1.4.0

What's Changed

Bug fixes

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

Maintenance

• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #99
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #101

Full Changelog: 1.3.0...1.4.0

MoSDeF-GOMC 1.3.0

What's Changed

Features

• fixed annoyance in AA mol2 reader by @bc118 in #81
• Add the Multi-particle move flags for GEMC-NVT and GEMC-NPT. by @bc118 in #83
• update to python 3.10 and 3.11 and update GMSO version by @bc118 in #94

Bug fixes (Important: From the GMSO dependency)

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

Maintenance

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

Deprecation

• Removed the old Parmed GOMC versions by @bc118 in #84
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #91
• updated mosdef packages to the latest versions by @bc118 in #92
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #93

New Contributors

• @latessa made their first contribution in #74
• @CalCraven made their first contribution in #78

Full Changelog: 1.2.0...1.3.0

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 #63
• Added Exp6 potential for GOMC in mosdef-gomc v1.2.0 by @bc118 in #65
• Added more checks for FF potential k-scalars in v1.2.0 by @bc118 in #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 #66

Maintenance

• Updated the mosdef-gomc syntax to fix the breaking, which occurred when using gmso v0.11.2 by @daico007 #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 #69

Full Changelog: 1.1.0...1.2.0

MoSDeF-GOMC 1.1.0

Features

• added to citations by @bc118 in #52
• added funding source by @bc118 in #53
• set the DCD writer as default=True and the coord writer option default=FALSE by @bc118 in #55
• sympy.simplify changed to symengine.sympify by @bc118 in #58

Bug fixes

• changed sympy code sections to be compatible with sympy 1.11 by @bc118 in #39
• Update functions to compatible with new mbuild by @daico007 in #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 #40
• added mamba install instructions, and a temporary fix for the conda install instructions by @bc118 in #42
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in (#43, #45, #47, #54)
• added the other order of asserted variables for test_charmm_a_few_mbuild_layers test by @bc118 in #48
• more individual test files for the specific_ff_to_residue files and the equation_compare files by @bc118 in #50
• Maintenance by @daico007 in #56

New Contributors

• @daico007 made their first contribution in #51

Full Changelog: 1.0.0...1.1.0

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 #18
• changed conversion.py header and added a space on 2 init.py files by @bc118 in #31
• In the README file, added links to readthedocs and reference page by @bc118 in #32
• added zenodo reference by @bc118 in #33
• added credits for main people involved in the project. by @bc118 in #34
• changed to correct conda-forge call on README by @bc118 in #35

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

MoSDeF-GOMC 0.1.0

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