How to run JOREK with neoclassical coefficient profiles

1. Calculate neoclassical coefficient profiles

1.1. Obtain JOREK data for calculating the coefficients

Running the JOREK equilibrium with neo=.false. produces the following files:

  • qprofile.dat, calculated in the qprofile subroutine, contains the normalized poloidal flux $\psi_{N,\mathrm{pol}}$ and the safety factor $q(\psi_N)$.
  • T_rho_profiles.dat, calculated in the equilibrium subroutine, contains $T(\psi_N)$ and $\rho(\psi_N)$ in JOREK units.

The neoclassical-coefficient calculation requires:

  • the normalized poloidal flux $\psi_N$;
  • the safety factor $q(\psi_N)$;
  • the electron temperature $T_e(\psi_N)$;
  • the electron density $N_e(\psi_N)$.

In JOREK, the poloidal flux and corresponding safety-factor profile are calculated by the qprofile subroutine, which is called from equilibrium and writes qprofile.dat. The $\psi$-dependent temperature and density profiles must have the same number of points as $q(\psi_N)$. The equilibrium subroutine writes these profiles to the ASCII file T_rho_profiles.dat.

For cleaner profiles, remove all points outside the separatrix from both qprofile.dat and T_rho_profiles.dat.

1.2. Run neoclassical_program

The program and its dedicated Makefile are located in util/neoclass_program/. This utility is not built by JOREK's top-level Makefile.

Prepare the input file

The namelist input for neoclassical_program must specify:

  • the central density in units of $10^{20}\,\mathrm{m}^{-3}$;
  • the magnetic field $B_t$ in tesla;
  • the major radius $R_0$ and minor radius $a_\mathrm{min}$;
  • the files containing the safety-factor and temperature-density profiles.

For example, for ITER-like parameters:

&in1
  central_density  = 1.0                 ! Units: 10^20 m^-3
  Bt               = 5.3d0               ! Magnetic field at the axis
  R0               = 6.19476d0           ! Major radius at the axis
  amin             = 2.d0                ! Minor radius of the equilibrium
  qprofile_file    = 'qprofile_ITER2.dat'
  T_Ne_profile_file = 'Te_ne_profiles_ITER.dat'
/

The utility directory contains the example files qprofile_ITER2.dat and Te_ne_profiles_ITER.dat. For a new JOREK case, replace these names with the paths to the corresponding qprofile.dat and T_rho_profiles.dat files, or copy those files into the utility's working directory. Both profile files must contain the same number of lines.

Compile neoclassical_program

The program requires BLAS. Its Makefile currently defaults to the Intel Fortran compiler and Intel MKL, using MKLROOT; adapt FC, BLAS_HOME, and BLASLIB if your system uses a different compiler or BLAS implementation. Compile from the utility directory:

cd util/neoclass_program
make neoclassical_program

Run neoclassical_program 

./neoclassical_program < input_neo_ITER

The program generates neoclass_coef.dat, which contains the normalized poloidal flux $\psi_N$, the neoclassical friction coefficient $\mu_{i,\mathrm{neo}}$, and the neoclassical heat-flux coefficient $k_i$ in JOREK units.

1.3. Use the coefficient profiles in JOREK

Add the following parameters to the JOREK input file:

neo      = .t.
neo_file = 'neoclass_coef.dat'

2. Alternative: constant neoclassical coefficients

Instead of using profiles, constant values can be used for $\mu_{i,\mathrm{neo}}$ and $k_i$. In this case, set typical coefficients in the JOREK input file:

neo           = .t.
aki_neo_const = -1.
amu_neo_const =  1.e-5