Code reference¶

Browse the source repository, or use MATLAB’s help and edit commands for local function documentation.

Entry points¶

Function	Purpose
`startupH2sim`	Initialize code and dependencies
`exampleBlackOilAquifer2D`	2D structural trapping and five storage cycles
`simple1DBacterialExampleMetacet`	MRST compositional microbial example
`setupH2StorageExampleWithSRB_benchmark`	Configure a multi-reaction benchmark
`exampleCompositionalBacterial1DPhreeqcMinerals`	Original MRST and three PHREEQC mineral configurations
`exampleSequentialBiochemistryPhreeqc1D`	Coarse-flow / local-reaction multirate example
`exampleCompositionalBacterial2DThreeReactions`	Existing 2D reservoir case with MET, ACE, SRB, packed cycles, and selectable scenarios
`runPhreeqcValidation`	Compositional PHREEQC injection benchmark against an external reference
`exampleH2BrineSolubilityStudy`	Phase-partition and salting-out comparisons
`setupOptimizedLinearSolver`	AMGCL CPR including bacterial and tracer unknowns; configurable native threads
`loadH2simResults`	Load result MAT files; optionally stage network files locally for HDF5
`activateH2simAMGCL`	Activate an optional locally compiled MRST gateway
`profilePhreeqcWorkflows`	Paired profiling and state comparisons

Output and replotting¶

The aquifer, compositional 2D, validation, and short chemistry examples save their setup and accepted states with MRST packed simulation output. packed_setup.mat sits beside the saved states, well solutions, and timestep reports. Changed inputs select a separate result directory. Returned results contain the setup and state histories; packedProblem identifies the black-oil and multirate output locations. The mineral comparison returns one result per model configuration.

plotBlackOilAquifer2D(result);
plotH2BrineSolubilityStudy(study);
plotCompositionalBacterial2DThreeReactions(results);
plotCompositionalPhreeqcValidation(validation);
plotPhreeqcMineralComparison(comparison);
plotSequentialBiochemistryPhreeqc(summary);
plotPhreeqcBackendComparison(scenarios);

The compositional 2D MAT results retain physical fields while omitting transient derivative/state-function caches. Complete restart states remain in the packed directory. A completed MAT result with matching packed setup can be reused without rereading every restart cache. Use loadH2simResults when loading large result files through a network path; it stages a temporary local copy for HDF5 and removes it after loading.

Plotting functions preserve values and export vector PDF and PNG figures. outputDirectory='' disables export. Dimensionless distance uses actual domain edges, rather than stretching cell centers to zero and one.

Hydrogen-consumption percentages refer to microbial reaction consumption, with the injection denominator stated by the figure. They are distinct from unrecovered gas or a production recovery factor.

Tests¶

checks = runtests('h2-biochem/tests');
assertSuccess(checks);

COM integration tests require the IPhreeqcCOM setup described in Installation. A skipped test does not validate a backend on that platform. The serial fallback tests cover both available and missing optional toolbox checks.

See PHREEQC coupling for the current conservation-audit limitations.