template_inputfile.inp

nout = 1000
timestep = 1e-1


grid = "cor_islanddivertor_260_4_1024_6.0_1.0_0.8_0.4_0.1_0.875_0.0_0.0_0.0.fci.grid.nc"


[mesh]
symmetricGlobalX = true

extrapolate_y = false   # Extrapolate metrics into Y boundary cells?

[mesh:paralleltransform]
type = fci

[input]
error_on_unused_options=false

[restart_files]
init_missing = true # initialize missing variables on restart?

##################################################
# derivative methods

[ddx]

first = C2
second = C2
upwind = W3

[ddy]

first = C2
second = C2
upwind = W3

[ddz]

first = C2
second = C2
upwind = W3

###################################################
# Time-integration solver

[solver]


# Note: If evolving neutrals, need preconditioning
type = cvode
#use_precon = true

atol = 1.0e-12  # absolute tolerance
rtol = 1.0e-5   # relative tolerance
mxstep = 1000000  # Maximum internal steps per output

cvode_max_order = 2
cvode_stability_limit_detection = true


########################################################################################

[phiSolver]

type   = petsc  # Needed if Boussinesq = false

ksptype = gmres # Linear iterative method

pctype = hypre # Preconditioner. Direct "lu" or "ilu"; iterative "jacobi", "sor"

atol=1e-12
rtol = 1e-5
# Set package to perform factorisation for direct solves
# "petsc" built-in solver only serial
# "superlu", "superlu_dist", "mumps", "cusparse"
factor_package = superlu_dist

inner_boundary_flags = 2
outer_boundary_flags = 16

all_terms = false
nonuniform = true   # NOTE: Necessary to avoid numerical instability

#########################################################################################

[aparSolver]
type = petsc

rtol=1e-5
atol=1e-12

# ksptype = gmres   # Linear iterative method

# pctype  = hypre   # Preconditioner. Direct "lu" or "ilu"; iterative "jacobi", "sor"

# # Set package to perform factorisation for direct solves
# # "petsc" built-in solver only serial
# # "superlu", "superlu_dist", "mumps", "cusparse"
# factor_package = superlu_dist


inner_boundary_flags = 2
outer_boundary_flags = 2

# all_terms = true
# nonuniform = true

# general settings for the model
[input]

transform_from_field_aligned=False


[Hermes]

electromagnetic = true
j_pol_pi = false
j_pol_simplified = true
boussinesq = true
FiniteElMass = true

evolve_ne = true
evolve_nvi = true
evolve_te = true
evolve_ti = true
evolve_vort = true
evolve_vepsi = true

TE_Ne = true
TE_NVi = true
TE_Pe = true
TE_Pi = true
TE_Vort = true
TE_VePsi = true


verbose = true
output_ddt = false

Tnorm = 20
Nnorm = 1e19
Bnorm = 1.0
AA = 2.0


[Transportcoefficients]


anomalous_D = 0.1
anomalous_nu = 0.1
anomalous_chi = 0.1

hyper_D = 1e-4
hyper_nu = 1e-4
hyper_chi = 1e-4

num_D = 1e-2
num_nu = 1e-2
num_chi = 1e-10

[Numerics]


use_Div_n_bxGrad_f_B_XPPM = true
use_bracket = true

ne_bndry_flux = false
pe_bndry_flux = false
vort_bndry_flux = false

flux_limit_alpha = -1
kappa_limit_alpha = -1
eta_limit_alpha = -1

resistivity_multiply = 1.0
electron_weight = 1.0
scale_ExB = 1.0


[Sheath]

sheath_model = 0
sheath_gamma_e = 6.0
sheath_gamma_i = 3.5

parallel_sheaths = true
sheath_allow_supersonic = true


########################################################################################
########################################################################################
########################################################################################
########################################################################################
########################################################################################

[all]

bndry_all = neumann_o2
bndry_xin = neumann_o2
bndry_xout =neumann_o2
bndry_par_all = parallel_neumann_o2

########################################################################################


[Ne] # Electron density
bndry_xin = neumann
bndry_xout =neumann
bndry_par = parallel_neumann_o1
scale = 1
function = 2.0 - x
source = 3e2*gauss(x, 0.24)


#Switches for terms

Ne_ExB = true
Ne_mag = true
Ne_parflow = true
Ne_collision = false
Ne_anomalous = true
Ne_sources = true
Ne_hyper = false
Ne_numdiff = true


########################################################################################


[NVi]
bndry_xin = neumann
bndry_xout =neumann
bndry_par = parallel_neumann_o1
scale = 1
function = 1e-2*sin(6*pi*x)*sin(12*z)*gauss(x,0.4)

#Switches for terms

NVi_ExB = true
NVi_mag = true
NVi_parflow = true
NVi_parpressure = true
NVi_parviscos = false
NVi_collision = false
NVi_anomalous = true
NVi_hyper = false
NVi_numdiff = true


########################################################################################


[Pe]  # Electron pressure

bndry_xin = neumann
bndry_xout =neumann
bndry_par_xin = parallel_neumann_o1
scale = 1
function = Ne:function + (2.0-x)*Ne:function
source = 5.0*Ne:source


#Switches for terms

Pe_ExB = true
Pe_mag = true
Pe_parflow = true
Pe_conduction = true
Pe_ohmic = true
Pe_thermalforce = true
Pe_thermalcurrent = true
Pe_collision = false
Pe_anomalous = true
Pe_sources = true
Pe_energyexchange = true
Pe_hyper = false
Pe_numdiff = false


####################################################################################


[Pi]
bndry_xin = neumann
bndry_xout =neumann
bndry_par = parallel_neumann_o1
scale = 1
function = Pe:function
source = Pe:source


#Switches for terms

Pi_ExB = true
Pi_mag = true
Pi_parflow = true
Pi_conduction = true
Pi_diamagenergyexchange = true
Pi_parviscousheat = true
Pi_resistivedrift = false
Pi_perpviscous = false
Pi_sources = true
Pi_hyper =false
Pi_numdiff = false
Pi_anomalous = true
Pi_energyexchange = true

####################################################################################


[Vort]
bndry_xin = neumann
bndry_xout =neumann
bndry_par = parallel_neumann_o1
scale=1.0
function=1e-3*sin(14*pi*x)*sin(8*z)*gauss(x,0.4)


#Switches for terms

Vort_mag = true
Vort_parcurrent = true
Vort_polarcurrent = true
Vort_collision = false
Vort_parviscous = false
Vort_anomalous = true
Vort_hyper = false
Vort_numdiff = true

########################################################################################


[VePsi] # Ve + 0.5*beta_e*mi_me*psi
bndry_xin = neumann
bndry_xout =neumann
bndry_par = parallel_neumann_o1
scale = 1
function = 1e-1*sin(14*pi*x)*sin(8*z)*gauss(x,0.4)

#Switches for terms

VePsi_parefield = true
VePsi_parpressure = true
VePsi_partemp = true
VePsi_parcurrent = true
VePsi_ExB = true
VePsi_parflow = true
VePsi_hyper = true
VePsi_numdiff = true