MoSDeF-dihedral-fit - MoSDeF-dihedral-fit 0.1.13

What's Changed

JOSS paper changes requested by editor to the paper

• Additional editor suggestions added to paper on the equations by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/140

Full Changelog: https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/compare/0.1.12...0.1.13

Scientific Software - Peer-reviewed - Python
Published by bc118 about 1 year ago

MoSDeF-dihedral-fit - MoSDeF-dihedral-fit 0.1.12

What's Changed

Changes to JOSS paper

• Added References title and fixed one reference for the JOSS paper. by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/139

Full Changelog: https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/compare/0.1.11...0.1.12

Scientific Software - Peer-reviewed - Python
Published by bc118 about 1 year ago

MoSDeF-dihedral-fit - MoSDeF-dihedral-fit 0.1.11

What's Changed

JOSS paper comments/suggestions

• Removed duplicate citation for JOSS publication by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/138

Full Changelog: https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/compare/0.1.10...0.1.11

Scientific Software - Peer-reviewed - Python
Published by bc118 about 1 year ago

MoSDeF-dihedral-fit - MoSDeF-dihedral-fit 0.1.10

Full Changelog: https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/compare/0.1.9...0.1.10

Changed so conda forge picks it up

Scientific Software - Peer-reviewed - Python
Published by bc118 about 1 year ago

MoSDeF-dihedral-fit - MoSDeF-dihedral-fit 0.1.8

What's Changed

JOSS paper edits

• Added some suggestions or clarifications that the editor suggested. by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/137

Full Changelog: https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/compare/0.1.7...0.1.8

Scientific Software - Peer-reviewed - Python
Published by bc118 about 1 year ago

MoSDeF-dihedral-fit - MoSDeF-dihedral-fit 0.1.7

Full Changelog: https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/compare/0.1.4...0.1.7

Scientific Software - Peer-reviewed - Python
Published by bc118 over 1 year ago

MoSDeF-dihedral-fit - MoSDeF-dihedral-fit 0.1.6

Fixed release name

Scientific Software - Peer-reviewed - Python
Published by bc118 over 1 year ago

MoSDeF-dihedral-fit - MoSDeF-dihedral-fit 0.1.5

What's Changed

• Update affiliation by @daico007 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/136

Full Changelog: https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/compare/0.014...0.1.5

Scientific Software - Peer-reviewed - Python
Published by bc118 over 1 year ago

MoSDeF-dihedral-fit - MoSDeF-dihedral-fit 0.1.4

Fix CITATION.ciff to allow DOI assignment by Zenodo

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

MoSDeF-dihedral-fit - MoSDeF-dihedral-fit 0.1.3

New version to obtain Zenodo DOI.

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

MoSDeF-dihedral-fit - MoSDeF-dihedral-fit 0.1.2

What's Changed

Bug fixes

• bug fix - randomly outputing misordered coord files by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/132

Changelog

Full Changelog: https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/compare/0.1.1...0.1.2

Scientific Software - Peer-reviewed - Python
Published by bc118 over 1 year ago

MoSDeF-dihedral-fit - 0.1.1

What's Changed

Removed Contributor's status as equal contributor as was an oversight.

• removed equal contributor for 1st Author on paper by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/131. Removed person as an equal contributor here as it was an somehow left in from the original template. Also, no one caught it as it the Authors are somehow not printed on the PDF when using Pandoc. Removed this person as an equal contributor here as it was an somehow left in from the original template. Also, no one caught it as it the Authors are somehow not printed on the PDF when using Pandoc.

Full Changelog: https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/compare/0.1.0...0.1.1

Scientific Software - Peer-reviewed - Python
Published by bc118 over 1 year ago

MoSDeF-dihedral-fit - MoSDeF-dihedral-fit 0.1.0

What's Changed

Features 

• added Mie and Exp6 F mixing rules for non-LJ parameters in docs by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/102
• added Exp6-AAD, AMBER-AA, TRAPPE-UA, Mie-UA, FF styles tests and XML … by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/108
• added links to examples for 4 more FFs to the README file by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/109
• Reviewer 2 request 1 changes for improved instructions on installing GOMC package by @CalCraven in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/107
• Update LICENSE and contributing guideline by @daico007 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/103
• Adds other ways to get FF or dihedral parameters by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/115
• Added better input tests for dihedral angle calc added all the functions with a warning by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/112
• More tests on read/write utils by @daico007 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/120
• Testing exceptions by @daico007 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/106

Bug fixes

• Added dihedral fits tests and updated/fixed build errors in the docs by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/111
• bug fix for other forms of Gaussian 16 dihedral output files by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/123
• added a HC-CT-CT-HC test on butane to ensure all the duplicate angles are being calculated properly by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/124
• fix unit tests by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/126
• fix unit tests by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/126

Maintenance 

• fixed the locked python versions to 3.11.xxx in yml files by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/83
• Update pre-commit badge link by @daico007 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/85
• Turn DOCKER build back on in CI.yml by @daico007 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/86
• added orig VMD license and updated paper to cite VMD. by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/88
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/87
• updated License to add VMD's license by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/89
• added text to specify the original VMD code was not used, just vmd-python by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/91
• made /mosdef-dihedral-fit lowercase in docker tags by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/92
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/90
• removed VMD from license by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/93
• Add authors and emails to setup.py by @daico007 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/104
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/110
• fixed citations on JOSS paper by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/113
• Paper updates: Added cites for all of 1st paragraph by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/116
• Made original lines 12-14 and 15 in the paper clearer for the reader by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/117
• Slimed down paper and fixed some doc typos by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/119
• fix readme periodic eqn typo by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/121
• Slimed down paper and fixed some doc typos by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/119
• fix readme periodic eqn typo by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/121
• Remove line 74, revise line 72 by @jpotoff in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/127
• changed paper date and fixed a few typos. by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/128
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/129
• Changed the wording on periodic form for CHARMM and equation math coverage. by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/130 Full Changelog: https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/compare/0.0.3...0.1.0

Scientific Software - Peer-reviewed - Python
Published by bc118 over 1 year ago

MoSDeF-dihedral-fit - MoSDeF-dihedral-fit 0.0.3

What's Changed

• Fix module not found error in CI by @daico007 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/80

Full Changelog: https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/compare/0.0.2...0.0.3

Scientific Software - Peer-reviewed - Python
Published by daico007 almost 2 years ago

MoSDeF-dihedral-fit - MoSDeF-dihedral-fit 0.0.2

What's Changed

• added a new line to init.py.py so it will hopefully pass on conda-forge by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/78
• Fix init py by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/79

Full Changelog: https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/compare/0.0.1...0.0.2

Scientific Software - Peer-reviewed - Python
Published by bc118 almost 2 years ago

MoSDeF-dihedral-fit - MoSDeF-dihedral-fit 0.0.1

What's Changed

• changed the git init.py file error by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/76
• Bump to version 0.0.1 by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/77

Full Changelog: https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/compare/0.0.0...0.0.1

Scientific Software - Peer-reviewed - Python
Published by bc118 almost 2 years ago

MoSDeF-dihedral-fit - MoSDeF-dihedral-fit

Initial Release PRs

• The initial files which are required to fit the dihedral. by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/1
• added setup files by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/2
• changed name of main folder by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/3
• added .files for project setup by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/4
• fix imports in python files by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/5
• add python vmd package and change os.waitpid to os.wait4 to be compatible with Mac by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/6
• changed CITATION.cff file to be MoSDeF-dihedral-fit references. by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/7
• fixed bug in the fitdihedral and filereadandwrite that was double printing dihedral constants if not set to 0 in xml file by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/9
• add the main testfitdihedralwithgomc.py file tests by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/10
• fixed dihedral naming for ethane by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/11
• Initial documentation by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/8
• fixed typos in simple example by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/12
• added testmathoperations.py. Not completed, but added from top of math_operations.py to and including the dihedral angle. by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/14
• Add unit tests for utils by @daico007 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/13
• fixed typo in installion docs, and removed the one in the wrong locat… by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/15
• Added general gaussain style output files to be used directly by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/16
• updated docs and docstrings by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/17
• updated docs to have no warning and look better. by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/18
• Added mol2 and QM file element matching check, in order. by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/19
• added comments/notes on the function of where fitted data points are … by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/20
• added comments/notes on the function of where fitted data points are … by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/21
• changed the opls energy equations to be the same in the docs by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/22
• Added unit tests for user input and other checks. by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/23
• changed fitvalidationrsquaredrtol range to 0 < fitminvalidatedrsquared < 1 by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/24
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/27
• Update CI.yml by @daico007 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/25
• Fix Dockerfile by @daico007 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/29
• Changed the example variables from override_VDWGeometricSigma to VDWGeometricSigma by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/30
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/33
• Added Mie and Exp6 FF for gmso FFs by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/34
• Fix typos by @CalCraven in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/35
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/37
• Initial tests for writing functions by @CalCraven in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/31
• added MoSDeF-GOMC to the citing repos by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/40
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/42
• Move tested files into files/tests by @CalCraven in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/44
• rename function variables by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/45
• add calculate a single dihedral angle to the docs by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/47
• added dihedral equations to docs by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/48
• add the dihedral angle calculation to the Doc by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/49
• Update docker actions by @daico007 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/50
• initial JOSS paper commit by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/46
• added chris's orchid by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/51
• Skeleton of README details by @CalCraven in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/36
• fixed Readme dihedral eqns by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/52
• adding the GOMC docker image to the CI.yml file by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/53
• added a check to ensure the GOMC binary is there and working. by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/54
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/55
• added spaces int he paper.md equations so it reads on GitHub Properly by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/56
• added the link to the docs webpage and updated the license reference. by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/57
• added some text and concepts to the paper.md file by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/58
• changed company name to only Atomfold by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/61
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/60
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/62
• changed assert condition in testfileread_write.py by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/64
• modified dockerfile by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/65
• modified dockerfile by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/67
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/63
• removed duplicate nomkl in mamba env create nomkl --file environment.yml in the Dockerfile by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/68
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/70
• added paper bib references and info in the docs on how to setup UA force fields with these AA QM data by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/71
• Pause Docker Build by @daico007 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/69
• Edits to paper by @jpotoff in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/72
• fixed a few typos in the paper and reworded 1 line. by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/73
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/74
• updated for v0.0.0 release by @bc118 in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/75

Contributors

• @bc118 made their first contribution in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/1
• @daico007 made their first contribution in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/13
• @pre-commit-ci made their first contribution in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/27
• @CalCraven made their first contribution in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/35
• @jpotoff made their first contribution in https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/pull/72

Full Changelog: https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/commits/0.0.0

Scientific Software - Peer-reviewed - Python
Published by bc118 almost 2 years ago