What's Changed

Features

Bug fixes

Fix sidemax test in test_packing.py by using a more reasonable length by @chrisjonesBSU in https://github.com/mosdef-hub/mbuild/pull/1256

Maintenance

Use numpy 2 in CI testing. Drop python 3.9, add python 3.13 to testing, remove openbabel from enviroment-dev.yml by @chrisjonesBSU in https://github.com/mosdef-hub/mbuild/pull/1252
[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #1251, #1253, #1254, #1255,

Full Changelog: https://github.com/mosdef-hub/mbuild/compare/1.2.0...1.2.1

- Python
Published by chrisjonesBSU 7 months ago

What's Changed

Features

Add method to Compound that checks for overlapping particles by @chrisjonesBSU in https://github.com/mosdef-hub/mbuild/pull/1225
Add option for periodic boundaries when using PACKMOL. by @chrisjonesBSU in https://github.com/mosdef-hub/mbuild/pull/1223

Bugfixes

Fix show ports by @chrisiacovella in https://github.com/mosdef-hub/mbuild/pull/1233

Maintenance

Fix and update Dockerfile by @chrisjonesBSU in https://github.com/mosdef-hub/mbuild/pull/1220
Remove windows tesitng, add separate WSL test, update readthedocs environment and remove documentation of deprecated modules. by @chrisjonesBSU in https://github.com/mosdef-hub/mbuild/pull/1227
Drop importlib.resources backport by @mattwthompson in https://github.com/mosdef-hub/mbuild/pull/1246
Add py3Dmol to dev env file by @chrisjonesBSU in https://github.com/mosdef-hub/mbuild/pull/1248
Remove experimental feature tag for freud generate_bonds by @CalCraven in https://github.com/mosdef-hub/mbuild/pull/1249
[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/mosdef-hub/mbuild/pull/1221 https://github.com/mosdef-hub/mbuild/pull/1222 https://github.com/mosdef-hub/mbuild/pull/1224 https://github.com/mosdef-hub/mbuild/pull/1228 https://github.com/mosdef-hub/mbuild/pull/1229 https://github.com/mosdef-hub/mbuild/pull/1230 https://github.com/mosdef-hub/mbuild/pull/1234 https://github.com/mosdef-hub/mbuild/pull/1235 https://github.com/mosdef-hub/mbuild/pull/1238 https://github.com/mosdef-hub/mbuild/pull/1239 https://github.com/mosdef-hub/mbuild/pull/1240 https://github.com/mosdef-hub/mbuild/pull/1241https://github.com/mosdef-hub/mbuild/pull/1242 https://github.com/mosdef-hub/mbuild/pull/1243 https://github.com/mosdef-hub/mbuild/pull/1244 https://github.com/mosdef-hub/mbuild/pull/1245 https://github.com/mosdef-hub/mbuild/pull/1247 https://github.com/mosdef-hub/mbuild/pull/1250

Full Changelog: https://github.com/mosdef-hub/mbuild/compare/1.1.1...1.2.0

- Python
Published by chrisjonesBSU 9 months ago

What's Changed

Features

Add Ruff to pre-commit hooks by @chrisjonesBSU in https://github.com/mosdef-hub/mbuild/pull/1207
Reformat loaders for different smiles paths by @CalCraven in https://github.com/mosdef-hub/mbuild/pull/1211
Replace setup.py with pyproject.toml, update actions to latest versions by @chrisjonesBSU in https://github.com/mosdef-hub/mbuild/pull/1217
Update 1.1.1 by @CalCraven in https://github.com/mosdef-hub/mbuild/pull/1219

Bugfixes

fix label handling during flatten by @CalCraven in https://github.com/mosdef-hub/mbuild/pull/1208

Maintenance

[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/mosdef-hub/mbuild/pull/1209 https://github.com/mosdef-hub/mbuild/pull/1210 https://github.com/mosdef-hub/mbuild/pull/1213 https://github.com/mosdef-hub/mbuild/pull/1214 https://github.com/mosdef-hub/mbuild/pull/1215 https://github.com/mosdef-hub/mbuild/pull/1216 https://github.com/mosdef-hub/mbuild/pull/1218

Full Changelog: https://github.com/mosdef-hub/mbuild/compare/1.0.0...1.1.1

- Python
Published by CalCraven about 1 year ago

What's Changed

Bugfixes * fix label handling during flatten by @CalCraven in https://github.com/mosdef-hub/mbuild/pull/1208 * Reformat loaders for different smiles paths by @CalCraven in https://github.com/mosdef-hub/mbuild/pull/1211

Maintenance * Add Ruff to pre-commit hooks by @chrisjonesBSU in https://github.com/mosdef-hub/mbuild/pull/1207 * [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/mosdef-hub/mbuild/pull/1209, https://github.com/mosdef-hub/mbuild/pull/1210, https://github.com/mosdef-hub/mbuild/pull/1213

Full Changelog: https://github.com/mosdef-hub/mbuild/compare/1.0.0...1.1.0

- Python
Published by CalCraven about 1 year ago

mbuild - mBuild 1.0 stable release

`mBuild` 1.0 Announcement

mBuild has reached a relatively feature complete stage. The core functionality of building up a wide array of systems is very stable and generalizeable through custom recipes. As GMSO has continued to inherit the workload of functionality, including being the nexus of conversion to other python objects and file readers and writers, many methods of mBuild have been exported. This leaves mBuild as a more focused package on handling diverse simulation configurations. Continued development will shift towards more complicated initialization utilities, such as energy minimization steps, quick and dirty Monte Carlo methods for thermodynamic configurations, polymer crosslinking, protein folding, and potentially more coarse grain accessibility and backmapping. We hope to continue to work with others who have developed these methods for their own research, and make them available to the community through mBuild routines.

What's Changed just in the last patch.

improve speedup of large lattice by @CalCraven in https://github.com/mosdef-hub/mbuild/pull/1198
Remove deprecated formats, update reader and writer backends by @chrisjonesBSU in https://github.com/mosdef-hub/mbuild/pull/1191
Remove rigid body data structure from Compound by @chrisjonesBSU in https://github.com/mosdef-hub/mbuild/pull/1203
[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/mosdef-hub/mbuild/pull/1201

Full Changelog: https://github.com/mosdef-hub/mbuild/compare/0.18.0...1.0.0

- Python
Published by CalCraven over 1 year ago

mbuild - 0.18.0

What's Changed

Features

Add packmol_args parameter to packing fucntions. Allows user to give additional commands to PACKMOL. by @chrisjonesBSU in https://github.com/mosdef-hub/mbuild/pull/787
Add cap hydrogens to head and tail compounds in the polymer builder by @chrisjonesBSU in https://github.com/mosdef-hub/mbuild/pull/1196

Bugfixes

resetlabels kwarg to forceoverlap, new method reset_labels by @jaclark5 in https://github.com/mosdef-hub/mbuild/pull/1195

Maintenance

Fix failing tests with latest version of packmol by @CalCraven in https://github.com/mosdef-hub/mbuild/pull/1189
Add warnings for deprecated file formats (protobuf, hoomdxml, Hoomd-Blue and LAMMPS simulation writers) by @chrisjonesBSU in https://github.com/mosdef-hub/mbuild/pull/1188
[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/mosdef-hub/mbuild/pull/1193
Fix deprecation warnig in packing.py and replace .format() with f-strings where possible. by @chrisjonesBSU in https://github.com/mosdef-hub/mbuild/pull/1192

Full Changelog: https://github.com/mosdef-hub/mbuild/compare/0.17.1...0.18.0

- Python
Published by CalCraven over 1 year ago

mbuild - 0.17.1

What's Changed

Features

Update README graphic by @daico007 in https://github.com/mosdef-hub/mbuild/pull/1178
Add option to reset child labels in Compound.remove() by @jaclark5 in https://github.com/mosdef-hub/mbuild/pull/1173
Periodic polymer by @jaclark5 in https://github.com/mosdef-hub/mbuild/pull/1170

Bugfixes

Attempt to fix docs build by @daico007 in https://github.com/mosdef-hub/mbuild/pull/1169
Fix failing doc build by @daico007 in https://github.com/mosdef-hub/mbuild/pull/1177

Maintenance

Bump to python 3.12 by @CalCraven in https://github.com/mosdef-hub/mbuild/pull/1180
[pre-commit.ci] pre-commit autoupdate by https://github.com/pre-commit-ci in https://github.com/mosdef-hub/mbuild/pull/1167, https://github.com/mosdef-hub/mbuild/pull/1176, https://github.com/mosdef-hub/mbuild/pull/1181, https://github.com/mosdef-hub/mbuild/pull/1183, https://github.com/mosdef-hub/mbuild/pull/1184
[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/mosdef-hub/mbuild/pull/1184

Full Changelog: https://github.com/mosdef-hub/mbuild/compare/0.17.0...0.17.1

- Python
Published by CalCraven almost 2 years ago

mbuild - mBuild 0.17.0

Features

Add export to RDKIT to allow for chemdraw style visualization. by @chrisiacovella in https://github.com/mosdef-hub/mbuild/pull/1137
Add check_box_size option for add method in Compound.add() by @daico007 in https://github.com/mosdef-hub/mbuild/pull/1149
Add new default option for combining_rule in Compound.save() by @daico007 in https://github.com/mosdef-hub/mbuild/pull/1153
Added ability to adjust bead_size by @jaclark5 in https://github.com/mosdef-hub/mbuild/pull/1158
Speed up json loader by @daico007 in https://github.com/mosdef-hub/mbuild/pull/1163

Bug fixes

fixed the tree print issue by @GuiLingfeng in https://github.com/mosdef-hub/mbuild/pull/1155

Maintenance

Fix Docker build by @daico007 in https://github.com/mosdef-hub/mbuild/pull/1147
[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1148, #1151, #1154, #1161, #1164, #1165
Update deprecated syntax in CI.yml by @daico007 in https://github.com/mosdef-hub/mbuild/pull/1160

New Contributors

@GuiLingfeng made their first contribution in https://github.com/mosdef-hub/mbuild/pull/1155

Full Changelog: https://github.com/mosdef-hub/mbuild/compare/0.16.4...0.17.0

- Python
Published by daico007 about 2 years ago

mbuild - mBuild 0.16.4

Features

Revised load_xyz function by @chrisiacovella in https://github.com/mosdef-hub/mbuild/pull/1140
Add new option for packing.solvate by @daico007 in https://github.com/mosdef-hub/mbuild/pull/1144

Bug fixes

Fix Treelib test by @daico007 in https://github.com/mosdef-hub/mbuild/pull/1142

Maintenance

Added extensions to savers doc string by @CalCraven in https://github.com/mosdef-hub/mbuild/pull/1146
[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/mosdef-hub/mbuild/pull/1136, https://github.com/mosdef-hub/mbuild/pull/1145

Full Changelog: https://github.com/mosdef-hub/mbuild/compare/0.16.3...0.16.4

- Python
Published by daico007 over 2 years ago

mbuild - mBuild 0.16.3

What's Changed

Features

Support GSD >= 2.9 by @chrisjonesBSU in https://github.com/mosdef-hub/mbuild/pull/1131
Turn off infer_residues for when converting to parmed by @daico007 in (#1129, #1134, #1135)

Full Changelog: https://github.com/mosdef-hub/mbuild/compare/0.16.2...0.16.3

- Python
Published by daico007 over 2 years ago

mbuild - mBuild 0.16.2

Features

speeding up add function for large compounds by @chrisiacovella in https://github.com/mosdef-hub/mbuild/pull/1107
Reduce charge particle warnings; add static particle_charge method by @chrisjonesBSU in https://github.com/mosdef-hub/mbuild/pull/1109
Extend ordering of rb torsions written out from parmed structure by @CalCraven in https://github.com/mosdef-hub/mbuild/pull/1112
New water box recipe by @chrisiacovella in https://github.com/mosdef-hub/mbuild/pull/1115
Add 2d checkered pattern by @daico007 in https://github.com/mosdef-hub/mbuild/pull/1118

Bug fixes

Fix lammps impropers docstring by @daico007 in https://github.com/mosdef-hub/mbuild/pull/1120
fixed freud bond issue by @chrisiacovella in https://github.com/mosdef-hub/mbuild/pull/1127

Maintenance

Add networkx to environment.yml by @daico007 in https://github.com/mosdef-hub/mbuild/pull/1103
Add testing for py3.10 and 3.11 by @daico007 in https://github.com/mosdef-hub/mbuild/pull/1110
Attempt to fix readthedocs build by @daico007 in https://github.com/mosdef-hub/mbuild/pull/1105
Use list to store compound.children by @daico007 in https://github.com/mosdef-hub/mbuild/pull/1121
Maintenance task by @daico007 in https://github.com/mosdef-hub/mbuild/pull/1123
handle hoomd 4 by @daico007 in https://github.com/mosdef-hub/mbuild/pull/1128

Full Changelog: https://github.com/mosdef-hub/mbuild/compare/0.16.1...0.16.2

- Python
Published by daico007 over 2 years ago

mbuild - mBuild 0.16.1

Features

Replaced bondgraph with networkx by @chrisiacovella in https://github.com/mosdef-hub/mbuild/pull/1087
Write LJ parameters with 5 decimal places instead of 3 with MCF writer. by @rwsmith7531 in https://github.com/mosdef-hub/mbuild/pull/1095
Add "metal" Unit for Lammps by @thangckt in https://github.com/mosdef-hub/mbuild/pull/1098
Print the hierarchy of a compound by @chrisiacovella in https://github.com/mosdef-hub/mbuild/pull/1097

Maintenance

[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/mosdef-hub/mbuild/pull/1099

New Contributors

@thangckt made their first contribution in https://github.com/mosdef-hub/mbuild/pull/1098

Full Changelog: https://github.com/mosdef-hub/mbuild/compare/0.16.0...0.16.1

- Python
Published by daico007 almost 3 years ago

mbuild - mBuild 0.16.0

Features

Add smiles string conversion using pybel backend by @daico007 in https://github.com/mosdef-hub/mbuild/pull/1056
Trim coordinate_transform.py, new features for spin method by @daico007 in https://github.com/mosdef-hub/mbuild/pull/1054
Updates to energy minimization routines by @chrisiacovella in #1061, #1076, #1078.
Produce n=2 when ports are not capped by @jaclark5 in https://github.com/mosdef-hub/mbuild/pull/1069
Add more notes about unit conversions to the hoomd functions by @chrisjonesBSU in https://github.com/mosdef-hub/mbuild/pull/1062
Reorder bond, angle, and dihedral in write_lammpsdata by @jaclark5 in https://github.com/mosdef-hub/mbuild/pull/1071
Lammps molecule number by @jaclark5 in https://github.com/mosdef-hub/mbuild/pull/1073
Lammps lj unit charges by @jaclark5 in https://github.com/mosdef-hub/mbuild/pull/1086
Clearer error message for fill_region by @RainierBarrett in https://github.com/mosdef-hub/mbuild/pull/1088

Bugfixes

Fix bug related to get_boundingbox() by @daico007 in https://github.com/mosdef-hub/mbuild/pull/1059
Patches for element reading in lattice builder by @CalCraven in https://github.com/mosdef-hub/mbuild/pull/1066

Maintenance

[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1053, #1058, #1063, #1074 #1075, #1079, #1083, #1089
Turn off fail-fast by @daico007 in https://github.com/mosdef-hub/mbuild/pull/1067
drop py3.7 from testing by @daico007 in https://github.com/mosdef-hub/mbuild/pull/1055
Migrate GOMC and CHARMM writer by @daico007 in https://github.com/mosdef-hub/mbuild/pull/1064

New Contributors

@jaclark5 made their first contribution in https://github.com/mosdef-hub/mbuild/pull/1069
@RainierBarrett made their first contribution in https://github.com/mosdef-hub/mbuild/pull/1088

Full Changelog: https://github.com/mosdef-hub/mbuild/compare/0.15.1...0.16.0

- Python
Published by daico007 about 3 years ago

mbuild - mBuild 0.15.1

Features

Default mass and charge of Compound to None by @daico007 in https://github.com/mosdef-hub/mbuild/pull/1047
Add refer_inhierarchy to gmso conversion by @daico007 in https://github.com/mosdef-hub/mbuild/pull/1051
Dihedral rotator function by @uppittu11 in https://github.com/mosdef-hub/mbuild/pull/1039

Bug fixes

Fix for bug with mbuild missing edges in bond graph by @CalCraven in https://github.com/mosdef-hub/mbuild/pull/1049

Maintenance

[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/mosdef-hub/mbuild/pull/1042

Full Changelog: https://github.com/mosdef-hub/mbuild/compare/0.15.0...0.15.1

- Python
Published by daico007 over 3 years ago

mbuild - mBuild 0.15.0

Features

Add is_independent() method for compound by @daico007 in https://github.com/mosdef-hub/mbuild/pull/1020
- Identify if a compound has bonds to compounds outside of its hierarchy.
Add method to flatten an mbuild compound by @daico007 in https://github.com/mosdef-hub/mbuild/pull/1027
- Take a hierarchical structure and reduce it to just a single container compound containing particles.
improve performance of is_independent by @daico007 in https://github.com/mosdef-hub/mbuild/pull/1037
- Check neighborlist for particle in self.particles() as an iterator, instead of particle in self to improve performance of molecule identification.
Add an attribute that tracks the number of bonds a particle is involved in by @chrisjonesBSU in https://github.com/mosdef-hub/mbuild/pull/1024
- Self.nbonds checks the number of bonds within a compound’s children. This returns a value of 0 for particles, as they have no children. To check for valency, self.ndirect_bonds can be useful to add ports or bonds into a compound.
Modify bond graph to include independent particle by @daico007 in https://github.com/mosdef-hub/mbuild/pull/1036
- The bond graph would only include particles that are members of bonds. This leaves out particles in the bond graph which are point particles, such as coarse grained beads or point atoms in a lattice.

Bug Fixes

Propagate kwargs in mb.load when backend is gmso. Fix #1034 by @umesh-timalsina in https://github.com/mosdef-hub/mbuild/pull/1035
Update port.access_labels by @daico007 in https://github.com/mosdef-hub/mbuild/pull/1032

Maintenance

[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in (#1021, #1026, #1040)
Switch from Azure to GHA by @daico007 in https://github.com/mosdef-hub/mbuild/pull/1033

Full Changelog: https://github.com/mosdef-hub/mbuild/compare/0.14.2...0.15.0

- Python
Published by daico007 over 3 years ago

mbuild - mBuild 0.14.2

Features

Add CITATION.cff file for easier repo citation by @justinGilmer in #1014, #1017, #1018

Bug fixes

Add missing file extensions in MANIFEST by @umesh-timalsina in https://github.com/mosdef-hub/mbuild/pull/1016
Change syntax to remove ghost ports by @daico007 in https://github.com/mosdef-hub/mbuild/pull/995

Maintenance

Exclude setup.cfg by @justinGilmer in https://github.com/mosdef-hub/mbuild/pull/1015

Full Changelog: https://github.com/mosdef-hub/mbuild/compare/0.14.1...0.14.2

- Python
Published by daico007 almost 4 years ago

mbuild - mBuild 0.14.1

Features

Use gmso backend to load Silica surfaces by @daico007 in https://github.com/mosdef-hub/mbuild/pull/1013

Bug fixes

Set periodicity correctly in freudgeneratebonds by @justinGilmer in https://github.com/mosdef-hub/mbuild/pull/1012
Fix charge scaling in HOOMD converters by @jennyfothergill in https://github.com/mosdef-hub/mbuild/pull/1011

Full Changelog: https://github.com/mosdef-hub/mbuild/compare/0.14.0...0.14.1

- Python
Published by daico007 almost 4 years ago

mbuild - mBuild 0.14.0

Breaking change

Dropping support of Python 3.6 and adding testing for Python 3.9 https://github.com/mosdef-hub/mbuild/pull/1000

Features

Add buffer argument for neighborlist by @jennyfothergill in https://github.com/mosdef-hub/mbuild/pull/988
Update the api for the cif file reader by @justinGilmer in https://github.com/mosdef-hub/mbuild/pull/989
Generate bonds with freud by @justinGilmer in https://github.com/mosdef-hub/mbuild/pull/969
Integrating GMSO as mbuild backend by @daico007 in https://github.com/mosdef-hub/mbuild/pull/971
Include box info when writing/reading json file by @daico007 in https://github.com/mosdef-hub/mbuild/pull/1005
Lammpswriter lj style by @CalCraven in https://github.com/mosdef-hub/mbuild/pull/993
Added TargetSwap move functionality and impulse correction to the GOMC control file writer by @bc118 in https://github.com/mosdef-hub/mbuild/pull/951
Update structure.defaults.comb_rule when saving by @daico007 in https://github.com/mosdef-hub/mbuild/pull/1010
Allow user to pad bounding box for small cmpds by @justinGilmer in https://github.com/mosdef-hub/mbuild/pull/1007

Bug fixes

Fix bug when having multiple dihedrals by @XiaoboLinlin in https://github.com/mosdef-hub/mbuild/pull/963
Copy input structure for write_lammpsdata by @rwsmith7531 in https://github.com/mosdef-hub/mbuild/pull/959
Use clone of solute in packing.solvate() method by @daico007 in https://github.com/mosdef-hub/mbuild/pull/985
Fix incorrect indexing of force constants in HOOMD forcefield by @jennyfothergill in https://github.com/mosdef-hub/mbuild/pull/996
Removed the C0 or K0 dihedral term from the Charmm writer by @bc118 in https://github.com/mosdef-hub/mbuild/pull/997
Ensure positions are casted to python floats before conversion to json by @umesh-timalsina in https://github.com/mosdef-hub/mbuild/pull/1002
Fix 1-4 LJ scaling detection for mcf writer by @rwsmith7531 in https://github.com/mosdef-hub/mbuild/pull/1004
Make Lammps Writer use correct indexing by @CalCraven in https://github.com/mosdef-hub/mbuild/pull/1009

Maintenance

Remove execution permission from files by @umesh-timalsina in https://github.com/mosdef-hub/mbuild/pull/960
Remove bash uploader in favor of codecov uploader by @umesh-timalsina in https://github.com/mosdef-hub/mbuild/pull/965
Use f-strings when applicable, add experimental by @justinGilmer in https://github.com/mosdef-hub/mbuild/pull/968
Use functools.wraps to preserve docstring by @justinGilmer in https://github.com/mosdef-hub/mbuild/pull/970
[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #975, #977, #978, #983, #992. #999
Fix mbuild version command in ISSUE TEMPLATE by @jennyfothergill in https://github.com/mosdef-hub/mbuild/pull/981
Modify bleeding test by @daico007 in https://github.com/mosdef-hub/mbuild/pull/982
Pin hoomdv3 to dev12 until the issue with hoomd.md.special_pair.LJ in dev13 is resolved by @justinGilmer in https://github.com/mosdef-hub/mbuild/pull/998

New Contributors

@XiaoboLinlin made their first contribution in https://github.com/mosdef-hub/mbuild/pull/963

Full Changelog: https://github.com/mosdef-hub/mbuild/compare/0.13.1...0.14.0

- Python
Published by daico007 almost 4 years ago

mbuild - mBuild 0.13.1

mBuild 0.13.1

Features

Add ExpertMode method for GOMC writer (#946)
Add precision kwarg to xyz writer (#948)

Bug fixes

Change default HOOMD r_cut values to 2.5 (#947)
Update PeriodicKDTree to support the new Box class (#952)
Update OpenMM references in energy_minimize (#953)
Include molecule ID offset in lammps writer (#954)
Fix bug in mbuild.clone (not cloning Compound.periodicity) (#955)

Maintenance

Pre-commit autoupdate (#949, #956)
Update docker image and re-add anaconda user (#957)

- Python
Published by daico007 over 4 years ago

mbuild - mBuild 0.13.0

Features

Add constraints options to Compound.energy_minimize() (#941)
Add mass as an attribute of Compound (#869)
Add support for HOOMD-Blue v3 (#871)
General improvements to the GOMC writer (#937)

Maintenance

Update windows installation instructions (#945)
Migrate azure pipeline environment creation to use mamba (#938)
Pre-commit autoupdate (#939)
Update docstring for conversion.py (#942)
Update Docker image information and entry point (#943)

- Python
Published by daico007 over 4 years ago

mbuild - mBuild 0.12.0

Major Bugfix - Impacted User Note

There was a bug in our native conversion from dihedral coefficients that were in the Ryckaert-Bellemans form. An incorrect method to convert these terms could lead to incorrect dihedral parameters when written out to file for our mbuild-native writers. The impacted file formats and objects are described below. We recommend all affected users to re-generate their parametrized files and inspect their dihedral terms.

Who is affected

Whoever has written out parametrized systems using the mbuild-native HOOMDXML or LAMMPS file extensions that contain dihedrals of the Ryckaert-Bellemans form (#916)
Whoever has written out parametrized systems using the mbuild-native create_hoomd_simulation with a system that contains dihedrals of the Ryckaert-Bellemans form (#916)
Whoever has written out to the above above formats using systems parametrized by foyer using the shipped oplsaa or trappe-ua potentials (#916)

Features

Add new MoSDeF graphic in README.md (#918)
Allow different neighborlist options to be passed in to create_hoomd_simulation (#913)
Add loading support for POSCAR files (#747)
Support converting HOOMD-Blue simulation snapshots to mbuild.Compounds (#834)
Remove improper atom sorting in the MCF file writer (#926)
Support for AMBER proper and improper dihedrals in write_lammpsdata (#896)
Overhaul of documentation pages mbuild.mosdef.org (#889)
Incorporate quality of life updates for lammpswriter (#924)
Add fixed-bonds and fixed-angles support for GOMC writer (#932)

Bugfixes

Changed the RB_to_OPLS function to an equation that works in all acceptable cases and errors out otherwise (#916)
Properly scale user inputs for GOMC writer (#923)
Fix function calls in axis transform functions (#928)

Maintenance

pre-commit autoupdate (#933)

- Python
Published by daico007 over 4 years ago

mbuild - mBuild 0.11.0

Breaking changes

Overhaul the mb.Box class (#774)
- Note: Any methods that relied on previous box behavior may be affected, Compound.get_boundingbox() should emulate that behavior if needed
mbuild.Compound.bounding_box is now a method called: mbuild.Compound.get_boundingbox() (#774)
mbuild.lattice.get_populated_box() has been removed, mbuild.lattice.populate() returns a Compound with a box attribute equivalent to the lattice parameters provided (#774)
Compound.periodicity has been changed to a tuple of booleans instead of lengths, use compound.box or compound.get_boundingbox() for the periodic distances (#774)

Features

Add edge adjustment for various packing functions (#837)
Allow restart.gsd file to be passed to create_hoomd_simulation (#844)
Migrate existing SMILES loader to RDKit (#854)
- Note: previous SMILES loading capability relied on openbabel, the user can still access that with mb.load(backend='pybel')
Add functionality to update mb.Port’s separation and orientation after creation (#839)
Add support for writing GOMC specific molecular and input files (#831)
Add library molecules for water models (#898)
Overhaul mbuild Polymer builder (#851)
Update ordered set usage (#904)
Add input coercion for mb.Compound xyz setter (#892)
Add write_atomnames option to xyz writer (#907)
Ensure deterministic order for bond creation (#905)
Update GOMC writers to support non-orthogonal boxes (#910)

Bug Fixes

Fix 1-4 scaling inference if one atom has zero epsilon (#847)
Fix bug and add unit tests for intermol conversion (#855)
Fix edge buffer for solvate method (#863)

Maintenance

Update azure pipelines (#849, #859)
Move has_nglview to corresponding test files (#842)
Start using conda yml files for requirements installation (#850)
Fix line continuation error in Dockerfile (#857)
Add units to docs (#858)
Convert TODO comments to issues (#876)
Update README (#873)
Add pre-commit (#868, #894, #902, #906, #911)
Fix autodoc issues in docs (#901)
Deprecate ATB client (#909)

- Python
Published by daico007 over 4 years ago

mbuild - mBuild 0.10.13

This version of mBuild now depends on parmed version v3.4.0 and later.

Bug Fixes

Update lammpsdata.py for nbfix_types index changes in parmed (#832)

Maintenance

Remove deprecated aliases from NumPy to built-in types (#828)

- Python
Published by umesh-timalsina about 5 years ago

mbuild - mBuild 0.10.12

Bug Fixes

Set element to None if it cannot be infered in read_xyz (#821)

Maintenance

Add python 3.8 support and remove channel mosdef (#823)

- Python
Published by umesh-timalsina about 5 years ago

mbuild - mBuild 0.10.11

Features

Integrate element attribute with object conversions and writers (#790)
Allow hoomd functions to read in and add to an existing snapshot (#808)

Maintenance

Fix deprecation warning on 'Iterable' import (#803)
Remove Travis CI (#812, #817)
Set ignore_box_warn to True for loading SMILES (#806)
Add hoomd to testing env (#810)

Bug Fixes

Fix particles out of box in to_hoomdsnapshot (#815)
Use correct lattice spacing when reading from cif (#819)

- Python
Published by umesh-timalsina about 5 years ago

mbuild - mBuild 0.10.10

Breaking Change

From this version, mBuild will no longer be distributed on Pypi

Features

Add sidemax argument for various packing functions (#795)

Bug Fixes

Fix conversion factor in file header when writing to hoomdxml (#798)
Fix syntax error in conversion.py (#797)

Maintenance

Simplify docker behavior (#791)
Update links in docs/installation.srt (#794)
Remove Deprecated messages in coordinate_transform.py and compound.py (#763)
Remove Pypi publish scripts (#801)

- Python
Published by daico007 over 5 years ago

mbuild - mBuild 0.10.9

Announcement

mBuild 0.10.9 will be the last version hosted on Pypi. In the future, all the versions on Pypi will be removed.

Breaking change

Refactor of mbuild.load() (#721)

Features

Add element attribute to Compound (#771)

Maintenance

Add links to github repository in documentation (#777)
Add OpenBabel as required dependency and pin its version to 0.3.0 (#779, #783)
Use setup.cfg for coverage, bump2version for versioning (#773)
Add docker release and pypi publish script (#778)

- Python
Published by daico007 over 5 years ago

mbuild - mBuild 0.10.8

Features

Support entry_point plugins for mbuild package distributed by conda (#754)

Bug fixes

Fix bug when cloning a Compound with Box (#753) Fix CIF module import statement, add more unit tests (#760) Include missing transpose of CIF box_matrix (#767) Fix command typo in packing.py (#761)

Maintenance

Update mBuild document link in README (#757) Replace instances of manual degree/rad conversion with numpy functions (#764)

- Python
Published by daico007 over 5 years ago

mbuild - mBuild 0.10.7

Features

Add box attribute to mb.Compound (#742)
Provide framework to load in .CIF files (#689)
Improve mass/pair/etc. ordering and improper atomtype comment order in lammps_writer (#673)

Bug Fixes

Fix MCF fragment identification for more complex ring system (#744)
Fix a bug with alkane recipe when dealing with n < 3 (#691)

Maintenance

Drop notebook-specific dependencies from requirements (#687)

- Python
Published by daico007 over 5 years ago

mbuild - mBuild 0.10.6

Feature

Update element name and atomtype name lengths in MCF writer (#719)
Automate Docker Image publishing with AZP (#728)
Add protobuf installation instructions (#738)

Maintenance

Include Licencse.rst in Manifest.in (#710)
Drop appveyor CI (#709)
Include Box and Lattice in Data Structure docs (#714)
Update conda channel order in one-liner in installation docs (#703)
Remove nglview as a hard dependency (#713)
Add documentation for plugin/recipes system (#634)
Fix conda download URL in Travis CI (#724)
Reformat docstring for Lattice class (#718)
Update non-element MOL2 test (unpin mdtraj version) (#733)
Update documentation to reflect refactoring and remove use of deprecated function (#730)

Bug fixes

Fix an issue with to_parmed regarding setting box's parameters (#699)
Fix the factor of 2 error in rmin/2 (#716)
Setting default of 1-4 interactions to 0.0 when structure.adjusts is empty (#664)
Typecast float to int to prevent NaNs in np.arange in SpherePattern class (#722)
Fix MCF charge accuracy issue (#731)

- Python
Published by daico007 over 5 years ago

mbuild - mBuild 0.10.5

Features

Add internal XYZ writer (#410)
Add Lennard-Jones unit systems to LAMMPS writer (#646)
Add a function that returns a populated lattice box (get_populated_box) (#661)
Add SDF reader/writer (via OpenBabel) (#674)
Add _BoxArray subclass that allows single box dimensions to be set for mbuild.Box instances (#672, #686)

Bug Fixes

Update deprecated GSD syntax after v2.0.0 (#682)
Fix MCF writer for systems with no defined bonds (#662)

Maintenance

Remove old landscape YAML (#669)
Add protobuf import message to io.py (#670)
Migrate mBuild documentation to Read the Docs (#693)

Miscellaneous

Add recipes links to README (#659)

- Python
Published by daico007 about 6 years ago

mbuild - mBuild 0.10.4

Features

Add wrap_coords function for wrapping particles into a box (#643)

Bug Fixes

Don't populate empty lists for hoomd snapshot (#647)

Maintenance

Add nbval as requirement for tests in conda recpe (#656)
Remove six and some Python 2 legacy code (#641)
Remove examples (from this repository) (#658)
Fix travis by not installing md5sha1sum (#660)
Add CHANGELOG (#632)

- Python
Published by mattwthompson about 6 years ago

mbuild - mBuild 0.10.3

Feature

Add Cassandra MCF writer (#636)
Add HOOMD snapshot converter (#622)
Generate mb.Compound from Parmed or MDTraj residues (#526)
Add **kwargs for write_gsd (#653)

Bug Fixes

Fix unique naming problem in to_networkx (#583)
Default the mBuild PAR-writer to use IMPROPER (#648)
Fix ghost ports attached to removed compound (#593)
Remove duplicate NP particles in TNP example (#625)
Only import MCF writer if networkx is installed (#654)

Maintenance

Add LGTM (#616)
Add Azure CI testing (#615, #617, #618, #630, #637, #638)
Update Travis CI (#649)
Update conda recipe to include nbval (#611, #656)
Pin nglview to 2.7+ (#651, #655)
Reduce length of some unit tests (#621)
Rename AmorphousSilica to be more descriptive (#630)

- Python
Published by daico007 about 6 years ago

mbuild - mBuild 0.10.1

This is a bugfix release to resolve a potential issue with a foyer dependency with mBuild 0.10.0.

Bugfixes

Remove a foyer import that was producing a circular dependency (#610)

- Python
Published by mattwthompson over 6 years ago

mbuild - mBuild 0.10.0

Breaking Change

Officially drop Python 2.7 (#573)

Features

Load mBuild compounds from existing ParmEd and MDTraj objects (#561)
Convert mBuild compound to and from JSON format (#581)
Include testing of notebooks in CI (#590)
Add NGLView tooltip (#600)
Initialize mBuild Compounds from SMILES strings (#598)
Write out parameterized structures to a CHARMM .par file (#508)
Add method to convert to and from Pybel (#555)
Add POSCAR file writer in an effort to incorporate VASP into mBuild (#468)

Bug Fixes

Remove unnecessary Pybel import statement in mb.load (#604)
Change how proxy compounds are named so that MOL2 files are in the correct format (#605)
Rename atom names in silica interface example to be compatible with recent mBuild release (#594)
Improve error handling for Box class (#576)
Add a with open block to manage file open (#585)
Add _clone() function to the Proxy class to properly clone an instance of Proxy (#592)

Miscellaneous

Add compound_pb2.py file generated from protoc compiler to gitignore (#602)
Improve documentation of various mBuild classes and functions (#577, #578, #579, #580)
Add additional testing for foyer_kwargs (#428)

- Python
Published by rmatsum836 over 6 years ago

mbuild - mBuild 0.9.3

Breaking Changes

This is the last release supporting Python 2.7

Features

A more descriptive exception is raised when attempting to access a non-existent Port (#544)
Element capitalization is better enforced in ParmEd conversions (#550)
The XYZ reader can now act on a passed compound (#567)
The LAMMPS writer now accurately prints residue IDs (#569)

Bugfixes

Visualizing compounds in notebooks no longer returns a duplicate widget (#545)
Names of custom elements are no longer clobbered during visualization (#563)

Maintenance

The image in our gitter link has been updated (#543)
Some links in tutorials have been corrected (#548)
Installation documentation has been updated to reflect changes in conda configurations (#558)
Some other documentation has been refreshed (#560)
The GSD version is pinned to 1.7 in order to continue Python 2.7 support (#572)

- Python
Published by mattwthompson over 6 years ago

mbuild - mBuild 0.9.2

Breaking Changes

Python 3.5 is no longer officially supported or tested on as part of the development process.

Features

mBuild is now tested and packaged on Python 3.7 (#542)

Maintenance

MDTraj is no longer pinned to an old version (#542)
Coveralls is dropped; we have been using codecov for a few months (#542)

- Python
Published by mattwthompson over 6 years ago

mbuild - mBuild 0.9.1

Breaking Changes

This is the last release including official support for Python 3.5. It will likely work for some time but mBuild will not be tested on Python 3.5 during development.

Features

Residue names can optionally be inferred from compound names in conversion to ParmEd (#475)
Custom cross-interactions (NBFIXES in ParmEd jargon) can now be written to LAMMPS data files (#456)
The LAMMPS writer now prints helpful comments to more verbosely describe which atom types are associated with each potential (#535)

Maintenance

Some stylistic changes were made as suggested by various linters (#522)
Appveyor now tests on Python 3.6 (#520)

Documentation

Installation docs were updated to explicitly list supported Python versions (#532)
A comment pointing to the glozter Anaconda channel has been updated to point to conda-forge (#534)

Miscellaneous

Some tests depending on foyer are now properly skipped when it it not installed (#521)
Some examples were updated in accordance with their new structure as internal recipes (#536, #538)

- Python
Published by mattwthompson over 6 years ago

mbuild - mBuild 0.9.0

Features

A plugin or "recipe" architecture has been added to allow external modules to be imported inside of mBuild (#501)
Python 3.6 is now explicitly supported and tested (#518)

Maintenance

A contributor's guide (#500) and .github issue & pull request templates (#498) have been added
A redundant and unused block of code was removed (#515)
The glotzer and bioconda channels, which are now obsolete in this scope, have been dropped (#516)

- Python
Published by mattwthompson almost 7 years ago

mbuild - mBuild 0.8.3

Breaking Changes

When writing hoomdxml files, units will now be in kJ/mol & nm instead of kcal/mol & ang, so particle positions will differ by a factor of 10.

Features

A to_networkx function was added to convert the hierarchy of a compound to a graph (#484)
Packing functions now use XYZ files while running PACKMOL, bypassing some issues with PDB files (#422)
When saving hoomdxml files, auto_scale=True will scale reference units from max forcefield parameters. (#488)

Maintenance

Switched to codecov for code coverage testing (#485)
Some dependencies accidentally missing in earlier PRs were cleaned up (#493)

Bugfixes

update_coordinates now behaves well when passed an XYZ file or operating on simple hierarchies (#496)
Internal conversion from ParmEd structures to HOOMDXML files was improved (#463, see above)

- Python
Published by mattwthompson almost 7 years ago

mbuild - mBuild 0.8.2

Features

Special Pair Support (1-4 pair information) to GSD writers (#473)
- GSD files now include 1-4 special pairs for use in OPLS

Misc and Bugfixes

Dependency requirements have been updated (#457)
- A dependency loop between Foyer and mBuild has been resolved
Fixed a bug that prevented Appveyor builds from running (#477)
Temporary PDB files left behind by packing functions are now properly removed (#471)
- Packing.py uses temporary files which were previously never closed. This sometimes caused the program to reach the limit of open files for a process set by the OS
pytest-ignore-flaky has been replaced in favor of xfail (#471)
Additonal fixes for PACKMOL input files (#474)
- Input files are now closed by mBuild in order to ensure it can be read by PACKMOL
- Error reporting is now caught when the subprocess returns an error code
Microsoft VSCode extraneous files are now ignored by git (#478)

- Python
Published by mattwthompson about 7 years ago

mbuild - mBuild 0.8.1

Features

Packing functions can optionally constrain the rotation of Compounds when using fill_box (#407)
Additional lammps datafile support (#412)
- Add functionality for atomic, charge, and molecular atom_styles
- Fix atomic and molecular atom-styles
- Add optional atom-style argument to save function
- Add tests to check for correct Atoms format
A Compound can be generated from a SMILES string if the user has Open Babel installed (#430)
The website was updated with details how to properly cite mBuild (#421)
OpenMM can now be used for energy minimization (#416)
A simple xyz file reader was added (#423)
Defaults in Compound.visualize have been improved (#438)
mBuild boxes can now store angles (#448)
mBuild boxes can now be passed to various writers (#448)
A changelog is now included in the root directory (#454)

Misc and Bugfixes

Switched from OpenMM to MDTraj to check for element existence (#408)
Changed bilayer notebook to use Compound methods for object manipulation (#406)
Added test to ensure that users can provide a custom forcefield XML file when applying a forcefield to a Compound (#431)
An error is now generated if the miniconda MD5 sum does not match when performing tests (#409)
LAMMPS box values are now written appropriately in Angstroms (#459)
Coordinates in HOOMDXML and GSD files are now correctly written in the range L /2 to L
A bug in the ordering of some Bravais angles of some non-rectangular lattices has been fixed (#450)

- Python
Published by mattwthompson about 7 years ago

mbuild - mBuild 0.8.0

Features

Improved packing API
- fill_box method now supports user-specified densities (#372)
- Support for non-cubic boxes (#385)
- Added edge buffer for pseudo-support of periodic boundaries (#385)
- Allow users to access PACKMOL raw output (#385)
- Improve documentation and removed repetitious code (#385)
Proper support for triclinic lattices (#386)
More intuitive Port behavior when adding/removing bonds
- Ports are now added along the bond vector when bonds are removed
- Ports are removed when using force_overlap when attribute add_bond is True (#390)

Misc and Bugfixes

Increased precision of PACKMOL overlap tolerance (#367)
Increased robustness for packing.py argument types (#368)
Continuous Integration (CI) fixes (#369, #375, #392, #402, #405)
Documentation updates (#371)
Combining rules for non-bonded interactions can now be specified when saving compounds (#377)
Remove ambigious data types for Box attributes (#384)
Fixed changing of basis for non-cubic lattices (#386)
Fixed issue where Ports were not aligned properly along user-specified direction (#390)
Add support for controlling Foyer warning verbosity when saving Compounds (#391)
Added more information to Port.__repr__ (#396)
Fixed bug in unit conversion for periodicity in Compound.from_parmed() (#401)
Rounding Lattice.lattice_point positions to 0. when below a certain threshold (#404)

- Python
Published by justinGilmer about 8 years ago

mbuild - 0.5.2

- Python
Published by ctk3b over 10 years ago

Recent Releases of mbuild

mbuild - 1.2.1

What's Changed

Features

Bug fixes

Maintenance

mbuild - 1.2.0

What's Changed

Features

Bugfixes

Maintenance

mbuild - 1.1.1

What's Changed

Features

Bugfixes

Maintenance

mbuild - 1.1.0

What's Changed

mbuild - mBuild 1.0 stable release

mBuild 1.0 Announcement

What's Changed just in the last patch.

mbuild - 0.18.0

What's Changed

Features

Bugfixes

Maintenance

mbuild - 0.17.1

What's Changed

Features

Bugfixes

Maintenance

mbuild - mBuild 0.17.0

Features

Bug fixes

Maintenance

New Contributors

mbuild - mBuild 0.16.4

Features

Bug fixes

Maintenance

mbuild - mBuild 0.16.3

What's Changed

Features

mbuild - mBuild 0.16.2

Features

Bug fixes

Maintenance

mbuild - mBuild 0.16.1

Features

Maintenance

New Contributors

mbuild - mBuild 0.16.0

Features

Bugfixes

Maintenance

New Contributors

mbuild - mBuild 0.15.1

Features

Bug fixes

Maintenance

mbuild - mBuild 0.15.0

Features

Bug Fixes

Maintenance

mbuild - mBuild 0.14.2

Features

Bug fixes

Maintenance

mbuild - mBuild 0.14.1

Features

Bug fixes

mbuild - mBuild 0.14.0

Breaking change

Features

Bug fixes

Maintenance

New Contributors

mbuild - mBuild 0.13.1

Features

Bug fixes

`mBuild` 1.0 Announcement