6. Run the complete workflow

Goal

Generate the mesh and both simulations with one command.

Command

pymm -i microsystem.png -p parameters.toml -t all

How it works

The all workflow executes image processing, mesh generation, steady flow, and tracer transport in dependency order.

Result

The output contains diagnostic PNGs, Gmsh input and mesh files, editable OpenFOAM cases, and VTK exports.

output/
├── binary_image.png
└── extracted_border.png
└── interior_grains_border.png
└── interior_grains.png
└── mesh.geo
└── mesh.msh
└── VTK_flowStokes/
└── VTK_tracerTransport/
└── OpenFOAM/
    ├──flowStokes/
    └──tracerTransport/