#include "cppdefs.h"

MODULE p4zmort
   !!======================================================================
   !!                         ***  MODULE p4zmort  ***
   !! TOP :   PISCES Compute the mortality terms for phytoplankton
   !!======================================================================
   !! History :   1.0  !  2002     (O. Aumont)  Original code
   !!             2.0  !  2007-12  (C. Ethe, G. Madec)  F90
#if defined key_pisces
   !!----------------------------------------------------------------------
   !!   p4z_mort       : Compute the mortality terms for phytoplankton
   !!   p4z_mort_init  : Initialize the mortality params for phytoplankton
   !!----------------------------------------------------------------------
   USE oce_trc         ! shared variables between ocean and passive tracers
   USE trc             ! passive tracers common variables 
   USE sms_pisces      ! PISCES Source Minus Sink variables
   USE p4zprod         ! Primary productivity 
   USE p2zlim          ! Phytoplankton limitation terms
   USE p4zlim          ! Phytoplankton limitation terms
   USE prtctl          ! print control for debugging

   !! * Substitutions
#  include "ocean2pisces.h90"   
#  include "do_loop_substitute.h90"
#  include "read_nml_substitute.h90"

   IMPLICIT NONE
   PRIVATE

   PUBLIC   p4z_mort           ! Called from p4zbio.F90 
   PUBLIC   p4z_mort_init      ! Called from trcini_pisces.F90 

   REAL(wp), PUBLIC ::   wchln    !: Quadratic mortality rate of nanophytoplankton
   REAL(wp), PUBLIC ::   wchld    !: Quadratic mortality rate of diatoms
   REAL(wp), PUBLIC ::   mpratn   !: Linear mortality rate of nanophytoplankton
   REAL(wp), PUBLIC ::   mpratd   !: Linear mortality rate of diatoms

   !!----------------------------------------------------------------------
   !! NEMO/TOP 4.0 , NEMO Consortium (2018)
   !! $Id: p4zmort.F90 15459 2021-10-29 08:19:18Z cetlod $ 
   !! Software governed by the CeCILL license (see ./LICENSE)
   !!----------------------------------------------------------------------
CONTAINS

   SUBROUTINE p4z_mort( kt, Kbb, Krhs )
      !!---------------------------------------------------------------------
      !!                     ***  ROUTINE p4z_mort  ***
      !!
      !! ** Purpose :   Calls the different subroutine to compute
      !!                the different phytoplankton mortality terms
      !!
      !! ** Method  : - ???
      !!---------------------------------------------------------------------
      INTEGER, INTENT(in) ::   kt ! ocean time step
      INTEGER, INTENT(in) ::   Kbb, Krhs  ! time level indices
      !!---------------------------------------------------------------------
      !
      CALL p4z_mort_nano( Kbb, Krhs )            ! nanophytoplankton
      CALL p4z_mort_diat( Kbb, Krhs )            ! diatoms
      !
   END SUBROUTINE p4z_mort


   SUBROUTINE p4z_mort_nano( Kbb, Krhs )
      !!---------------------------------------------------------------------
      !!                     ***  ROUTINE p4z_mort_nano  ***
      !!
      !! ** Purpose :   Compute the mortality terms for nanophytoplankton
      !!
      !! ** Method  :   Both quadratic and simili linear mortality terms
      !!---------------------------------------------------------------------
      INTEGER, INTENT(in) ::   Kbb, Krhs  ! time level indices
      INTEGER  ::   ji, jj, jk
      REAL(wp) ::   zcompaph
      REAL(wp) ::   zfactfe, zfactch, zprcaca, zfracal
      REAL(wp) ::   ztortp , zrespp , zmortp, zlim1, zlim2 
      CHARACTER (len=25) ::   charout
      !!---------------------------------------------------------------------
      !
      IF( ln_timing )   CALL timing_start('p4z_mort_nano')
      !
      prodcal(:,:,:) = 0._wp   ! calcite production variable set to zero
      DO_3D( 0, 0, 0, 0, 1, jpkm1)
         zcompaph = MAX( ( tr(ji,jj,jk,jpphy,Kbb) - 1e-9 ), 0.e0 )

         ! Quadratic mortality of nano due to aggregation during
         ! blooms (Doney et al. 1996)
         ! -----------------------------------------------------
         zlim2   = xlimphy(ji,jj,jk) * xlimphy(ji,jj,jk)
         zlim1   = 0.25 * ( 1. - zlim2 ) / ( 0.25 + zlim2 ) * tr(ji,jj,jk,jpphy,Kbb)
         zrespp  = wchln * 1.e6 * xstep * zlim1 * xdiss(ji,jj,jk) * zcompaph

         ! Phytoplankton linear mortality
         ! A michaelis-menten like term is introduced to avoid 
         ! extinction of nanophyto in highly limited areas
         ! ----------------------------------------------------
         ztortp = mpratn * xstep * zcompaph / ( xkmort + tr(ji,jj,jk,jpphy,Kbb) ) &
             &    * tr(ji,jj,jk,jpphy,Kbb)

         zmortp = zrespp + ztortp
         
         !   Update the arrays TRA which contains the biological sources and sinks
         zfactfe = tr(ji,jj,jk,jpnfe,Kbb)/(tr(ji,jj,jk,jpphy,Kbb)+rtrn)
         zfactch = tr(ji,jj,jk,jpnch,Kbb)/(tr(ji,jj,jk,jpphy,Kbb)+rtrn)
         tr(ji,jj,jk,jpphy,Krhs) = tr(ji,jj,jk,jpphy,Krhs) - zmortp
         tr(ji,jj,jk,jpnch,Krhs) = tr(ji,jj,jk,jpnch,Krhs) - zmortp * zfactch
         tr(ji,jj,jk,jpnfe,Krhs) = tr(ji,jj,jk,jpnfe,Krhs) - zmortp * zfactfe

         ! Production PIC particles due to mortality
         zprcaca = xfracal(ji,jj,jk) * zmortp
         prodcal(ji,jj,jk) = prodcal(ji,jj,jk) + zprcaca  ! prodcal=prodcal(nanophy)+prodcal(microzoo)+prodcal(mesozoo)

         ! POC associated with the shell is supposed to be routed to 
         ! big particles because of the ballasting effect
         zfracal = 0.5 * xfracal(ji,jj,jk)
         tr(ji,jj,jk,jpdic,Krhs) = tr(ji,jj,jk,jpdic,Krhs) - zprcaca
         tr(ji,jj,jk,jptal,Krhs) = tr(ji,jj,jk,jptal,Krhs) - 2. * zprcaca
         tr(ji,jj,jk,jpcal,Krhs) = tr(ji,jj,jk,jpcal,Krhs) + zprcaca
         tr(ji,jj,jk,jppoc,Krhs) = tr(ji,jj,jk,jppoc,Krhs) + zmortp
         prodpoc(ji,jj,jk) = prodpoc(ji,jj,jk) + zmortp

         ! Update the arrays TRA which contains the biological sources and sinks
         tr(ji,jj,jk,jpsfe,Krhs) = tr(ji,jj,jk,jpsfe,Krhs) + zmortp * zfactfe
         !
      END_3D
      !
       IF(sn_cfctl%l_prttrc)   THEN  ! print mean trends (used for debugging)
         WRITE(charout, FMT="('nano')")
         CALL prt_ctl_info( charout, cdcomp = 'top' )
     !    CALL prt_ctl(tab4d_1=tr(:,:,:,:,Krhs), mask1=tmask, clinfo=ctrcnm)
       ENDIF
      !
      IF( ln_timing )   CALL timing_stop('p4z_mort_nano')
      !
   END SUBROUTINE p4z_mort_nano


   SUBROUTINE p4z_mort_diat( Kbb, Krhs )
      !!---------------------------------------------------------------------
      !!                     ***  ROUTINE p4z_mort_diat  ***
      !!
      !! ** Purpose :   Compute the mortality terms for diatoms
      !!
      !! ** Method  : - Both quadratic and simili linear mortality terms
      !!---------------------------------------------------------------------
      INTEGER, INTENT(in) ::   Kbb, Krhs  ! time level indices
      INTEGER  ::   ji, jj, jk
      REAL(wp) ::   zfactfe,zfactsi,zfactch, zcompadi
      REAL(wp) ::   zrespp2, ztortp2, zmortp2
      REAL(wp) ::   zlim2, zlim1
      CHARACTER (len=25) ::   charout
      !!---------------------------------------------------------------------
      !
      IF( ln_timing )   CALL timing_start('p4z_mort_diat')
      !
      ! Aggregation term for diatoms is increased in case of nutrient
      ! stress as observed in reality. The stressed cells become more
      ! sticky and coagulate to sink quickly out of the euphotic zone
      ! This is due to the production of EPS by stressed cells
      ! -------------------------------------------------------------

      DO_3D( 0, 0, 0, 0, 1, jpkm1)

         zcompadi = MAX( ( tr(ji,jj,jk,jpdia,Kbb) - 1e-9), 0. )

         ! Aggregation term for diatoms is increased in case of nutrient
         ! stress as observed in reality. The stressed cells become more
         ! sticky and coagulate to sink quickly out of the euphotic zone
         ! ------------------------------------------------------------
         zlim2   = xlimdia(ji,jj,jk) * xlimdia(ji,jj,jk)
         zlim1   = 0.25 * ( 1. - zlim2 ) / ( 0.25 + zlim2 ) 
         zrespp2 = 1.e6 * xstep * wchld * zlim1 * xdiss(ji,jj,jk) * zcompadi * tr(ji,jj,jk,jpdia,Kbb)

         ! Phytoplankton linear mortality
         ! A michaelis-menten like term is introduced to avoid 
         ! extinction of diatoms in highly limited areas
         !  ---------------------------------------------------
         ztortp2 = mpratd * xstep * tr(ji,jj,jk,jpdia,Kbb)  &
            &     / ( xkmort + tr(ji,jj,jk,jpdia,Kbb) ) * zcompadi 

         zmortp2 = zrespp2 + ztortp2

         !   Update the arrays trends which contains the biological sources and sinks
         !   ---------------------------------------------------------------------
         zfactch = tr(ji,jj,jk,jpdch,Kbb) / ( tr(ji,jj,jk,jpdia,Kbb) + rtrn )
         zfactfe = tr(ji,jj,jk,jpdfe,Kbb) / ( tr(ji,jj,jk,jpdia,Kbb) + rtrn )
         zfactsi = tr(ji,jj,jk,jpdsi,Kbb) / ( tr(ji,jj,jk,jpdia,Kbb) + rtrn )
         tr(ji,jj,jk,jpdia,Krhs) = tr(ji,jj,jk,jpdia,Krhs) - zmortp2 
         tr(ji,jj,jk,jpdch,Krhs) = tr(ji,jj,jk,jpdch,Krhs) - zmortp2 * zfactch
         tr(ji,jj,jk,jpdfe,Krhs) = tr(ji,jj,jk,jpdfe,Krhs) - zmortp2 * zfactfe
         tr(ji,jj,jk,jpdsi,Krhs) = tr(ji,jj,jk,jpdsi,Krhs) - zmortp2 * zfactsi
         tr(ji,jj,jk,jpgsi,Krhs) = tr(ji,jj,jk,jpgsi,Krhs) + zmortp2 * zfactsi

         ! Half of the linear mortality term is routed to big particles
         ! becaue of the ballasting effect
         tr(ji,jj,jk,jpgoc,Krhs) = tr(ji,jj,jk,jpgoc,Krhs) + zrespp2
         tr(ji,jj,jk,jppoc,Krhs) = tr(ji,jj,jk,jppoc,Krhs) + ztortp2
         prodpoc(ji,jj,jk) = prodpoc(ji,jj,jk) + ztortp2
         prodgoc(ji,jj,jk) = prodgoc(ji,jj,jk) + zrespp2
         tr(ji,jj,jk,jpsfe,Krhs) = tr(ji,jj,jk,jpsfe,Krhs) + ztortp2 * zfactfe
         tr(ji,jj,jk,jpbfe,Krhs) = tr(ji,jj,jk,jpbfe,Krhs) + zrespp2 * zfactfe
      END_3D
      !
      IF(sn_cfctl%l_prttrc) THEN      ! print mean trends (used for debugging)
         WRITE(charout, FMT="('diat')")
         CALL prt_ctl_info( charout, cdcomp = 'top' )
   !      CALL prt_ctl(tab4d_1=tr(:,:,:,:,Krhs), mask1=tmask, clinfo=ctrcnm)
      ENDIF
      !
      IF( ln_timing )   CALL timing_stop('p4z_mort_diat')
      !
   END SUBROUTINE p4z_mort_diat


   SUBROUTINE p4z_mort_init
      !!----------------------------------------------------------------------
      !!                  ***  ROUTINE p4z_mort_init  ***
      !!
      !! ** Purpose :   Initialization of phytoplankton parameters
      !!
      !! ** Method  :   Read the namp4zmort namelist and check the parameters
      !!              called at the first timestep
      !!
      !! ** input   :   Namelist namp4zmort
      !!
      !!----------------------------------------------------------------------
      INTEGER ::   ios   ! Local integer
      !
      NAMELIST/namp4zmort/ wchln, wchld, mpratn, mpratd
      !!----------------------------------------------------------------------
      !
      IF(lwp) THEN
         WRITE(numout,*) 
         WRITE(numout,*) 'p4z_mort_init : Initialization of phytoplankton mortality parameters'
         WRITE(numout,*) '~~~~~~~~~~~~~'
      ENDIF
      !
      READ_NML_REF(numnatp,namp4zmort)
      READ_NML_CFG(numnatp,namp4zmort)
      IF(lwm) WRITE( numonp, namp4zmort )
      !
      IF(lwp) THEN                         ! control print
         WRITE(numout,*) '   Namelist : namp4zmort'
         WRITE(numout,*) '      quadratic mortality of phytoplankton        wchln  =', wchln
         WRITE(numout,*) '      maximum quadratic mortality of diatoms      wchld  =', wchld
         WRITE(numout,*) '      phytoplankton mortality rate                mpratn =', mpratn
         WRITE(numout,*) '      Diatoms mortality rate                      mpratd =', mpratd
      ENDIF
      !
   END SUBROUTINE p4z_mort_init

#else
   !!======================================================================
   !!  Dummy module :                                   No PISCES bio-model
   !!======================================================================
CONTAINS
   SUBROUTINE p4z_mort                    ! Empty routine
   END SUBROUTINE p4z_mort
#endif

   !!======================================================================
END MODULE p4zmort
