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implement molecular-mechanics-type EnergyFn functionality and construction #199

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implement molecular-mechanics-type EnergyFn functionality and construction #199

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dominicrufa
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@dominicrufa dominicrufa commented Jun 6, 2022 •
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A first pass on implementing molecular mechanics (MM) style EnergyFn functionality and parameter construction.

  • parameter data structure creation/documentation
  • implementing/testing all 4 "canonical" mm forces (bonds/angles/torsions/nonbondeds)
  • support interoperability for different valence/nonbonded implementations
  • conversion of openmm.System or .xml to jax_md.mm canonical parameter structure and assert energy equivalence.
  • test nonbonded neighbor masking/energy calculations speed versus post-neighborhood creation masking/exception handling.
  • test converage

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dominicrufa and others added 26 commits June 7, 2022 18:49
add box_handler for displacements and exception masking fn
cfd450c
add geometry handlers, omm decay fn, and adapt smap.bond to handle …
fce795a 
…generalized ordered n-particle tuples with kwarg params
add vacuum coulomb, reorganize Parameters, check bond parameters, add…
e48a7e4 
… check for smap.bond
forgot smap.bond updates (just validation checks)
ffd7a8a
default Q_sq by requirement; match parameters to those in energy.py
1421dd4
forgot parameter change.
f026736
use _asdict for NamedTuple instead of manual dict creation.
9dc5d82
handle nonbonded force
ef427b2
handle implicit parameters; build nonbonded neighbor list regardless …
ac4e521 
…of whether exception kwargs are provided.
if/else typo
60248da
unload params as None before unchanged pass
5a01ee6
move geometry_handler arg to pass predefined tests
05178b6
extend dynamic bondtype tests
bf4858c
safe mask cosine angle
e0ade60
add quantity, remove explicit vmap axes
69e021a
fix typos and default MMEnergyFnParameters to omit canonical forces
3deba71
built utilties to convert openmm.System to mm.MMEnergyFnParameters
56e65b1
simple example for get_parameters_from_omm_system
06944de
rename parameter conversion fn
3ee472d
satisfy default canonicalization
4d35aa0
fix cross product calculation for normal plane angle calculation
bf8881e
try an openmm import (lazy)
af55dfc
fix automated bond fn calculation (bond, angle, torsion, nonbonded exc.)
b0ad524
@dominicrufa
Merge branch 'google:main' into main
110c771
remove "validation" functions; allow custom_masking for smap.pair…
b8e8bc8 
… (for non-neighbor-listed systems)
Merge branch 'main' of https://github.com/dominicrufa/jax-md into main
6941160
dominicrufa and others added 30 commits August 15, 2022 12:08
avoid long lines
dc0c48f
add coulomb-rf implementation
4d57e4a
add reaction field converter
e0f6462
format jax_md.energy
248fb70
change rf converter formatting
66502d7
Merge branch 'main' of https://github.com/google/jax-md into google-main
63e2450
@dominicrufa
Merge pull request #5 from dominicrufa/google-main
a0bd92c 
Google main
drop/replace nvt langevin with baoab from schsam
7a96c6a
pop dt from kwargs
e156308
merge kwargs to pass bvs for space.periodic_general?
e2e8ce0
fix typing
af5c770
remove import error messaging classes
8fc2529
explicitly convert namedtuple._asdict to dict for python3.7
26bddbe
use manual dense mask generator
158b957
change dense mask construction
7b4e663
separate mask tuple
7999a3c
add stochastic step for remote
c0e3c6f
remove extra sorting in dense mask
4dc3f23
remove dictionary bond manager
0035f5f
rename capturing of geometry kwargs
ba02089
use different bond parameter register if bond_types is a dict; mod no…
9215b50 
…nbonded neighbor
add reaction field helper functionality.
474fa15
allow for auxiliary neighbor kwargs
d92ed81
add dense mask test
cc099f5
profiling script
3f4d053
sans-openmm testing purposes.
efc8e27
fix hastily constructed .py
ba6b073
remove perfetto tracing in favor of internal profiling
37a2ecd
@dominicrufa
Merge branch 'main' into update_main
e6c03a3
@dominicrufa
Merge pull request #6 from dominicrufa/update_main
6bbea3b 
Update main
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