Fluid and kinetic studies of tokamak disruptions using Bayesian optimization

The codes and the data in this directory corresponds to the code and results used in the paper [I. Ekmark et al (2024) J. Plasma Phys., Fluid and kinetic studies of tokamak disruptions using Bayesian optimization, http://arxiv.org/abs/2402.05843]. References to figures below refer to this publication. 

The optimizations have been performed using the Python package by Fernando Nogueira [https://github.com/bayesian-optimization/BayesianOptimization] and the simulations are performed using the disruptions simulation simulation tool DREAM [https://github.com/chalmersplasmatheory/DREAM, git hash: 0d786e859f6228185ef68b6b3639747e8d96172d], for more information on the latter code visit https://ft.nephy.chalmers.se/dream/.

The codes:
 - BayesianOptimization.py: Runs the optimization, first in fluid and then in isotropic mode. For activated simulations, use the flag "-A".
     - BlackBox.py: Contains the functions that are run in the optimizations and sets up the simulations.
     - utils.py: Contains the settings for the simulations as well as some other functions needed in BlackBox.py
     - ITER.py: Contains all the ITER specific settings.
     - Exceptions.py: Contains exceptions needed during the simulations. 
     - CostFunction.py: Contains the functions used for evaluating the cost function value for specified values of the representative runaway current, final Ohmic current, current quench time and transported heat fraction.
 - RunCases.py: Sets up simulations for the cases of table 1 in the paper, as well as for all the optima found.

The data:
 - Optimization results:
 
    - Data/OptimizationResults/optresult_fluid.json: Contains the optimization data for the non-activated case using the fluid model. Used to produce figure 1.a. 
    - Data/OptimizationResults/optresult_isotropic.json: Contains the optimization data for the non-activated case using the isotropic model. Used to produce figure 1.b. 
    - Data/OptimizationResults/optresult_fluid_activated.json: Contains the optimization data for the activated case using the fluid model. Used to produce figure 5.a.
    - Data/OptimizationResults/optresult_isotropic_activated.json: Contains the optimization data for the activated case using the isotropic model. Used to produce figure 5.b.
    
    - Data/OptimizationResults/components_fluid.json: Contains the cost function components for each sample from the optimization of the non-activated case using the fluid model. Used to produce figure 2.a. 
    - Data/OptimizationResults/components_isotropic.json: Contains the cost function components for each sample from the optimization of the non-activated case using the isotropic model. Used to produce figure 2.b. 
    - Data/OptimizationResults/components_fluid_activated.json: Contains the cost function components for each sample from the optimization of the activated case using the fluid model. Used to produce figure 6.a.
    - Data/OptimizationResults/components_isotropic_activated.json: Contains the cost function components for each sample from the optimization of the activated case using the isotropic model. Used to produce figure 6.b.
    
 - Cases:
    - Data/Cases/nonActivatedOpts/fluidOpt/: Contains outputfiles for fluid and isotropic simulations of the optimal case found for the non-activated scenario using the fluid model.
    - Data/Cases/nonActivatedOpts/isoOpt/: Contains outputfiles for fluid and isotropic simulations of the optimal case found for the non-activated scenario using the isotropic model.
    - Data/Cases/activatedOpts/fluidOpt/: Contains outputfiles for fluid and isotropic simulations of the optimal case found for the activated scenario using the fluid model.
    - Data/Cases/activatedOpts/isoOpt/: Contains outputfiles for fluid and isotropic simulations of the optimal case found for the activated scenario using the isotropic model.
    - Data/Cases/[circle, cross, square, triangle]: Contains outputfiles for fluid and isotropic simulations corresponding to the cases presented in table 1.