GitLab

* Correct AmoebaAngleTorsion in test_Amoeba18Nucleic of TestForceField

* Update processTinkerForceField to handle latest .prm Tinker files

* Update amoeba2018 XML files

* Update amoeba2013 XML files

* Update amoeba2009 XML files

* Adapt addTorTor to new format in the .prm files

* Fix TorsionTorsion

* Also update the total energy in test_Amoeba18Nucleic

* Update amoebabio18.prm

* Fix nucleic acid test energies

* Correct AmoebaAngleTorsionForce params

* Add new addTorTor to TinkerFiles

* Revert unit fix

* Change to .pdb file which Tinker likes

* Update test_Amoeba18BPTI

* Remove trailing zeros from XML files

* Leave trailing zeros only on 2018 ff

* New element names in 2018

* More digits for surfaceAreaFactor

* More digits for surfaceAreaFactor

* More digits

* Remove debugging print

* Add support to 2009 and 2013 AMOEBA ffs to processTinkerForceField.py

* Add FF specific residues XML files

* Delete old residuesFinal.xml

* Update AMOEBA XML ffs

* Update FFs

* Fix some formatting issues

* Fix "." in scientific notation

* Remove old assertions

* Initial implementation of C++ API

* Add kernel interface and information for API generation

* API updates for updating electrode parameters

* Add serialization proxy for ConstantPotentialForce

* Update file headers

* Add CG error tolerance and fix units on getCharges() return value

* Initial implementation of matrix solver

* Fixes and conjugate gradient solver

* Try to fix Linux and Windows builds

* Make sure charge constraint target is on total charge

* Restore handling of exceptions like NonbondedForce since they won't involve electrode atoms

* Ameliorate numerical instability in constrained conjugate gradient

* Fix uninitialized pointers, memory leak, and style

* Set CG tolerance units in Python API

* Test ConstantPotentialForce serialization

* Read/write ExceptionsUsePeriodicBoundaryConditions as bool

* Improve constrained conjugate gradient robustness to roundoff error accumulation

* Recompute matrix if electrode atoms move due to setPositions()

* Tolerance is now in gradient (potential) units again

* Add neutralizing background correction

* Add Python API tests

* Fixes for CG and nonbonded exceptions

* Add initial tests checking against existing NonbondedForce behavior

* Expand test suite and fix some implementation issues

* Add additional tests using larger reference system

* Add Gaussian test

* Finish test against reference computation

* CPU platform implementation

* Fixes for compilation on some platforms

* Fixes for constant potential with AVX/AVX2

* Test linking CPU PME library to constant potential test directly

* Older SWIG versions don't support Python set to C++ set conversion

* Add user guide entry

* Increase speed of reference test

* Conditional building constant potential CPU test is unreliable

* Debugging

* Miscellaneous fixes and improvements for CI

* Cache charges so solver will not run if system and coordinates have not changed

* Preconditioner flag, stability, and automatic detection improvements

* Add GPU platform-specific constant potential kernel classes

* PME and device-host I/O changes to support constant potential

* Initial common constant potential implementation

* Constant potential fixes:

* Fix preconditioner PME position/charge save/restore logic

* Fix reduction synchronization in constant potential solver kernels

* Add double-float accumulation for conjugate gradient solver when
  double unsupported by hardware

* Improve conditioning of a test system, and make sure particles are in or
out of cutoff for consistency and ease of comparing between platforms

* Reorder guess charges for CG when atom reordering changes positions

* Remove PME queue for now

* Trying to debug optimized direct space derivative kernel

* Remove extraneous debugging lines

* Style updates; just make CPU preconditioner double precision

* Debugging updated optimized direct derivatives kernel for all but OpenCL CPU

* OpenCL CPU implementation of direct space derivatives, and cleanup

* Try to make test even shorter to not time out on CI

* Temporary - Debugging

* Debugging

* Debugging

* Debugging

* Debugging

* Remove debugging code and fix reduction synchronization

* Fix other reductions

* Debugging - are tests hanging or just slow on CI?

* Debugging

* Debugging

* Fix macro for case when double precision is available on hardware

* Remove changes for debugging again

* Try to improve matrix solver cache locality by uploading transpose

* Fixes for atom ordering and periodic images

* Can't rely on reorder listener for cell offset updates

* Test reducing number of contexts and timing for CI

* Debugging

* Remove timing code and revert debugging changes

* Matrix solver and plasma term optimizations

* Reduce CG solver kernel calls and downloads

* Don't read back convergence flag from global memory

* Update PME due to refactoring in master branch

* Faster matrix solver (1st step)

* Faster matrix solver for CUDA

* Faster matrix solver compatibility with non-CUDA platforms

* Matrix solver fixes

* Use warp shuffle reductions when possible

* Attempt to work around intermittent compiler crash in Intel CPU OpenCL

* Optimize CG solver kernel 1

* Rework CG solver so some kernels can use more than 1 block

* Don't run out of shared memory

* Asynchronously download convergence flag while clearing buffers

---------
Co-authored-by: Evan Pretti <pretti@sh03-17n15.int>

* Replace C++ code examples in Python API docs

* Use newer Python for building docs

* Remove sphinx version pin

* Add Python versions of code examples

* Minor edit

* Add Python version of one more code example

* Remove includes for Dart

* Fix CMake error

* Fixed broken link

* Pin to cmake<4.0

* Try to make the link checker stop complaining

* Use Intel OpenCL for CI

* Set environment variables

* Try to get CI to run

* Debugging

* Debugging

* Fixes for Intel OpenCL

* Updated Python versions for CI

* Install setuptools

* CI build for HIP

* Removed some unneeded dependencies

* Fix test for which libraries are present

* Support numpy 2

* Debugging

* Removed debugging code

* Run Mac tests on ARM and Intel

* Added missing environment file

* Removed obsolete code for M1 runner

* Removed obsolete code for M1 runner

* Debug CI failures

* Debugging

* Debugging

* Debugging

* Debugging

* Debugging

* Debugging

* Debugging

* Debugging

* Removed build that was failing

* Fixed URL that had changed

* addHydrogens() allows specifying exactly what hydrogens to add

* Prevent CI from using numpy 2.0

* Revised code from installing CUDA on CI

* Debugging

* Debugging

* Debugging

* Debugging

* Debugging

* Debugging

* Debugging

* Remove support for Gromacs implicit solvent

* Removed tests of implicit solvent

* Always use nvrtc for compilation

* Install nvrtc on CI

* Workaround for compiler error

* Set empty values for deprecated properties

* update to use newer openmm-torch version

* openmm8 rc1 envs

* forgot to bump nnpops

* Attempt at fixing failing pypy build

* Try using mambaforge

* Debugging

* A different approach to using mambaforge

* Try a separate environment file for pypy

* add guide for dev builds

* hosted env file for openmm-8 beta

* explain how to host an env

* add a namespace to support different os

* pin all the versions

* add version pins and env name

* Added pytest

* update envs

* add guide for dev builds

* hosted env file for openmm-8 beta

* explain how to host an env

* add a namespace to support different os

* pin all the versions

* add version pins and env name

* Added pytest

* add guide for dev builds

* hosted env file for openmm-8 beta

* explain how to host an env

* add a namespace to support different os

* 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

* Update CUDA keys

* Fixed typo

* Optimized computing powers in CompiledExpression

* Fixed compilation error

* Attempt at fixing compilation error

* lets see what blows up!

* need to add env file, different name than normal

* lets see if setting an env will help it find the base

* try forcing the use of mamba

* this should break everything, but might make osx work

* lets see if this fixes the issue with the extension

* ci bump

* lets see if a different installer will work

* single thread build to see error better

* ci bump

* ci bump

* can't build opencl on m1

* add salt to url to prevent caching

* rename to reflect that we can just build CPU

* going to add a M1 x86_64 buld and an arm64 build

* lets see if I broke 86

* now lets see what happens with arm

* forgot to add new build files

* try older python version

* newer python?

* try mini forge

* ci bump

* unpin doxygen and remove gromacs as a dep

* double check where x86_64 libs are getting pulled in

* ci bump

* try and use conda compiler toolchain and set arch

* weird things happend with setting arch

* lets see what the arch the runner thinks it is using

* try printing arch again

* undo shell change

* remove changes to shell

* make sure I don't break other buikds

* fix syntax issue and add new label to actionlint

* ci bump

* ci bump

* lets focus on arm64 builds for now

* ci bump

* ci bump

* try setting arch to build with arch command

* split steps up so other builds don't break

* see if the cmake step is the only one we need to arch-ify

* cleaning things up

* cleaning things up

* set -j2 for make

* we can use the same build step as the otehr builds

* now lets see if it can install gromacs

* no gromacs, no problem?

* remove bit of logic stopping the build

* pin doxygen to 1.9.1

* try building openCL

* ci bump

* ci bump

* 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

* 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

* Changes to work with recent versions of Sphinx

* Updated Sphinx version used for CI

* add docs for conda forge releases

* adapt to openmm git_url

* Use command line compiler if it is explicitly specified

* Don't set OPENMM_CUDA_COMPILER on Jenkins

* 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

* 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

* Use list-comprehension in Python code

A minor change, but slighly easier to understand the initialization of
`parent_exclude_list` in my opinion.

* Implement __ne__ in Python classes that has __eq__

In Python 3, `__ne__` is automatically implemented as `not __eq__`.

However, in Python 2 it seems to be implemented as `not is` (so based on object
identity).

Based on setup.py [0] which says that "OpenMM requires Python 2.7 or better", it
should be useful to have better support for Python 2 :)

This was already done in 4 of the 12 classes that implements `__eq__`

```
>>> class WildCard(object):
...     def __eq__(self, other): return True

>>> w = WildCard()

>>> w == 42
True

>>> w != 42
True

>>> w != w
False
```

[0]: https://github.com/openmm/openmm/blob/5cef29ce8d4e17b6d0f9fd8a3c6cc1669ca0ba2b/wrappers/python/setup.py#L237

* Use umambiguous floor division for index calculations in Python

This makes the code work as intended if run...