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Switch from Zygote to Enzyme #182

Merged
merged 74 commits into from
Oct 30, 2024
Merged

Switch from Zygote to Enzyme #182

merged 74 commits into from
Oct 30, 2024

Commits on Oct 30, 2024

  1. no branching for cutoffs

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  2. coord not needed for cutoff function

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  3. potential cutoff args

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  4. check units changes

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  5. pairwise interaction arguments and fields

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  6. remove Zygote functions

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  7. remove chain rules

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  8. interaction arguments

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  9. pairwise interaction docs

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  10. rename test groups

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  11. remove deps

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  12. force and energy arguments

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  13. fix unit check

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  14. rename coulombconst to coulomb_const

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  15. change specific interaction arguments

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  16. forces reuse memory

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  17. add step_n to virial

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  18. refactor energy functions

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  19. step_n for general interactions

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  20. loggers use step_n

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  21. use step_n throughout

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  22. reuse memory in simulators

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  23. reuse memory in simulators and couplers

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  24. gradient tests use Enzyme

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  25. move Enzyme code to extension

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  26. gradient test clearer typing

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  27. LennardJones mixing and shortcut

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  28. Mie mixing and shortcut

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  29. soft sphere mixing and shortcut

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  30. Buckingham mixing and shortcut

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  31. Coulomb mixing

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  32. Gravity zero and + functions

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  33. add atom_type to Atom, reorder fields

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  34. rename run_loggers! to apply_loggers!

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  35. Use @kwdef for interactions

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  36. concrete function typing for interactions

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  37. fix tests

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  38. remove abstract interaction types

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  39. rng arg for coordinate setup

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  40. make DMS test pass with Enzyme

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  41. broadcast gradient injection

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  42. DMS protein gradient tests

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  43. move gradient code to relevant places

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  44. move parameter extraction to files

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  45. deepcopy to copy

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  46. Add @inline to simulators for Enzyme

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  47. Enzyme loggers fix

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  48. Enzyme compat

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  49. test simulation gradients on CI

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  50. remove unused gradient dependencies

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  51. OBC Born radii don't broadcast

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  52. GBSA energy don't broadcast

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  53. GBn2 force don't broadcast 1

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  54. GBn2 force don't broadcast 2

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  55. fix Colors weakdep

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  56. fix Enzyme weakdep

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  57. rename box_volume to volume

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  58. density function and logger

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  59. add VolumeLogger

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  60. dipole_moment function

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  61. density test

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  62. update Enzyme version

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  63. add paper to docs

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  64. remove redundant method

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  65. test options

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  66. n_dimensions fixes

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  67. don't do sim gradient tests on CI

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  68. rename ForceLogger to ForcesLogger

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  69. rename VelocityLogger to VelocitiesLogger

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  70. rename CoordinateLogger to CoordinatesLogger

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  71. update API docs

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  72. KernelDensity extension

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  73. docs cover all docstrings

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  74. Colors compat

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