Processing Tools for HemeLB Simulations

<p>This repository contains the pre-processing and post-processing tools used in the simulations described in the referenced paper.</p> <p><br></p> <p>Here <em>FiveExit</em> and <em>ProfundaFemoris2</em> refer to the five-outlets model and the <em>profunda femoris</em> model described in the paper, respectively.</p> <p><br></p> <p>The simulation cases studied are listed in the file <strong>experiments.csv</strong> in the corresponding sub-folders. For example, <strong>FiveExit_coarse</strong> refers to the simulations using the coarse grid and the five-outlets model.</p> <p><br></p> <p>The simulations described in the paper were performed using <a href="https://github.com/hemelb-codes/HemePure" target="_blank">HemePure</a>, a HemeLB version with improved memory, compilation and scaling. The input files for these simulations were generated by the Python script <strong>writeInput.py</strong>. This script imports <strong>MyModules/InputOutput.py</strong> and reads <strong>experiments.csv</strong> and <strong>input_VfWKf.xml</strong> in the corresponding sub-folders, where the constant parameters for each simulation domain are provided in <strong>const_param.csv</strong>. To use this script, execute the command "python writeInput.py" with Python of version 3.6 or above.</p> <p><br></p> <p>The outputs of HemeLB were first processed using <strong>paraviewPreprocess.sh</strong> to obtain human-readable outputs. These outputs were analysed using <strong>verification.py</strong>. The figures in the paper and its supplementary figures were generated using <strong>analysis.py</strong>.</p>