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Evan Pretti authored
* 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
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