One shearing cell

The example in examples/oneCellShear presents a single red blood cell (RBC) subjected to a shearing flow. The example provides a validation case for the different material models used in HemoCell.

A single RBC is initialised in a fully periodic domain, i.e. periodicity is enabled for all boundaries. The domain is then subjected to a shearing flow in the x-direction. To achieve this flow field, the top and bottom surfaces are subjected to velocity boundary conditions in opposing directions. The largest diameter achieved by the RBC is reported and can be compared with respect to experimental data.

After compilation, the example can be run using single core as:

# run the simulation from the `examples/oneCellShear` directory
mpirun -n 1 ./oneCellShear config.xml

# generate Paraview compatible output files
../../scripts/batchPostProcess.sh

The outcome files are generated in tmp/, where the flow field and particle fields can be visualised separately by respectively viewing the tmp/Fluid.*.xmf and tmp/RBC.*.xmf files.

A single red blood cell subjected to a shearing flow in x-direction. The colours and glyps indicate the flow velocity and direction. The effect of the shearing flow becomes visible in the deformations of the RBC.

A gnuplot script is provided as well to visualise the largest diameter of the cell over the iterations, which can be invoked through

gnuplot shear.gpl

Tank treading

A simple variation of the single shearing RBC, is to consider the “tank treading” case. This considers a problem where the RBC is rotated in the domain and can be achieved by changing the loaded RBC properties by updating "RBC" used in the oneCellShear.cpp example to "RBC_tt".

A single red blood cell subjected to a shearing flow in x-direction in the “tank treading” configuration. The colours and glyps indicate the flow velocity and direction. The cell now “rotates” along with the shearing flow resulting in different deformations.

Configuration

The imposed velocity is derived from the shear rate provided in the configuration file config.xml, where the shear rate can be set manually by updating the <domain><shearrate> entry. Note, this value specifies the shear rate in 1/s.

Rendering

An example rendering pipeline with Blender is illustrated in the hemocell/scripts/visualization/render_oneCellShear.py script, for more information see Rendering with Blender.

An example rendering of the RBC using Blender.