GitLab

* Use PocketFFT instead of FFTW

* Minor cleanup

* Use PocketFFT instead of fftpack for reference platform

* Remove FFTW as a dependency

* Converted a test case to use PocketFFT

* Fixed an incorrect comment

* 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 documentation to clarify behavior of nonbonded exceptions

* Added documentation to clarify behavior of nonbonded exceptions

* Reference implementation of computed values for CustomNonbondedForce

* CPU implementation of computed values for CustomNonbondedForce

* Common implementation of computed values for CustomNonbondedForce

* Serialization of computed values

* ForceField supports computed values

* Minor clarification to manual

* Another minor clarification

* 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 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

* 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

* 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

* Update instructions on compiling from source

* Minor changes based on feedback

* 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 ..

* Changes to work with recent versions of Sphinx

* Updated Sphinx version used for CI

* Add draft GHA-based CI for Linux

* Fix events

* Dup key

* Fix path

* Update env vars

* More fixes

* Fix env vars again

* add doxygen

* add sudo

* Typo

* upgrade CUDA

* escape newlines

* more backslashes

* fix CUDA_APT

* more env vars fixes

* fix missing file

* acumulate env_vars

* build python wrappers only if requested

* add pytest

* use $GITHUB_ENV

https://docs.github.com/en/free-pro-team@latest/actions/reference/workflow-commands-for-github-actions#environment-files

* use ${GITHUB_WORKSPACE}

* Pin older gromacs

* add windows

* Provide default values for unbound vars

* fixes

* this is powershell not cmd

* update envs

* win fix

* make windows use cmd

* Change install prefix

* fixes

* better env files

* Increase timeout threshold

* set xcode to 10.x

* specify action version

* fix sdk in macos

* split jobs a bit more

* build wrappers even if tests failed for c...

* Top level Python module is now "openmm"

* Updated module names in examples

* Updated module names in documentation

* Updated module in CI scripts

* Added deprecation warning

* Start branch

* Update installation instructions for conda-forge

* Update instructions for openmm-setup and openmmforcefields

* Updated to latest values for physical constants

* Updated documentation on physical constants

* Updated Python unit definitions

* Fixed constants in test case

* Added a comment