GitLab

* 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

Without this restriction, the compilation fails if the project folder has parent folders called "tests", "internal" or other words in these generic patterns.

* Fixed potential invalid memory access

* Fixed exception

* Support prmtop files created by chamber

* Support CHARMM CMAP flags

* Changed handling of SCEE and SCNB scale factors

* fix barostat frequency check

* fix other barostats

* fix error messages

* Add Fortran type translation for `long long`

* Replaced tabs with spaces
Co-authored-by: Peter Eastman <peter.eastman@gmail.com>

* Optimized CudaSort for non-uniformly distributed data

* Optimized OpenCLSort for non-uniformly distributed data

* Further tuned distributing elements between buckets

* Copied optimizations over to OpenCL

* Try older miniforge version

Use miniforge version that was known to be working

* ci bump

* switch back to using latest miniforge3 + cleanup miniconda folder at the end of testing for the self-hosted runner'

* ci bump

* ci bump

* Minor clarification to manual

* Another minor clarification

* Use multiple streams to broadcast positions

* Use multiple streams to reduce forces

* Adds sync between default stream and peer-copy

* Minor cleanup
Co-authored-by: David Clark <daclark@nvidia.com>

* 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

* updateParametersInContext() can change tabulated functions

* Fixed error in building C wrappers

* updateParametersInContext() can change tabulated functions for CustomCentroidBondForce

* CustomNonbondedForce can update tabulated functions

* CustomGBForce can update tabulated functions

* CustomManyParticleForce can update tabulated functions

* CustomHbondForce can update tabulated functions

* 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

* Added lots of checks for invalid parameter values

* Fixed test failures

* More checks for incorrect parameters

* Fixed test failures

* 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