mosdef-gomc - MoSDeF-GOMC 1.5.0

What's Changed

Features 

• update python versions to 3.12 and 3.13 by @bc118 in https://github.com/GOMC-WSU/MoSDeF-GOMC/pull/111

Bug fixes

• Need to lock GSD at gsd =3.3.2 until it is compatible (and others) with NumPy=>2.x by @bc118 in https://github.com/GOMC-WSU/MoSDeF-GOMC/pull/105
• Fix fit by @bc118 in https://github.com/GOMC-WSU/MoSDeF-GOMC/pull/106

Maintenance 

• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/GOMC-WSU/MoSDeF-GOMC/pull/103
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/GOMC-WSU/MoSDeF-GOMC/pull/107
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/GOMC-WSU/MoSDeF-GOMC/pull/108

Full Changelog: https://github.com/GOMC-WSU/MoSDeF-GOMC/compare/1.4.0...1.5.0

- Python
Published by bc118 8 months ago

mosdef-gomc - 1.4.0

What's Changed

Bug fixes

• fixed the locked python versions to 3.11.xxx in yml files by @bc118 in https://github.com/GOMC-WSU/MoSDeF-GOMC/pull/96
• removed all printing of duplicate atom classes/types in bonded or non-bonded parameters in the FF file by @bc118 in https://github.com/GOMC-WSU/MoSDeF-GOMC/pull/102
• 'symengine.sympify' changed to 'sympy.nsimplify' to solve for non-integers by @bc118 in https://github.com/GOMC-WSU/MoSDeF-GOMC/pull/100

Maintenance

• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/GOMC-WSU/MoSDeF-GOMC/pull/99
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/GOMC-WSU/MoSDeF-GOMC/pull/101

Full Changelog: https://github.com/GOMC-WSU/MoSDeF-GOMC/compare/1.3.0...1.4.0

- Python
Published by bc118 over 1 year ago

mosdef-gomc - MoSDeF-GOMC 1.3.0

What's Changed

Features

• fixed annoyance in AA mol2 reader by @bc118 in https://github.com/GOMC-WSU/MoSDeF-GOMC/pull/81
• Add the Multi-particle move flags for GEMC-NVT and GEMC-NPT. by @bc118 in https://github.com/GOMC-WSU/MoSDeF-GOMC/pull/83
• update to python 3.10 and 3.11 and update GMSO version by @bc118 in https://github.com/GOMC-WSU/MoSDeF-GOMC/pull/94

Bug fixes (Important: From the GMSO dependency)

• Sorting of improper types by @CalCraven in https://github.com/mosdef-hub/gmso/pull/796
• Update connection members during parameterization by @CalCraven in https://github.com/mosdef-hub/gmso/pull/808
• @daico007 Fix order of matching when atomtyping by @daico007 in https://github.com/mosdef-hub/gmso/pull/802

Maintenance

• updated version on .github/workflows/CI.yml, hoping to fix the docker build by @bc118 in https://github.com/GOMC-WSU/MoSDeF-GOMC/pull/73
• adding the libarchive package needed by mamba by @latessa in https://github.com/GOMC-WSU/MoSDeF-GOMC/pull/74
• added docs/environment_docs.yml back in, as it appeard read the docs requires it by @bc118 in https://github.com/GOMC-WSU/MoSDeF-GOMC/pull/75
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/GOMC-WSU/MoSDeF-GOMC/pull/76
• Update Forcefield loading by @CalCraven in https://github.com/GOMC-WSU/MoSDeF-GOMC/pull/78
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/GOMC-WSU/MoSDeF-GOMC/pull/79
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/GOMC-WSU/MoSDeF-GOMC/pull/86
• removed duplicate nomkl in mamba env create nomkl --file environment.yml in the Dockerfile by @bc118 in https://github.com/GOMC-WSU/MoSDeF-GOMC/pull/90

Deprecation

• Removed the old Parmed GOMC versions by @bc118 in https://github.com/GOMC-WSU/MoSDeF-GOMC/pull/84
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/GOMC-WSU/MoSDeF-GOMC/pull/91
• updated mosdef packages to the latest versions by @bc118 in https://github.com/GOMC-WSU/MoSDeF-GOMC/pull/92
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/GOMC-WSU/MoSDeF-GOMC/pull/93

New Contributors

• @latessa made their first contribution in https://github.com/GOMC-WSU/MoSDeF-GOMC/pull/74
• @CalCraven made their first contribution in https://github.com/GOMC-WSU/MoSDeF-GOMC/pull/78

Full Changelog: https://github.com/GOMC-WSU/MoSDeF-GOMC/compare/1.2.0...1.3.0

- Python
Published by bc118 about 2 years ago

mosdef-gomc - MoSDeF-GOMC 1.2.0

What's Changed

Features

• Updated installation.rst file for the instructions to mosdef-gomc v1.2.0 by @bc118 in https://github.com/GOMC-WSU/MoSDeF-GOMC/pull/63
• Added Exp6 potential for GOMC in mosdef-gomc v1.2.0 by @bc118 in https://github.com/GOMC-WSU/MoSDeF-GOMC/pull/65
• Added more checks for FF potential k-scalars in v1.2.0 by @bc118 in https://github.com/GOMC-WSU/MoSDeF-GOMC/pull/67

Bug fixes

• Now accounting for the non-bonded interaction equation scalars for LJ, Mie, or Exp6 GMSO in v1.2.0 by @bc118 in https://github.com/GOMC-WSU/MoSDeF-GOMC/pull/66

Maintenance

• Updated the mosdef-gomc syntax to fix the breaking, which occurred when using gmso v0.11.2 by @daico007 https://github.com/GOMC-WSU/MoSDeF-GOMC/pull/71
• In mosdef-gomc 1.1.0, locked gmso version to 0.11.1 to fix the breaking, which occurred when using gmso v0.11.2 @bc118 in https://github.com/GOMC-WSU/MoSDeF-GOMC/pull/69

Full Changelog: https://github.com/GOMC-WSU/MoSDeF-GOMC/compare/1.1.0...1.2.0

- Python
Published by bc118 over 2 years ago

mosdef-gomc - MoSDeF-GOMC 1.1.0

Features

• added to citations by @bc118 in https://github.com/GOMC-WSU/MoSDeF-GOMC/pull/52
• added funding source by @bc118 in https://github.com/GOMC-WSU/MoSDeF-GOMC/pull/53
• set the DCD writer as default=True and the coord writer option default=FALSE by @bc118 in https://github.com/GOMC-WSU/MoSDeF-GOMC/pull/55
• sympy.simplify changed to symengine.sympify by @bc118 in https://github.com/GOMC-WSU/MoSDeF-GOMC/pull/58

Bug fixes

• changed sympy code sections to be compatible with sympy 1.11 by @bc118 in https://github.com/GOMC-WSU/MoSDeF-GOMC/pull/39
• Update functions to compatible with new mbuild by @daico007 in https://github.com/GOMC-WSU/MoSDeF-GOMC/pull/51
• updated docs and locked sphinx to 6.1.1 until error fixed by @bc118 in (#59, 61)

Maintenance

• For the writers, changed build via mBuild to MoSDeF-GOMC, and removed misspelling of orthogonal by @bc118 in https://github.com/GOMC-WSU/MoSDeF-GOMC/pull/40
• added mamba install instructions, and a temporary fix for the conda install instructions by @bc118 in https://github.com/GOMC-WSU/MoSDeF-GOMC/pull/42
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in (#43, #45, #47, #54)
• added the other order of asserted variables for testcharmmafewmbuild_layers test by @bc118 in https://github.com/GOMC-WSU/MoSDeF-GOMC/pull/48
• more individual test files for the specificfftoresidue files and the equationcompare files by @bc118 in https://github.com/GOMC-WSU/MoSDeF-GOMC/pull/50
• Maintenance by @daico007 in https://github.com/GOMC-WSU/MoSDeF-GOMC/pull/56

New Contributors

• @daico007 made their first contribution in https://github.com/GOMC-WSU/MoSDeF-GOMC/pull/51

Full Changelog: https://github.com/GOMC-WSU/MoSDeF-GOMC/compare/1.0.0...1.1.0

- Python
Published by daico007 over 2 years ago

mosdef-gomc - 1.0.0

What's Changed

• Major Update: The new gmso-mosdef-gomc files were created, which allows GOMC to use the LJ and Mie FFs via GMSO format. This allows the user to specify the potential energy equations explicitly in the FF file via a string for the bonded and non-bonded interactions, including different units (unyt package) and scalar values. These are different files in the formats folder. Minor Update: The parmed-mosdef-gomc updates are for changing the occupancy and beta numbers in the PDB file to fix molecules/atoms in GOMC or NAMD or both for a hybrid simulation. This is mostly for NAMD when running hybrid MCMD simulations via the py-MCMD software. Note: The plan is for the parmed mosdef-gomc version to be deprecated by the end of 2022 @bc118 in https://github.com/GOMC-WSU/MoSDeF-GOMC/pull/18
• changed conversion.py header and added a space on 2 init.py files by @bc118 in https://github.com/GOMC-WSU/MoSDeF-GOMC/pull/31
• In the README file, added links to readthedocs and reference page by @bc118 in https://github.com/GOMC-WSU/MoSDeF-GOMC/pull/32
• added zenodo reference by @bc118 in https://github.com/GOMC-WSU/MoSDeF-GOMC/pull/33
• added credits for main people involved in the project. by @bc118 in https://github.com/GOMC-WSU/MoSDeF-GOMC/pull/34
• changed to correct conda-forge call on README by @bc118 in https://github.com/GOMC-WSU/MoSDeF-GOMC/pull/35

Full Changelog: https://github.com/GOMC-WSU/MoSDeF-GOMC/commits/1.0.0

- Python
Published by bc118 over 3 years ago

mosdef-gomc - MoSDeF-GOMC 0.1.0

First release of MoSDeF-GOMC, forked from mbuild for separating GOMC specific functionality from the main mbuild repository.

- Python
Published by umesh-timalsina about 4 years ago