commit autoupdate
pre-commit-ci[bot]
authored

Commits on Aug 20, 2025

finding low density points returns all tested points, sorted from low to high density
chrisjonesBSU
committed

Commits on Aug 21, 2025

Add a new random walk method that operates with compounds instead of hard spheres
chrisjonesBSU
committed

Commits on Aug 22, 2025

Replace param name in volume classes
chrisjonesBSU
committed

Commits on Aug 25, 2025

Commits on Aug 26, 2025

Commits on Aug 27, 2025

Add beginning of data structure for RW bias
chrisjonesBSU
committed

Commits on Aug 28, 2025

bug fix, some progress on coordinate bias
chrisjonesBSU
committed

Commits on Aug 29, 2025

CodeQL Fixes
chrisjonesBSU
committed

Commits on Sep 1, 2025

[pre-commit.ci] pre-commit autoupdate
pre-commit-ci[bot]
authored

Commits on Sep 2, 2025

Merge pull request #1266 from mosdef-hub/pre-commit-ci-update-config
chrisjonesBSU
authored

Commits on Sep 15, 2025

[pre-commit.ci] pre-commit autoupdate
pre-commit-ci[bot]
authored

Commits on Sep 16, 2025

Merge pull request #1267 from mosdef-hub/pre-commit-ci-update-config
chrisjonesBSU
authored

Commits on Sep 22, 2025

[pre-commit.ci] pre-commit autoupdate
pre-commit-ci[bot]
authored

Commits on Sep 23, 2025

Merge pull request #1269 from mosdef-hub/pre-commit-ci-update-config
chrisjonesBSU
authored

Commits on Sep 29, 2025

[pre-commit.ci] pre-commit autoupdate
pre-commit-ci[bot]
authored

Commits on Sep 30, 2025

Merge pull request #1271 from mosdef-hub/pre-commit-ci-update-config
chrisjonesBSU
authored

Commits on Oct 6, 2025

[pre-commit.ci] pre-commit autoupdate
pre-commit-ci[bot]
authored

Commits on Oct 7, 2025

Merge pull request #1272 from mosdef-hub/pre-commit-ci-update-config
chrisjonesBSU
authored

Commits on Oct 13, 2025

[pre-commit.ci] pre-commit autoupdate
pre-commit-ci[bot]
authored

Commits on Oct 14, 2025

Merge pull request #1273 from mosdef-hub/pre-commit-ci-update-config
chrisjonesBSU
authored

Commits on Oct 17, 2025

Bond Order Handling (#1274)

CalCraven
and
pre-commit-ci[bot]
authored

Commits on Oct 20, 2025

auto set box
chrisjonesBSU
committed
[pre-commit.ci] pre-commit autoupdate
pre-commit-ci[bot]
authored

Commits on Oct 21, 2025

Merge pull request #1275 from mosdef-hub/pre-commit-ci-update-config
chrisjonesBSU
authored

Commits on Oct 27, 2025

[pre-commit.ci] pre-commit autoupdate
pre-commit-ci[bot]
authored

Commits on Oct 28, 2025

Merge pull request #1277 from mosdef-hub/pre-commit-ci-update-config
chrisjonesBSU
authored

Commits on Oct 29, 2025