Bilayer support

[rozyczko]

As requested and described by @jfkcooper this is the library implementation of bilayers in EasyReflectometryLib.

Please scrutinize docs\tutorials\simulation\bilayer.ipynb for correctness and API.

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[codecov]

Codecov Report

❌ Patch coverage is 91.26984% with 11 lines in your changes missing coverage. Please review.
✅ Project coverage is 88.29%. Comparing base (205db70) to head (4333c43).

Files with missing lines	Patch %	Lines
src/easyreflectometry/sample/assemblies/bilayer.py	91.20%	0 Missing and 11 partials ⚠️

Additional details and impacted files

@@                Coverage Diff                @@
##           append_sample     #292      +/-   ##
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+ Coverage          88.10%   88.29%   +0.19%     
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  Files                 45       46       +1     
  Lines               2471     2597     +126     
  Branches             288      307      +19     
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+ Hits                2177     2293     +116     
+ Misses               233      232       -1     
- Partials              61       72      +11     

Flag	Coverage Δ
unittests	88.29% <91.26%> (+0.19%)	⬆️

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Files with missing lines	Coverage Δ
src/easyreflectometry/sample/__init__.py	100.00% <100.00%> (ø)
src/easyreflectometry/sample/assemblies/bilayer.py	91.20% <91.20%> (ø)

... and 1 file with indirect coverage changes

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[jfkcooper]

Basically only one comment on the code parts, and easily rectified. I will run the notebook now and give you feedback on this, but doing it in github is not fun for notebooks, so I submit these comments now

[jfkcooper]

Notes from the notebook:

• Depending on what the aim for the notebook is, I would remove all of the cells doing checking an printing, as they would not be interesting to a user - it would be assumed that they just work.

• The superphase for the complete sample should be silicon. The structure should be:
  Si | SiO2 | head | tail | tail | head | water it should look something like this:

• For the tail groups, I believe you have the SLD for a deuterated version of the tails, but this is not the 'normal' configuration, and I think for an exemplar notebook it is better to use the hydrogenous version.

• For the asymmetric hydration, it isn't clear where but there seems to be a bug or something, as you would expect a difference in the curves. I would highlight the change by showing the SLD curves rather than just the reflectivity though, as this is where you can know that it is being done correctly

[jfkcooper]

image from https://www.researchgate.net/publication/273159532_Cationic_liposomes_as_efficient_nanocarriers_for_the_drug_delivery_of_an_anticancer_cholesterol-based_ruthenium_complex

[jfkcooper]

Thinking on it, I would also use this as a way to demonstrate mutliple contrasts for the lipid model, so using H2O as the solvent and subphase as well as D2O, and then showing the SLD curves, and the reflectivity curves (and the ability to set the constraints between the two models (or however you would put the models together).

The most common use case of the lipid bilayer would be for fitting mulitple contrast (water) data.

[rozyczko]

Addressed the code issues and modified the notebook to reflect Jos' comments.

[jfkcooper]

Thanks for the changes, though I just noticed a couple more things:

• In cell 3 you solvate the head and the tail with different solvents. These should strictly always be the same solvent
• The inner and outer headgroups are hydrated differently - but it isn't clear how this happened, or how one would set them separately ('front_head_layer' and 'back_head_layer' are not mentioned before cell 7
• Cell 8 has the same parameter being printed as cell 6, so, not really demonstrating that the roughness is conformal.
• I think cell 13 has some bug as the two curves should be different, but aren't
• Same bug with cell 14
• cell 15 - the head and tails should be solvated with the same liquid. It is also a little confusing that the tails are now a different lipid (hydrogenous rather than deuterated tail group), I would keep it consistent throughout the notebook
• The above point is especially important in cells 18 and 19, since the two curves are not presenting the same lipid system.

Let me know if you want a chat about any of these points, and thanks again for the progress!

[jfkcooper]

Thanks for the changes, though I just noticed a couple more things:

• In cell 3 you solvate the head and the tail with different solvents. These should strictly always be the same solvent
• The inner and outer headgroups are hydrated differently - but it isn't clear how this happened, or how one would set them separately ('front_head_layer' and 'back_head_layer' are not mentioned before cell 7
• Cell 8 has the same parameter being printed as cell 6, so, not really demonstrating that the roughness is conformal.
• I think cell 13 has some bug as the two curves should be different, but aren't
• Same bug with cell 14
• cell 15 - the head and tails should be solvated with the same liquid. It is also a little confusing that the tails are now a different lipid (hydrogenous rather than deuterated tail group), I would keep it consistent throughout the notebook
• The above point is especially important in cells 18 and 19, since the two curves are not presenting the same lipid system.

Let me know if you want a chat about any of these points, and thanks again for the progress!