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 namespace hemo 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, described by XDMF files for ParaView (see Files), and cell scalar data additionally in tmp/csv (see Post-processing the output of a HemoCell case).

Files

Each writeOutput() writes, in the output directory (tmp/ by default):

hdf5/<iteration>/<name>.<iteration>.p.<block>.h5

One file per atomic block for every cell type (<name> is the cell type, without a directory part), the fluid (Fluid) and the CEPAC field (CEPAC); _PRE is appended in a pre-inlet. Datasets are single precision (the triangle and inner-link lists are integers), byte-shuffled and deflate-compressed. The attributes hold dx, dt and the iteration.

<name>.<iteration>.xmf

XDMF (version 3) description of that step: all blocks with the time of the step.

<name>.xmf

All steps of <name> in the directory, with their time (seconds, or iterations for lattice-unit output). Open this file in ParaView to get a time series.

The XDMF files are rewritten at every output, so a running simulation can be inspected. ParaView reads them with its XDMF3 readers and with the legacy XDMF reader. For output of HemoCell versions that did not write XDMF files, generate them with batchPostProcess.sh.

Cell files hold the vertices of the cells a block writes: every cell is written once, by the block whose bulk contains the cell’s vertex 0, with all its vertices in vertex order (numVertex rows per cell, cells in ascending cell ID). A cell crossing a periodic boundary is written once, at the position of its vertex 0, and may therefore extend past the domain boundary. Triangles and InnerLinks index the rows of the block’s Position.

Fluid files hold the values of the block’s bulk lattice nodes as (z, y, x, component) arrays (attribute subdomainSize is (nz, ny, nx)). Every node is the centre of one cell of size dx of a regular grid whose lower corner is relativePosition (z, y, x, the first node minus dx/2), so the blocks tile the domain without overlap and every node is written once.

Note

Older versions wrote every cell from each block that held part of it (and both images of a cell crossing a periodic boundary), and wrote one extra node layer around each fluid block. Analysis scripts that removed duplicate cells or the extra layer are not needed for current output.

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: the membrane force plus the repulsion force that will be applied to the fluid in the next iteration. For cell types with a material time-scale separation > 1 this is the force from the last material update, while the individual components below are evaluated for the current shape, so they need not add up exactly.
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), as computed at the last repulsion update.
OUTPUT_INNER_LINKS	The inner-edge connectivity of the cell.
OUTPUT_CELL_ID	The unique id of the cell each vertex belongs to, as a 64-bit integer (exact; IDs grow with every periodic crossing, see Cell IDs and periodicity).
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 (kg/m3 in SI output; for the CEPAC field the transported concentration, unscaled).
OUTPUT_FORCE	Total force field acting on the fluid: the external (body) force plus the force spread from the immersed cells. Writing it leaves the lattice force unchanged, so a body force set before writeOutput() does not need to be re-applied.
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, dimensionless) field.
OUTPUT_BOUNDARY	Boundary/solid mask of the domain.
OUTPUT_CELL_DENSITY	Number density of cells mapped onto the fluid grid, one dataset CellDensity_<name> per cell type: the number of vertices nearest to each node, times the volume fraction of a vertex in SI output.

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.