Generate an input file from equilibrium and profiles

Here a step-by-step guide on how to generate an input file for any gyrokinetic codes supported in pyrokinetics, starting from equilibrium and profile files.

Let’s first import pyrokinetics and define our equilibrium and input files.

>>> from pyrokinetics import Pyro, template_dir
>>> eq_file = template_dir / "test.geqdsk"
>>> kinetics_file = template_dir / "jetto.jsp"
>>> gk_file = template_dir / "input.cgyro"

The equilibrium file test.geqdsk and the kinetics file jetto.jsp are stored in the template folder and used here as an example. The gyrokinetic file input.cgyro is our input file template where we set all the extra flags we need. The input parameters related to the geometry and species will be added to this template by pyrokinetics. We now load these files into pyrokinetics:

>>> pyro = Pyro(
     eq_file=eq_file,
     kinetics_file=kinetics_file,
     kinetics_type="JETTO",
     kinetics_kwargs={"time": 550},
     gk_file=gk_file,
 )

During initialization, Pyro calls read_equilibrium from the class Equilibrium and initializes the class Kinetics. The global equilibrium and profiles are now stored in pyro. Let’s suppose we want to generate an input file for a local gyrokinetic simulation at \(\Psi_n = 0.5\). This requires loading the local geometry at the chosen surface, which can be done by simply calling the load_local method:

>>> pyro.load_local(psi_n=0.5, local_geometry="Miller")

Here we have used the Miller parametrization of the local surface. Other parametrizations are possible in pyrokinetics. See the output of pyro.supported_local_geometries. Before generating an input file, we need to specify gk_code:

>>> pyro.gk_code = "CGYRO"

Note that gk_code can be any code supported in pyrokinetics, which can be found in pyro.supported_gk_inputs. We are now ready to write our input file:

>>> pyro.write_gk_file(file_name="test_jetto.cgyro")

Alternatively, gk_code can be pass as keyword argument to write_gk_file,

>>> pyro.write_gk_file(file_name="test_jetto.cgyro", gk_code="CGYRO")