GitLab

* copy opc ions and opc*standard.xml from https://github.com/openmm/openmmforcefields/commit/b12c2e871b60275a10b3f8f56dfc2f6d5447591f

* auto-merged files

* move charges to residue definition

* remove unmerged files

* add docs

* rename U to U4+

* rename Ag+, Tl+, Gd3+ and I- residue names

* fix O-H bond length typo

* add opc3 constraints test

* Add benchmarks from Amber20 benchmark suite to standard benchmark script

* Add ensemble option; don't change hydrogen mass in amber input files

* Download and extract .tar.gz using pure python code, no wget/tar dependencies

* Rename amber tests

* add opc and opc3 models

* update to match https://bioinformatics.cs.vt.edu/~izadi/OPC_Gromacs/opc.top



* opc box, converted from ambertools-22.0-py38h6177452_1/dat/leap/lib/opcbox.off

* change values to make serialized system match one created from prmtop as close as possible

* unit test for opc water

* opc - final values, match frcmod.opc; derivation in comments

* opc3 water - final values, shows derivation

* opc3box made from ambertools 22 dat/leap/lib/opc3box.off

* add opc3 water test

* add opc and opc3 to docs

* move tests to TestForceField.py

* move opc tests out of amoeba tests, oops

* move opcbox and opc3box pdb files
Co-authored-by: Alex Izvorski <alex@genesistherapeutics.ai>

* Added GLYCAM

* Improved tests and documentation

* Fixed incorrect external bonds

* Adding support for new AMOEBA features

* Support modern method of specifying in-plane angles

* Implemented stretch-torsions

* Implemented angle-torsions

* More AMOEBA fixes

* Bug fix

* Converted AMOEBA 2018 force field

* Added documentation for AMOEBA 2018

* Added a missing file for tests

* Created OBC2 that works with current force fields

* Created HCT, OBC1, GBn, and GBn2 that works with current force fields

* Added documentation for GB models

* Updates to documentation and tests based on comments

* Added formula for screening parameter

* Break user guide into parts

* Break up file I missed

* Add basic .gitignore to suit out-of-tree builds in build, build1, build2 ... build9

* Small changes to autonumber.py for doc compilation

This is a small change designed not to fix the incorrect logic of
autonumber.py, but just to get the docs compiling. While assigning
numbers, the code now just ignores the autonumber_by_chapter
setting for a particular object if it can't find the appropriate
section in section_numbers. This is a temporary fix!

* Include part and chapter in autonumbered objects

* Fix autonumber.py to correctly reference autonumber roles in file-level sections

* Unify and simplify styling across documentation

* Break dev docs down into individual chapter-files

* Correct absolute links to relative

* Disable browser suggestions for lunrsearch box in API docs

* Remove part name from chapter 2.1

* Rename ambiguous 'Home' link to OpenMM.org

* Typo

* Minor fixes and reversions

Reverts some changes I had made and later thought better of,
and fixes some recurring typos across the documentation.

* Number developers guide chapters

* Fix responsiveness

* Remove header.rst and center captions

* Add a level of depth to main TOC and styling to accomodate

* Add third level to Part-level TOCs

* Use :numref: instead of :ref: to number links to sections

* Continuously number chapters in user guide

* navbar links to other docs relative, not absolute

* Improve navbar spacing with new template

* Fix sidebar while allowing it to scroll

* Hard -> Soft links for navigation.html template

* Add navigation.html template to cmakelists

* Add another level of .. to relative links

* Fix flex on C++ and remove layer of ..