Helper scripts

A number of helper scripts for working with HemoCell.


HemoCell is build on top of Palabos and has added a number of additional features to the source of Palabos. These additional features are contained as a patch file in hemocell/patch/palabos.patch which is applied by the hemocell/patch/ script.

The script can be evaluated from the hemocell/patch directory as



This scripts uses the * files to generate all necessary xmf-files so that the output of a job can be read into ParaView and others. This script should be run within the hemocell/examples/<case> or hemocell/examples/<case>/tmp directory. For instance:

cd hemocell/examples/<case>


These files contain the corresponding build dependencies on the Cartesius system of SurfSara. They should be sourced instead of executed:

. ./scripts/


This script merges the CSV output from multiple processors into a single one in the current directory. Use it in the tmp directory like this:

cd hemocell/examples/<case>/tmp/
. ./scripts/

This script converts generated *.xmf particle files (RBC, PLT, etc.) to the X3D format for rendering purposes, e.g. using Blender. The script creates a x3d directory in the output directory of an example case and populates this with the *.x3d files. The script is used as follows

usage: [-h] [--view-size width height]
                             [--smooth SMOOTH]
                             path [path ...]

positional arguments:
  path                  Directories containing XMF output files to
                        convert to X3D scenes

optional arguments:
  -h, --help            show this help message and exit
  --view-size width height
                        Set the render view-size in Paraview
  --smooth SMOOTH       Number of mesh smoothing iterations