Examples

This directory contains example simulations using hemocell. Each directory represents a separate case study.

Compilation

When compiling hemocell without providing a specific compilation target, all examples will be compiled. Each example registers itself with a CMakeLists.txt file, as described in the next section. To compile an individual, specific example, the directory name can be passed as a compile target to CMake. To compile an example, run the following code from within the hemocell/build/ directory and replace $example by the desired example's directory name.

cmake --build . --parallel $(nproc) --target "$example"

Adding examples

To add example case $new_example:

• Copy the template directory: cp -r examples/template examples/$new_example.
• Add the example directory to examples/CMakeLists.txt by appending a line containing add_subdirectory("$new_example").
• Include your code that defines the main in $new_example/$new_example.cpp. This file is automatically included for compilation by the template CMakeLists.txt. If you would like to compile additional *.cpp or *.h files, make sure to register them within $new_example/CMakeLists.txt.
• Ensure the right variant of the available hemocell libraries is linked against. By default the standard library is used, i.e. libhemocell.a. However, when requiring specific compilation features, such as interior viscosity, solidification mechanics, or parmetis, the corresponding library needs to be selected. If this applies, change the last argument ${PROJECT_NAME} in following line target_link_libraries(${EXEC_NAME} ${PROJECT_NAME}) to one of the following
  • ${PROJECT_NAME}_interior_viscosity
  • ${PROJECT_NAME}_solidify_mechanics
  • ${PROJECT_NAME}_parmetis
• Build hemocell as usual or provide --target "$new_example$" to only compile the newly added example.

Cell parameters

Example properties for red blood cells (RBC), white blood cells (WBC) and platelets (PLT) are given in RBC_template.xml, WBC_template, and PLT_template.xml respectively. These can be used as initial starting point to define the properties of these cells. Alternatively, you can consider the RBC.xml, WBC.xml, or PLT.xml files that are present in most examples herein.