Data and figure-generating scripts for: On shear Alfvén wave-induced energetic ion transport in optimized stellarators.

This archive stores data and simulations used for the paper “On shear Alfvén wave-induced energetic ion transport in optimized stellarators” by Knyazev et al., accepted for publication in Journal of Plasma Physics.

A preprint of the article is available at: https://arxiv.org/abs/2603.03118

Codes used for calculations. 

For calculations in this paper, we used:

1. `VMEC` for equilibria calculations. 

More details on VMEC can be found in https://doi.org/10.1063/1.864116 

2. `STELLGAP` for calculating the shear Alfvén continua

More details on STELLGAP can be found in https://doi.org/10.1063/1.1590316

3. `AE3D` for shear Alfvén wave calculations, with the kink term removed by setting the 
   corresponding matrix elements to zero.

More details on AE3D code can be found in https://doi.org/10.1063/1.3313818 

4. `FIRM3D` for Poincaré cross-section, loss fraction calculation, orbit classification,
   and digit accuracy measurements of weighted Birkhoff average convergence of canonical
   momentum.
Version with git commit bc65bab877d88b6b00d6d248f54e5c75d893e6ac
available at
https://github.com/ColumbiaStellaratorTheory/firm3d/tree/bc65bab877d88b6b00d6d248f54e5c75d893e6ac

More details on FIRM3D code can be found in https://arxiv.org/abs/2605.16734

Calculation results organization

Calculation results are organized based on figures in the paper, numbered as they appear in the manuscript.

Each `FIG` folder has script `run.sh` that produces the corresponding figure from the paper.

The inputs for AE3D and STELLGAP codes are described in the paper. Inputs for FIRM3D analysis are included in `./simulations_fig4_fig5`

Environment and simulation scripts

All AE3D, STELLGAP and FIRM3D data used to produce figures is available in the respective `inputs/` subfolders.

The conda environment `jpp26` used for producing the figures is in `environment/environment_full.yml` for reference. If installing, remove the firm3d reference and install it from github link:

pip install git+https://github.com/ColumbiaStellaratorTheory/firm3d@bc65bab877d88b6b00d6d248f54e5c75d893e6ac