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

* Add basic version of TinkerFiles

* Refactor TinkerFiles

* Update docstring, type hints, and fix bug when setting box vectors

* Small fixes

* Add unit tests for the TinkerFiles class

* Fixes and updates to TinkerFiles

* Add simuteTinker example

* Update Modeller to work with AMOEBA force fields

* Small fixes

* Relax type hinting

* Fix indices in modeller

* Fix modeller indices

* Fix type hints and usage of Quantity

* Remove numpy protector

* Add reader of .seq files

* Add topology parsing of some protein residues, waters, ions, and generic molecules.

* Miscellaneous improvements

* Update amino acids and nucleotides list

* Various fixes to XML writing, and separate XML writing into a new class

* Comments/warnings

* Add nucleic topological definitions

* Improved handling of peptide residues

* Fix for CYX (disulfide bonds)

* Refactor the topology creation methods

* General improvements, and add support for nucleic-like residues

* No need to handle MP, DP, TP

* Minor improvements

* General refactoring, add automatic determination of topology

* Add TinkerAtomType dataclass, and remove references to biotypes as they are not needed

* Re-add missing parsing of forces and scalars

* Updates to createSystem()

* Add AMOEBA forces

* Add angle-related forces to createSystem

* Add placeholders for missing forces

* Beginning of support for AmoebaMultipoleForce

* Finished support for AmoebaMultipoleForce

* Support for AmoebaVdwForce

* TinkerFiles supports vdw

* Misc updates, and add AmoebaTorsionTorsion, AmoebaWcaDispersion, and AmoebaGeneralizedKirkwood

* Remove XML writer

* Fixes

* Fix wrong indentation in _findBitorsions

* Remove pdb debugging

* Documentation and fixes

* Remove files

* Revert checks in AmoebaVdwForceBuilder and ## @private  markers

* Remove duplicated static methods _getChiralAtomIndex

* Fix GK force

* Fix WcaDispersion force

* Fix WcaDisp

* Fixes and updates

* Cleanup and removing duplicated code

* Bug fixes

* A few more unit conversions

* Minor cleanup

* Misc fixes and updates

* Fix Add AmoebaStretchBendForce

* Simplify force builders

* Update ForceField

* Fix AmoebaPiTorsionForce

* Only add AmoebaWcaDispersionForce if using implicitSolvent

* Simplify amoebaforces

* Stretch torsion and angle torsion

* Misc. fixes

* Improve tests

* Fix cap group identification

* Add/improve tests

* Remove whitespaces from residue names

* Improve tests

* Consistent use of atomClasses list

* Fix match condition in AmoebaOutOfPlaneBendForceBuilder

* Fix AmoebaStretchBendForce

* Final fix for AmoebaStretchBendForce

* Fix AmoebaAngleForce

* Small fixes and improvements

* Update assertion tolerances

* Simplify torsion-torsion force creation

* Small fixes in the tests

* Review comments, type hints, docs for tinkerfiles.py

* Only use standard PDB for AA

* Type hint and docs for amoebaforces

* Reduce tolerances for failing tests

* Fixed error with ZOnly axis type when x particle is not specified

---------
Co-authored-by: peastman <peastman@stanford.edu>

* Benchmark enhancements

- Add `--disable-pme-stream` to benchmark.py to easily compare performance without having to build with different default values for `DisablePmeSteam`
- Replace utcnow to remove DeprecationWarning
- Check for nvidia-smi before attempting to launch it
- Mention HIP where appropriate

* Adjust option

* Can use getPlatform() instead of getPlatformByName()

* More concise arguments for getState()

Test no longer runs and prints out a warning when running benchmark.py with --verbose. Fixes #3391

* Draft integration of the Alchemical Transfer Method (ATM) plugin

* Attempt to store and retrieve forces--does not compile

* Implement addForce()/getForce() methods

* Throw exception when specifying properties without a Platform (#4130)

* Fixed DOF calculation for NoseHooverIntegrator (#4128)

* Fix variance in documentation of VerletIntegrator (#4138)

* Python API for ATMForce

* Fixed compilation error

* Minor cleanup of formatting and documentation

* Files for ATMForce test cases

* More cleanup

* Removed variable groups

* Test ATMForce with two particles

* More tests for ATMForce plus fixes

* Added missing header

* Rework interface to pass displacements as vector of parameters

* Revert "Rework interface to pass displacements as vector of parameters"

This reverts commit 5e092031f31ded1137b677588f007add1c2d6f82.

* Test with nonbonded force

* Allow energy expression to be custom...

* Detect NaN to avoid infinite loop in JAMA::Eigenvalue

* Update to more modern version of pymbar

* No reason to modify spacing

Fix specifying a device will fail to run when multiple OpenCL platforms are available. Specifying `--verbose` prints the following exception:
```
Specified DeviceIndex but not OpenCLPlatformIndex. When multiple platforms are available, a platform index is needed to specify a device.
```

* Overhaul benchmarking script to add lots of new features

* Added another example

* Changes hydrogen mass for benchmarks

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

* 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

* 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

* Added HMR to make ApoA1 benchmark more stable

* Removed debugging code