[markbujehein]

Summary

This is an implementation of the Chudley-Elliott Jump Diffusion Model. The model is described in old Mantid documentation and in literature¹, and provides a physical model of jump diffusion different from existing ones.

What Changed

The implementation adds:

• New model: ChudleyElliottJumpDiffusion class implementing the jump diffusion model by Chudley and Elliott²

  • $Q$-dependent HWHM, calculated from $\Gamma(Q) = \hbar / \tau \left( 1 - \frac{\sin(Q l)}{Q l} \right)$, in meV (if $\tau$ is in ps).
  • residence_time ($\tau$) parameter: relaxation time in picoseconds
  • jump_length ($l$) parameter: jump distance in angstroms (inverse units of $Q$)
  • Written using JumpTranslationalDiffusion as a template as the two are practically very similar (besides parameters and model).

• Unit Tests:

  • Tests for JumpTranslationalDiffusion has been adapted to ChudleyElliottJumpDiffusion to cover equivalent sanity checks and edge cases, and thus TestChudleyElliottJumpDiffusion is also written by using TestJumpTranslationalDiffusion as a template.
  • Cross-checks on the use of np.sinc(x) vs. sc.sin(x) / x in the width calculation.

• Configuration updates: I've followed CONTRIBUTING.md step-by-step which also introduced linting of the various files, such as pyproject.toml and pixi.toml. I've committed these as well as the changed would otherwise live in my working tree for ever; feel free to disregard these and tell me why I'm wrong!

Why

Addresses #46

Scope Label

[scope] enhancement: This PR adds a new diffusion model feature, requiring a minor version bump (major.MINOR.patch)

Implementation Notes

• Linting corrected with pixi run fix.
• All checks, tests and cov-tests, passed.

References

Footnotes

1. Mantid 6.1.0 - Chudley-Elliot ↩

2. C T Chudley and R J Elliott 1961 Proc. Phys. Soc. 77 353, doi:10.1088/0370-1328/77/2/319 ↩

[markbujehein]

Btw: I tried adding a label properly, but think I don't have the permission to do so.

[henrikjacobsenfys]

Very nice, just want a few small changes here and there.

Also, you'll need to rebase to the new develop (and perhaps fix a formatting issue there, we'll look at it together)

When you are done please run pixi update

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 98.18%. Comparing base (762b081) to head (7f2f8a5).
⚠️ Report is 6 commits behind head on develop.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop     #246      +/-   ##
===========================================
+ Coverage    98.15%   98.18%   +0.02%     
===========================================
  Files           60       61       +1     
  Lines         6066     6162      +96     
  Branches      1022     1033      +11     
===========================================
+ Hits          5954     6050      +96     
  Misses          58       58              
  Partials        54       54              

Flag	Coverage Δ
unittests	98.18% <100.00%> (+0.02%)	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files with missing lines	Coverage Δ
src/easydynamics/__init__.py	100.00% <100.00%> (ø)
src/easydynamics/sample_model/__init__.py	100.00% <100.00%> (ø)
...ydynamics/sample_model/diffusion_model/__init__.py	100.00% <100.00%> (ø)
.../diffusion_model/chudley_elliott_jump_diffusion.py	100.00% <100.00%> (ø)

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• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

[markbujehein]

@henrikjacobsenfys the missing tutorial has been added for ChudleyElliottJumpDiffusion (and JumpTranslationalDiffusion). I expect the remaining checks to fail by default because they break on PRs opened from a fork. This is also the case for core.

[henrikjacobsenfys]

Thanks!