Addition of Stellarator to OPENPOPCON

.gitignore

@@ -2,4 +2,8 @@
 .conda/*
 __*
 .vscode
-outputs/*
+outputs/*
+.ipynb_checkpoints/
+**/.ipynb_checkpoints/
+.DS_Store
+**/.DS_Store

environment.yml

@@ -8,4 +8,5 @@ dependencies:
 - scipy
 - matplotlib
 - numba
-- pyyaml
+- pyyaml
+- netcdf4  # For VMEC file reading

resources/examples/MANTA/POPCON_input_example.yaml

@@ -5,6 +5,8 @@
 
 name: "MANTA"
 
+device_type: "tokamak"
+
 R: 4.55 # major radius in meters
 a: 1.2 # minor radius in meters
 kappa: 1.4 # elongation

resources/examples/Stellarator/Stellarator_example.yaml

@@ -0,0 +1,111 @@
+# OpenPOPCON input file
+#-----------------------------------------------------------------------
+# Machine Paramters
+#-----------------------------------------------------------------------
+
+name: "Stellarator"
+
+device_type: "stellarator"
+
+vmecfile: /path/to/wout_stellarator.nc
+# If vmecfile is given, iota_23 will be extracted automatically.
+
+R: 4.55 # major radius in meters
+a: 1.2 # minor radius in meters
+kappa: 1.4 # elongation
+delta: -0.5 # triangularity
+
+
+iota_23: 0.7 # iota 2/3 value (only for stellarators) 
+# should be defined as the value of the rotational transform at 2/3 of the minor radius (normalized radius)
+
+
+#----------------------
+# I_P and q* can be calculated from each other. Pick one to specify:
+I_P: 10. # plasma current in MA
+# or
+# qstar: 2.5
+#----------------------
+
+#----------------------
+# B_0 and B_coil can be calculated from each other. Pick one to specify:
+B_0: 11.0 # on-axis magnetic field in Tesla
+# or
+# B_coil: 24.0 # magnetic field at the coil in Tesla
+# wall_thickness: 1.1 # wall thickness between magnet and separatrix in meters
+#----------------------
+
+#----------------------
+tipeak_over_tepeak: 0.9894 # ratio of ion to electron temperature at peak
+fuel: 2 # 1 for D-D, 2 for D-T, 3 for D-He3
+#----------------------
+
+#----------------------
+# Impurity Fractions
+# In order, the fractions of:
+# 0 He ash
+# 1 Ne
+# 2 Ar
+# 3 Kr
+# 4 Xe
+# 5 W
+# Impfracs and Z_eff can be calculated from each other. If you specify
+# Z_eff, the impurity fraction for the specified impurity will be overwritten.
+impurityfractions: [0.025, 0., 0., 0.00075, 0., 0.]
+Zeff_target: 2.26 # average effective charge of plasma
+impurity: 3 # 0 for He, 1 for Ne, 2 for Ar, 3 for Kr, 4 for Xe, 5 for W
+#----------------------
+
+#----------------------
+scalinglaw: "ISS04" # Name of tau_E scaling law as defined in scaling_laws.yaml
+H_fac: 0.79 # Factor by which to multiply the scaling law
+#----------------------
+
+#----------------------
+# Profiles
+# If you specify a filename, the profiles will be read from that file and normalized.
+# Otherwise, the normalized profiles will be parabolic of the form
+# f(r) = (1 - offset)*(1 - r**alpha1)**alpha2 + offset
+# j profile comes from the equilibrium, the others come from the profs file.
+gfilename: "gMANTA"
+profsfilename: "profsMANTA.csv"
+
+# Stellarator-optimized profile parameters (uncomment to use)
+j_alpha1: 2.0
+j_alpha2: 2.5
+j_offset: 0.0
+
+ne_alpha1: 2.0
+ne_alpha2: 1.8
+ne_offset: 0.05
+
+ni_alpha1: 2.0
+ni_alpha2: 1.8
+ni_offset: 0.05
+
+Ti_alpha1: 2.0
+Ti_alpha2: 2.0
+Ti_offset: 0.1
+
+Te_alpha1: 2.0
+Te_alpha2: 2.0
+Te_offset: 0.1
+#----------------------
+
+
+#----------------------
+# Algorithm settings
+#----------------------
+Nn: 50 # resolution of densities
+NTi: 50 # resolution of ion temperatures
+nr: 200 # number of radial grid points
+nmax_frac: 1.0 # maximum electron density as a fraction of the Greenwald density
+nmin_frac: 0.3 # minimum electron density as a fraction of the Greenwald density
+Tmax_keV: 11. # maximum volume-averaged temperature in keV
+Tmin_keV: 6. # minimum volume-averaged temperature in keV
+resistivity_model: "Jardin" # Jardin, Paz-Soldan or maximum (suggested: Jardin)
+maxit: 1000 # maximum number of iterations
+accel: 1.5 # acceleration factor
+err: 1e-6 # error tolerance
+verbosity: 2 # 0 for no output, 1 for minimal output, 2 for verbose output
+parallel: True