&input_parameters

! control parameters
  irun=1        	    ! 0 for initial run, any non-zero value for restart
  mstep=5000	            ! # of ion and field time steps
  msnap=10		    ! # of snapshots and restarts
  ndiag=10	  	    ! do diagnosis when mod(istep,ndiag)=0
  nonlinear=1		    ! 1: nonlinear run; 
                            ! 0: linear run
  toroidaln=1               ! must be >=1: toroidal simulation domain zeta=[0,2pi/toroidaln]
  nfilter=0                 ! 0: keep all modes; 
                            ! 1: select n-mode in setup.F90; 
                            ! 2: select n & m mode;
                            ! >2: select n & m and k_para<<k_perp 
  tstep=0.02		    ! time step size, unit=R_0/c_s (c_s^2=T_e/m_i: main ion species)
  paranl=0.0		    ! 0: no parallel nonlinearity;
                            ! 1: keep parallel nonlinearity
  track_particles=0	    ! 0: no tracking;
                            ! 1: track particles 
  ndata3D=0		    ! 0: no 3D data;
                            ! 1: write out 3D field data 
  magnetic=0		    ! 0: electrostatic; 
                            ! 1: electromagnetic
  cs_method=0               ! 0: without conservative scheme
                            ! 1: with conservative scheme(magnetic=1 and nhybrid=1)
 
! Radial Boundary Decay Controls
  BC_type=2   		! 0: NO Radial Boundary Decay 
  			! 1: Linear Radial Boundary Decay
 			! 2: Gaussian Radial Boundary Decay
  BC_nbound=10	            ! # of radial grid cells on inner boundary subjected to boundary decay. 
                            ! At least 10 points recommented for gaussian boundary.
                            ! Same number of points for fields and particle drives.

  BC_nboundR=0              ! # of radial grid cells on outer boundary subjected to boundary decay 
                            ! 0: same number of points subject to boundary condition on both sides.

! parallel magnetic perturbation
  deltabpara=0          ! 0: without delta B_para 
                        ! 1: with delta B_para (magnetic=1)
                           
  ismooth=1                 ! # of iterations of smoothing in smooth.F90
  numereq=0		    ! 0: analytic equilibrium
                            ! 1: numerical equilibrium; EFIT input
			    ! 2: VMEC input [See also: ndim]
			    ! 3: M3DC1 equilibrium geometry [See also: ndim, nzsp_sec]

  ndim=0                    ! number of toroidal modes used for 3D field structure, including the n=0 axisymmetric component
			    ! For example: ndim=3 uses the axisymmetric component plus the first 2 additional n numbers provided 
			    ! by VMEC or M3DC1 input file(s).  
                            ! ndim=0 automatically use the default value in different scenarios. 
  			    ! Defaults: M3DC1: ndim=1 (equilibrium only)
                            !           VMEC:  ndim=ndim_total (all 3D harmonics available)
 
  nzsp_sec=3              ! number of sub-sections for equilibrium island spline within one toroidal 
                            ! simulation section
  alpha_scale=1.0           ! rescale factor for equilbrium island data from M3DC1
  island=0                  ! 0: no analytic islands
                            ! 1: with analytic islands
! diagnostics and filtering specifics
  n_modes= 10 5 15 20 25 30 35 40 ! for frc case, use single n for now
  m_modes= 14 7 21 28 35 42 49 56  ! 

! field grids
  eq_flux=48                  ! equilirium reference flux surface label. Used only in iload=1 
                            ! Usually, eq_flux=mpsi/2. rho0 defined w.r.t. eq_flux
  diag_flux=48              ! diagnostic flux surface label.
  mpsi=96 		    ! # of radial grid points
  mthetamax=394	            ! # poloidal grid points (in fieldline following coordinate)
  mtoroidal=32		    ! # of toroidal grids=MPI DD, 64 needed for ITG linear dispersion
  psi0=0.02		    ! inner boundary, psi_inner/psiw
  psi1=0.88		    ! outer boundary, psi_outer/psiw
  neop=16		    ! radial grids for collision
  neot=16	            ! poloidal grids for collision (in magnetic coordiante)
  neoz=3		    ! toroidal grids. 1 or >9: normal;

! thermal (main) ion
  micell=100		    ! particle per cell for ion
  aion=1.0		    ! ion mass, unit=proton mass
  qion=1.0		    ! ion charge, unit=proton charge
  ngyroi=4		    ! N-point gyro-averaging, N=1, 4, or 8
  iload=1		    ! 0: ideal MHD; 
                            ! 1: uniform marker & MHD, 
                            ! >1: non-uniform marker & MHD
  icoll=0		    ! 0: no collisions; 
                            ! >0: collisions when mod(istep,ndiag)=0

! fast ion
  mfcell=1		    ! particle per cell for fast ion
  afast=1.0     	    ! fast ion mass, unit=proton mass
  qfast=1.0		    ! fast ion charge, unit=proton charge
  ngyrof=1		    ! N-point gyro-averaging, N=1, 4, or 8
  fload=0		    ! 0: no fast ion;
                            ! 1: uniform marker temperature;
                            ! 2: non-uniform marker
                            ! 11: slowing down distribution; uniform marker temperature

! fast electron
  mfecell=10                ! particle per cell for fast electron
  afaste=5.44618e-4         ! fast electron mass, uint=proton mass
  qfaste=-1.0               ! fast electron charge, uint=proton charge
  ngyrofe=1                 ! N-point gyro-averaging,default=1 for drift kinetic
  ncyclefe=7                ! # of fast electron subcycle
  fetrap=2                  ! 1: load all fast electrons;
                            ! 2: load trapped fast electrons
  feload=0                  ! 1: uniform marker temperature;
                            ! 2: non-uniform marker

! electron
  mecell=100		    ! particle per cell for electron
  nhybrid=2		    ! fluid-kinetic hybrid electron model, 0: no kinetic electron
  ncyclee=4		    ! # of electron subcycle
  qelectron=-1.0 	    ! electron charge, unit=proton charge
  aelectron=5.44618e-4	    ! electron mass, unit=proton mass
  eload=1		    ! 1: uniform marker temperature, 
                            ! >1: non-uniform marker
  etrap=1                   ! 1: load trapped electrons; 
                            ! 2: load all electrons
  ecoll=0		    ! 0: no collisions; 
                            ! >0: collisions when mod(istep,ndiag)=0

!Newly added parameters
  ilaplacian=0              !0: integral form of phi tilde in gk poisson eq.(Lin & Lee, PRE95)
                            !1: Pade approximation with finite difference
  eqcurrent=0   	    ! eqcurrent=0: drop curl B terms; 
                            ! eqcurrent=1: keep curl B terms
  ier = 0                   !0: no er, 1: er                           
  iupara0 = 0               !0: no toroidal rotation
                            !1: calculate from radial forcebalance (should be used with er)
                            !2: load from profile.dat (should not be used for analytic eq)
  eta=0.0                   ! Resistivity magnitude for tearing mode
                            ! 0:  no resistivity 
                            ! >0: resistivity, unit: Ohm*cm
  fieldmodel=1  	    ! Analytic eq field model: 0: s-alpha like (cyclone) model;
                            ! 1: first order (in r/R_0) model with parallel current
  bcond=0       	    ! 0: fixed zero boundary; 
                            ! 1:linear inner boundary in r 
  fielddir=0    	    ! Equilibrium magnetic field and current direction
  hypr1=0.0		    ! Parallel hyperviscosity
  hypr2=0.0E-2     	    ! Perpendicular hyperviscosity 
  antenna_on=0              ! 0: no antenna
                            ! 1: antenna with structure = cos(m(1)*theta-n(1)*zeta) 
  alcon_on=0                ! 0: do nothing
                            ! 1: write out parameters for ALCON
                            ! When running python, need: alcon.dat, equilibrium.out, profile.dat
  izonal=1                  ! zonal component solver
                            ! 0: no zonal phi
                            ! 1: general geometry zonal phi solver
                            ! 2: zonal phi solver for concentric flux surfaces
  irestore=1                ! 0: Allow temperature gradient to relax in nl runs
                            ! 1: Keep temperature gradients fixed for nl runs
!> @note
!> The parameter ipoincare is only effective
!> when 'track_particle' is set to 1.
!> if not, the poincare file wouldn't output,
!> and the particles would be loaded in the manner of poincare
  ipoincare=0               ! 0: no poincare plot
                            ! 1: poincare plot

! slowing down distribution parameters
  sd_v0=0.01!0.00299123                 !birth velocity
  sd_vc=.03!1.07*0.00299123             !critical velocity
  sd_l0=0.5                             !control for injection angle
  sd_widthInv=0                         ! inverse anisotropic distribution pitch width; 
                                        ! 0 for isotropic limit


! normalization for physical quantities
!> @note
!> The pass-in electron temperature and density is only used in analytic equilibrium cases.
!> For iload==2 or 3, these should be the on-axis values
!> For iload==1, these are the local values
  etemp0=2223               ! electron temperature normalization value, unit=ev
  eden0=0.1130e14           ! electron number density normalization value, unit=1/cm^3

! GTC Length and magnetic field are normalized to major radius and on-axis B field
!> @note
!> The pass-in major radius and on-axis magnetic field are used only in analytic and EFIT equilibria
!> (numereq==0 and 1)
  r0=83.5                   ! major radius, unit=cm
  b0=20125.40               ! on-axis magnetic field, unit=gauss
 /

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

&equilibrium_parameters

! example numerical/analytical equilibrium using variables from numereq=1 
  
psiw_analytic= 3.75e-2         ! poloidal flux at wall
ped_analytic=  3.75e-2         ! poloidal flux at separatrix

! q, zeff and er profile is parabolic: q=q1+q2*psi/psiw+q3*(psi/psiw)^2
q_analytic=   0.82  1.1 1.0  !
ze_analytic=  1.0  0.0  0.0   !
er_analytic=  0.0  0.18016647  0.0  !er(1) is mach number [rad/s]/[Cs/r0] @ psi=0. 
                             
itemp0_analytic=  1.0          ! on-axis thermal ion temperature, unit=T_e0
ftemp0_analytic=  2.0          ! on-axis fast ion temperature, unit=T_e0
fden0_analytic=   1.0e-5       ! on-axis fast ion density, unit=n_e0
fetemp0_analytic= 1.0          ! on-axis fast electron temperature, unit=T_e0
feden0_analytic=  1.0          ! on-axis fast electron density, unit=n_e0


! density and temperature profiles are hyperbolic: ne=1.0+ne1*(tanh((ne2-(psi/psiw))/ne3)-1.0)
ne_analytic=  0.205 0.30 0.4   ! Cyclone base case, R0/L_ne = 2.2 (Lin 2007), ni determined by quasi-neutrality
te_analytic=  0.415 0.18 0.4   !                    R0/L_te = 6.9 (Lin 2007)
ti_analytic=  0.415 0.18 0.4   ! 0.115 0.3384 0.4 !                    R0/L_ti = 1.1 (Lin 2007, Fig 1a)
tf_analytic=  0.0  0.0  1.0    ! fast ion temperature profile
nf_analytic=  0.0  0.0  1.0    ! fast ion density profile
tfe_analytic= 0.415 0.18 0.4   ! fast electron density profile
nfe_analytic= 0.205 0.30 0.4   ! fast electron density profile

/

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!
! GTC unit: R_0=1, Omega_proton=1, B_0=1, m_p=1, e=1.
!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!
! IMPORTANT: make sure that multiple OpenMP threads produce identical output in 
! gtc.out as with a single Openmp thread (up to 6 digits in single precision).
!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!
! repeatibility in linear runs:
! 1) Random # generator in loading is the only source for different output in gtc.out.
! 2) Particle decomposition # leads to difference in ~3 digits due to random # generator.
!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!
! Non-perturbative (full-f) simulation steps:
! 1) Initial linear run for a few bounce times with irun=0, nonlinear=0.0, iload>99
! 2) Continue linear run for a few bounce times with irun=1
! 3) Continue nonlinear run with nonlinear=1.0 and reduce tstep
! 4) If needed, continue nonlienar run with irun>9
!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!