Rewrite pair list class; large speedup for 'checkstructure' #530
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…x in a 5827 atom system
…ical pragma in the middle of the loop and will eventually allow for consistent output between serial/openmp.
…e functionality into its own subroutine.
…the same structure.
…used, adjust the pairlist accordingly.
…ames because its way faster now.
…ots of validation still.
…tructureCheck; will suppress non-warning/error setup messages in permutedihedrals.
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Jenkins failure looks like an issue with the build system - safe to merge. |
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This PR consists of two major changes/improvements to cpptraj:
checkstructureAction to speed up systems with box info, which tend to be large.The PairList class was originally written for the Ewald class and was based on how SANDER employed a pair list. While it worked, it was not written in a very user-friendly or object-oriented way. It has now been written to be much more object oriented: the pair list consists of cells (
CellType), to which atoms are added (AtmType). Cells contain information on all neighboring cells. The performance is unchanged from the previous implementation (based on tests of theenergy ewaldcommand) and it is now easier to iterate over cells and atoms in cells.With the PairList class now being easier to use it has been incorporated into the
checkstructureAction as a proof-of-concept and performs extremely well. In tests of some large systems (thousands to tens of thousands of atoms) the version ofcheckstructurewith a pair list shows a speedup of over 100x compared to the non-pair list version.The structure checking aspect of Action_CheckStructure has now been properly separated into the new
StructureCheckclass so that other parts of the code (e.g.Exec_PermuteDihedrals) get access to only the functionality they need. Thecheckstructurecommand now also works properly with MPI and gives consistent results when used with MPI and/or OpenMP (i.e. order of problems found is the same no matter what). The OpenMP version scales slightly better now due to the removal ofcriticalpragmas.This PR also adds more tests for
checkstructure, including for the new pair list functionality.