Walls, Flow, and Microfluidics 🧬 - #1

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marpaia wants to merge 55 commits into

marpaia/microfluidics

Commits on Aug 17, 2026

Add ADR 0016 for axis-aligned box constraints
marpaia
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286216b
Add axis-aligned box constraints to CPU, Metal, and CUDA mechanics
marpaia
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1229939
Expose box constraints in Python API with checkpoint schema v8
marpaia
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0ca4737
Build the Danino trap from box constraints instead of sphere rows
marpaia
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e6fa52b
Add ADR 0017 for signal grid obstacles
marpaia
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a3e103f
Add signal grid obstacle masks to CPU, Metal, and CUDA transport
marpaia
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48a6573
Expose signal grid obstacle masks in Python and checkpoint schema
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92ad260
Carry external constraints in scene format v2
marpaia
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7ed71be
Render scene v2 device constraints in the viewer
marpaia
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01bf626
Add ADR 0018 for axis-aligned cylinder constraints
marpaia
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d0403c0
Add axis-aligned cylinder constraints to CPU, Metal, and CUDA mechanics
marpaia
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cf542eb
Expose cylinder constraints in Python, scene v2, and the viewer
marpaia
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e02eaa4
Add ADR 0019 for face-staggered signal velocity fields
marpaia
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7a2fe42
Add face-staggered velocity fields to CPU, Metal, and CUDA transport
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5889f26
Expose signal velocity fields in Python and checkpoint schema
marpaia
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0f16aef
Add microfluidics device authoring and a flow-fed trap example
marpaia
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b4d0b3e
Type-narrow the microfluidics tests
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3650e72
Add cell removal with StepPlan washout support
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2447233
Add advective flow drift on cells with controller wiring
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9f7492c
Rebuild Danino and trap models on device flow with washout
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b9179d0
Add Prindle biopixel trap device, tutorial model, and CAD masks
marpaia
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a5004fb
Permit module-internal protected use in microfluidics helpers
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4b56c33
Extract the biopixel trap array from the mask DXF
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0941fe4
Model the biopixel trap under its millimeter-wide flow layer
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e9eff2c
Let the biopixel colony break planarity for trap overflow
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eba48a5
Guard the biopixel lattice for tilted endpoint sampling
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cda00b3
Read the biopixel trap footprint from the mask and restore its ceiling
marpaia
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d8a1e2c

Commits on Aug 18, 2026

Commits on Aug 19, 2026

Clamp flow drift endpoint sampling to the signal lattice
marpaia
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d2f877d
Add gap-height and per-site base mobility to the flow solver
marpaia
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87a9a29
Drive device grids and trap models with the solved Brinkman flow
marpaia
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630b9ab
Solve staggered MAC Stokes-Brinkman flow in the authoring layer
marpaia
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68fa478
Benchmark both flow solvers against literature references
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dd69a70
Let divisions and plan removals share a controller step
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bb1bd82
Add the pillar-channel tutorial for the flow solvers
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029bb39
Fix and cheapen signal grid sampling on device grids
marpaia
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e8c7753
Match ADR 0021 to the drift clamp and rotation limit
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1afaaab
Make device model chemistry reach the signal grid
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d6bf3af
Sharpen the flow benchmarks and cover the solvers' gaps
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30dc0c1
Correct the flow tutorials and record the solvers' limits
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8bbdde5
Share the flow solvers' internals and drop dead code
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5efac3b
Give every constraint kind one contact pass
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6955e95
Tidy the dish example and the drift call site
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65059b7
Declare the CUDA coupled grid spec before its buffers reserve
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d695811
Scatter into a cell's own stencil without reading the mask
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592c303
Judge implicit convergence against the step, not the field
marpaia
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1c068e1
Share the CUDA grid transport helpers between kernels
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3d138da
Share the Metal grid transport helpers between kernels
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07161df
Sample no flow where a stencil holds no fluid
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75bf7c6
Format the native sources with the repo's clang-format
marpaia
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530657a
Add commit hooks for formatting, linting, and typing
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c33031f
Make the Danino clock a clock
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15f2cb7
Refresh the clock's AHL loss field on a cadence
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ac9ec36