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[WIP] jitted just the inner loop of the adaptive loop #402

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[WIP] jitted just the inner loop of the adaptive loop #402

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Discussion is in #340. This is one of the faster options, will need to do more careful examination of the timing to see which is better, this one or #399 (or something else!)

@mrshirts
Changed to umbrella sampling for PMF.
7e6436f
@mrshirts
Remove debugging.
f374859
@mrshirts
Merge branch 'master' of https://github.com/choderalab/pymbar
1d8dabe 
Merging in recent changes from upstream.
@mrshirts
Merge branch 'master' of https://github.com/choderalab/pymbar
871db11
@mrshirts
adding profiling.
8d1bc64
@mrshirts
partial jax.
bce97f9
@mrshirts
mostly working jax partial.
4810131
@mrshirts
Running with jax
1fa4c69
@mrshirts
working with jit.
70c40c4
@mrshirts
Working with jit and jax
60bc37b
@mrshirts
Updating solvers for more jaxness.
7070040
@mrshirts
trying to jit all of adaptive.
8e754b9
@mrshirts
working on more complete jax.
0b1c7ad
@mrshirts
Remove some unneeded conversions
2e4380c
@mrshirts
Adding a test file.
db13aab
@mrshirts
different choices in profiler.
b78d0bf
@mrshirts
Changes in profiling script
b27f1a5
@mrshirts
more script changes for profiling.
dc3d581
@mrshirts
Cleaning up jitting the whole adaptive path.
855851b
@mrshirts
add profiling script.
c93a8ef
@mrshirts
Merge branch 'partial_jax' into pymbar4_partial_jit
e2ac7f7 
Merging jit changes into pymbar4
@mrshirts
Partial jit code.
7be779f
@mrshirts
Merge branch 'more_jit' into adaptive_jit
a071c6b 
made adaptive for pymbar jittable.
@mrshirts
Updated parameters.
44a9f93
@mrshirts
revisiting maximal jitting.
f2f59d9
@mrshirts
Change the acceleration of the adaptive code so we just accelerate
fce8daa 
the inner part of the adaptive loop.
@mrshirts mrshirts changed the base branch from master to pymbar4 June 30, 2020 05:27
@mrshirts mrshirts requested a review from jchodera June 30, 2020 05:28
@mrshirts mrshirts mentioned this pull request Jun 30, 2020
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@mrshirts mrshirts mentioned this pull request Jun 28, 2022
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@mrshirts @mikemhenry