Improve performance of from_mbuild #470
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@@ Coverage Diff @@
## master #470 +/- ##
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Coverage 88.96% 88.96%
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Files 46 46
Lines 3027 3028 +1
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+ Hits 2693 2694 +1
Misses 334 334
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daico007
approved these changes
Oct 15, 2020
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| is an gmso.AtomType associated with the site and | ||
| it to the sub-topology's AtomTypes collection. |
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I think you miss a word here. Is it supposed to be ... the site and add it to the sub-...
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| Parameters | ||
| ---------- | ||
| site : gmso.Atom | ||
| The site to be added to this sub-topology | ||
| update_types : (bool), default=True |
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This is just nitpicking, but can you remove the parentheses (so just update_types : bool, default=True) just so we are consistent with other method.
justinGilmer
approved these changes
Oct 21, 2020
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The
from_mbuildconversion is very costly. As per previous discussions, we hypothesized that this was because we are repeatedly and unnecessarily runningupdate_types/update_connections/etc. commands which loop through every atom (O(N^2) complexity). Here I'm trying to reduce the number of calls to cut down the time it takes to convert from mbuild by applying theupdate_types=Falseflag when adding sites and connections. As of this first commit, here are the performance gains forfrom_mbuildconversions for boxes of tip3p water.