Dependencies

The standard workflows run serially. Plain startupH2sim initializes core modules and MRST without checking or fetching chemistry libraries. Request startupH2sim('phreeqc', true) only for chemistry workflows, or initialize chemistry later with initializeH2simPhreeqc. See Installation for explicit setup, first-use downloads and offline chemistry requirements.

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	Optional chemistry integration tools	Pinned submodule; initialized only by explicit chemistry setup
IPhreeqc (Linux) / IPhreeqcCOM (Windows)	The two sequential PHREEQC backends	Native shared library through PhreeqcMatlab on Linux; registered COM server on Windows; see Optional PHREEQC setup
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 three-backend comparison and standalone PHREEQC validation use only H2sim and the bundled database. No external reference checkout is required. To reproduce an optional external comparison, pass its checkout explicitly as referenceRoot to runPhreeqcValidation. The reference files and platform are checked before simulation starts. All cases run serially.

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

Both sequential PHREEQC backends support Linux MATLAB through the native IPhreeqc shared library supplied by PhreeqcMatlab, and Windows MATLAB through a registered IPhreeqcCOM server. Linux uses the native C interface and requires no COM registration. See Optional PHREEQC setup for platform-specific installation, the Linux runtime setup, and verification commands. The core black-oil, compositional bacterial, and thermodynamic workflows run independently of the optional PHREEQC coupling.

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.