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sfincs_interface.fpp
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module sfincs_interface
implicit none
public :: get_neo_from_sfincs
private
# ifdef USE_SFINCS
integer :: nproc_sfincs
integer :: irad_min, irad_max
real :: Er_window
logical :: includeXDotTerm
logical :: includeElectricFieldTermInXiDot
! logical :: includeRadialExBDrive
integer :: magneticDriftScheme
logical :: includePhi1
logical :: includePhi1InKineticEquation
! logical :: includePhi1InCollisionOperator
integer :: geometryScheme
integer :: VMECRadialOption
integer :: coordinateSystem
integer :: inputRadialCoordinate
integer :: inputRadialCoordinateForGradients
character (200) :: equilibriumFile
real :: aHat, psiAHat, Delta
real :: nu_n, dPhiHatdrN
integer :: nxi, nx, ntheta, nzeta
logical :: calculate_radial_electric_field
logical :: read_sfincs_output_from_file
logical :: sfincs_finished = .true.
real, dimension (:), allocatable :: fprim_local, tprim_local
# endif
contains
subroutine get_neo_from_sfincs (nradii, drho, f_neoclassical, phi_neoclassical, &
dfneo_dalpha, dphineo_dalpha)
# ifdef USE_SFINCS
use mp, only: proc0, iproc
use mp, only: comm_split, comm_free
use stella_geometry, only: geo_surf
use species, only: spec, nspec
# endif
use mp, only: mp_abort
use zgrid, only: nzgrid
implicit none
integer, intent (in) :: nradii
real, intent (in) :: drho
real, dimension (:,-nzgrid:,:,:,:,-nradii/2:), intent (out) :: f_neoclassical
real, dimension (:,-nzgrid:,-nradii/2:), intent (out) :: phi_neoclassical
real, dimension (:,-nzgrid:,:,:,:), intent (out) :: dfneo_dalpha
real, dimension (:,-nzgrid:), intent (out) :: dphineo_dalpha
# ifdef USE_SFINCS
integer :: sfincs_comm
integer :: color, ierr
integer :: irad
real :: dPhiHatdrN_best_guess
logical :: Er_converged
integer :: nsfincs_calls
if (.not.allocated(fprim_local)) allocate (fprim_local(nspec))
if (.not.allocated(tprim_local)) allocate (tprim_local(nspec))
if (proc0) call read_sfincs_parameters (nradii)
call broadcast_sfincs_parameters
if (iproc < nproc_sfincs) then
color = 0
else
color = 1
end if
call comm_split (color, sfincs_comm, ierr)
if (iproc < nproc_sfincs) then
do irad = irad_min, irad_max
! get local values of -dlog(ns)/drho and -dlog(Ts)/drho
! using dlog(n)/drho = dlog(n0)/drho + delrho*d/drho(dlog(n)/drho)
fprim_local = 1.0/geo_surf%drhotordrho*(spec%fprim &
+ irad*drho*(spec%fprim**2-spec%d2ndr2)/geo_surf%drhotordrho)
tprim_local = 1.0/geo_surf%drhotordrho*(spec%tprim &
+ irad*drho*(spec%tprim**2-spec%d2Tdr2)/geo_surf%drhotordrho)
! fprim_local = 1.0/geo_surf%drhotordrho*(spec%fprim - irad*drho*spec%d2ndr2)
! tprim_local = 1.0/geo_surf%drhotordrho*(spec%tprim - irad*drho*spec%d2Tdr2)
if (calculate_radial_electric_field) then
! get best guess at radial electric field
! using force balance with radial pressure gradient
if (dPhiHatdrN > -9999.0) then
dPhiHatdrN_best_guess = dPhiHatdrN
else
dPhiHatdrN_best_guess = fprim_local(1)+tprim_local(1)
end if
call iterate_sfincs_until_electric_field_converged (sfincs_comm, &
irad, drho, irad_max, dPhiHatdrN_best_guess, &
Er_converged, nsfincs_calls)
if (proc0) then
write (*,*)
write (*,*) 'At irad= ', irad, 'Er_converged= ', Er_converged, &
'nsfincs_calls_required= ', nsfincs_calls, 'dPhiHatdrN= ', dPhiHatdrN
write (*,*)
end if
! write_and_finish_sfincs manipulates sfincs output
! to get the neoclassical distribution function and potential
! on the stella (zed,alpha,vpa,mu) grid; it then
! deallocates sfincs arrays, etc. to make it ready
! for running again if need be
call write_and_finish_sfincs (f_neoclassical(:,:,:,:,:,irad), &
phi_neoclassical(:,:,irad), dfneo_dalpha, dphineo_dalpha, irad)
else
! init_and_run_sfincs initializes sfincs,
! including passing geometry info if necessary;
! and runs sfincs (if requested)
call init_and_run_sfincs (sfincs_comm, irad, drho, irad_max)
! write_and_finish_sfincs manipulates sfincs output
! to get the neoclassical distribution function and potential
! on the stella (zed,alpha,vpa,mu) grid; it then
! deallocates sfincs arrays, etc. to make it ready
! for running again if need be
call write_and_finish_sfincs (f_neoclassical(:,:,:,:,:,irad), &
phi_neoclassical(:,:,irad), dfneo_dalpha, dphineo_dalpha, irad)
end if
end do
end if
call comm_free (sfincs_comm, ierr)
! NB: NEED TO CHECK THIS BROADCAST OF SFINCS RESULTS
do irad = irad_min, irad_max
call broadcast_sfincs_output &
(f_neoclassical(:,:,:,:,:,irad), phi_neoclassical(:,:,irad))
end do
call broadcast_sfincs_output (dfneo_dalpha, dphineo_dalpha)
deallocate (fprim_local, tprim_local)
if (proc0) then
write (*,*)
write (*,*) 'maxval(fneo): ', maxval(f_neoclassical(:,:,:,:,:,irad_min:irad_max)), &
'maxval(phineo): ', maxval(phi_neoclassical(:,:,irad_min:irad_max))
write (*,*)
end if
if ((irad_min /= -nradii/2) .or. (irad_max /= nradii/2)) &
call mp_abort ('WARNING: irad_min must equal -nradii/2 and irad_max must equal &
& nradii/2 to proceed to stella calculation. aborting.')
# else
real :: dum
! this pointless dum assignment only here to avoid
! annoying warning messages during compilation
! about unused variable drho
dum = drho
f_neoclassical = 0. ; phi_neoclassical = 0.
dfneo_dalpha = 0. ; dphineo_dalpha = 0.
call mp_abort ("to run with include_neoclassical_terms=.true., &
& USE_SFINCS must be defined at compilation time. Aborting.")
# endif
end subroutine get_neo_from_sfincs
# ifdef USE_SFINCS
subroutine iterate_sfincs_until_electric_field_converged (sfincs_comm, irad, drho, &
nrad_max, dPhiHatdrN_best_guess, dphiHatdrN_is_converged, number_of_sfincs_calls_for_convergence)
use mp, only: proc0, iproc
implicit none
integer, intent (in) :: sfincs_comm, irad, nrad_max
real, intent (in) :: drho, dPhiHatdrN_best_guess
logical, intent (out) :: dPhiHatdrN_is_converged
integer, intent (out) :: number_of_sfincs_calls_for_convergence
integer :: itmax_bracket = 10
integer :: itmax_root = 10
real :: window = 0.3
real :: tol = 0.1
integer :: it
real :: a,b,c,d,e,fa,fb,fc,p,q,r,s,tol1,xm,eps
real :: converged_dPhiHatdrN
dPhiHatdrN_is_converged = .false.
a = dPhiHatdrN_best_guess*(1.0-Er_window)
b = dPhiHatdrN_best_guess*(1.0+Er_window)
! initialize sfincs, run it, and return the total charge flux as fa
call get_total_charge_flux (sfincs_comm, irad, drho, nrad_max, a, fa)
call get_total_charge_flux (sfincs_comm, irad, drho, nrad_max, b, fb)
number_of_sfincs_calls_for_convergence = 2
do it = 1, itmax_bracket
eps = epsilon(a)
if ((fa > 0.0 .and. fb > 0.0) .or. (fa < 0.0 .and. fb < 0.0)) then
if (proc0) then
write (*,*)
write (*,*) 'dPhiHatdrN values ', a, ' and ', b, ' do not bracket root.'
write (*,*) 'flux at ', a, ' is ', fa, '.'
write (*,*) 'flux at ', b, ' is ', fb, '.'
end if
a = a*(1.0-Er_window)
b = b*(1.0+Er_window)
if (proc0) then
write (*,*) 'Trying again with values ', a, ' and ', b, ' .'
write (*,*)
end if
call get_total_charge_flux (sfincs_comm, irad, drho, nrad_max, a, fa)
call get_total_charge_flux (sfincs_comm, irad, drho, nrad_max, b, fb)
number_of_sfincs_calls_for_convergence = number_of_sfincs_calls_for_convergence + 2
! ! eliminate the endpoint corresonding to the flux that is furthest from zero in magnitude
! if (abs(fa) > abs(fb)) then
! ! keep b as an endpoint and eliminate a
! a = b ; fa = fb
! b = a*(1.0+window)
! if (proc0) then
! write (*,*) 'Trying again with values ', a, ' and ', b, ' .'
! write (*,*)
! end if
! call get_total_charge_flux (sfincs_comm, irad, drho, nrad_max, b, fb)
! else
! ! keep a as an endpoint and eliminate b
! b = a ; fb = fa
! a = b*(1.0-window)
! if (proc0) then
! write (*,*) 'Trying again with values ', a, ' and ', b, ' .'
! write (*,*)
! end if
! call get_total_charge_flux (sfincs_comm, irad, drho, nrad_max, a, fa)
! end if
else
exit
end if
end do
c=b
fc=fb
do it = 1, itmax_root
if ((fb > 0.0 .and. fc > 0.0) .or. (fb < 0.0 .and. fc < 0.0)) then
c=a
fc=fa
d=b-a
e=d
end if
if (abs(fc) < abs(fb)) then
a=b
b=c
c=a
fa=fb
fb=fc
fc=fa
end if
tol1=2.0*eps*abs(b)+0.5*tol
xm=0.5*(c-b)
if (abs(xm) <= tol1 .or. fb == 0.0) then
converged_dPhiHatdrN = b
dPhiHatdrN_is_converged = .true.
! number_of_sfincs_calls_for_convergence = it+1
exit
end if
if (abs(e) >= tol1 .and. abs(fa) > abs(fb)) then
s=fb/fa
if (a==c) then
p=2.0*xm*s
q=1.0-s
else
q=fa/fc
r=fb/fc
p=s*(2.0*xm*q*(q-r)-(b-a)*(r-1.0))
q=(q-1.0)*(r-1.0)*(s-1.0)
end if
if (p > 0.0) q=-q
p=abs(p)
if (2.0*p < min(3.0*xm*q-abs(tol1*q),abs(e*q))) then
e=d
d=p/q
else
d=xm
e=d
end if
else
d=xm
e=d
end if
a=b
fa=fb
b=b+merge(d,sign(tol1,xm), abs(d) > tol1)
call get_total_charge_flux (sfincs_comm, irad, drho, nrad_max, b, fb)
number_of_sfincs_calls_for_convergence = number_of_sfincs_calls_for_convergence + 1
end do
end subroutine iterate_sfincs_until_electric_field_converged
subroutine get_total_charge_flux (sfincs_comm, irad, drho, nrad_max, &
dPhiHatdrN_in, total_charge_flux)
use mp, only: iproc, broadcast_with_comm
use sfincs_main, only: finish_sfincs
use globalVariables, only: Zs, particleFlux_vd_psiHat
use species, only: nspec
implicit none
integer, intent (in) :: sfincs_comm, irad, nrad_max
real, intent (in) :: drho
real, intent (in) :: dPhiHatdrN_in
real, intent (out) :: total_charge_flux
dPhiHatdrN = dPhiHatdrN_in
call init_and_run_sfincs (sfincs_comm, irad, drho, nrad_max)
call broadcast_with_comm (Zs, sfincs_comm)
call broadcast_with_comm (particleFlux_vd_psiHat, sfincs_comm)
total_charge_flux = sum(Zs(:nspec)*particleFlux_vd_psiHat(:nspec))
end subroutine get_total_charge_flux
subroutine init_and_run_sfincs (sfincs_comm, irad, drho, nrad_max)
use mp, only: proc0, iproc
use sfincs_main, only: init_sfincs, prepare_sfincs, run_sfincs, finish_sfincs
use globalVariables, only: Zs, particleFlux_vd_psiHat
use species, only: nspec
implicit none
integer, intent (in) :: sfincs_comm, irad, nrad_max
real, intent (in) :: drho
if (.not.sfincs_finished) then
call finish_sfincs
sfincs_finished = .true.
end if
call init_sfincs (sfincs_comm)
call pass_inputoptions_to_sfincs (irad*drho)
call pass_outputoptions_to_sfincs
call prepare_sfincs
! if geometryScheme = 5, then sfincs will read in equilibrium
! parameters from vmec file separately
! otherwise, assume system is axisymmetric and pass geometry
! from stella (miller local equilibrium or similar)
if (geometryScheme /= 5) call pass_geometry_to_sfincs (irad*drho)
if (read_sfincs_output_from_file) then
if (proc0) call read_sfincs_output (irad, nrad_max)
else
if (proc0) then
write (*,*)
write (*,*) 'Running sfincs at irad= ', irad, ', with dPhiHatdrN= ', dPhiHatdrN
end if
call run_sfincs
if (proc0) then
write (*,*) 'sfincs finished running. total charge flux= ', sum(Zs(:nspec)*particleFlux_vd_psiHat(:nspec))
write (*,*)
end if
! write Phi1Hat and delta_f to file
! so we have the option of using it
! again without re-running sfincs
if (proc0) call write_sfincs (irad, nrad_max)
end if
sfincs_finished = .false.
end subroutine init_and_run_sfincs
subroutine write_and_finish_sfincs (fneo, phineo, dfneo, dphineo, irad)
use mp, only: proc0
use sfincs_main, only: finish_sfincs
use zgrid, only: nzgrid
implicit none
real, dimension (:,-nzgrid:,:,:,:), intent (out) :: fneo
real, dimension (:,-nzgrid:), intent (out) :: phineo
real, dimension (:,-nzgrid:,:,:,:), intent (in out) :: dfneo
real, dimension (:,-nzgrid:), intent (in out) :: dphineo
integer, intent (in) :: irad
if (proc0) then
! only need to compute dfneo_dalpha and dphineo_dalpha
! for central radius and for stellarator calculation
if (irad == 0 .and. geometryScheme == 5) then
call get_sfincs_output (fneo, phineo, dfneo, dphineo)
else
call get_sfincs_output (fneo, phineo)
end if
end if
call finish_sfincs
end subroutine write_and_finish_sfincs
subroutine read_sfincs_parameters (nradii)
use constants, only: pi
use mp, only: nproc
use file_utils, only: input_unit_exist
use species, only: nspec
use physics_parameters, only: rhostar, vnew_ref
use stella_geometry, only: geo_surf, aref, bref
implicit none
integer, intent (in) :: nradii
namelist /sfincs_input/ nproc_sfincs, &
calculate_radial_electric_field, &
includeXDotTerm, &
includeElectricFieldTermInXiDot, &
irad_min, irad_max, &
magneticDriftScheme, &
includePhi1, &
includePhi1InKineticEquation, &
! includePhi1InCollisionOperator, &
geometryScheme, &
VMECRadialOption, &
equilibriumFile, &
coordinateSystem, &
inputRadialCoordinate, &
inputRadialCoordinateForGradients, &
aHat, psiAHat, nu_N, nxi, nx, Delta, &
dPhiHatdrN, &
ntheta, nzeta, &
read_sfincs_output_from_file, Er_window
logical :: exist
integer :: in_file
! if read_sfincs_output_from_file=.true.,
! will try to read in Phi1Hat and delta_f
! from pre-saved file named sfincs.output
! otherwise, run sfincs to compute these
! quantities on the fly
read_sfincs_output_from_file = .false.
! number of processors to use for sfincs calculation
nproc_sfincs = 1
! minimum and maximum radial index (irad=0 corresponds to central radius)
irad_min = -nradii/2 ; irad_max = nradii/2
! if calculate_radial_electric_field, then
! will scan in radial electric field to find value
! for which ambipolarity is satisfied, and then
! use this value to obtain neoclassical fluxes,
! distribution function, and potential
calculate_radial_electric_field = .true.
! do not include radial electric field term if set to .false.
includeXDotTerm = .true.
includeElectricFieldTermInXiDot = .true.
! include v_E . grad r term
! includeRadialExBDrive = .true.
! no poloidal or toroidal magnetic drifts
magneticDriftScheme = 0
! combo of next two variables means
! phi1 will be calculated via quasineutrality
includePhi1 = .true.
includePhi1InKineticEquation = .false.
! includePhi1InCollisionOperator = .false.
! will be overridden by direct input of geometric quantities
! unless geometryScheme = 5 (vmec equilibrium)
geometryScheme = 1
! only relevant if geometryScheme = 5
! radial option to use for vmec equilibrium
! 0 corresponds to using radial interpolation to get desired surface
! 1 corresponds to using nearest surface on VMEC HALF grid
! 2 corresponds to using nearest surface on VMEC FULL grid
! should not change this unless self-consistently change in the
! vmec input namelist
VMECRadialOption = 0
! path of vmec equilibrium file
equilibriumFile = 'wout_161s1.nc'
! seems to be a nonsensical option
coordinateSystem = 3
! option 3 corresponds to using sqrt of toroidal flux
! normalized by toroidal flux enclosed by the LCFS
inputRadialCoordinate = 3
! option 3 corresponds to same choice
! when calculating gradients of density, temperature, and potential
inputRadialCoordinateForGradients = 3
! corresponds to r_LCFS as reference length in sfincs
! only used in sfincs when geometryScheme=1
aHat = 1.0
! psitor_LCFS / (B_ref * a_ref^2)
psiAHat = geo_surf%psitor_lcfs
! Delta is rho* = mref*vt_ref/(e*Bref*aref), with reference
! quantities given in SI units
! unless geometryScheme = 5, in which case Bref=1T
! and aref = 1m (these are hardwired in sfincs)
! set negative to allow check later to see if any value given in input file
Delta = -1.0
! nu_n = nu_ref * aref/vt_ref
! nu_ref = 4*sqrt(2*pi)*nref*e**4*loglam/(3*sqrt(mref)*Tref**3/2)
! (with nref, Tref, and mref in Gaussian units)
! set negative to allow check later to see if any value given in input file
nu_n = -1.0
! radial derivative of normalized phi
dPhiHatdrN = -9999.9
Er_window = 0.3
! number of spectral coefficients in pitch angle
nxi = 48
! number of speeds
nx = 12
! number of poloidal angles
Ntheta = 65
! number of toroidal angles, 1 is appropriate for tokamak
Nzeta = 1
in_file = input_unit_exist("sfincs_input", exist)
if (exist) read (unit=in_file, nml=sfincs_input)
if (nproc_sfincs > nproc) then
write (*,*) 'requested number of processors for sfincs is greater &
& than total processor count.'
write (*,*) 'allocating ', nproc, ' processors for sfincs.'
end if
if (Delta < 0.0) then
Delta = rhostar
! if geometryScheme=5, Bref=1T and aref=1m are hard-wired in sfincs
! but these are not the values used in stella to define rhostar
if (geometryScheme == 5) Delta = rhostar*bref*aref
end if
if (nu_n < 0.0) then
nu_n = vnew_ref*(4./(3.*sqrt(pi)))
! if geometryScheme=5, aref=1m is hard-wired in sfincs
! but this is not the value used in stella
if (geometryScheme == 5) nu_n = nu_n/aref
end if
! FLAG -- NOT YET SURE IF THIS SHOULD BE HERE
! if (nspec == 1 .and. includePhi1) then
! write (*,*) 'includePhi1 = .true. is incompatible with a single-species run.'
! write (*,*) 'forcing includePhi1 = .false.'
! includePhi1 = .false.
! end if
! ensure that ntheta and nzeta are odd for SFINCS
ntheta = 2*(ntheta/2)+1
nzeta = 2*(nzeta/2)+1
end subroutine read_sfincs_parameters
subroutine broadcast_sfincs_parameters
use mp, only: broadcast
use physics_parameters, only: rhostar
implicit none
call broadcast (read_sfincs_output_from_file)
call broadcast (nproc_sfincs)
call broadcast (irad_min)
call broadcast (irad_max)
call broadcast (calculate_radial_electric_field)
call broadcast (includeXDotTerm)
call broadcast (includeElectricFieldTermInXiDot)
! call broadcast (includeRadialExBDrive)
call broadcast (magneticDriftScheme)
call broadcast (includePhi1)
call broadcast (includePhi1InKineticEquation)
! call broadcast (includePhi1InCollisionOperator)
call broadcast (geometryScheme)
call broadcast (VMECRadialOption)
call broadcast (equilibriumFile)
call broadcast (coordinateSystem)
call broadcast (inputRadialCoordinate)
call broadcast (inputRadialCoordinateForGradients)
call broadcast (aHat)
call broadcast (psiAHat)
call broadcast (Delta)
call broadcast (nu_N)
call broadcast (dPhiHatdrN)
call broadcast (Er_window)
call broadcast (nxi)
call broadcast (nx)
call broadcast (ntheta)
call broadcast (nzeta)
write (*,*) 'Delta stella', Delta, rhostar
end subroutine broadcast_sfincs_parameters
subroutine pass_inputoptions_to_sfincs (delrho)
use mp, only: mp_abort
use stella_geometry, only: geo_surf
use species, only: spec, nspec
use zgrid, only: nzed
use physics_parameters, only: nine, tite
use globalVariables, only: includeXDotTerm_sfincs => includeXDotTerm
use globalVariables, only: includeElectricFieldTermInXiDot_sfincs => includeElectricFieldTermInXiDot
! use globalVariables, only: includeRadialExBDrive_sfincs => includeRadialExBDrive
use globalVariables, only: magneticDriftScheme_sfincs => magneticDriftScheme
use globalVariables, only: includePhi1_sfincs => includePhi1
use globalVariables, only: includePhi1InKineticEquation_sfincs => includePhi1InKineticEquation
! use globalVariables, only: includePhi1InCollisionOperator_sfincs => includePhi1InCollisionOperator
use globalVariables, only: geometryScheme_sfincs => geometryScheme
use globalVariables, only: equilibriumFile_sfincs => equilibriumFile
use globalVariables, only: VMECRadialOption_sfincs => VMECRadialOption
use globalVariables, only: coordinateSystem_sfincs => coordinateSystem
use globalVariables, only: RadialCoordinate => inputRadialCoordinate
use globalVariables, only: RadialCoordinateForGradients => inputRadialCoordinateForGradients
use globalVariables, only: rN_wish
use globalVariables, only: Nspecies, nHats, THats, MHats, Zs
use globalVariables, only: adiabaticNHat, adiabaticTHat, adiabaticZ
use globalVariables, only: nxi_sfincs => Nxi
use globalVariables, only: nx_sfincs => Nx
use globalVariables, only: ntheta_sfincs => Ntheta
use globalVariables, only: nzeta_sfincs => Nzeta
use globalVariables, only: dnHatdrNs, dTHatdrNs
use globalVariables, only: aHat_sfincs => aHat
use globalVariables, only: psiAHat_sfincs => psiAHat
use globalVariables, only: Delta_sfincs => Delta
use globalVariables, only: nu_n_sfincs => nu_n
use globalVariables, only: dPhiHatdrN_sfincs => dPhiHatdrN
use globalVariables, only: withAdiabatic
implicit none
real, intent (in) :: delrho
includeXDotTerm_sfincs = includeXDotTerm
includeElectricFieldTermInXiDot_sfincs = includeElectricFieldTermInXiDot
! includeRadialExBDrive_sfincs = includeRadialExBDrive
magneticDriftScheme_sfincs = magneticDriftScheme
includePhi1_sfincs = includePhi1
includePhi1InKineticEquation_sfincs = includePhi1InKineticEquation
! includePhi1InCollisionOperator_sfincs = includePhi1InCollisionOperator
geometryScheme_sfincs = geometryScheme
VMECRadialOption_sfincs = VMECRadialOption
equilibriumFile_sfincs = trim(equilibriumFile)
coordinateSystem_sfincs = coordinateSystem
RadialCoordinate = inputRadialCoordinate
RadialCoordinateForGradients = inputRadialCoordinateForGradients
Nspecies = nspec
nHats(:nspec) = spec%dens*(1.0-delrho*spec%fprim)
THats(:nspec) = spec%temp*(1.0-delrho*spec%tprim)
mHats(:nspec) = spec%mass
Zs(:nspec) = spec%z
nzeta_sfincs = nzeta
ntheta_sfincs = ntheta
nx_sfincs = nx
nxi_sfincs = nxi
aHat_sfincs = aHat
psiAHat_sfincs = psiAHat
Delta_sfincs = Delta
nu_n_sfincs = nu_n
dPhiHatdrN_sfincs = dPhiHatdrN
if (nspec == 1) then
withAdiabatic = .true.
adiabaticNHat = nHats(1)/nine
adiabaticTHat = THats(1)/tite
adiabaticZ = -1
end if
if (inputRadialCoordinate == 3) then
rN_wish = geo_surf%rhotor + delrho*geo_surf%drhotordrho
else
call mp_abort ('only inputRadialCoordinate=3 currently supported. aborting.')
end if
if (inputRadialCoordinateForGradients == 3) then
! radial density gradient with respect to rhotor = sqrt(psitor/psitor_LCFS)
! normalized by reference density (not species density)
dnHatdrNs(:nspec) = -spec%dens*fprim_local
! radial temperature gradient with respect to rhotor = sqrt(psitor/psitor_LCFS)
! normalized by reference tmperatures (not species temperature)
dTHatdrNs(:nspec) = -spec%temp*tprim_local
else
call mp_abort ('only inputRadialCoordinateForGradients=3 currently supported. aborting.')
end if
end subroutine pass_inputoptions_to_sfincs
subroutine pass_outputoptions_to_sfincs
use export_f, only: export_f_theta_option
use export_f, only: export_f_zeta_option
use export_f, only: export_f_xi_option
use export_f, only: export_f_x_option
use export_f, only: export_delta_f, export_full_f
use export_f, only: export_f_stella
implicit none
export_f_theta_option = 0
export_f_zeta_option = 0
export_f_xi_option = 0
export_f_x_option = 0
export_delta_f = .true.
export_full_f = .false.
export_f_stella = .true.
end subroutine pass_outputoptions_to_sfincs
! if this subroutine is being called, then
! using sfincs in tokamak geometry
! so zed in stella is theta
subroutine pass_geometry_to_sfincs (delrho)
use constants, only: pi
use splines, only: linear_interp_periodic
use zgrid, only: nz2pi, zed
use stella_geometry, only: bmag, dbdzed, gradpar
use stella_geometry, only: dBdrho, d2Bdrdth, dgradpardrho, dIdrho
use stella_geometry, only: geo_surf
use globalVariables, only: BHat
use globalVariables, only: dBHatdtheta
use globalVariables, only: iota
use globalVariables, only: DHat
use globalVariables, only: BHat_sup_theta
use globalVariables, only: BHat_sub_zeta
use export_f, only: export_f_theta
implicit none
real, intent (in) :: delrho
integer :: nzeta = 1
integer :: nzpi
real :: q_local
real, dimension (:), allocatable :: B_local, dBdz_local, gradpar_local
real, dimension (:), allocatable :: zed_stella
real, dimension (:), allocatable :: theta_sfincs
nzpi = nz2pi/2
allocate (B_local(-nzpi:nzpi))
allocate (dBdz_local(-nzpi:nzpi))
allocate (gradpar_local(-nzpi:nzpi))
allocate (theta_sfincs(ntheta))
allocate (zed_stella(-nzpi:nzpi))
call init_zero_arrays
! first get some geometric quantities at this radius
! for theta from -pi to pi
q_local = geo_surf%qinp*(1.0+delrho*geo_surf%shat/geo_surf%rhoc)
B_local = bmag(1,-nzpi:nzpi) + delrho*dBdrho(-nzpi:nzpi)
dBdz_local = dbdzed(1,-nzpi:nzpi) + delrho*d2Bdrdth(-nzpi:nzpi)
gradpar_local = gradpar(-nzpi:nzpi) + delrho*dgradpardrho(-nzpi:nzpi)
zed_stella = zed(-nzpi:nzpi)+pi
theta_sfincs = export_f_theta(:ntheta)
iota = 1./q_local
! interpolate from stella zed-grid to sfincs theta grid
! point at -pi (stella) is same as point at 0 (sfincs)
BHat(1,1) = B_local(-nzpi)
call linear_interp_periodic (zed_stella, B_local, theta_sfincs(2:), BHat(2:,1))
! FLAG -- needs to be changed for stellarator runs
BHat = spread(BHat(:,1),2,nzeta)
dBHatdtheta(1,1) = dBdz_local(-nzpi)
call linear_interp_periodic (zed_stella, dBdz_local, theta_sfincs(2:), dBHatdtheta(2:,1))
dBHatdtheta = spread(dBHatdtheta(:,1),2,nzeta)
! this is bhat . grad theta
BHat_sup_theta(1,1) = B_local(-nzpi)*gradpar_local(-nzpi)
call linear_interp_periodic (zed_stella, B_local*gradpar_local, theta_sfincs(2:), BHat_sup_theta(2:,1))
BHat_sup_theta = spread(BHat_sup_theta(:,1),2,nzeta)
! this is I(psi) / (aref*Bref)
BHat_sub_zeta = geo_surf%rgeo + delrho*dIdrho
! this is grad psitor . (grad theta x grad zeta)
! note that + sign below relies on B = I grad zeta + grad zeta x grad psi
DHat = q_local*BHat_sup_theta
deallocate (B_local, dBdz_local, gradpar_local)
deallocate (theta_sfincs, zed_stella)
end subroutine pass_geometry_to_sfincs
subroutine init_zero_arrays
use globalVariables, only: dBHatdzeta
use globalVariables, only: dBHatdpsiHat
use globalVariables, only: BHat_sup_zeta
use globalVariables, only: BHat_sub_psi
use globalVariables, only: BHat_sub_theta
use globalVariables, only: dBHat_sub_psi_dtheta
use globalVariables, only: dBHat_sub_psi_dzeta
use globalVariables, only: dBHat_sub_theta_dpsiHat
use globalVariables, only: dBHat_sub_theta_dzeta
use globalVariables, only: dBHat_sub_zeta_dpsiHat
use globalVariables, only: dBHat_sub_zeta_dtheta
use globalVariables, only: dBHat_sup_theta_dpsiHat
use globalVariables, only: dBHat_sup_theta_dzeta
use globalVariables, only: dBHat_sup_zeta_dpsiHat
use globalVariables, only: dBHat_sup_zeta_dtheta
implicit none
dBHatdzeta = 0.
dBHatdpsiHat = 0.
BHat_sup_zeta = 0.
BHat_sub_psi = 0.
BHat_sub_theta = 0.
dBHat_sub_psi_dtheta = 0.
dBHat_sub_psi_dzeta = 0.
dBHat_sub_theta_dpsiHat = 0.
dBHat_sub_theta_dzeta = 0.
dBHat_sub_zeta_dpsiHat = 0.
dBHat_sub_zeta_dtheta = 0.
dBHat_sup_theta_dpsiHat = 0.
dBHat_sup_theta_dzeta = 0.
dBHat_sup_zeta_dpsiHat = 0.
dBHat_sup_zeta_dtheta = 0.
end subroutine init_zero_arrays
subroutine get_sfincs_output (f_neoclassical, phi_neoclassical, &
dfneo_dalpha, dphineo_dalpha)
use constants, only: pi
use sort, only: sort_array_ascending, unsort_array_ascending
use species, only: nspec
use zgrid, only: nzgrid, nz2pi
use export_f, only: h_sfincs => delta_f
use globalVariables, only: Phi1Hat
use kt_grids, only: nalpha
implicit none
real, dimension (:,-nzgrid:,:,:,:), intent (out) :: f_neoclassical
real, dimension (:,-nzgrid:), intent (out) :: phi_neoclassical
real, dimension (:,-nzgrid:,:,:,:), intent (out), optional :: dfneo_dalpha
real, dimension (:,-nzgrid:), intent (out), optional :: dphineo_dalpha
integer :: i, j
integer :: ialpha, iz, is
real, dimension (:), allocatable :: zed_stella
integer :: nfp, nfp_stella
integer, dimension (:), allocatable :: nzed_per_field_period
real, dimension (:,:), allocatable :: zed_stella_by_field_period
real, dimension (:,:), allocatable :: alpha_like_stella
integer, dimension (:,:), allocatable :: alpha_sort_map
integer :: nzed_sfincs, nalpha_sfincs
real, dimension (:), allocatable :: zed_sfincs, alpha_like_sfincs
real, dimension (:,:), allocatable :: phi_sfincs
real, dimension (:,:), allocatable :: phi_stella_zgrid, phi_stella
real, dimension (:,:), allocatable :: dphi_dalpha_stella_zgrid
real, dimension (:,:), allocatable :: tmp_sfincs, tmp_stella_zgrid, tmp_stella
real, dimension (:,:), allocatable :: dh_stella_zgrid
real, dimension (:,:,:,:), allocatable :: h_stella, dh_stella
! zed coordinate in stella is zeta when simulating stellarators (using vmec)
! and theta otherwise. this leads to some complications, treated below
allocate (zed_stella(nz2pi))
allocate (alpha_like_stella(nalpha,nz2pi))
allocate (alpha_sort_map(nalpha,nz2pi))
! obtain theta and zeta grids used in stella, and assign them
! to the zed and alpha-like coordinates.
! for stellarator, zed=zeta and alpha_like=theta.
! for tokamak, zed=theta and alpha_like = zeta.
call get_stella_theta_zeta_grids (alpha_like_stella, zed_stella)
! do iz = 1, nz2pi
! do ialpha = 1, size(alpha_like_stella,1)
! write (*,*) 'unsorted_alpha_like_stella', alpha_like_stella(ialpha,iz)
! end do
! write (*,*)
! end do
! rearrange alpha_like_stella to be in ascending order and store map
! so that sorting can be undone later
do iz = 1, nz2pi
call sort_array_ascending (alpha_like_stella(:,iz), alpha_sort_map(:,iz))
end do
! do iz = 1, nz2pi
! do ialpha = 1, size(alpha_like_stella,1)
! write (*,*) 'sorted_alpha_like_stella', alpha_like_stella(ialpha,iz)
! end do
! write (*,*)
! end do
! obtain the number of alpha-like and zed grid points to use in sfincs theta-zeta grid
! also obtain the number of field periods per 2*pi segment in zed
call get_sfincs_theta_zeta_grid_sizes (nalpha_sfincs, nzed_sfincs, nfp)
! obtain the alpha-like and zed coordinate grids
! note that additional points are added at periodic points
! that are not sampled in sfincs
allocate (zed_sfincs(nzed_sfincs))
allocate (alpha_like_sfincs(nalpha_sfincs))
call get_sfincs_theta_zeta_grids (alpha_like_sfincs, zed_sfincs)
allocate (phi_sfincs(nalpha_sfincs,nzed_sfincs))
call get_sfincs_field_theta_zeta (Phi1Hat, phi_sfincs)
! this is the number of field periods included in stella
! simulation domain
nfp_stella = int((zed_stella(nz2pi)*nfp-100.*epsilon(0.))/(2.*pi)) + 1
! obtain the number of zed grid points in each field period within the zed domain
allocate (nzed_per_field_period(nfp_stella))
call get_nzed_per_field_period (zed_stella, nfp, nzed_per_field_period)
! obtain the zed grid within each field period
allocate (zed_stella_by_field_period(maxval(nzed_per_field_period),nfp_stella))
call sort_zed_by_field_period (zed_stella, nzed_per_field_period, nfp, zed_stella_by_field_period)
! interpolate phi from sfincs zed grid to stella zed grid
allocate (phi_stella_zgrid(nalpha_sfincs,nz2pi))
call get_field_on_stella_zed_grid (phi_sfincs, nfp_stella, nfp, nzed_per_field_period, &
nalpha_sfincs, zed_sfincs, zed_stella_by_field_period, phi_stella_zgrid)
allocate (phi_stella(nalpha,nz2pi))
! interpolate onto stella (sorted) alpha grid
call get_field_stella (phi_stella_zgrid, alpha_like_sfincs, alpha_like_stella, phi_stella)
! need to remap from ascending (sorted) alpha grid to original ordering
do iz = 1, nz2pi
call unsort_array_ascending (phi_stella(:,iz), alpha_sort_map(:,iz))
end do
call get_field_on_extended_zed (phi_stella, phi_neoclassical)
if (present(dphineo_dalpha)) then
allocate (dphi_dalpha_stella_zgrid(nalpha_sfincs,nz2pi))
call get_dfield_dalpha (phi_stella_zgrid, alpha_like_sfincs, dphi_dalpha_stella_zgrid)
call get_field_stella (dphi_dalpha_stella_zgrid, alpha_like_sfincs, alpha_like_stella, phi_stella)
do iz = 1, nz2pi
call unsort_array_ascending (phi_stella(:,iz), alpha_sort_map(:,iz))
end do
call get_field_on_extended_zed (phi_stella, dphineo_dalpha)
deallocate (dphi_dalpha_stella_zgrid)
end if
deallocate (phi_stella, phi_stella_zgrid, phi_sfincs)
allocate (tmp_sfincs(nalpha_sfincs,nzed_sfincs))
allocate (tmp_stella_zgrid(nalpha_sfincs,nz2pi))
allocate (tmp_stella(nalpha,nz2pi))
allocate (h_stella(nalpha,nz2pi,size(h_sfincs,4),size(h_sfincs,5)))
if (present(dfneo_dalpha)) then
allocate (dh_stella_zgrid(nalpha_sfincs,nz2pi))
allocate (dh_stella(nalpha,nz2pi,size(h_sfincs,4),size(h_sfincs,5)))
end if
do is = 1, nspec
do i = 1, size(h_sfincs,5)
do j = 1, size(h_sfincs,4)
! re-order theta and zeta indices for sfincs h to ensure alpha-like coordinate
! appears before zed coordinate
call get_sfincs_field_theta_zeta (h_sfincs(is,:,:,j,i), tmp_sfincs)
! interpolate onto stella zed grid
call get_field_on_stella_zed_grid (tmp_sfincs, nfp_stella, nfp, nzed_per_field_period, &
nalpha_sfincs, zed_sfincs, zed_stella_by_field_period, tmp_stella_zgrid)
! interpolate onto (sorted) stella alpha-like coordinate
call get_field_stella (tmp_stella_zgrid, alpha_like_sfincs, alpha_like_stella, tmp_stella)
do iz = 1, nz2pi
call unsort_array_ascending (tmp_stella(:,iz), alpha_sort_map(:,iz))
end do
! use periodicity to copy onto extended zed grid if nperiod > 1
call get_field_on_extended_zed (tmp_stella, h_stella(:,:,j,i))
if (present(dfneo_dalpha)) then
call get_dfield_dalpha (tmp_stella_zgrid, alpha_like_sfincs, dh_stella_zgrid)
call get_field_stella (dh_stella_zgrid, alpha_like_sfincs, &
alpha_like_stella, tmp_stella)
do iz = 1, nz2pi
call unsort_array_ascending (tmp_stella(:,iz), alpha_sort_map(:,iz))
end do
call get_field_on_extended_zed (tmp_stella, dh_stella(:,:,j,i))
end if
end do
end do
do ialpha = 1, nalpha
do iz = -nzgrid, nzgrid
call sfincs_vspace_to_stella_vspace (ialpha, iz, is, h_stella(ialpha,iz+nzgrid+1,:,:), &
phi_neoclassical(ialpha,iz), f_neoclassical(ialpha,iz,:,:,is))
if (present(dfneo_dalpha)) call sfincs_vspace_to_stella_vspace (ialpha, iz, is, &
dh_stella(ialpha,iz+nzgrid+1,:,:), dphineo_dalpha(ialpha,iz), &
dfneo_dalpha(ialpha,iz,:,:,is))
end do
end do
end do
deallocate (tmp_sfincs, tmp_stella_zgrid, tmp_stella)
deallocate (zed_stella, alpha_like_stella)
deallocate (alpha_sort_map)
deallocate (zed_sfincs, alpha_like_sfincs)
deallocate (nzed_per_field_period, zed_stella_by_field_period)
deallocate (h_stella)
if (present(dfneo_dalpha)) deallocate (dh_stella, dh_stella_zgrid)
end subroutine get_sfincs_output
subroutine get_stella_theta_zeta_grids (alpha_like_stella, zed_stella)
use constants, only: pi
use zgrid, only: nz2pi, zed
use stella_geometry, only: zed_scalefac
use stella_geometry, only: alpha
use kt_grids, only: nalpha
use globalVariables, only: iota
implicit none
real, dimension (:,:), intent (out) :: alpha_like_stella
real, dimension (:), intent (out) :: zed_stella
integer :: nzpi
nzpi = nz2pi/2
! convert from scaled zed grid on [-pi,pi]