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[WIP] HTF speedup and cmap support#142

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jthorton wants to merge 2 commits into
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htf_speed2
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[WIP] HTF speedup and cmap support#142
jthorton wants to merge 2 commits into
mainfrom
htf_speed2

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@jthorton

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Copy of OpenFreeEnergy/openfe#1858 to make sure tests pass, speeds up HTF creation and adds cmap support.

@ijpulidos

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This is looking good to me! As far as I can tell, all the tests in test_relative.py are passing. There was a change in the attribute changes for old/initial atom indices, but that should be easy to fix.

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