Output fields

You select what HemoCell writes to disk with two calls from your case:

• hemocell.setOutputs("RBC", { ... }) — per-cell fields, once per cell type, and

• hemocell.setFluidOutputs({ ... }) — fluid (lattice) fields.

Each takes a list of OUTPUT_* constants defined in config/constant_defaults.h. Requesting only what you need keeps the output smaller and the simulation faster. By default the values are written in SI units (set hemocell.outputInSiUnits = false for lattice units). The fields end up in compressed HDF5 files under tmp/hdf5 (convert them for ParaView with batchPostProcess.sh), and cell scalar data additionally in tmp/csv (see Post-processing the output of a HemoCell case).

Per-cell outputs

Pass these to setOutputs(name, {...}).

Constant	Field written
OUTPUT_POSITION	Position of each membrane vertex.
OUTPUT_TRIANGLES	The triangulated surface mesh (connectivity), needed to render the cell surface.
OUTPUT_VELOCITY	Velocity of each membrane vertex.
OUTPUT_FORCE	Total force on each vertex (sum of all force terms below).
OUTPUT_FORCE_VOLUME	Volume-conservation force contribution.
OUTPUT_FORCE_AREA	Local area-conservation force contribution.
OUTPUT_FORCE_BENDING	Bending force contribution.
OUTPUT_FORCE_LINK	Link (stretching) force contribution.
OUTPUT_FORCE_VISC	Viscous force contribution.
OUTPUT_FORCE_INNER_LINK	Inner-link force contribution (models with internal structure).
OUTPUT_FORCE_REPULSION	Repulsion force contribution (requires repulsion enabled).
OUTPUT_INNER_LINKS	The inner-edge connectivity of the cell.
OUTPUT_CELL_ID	The unique id of the cell each vertex belongs to.
OUTPUT_VERTEX_ID	The id of each vertex.
OUTPUT_RES_TIME	Residence time of the cell in the domain.

Note

OUTPUT_BINDING_SITES and OUTPUT_INTERIOR_POINTS are also defined and relate to the binding/solidification and interior-viscosity features respectively. They are only meaningful when those features are enabled; verify against the model you use before relying on them.

Fluid outputs

Pass these to setFluidOutputs({...}).

Constant	Field written
OUTPUT_VELOCITY	Fluid velocity field.
OUTPUT_DENSITY	Fluid density field.
OUTPUT_FORCE	Force field acting on the fluid (e.g. from the immersed cells).
OUTPUT_SHEAR_STRESS	Shear stress field.
OUTPUT_SHEAR_RATE	Shear rate field.
OUTPUT_STRAIN_RATE	Strain-rate field.
OUTPUT_OMEGA	Relaxation parameter (omega = 1/tau) field.
OUTPUT_BOUNDARY	Boundary/solid mask of the domain.
OUTPUT_CELL_DENSITY	Number density of cells mapped onto the fluid grid.

Tip

The full list of OUTPUT_* constants lives in config/constant_defaults.h. If a constant is not listed above, it is either experimental or specific to an optional feature.