Scripts within HemoCell

TODO

hemocell/cases/MakeFile

make cmakefiles

replace <case>/CmakeLists.txt with ./CmakeLists_template.txt if you want to update the build process for all cases.

make executables

compile every case

make all

synonym for make executables

make clean

remove all build directories, CMakeLists.txt and executables

hemocell/patch/patchPLB.sh

used to patch Palabos to add some features that HemoCell needs but are by default not available.

hemocell/scripts/batchPostProcess.sh

This scripts uses the *XMF.py 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/cases/<case> or hemocell/cases/<case>/tmp directory. like so:

cd hemocell/cases/<case>
../../scripts/batchPostProcess.sh

hemocell/scripts/cartesius[_intel]_env.sh

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

. ./scripts/cartesius_env.sh

hemocell/scripts/CellInfoMergeCSV.sh

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/cases/<case>/tmp/
. ./scripts/CellInfoMergeCSV.sh