Rewrite pair list class; large speedup for 'checkstructure'#530

Merged

drroe merged 43 commits into

Amber-MD:masterfrom

drroe:new_pairlist

Aug 21, 2017

Commits on Aug 17, 2017

DRR - Cpptraj: Test direct calc with new pairlist
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DRR - Cpptraj: Enable new pairlist calc
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DRR - Cpptraj: Add some timing data. Use wrapped fractional coords.
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DRR - Cpptraj: Properly clear cells
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DRR - Cpptraj: Make naming consistent
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DRR - Cpptraj: Improve code docs.
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DRR - Cpptraj: Look at delta E
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DRR - Cpptraj: Replace PairList with PairList2
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DRR - Cpptraj: Start replacing PairList with PairList2 in Ewald
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DRR - Cpptraj: Store fractional coords separately for recip calc
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DRR - Cpptraj: Do not store fractional wrapped coords in AtmType anymore
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DRR - Cpptraj: Code comments and cleanup
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DRR - Cpptraj: Print grid dimensions
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DRR - Cpptraj: Version of check using pairlist. So far speedup of ~10x in a 5827 atom system
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DRR - Cpptraj: OpenMP-parallelize
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DRR - Cpptraj: Add ability to change pairlist cutoff
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DRR - Cpptraj: Make 4.0 the default cutoff for pairlist
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DRR - Cpptraj: Use Problem to track long bonds - gets rid of omp critical pragma in the middle of the loop and will eventually allow for consistent output between serial/openmp.
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DRR - Cpptraj: Use Problem for CheckOverlap. Separate out common write functionality into its own subroutine.
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DRR - Cpptraj: Consolidate code for writing out individual problems.
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DRR - Cpptraj: Use Problem class in place of BondType since they are the same structure.
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DRR - Cpptraj: Sort bond list. Will help with output, may help locality of reference.
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DRR - Cpptraj: Check test output order no longer varies based on number of threads
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DRR - Cpptraj: If for some reason a really large cutoff for check is used, adjust the pairlist accordingly.
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Commits on Aug 18, 2017