Changeset 12537 for NEMO/branches/2019/dev_r11708_aumont_PISCES_QUOTA/src/TOP/PISCES/P4Z/p4zmort.F90

Timestamp:

2020-03-11T16:02:54+01:00 (4 years ago)

Author:

aumont

Message:

Comments in routines have been revised and significantly augmented

File:

• NEMO/branches/2019/dev_r11708_aumont_PISCES_QUOTA/src/TOP/PISCES/P4Z/p4zmort.F90 (modified) (9 diffs)

NEMO/branches/2019/dev_r11708_aumont_PISCES_QUOTA/src/TOP/PISCES/P4Z/p4zmort.F90

@@ -20 +20 @@
    PRIVATE
 
-   PUBLIC   p4z_mort    
-   PUBLIC   p4z_mort_init    
-
-   REAL(wp), PUBLIC ::   wchln    !:
-   REAL(wp), PUBLIC ::   wchld    !:
-   REAL(wp), PUBLIC ::   wchldm   !:
-   REAL(wp), PUBLIC ::   mpratn   !:
-   REAL(wp), PUBLIC ::   mpratd   !:
+   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 ::   wchldm   !: Maximum quadratic mortality rate of diatoms
+   REAL(wp), PUBLIC ::   mpratn   !: Linear mortality rate of nanophytoplankton
+   REAL(wp), PUBLIC ::   mpratd   !: Linear mortality rate of diatoms
 
    !!----------------------------------------------------------------------
@@ -40 +40 @@
       !!                     ***  ROUTINE p4z_mort  ***
       !!
-      !! ** Purpose :   Calls the different subroutine to initialize and compute
+      !! ** Purpose :   Calls the different subroutine to compute
       !!                the different phytoplankton mortality terms
       !!
@@ -49 +49 @@
       !
       CALL p4z_nano            ! nanophytoplankton
-      !
       CALL p4z_diat            ! diatoms
       !
@@ -82 +81 @@
                !     to 0
                zsizerat = MIN(1., MAX( 0., (quotan(ji,jj,jk) - 0.2) / 0.3) ) * trb(ji,jj,jk,jpphy)
-               !     Squared mortality of Phyto similar to a sedimentation term during
-               !     blooms (Doney et al. 1996)
+
+               ! Quadratic mortality of nano due to aggregation during
+               ! blooms (Doney et al. 1996)
+               ! -----------------------------------------------------
                zrespp = wchln * 1.e6 * xstep * xdiss(ji,jj,jk) * zcompaph * zsizerat 
 
-               !     Phytoplankton mortality. This mortality loss is slightly
-               !     increased when nutrients are limiting phytoplankton growth
-               !     as observed for instance in case of iron limitation.
+               ! Phytoplankton linear mortality
+               ! A michaelis-menten like term is introduced to avoid 
+               ! extinction of nanophyto in highly limited areas
+               ! ----------------------------------------------------
                ztortp = mpratn * xstep * zcompaph / ( xkmort + trb(ji,jj,jk,jpphy) ) * zsizerat
 
                zmortp = zrespp + ztortp
 
-               !   Update the arrays TRA which contains the biological sources and sinks
-
+               ! Update the arrays TRA which contains the biological sources and sinks
                zfactfe = trb(ji,jj,jk,jpnfe)/(trb(ji,jj,jk,jpphy)+rtrn)
                zfactch = trb(ji,jj,jk,jpnch)/(trb(ji,jj,jk,jpphy)+rtrn)
@@ -100 +101 @@
                tra(ji,jj,jk,jpnch) = tra(ji,jj,jk,jpnch) - zmortp * zfactch
                tra(ji,jj,jk,jpnfe) = tra(ji,jj,jk,jpnfe) - 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)
-               !
                zfracal = 0.5 * xfracal(ji,jj,jk)
                tra(ji,jj,jk,jpdic) = tra(ji,jj,jk,jpdic) - zprcaca
@@ -146 +146 @@
       IF( ln_timing )   CALL timing_start('p4z_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
-      !     ------------------------------------------------------------
+      ! 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
+      ! -------------------------------------------------------------
 
       DO jk = 1, jpkm1
@@ -157 +157 @@
                zcompadi = MAX( ( trb(ji,jj,jk,jpdia) - 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
-               !     ------------------------------------------------------------
-               !  Phytoplankton respiration 
-               !     ------------------------
+               ! 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 + wchldm * zlim1 ) * xdiss(ji,jj,jk) * zcompadi * trb(ji,jj,jk,jpdia)
 
-               !     Phytoplankton mortality. 
-               !     ------------------------
+               ! Phytoplankton linear mortality
+               ! A michaelis-menten like term is introduced to avoid 
+               ! extinction of diatoms in highly limited areas
+               !  ---------------------------------------------------
                ztortp2 = mpratd * xstep * trb(ji,jj,jk,jpdia)  / ( xkmort + trb(ji,jj,jk,jpdia) ) * zcompadi 
 
                zmortp2 = zrespp2 + ztortp2
 
-               !   Update the arrays tra which contains the biological sources and sinks
+               ! Update the arrays tra which contains the biological sources and sinks
                !   ---------------------------------------------------------------------
                zfactch = trb(ji,jj,jk,jpdch) / ( trb(ji,jj,jk,jpdia) + rtrn )
@@ -210 +210 @@
       !! ** Purpose :   Initialization of phytoplankton parameters
       !!
-      !! ** Method  :   Read the nampismort namelist and check the parameters
+      !! ** Method  :   Read the namp4zmort namelist and check the parameters
       !!              called at the first timestep
       !!
-      !! ** input   :   Namelist nampismort
+      !! ** input   :   Namelist namp4zmort
       !!
       !!----------------------------------------------------------------------
@@ -227 +227 @@
       ENDIF
       !
-      REWIND( numnatp_ref )              ! Namelist nampismort in reference namelist : Pisces phytoplankton
+      REWIND( numnatp_ref )              ! Namelist namp4zmort in reference namelist : Pisces phytoplankton
       READ  ( numnatp_ref, namp4zmort, IOSTAT = ios, ERR = 901)
 901   IF( ios /= 0 )   CALL ctl_nam ( ios , 'namp4zmort in reference namelist' )
-      REWIND( numnatp_cfg )              ! Namelist nampismort in configuration namelist : Pisces phytoplankton
+      REWIND( numnatp_cfg )              ! Namelist namp4zmort in configuration namelist : Pisces phytoplankton
       READ  ( numnatp_cfg, namp4zmort, IOSTAT = ios, ERR = 902 )
 902   IF( ios >  0 )   CALL ctl_nam ( ios , 'namp4zmort in configuration namelist' )