├── .coveragerc ├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ └── feature_request.md ├── release.yml └── workflows │ ├── bump-version.yml │ ├── generate-docs.yml │ ├── generate-release-notes.yml │ ├── logger.sh │ ├── nightly.yml │ ├── publish-to-pypi.yml │ ├── ruff.yml │ ├── run-examples.yml │ ├── run-tests.yml │ └── utils.sh ├── .gitignore ├── CITATION.cff ├── CODE_OF_CONDUCT.md ├── DEV_GUIDE.md ├── LICENSE ├── Makefile ├── README.md ├── VERSIONING.md ├── codecov.yml ├── docs ├── Makefile ├── _examples │ ├── applications.rst │ ├── index.rst │ ├── reference.rst │ └── tutorials.rst ├── _static │ ├── css │ │ └── custom.css │ ├── images │ │ ├── conc_dist.png │ │ ├── droplet.png │ │ ├── extracted_berea.png │ │ ├── find_neighbor_pores_three_labels.png │ │ ├── find_neighbor_pores_three_labels_version_three.png │ │ ├── generic_geometry_histogram.png │ │ ├── histogram.png │ │ ├── openpnm_logo.jpg │ │ ├── percolation.png │ │ ├── quick_start_drainage_curve.png │ │ ├── reactive_diffusion.png │ │ ├── rel_diff.png │ │ ├── stick_and_ball_histogram.png │ │ └── transient.png │ └── js │ │ └── custom.js ├── _templates │ └── autosummary │ │ ├── base.rst │ │ ├── class.rst │ │ ├── method.rst │ │ └── module.rst ├── conf.py ├── index.rst ├── installation.rst ├── make.bat └── modules │ └── index.rst ├── example.py ├── examples ├── applications │ ├── Sandstone.csv │ ├── absolute_permeability.ipynb │ ├── adjusting_pore_size_distributions.ipynb │ ├── dispersion_coefficient.ipynb │ ├── effective_diffusivity_and_tortuosity.ipynb │ ├── formation_factor.ipynb │ ├── mercury_intrusion.ipynb │ ├── network_extraction.ipynb │ ├── porosity.ipynb │ ├── relative_diffusivity.ipynb │ └── relative_permeability.ipynb ├── contrib │ └── README.rst ├── getting_started.ipynb ├── reference │ ├── architecture │ │ ├── pore_scale_models.ipynb │ │ ├── settings_attribute_machinery.ipynb │ │ └── workspace_and_projects.ipynb │ ├── networks │ │ └── managing_clustered_networks.ipynb │ └── simulations │ │ ├── available_matrix_solvers.ipynb │ │ ├── basic_transport.ipynb │ │ ├── explanation_of_units.ipynb │ │ ├── reactive_transport.ipynb │ │ ├── size_factors_and_transport_conductance.ipynb │ │ └── transient_transport.ipynb └── tutorials │ ├── 01_numerical_python_primer.ipynb │ ├── 02_network_generation_and_visualization.ipynb │ ├── 03_data_and_topology_storage.ipynb │ ├── 04_graph_queries_and_manipulation.ipynb │ ├── 05_defining_geometry.ipynb │ ├── 06_labels_and_domains.ipynb │ ├── 07_phases_and_mixtures.ipynb │ ├── 08_simulating_transport.ipynb │ ├── 09_simulating_invasion.ipynb │ └── 10_visualization_options.ipynb ├── pyproject.toml ├── pytest.ini ├── requirements.txt ├── requirements ├── conda.txt ├── docs.txt └── tests.txt ├── scripts ├── chemical_example.py ├── example_advection_diffusion ├── example_bundle_of_tubes.py ├── example_knudsen_diffusion.py ├── example_mass_partitioning.py ├── example_mixtures.py ├── example_multiphase_diffusion.py ├── example_multiphysics_solver.py ├── example_nernst_planck2d ├── example_nernst_planck3d ├── example_new_solvers.py ├── example_non_newtonian.py ├── example_pnflow.py ├── example_salome_export.py ├── example_statoil.py ├── example_subdomains.py ├── example_transient_diffusion.py ├── example_transient_dispersion.py ├── example_transient_nernst_planck └── tmp_comsol_data.npz ├── src └── openpnm │ ├── __init__.py │ ├── _skgraph │ ├── __init__.py │ ├── generators │ │ ├── __init__.py │ │ ├── _bcc.py │ │ ├── _cubic.py │ │ ├── _delaunay.py │ │ ├── _fcc.py │ │ ├── _gabriel.py │ │ ├── _template.py │ │ ├── _voronoi.py │ │ ├── _voronoi_delaunay_dual.py │ │ ├── network │ │ └── tools │ │ │ ├── __init__.py │ │ │ └── _funcs.py │ ├── io │ │ ├── __init__.py │ │ └── _funcs.py │ ├── operations │ │ ├── __init__.py │ │ ├── _binary.py │ │ ├── _funcs.py │ │ └── _unary.py │ ├── queries │ │ ├── QuickUnion.py │ │ ├── __init__.py │ │ ├── _funcs.py │ │ └── _qupc.py │ ├── simulations │ │ ├── __init__.py │ │ ├── _funcs.py │ │ └── _percolation.py │ ├── tools │ │ ├── GraphBundle.py │ │ ├── __init__.py │ │ ├── _coords_transforms.py │ │ └── _funcs.py │ └── visualization │ │ ├── __init__.py │ │ └── _funcs.py │ ├── algorithms │ ├── __init__.py │ ├── _advection_diffusion.py │ ├── _algorithm.py │ ├── _drainage.py │ ├── _fickian_diffusion.py │ ├── _fourier_conduction.py │ ├── _invasion_percolation.py │ ├── _ohmic_conduction.py │ ├── _reactive_transport.py │ ├── _solution.py │ ├── _stokes_flow.py │ ├── _transient_advection_diffusion.py │ ├── _transient_fickian_diffusion.py │ ├── _transient_fourier_conduction.py │ ├── _transient_reactive_transport.py │ └── _transport.py │ ├── beta │ ├── __init__.py │ └── _funcs.py │ ├── contrib │ ├── __init__.py │ ├── _multiphase.py │ └── _transient_multiphysics.py │ ├── core │ ├── __init__.py │ ├── _base2.py │ ├── _mixins.py │ └── _models.py │ ├── integrators │ ├── __init__.py │ ├── _base.py │ └── _scipy.py │ ├── io │ ├── __init__.py │ ├── _comsol.py │ ├── _csv.py │ ├── _dict.py │ ├── _hdf5.py │ ├── _jsongraph.py │ ├── _marock.py │ ├── _networkx.py │ ├── _pandas.py │ ├── _paraview.py │ ├── _pergeos.py │ ├── _porespy.py │ ├── _salome.py │ ├── _statoil.py │ ├── _stl.py │ ├── _utils.py │ ├── _vtk.py │ └── _xdmf.py │ ├── models │ ├── __init__.py │ ├── _doctxt.py │ ├── collections │ │ ├── __init__.py │ │ ├── geometry │ │ │ ├── __init__.py │ │ │ ├── circles_and_rectangles.py │ │ │ ├── cones_and_cylinders.py │ │ │ ├── cubes_and_cuboids.py │ │ │ ├── pyramids_and_cuboids.py │ │ │ ├── spheres_and_cylinders.py │ │ │ ├── squares_and_rectangles.py │ │ │ └── trapezoids_and_rectangles.py │ │ ├── network │ │ │ └── __init__.py │ │ ├── phase │ │ │ ├── __init__.py │ │ │ ├── air.py │ │ │ ├── gas.py │ │ │ ├── liquid.py │ │ │ ├── mercury.py │ │ │ └── water.py │ │ └── physics │ │ │ ├── __init__.py │ │ │ ├── basic.py │ │ │ └── standard.py │ ├── geometry │ │ ├── __init__.py │ │ ├── _geodocs.py │ │ ├── conduit_lengths │ │ │ ├── __init__.py │ │ │ └── _funcs.py │ │ ├── diffusive_size_factors │ │ │ ├── __init__.py │ │ │ └── _funcs.py │ │ ├── hydraulic_size_factors │ │ │ ├── __init__.py │ │ │ └── _funcs.py │ │ ├── pore_cross_sectional_area │ │ │ ├── __init__.py │ │ │ └── _funcs.py │ │ ├── pore_seed │ │ │ ├── __init__.py │ │ │ └── _funcs.py │ │ ├── pore_size │ │ │ ├── __init__.py │ │ │ └── _funcs.py │ │ ├── pore_surface_area │ │ │ ├── __init__.py │ │ │ └── _funcs.py │ │ ├── pore_volume │ │ │ ├── __init__.py │ │ │ └── _funcs.py │ │ ├── throat_capillary_shape_factor │ │ │ ├── __init__.py │ │ │ └── _funcs.py │ │ ├── throat_centroid │ │ │ ├── __init__.py │ │ │ └── _funcs.py │ │ ├── throat_cross_sectional_area │ │ │ ├── __init__.py │ │ │ └── _funcs.py │ │ ├── throat_endpoints │ │ │ ├── __init__.py │ │ │ └── _funcs.py │ │ ├── throat_length │ │ │ ├── __init__.py │ │ │ └── _funcs.py │ │ ├── throat_perimeter │ │ │ ├── __init__.py │ │ │ └── _funcs.py │ │ ├── throat_seed │ │ │ ├── __init__.py │ │ │ └── _funcs.py │ │ ├── throat_size │ │ │ ├── __init__.py │ │ │ └── _funcs.py │ │ ├── throat_surface_area │ │ │ ├── __init__.py │ │ │ └── _funcs.py │ │ ├── throat_vector │ │ │ ├── __init__.py │ │ │ └── _funcs.py │ │ └── throat_volume │ │ │ ├── __init__.py │ │ │ └── _funcs.py │ ├── misc │ │ ├── __init__.py │ │ ├── _basic_math.py │ │ ├── _neighbor_lookups.py │ │ ├── _simple_equations.py │ │ └── _statistical_distributions.py │ ├── network │ │ ├── __init__.py │ │ ├── _health.py │ │ └── _topology.py │ ├── phase │ │ ├── __init__.py │ │ ├── _phasedocs.py │ │ ├── critical_props │ │ │ ├── __init__.py │ │ │ └── _funcs.py │ │ ├── density │ │ │ ├── __init__.py │ │ │ └── _funcs.py │ │ ├── diffusivity │ │ │ ├── __init__.py │ │ │ └── _funcs.py │ │ ├── heat_capacity │ │ │ ├── __init__.py │ │ │ └── _funcs.py │ │ ├── misc │ │ │ ├── __init__.py │ │ │ └── _funcs.py │ │ ├── mixtures │ │ │ ├── __init__.py │ │ │ └── _funcs.py │ │ ├── partition_coefficient │ │ │ ├── __init__.py │ │ │ ├── _funcs.py │ │ │ └── gas_water_henry.csv │ │ ├── surface_tension │ │ │ ├── __init__.py │ │ │ └── _funcs.py │ │ ├── thermal_conductivity │ │ │ ├── __init__.py │ │ │ └── _funcs.py │ │ ├── vapor_pressure │ │ │ ├── __init__.py │ │ │ └── _funcs.py │ │ └── viscosity │ │ │ ├── __init__.py │ │ │ └── _funcs.py │ └── physics │ │ ├── __init__.py │ │ ├── _utils.py │ │ ├── ad_dif_conductance │ │ ├── __init__.py │ │ └── _funcs.py │ │ ├── capillary_pressure │ │ ├── __init__.py │ │ └── _funcs.py │ │ ├── diffusive_conductance │ │ ├── __init__.py │ │ └── _funcs.py │ │ ├── electrical_conductance │ │ ├── __init__.py │ │ └── _funcs.py │ │ ├── hydraulic_conductance │ │ ├── __init__.py │ │ └── _funcs.py │ │ ├── meniscus │ │ ├── __init__.py │ │ └── _funcs.py │ │ ├── multiphase │ │ ├── __init__.py │ │ └── _funcs.py │ │ ├── source_terms │ │ ├── __init__.py │ │ └── _funcs.py │ │ └── thermal_conductance │ │ ├── __init__.py │ │ └── _funcs.py │ ├── network │ ├── __init__.py │ ├── _bcc.py │ ├── _cubic.py │ ├── _cubic_template.py │ ├── _delaunay.py │ ├── _delaunay_voronoi_dual.py │ ├── _demo.py │ ├── _fcc.py │ ├── _network.py │ └── _voronoi.py │ ├── phase │ ├── __init__.py │ ├── _air.py │ ├── _mercury.py │ ├── _mixture.py │ ├── _phase.py │ ├── _species.py │ └── _water.py │ ├── solvers │ ├── __init__.py │ ├── _base.py │ ├── _pardiso.py │ ├── _petsc.py │ ├── _pyamg.py │ └── _scipy.py │ ├── topotools │ ├── __init__.py │ ├── _graphtools.py │ ├── _perctools.py │ └── _topotools.py │ ├── utils │ ├── __init__.py │ ├── _health.py │ ├── _misc.py │ ├── _project.py │ ├── _settings.py │ ├── _workspace.py │ └── jgf_schema.pkl │ └── visualization │ ├── __init__.py │ ├── _conduit_visualizer.py │ └── _plottools.py ├── tests ├── fixtures │ ├── 3DMA-Castlegate │ │ ├── castle_cln.np2th │ │ └── castle_cln.th2np │ ├── ICL-SandPack(F42A) │ │ ├── F42A_link1.dat │ │ ├── F42A_link2.dat │ │ ├── F42A_node1.dat │ │ └── F42A_node2.dat │ ├── ICL-Sandstone(Berea) │ │ ├── Berea_link1.dat │ │ ├── Berea_link2.dat │ │ ├── Berea_node1.dat │ │ └── Berea_node2.dat │ ├── JSONGraphFormat │ │ ├── invalid.json │ │ └── valid.json │ ├── OpenPNM-Objects │ │ └── net_01.net │ ├── PerGeos │ │ ├── flooded.am │ │ ├── mandatory.am │ │ └── simplePNM.am │ ├── VTK-VTP │ │ ├── test.pvsm │ │ ├── test_save_vtk_1.vtp │ │ └── test_save_vtk_2.vtp │ ├── berea_100_to_300.npz │ └── iMorph-Sandstone │ │ ├── throats_cellsThroatsGraph.txt │ │ └── throats_cellsThroatsGraph_Nodes.txt ├── integration │ ├── Flow_in_straight_conduit.py │ └── PoreSpyIO_on_Berea.py └── unit │ ├── algorithms │ ├── AdvectionDiffusionTest.py │ ├── BCTest.py │ ├── DrainageTest.py │ ├── GenericTransportTest.py │ ├── IPTest.py │ ├── NernstPlanckTest.py │ ├── ReactiveTransportTest.py │ ├── SolversTest.py │ ├── SubclassedTransportTest.py │ ├── TransientAdvectionDiffusionTest.py │ ├── TransientFickianDiffusionTest.py │ ├── TransientMultiPhysicsTest.py │ └── TransientReactiveTransportTest.py │ ├── core │ ├── Base2Test.py │ ├── BaseTest.py │ ├── HealthCheckTest.py │ └── ModelsWrapperTest.py │ ├── io │ ├── COMSOLTest.py │ ├── CSVTest.py │ ├── DictTest.py │ ├── HDF5Test.py │ ├── IOUtilsTest.py │ ├── JSONGraphFormatTest.py │ ├── MARockTest.py │ ├── NetworkXTest.py │ ├── PandasTest.py │ ├── ParaViewTest.py │ ├── PerGeosTest.py │ ├── PoreSpyTest.py │ ├── STLTest.py │ ├── SalomeTest.py │ ├── StatoilTest.py │ ├── VTKTest.py │ ├── XDMFTest.py │ ├── berea.net │ └── custom_code.py │ ├── models │ ├── geometry │ │ ├── ConduitDiffusiveSizeFactorsTest.py │ │ ├── ConduitHydraulicSizeFactorsTest.py │ │ ├── ConduitLengthsTest.py │ │ ├── PoreAreaTest.py │ │ ├── PoreCentroidTest.py │ │ ├── PoreSeedTest.py │ │ ├── PoreSizeTest.py │ │ ├── PoreSurfaceAreaTest.py │ │ ├── PoreVolumeTest.py │ │ ├── ThroatCapillaryShapeFactorTest.py │ │ ├── ThroatCentroidTest.py │ │ ├── ThroatCrossSectionalAreaTest.py │ │ ├── ThroatEndpointsTest.py │ │ ├── ThroatLengthTest.py │ │ ├── ThroatNormalTest.py │ │ ├── ThroatOffsetVerticesTest.py │ │ ├── ThroatPerimeterTest.py │ │ ├── ThroatSIzeTest.py │ │ ├── ThroatSeedTest.py │ │ ├── ThroatSurfaceAreaTest.py │ │ ├── ThroatVectorTest.py │ │ └── ThroatVolumeTest.py │ ├── misc │ │ └── MiscTest.py │ ├── network │ │ └── TestTopologyModels.py │ ├── phase │ │ ├── DensityTest.py │ │ ├── DiffusivityTest.py │ │ ├── HeatCapacityTest.py │ │ ├── LatentHeatOfVaporizationTest.py │ │ ├── MixturesTest.py │ │ ├── SurfaceTensionTest.py │ │ ├── ThermalConductivityTest.py │ │ ├── VaporPressureTest.py │ │ └── ViscosityTest.py │ └── physics │ │ ├── AdvectiveDiffusiveConductanceTest.py │ │ ├── CapillaryPressureTest.py │ │ ├── DiffusiveConductanceTest.py │ │ ├── ElectricalConductanceTest.py │ │ ├── HydraulicConductanceTest.py │ │ ├── MeniscusTest.py │ │ ├── MultiPhaseModelsTest.py │ │ ├── SourceTermTest.py │ │ └── ThermalConductanceTest.py │ ├── network │ ├── BravaisTest.py │ ├── CubicTemplateTest.py │ ├── CubicTest.py │ ├── DelaunayTest.py │ ├── GenericNetworkTest.py │ ├── LabelTest.py │ ├── NetworkHealthCheckTest.py │ ├── VoronoiDelaunayDualTest.py │ └── VoronoiTest.py │ ├── phase │ ├── AirTest.py │ ├── MercuryTest.py │ 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