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Rate equations or MC approaches for modelling growth

The following is a project submission for the Numerical Methods 2 unit of Master 2 CompuPhys. Documentation on the code can be found on O10-Technical-Report. Exloitations and results can be found in notebooks 001 to 004. Finally, a benchmark can be found in notebook 012.

License

This work is provided under the CC-BY-NC-SA licence.

Notes on the project

Notebooks

Jupyter notebooks can be found in the Numerical Work folder. They use the simulation implementation files to execute simulations and answer questions.

Task notebooks

  • 001-notebook-task1
  • 002-notebook-task2
  • 003-notebook-task3
  • 004-notebook-task4

Simulation related

  • 012-notebook-benchmark

Markdown

Markdown reports are available in the numerical work. They are used when no computations are required.

  • 010-Technical-Report
  • 011-writeup_better_implementation

Reports

Reports can be found in the PDF format inside the PDF reports folder. Additionally, HTML versions can be found in Numerical Work/HTML reports. Notebooks can also be found and ran directly in Numerical Work.

Markdown files can be found in HTML reports.

graphs folder are identical and contain image ressources used in mardown inside of the notebook of task 2.

Python files

Multiple python files can be found in Numerical Work.

Simulation related

  • task2and3 : Single-threaded version of the simulation used in task 2 and 3.
  • task2_parallel : Parallel version of the simulation used in task 2 and 3.
  • task4_parallel : Parallel version of the simulation used in task 4.

Other files

  • cluster : Sandbox file, code version used on the cluster. was modified multiple time.
  • video_converter : can be used to convert hdf5 data from simulation to mp4 videos.
  • test : self explanatory

Saved data format.

Saved data are stored in hdf5 files using the h5 extension.

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Python implementation of rate equation or MC approaches for modeling growth.

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