GitLab

* 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

* Added lots of checks for invalid parameter values

* Fixed test failures

* More checks for incorrect parameters

* Fixed test failures

* Created MonteCarloFlexibleBarostat

* Improved test cases

* Documentation for MonteCarloFlexibleBarostat

* Added a missing include

* Serialization for MonteCarloFlexibleBarostat

* Added MonteCarloFlexibleBarostat to C++ API docs index

* Added citation for MonteCarloFlexibleBarostat

* Atom types in CHARMM FF are non-case-sensitive

* Atom type name in CHARMM RTF

* Make atom section in CHARMM PSF file to be uppercase

* Further optimization to updating long range correction

* Bug fix

* Improved handling of atoms with alternate locations

* Fixed a test failure caused by an invalid PDB file

* Improve accuracy of constants in Fortran interface

* Use different suffix for Fortran constants

* Use cuCtxPushCurrent() and cuCtxPopCurrent() for selecting CUDA context

* Fixed errors in amoeba coda

* Fixed more errors in context selection

* Added option for CheckpointReporter to save States

* Try to fix test failure on Windows

* Allow querying current step count

* Fixed error building Python wrapper

* Check for keyword args to createSystem() that are never used

* Fixed incorrect arguments in test cases

* Simplified derivatives of min() and max()

* Fixed compilation error in kernel

* 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

Made OpenCLContext::reduceBuffer additionally store the result into a 64-bit fixed point buffer. (#3209)

* Changes hydrogen mass for benchmarks

* Adds amber case for hydrogen mass
Co-authored-by: David Clark <daclark@nvidia.com>

* Proof of concept matching current behaviour with Breathe

* Reorganise C++ API docs to work without autosummary

* Revert to Sphinx-native search

* Move remaining pip deps to conda

* Remove unnecessary lunrsearch templates

* Remove lunrsearch from cmake

* Tidy up layout of API docs

* Get code blocks to work with Breathe

Breathe doesn't seem to support the Doxygen <preformatted> tag.
It does support the <code> tag, but better yet it supports using
<verbatim> tags to embed rst into docstrings. This commit changes
all <pre> tags to use RST verbatim, and updates the Python
documentation machinery to support it too.

* Clarified some language

* Have doxygen exclude undocumented classes and have sphinx fail on warnings for C++ API docs

* List custom forces and integrators last

* Add breathe to documentation CI

* Typo

* Fix link to custom forces in extras.rst

* Have Breathe process only public classes

* Strip OpenMM:: prefix from rst files to avoid colons in links

* Remove existing private classes from EXCLUDE_SYMBOLS

* Add comment to C++ cmake describing why we promote warnings to errors

* Revise documentation build instructions for new dependencies

* Remove tri-sulfite bond formation.

Pdbfixer attempts to add di-sulfide bonds to any pair of CYS "S" atoms that are less than 3 A. This procedure fails when multiple such bonds are assigned to a given atom. 

Here we rectify this issue by a greedy algorithm: Atom I is chosen to be bonded to `argmin(distance([:I-1, I])` over all candidate di-sulfide bonds. This procedure will not generally result in a set of minimal distance di-sulfide bonds, but will fix the "tri-sulfide bond" problem. Fixing the more general case would require a solution to global constraint satisfaction problem.

**Legal**
This patch is provided under the CC0 license (https://creativecommons.org/share-your-work/public-domain/cc0/).
This is not an officially-supported Google product. It is provided ‘as-is’ without any warranty of any kind, whether expressed or implied.

* Update topology.py

Remove a redundant comment.

* Accept relative links between documentation sites

* add glob to linkinator

* Recurse from index.html

* Path is relative to server-root

* Get all the dots and slashes just right

* Report only the broken links

* Treat linkinator's --skip argument as regex and skip the ks.uiuc.edu domain

* Increase linkinator timeout rather than skip ks.uiuc.edu

* typo

* another typo

* Delete .confirm_shortcut_change

* Update instructions on compiling from source

* Minor changes based on feedback

* Deleted the default copy-constuctor for ContextImpl.

* Deleted the default copy assignment operator for ContextImpl.

* 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 ..