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reflectivity
orsopy
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Lipid bilayer model
- #160
#160
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aglavic
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reflectivity:main
reflectivity/orsopy:main
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Lipid bilayer model
#160
aglavic
wants to merge 22 commits into
reflectivity:main
reflectivity/orsopy:main
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aglavic:lipid_bilayer_model
aglavic/orsopy:lipid_bilayer_model
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Commits
Commits on May 13, 2026
Allow new curly bracket syntax in stack for SubStackType objects
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68dc3d6
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Commits on May 18, 2026
Start creating class for lipid Bilayer using build-in lipids or two materials, still missing correct layer calculation
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Minor improvements for resolution of default_solvent and lipid name implementation
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default apm unit resolution
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Commits on May 19, 2026
Add example for Bilayer and first version resolving to layers with thickness and density, math needs checking
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Add volume property to Material if number_density is already defined
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Add coverage parameter
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minor fix
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7ab6f3e
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Commits on Jun 3, 2026
Remove option for lipid to be explicit, add Leaflet class
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Make sure that resolve_to_blocks includes all density information needed
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Fix model 10 test values
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ed37922
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Calculate number density in Material and don't overwrite Header __repr__ with dataclass default
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b0584c3
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Fix mixing calculation, add hydration to thickness calculation, create neutorn refnx model with blocks
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Commits on Jun 4, 2026
Allow named component resolution with LateResolver, currently implemented for hardcoded Lipids
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Add simple example showing multiple lipids with just using stack string
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Fix test values for changed models
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5d88585
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Still needs to validate refnx implementation of leaflet
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Commits on Jun 5, 2026
Fix resolver for refnx LipidLeaflet to calculate b correctly and include coverage parameter
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Change resolve_and_plot_model to first generate refnx model code and print the results
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4be1993
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Minor fix
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659feb0
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Commits on Jun 15, 2026
Modify definition for heads/tails instead of inner/outer and only define one hydration parameter per leaflet
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minor fix to keep tails_2/heads_2 None for resolve_to_block to signify symmetric bi-layer.
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62d0a62
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