Selected examples and notebooks¶

Run the MATLAB commands locally and inspect their saved results in the notebooks. Start with a representative storage or validation case, then use the smaller workflow checks to explore chemistry settings.

Choose how to run an example¶

Setup check: use runPhreeqcValidation('totalDays', 2, 'plotResults', false) or the four-cell mineral notebook to check dependencies. These short runs do not reproduce full-duration figures.
Tutorial run: follow a notebook’s stated grid, schedule, and physical switches. Storage examples can be substantially larger than setup checks.
Exact reproduction: use the configuration and source dataset identified for the displayed result. A default example with a different cycle count, grid, or kinetic model does not reproduce that figure.
Saved-result exploration: redraw the exported multirate histories or inspect the three-cycle animation. Their provenance records identify the saved inputs; the documentation build does not rerun MATLAB simulations.

Open h2-biochem/examples/Contents.m in this checkout for the example catalogue. Initialize H2sim with startupH2sim before running examples.

Small hydrogen-mixing animation¶

Hydrogen–methane mixing in a sealed section

A small adaptation of a published hydrogen benchmark. Watch gravity and diffusion redistribute two gases; no PHREEQC is required.

Hydrogen–methane mixing

Cyclic storage beneath an anticline

A four-layer Gaussian structure, cushion injection, shut-in and ten storage cycles. Watch the plume, well operation and hydrogen inventory.

Anticlinal hydrogen storage

Storage in saline aquifers¶

2D aquifer storage cycle

Hydrogen build-up, structural trapping, injection, and withdrawal in the existing aquifer model. Gravity, capillarity, and dissolved hydrogen.

2D hydrogen storage in an aquifer

Storage in depleted gas reservoirs¶

Five-cycle 2D storage with three reactions

The existing 2D case with residual methane, MET, ACE, and SRB. Compare bacterial and abiotic injection and withdrawal on the original grid.

2D compositional storage with three reactions

Thermodynamics¶

Phase partitioning and salting-out

Compare RK, SW, PR, and Henry–Setschenow calculations with supplied ePC-SAFT reference tables. Inspect the route to black-oil PVT tabulation.

Hydrogen–brine phase behavior

PHREEQC validation¶

Compositional PHREEQC full-cycle validation

A 20-cell, 250-day injection–storage–production comparison with a separate reference implementation. Compare H₂ consumption, dissolved hydrogen, pH, DIC, and the three metabolic pathways.

Complete-cycle PHREEQC validation