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 build dependency module setup on various HPC systems. For instance, contains the module settings to compile on the Snellius system of SURF. These scripts 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/

Note: this script is depracated, HemoCell now does this automatically on saving.

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