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Recent Releases of FlowerMD

FlowerMD - 1.4.1

What's Changed

  • Fix pyproject.toml by @chrisjonesBSU in https://github.com/cmelab/flowerMD/pull/199

Full Changelog: https://github.com/cmelab/flowerMD/compare/1.4.0...1.4.1

Scientific Software - Peer-reviewed - Python
Published by chrisjonesBSU 9 months ago

FlowerMD - 1.4.0

What's Changed

  • Fix name in environment.yml file. by @chrisjonesBSU in https://github.com/cmelab/flowerMD/pull/145
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/cmelab/flowerMD/pull/146
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/cmelab/flowerMD/pull/147
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/cmelab/flowerMD/pull/150
  • Add support for mBuild's periodic polymer bonding by @chrisjonesBSU in https://github.com/cmelab/flowerMD/pull/148
  • Add data structure to save and restart a simulation. by @chrisjonesBSU in https://github.com/cmelab/flowerMD/pull/149
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/cmelab/flowerMD/pull/151
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/cmelab/flowerMD/pull/152
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/cmelab/flowerMD/pull/155
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/cmelab/flowerMD/pull/156
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/cmelab/flowerMD/pull/157
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/cmelab/flowerMD/pull/158
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/cmelab/flowerMD/pull/159
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/cmelab/flowerMD/pull/162
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/cmelab/flowerMD/pull/163
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/cmelab/flowerMD/pull/164
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/cmelab/flowerMD/pull/165
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/cmelab/flowerMD/pull/166
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/cmelab/flowerMD/pull/167
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/cmelab/flowerMD/pull/168
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/cmelab/flowerMD/pull/169
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/cmelab/flowerMD/pull/170
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/cmelab/flowerMD/pull/171
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/cmelab/flowerMD/pull/172
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/cmelab/flowerMD/pull/173
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/cmelab/flowerMD/pull/174
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/cmelab/flowerMD/pull/175
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/cmelab/flowerMD/pull/176
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/cmelab/flowerMD/pull/177
  • Update CI file and environments by @chrisjonesBSU in https://github.com/cmelab/flowerMD/pull/180
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/cmelab/flowerMD/pull/179
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/cmelab/flowerMD/pull/181
  • Replace setup.py with pyproject.toml, update CI by @chrisjonesBSU in https://github.com/cmelab/flowerMD/pull/182
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/cmelab/flowerMD/pull/185
  • Add seed parameter and kwargs to Pack by @StephMcCallum in https://github.com/cmelab/flowerMD/pull/184
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/cmelab/flowerMD/pull/186
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/cmelab/flowerMD/pull/187
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/cmelab/flowerMD/pull/189
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/cmelab/flowerMD/pull/193
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/cmelab/flowerMD/pull/194
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/cmelab/flowerMD/pull/195
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/cmelab/flowerMD/pull/196
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/cmelab/flowerMD/pull/197
  • Revamp Ellipsoid Class, add method to create bond constraints in a system's snapshot. by @chrisjonesBSU in https://github.com/cmelab/flowerMD/pull/191
  • Adding Single Chain system class by @StephMcCallum in https://github.com/cmelab/flowerMD/pull/192
  • Add support for Hoomd 5 by @chrisjonesBSU in https://github.com/cmelab/flowerMD/pull/198

New Contributors

  • @StephMcCallum made their first contribution in https://github.com/cmelab/flowerMD/pull/184

Full Changelog: https://github.com/cmelab/flowerMD/compare/1.3.1...1.4.0

Scientific Software - Peer-reviewed - Python
Published by chrisjonesBSU 9 months ago

FlowerMD - 1.3.1

What's Changed

  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/cmelab/flowerMD/pull/133
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/cmelab/flowerMD/pull/134
  • Update MacOS images used in os-matrix in CI workflow by @chrisjonesBSU in https://github.com/cmelab/flowerMD/pull/135
  • Add ruff-precommit, remove pydocstyle by @chrisjonesBSU in https://github.com/cmelab/flowerMD/pull/138
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/cmelab/flowerMD/pull/139
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/cmelab/flowerMD/pull/140
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/cmelab/flowerMD/pull/141
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/cmelab/flowerMD/pull/142
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/cmelab/flowerMD/pull/143
  • Update dependancies by @chrisjonesBSU in https://github.com/cmelab/flowerMD/pull/144

Full Changelog: https://github.com/cmelab/flowerMD/compare/1.3.0...1.3.1

Scientific Software - Peer-reviewed - Python
Published by chrisjonesBSU over 1 year ago

FlowerMD - v1.3.0

What's Changed

  • Update installation guide and add citation by @marjanalbooyeh in https://github.com/cmelab/flowerMD/pull/117
  • Add type check for forcefield parameter in Simulation by @chrisjonesBSU in https://github.com/cmelab/flowerMD/pull/118
  • Update README by @chrisjonesBSU in https://github.com/cmelab/flowerMD/pull/123
  • Bug fix in Interface to duplicate and shift along the correct axis by @chrisjonesBSU in https://github.com/cmelab/flowerMD/pull/125
  • Including testing tutorial notebooks in PR unit CI workflow by @chrisjonesBSU in https://github.com/cmelab/flowerMD/pull/127
  • Fix Lattice system class for coarse-grained molecules by @chrisjonesBSU in https://github.com/cmelab/flowerMD/pull/129
  • Add classes for simulating ellipsoid polymer systems. by @chrisjonesBSU in https://github.com/cmelab/flowerMD/pull/102
  • Release 1.3.0; update environment files. by @chrisjonesBSU in https://github.com/cmelab/flowerMD/pull/132

Full Changelog: https://github.com/cmelab/flowerMD/compare/1.2.0...1.3.0

Scientific Software - Peer-reviewed - Python
Published by chrisjonesBSU over 1 year ago

FlowerMD - v1.2.0

What's Changed

  • Update wetting tutorial visualization by @marjanAlbouye in https://github.com/cmelab/flowerMD/pull/101
  • Align chains along z-axis when using system.Lattice by @chrisjonesBSU in https://github.com/cmelab/flowerMD/pull/107
  • Fix import for add_void_particles in modules.welding.utils by @chrisjonesBSU in https://github.com/cmelab/flowerMD/pull/108
  • Add KremerGrestBeadSpring class to library.forcefields, remove r_cut from various Simulation classes. by @chrisjonesBSU in https://github.com/cmelab/flowerMD/pull/109
  • Add ability to use number density when calculating target box lengths for shrinking and NVT. by @chrisjonesBSU in https://github.com/cmelab/flowerMD/pull/112
  • We can now use two GSD files in welding.Interface by @chrisjonesBSU in https://github.com/cmelab/flowerMD/pull/113

New Contributors

  • @erjank made their first contribution in https://github.com/cmelab/flowerMD/pull/103

Full Changelog: https://github.com/cmelab/flowerMD/compare/1.1.1...1.2.0

Scientific Software - Peer-reviewed - Python
Published by chrisjonesBSU almost 2 years ago

FlowerMD - v1.1.1

What's Changed

  • fix setup.py to install all modules by @chrisjonesBSU in https://github.com/cmelab/flowerMD/pull/99

Full Changelog: https://github.com/cmelab/flowerMD/compare/1.1.0...1.1.1

Scientific Software - Peer-reviewed - Python
Published by chrisjonesBSU about 2 years ago

FlowerMD - v1.1.0

What's Changed

  • Add initial classes for surface wetting module by @chrisjonesBSU in https://github.com/cmelab/flowerMD/pull/90
  • Add need statement to main docs page by @RainierBarrett in https://github.com/cmelab/flowerMD/pull/92
  • Graphene now inherits from Molecule by @chrisjonesBSU in https://github.com/cmelab/flowerMD/pull/93
  • Fix hyperlink for TRUE by @chrisjonesBSU in https://github.com/cmelab/flowerMD/pull/94
  • Add more descriptions to tutorials, update links to base code by @marjanAlbouye in https://github.com/cmelab/flowerMD/pull/95
  • Update README and documentation with new installation instructions. by @chrisjonesBSU in https://github.com/cmelab/flowerMD/pull/98
  • Add surface wetting module by @chrisjonesBSU in https://github.com/cmelab/flowerMD/pull/96

Full Changelog: https://github.com/cmelab/flowerMD/compare/1.0.0...1.1.0

Scientific Software - Peer-reviewed - Python
Published by chrisjonesBSU about 2 years ago

FlowerMD - release 1.0.0

What's Changed

  • Add/unit tests by @chrisjonesBSU in https://github.com/cmelab/flowerMD/pull/3
  • add doc strings to Systems by @chrisjonesBSU in https://github.com/cmelab/flowerMD/pull/4
  • Add/unit tests by @chrisjonesBSU in https://github.com/cmelab/flowerMD/pull/5
  • more tests for Simulation by @chrisjonesBSU in https://github.com/cmelab/flowerMD/pull/6
  • Make LJ chain class more flexible, add unit tests by @chrisjonesBSU in https://github.com/cmelab/flowerMD/pull/7
  • Add DisplacementCapped Integrator to simulation by @marjanAlbouye in https://github.com/cmelab/flowerMD/pull/9
  • Refactoring hoomd polymers by @marjanAlbouye in https://github.com/cmelab/flowerMD/pull/8
  • Refactor by @chrisjonesBSU in https://github.com/cmelab/flowerMD/pull/10
  • Change hoomdpolymers to hoomdorganics by @marjanAlbouye in https://github.com/cmelab/flowerMD/pull/26
  • include assets dir in setup.py by @chrisjonesBSU in https://github.com/cmelab/flowerMD/pull/27
  • Fix for Lattice box and Tensile simulation. Add more unit tests by @chrisjonesBSU in https://github.com/cmelab/flowerMD/pull/29
  • update pytest codecov links, remove old code from README by @chrisjonesBSU in https://github.com/cmelab/flowerMD/pull/30
  • Update and simplify environment files by @chrisjonesBSU in https://github.com/cmelab/flowerMD/pull/32
  • Add system and utils unit tests by @marjanAlbouye in https://github.com/cmelab/flowerMD/pull/34
  • Fix scale charges, add unit tests by @chrisjonesBSU in https://github.com/cmelab/flowerMD/pull/33
  • Move reference values unit validation to utils by @marjanAlbouye in https://github.com/cmelab/flowerMD/pull/36
  • Fix mismatched gmso residue name when molecule is loaded from mol2 by @marjanAlbouye in https://github.com/cmelab/flowerMD/pull/37
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/cmelab/flowerMD/pull/43
  • Updates to remove hydrogens by @chrisjonesBSU in https://github.com/cmelab/flowerMD/pull/44
  • Update simulation interface and add density to update_volume by @marjanAlbouye in https://github.com/cmelab/flowerMD/pull/42
  • add writeatstart parameters to run functions by @chrisjonesBSU in https://github.com/cmelab/flowerMD/pull/46
  • Add GSD Logger and Pressure Tensor by @chrisjonesBSU in https://github.com/cmelab/flowerMD/pull/53
  • Change behavior of hoomd object properties by @chrisjonesBSU in https://github.com/cmelab/flowerMD/pull/56
  • Migrate to hoomd v4 by @marjanAlbouye in https://github.com/cmelab/flowerMD/pull/54
  • Update to GSD 3 by @chrisjonesBSU in https://github.com/cmelab/flowerMD/pull/57
  • Refactor apply_forcefield by @chrisjonesBSU in https://github.com/cmelab/flowerMD/pull/61
  • Complete docstrings by @marjanAlbouye in https://github.com/cmelab/flowerMD/pull/50
  • Update apply_forcefield and molecule forcefield by @marjanAlbouye in https://github.com/cmelab/flowerMD/pull/62
  • Tutorials by @marjanAlbouye in https://github.com/cmelab/flowerMD/pull/38
  • Add graphene surface to library by @chrisjonesBSU in https://github.com/cmelab/flowerMD/pull/67
  • Update readthedoc setup by @marjanAlbouye in https://github.com/cmelab/flowerMD/pull/66
  • Dockerfile with GPU support by @RainierBarrett in https://github.com/cmelab/flowerMD/pull/40
  • Add table potential class to forcefields library by @chrisjonesBSU in https://github.com/cmelab/flowerMD/pull/65
  • Finish welding tutorial by @chrisjonesBSU in https://github.com/cmelab/flowerMD/pull/49
  • Change name from hoomd-organics to jankflow by @marjanAlbouye in https://github.com/cmelab/flowerMD/pull/68
  • remove box resizer in runupdatevolume by @chrisjonesBSU in https://github.com/cmelab/flowerMD/pull/70
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/cmelab/flowerMD/pull/71
  • Update package name to flower by @marjanAlbouye in https://github.com/cmelab/flowerMD/pull/72
  • Set logger to log hours+mins for mins>60 by @RainierBarrett in https://github.com/cmelab/flowerMD/pull/73
  • Fix translation in Lattice by @chrisjonesBSU in https://github.com/cmelab/flowerMD/pull/74
  • fix assets in setup.py by @chrisjonesBSU in https://github.com/cmelab/flowerMD/pull/75
  • update assets path in setup by @marjanAlbouye in https://github.com/cmelab/flowerMD/pull/77
  • Joss paper md files by @marjanAlbouye in https://github.com/cmelab/flowerMD/pull/69
  • fix asset paths by @chrisjonesBSU in https://github.com/cmelab/flowerMD/pull/79
  • Address JOSS prereview comments by @marjanAlbouye in https://github.com/cmelab/flowerMD/pull/80
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/cmelab/flowerMD/pull/81
  • Fix charge units when charge is 0 by @chrisjonesBSU in https://github.com/cmelab/flowerMD/pull/82
  • Fix PEKK, remove random_sequence parameter from CoPolymer by @chrisjonesBSU in https://github.com/cmelab/flowerMD/pull/83
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/cmelab/flowerMD/pull/84
  • Round minutes in StdOutLogger; add forcefield pickle method to System, fix write mode in to_gsd, add flush_writers method and add parameter for max buffer size. by @chrisjonesBSU in https://github.com/cmelab/flowerMD/pull/85
  • JOSS: Fix 2 spelling typos, and correct hoomd citaiton by @chrisjonesBSU in https://github.com/cmelab/flowerMD/pull/86
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/cmelab/flowerMD/pull/88
  • Update environment.yml to use conda-forge versions of grits and cmeutils by @chrisjonesBSU in https://github.com/cmelab/flowerMD/pull/89

New Contributors

  • @chrisjonesBSU made their first contribution in https://github.com/cmelab/flowerMD/pull/3
  • @marjanAlbouye made their first contribution in https://github.com/cmelab/flowerMD/pull/9
  • @pre-commit-ci made their first contribution in https://github.com/cmelab/flowerMD/pull/43
  • @RainierBarrett made their first contribution in https://github.com/cmelab/flowerMD/pull/40

Full Changelog: https://github.com/cmelab/flowerMD/commits/1.0.0

Scientific Software - Peer-reviewed - Python
Published by marjanAlbouye about 2 years ago

FlowerMD - 1.0.0

Releasing the first version of JankFlow.

Scientific Software - Peer-reviewed - Python
Published by marjanAlbouye about 2 years ago