GitLab

* Added documentation on HIP

* Instructions for building HIP on Windows

* Can use getPlatform() instead of getPlatformByName()

* More concise arguments for getState()

* Implemented CustomCPPForceImpl

* Documentation for CustomCPPForceImpl

* Attempt at fixing Windows compilation error

* Improved documentation

* Always use nvrtc for compilation

* Install nvrtc on CI

* Workaround for compiler error

* Set empty values for deprecated properties

* Update 05_cpu_platform.rst

* Update 04_platform_specifics.rst

* 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 ..

* 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 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 core

* revert & resort build/test

* fix run logic?

* install envs in D:\

* add more cudas

* allow longer test times

* sudo that

* fix cuda ver checks

* another little fix

* one more

* missing package

* missing dev packages

* missing backslash

* add nvprof

* factor scripts out

* export CUDA_PATH

* no quotes in env var

* add more cudas

* fix ci name

* fix flags

* typo

* missing parenthesis

* add cuda 11.2 urls

* add retry loops for online installations

* add library existence tests

* verbose

* fix sets

* CPU and PME are not built in GPU variants; do not test for those

* quote?

* fix windows checks

* add macos opencl

* disable opencl tests on macos (but build anyway)

* add docs

* cd into build for docs!

* install then cd

* pin sphinxcontrib-bibtex

* we need tex in the system

* split docs into a separate job

* simplify retrying

* simplify retrying 2

* do install

* fix tlmgr installation

* more tex packages

* one more

* one more

* add textcomp to docs

* usepackage[utf8]{inputenc}

* switch to xelatex?

* add xetex

* more fonts

* do not use xindy

* tables can't contain blocks and use tabularcolumns at the same time

https://www.sphinx-doc.org/en/master/usage/restructuredtext/directives.html?highlight=tabular#directive-tabularcolumns

* build libs in docs too

* update docs deps; bring in pdfs

* kill server after 404 checks

* chage 404 checker

* explicit locations needed

* cumulative exit codes

* override set -e

* update README badges

* add ppc / arm

* missing vbar

* not it

* one too many extensions

* do not test gromacs

* manage workspace

* source conda.sh

* add python version to matrix vars

* source first thing

* disable unbound checks

* add compilers

* some more cuda stuff

* add CPU only ppc64le

* link through stubs

* One more way to obtain HOST_USER_ID?

* let cmake find cf's opencl

* Try with GCC7

* add timeouts for docker based runs

* add several attempts for stochastic failures

* add tests with conda forge compilers

* do not parallelize pytest in docker runs

* exclude some known slow tests

* enable ccache

* forgot conda shell

* No need for macos sdk retries

* \  -> ^

* fix timestampt windows

* export env vars for current step too

* unneeded quotes windows?

* disable compression on windows?

* add ccache in docker too

* group commands

* fix syntax error

* fix version spec

* Increase timeout in Docker runs

* heh, it's double colon

* fix cache timestamp in windows

* escape % with %%

* ccache in docs too

* don't use wrapper package in windows; call vcvarsall directly

* More docker variants

* Handle ccache env vars in yaml

* Re-enable parallel pytest in Docker runs

* Delete unwanted azure ymls that I didn't end up using

* add some comments

* Update badge URL

* is that path messing with windows ccache?

* add CI-README

* Reduce CI matrix

* increase timeouts

* Add GCC7 on PPC QEmu again (temporarily, just for debugging)

* add docker instructions for local debugging

* fix start_docker_locally

* skip some url checks in docs

* Use new package name

* update link

* Updated to latest values for physical constants

* Updated documentation on physical constants

* Updated Python unit definitions

* Fixed constants in test case

* Added a comment

* Began creating common compute framework to unify code between CUDA and OpenCL

* Began OpenCL implementation of common compute framework

* Common implementation of CMMotionRemover

* CUDA implementation of common compute interface

* Converted HarmonicBondForce to common compute API

* Converted standard bonded forces to common compute API

* Converted ExpressionUtilities to common compute API

* Created ComputeParameterSet

* Converted custom bonded forces to common compute API

* Converted CustomCentroidBondForce to common compute API

* Converted CustomManyParticleForce to common compute API

* Moved lots of duplicate code from CudaContext and OpenCLContext to ComputeContext

* Converted GayBerneForce to common compute API

* Removed obsolete kernels

* Converted verlet integrators to common compute API

* Converted Langevin and Brownian integrators to common compute API

* Converted CustomIntegrator to common compute API

* Converted CustomNonbondedForce to common compute API

* Removed uses of a deprecated API

* Fixed failing test cases

* Converted GBSAOBCForce to common compute API

* Began converting CustomGBForce to common compute API

* Finished converting CustomGBForce to common compute API

* Merged duplicated code in CudaIntegrationUtilities and OpenCLIntegrationUtilities

* Converted RMSDForce and AndersenThermostat to common compute API

* Converted CustomHbondForce to common compute API

* Merged scripts for encoding kernel sources

* Converted Drude plugin to common compute API

* Fixed errors in CMake scripts

* Attempt at fixing errors on Windows

* Added discussion of common compute API to developer guide

* Added Windows export macro for common classes

* Fixed error in CMMotionRemover

* Ubdated travis to newer Ubuntu version

* Fixed errors on CPU OpenCL

* Fixed Windows linking errors

* Added missing pragma for 32 bit atomics

* Replaced long long with mm_long

* More fixes to Windows linking

* Bug fix