geometry_mod.F90

module geometry
! computes geometrical quantities
! Adapted from B.J.Frei MOLIX code (2021)

  use prec_const
  use model
  use grid
  use array
  use fields
  use basic
  use calculus, ONLY: simpson_rule_z
  use miller, ONLY: set_miller_parameters, get_miller
implicit none
  PRIVATE
  ! Geometry input parameters
  CHARACTER(len=16), &
               PUBLIC, PROTECTED :: geom
  REAL(dp),    PUBLIC, PROTECTED :: q0        = 1.4_dp  ! safety factor
  REAL(dp),    PUBLIC, PROTECTED :: shear     = 0._dp   ! magnetic field shear
  REAL(dp),    PUBLIC, PROTECTED :: eps       = 0.18_dp ! inverse aspect ratio
  REAL(dp),    PUBLIC, PROTECTED :: alpha_MHD = 0 ! shafranov shift effect alpha = -q2 R dbeta/dr
  ! parameters for Miller geometry
  REAL(dp),    PUBLIC, PROTECTED :: kappa     = 1._dp ! elongation (1 for circular)
  REAL(dp),    PUBLIC, PROTECTED :: s_kappa   = 0._dp ! r normalized derivative skappa = r/kappa dkappa/dr
  REAL(dp),    PUBLIC, PROTECTED :: delta     = 0._dp ! triangularity
  REAL(dp),    PUBLIC, PROTECTED :: s_delta   = 0._dp ! '' sdelta = r/sqrt(1-delta2) ddelta/dr
  REAL(dp),    PUBLIC, PROTECTED :: zeta      = 0._dp ! squareness
  REAL(dp),    PUBLIC, PROTECTED :: s_zeta    = 0._dp ! '' szeta = r dzeta/dr
  ! to apply shift in the parallel z-BC if shearless
  REAL(dp),    PUBLIC, PROTECTED :: shift_y   = 0._dp ! for Arno
  ! Chooses the type of parallel BC we use for the unconnected kx modes (active for non-zero shear only)
  !  'periodic'     : Connect a disconnected kx to a mode on the other cadran
  !  'dirichlet'    : Connect a disconnected kx to 0
  !  'disconnected' : Connect all kx to 0
  !  'shearless'    : Connect all kx to itself
  CHARACTER(len=256), &
               PUBLIC, PROTECTED :: parallel_bc

  ! GENE unused additional parameters for miller_mod
  REAL(dp), PUBLIC, PROTECTED :: edge_opt      = 0._dp ! meant to redistribute the points in z
  REAL(dp), PUBLIC, PROTECTED :: major_R       = 1._dp ! major radius
  REAL(dp), PUBLIC, PROTECTED :: major_Z       = 0._dp ! vertical elevation
  REAL(dp), PUBLIC, PROTECTED :: dpdx_pm_geom  = 0._dp ! amplitude mag. eq. pressure grad.
  REAL(dp), PUBLIC, PROTECTED ::          C_y  = 0._dp ! defines y coordinate : Cy (q theta - phi)
  REAL(dp), PUBLIC, PROTECTED ::         C_xy  = 1._dp ! defines x coordinate : B = Cxy Vx x Vy

  ! Geometrical auxiliary variables
  LOGICAL,     PUBLIC, PROTECTED :: SHEARED  = .false. ! flag for shear magn. geom or not
  ! Curvature
  REAL(dp),    PUBLIC, DIMENSION(:,:,:,:), ALLOCATABLE :: Ckxky  ! dimensions: kx, ky, z, odd/even p
  ! Jacobian
  REAL(dp),    PUBLIC, DIMENSION(:,:), ALLOCATABLE :: Jacobian ! dimensions: z, odd/even p
  COMPLEX(dp), PUBLIC, PROTECTED        :: iInt_Jacobian ! Inverse integrated Jacobian
  ! Metric
  REAL(dp),    PUBLIC, DIMENSION(:,:), ALLOCATABLE :: gxx, gxy, gxz, gyy, gyz, gzz ! dimensions: z, odd/even p
  REAL(dp),    PUBLIC, DIMENSION(:,:), ALLOCATABLE :: dxdr, dxdZ, Rc, phic, Zc
  ! derivatives of magnetic field strength
  REAL(dp),    PUBLIC, DIMENSION(:,:), ALLOCATABLE :: dBdx, dBdy, dBdz, dlnBdz
  ! Relative magnetic field strength
  REAL(dp),    PUBLIC, DIMENSION(:,:), ALLOCATABLE :: hatB
  ! Relative strength of major radius
  REAL(dp),    PUBLIC, DIMENSION(:,:), ALLOCATABLE :: hatR, hatZ
  ! Some geometrical coefficients
  REAL(dp),    PUBLIC, DIMENSION(:,:) , ALLOCATABLE :: gradz_coeff  ! 1 / [ J_{xyz} \hat{B} ]
  ! Array to map the index of mode (kx,ky,-pi) to (kx+2pi*s*ky,ky,pi) for sheared periodic boundary condition
  INTEGER,     PUBLIC, DIMENSION(:,:), ALLOCATABLE :: ikx_zBC_L, ikx_zBC_R
  ! Geometric factor in front of the parallel phi derivative (not implemented)
  ! REAL(dp),    PUBLIC, DIMENSION(:,:), ALLOCATABLE :: Gamma_phipar
  ! pb_phase, for parallel boundary phase, contains the factor that occurs when taking into account
  !   that q0 is defined in the middle of the fluxtube whereas the radial position spans in [0,Lx)
  !   This shift introduces a (-1)^(Nexc*iky) phase change that is included in GENE
  COMPLEX(dp), PUBLIC, DIMENSION(:),   ALLOCATABLE :: pb_phase_L, pb_phase_R

  ! Functions
  PUBLIC :: geometry_readinputs, geometry_outputinputs,&
            eval_magnetic_geometry, set_ikx_zBC_map
CONTAINS


  SUBROUTINE geometry_readinputs
    ! Read the input parameters
    IMPLICIT NONE
    NAMELIST /GEOMETRY/ geom, q0, shear, eps,&
      kappa, s_kappa,delta, s_delta, zeta, s_zeta,& ! For miller
      parallel_bc, shift_y
    READ(lu_in,geometry)
    IF(shear .NE. 0._dp) SHEARED = .true.
    SELECT CASE(parallel_bc)
      CASE ('dirichlet')
      CASE ('periodic')
      CASE ('shearless')
      CASE ('disconnected')
      CASE DEFAULT
        ERROR STOP '>> ERROR << Parallel BC not recognized'
    END SELECT
    IF(my_id .EQ. 0) print*, 'Parallel BC : ', parallel_bc

  END SUBROUTINE geometry_readinputs

  subroutine eval_magnetic_geometry
    ! evalute metrix, elementwo_third_kpmaxts, jacobian and gradient
    implicit none
    REAL(dp) :: kx,ky
    COMPLEX(dp), DIMENSION(izs:ize) :: integrant
    real(dp) :: G1,G2,G3,Cx,Cy

    ! Allocate arrays
    CALL geometry_allocate_mem
    !
    IF( (Ny .EQ. 1) .AND. (Nz .EQ. 1)) THEN !1D perp linear run
      IF( my_id .eq. 0 ) WRITE(*,*) '1D perpendicular geometry'
      call eval_1D_geometry
    ELSE
      SELECT CASE(geom)
        CASE('s-alpha')
          IF( my_id .eq. 0 ) WRITE(*,*) 's-alpha geometry'
          call eval_salpha_geometry
        CASE('Z-pinch')
          IF( my_id .eq. 0 ) WRITE(*,*) 'Z-pinch geometry'
          call eval_zpinch_geometry
          SHEARED = .FALSE.
          shear   = 0._dp
        CASE('miller')
          IF( my_id .eq. 0 ) WRITE(*,*) 'Miller geometry'
          call set_miller_parameters(kappa,s_kappa,delta,s_delta,zeta,s_zeta)
          call get_miller(eps,major_R,major_Z,q0,shear,alpha_MHD,edge_opt,&
               C_y,C_xy,dpdx_pm_geom,gxx,gyy,gzz,gxy,gxz,gyz,&
               dBdx,dBdy,hatB,jacobian,dBdz,hatR,hatZ,dxdR,dxdZ,&
               Ckxky,gradz_coeff)
        CASE DEFAULT
          ERROR STOP '>> ERROR << geometry not recognized!!'
        END SELECT
    ENDIF
    !
    ! Evaluate perpendicular wavenumber
    !  k_\perp^2 = g^{xx} k_x^2 + 2 g^{xy}k_x k_y + k_y^2 g^{yy}
    !  normalized to rhos_
    DO eo = 0,1
      DO iz = izgs,izge
        DO iky = ikys, ikye
          ky = kyarray(iky)
          DO ikx = ikxs, ikxe
            kx = kxarray(ikx)
            ! there is a factor 1/B from the normalization; important to match GENE
            ! this factor comes from $b_a$ argument in the Bessel. Kperp is not used otherwise.
            kparray(iky, ikx, iz, eo) = &
            SQRT( gxx(iz,eo)*kx**2 + 2._dp*gxy(iz,eo)*kx*ky + gyy(iz,eo)*ky**2)/ hatB(iz,eo)
          ENDDO
        ENDDO
      ENDDO
      ! Curvature operator (Frei et al. 2022 eq 2.15)
      DO iz = izgs,izge
        G1 = gxx(iz,eo)*gyy(iz,eo)-gxy(iz,eo)*gxy(iz,eo)
        G2 = gxx(iz,eo)*gyz(iz,eo)-gxy(iz,eo)*gxz(iz,eo)
        G3 = gxy(iz,eo)*gyz(iz,eo)-gyy(iz,eo)*gxz(iz,eo)
        ! Here we divide by hatB because our equation is formulated with grad(lnB) terms (not gradB like in GENE)
        Cx =-(dBdy(iz,eo) + G2/G1*dBdz(iz,eo))/hatB(iz,eo)
        Cy = (dBdx(iz,eo) - G3/G1*dBdz(iz,eo))/hatB(iz,eo)

        DO iky = ikys, ikye
          ky = kyarray(iky)
           DO ikx= ikxs, ikxe
             kx = kxarray(ikx)
             Ckxky(iky, ikx, iz,eo) = (Cx*kx + Cy*ky)/C_xy
           ENDDO
        ENDDO
        ! coefficient in the front of parallel derivative
        gradz_coeff(iz,eo) = 1._dp /(jacobian(iz,eo)*hatB(iz,eo))
        ! d/dz(ln B) to correspond to the formulation in paper 2023
        dlnBdz(iz,eo)      = dBdz(iz,eo)/hatB(iz,eo)
        ! Geometric factor in front to the maxwellian dzphi term (not implemented)
        ! Gamma_phipar(iz,eo) = G2/G1
      ENDDO
    ENDDO


    ! set the mapping for parallel boundary conditions
    CALL set_ikx_zBC_map

    two_third_kpmax = 2._dp/3._dp * MAXVAL(kparray)
    !
    ! Compute the inverse z integrated Jacobian (useful for flux averaging)
    integrant = Jacobian(izs:ize,0) ! Convert into complex array
    CALL simpson_rule_z(integrant,iInt_Jacobian)
    iInt_Jacobian = 1._dp/iInt_Jacobian ! reverse it
  END SUBROUTINE eval_magnetic_geometry
  !
  !--------------------------------------------------------------------------------
  !

  SUBROUTINE eval_salpha_geometry
  ! evaluate s-alpha geometry model
  implicit none
  REAL(dp) :: z
  alpha_MHD = 0._dp

  parity: DO eo = 0,1
  zloop: DO iz = izgs,izge
    z = zarray(iz,eo)

    ! metric
      gxx(iz,eo) = 1._dp
      gxy(iz,eo) = shear*z - alpha_MHD*SIN(z)
      gxz(iz,eo) = 0._dp
      gyy(iz,eo) = 1._dp + (shear*z - alpha_MHD*SIN(z))**2
      gyz(iz,eo) = 1._dp/eps
      gzz(iz,eo) = 1._dp/eps**2
      dxdR(iz,eo)= COS(z)
      dxdZ(iz,eo)= SIN(z)

    ! Poloidal plane coordinates
      hatR(iz,eo) = 1._dp + eps*COS(z)
      hatZ(iz,eo) = 1._dp + eps*SIN(z)

    ! toroidal coordinates
      Rc  (iz,eo) = hatR(iz,eo)
      phic(iz,eo) = z
      Zc  (iz,eo) = hatZ(iz,eo)

    ! Relative strengh of modulus of B
      hatB(iz,eo) = 1._dp/(1._dp + eps*COS(z))

    ! Jacobian
      Jacobian(iz,eo) = q0/hatB(iz,eo)

    ! Derivative of the magnetic field strenght
      dBdx(iz,eo) = -COS(z)*hatB(iz,eo)**2 ! LB = 1
      dBdy(iz,eo) =  0._dp
      dBdz(iz,eo) =  eps*SIN(z)*hatB(iz,eo)**2

    ! Curvature factor
      C_xy = 1._dp

  ENDDO zloop
  ENDDO parity

  END SUBROUTINE eval_salpha_geometry
  !
  !--------------------------------------------------------------------------------
  !

  SUBROUTINE eval_zpinch_geometry
  implicit none
  REAL(dp) :: z
  alpha_MHD = 0._dp

  parity: DO eo = 0,1
  zloop: DO iz = izgs,izge
    z = zarray(iz,eo)

    ! metric
      gxx(iz,eo) = 1._dp
      gxy(iz,eo) = 0._dp
      gxz(iz,eo) = 0._dp
      gyy(iz,eo) = 1._dp ! 1/R but R is the normalization length
      gyz(iz,eo) = 0._dp
      gzz(iz,eo) = 1._dp
      dxdR(iz,eo)= COS(z)
      dxdZ(iz,eo)= SIN(z)

    ! Relative strengh of radius
      hatR(iz,eo) = 1._dp ! R but R is the normalization length
      hatZ(iz,eo) = 1._dp

    ! toroidal coordinates
      Rc  (iz,eo) = hatR(iz,eo)
      phic(iz,eo) = z
      Zc  (iz,eo) = hatZ(iz,eo)

    ! Jacobian
      Jacobian(iz,eo) = 1._dp ! R but R is the normalization length

    ! Relative strengh of modulus of B
      hatB   (iz,eo) = 1._dp

    ! Derivative of the magnetic field strenght
      dBdx(iz,eo) = -hatB(iz,eo) ! LB = 1
      dBdy(iz,eo) = 0._dp
      dBdz(iz,eo) = 0._dp ! Gene put a factor hatB or 1/hatR in this

  ENDDO zloop
  ENDDO parity

  ! Curvature factor
    C_xy = 1._dp
  END SUBROUTINE eval_zpinch_geometry
    !
    !--------------------------------------------------------------------------------
    !
  subroutine eval_1D_geometry
    ! evaluate 1D perp geometry model
    implicit none
    REAL(dp) :: z, kx, ky

    parity: DO eo = 0,1
    zloop: DO iz = izs,ize
     z = zarray(iz,eo)

    ! metric
       gxx(iz,eo) = 1._dp
       gxy(iz,eo) = 0._dp
       gyy(iz,eo) = 1._dp

    ! Relative strengh of radius
       hatR(iz,eo) = 1._dp

    ! Jacobian
       Jacobian(iz,eo) = 1._dp

    ! Relative strengh of modulus of B
       hatB(iz,eo) = 1._dp

    ! Curvature operator
       DO iky = ikys, ikye
         ky = kyarray(iky)
          DO ikx= ikxs, ikxe
            kx = kxarray(ikx)
            Ckxky(ikx, iky, iz,eo) = -kx ! .. multiply by hatB to cancel the 1/ hatB factor in moments_eqs_rhs.f90 routine
          ENDDO
       ENDDO
    ! coefficient in the front of parallel derivative
       gradz_coeff(iz,eo) = 1._dp
  ENDDO zloop
  ENDDO parity

   END SUBROUTINE eval_1D_geometry

   !
   !--------------------------------------------------------------------------------
   !

 SUBROUTINE set_ikx_zBC_map
 IMPLICIT NONE
 REAL :: shift

 ALLOCATE(ikx_zBC_L(ikys:ikye,ikxs:ikxe))
 ALLOCATE(ikx_zBC_R(ikys:ikye,ikxs:ikxe))
 ALLOCATE(pb_phase_L(ikys:ikye))
 ALLOCATE(pb_phase_R(ikys:ikye))
 !! No shear case (simple id mapping) or not at the end of the z domain
 !3            | 1    2    3    4    5    6 |  ky = 3 dky
 !2   ky       | 1    2    3    4    5    6 |  ky = 2 dky
 !1   A        | 1    2    3    4    5    6 |  ky = 1 dky
 !0   | -> kx  | 1____2____3____4____5____6 |  ky = 0 dky
 !(e.g.) kx =    0   0.1  0.2  0.3 -0.2 -0.1  (dkx=free)
 DO iky = ikys,ikye
   DO ikx = ikxs,ikxe
     ikx_zBC_L(iky,ikx) = ikx ! connect to itself per default
     ikx_zBC_R(iky,ikx) = ikx
   ENDDO
   pb_phase_L(iky) = 1._dp ! no phase change per default
   pb_phase_R(iky) = 1._dp
 ENDDO
 ! Parallel boundary are not trivial for sheared case and if
 !  the user does not ask explicitly for shearless bc
 IF(SHEARED .AND. (parallel_bc .NE. 'shearless')) THEN
   !!!!!!!!!! LEFT PARALLEL BOUNDARY
   ! Modify connection map only at border of z (matters for MPI z-parallelization)
   IF(contains_zmin) THEN ! Check if the process is at the start of the fluxtube
     DO iky = ikys,ikye
       ! Formula for the shift due to shear after Npol turns
       shift = 2._dp*PI*shear*kyarray(iky)*Npol
         DO ikx = ikxs,ikxe
           ! Usual formula for shifting indices using that dkx = 2pi*shear*dky/Nexc
           ikx_zBC_L(iky,ikx) = ikx-(iky-1)*Nexc
           ! Check if it points out of the kx domain
           ! IF( (kxarray(ikx) - shift) .LT. kx_min ) THEN
           IF( (ikx-(iky-1)*Nexc) .LT. 1 ) THEN ! outside of the frequ domain
             SELECT CASE(parallel_bc)
               CASE ('dirichlet')! connected to 0
                 ikx_zBC_L(iky,ikx) = -99
               CASE ('periodic')
                 ikx_zBC_L(iky,ikx) = ikx
               CASE ('cyclic')! reroute it by cycling through modes
                 ikx_zBC_L(iky,ikx) = MODULO(ikx_zBC_L(iky,ikx)-1,Nkx)+1
             END SELECT
           ENDIF
         ENDDO
         ! phase present in GENE from a shift of the x origin by Lx/2 (useless?)
         ! We also put the user defined shift in the y direction (see Volcokas et al. 2022)
         pb_phase_L(iky) = (-1._dp)**(Nexc*(iky-1))*EXP(imagu*REAL(iky-1,dp)*2._dp*pi*shift_y)
     ENDDO
   ENDIF
   ! Option for disconnecting every modes, viz. connecting all boundary to 0
   IF(parallel_bc .EQ. 'disconnected') ikx_zBC_L = -99
   !!!!!!!!!! RIGHT PARALLEL BOUNDARY
   IF(contains_zmax) THEN ! Check if the process is at the end of the flux-tube
     DO iky = ikys,ikye
       ! Formula for the shift due to shear after Npol
       shift = 2._dp*PI*shear*kyarray(iky)*Npol
         DO ikx = ikxs,ikxe
           ! Usual formula for shifting indices
           ikx_zBC_R(iky,ikx) = ikx+(iky-1)*Nexc
           ! Check if it points out of the kx domain
           ! IF( (kxarray(ikx) + shift) .GT. kx_max ) THEN ! outside of the frequ domain
           IF( (ikx+(iky-1)*Nexc) .GT. Nkx ) THEN ! outside of the frequ domain
             SELECT CASE(parallel_bc)
               CASE ('dirichlet') ! connected to 0
                 ikx_zBC_R(iky,ikx) = -99
               CASE ('periodic') ! connected to itself as for shearless
                 ikx_zBC_R(iky,ikx) = ikx
               CASE ('cyclic')
                 ! write(*,*) 'check',ikx,iky, kxarray(ikx) + shift, '>', kx_max
                 ikx_zBC_R(iky,ikx) = MODULO(ikx_zBC_R(iky,ikx)-1,Nkx)+1
             END SELECT
           ENDIF
         ENDDO
         ! phase present in GENE from a shift ofthe x origin by Lx/2 (useless?)
         ! We also put the user defined shift in the y direction (see Volcokas et al. 2022)
         pb_phase_R(iky) = (-1._dp)**(Nexc*(iky-1))*EXP(-imagu*REAL(iky-1,dp)*2._dp*pi*shift_y)
     ENDDO
   ENDIF
   ! Option for disconnecting every modes, viz. connecting all boundary to 0
   IF(parallel_bc .EQ. 'disconnected') ikx_zBC_R = -99
  ENDIF
  ! write(*,*) kxarray
  ! write(*,*) kyarray
  ! write(*,*) 'ikx_zBC_L :-----------'
  ! DO iky = ikys,ikye
  !   print*, ikx_zBC_L(iky,:)
  ! enddo
  ! print*, pb_phase_L
  ! write(*,*) 'ikx_zBC_R :-----------'
  ! DO iky = ikys,ikye
  !   print*, ikx_zBC_R(iky,:)
  ! enddo
  ! print*, pb_phase_R
  ! print*, shift_y
  ! stop
  !!!!!!! Example of maps ('x' means connected to 0 value, in the table it is -99)
  ! dirichlet connection map BC of the RIGHT boundary (z=pi*Npol-dz)
  !3            | 4    x    x    x    2    3 |  ky = 3 dky
  !2   ky       | 3    4    x    x    1    2 |  ky = 2 dky
  !1   A        | 2    3    4    x    6    1 |  ky = 1 dky
  !0   | -> kx  | 1____2____3____4____5____6 |  ky = 0 dky
  !kx =           0   0.1  0.2  0.3 -0.2 -0.1  (dkx=2pi*shear*npol*dky)

  ! periodic connection map BC of the RIGHT boundary (z=pi*Npol-dz)
  !3            | 4    2    3    4    2    3 |  ky = 3 dky
  !2   ky       | 3    4    3    4    1    2 |  ky = 2 dky
  !1   A        | 2    3    4    4    6    1 |  ky = 1 dky
  !0   | -> kx  | 1____2____3____4____5____6 |  ky = 0 dky
  !kx =           0   0.1  0.2  0.3 -0.2 -0.1  (dkx=2pi*shear*npol*dky)

  ! cyclic connection map BC of the LEFT boundary (z=-pi*Npol)
  !3            | 4    5    6    1    2    3 |  ky = 3 dky
  !2   ky       | 5    6    1    2    3    4 |  ky = 2 dky
  !1   A        | 6    1    2    3    4    5 |  ky = 1 dky
  !0   | -> kx  | 1____2____3____4____5____6 |  ky = 0 dky
  !(e.g.) kx =    0   0.1  0.2  0.3 -0.2 -0.1  (dkx=2pi*shear*npol*dky)

  ! shearless connection map BC of the LEFT/RIGHT boundary (z=+/-pi*Npol)
  !3            | 1    2    3    4    5    6 |  ky = 3 dky
  !2   ky       | 1    2    3    4    5    6 |  ky = 2 dky
  !1   A        | 1    2    3    4    5    6 |  ky = 1 dky
  !0   | -> kx  | 1____2____3____4____5____6 |  ky = 0 dky
  !(e.g.) kx =    0   0.1  0.2  0.3 -0.2 -0.1  (dkx=2pi*shear*npol*dky)

  ! disconnected connection map BC of the LEFT/RIGHT boundary (z=+/-pi*Npol)
  !3            | x    x    x    x    x    x |  ky = 3 dky
  !2   ky       | x    x    x    x    x    x |  ky = 2 dky
  !1   A        | x    x    x    x    x    x |  ky = 1 dky
  !0   | -> kx  | x____x____x____x____x____x |  ky = 0 dky
  !(e.g.) kx =    0   0.1  0.2  0.3 -0.2 -0.1  (dkx=2pi*shear*npol*dky)
END SUBROUTINE set_ikx_zBC_map

!
!--------------------------------------------------------------------------------
!

   SUBROUTINE geometry_allocate_mem

       ! Curvature and geometry
       CALL allocate_array( Ckxky,   ikys,ikye, ikxs,ikxe,izgs,izge,0,1)
       CALL allocate_array(   Jacobian,izgs,izge, 0,1)
       CALL allocate_array(        gxx,izgs,izge, 0,1)
       CALL allocate_array(        gxy,izgs,izge, 0,1)
       CALL allocate_array(        gxz,izgs,izge, 0,1)
       CALL allocate_array(        gyy,izgs,izge, 0,1)
       CALL allocate_array(        gyz,izgs,izge, 0,1)
       CALL allocate_array(        gzz,izgs,izge, 0,1)
       CALL allocate_array(       dBdx,izgs,izge, 0,1)
       CALL allocate_array(       dBdy,izgs,izge, 0,1)
       CALL allocate_array(       dBdz,izgs,izge, 0,1)
       CALL allocate_array(     dlnBdz,izgs,izge, 0,1)
       CALL allocate_array(       hatB,izgs,izge, 0,1)
       ! CALL allocate_array(Gamma_phipar,izgs,izge, 0,1) (not implemented)
       CALL allocate_array(       hatR,izgs,izge, 0,1)
       CALL allocate_array(       hatZ,izgs,izge, 0,1)
       CALL allocate_array(         Rc,izgs,izge, 0,1)
       CALL allocate_array(       phic,izgs,izge, 0,1)
       CALL allocate_array(         Zc,izgs,izge, 0,1)
       CALL allocate_array(       dxdR,izgs,izge, 0,1)
       CALL allocate_array(       dxdZ,izgs,izge, 0,1)
       call allocate_array(gradz_coeff,izgs,izge, 0,1)
       CALL allocate_array( kparray, ikys,ikye, ikxs,ikxe,izgs,izge,0,1)

   END SUBROUTINE geometry_allocate_mem

   SUBROUTINE geometry_outputinputs(fidres, str)
     ! Write the input parameters to the results_xx.h5 file

     USE futils, ONLY: attach

     USE prec_const
     IMPLICIT NONE

     INTEGER, INTENT(in) :: fidres
     CHARACTER(len=256), INTENT(in) :: str
     CALL attach(fidres, TRIM(str),"geometry",  geom)
     CALL attach(fidres, TRIM(str),      "q0",    q0)
     CALL attach(fidres, TRIM(str),   "shear", shear)
     CALL attach(fidres, TRIM(str),     "eps",   eps)
   END SUBROUTINE geometry_outputinputs
end module geometry