The femtoscope software was written as part of Hugo Lévy's PhD thesis (2021-2024). This Python code can be used to investigate different models of modified gravity within complex geometries on unbounded domains.

Installation from YAML

YAML (stands for YAML Ain't Markup Language) is a serialization language which is often used as a format for configuration files. Anaconda allows the creation of an environment file (with .yml extension) in order to share with others.

>> conda env export --name femtoscope > femtoscope.yml

This will create femtoscope.yml at current location. This file can then be used by another Anaconda user to re-create the same environment. The steps to follow (from official conda online documentation) are:

1. Create the environment

   >> conda env create -f femtoscope.yml

2. Activate the new environment

   >> conda activate femtoscope

3. Verify that the new environment was installed correctly

   >> conda env list

   and make sure femtoscope appears in the list. This process is likely to take several tens of minutes.

note The project uses Python >= 3.9

Main dependencies

• Python >= 3.9
• meshio == 4.4.6 (read & write mesh files)
• numpy < 2 (sfepy is not yet compatible with numpy 2.x)
• pandas >= 1.5.3
• pyevtk (creation of .vtk files)
• pyvista (visualization of FEM results)
• scipy
• sfepy >= 2024.3 (FEM engine)
• pdoc >= 14.5.1 (patch against polyfill.io malicious CDN)
• gmsh == 4.11.1 (some features of femtoscope are broken in newer versions)

Tree structure

├───data		# I/O files
│   ├───mesh
│   │   └───geo
│   ├───model
│   ├───result
│   └───tmp
│
├───doc
│
├───femtoscope
│   ├───core	# weak form representation & solvers
│   ├───display
│   ├───inout	# mesh & VTK generation
│   ├───misc
│   ├───physics	# Poisson & Chameleon classes	
│   ├───tests	# unit & integration tests
│
├───images
│
├───script		# Examples
│
└───tutorials	# hands-on notebooks

Citing

If you would like to cite femtoscope in a paper or presentation, please use the following reference:

@article{hlevy:femtoscope,
	doi = {10.1103/PhysRevD.106.124021},
	url = {https://link.aps.org/doi/10.1103/PhysRevD.106.124021},
	author = {Lévy, Hugo and Bergé, Joël and Uzan, Jean-Philippe},
	title = {Solving nonlinear Klein-Gordon equations on unbounded domains via
	the Finite Element Method},
	month = {09},
	year = {2022}
}

Generate documentation

The documentation is generated using pdoc by running the Python script "generate_documentation.py" located in the "script" directory.