mBuild 0.16.2

Features

• speeding up add function for large compounds by @chrisiacovella in #1107
• Reduce charge particle warnings; add static particle_charge method by @chrisjonesBSU in #1109
• Extend ordering of rb torsions written out from parmed structure by @CalCraven in #1112
• New water box recipe by @chrisiacovella in #1115
• Add 2d checkered pattern by @daico007 in #1118

Bug fixes

• Fix lammps impropers docstring by @daico007 in #1120
• fixed freud bond issue by @chrisiacovella in #1127

Maintenance

• Add networkx to environment.yml by @daico007 in #1103
• Add testing for py3.10 and 3.11 by @daico007 in #1110
• Attempt to fix readthedocs build by @daico007 in #1105
• Use list to store compound.children by @daico007 in #1121
• Maintenance task by @daico007 in #1123
• handle hoomd 4 by @daico007 in #1128

Full Changelog: 0.16.1...0.16.2

mBuild 0.16.1

Features

• Replaced bondgraph with networkx by @chrisiacovella in #1087
• Write LJ parameters with 5 decimal places instead of 3 with MCF writer. by @rwsmith7531 in #1095
• Add "metal" Unit for Lammps by @thangckt in #1098
• Print the hierarchy of a compound by @chrisiacovella in #1097

Maintenance

• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1099

New Contributors

• @thangckt made their first contribution in #1098

Full Changelog: 0.16.0...0.16.1

mBuild 0.16.0

Features

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

Bugfixes

• Fix bug related to get_boundingbox() by @daico007 in #1059
• Patches for element reading in lattice builder by @CalCraven in #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 #1067
• drop py3.7 from testing by @daico007 in #1055
• Migrate GOMC and CHARMM writer by @daico007 in #1064

New Contributors

• @jaclark5 made their first contribution in #1069
• @RainierBarrett made their first contribution in #1088

Full Changelog: 0.15.1...0.16.0

mBuild 0.15.1

Features

• Default mass and charge of Compound to None by @daico007 in #1047
• Add refer_inhierarchy to gmso conversion by @daico007 in #1051
• Dihedral rotator function by @uppittu11 in #1039

Bug fixes

• Fix for bug with mbuild missing edges in bond graph by @CalCraven in #1049

Maintenance

• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1042

Full Changelog: 0.15.0...0.15.1

mBuild 0.15.0

Features

• Add is_independent() method for compound by @daico007 in #1020
  • Identify if a compound has bonds to compounds outside of its hierarchy.
• Add method to flatten an mbuild compound by @daico007 in #1027
  • Take a hierarchical structure and reduce it to just a single container compound containing particles.
• improve performance of is_independent by @daico007 in #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 #1024
  • Self.n_bonds 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.n_direct_bonds can be useful to add ports or bonds into a compound.
• Modify bond graph to include independent particle by @daico007 in #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 #1035
• Update port.access_labels by @daico007 in #1032

Maintenance

• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in (#1021, #1026, #1040)
• Switch from Azure to GHA by @daico007 in #1033

Full Changelog: 0.14.2...0.15.0

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 #1016
• Change syntax to remove ghost ports by @daico007 in #995

Maintenance

• Exclude setup.cfg by @justinGilmer in #1015

Full Changelog: 0.14.1...0.14.2

mBuild 0.14.1

Features

• Use gmso backend to load Silica surfaces by @daico007 in #1013

Bug fixes

• Set periodicity correctly in freud_generate_bonds by @justinGilmer in #1012
• Fix charge scaling in HOOMD converters by @jennyfothergill in #1011

Full Changelog: 0.14.0...0.14.1

mBuild 0.14.0

Breaking change

• Dropping support of Python 3.6 and adding testing for Python 3.9 #1000

Features

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

Bug fixes

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

Maintenance

• Remove execution permission from files by @umesh-timalsina in #960
• Remove bash uploader in favor of codecov uploader by @umesh-timalsina in #965
• Use f-strings when applicable, add experimental by @justinGilmer in #968
• Use functools.wraps to preserve docstring by @justinGilmer in #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 #981
• Modify bleeding test by @daico007 in #982
• Pin hoomdv3 to dev12 until the issue with hoomd.md.special_pair.LJ in dev13 is resolved by @justinGilmer in #998

New Contributors

• @XiaoboLinlin made their first contribution in #963

Full Changelog: 0.13.1...0.14.0

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)

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)