GitLab

* Update charmmparameterset.py

* Update charmmpsffile.py

* Made ComputeContext worker threads rethrow encountered exceptions into the main thread.

* Changed misleading variable names.

* Changed a misleading exception description

* Optimizations to Lepton

* More optimizations to Lepton

* Began implementing geometric functions on points

* Started common implementation of point functions

* Completed implementation of point functions for CustomCompoundBondForce

* Implemented point functions for CustomCentroidBondForce

* Implemented point functions for CustomManyParticleForce

* Use point functions to simplify implementation of custom forces

* Removed unnecessary code

* Fixed typo

* Improve selection of architecture to compile for

* Fixed compilation errors on older CUDA versions

* 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 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

* Frames distance calculation as matrix multiplciation

* Adds comment explaining distance calculation

* Tunes launch bound for cuda11.2

* Simplifies the effective matrix multiplication
Co-authored-by: David Clark <daclark@nvidia.com>

* Made ordering of impropers more deterministic

* Fixed typo

* 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

* Initial fixes for Apple silicon

Doesn't work yet

* assume vec4 is supported on apple

* Trust the user with env variables

* Fix macos-version-min logic

* Do not alter mass of hydrogens in rigid water

* Do not alter mass of hydrogens in rigid water

* Update IntegrationUtilities.cpp

* Use pinned buffer and for context download
* use template to reduce duplicate code

* Remove template and only add PinnedBuffer for minor performance improvement

* Use pinned buffer for minor performance improvement

Co-authored-by: xxx <yyy>

* nbthole

* Update charmmpsffile.py

* Update charmmpsffile.py

* Update charmmparameterset.py

fix multiple dihedral with the same periodicity and add a warning reminder for improper dihedral

* add test example for NBTHole

add system files of CYT-GUA-CYT DNA segment for testing NBThole

* Update TestCharmmFiles.py

* Changes name of NVRTC program

* Adds launch bounds for findInteractingBlocks

* Replaces launch bound parameter with named constant
Co-authored-by: David Clark <daclark@nvidia.com>

* Adds cuFFT error checking for execution

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