Choose a model

Start with the physical processes your question needs. All simulation families use MATLAB and the pinned MRST checkout. Initialize H2sim from the repository root with startupH2sim; PHREEQC is an additional, explicit setup. See Installation before running the Quick start commands. On a narrow screen, scroll the comparison table sideways to see every column.

Model families and first examples

Family	Choose it for	Additional dependencies	Start here
Black-oil storage	Hydrogen–brine injection, withdrawal, trapping and dissolution using PVT tables	None for the bundled aquifer and anticline cases	Small aquifer run; then Hydrogen storage in saline aquifers or Anticlinal hydrogen storage
Compositional biochemistry	Gas composition, residual methane and microbial hydrogen consumption	None for serial execution; PHREEQC is unnecessary	Two-step comparison; then Hydrogen storage in depleted gas reservoirs
PHREEQC coupling	Aqueous speciation, pH and mineral feedback alongside compositional flow	PhreeqcMatlab, a working IPhreeqc engine and a chemistry database	Four-cell setup check; then PHREEQC coupling
Thermodynamics	Compare gas–liquid partitioning and salinity effects, or prepare PVT tables	None for the supplied study; internet access for new NIST downloads	Property study; then Thermodynamics and PVT tabulation

For gas mixing without water or reactions, start with Hydrogen–methane mixing. That small compositional example needs only core startup.

What changes between families?

Black-oil models use supplied phase-property tables; they do not resolve a multicomponent gas composition. Compositional models use an equation of state and track components. Biochemistry adds microbial kinetics to that transport. PHREEQC adds aqueous chemistry, with two different assignments of microbial kinetics: compositional PHREEQC uses cell-local PHREEQC kinetics; multirate PHREEQC retains MRST kinetics and calls equilibrium chemistry after reaction substeps. Read PHREEQC coupling before attributing differences between these workflows to a single physical process.

The example name does not select every process automatically. Check its transport switches, initial composition, mineral inventory and schedule. A short prefix checks setup; a complete cycle is needed to inspect recovery. Neither establishes agreement with published results or grid convergence.

Time and run size

Start with the coarse aquifer or a limited-step example in Quick start. The Run sizes and recorded timings distinguishes measured wall-clock times from cases without a recorded timing. Simulated days and animation length are not execution times. Full 2D reactive cases are intended for subsequent study, not as installation checks.

PHREEQC has platform-specific setup: native IPhreeqc on Linux, IPhreeqcCOM on Windows. See Optional PHREEQC setup and the tested-platform limits in Local verification. Parallel Computing Toolbox and AMGCL are optional; no example on this selection path requires them.