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README.md

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+---
+pretty_name: PoreML-Geo
+license: cc-by-4.0
+tags:
+  - porous-media
+  - digital-rock
+  - multiphase-flow
+  - 3d
+size_categories:
+  - 1K<n<10K
+---
+
+# PoreML-Geo
+
+3D porous geometries for pore-scale drainage LBM simulation and ML surrogate modelling: ten rock/fiber subsets (synthetic + real micro-CT) and one designed flip-chip geometry, all with identical layout and deterministic seeded generation.
+
+**Conventions** — arrays are boolean voxels with **`True` = solid**, axes ordered (z, y, x); fluid drains along the flow axis x (last), from x = 0 to x = −1. All samples percolate along the flow axis. Every size folder and asset is named by the **saved array shape in that same (z, y, x) order** — `128`/`256` for the cubic subsets, `256x256x128`/`128x128x64` for the anisotropic ones (so the trailing number is always the flow-axis length).
+
+## Quick start
+
+```python
+from huggingface_hub import hf_hub_download
+import numpy as np
+solid = np.load(hf_hub_download("PoreML/PoreML_geo", "poly/128/poly128_0000.npy", repo_type="dataset"))
+```
+
+## Subsets
+
+| Subset | Domain | N | Final porosity |
+|---|---|---|---|
+| `poly/128/` | 128³ | 64 | 0.16 – 0.38 |
+| `poly/256/` | 256³ | 64 | 0.21 – 0.31 |
+| `blob/128/` | 128³ | 64 | 0.22 – 0.31 |
+| `blob/256/` | 256³ | 64 | 0.22 – 0.31 |
+| `sphere/128/` | 128³ | 64 | 0.17 – 0.33 |
+| `sphere/256/` | 256³ | 64 | 0.16 – 0.33 |
+| `bentheimer/128/` | 128³ | 64 | 0.17 – 0.42 |
+| `bentheimer/256/` | 256³ | 64 | 0.19 – 0.29 |
+| `castlegate/128/` | 128³ | 64 | 0.10 – 0.36 |
+| `castlegate/256/` | 256³ | 64 | 0.18 – 0.26 |
+| `buffberea/128/` | 128³ | 64 | 0.05 – 0.39 |
+| `buffberea/256/` | 256³ | 64 | 0.10 – 0.28 |
+| `gdl_ct/128x128x64/` | 128×128×64 | 64 | 0.48 – 0.67 |
+| `gdl_ct/256x256x128/` | 256×256×128 | 64 | 0.53 – 0.62 |
+| `gdl_ct_20/128x128x64/` | 128×128×64 | 64 | 0.43 – 0.68 |
+| `gdl_ct_20/256x256x128/` | 256×256×128 | 64 | 0.53 – 0.63 |
+| `gdl_ct_40/128x128x64/` | 128×128×64 | 64 | 0.52 – 0.68 |
+| `gdl_ct_40/256x256x128/` | 256×256×128 | 64 | 0.56 – 0.63 |
+| `fiber/128x128x64/` | 128×128×64 | 64 | 0.53 – 0.77 |
+| `fiber/256x256x128/` | 256×256×128 | 64 | 0.53 – 0.77 |
+| `flipchip/samples/` | (gap+2)×482×(432–476) | 64 | see per-sample JSON (array region) |
+
+## Geometry sources
+
+Parameter sampling is deterministic (fixed seeds), and the realized generation parameters of every sample are recorded in its `.json`. Generation code is not included in this anonymized release.
+
+- **`poly/`** — synthetic polydisperse overlapping spheres (porespy, lognormal grain radii); poorly-sorted sandstone analogue.
+- **`blob/`** — thresholded Gaussian random fields (porespy blobs); tight/carbonate-like irregular pore morphology.
+- **`sphere/`** — monodisperse overlapping spheres at 2 μm/voxel; well-sorted sandstone as a zoomed-in high-resolution patch with wide throats.
+- **`bentheimer/`** — random crops of the DRP-317 Bentheimer sandstone micro-CT binary volume (1000³, 2.25 μm/voxel), augmented with random axis permutations + flips (full octahedral symmetry group).
+- **`castlegate/`** — same recipe applied to the DRP-317 CastleGate sandstone micro-CT binary volume (1000³, 2.25 μm/voxel; raw porosity ≈ 0.25).
+- **`buffberea/`** — same recipe applied to the DRP-317 Buff Berea sandstone micro-CT binary volume (1000³, 2.25 μm/voxel; raw porosity ≈ 0.23).
+- **`gdl_ct/`** — random crops of the real DRP-462 5% PTFE carbon-paper GDL micro-CT scan (Shojaei et al., Fuel 2023; 2.05 μm/voxel, 151 through-plane voxels of which 128 are cropped). No permutation/flip augmentation — one fixed transpose so the flow axis x is the GDL through-plane direction. Two sizes: the full 256×256×128 set and a half-linear-extent (1/8 volume) 128×128×64 set at the same 2.05 μm/voxel resolution and identical post-processing.
+- **`gdl_ct_20/`**, **`gdl_ct_40/`** — the same recipe (same seed-42 origin stream) applied to the DRP-462 **20 %** and **40 %** PTFE-coating dry scans of the same GDL family (168 and 155 through-plane voxels; 1239² and 1284² in-plane inscribed-square parents, porosity ≈ 0.673 / 0.670). Together with `gdl_ct` (5 %) they form a PTFE-loading series at identical resolution and post-processing.
+- **`fiber/`** — synthetic in-plane fiber mats (porespy `cylinders`), the synthetic analog of `gdl_ct`: fibers lie in the transverse 256×256 (z, y) plane, isotropic in-plane with a small sampled out-of-plane tilt bound (phi_max 0–20°; fiber radius 3–5 vox); drainage is through-plane across the mat. Porosity-tolerance retry per sample. Two sizes matching `gdl_ct`: the full 256×256×128 set and a half-linear-extent (1/8 volume) 128×128×64 set at the same 1 μm/voxel resolution, fiber radii and porosity targets.
+- **`flipchip/`** — DESIGNED (non-rock) flip-chip underfill gaps for capillary underfill studies: a staggered array of truncated-sphere solder balls between a substrate and a die plate, compressed joint with real contact patches on both plates. Per sample, ball diameter D, standoff gap = squish·D (squish 0.60–0.95) and staggered pitch (1.5–2.1 D) are drawn deterministically, then every length is multiplied by a resolution `scale` of 1.5, giving the shipped D = 32–54 cells and gap ≥ 18 fluid layers; all balls share one voxel stencil, the array region is square, and balls keep ≥ 2 D clearance to the sealed y walls. x is open flow with 30-slab buffers and 1 D ball-free entry/vent margins.
+
+## Post-processing
+
+All rock/fiber subsets: ball(3) morphological opening of the pore space (throats < 3 vox removed) + fill of face-disconnected pore pockets. `flipchip` is analytic — throats are designed (at the default 1.5 scale: ball–ball ≥ 15 cells at the equator, wall ≥ 9 cells) and recorded exactly in each JSON, so no morphological opening or SNOW2 extraction is applied.
+
+## Files per sample
+
+Samples are named `poly{size}_{NNNN}`, `blob{size}_{NNNN}`, `sphere{size}_{NNNN}`, `bent{size}_{NNNN}`, `castle{size}_{NNNN}`, `buff{size}_{NNNN}`, `gdl_{NNNN}`, `fiber_{NNNN}`, `flipchip_{NNNN}`:
+
+- `.npy` — boolean solid mask (see conventions above);
+- `.json` — generation params + SNOW2 pore-network stats (flipchip: exact designed-geometry stats — ball centers, throats, contact-patch size);
+- throat-distribution, cross-section and 3D-render figures with backing CSVs (flipchip: mid-gap top view instead of the throat histogram);
+- per size folder: `summary.csv`.
+
+## Previews
+
+Samples 0000–0015 of each subset; solid phase in 3D (left) and mid-plane slices with solid = gray, pore = white (right).
+
+### 256³
+
+| | Solid phase (3D) | Mid-plane slices |
+|---|---|---|
+| `poly` | <img src="assets/poly_256_3d.png" width="420"> | <img src="assets/poly_256_slices.png" width="420"> |
+| `blob` | <img src="assets/blob_256_3d.png" width="420"> | <img src="assets/blob_256_slices.png" width="420"> |
+| `sphere` | <img src="assets/sphere_256_3d.png" width="420"> | <img src="assets/sphere_256_slices.png" width="420"> |
+| `bentheimer` | <img src="assets/bentheimer_256_3d.png" width="420"> | <img src="assets/bentheimer_256_slices.png" width="420"> |
+| `castlegate` | <img src="assets/castlegate_256_3d.png" width="420"> | <img src="assets/castlegate_256_slices.png" width="420"> |
+| `buffberea` | <img src="assets/buffberea_256_3d.png" width="420"> | <img src="assets/buffberea_256_slices.png" width="420"> |
+
+### 128³
+
+| | Solid phase (3D) | Mid-plane slices |
+|---|---|---|
+| `poly` | <img src="assets/poly_128_3d.png" width="420"> | <img src="assets/poly_128_slices.png" width="420"> |
+| `blob` | <img src="assets/blob_128_3d.png" width="420"> | <img src="assets/blob_128_slices.png" width="420"> |
+| `sphere` | <img src="assets/sphere_128_3d.png" width="420"> | <img src="assets/sphere_128_slices.png" width="420"> |
+| `bentheimer` | <img src="assets/bentheimer_128_3d.png" width="420"> | <img src="assets/bentheimer_128_slices.png" width="420"> |
+| `castlegate` | <img src="assets/castlegate_128_3d.png" width="420"> | <img src="assets/castlegate_128_slices.png" width="420"> |
+| `buffberea` | <img src="assets/buffberea_128_3d.png" width="420"> | <img src="assets/buffberea_128_slices.png" width="420"> |
+
+### GDL, fiber & flipchip
+
+| | Solid phase (3D) | Mid slices / top views |
+|---|---|---|
+| `gdl_ct` 256×256×128 | <img src="assets/gdl_ct_256x256x128_3d.png" width="420"> | <img src="assets/gdl_ct_256x256x128_slices.png" width="420"> |
+| `gdl_ct` 128×128×64 | <img src="assets/gdl_ct_128x128x64_3d.png" width="420"> | <img src="assets/gdl_ct_128x128x64_slices.png" width="420"> |
+| `gdl_ct_20` 256×256×128 | <img src="assets/gdl_ct_20_256x256x128_3d.png" width="420"> | <img src="assets/gdl_ct_20_256x256x128_slices.png" width="420"> |
+| `gdl_ct_20` 128×128×64 | <img src="assets/gdl_ct_20_128x128x64_3d.png" width="420"> | <img src="assets/gdl_ct_20_128x128x64_slices.png" width="420"> |
+| `gdl_ct_40` 256×256×128 | <img src="assets/gdl_ct_40_256x256x128_3d.png" width="420"> | <img src="assets/gdl_ct_40_256x256x128_slices.png" width="420"> |
+| `gdl_ct_40` 128×128×64 | <img src="assets/gdl_ct_40_128x128x64_3d.png" width="420"> | <img src="assets/gdl_ct_40_128x128x64_slices.png" width="420"> |
+| `fiber` 256×256×128 | <img src="assets/fiber_256x256x128_3d.png" width="420"> | <img src="assets/fiber_256x256x128_slices.png" width="420"> |
+| `fiber` 128×128×64 | <img src="assets/fiber_128x128x64_3d.png" width="420"> | <img src="assets/fiber_128x128x64_slices.png" width="420"> |
+| `flipchip` | <img src="assets/flipchip_samples_3d.png" width="420"> | <img src="assets/flipchip_samples_slices.png" width="420"> |
+
+## Pore & throat size distributions
+
+SNOW2 inscribed radii aggregated over every sample in each subset; raw values back each figure in `assets/{geom}_{size}_dist.csv`.
+
+| | 256³ | 128³ |
+|---|---|---|
+| `poly` | <img src="assets/poly_256_dist.png" width="420"> | <img src="assets/poly_128_dist.png" width="420"> |
+| `blob` | <img src="assets/blob_256_dist.png" width="420"> | <img src="assets/blob_128_dist.png" width="420"> |
+| `sphere` | <img src="assets/sphere_256_dist.png" width="420"> | <img src="assets/sphere_128_dist.png" width="420"> |
+| `bentheimer` | <img src="assets/bentheimer_256_dist.png" width="420"> | <img src="assets/bentheimer_128_dist.png" width="420"> |
+| `castlegate` | <img src="assets/castlegate_256_dist.png" width="420"> | <img src="assets/castlegate_128_dist.png" width="420"> |
+| `buffberea` | <img src="assets/buffberea_256_dist.png" width="420"> | <img src="assets/buffberea_128_dist.png" width="420"> |
+
+| | 256×256×128 | 128×128×64 |
+|---|---|---|
+| `gdl_ct` | <img src="assets/gdl_ct_256x256x128_dist.png" width="420"> | <img src="assets/gdl_ct_128x128x64_dist.png" width="420"> |
+| `gdl_ct_20` | <img src="assets/gdl_ct_20_256x256x128_dist.png" width="420"> | <img src="assets/gdl_ct_20_128x128x64_dist.png" width="420"> |
+| `gdl_ct_40` | <img src="assets/gdl_ct_40_256x256x128_dist.png" width="420"> | <img src="assets/gdl_ct_40_128x128x64_dist.png" width="420"> |
+| `fiber` | <img src="assets/fiber_256x256x128_dist.png" width="420"> | <img src="assets/fiber_128x128x64_dist.png" width="420"> |
+
+`flipchip` parameter coverage (ball diameter D vs gap height, colored by pitch):
+
+<img src="assets/flipchip_params.png" width="420">

sphere/128/sphere128_0000.json

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+{
+  "generator": "overlapping_spheres",
+  "shape": [
+    128,
+    128,
+    128
+  ],
+  "porosity": 0.31609340728339447,
+  "seed": 1405681632,
+  "grain_radius": 20,
+  "opening_radius": 3,
+  "porosity_pre": 0.31846,
+  "pre_opening_porosity": 0.31846,
+  "post_opening_porosity": 0.30307,
+  "closed_pore_voxels": 0,
+  "post_fill_porosity": 0.30307,
+  "porosity_post": 0.30307,
+  "stats": {
+    "post_processing": {
+      "description": "ball(3) morphological opening of the pore space (closes throats with inscribed-sphere radius < 3 vox) + fill of face-disconnected dead pore pockets",
+      "opening_radius_vox": 3,
+      "closed_pore_voxels": 0
+    },
+    "porosity": 0.30307,
+    "n_pores": 49,
+    "n_throats": 73,
+    "throat_inscribed_radius_vox": {
+      "n": 73,
+      "mean": 6.729,
+      "std": 3.951,
+      "min": 1.414,
+      "p10": 3.162,
+      "p25": 4.243,
+      "median": 5.385,
+      "p75": 7.616,
+      "p90": 12.441,
+      "max": 19.313
+    },
+    "pore_inscribed_radius_vox": {
+      "n": 49,
+      "mean": 7.139,
+      "std": 3.749,
+      "min": 2.0,
+      "p10": 3.0,
+      "p25": 4.899,
+      "median": 6.0,
+      "p75": 9.0,
+      "p90": 12.2,
+      "max": 17.117
+    },
+    "network_extraction": "porespy.networks.snow2 (boundary_width=0, voxel_size=1) on the post-processed geometry"
+  }
+}

sphere/128/sphere128_0000_slices.csv

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+slice_axis,slice_index,depth_fraction,slice_porosity
+x,32,0.25,0.23871
+x,64,0.5,0.37006
+x,95,0.75,0.30518
+y,32,0.25,0.19037
+y,64,0.5,0.26691
+y,95,0.75,0.33136
+z,32,0.25,0.33777
+z,64,0.5,0.41974
+z,95,0.75,0.33765

sphere/128/sphere128_0000_throat_dist.csv

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+throat_inscribed_radius_vox
+3.1623
+7.8740
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+4.3589
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+12.0830
+19.3132
+4.5826
+12.0416
+5.0000
+5.0000
+5.0000
+16.4012
+7.6158

sphere/128/sphere128_0001.json

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+{
+  "generator": "overlapping_spheres",
+  "shape": [
+    128,
+    128,
+    128
+  ],
+  "porosity": 0.3287896879867074,
+  "seed": 184566854,
+  "grain_radius": 24,
+  "opening_radius": 3,
+  "porosity_pre": 0.33737,
+  "pre_opening_porosity": 0.33737,
+  "post_opening_porosity": 0.32603,
+  "closed_pore_voxels": 999,
+  "post_fill_porosity": 0.32555,
+  "porosity_post": 0.32555,
+  "stats": {
+    "post_processing": {
+      "description": "ball(3) morphological opening of the pore space (closes throats with inscribed-sphere radius < 3 vox) + fill of face-disconnected dead pore pockets",
+      "opening_radius_vox": 3,
+      "closed_pore_voxels": 999
+    },
+    "porosity": 0.32555,
+    "n_pores": 32,
+    "n_throats": 42,
+    "throat_inscribed_radius_vox": {
+      "n": 42,
+      "mean": 9.5,
+      "std": 4.406,
+      "min": 2.236,
+      "p10": 4.211,
+      "p25": 6.204,
+      "median": 9.0,
+      "p75": 12.443,
+      "p90": 15.652,
+      "max": 19.339
+    },
+    "pore_inscribed_radius_vox": {
+      "n": 32,
+      "mean": 7.801,
+      "std": 4.278,
+      "min": 1.732,
+      "p10": 3.016,
+      "p25": 4.092,
+      "median": 7.036,
+      "p75": 9.212,
+      "p90": 14.849,
+      "max": 19.0
+    },
+    "network_extraction": "porespy.networks.snow2 (boundary_width=0, voxel_size=1) on the post-processed geometry"
+  }
+}

sphere/128/sphere128_0001_throat_dist.csv

@@ -0,0 +1,43 @@
+throat_inscribed_radius_vox
+5.0000
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