Other topics

Loading a cell from an stl file

Usually a cell is defined to be generated mathematically, this means that the vertex locations are gathered from describing equations. The place where the method for generating the cell is defined is in the hemocell.addCellType<>() function.

To load a celltype from stl you have to change the second argument to MESH_FROM_STL. This means that HemoCell will look at the stl file located at the place specified in the CELL.xml file. The specification of this file should be in the <hemocell><MaterialModel><StlFile> tag.

Note

The stl file should only contain triangles. The stl file reader that is used by HemoCell is the one already present in Palabos

• This reader has no capabilities to triangulate squares and will crash on stl files that do not follow this rule.
• Furthermore the STL file needs to be in ASCII format. Nowadays most readers save in Binary format by default.

Running a pure fluid flow (without cells)

With HemoCell it is possible to run a pure fluid flow, meaning that no cells are present within the domain. This is actually the same as just running a fluid simulation with palabos. The simplest way to remove all the cells is to set the number of cells in the CELL.pos files to zero (first line). Or to remove the addCellType and all subsequent functions that request that specific celltype (such as setOutputs) from the case.cpp file.

However this still leaves a small overhead as the function for the material model are still called (although little work is done inside them as there are no cells). This can be circumvented by replacing

hemocell.iterate()

With

hemocell.lattice->collideAndStream(); hemocell.iter++;

within the case.cpp file

Saving only the CSV output and not the HDF5 output

This is possible with the extra <sim><tcsv> parameter which is already added in the Pipeflow case. This parameter then controls a seperate call to writeCellInfo_CSV that writes only CSV output. To reduce the HDF5 output you can simply increate <sim><tmeas> in the config file.

Note

Don’t forget to include the right header:

#include "writeCellInfoCSV.h"

HemoCell related papers

References

[1]	Cellular Level In-silico Modeling of Blood Rheology with An Improved Material Model for Red Blood Cells, Fronties in physiology, 8, 563. Závodszky, G., van Rooij, B., Azizi, V., Alowayyed, S., & Hoekstra, A.

[2]	Numerical Investigation of the Effects of Red Blood Cell Cytoplasmic Viscosity Contrasts on Single Cell and Bulk Transport Behaviour. Applied Sciences 8. M de Haan, G Závodszky, V Azizi, A Hoekstra.

[3]	Load balancing of parallel cell-based blood flow simulations. Journal of computational science 24, 1-7. S Alowayyed, G Závodszky, V Azizi & AG Hoekstra.