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)

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)

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)

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)