GitLab

* 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 ..

* Switches to using FindCUDAToolkit

* Increases minimum CMake version to 3.17 for FindCUDAToolkit
Co-authored-by: David Clark <daclark@nvidia.com>

* Support of Amber FF19SB CMAP

* Update: Support of Amber FF19SB CMAP
Co-authored-by: Kye Won Wang <kyw220@sol.cc.lehigh.edu>

* Changes to work with recent versions of Sphinx

* Updated Sphinx version used for CI

* Began converting AMOEBA to common platform

* Beginning of OpenCL platform for AMOEBA

* Converted AmoebaVdwForce to common platform

* Cleaned up reference AMOEBA tests

* Began converting AmoebaMultipoleForce to common platform

* Continue converting AmoebaMultipoleForce to common platform

* Bug fixes

* Bug fix

* Continue converting AmoebaMultipoleForce to common platform

* Converting AmoebaMultipoleForce and AmoebaGeneralizedKirkwoodForce to common platform

* Converting AmoebaMultipoleForce and AmoebaGeneralizedKirkwoodForce to common platform

* Creating OpenCL version of AmoebaMultipoleForce and AmoebaGeneralizedKirkwoodForce

* Creating OpenCL version of AmoebaMultipoleForce and AmoebaGeneralizedKirkwoodForce

* Creating OpenCL version of AmoebaMultipoleForce and AmoebaGeneralizedKirkwoodForce

* Converted arrays from real3 to real

* Bug fix to OpenCL AmoebaGeneralizedKirkwoodForce

* Fixes for AMD GPUs

* Began converting HippoNonbondedForce to common platform

* Continuing to convert HippoNonbondedForce to common platform

* Continuing to convert HippoNonbondedForce to common platform

* Working on unifying PME kernels

* Fixed error on devices without 64 bit atomics

* Unified PME kernels

* Converted HippoNonbondedForce to common platform

* Creating OpenCL implementation of HippoNonbondedForce

* Continuing OpenCL implementation of HippoNonbondedForce

* Mostly finished OpenCL implementation of HippoNonbondedForce

* Eliminated three component vector types in host code

* Fix errors on CPU OpenCL

* Skip double precision tests for AMOEBA on OpenCL

* Bug fixes

* Bug fixes

* Fixed compilation error

* add docs for conda forge releases

* adapt to openmm git_url

Update openforcefield namespace to new conda-forge namespace in User guide

* Converted RPMD plugin to common platform

* Merged RPMD tests for different platforms

* Try to fix errors on CPU OpenCL

* Converted more code to common platform

* Converted more code to common platform

* Cleanup to CUDA AmoebaMultipoleForce

* Deleted obsolete SOR code

Co-authored-by: David Clark <daclark@nvidia.com>

* Use the force group which is assigned to the metadynamics force

* Handle a case when all the force groups are already used

* Fix a typo

Moved _syncWithDisk in init before adding table of biases to CustomCVForce so that loaded biases are included in the biasing potential. (#3052)