GitLab

* Basic LCPO support

* Add basic test for LCPO from a prmtop file

* API for LCPOForce

* Started LCPO reference implementation

* Finished reference forces & test cases

* Use other test for finite difference since grid might have discontinuous forces

* Reference platform formatting

* Initial implementation of CPU platform

* Bugfixes

* More vectorization and improve neighbor list query speed

* Parallelize part of neighbor search

* Check box size for LCPO with periodic boundary conditions

* Fixes for updating parameters in context

* GBSAOBCForce doesn't use first & last indices for updates, so no need for this optimization here

* Changes to neighbor checking and optimization

* Fixes and minor changes

* Add global surface tension parameter

* Only process half of the pairs in the neighbor list

* Remove unnecessary checks

* Initial version of common platform implementation

* Asynchronously download neighbor list size

* Debugging

* Do pair precomputation in copyPairsToNeighborList

* Recompute interactions instead of scanning neighbor list in inner loop

* Condense position array before computations

* Also make neighbor count download asynchronous on device

* Fixes for kernel launching

* Topology-based LCPO parameter assignment

* Fixes, and use test system for LCPO with nucleic acids

* Always raise instead of warn when LCPO parameters can't be assigned

* Use Amber convention for phosphates

* Replace SimTK-containing file headers

* Update file headers for new Tinker reader files added

* Vectorize NonbondedForce with no cutoff

* Vectorize CustomNonbondedForce with no cutoff

* Memory efficient dense neighbor list

* Fixed errors

The exclusion mask was 8-bits wide, but future CPU support will require
more bits than this (e.g., AVX-512 will be 16-bit).

Enforce memory alignment to improve performance of vector operations.  Also fixed bugs in an earlier optimization.