Add pair list to SPAM pure water calc and properly image distances#539
Merged
drroe merged 13 commits intoAmber-MD:masterfrom Sep 5, 2017
Merged
Add pair list to SPAM pure water calc and properly image distances#539drroe merged 13 commits intoAmber-MD:masterfrom
drroe merged 13 commits intoAmber-MD:masterfrom
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…>i residues calcd. Results are still off though.
…ure how this was missed before.
…is time it works.
… reorganize code. Improve code docs.
…re it is properly cleaned.
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This PR started out as an enhancement but ended up being a bug fix as well.
The
purewatercalculation for the SPAM action was very time-consuming since it scaled O(N^2). This PR improves the speed of this calculation by using a pair list. Note thatpurewateris no longer OpenMP parallelized; however, the speedup from the pair list is such that even vs 4 threads with the old code the new code is almost 2x as fast (not taking into account the imaging issue detailed in the next paragraph).In the course of testing the new pair list implementation, inconsistencies with results from the old code revealed that distances were not being imaged. The problem was that the ImagedAction class was being employed but not properly set up in
Action_Spam::Setup, resulting in the non-imaged distance always being used. Now the minimum imaged distance is actually used throughout Action_Spam and the test results have been updated to reflect this.Also includes general code cleanup of Action_Spam and removal of a test file that should not have been tracked.