Greg Landrum 2c5ae534f2 Optimizations of the DistanceGeometry forcefield (#7600) ...

* First try at using DistViolationContribs

only the most basic of testing has been done

also add ForceField::distance2 to allow some optimizations

* allow testing using old approach

* optimization

At this point testUFFForceFieldHelpers fails since the check for std::max_element
in the e_contribs vector at Embedder.cpp:513 is now doing something totally different
(instead of a bunch of small distance violation contribs, we have one big one).
We'll need to come up with something for this.

With the benchmarking set that I'm using - 500 DG conformers for ~465 COD molecules
using 10 threads - this runs in almost 10% less time than master.

* backup;
builds, tests do not pass

* all tests pass except the old failure

* more constification

* backup/debugging

* add fourthdim contribs the same way

* tests now pass

* deprecations

* remove unused vars and code

* changes in response to review

2024-07-15 14:14:39 -04:00

9.1 KiB

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