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…hance shape factor methods
…to 'valvatne_blunt' in tests
This notebook compares the default circular `generic_poiseuille` conductance with new shape-factor-aware Valvatne-Blunt models. It includes a synthetic Cartesian network and a real extracted Ketton rock network to evaluate the impact on absolute permeability estimation. Key findings include the recovery of the circular limit for throat-only shape-factor closure and the quantification of changes in throat conductance and absolute permeability for non-circular ducts.
… conductance models - Updated binary images for permeability and porosity scatter plots. - Modified CSV files for Stokes case results and limit representative data to reflect new calculations. - Expanded background documentation with detailed explanations of the equivalent duct concept and shape-aware conductance models. - Clarified hydraulic geometry fields and their significance in single-phase conductance models in the concepts documentation. - Revised verification documentation to reflect the transition from `valvatne_blunt_baseline` to the complete `valvatne_blunt` model.
…lidations and shape factor calculations
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… and PoreSpy import
…s for Imperial export repairs
This notebook compares the `voids` workflow against a committed reference dataset produced with the Imperial College `pnextract` and `pnflow` workflow. It includes functionality to load reference data, run the `voids` extraction, and generate comparative metrics and visualizations for permeability and porosity. The results are saved for documentation and review.
…, and improve plotting structure
…ct/pnflow benchmark, including new figures and CSV results
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Pull request overview
This PR updates voids’ single-phase hydraulic conductance modeling to implement the full Valvatne–Blunt-style shape-factor closure, and aligns the image-extraction/import pipeline and verification artifacts (benchmarks, docs, notebooks, and reference datasets) with that model.
Changes:
- Implement Valvatne–Blunt single-phase conductance with shape-dependent coefficients and add explicit model names (
valvatne_blunt,valvatne_blunt_throat), while keepingvalvatne_blunt_baselineas a compatibility alias. - Add “Imperial export” (
pnextract-style) geometry repair heuristics to the PoreSpy importer, and enable those repairs by default in the image extraction workflow. - Add/refresh verification reports, notebooks, and a committed external
pnextract/pnflowreference dataset; update benchmark expectations and documentation accordingly.
Reviewed changes
Copilot reviewed 76 out of 109 changed files in this pull request and generated 2 comments.
Show a summary per file
| File | Description |
|---|---|
| tests/test_workflows_porespy_volume.py | Adds tests asserting default Imperial-export geometry repairs in image extraction and acceptance of the legacy pnextract alias. |
| tests/test_porespy_import_aliases.py | Removes importer alias/derivation tests (file deleted). |
| tests/test_porespy_import.py | Removes minimal importer tests (file deleted). |
| tests/test_legacy_solver_coverage.py | Extends solver coverage tests to include the new model names and the new direct API function. |
| tests/test_benchmark_xlb.py | Updates benchmark expectation from valvatne_blunt_baseline to valvatne_blunt. |
| tests/test_benchmark_segmented_volume.py | Updates benchmark expectations and crosscheck assertions to use valvatne_blunt. |
| src/voids/io/porespy.py | Adds Imperial-export geometry repair mode, legacy alias normalization, and additional geometry derivation/override logic during import. |
| src/voids/image/network_extraction.py | Enables Imperial-export geometry repairs by default in the extraction workflow and threads seed/provenance through. |
| src/voids/geom/hydraulic.py | Implements the complete Valvatne–Blunt single-phase closure (triangle/square/circle coefficients), adds throat-only and full-conduit variants, and expands geometry derivations (area/shape-factor inference). |
| src/voids/benchmarks/xlb.py | Switches default benchmark options to valvatne_blunt. |
| src/voids/benchmarks/segmented_volume.py | Switches default OpenPNM benchmark options/documentation to valvatne_blunt. |
| notebooks/14_mwe_shape_factor_conductance_comparison.py | New notebook comparing generic Poiseuille vs shape-factor-aware conductance models on synthetic + extracted networks. |
| notebooks/13_mwe_synthetic_volume_xlb_benchmark.py | Updates notebook options to valvatne_blunt. |
| notebooks/12_mwe_synthetic_volume_openpnm_benchmark.py | Updates options to valvatne_blunt and adds report/asset export paths and saved figures/CSVs. |
| notebooks/09_mwe_image_based_vug_sensitivity_2d.py | Updates options to valvatne_blunt. |
| notebooks/08_mwe_image_based_vug_shape_sensitivity.py | Updates options and documentation text to valvatne_blunt. |
| notebooks/07_mwe_synthetic_vug_case.py | Updates options to valvatne_blunt. |
| notebooks/06_mwe_real_porespy_extraction.py | Updates options to valvatne_blunt. |
| notebooks/04_mwe_manufactured_porespy_extraction.py | Updates options to valvatne_blunt. |
| mkdocs.yml | Adds new verification pages for OpenPNM cross-check and external pnflow benchmark. |
| examples/data/external_pnflow_benchmark/README.md | Adds documentation for the committed external reference dataset and its intent. |
| examples/data/external_pnflow_benchmark/manifest.csv | Adds manifest describing committed external benchmark cases and file paths. |
| examples/data/external_pnflow_benchmark/phi041_b20/phi041_b20_upscaled.tsv | Adds saved pnflow outputs for case phi041_b20. |
| examples/data/external_pnflow_benchmark/phi041_b20/phi041_b20_pnflow.prt | Adds saved pnflow report for case phi041_b20. |
| examples/data/external_pnflow_benchmark/phi041_b20/phi041_b20_node2.dat | Adds saved pnextract node data for case phi041_b20. |
| examples/data/external_pnflow_benchmark/phi041_b20/input_pnflow.dat | Adds pnflow input deck for case phi041_b20. |
| examples/data/external_pnflow_benchmark/phi040_b18/phi040_b18_upscaled.tsv | Adds saved pnflow outputs for case phi040_b18. |
| examples/data/external_pnflow_benchmark/phi040_b18/phi040_b18_pnflow.prt | Adds saved pnflow report for case phi040_b18. |
| examples/data/external_pnflow_benchmark/phi040_b18/phi040_b18_node2.dat | Adds saved pnextract node data for case phi040_b18. |
| examples/data/external_pnflow_benchmark/phi040_b18/input_pnflow.dat | Adds pnflow input deck for case phi040_b18. |
| examples/data/external_pnflow_benchmark/phi038_b18/phi038_b18_upscaled.tsv | Adds saved pnflow outputs for case phi038_b18. |
| examples/data/external_pnflow_benchmark/phi038_b18/phi038_b18_pnflow.prt | Adds saved pnflow report for case phi038_b18. |
| examples/data/external_pnflow_benchmark/phi038_b18/phi038_b18_node2.dat | Adds saved pnextract node data for case phi038_b18. |
| examples/data/external_pnflow_benchmark/phi038_b18/phi038_b18_node1.dat | Adds saved pnextract node data for case phi038_b18. |
| examples/data/external_pnflow_benchmark/phi038_b18/input_pnflow.dat | Adds pnflow input deck for case phi038_b18. |
| examples/data/external_pnflow_benchmark/phi035_b16/phi035_b16_upscaled.tsv | Adds saved pnflow outputs for case phi035_b16. |
| examples/data/external_pnflow_benchmark/phi035_b16/phi035_b16_pnflow.prt | Adds saved pnflow report for case phi035_b16. |
| examples/data/external_pnflow_benchmark/phi035_b16/phi035_b16_node2.dat | Adds saved pnextract node data for case phi035_b16. |
| examples/data/external_pnflow_benchmark/phi035_b16/phi035_b16_node1.dat | Adds saved pnextract node data for case phi035_b16. |
| examples/data/external_pnflow_benchmark/phi035_b16/input_pnflow.dat | Adds pnflow input deck for case phi035_b16. |
| examples/data/external_pnflow_benchmark/phi032_b14/phi032_b14_upscaled.tsv | Adds saved pnflow outputs for case phi032_b14. |
| examples/data/external_pnflow_benchmark/phi032_b14/phi032_b14_pnflow.prt | Adds saved pnflow report for case phi032_b14. |
| examples/data/external_pnflow_benchmark/phi032_b14/phi032_b14_node2.dat | Adds saved pnextract node data for case phi032_b14. |
| examples/data/external_pnflow_benchmark/phi032_b14/input_pnflow.dat | Adds pnflow input deck for case phi032_b14. |
| examples/data/README.md | Documents the new external pnflow benchmark dataset directory. |
| docs/verification/xlb.md | Updates documentation to reference valvatne_blunt as the conductance model. |
| docs/verification/pnflow.md | Adds a new narrative verification report for the external pnextract/pnflow benchmark. |
| docs/verification/openpnm.md | Adds a new narrative verification report for the OpenPNM extracted-network cross-check. |
| docs/verification/index.md | Expands verification index to include new reports and a comparison table. |
| docs/index.md | Renames the top-level heading to “Overview”. |
| docs/examples.md | Adds references to new verification reports and the external pnflow benchmark notebook/report. |
| docs/concepts.md | Adds a section documenting hydraulic geometry fields and how the conductance models use them. |
| docs/background.md | Adds substantial background documentation for equivalent-duct/shape-factor conductance and conduit decomposition, and updates assumptions accordingly. |
| docs/assets/verification/xlb_stokes_limit_representative.csv | Updates stored representative benchmark results. |
| docs/assets/verification/xlb_stokes_15_case_results.csv | Updates stored 15-case Stokes-limit results. |
| docs/assets/verification/xlb_15_case_results.csv | Updates stored 15-case XLB results. |
| docs/assets/verification/pnflow_5_case_results.csv | Adds stored 5-case external pnflow comparison results. |
| docs/assets/verification/openpnm_5_case_results.csv | Adds stored 5-case OpenPNM cross-check results. |
| docs/assets/valvatne_equivalent_shape_factor.svg | Adds an accessible SVG wrapper for the Valvatne equivalent-shape figure. |
| docs/assets/valvatne_conduit_series_model.svg | Adds an accessible SVG schematic for the pore–throat–pore conduit decomposition. |
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…py importer (#34) * Initial plan * Validate shape_factor and throat area before overriding area in porespy importer Co-authored-by: volpatto <5941226+volpatto@users.noreply.github.com> * Guard computed area against overflow; fix test throat_conns alignment; add coverage tests Co-authored-by: volpatto <5941226+volpatto@users.noreply.github.com> --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: volpatto <5941226+volpatto@users.noreply.github.com>
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This PR adds the complete Valvatne-Blunt conductance model to single-phase flow, with a bunch of benchmarks, including against
pnextractandpnflow.