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 #1198
• Remove deprecated formats, update reader and writer backends by @chrisjonesBSU in #1191
• Remove rigid body data structure from Compound by @chrisjonesBSU in #1203
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1201

Full Changelog: 0.18.0...1.0.0

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 #787
• Add cap hydrogens to head and tail compounds in the polymer builder by @chrisjonesBSU in #1196

Bugfixes

• reset_labels kwarg to force_overlap, new method reset_labels by @jaclark5 in #1195

Maintenance

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

Full Changelog: 0.17.1...0.18.0

0.17.1

What's Changed

Features

• Update README graphic by @daico007 in #1178
• Add option to reset child labels in Compound.remove() by @jaclark5 in #1173
• Periodic polymer by @jaclark5 in #1170

Bugfixes

• Attempt to fix docs build by @daico007 in #1169
• Fix failing doc build by @daico007 in #1177

Maintenance

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

Full Changelog: 0.17.0...0.17.1

mBuild 0.17.0

Features

• Add export to RDKIT to allow for chemdraw style visualization. by @chrisiacovella in #1137
• Add check_box_size option for add method in Compound.add() by @daico007 in #1149
• Add new default option for combining_rule in Compound.save() by @daico007 in #1153
• Added ability to adjust bead_size by @jaclark5 in #1158
• Speed up json loader by @daico007 in #1163

Bug fixes

• fixed the tree print issue by @GuiLingfeng in #1155

Maintenance

• Fix Docker build by @daico007 in #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 #1160

New Contributors

• @GuiLingfeng made their first contribution in #1155

Full Changelog: 0.16.4...0.17.0

mBuild 0.16.4

Features

• Revised load_xyz function by @chrisiacovella in #1140
• Add new option for packing.solvate by @daico007 in #1144

Bug fixes

• Fix Treelib test by @daico007 in #1142

Maintenance

• Added extensions to savers doc string by @CalCraven in #1146

• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1136, #1145

Full Changelog: 0.16.3...0.16.4

mBuild 0.16.3

What's Changed

Features

• Support GSD >= 2.9 by @chrisjonesBSU in #1131
• Turn off infer_residues for when converting to parmed by @daico007 in (#1129, #1134, #1135)

Full Changelog: 0.16.2...0.16.3

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