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

Implemented setting random seed for reference platform, as well as adding it as an option to BrownianIntegrator and AndersenThermostat.

Implemented dynamic loading of platforms from DLLs.  Also fixed a lot of compilation errors and warnings under Windows.

Modified the initialization order of ForceImpls to prevent them from trying to initialize themselves before the Platform had been chosen