Dependencies¶

The standard workflows run serially. Install optional components only when your selected model needs them.

What you need¶
Component	Required for	Installation
MATLAB	Core examples; R2021a or newer	Your MATLAB installation and license
MRST	All simulation workflows	Pinned Git submodule; initialized by `startupH2sim`
PhreeqcMatlab	Included chemistry integration tools	Pinned Git submodule
IPhreeqcCOM	The two sequential PHREEQC backends	Platform-specific COM setup; see installation
`h2_biogeochemistry.dat`	Selected PHREEQC examples	Bundled under `h2-biochem/database`
Parallel Computing Toolbox	Optional parallel pressure flashes	Optional; serial is the default
AMGCL and a supported C++ compiler	Optional acceleration of large compositional cases	MRST linear-solver MEX gateway; no Parallel Computing Toolbox needed
Internet access to NIST	Pure-component table-generation scripts	Needed when fetching data, not for the compact notebooks

Reference validation¶

The PHREEQC validation case additionally uses a separate UGFACT checkout. Pass its root directory as ugfactRoot to runPhreeqcValidation. All selected examples and the reference run use serial execution.

Without Parallel Computing Toolbox¶

Leave phreeqcReflashParallel=false (the default). The selected models and notebooks do not call parpool or require worker processes.

summary = exampleSequentialBiochemistryPhreeqc1D( ...
    'maximumFlowSteps', 2, 'phreeqcReflashParallel', false);

If parallel pressure flashes are explicitly requested but the toolbox or its license is unavailable, H2sim reports the fallback and uses the serial loop. Parallel execution is an optional optimization, not a different model.

Dependency revisions¶

Git records the exact MRST and PhreeqcMatlab revisions used by the checkout:

git submodule status
git submodule update --init --recursive

H2sim’s acetate component parameters live in its own helper; no local edit to MRST’s property table is required. Avoid recursively adding an entire MRST checkout to MATLAB’s path. Its startup and module manager select the needed paths.

Platform requirements¶

The core black-oil, compositional bacterial, and thermodynamic workflows do not depend on the Windows COM interface. The two sequential PHREEQC backends currently use IPhreeqcCOM; their platform requirement and setup check are documented in Installation.

Database source¶

h2_biogeochemistry.dat is an unmodified copy of the database distributed with UGFACT, developed by Ahmadreza Shojaee at Heriot-Watt University. H2sim changes only its filename. The exact source revision is recorded alongside the checksum in h2-biochem/database/README.md. The original USGS PHREEQC database credits are preserved. Cite UGFACT’s framework publication when using this database.