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Changeset 12340 for NEMO/branches/2019/dev_r11943_MERGE_2019/src/TOP/PISCES/P4Z/p5zmeso.F90 – NEMO

Ignore:
Timestamp:
2020-01-27T15:31:53+01:00 (4 years ago)
Author:
acc
Message:

Branch 2019/dev_r11943_MERGE_2019. This commit introduces basic do loop macro
substitution to the 2019 option 1, merge branch. These changes have been SETTE
tested. The only addition is the do_loop_substitute.h90 file in the OCE directory but
the macros defined therein are used throughout the code to replace identifiable, 2D-
and 3D- nested loop opening and closing statements with single-line alternatives. Code
indents are also adjusted accordingly.

The following explanation is taken from comments in the new header file:

This header file contains preprocessor definitions and macros used in the do-loop
substitutions introduced between version 4.0 and 4.2. The primary aim of these macros
is to assist in future applications of tiling to improve performance. This is expected
to be achieved by alternative versions of these macros in selected locations. The
initial introduction of these macros simply replaces all identifiable nested 2D- and
3D-loops with single line statements (and adjusts indenting accordingly). Do loops
are identifiable if they comform to either:

DO jk = ....

DO jj = .... DO jj = ...

DO ji = .... DO ji = ...
. OR .
. .

END DO END DO

END DO END DO

END DO

and white-space variants thereof.

Additionally, only loops with recognised jj and ji loops limits are treated; these are:
Lower limits of 1, 2 or fs_2
Upper limits of jpi, jpim1 or fs_jpim1 (for ji) or jpj, jpjm1 or fs_jpjm1 (for jj)

The macro naming convention takes the form: DO_2D_BT_LR where:

B is the Bottom offset from the PE's inner domain;
T is the Top offset from the PE's inner domain;
L is the Left offset from the PE's inner domain;
R is the Right offset from the PE's inner domain

So, given an inner domain of 2,jpim1 and 2,jpjm1, a typical example would replace:

DO jj = 2, jpj

DO ji = 1, jpim1
.
.

END DO

END DO

with:

DO_2D_01_10
.
.
END_2D

similar conventions apply to the 3D loops macros. jk loop limits are retained
through macro arguments and are not restricted. This includes the possibility of
strides for which an extra set of DO_3DS macros are defined.

In the example definition below the inner PE domain is defined by start indices of
(kIs, kJs) and end indices of (kIe, KJe)

#define DO_2D_00_00 DO jj = kJs, kJe ; DO ji = kIs, kIe
#define END_2D END DO ; END DO

TO DO:

Only conventional nested loops have been identified and replaced by this step. There are constructs such as:

DO jk = 2, jpkm1

z2d(:,:) = z2d(:,:) + e3w(:,:,jk,Kmm) * z3d(:,:,jk) * wmask(:,:,jk)

END DO

which may need to be considered.

File:
1 edited

Legend:

Unmodified
Added
Removed

  • NEMO/branches/2019/dev_r11943_MERGE_2019/src/TOP/PISCES/P4Z/p5zmeso.F90

    r12260 r12340  
    5151   LOGICAL,  PUBLIC ::  bmetexc2     !: Use of excess carbon for respiration 
    5252 
     53   !! * Substitutions 
     54#  include "do_loop_substitute.h90" 
    5355   !!---------------------------------------------------------------------- 
    5456   !! NEMO/TOP 4.0 , NEMO Consortium (2018) 
    … …  
    9698      IF ( bmetexc2 ) zmetexcess = 1.0 
    9799 
    98       DO jk = 1, jpkm1 
    99          DO jj = 1, jpj 
    100             DO ji = 1, jpi 
    101                zcompam   = MAX( ( tr(ji,jj,jk,jpmes,Kbb) - 1.e-9 ), 0.e0 ) 
    102                zfact     = xstep * tgfunc2(ji,jj,jk) * zcompam 
    103  
    104                !   Michaelis-Menten mortality rates of mesozooplankton 
    105                !   --------------------------------------------------- 
    106                zrespz   = resrat2 * zfact * ( tr(ji,jj,jk,jpmes,Kbb) / ( xkmort + tr(ji,jj,jk,jpmes,Kbb) )  & 
    107                &          + 3. * nitrfac(ji,jj,jk) ) 
    108  
    109                !   Zooplankton mortality. A square function has been selected with 
    110                !   no real reason except that it seems to be more stable and may mimic predation 
    111                !   --------------------------------------------------------------- 
    112                ztortz   = mzrat2 * 1.e6 * zfact * tr(ji,jj,jk,jpmes,Kbb) * (1. - nitrfac(ji,jj,jk)) 
    113  
    114                !   Computation of the abundance of the preys 
    115                !   A threshold can be specified in the namelist 
    116                !   -------------------------------------------- 
    117                zcompadi  = MAX( ( tr(ji,jj,jk,jpdia,Kbb) - xthresh2dia ), 0.e0 ) 
    118                zcompaz   = MAX( ( tr(ji,jj,jk,jpzoo,Kbb) - xthresh2zoo ), 0.e0 ) 
    119                zcompaph  = MAX( ( tr(ji,jj,jk,jpphy,Kbb) - xthresh2phy ), 0.e0 ) 
    120                zcompapoc = MAX( ( tr(ji,jj,jk,jppoc,Kbb) - xthresh2poc ), 0.e0 ) 
    121                zcompames = MAX( ( tr(ji,jj,jk,jpmes,Kbb) - xthresh2mes ), 0.e0 ) 
    122  
    123                !   Mesozooplankton grazing 
    124                !   ------------------------ 
    125                zfood     = xpref2d * zcompadi + xpref2z * zcompaz + xpref2n * zcompaph + xpref2c * zcompapoc   & 
    126                &           + xpref2m * zcompames  
    127                zfoodlim  = MAX( 0., zfood - MIN( 0.5 * zfood, xthresh2 ) ) 
    128                zdenom    = zfoodlim / ( xkgraz2 + zfoodlim ) 
    129                zgraze2   = grazrat2 * xstep * tgfunc2(ji,jj,jk) * tr(ji,jj,jk,jpmes,Kbb) * (1. - nitrfac(ji,jj,jk))  
    130  
    131                !   An active switching parameterization is used here. 
    132                !   We don't use the KTW parameterization proposed by  
    133                !   Vallina et al. because it tends to produce to steady biomass 
    134                !   composition and the variance of Chl is too low as it grazes 
    135                !   too strongly on winning organisms. Thus, instead of a square 
    136                !   a 1.5 power value is used which decreases the pressure on the 
    137                !   most abundant species 
    138                !   ------------------------------------------------------------   
    139                ztmp1 = xpref2n * zcompaph**1.5 
    140                ztmp2 = xpref2m * zcompames**1.5 
    141                ztmp3 = xpref2c * zcompapoc**1.5 
    142                ztmp4 = xpref2d * zcompadi**1.5 
    143                ztmp5 = xpref2z * zcompaz**1.5 
    144                ztmptot = ztmp1 + ztmp2 + ztmp3 + ztmp4 + ztmp5 + rtrn 
    145                ztmp1 = ztmp1 / ztmptot 
    146                ztmp2 = ztmp2 / ztmptot 
    147                ztmp3 = ztmp3 / ztmptot 
    148                ztmp4 = ztmp4 / ztmptot 
    149                ztmp5 = ztmp5 / ztmptot 
    150  
    151                !   Mesozooplankton regular grazing on the different preys 
    152                !   ------------------------------------------------------ 
    153                zgrazdc   = zgraze2 * ztmp4 * zdenom 
    154                zgrazdn   = zgrazdc * tr(ji,jj,jk,jpndi,Kbb) / ( tr(ji,jj,jk,jpdia,Kbb) + rtrn) 
    155                zgrazdp   = zgrazdc * tr(ji,jj,jk,jppdi,Kbb) / ( tr(ji,jj,jk,jpdia,Kbb) + rtrn) 
    156                zgrazdf   = zgrazdc * tr(ji,jj,jk,jpdfe,Kbb) / ( tr(ji,jj,jk,jpdia,Kbb) + rtrn) 
    157                zgrazz    = zgraze2 * ztmp5 * zdenom 
    158                zgrazm    = zgraze2 * ztmp2 * zdenom 
    159                zgraznc   = zgraze2 * ztmp1 * zdenom 
    160                zgraznn   = zgraznc * tr(ji,jj,jk,jpnph,Kbb) / ( tr(ji,jj,jk,jpphy,Kbb) + rtrn) 
    161                zgraznp   = zgraznc * tr(ji,jj,jk,jppph,Kbb) / ( tr(ji,jj,jk,jpphy,Kbb) + rtrn) 
    162                zgraznf   = zgraznc * tr(ji,jj,jk,jpnfe,Kbb) / ( tr(ji,jj,jk,jpphy,Kbb) + rtrn) 
    163                zgrazpoc  = zgraze2 * ztmp3 * zdenom 
    164                zgrazpon  = zgrazpoc * tr(ji,jj,jk,jppon,Kbb) / ( tr(ji,jj,jk,jppoc,Kbb) + rtrn) 
    165                zgrazpop  = zgrazpoc * tr(ji,jj,jk,jppop,Kbb) / ( tr(ji,jj,jk,jppoc,Kbb) + rtrn) 
    166                zgrazpof  = zgrazpoc * tr(ji,jj,jk,jpsfe,Kbb) / ( tr(ji,jj,jk,jppoc,Kbb) + rtrn) 
    167  
    168                !   Mesozooplankton flux feeding on GOC 
    169                !   ---------------------------------- 
    170                zgrazffeg = grazflux  * xstep * wsbio4(ji,jj,jk)      & 
    171                &           * tgfunc2(ji,jj,jk) * tr(ji,jj,jk,jpgoc,Kbb) * tr(ji,jj,jk,jpmes,Kbb)  & 
    172                &           * (1. - nitrfac(ji,jj,jk)) 
    173                zgrazfffg = zgrazffeg * tr(ji,jj,jk,jpbfe,Kbb) / (tr(ji,jj,jk,jpgoc,Kbb) + rtrn) 
    174                zgrazffng = zgrazffeg * tr(ji,jj,jk,jpgon,Kbb) / (tr(ji,jj,jk,jpgoc,Kbb) + rtrn) 
    175                zgrazffpg = zgrazffeg * tr(ji,jj,jk,jpgop,Kbb) / (tr(ji,jj,jk,jpgoc,Kbb) + rtrn) 
    176                zgrazffep = grazflux  * xstep *  wsbio3(ji,jj,jk)     & 
    177                &           * tgfunc2(ji,jj,jk) * tr(ji,jj,jk,jppoc,Kbb) * tr(ji,jj,jk,jpmes,Kbb)   & 
    178                &           * (1. - nitrfac(ji,jj,jk)) 
    179                zgrazfffp = zgrazffep * tr(ji,jj,jk,jpsfe,Kbb) / (tr(ji,jj,jk,jppoc,Kbb) + rtrn) 
    180                zgrazffnp = zgrazffep * tr(ji,jj,jk,jppon,Kbb) / (tr(ji,jj,jk,jppoc,Kbb) + rtrn) 
    181                zgrazffpp = zgrazffep * tr(ji,jj,jk,jppop,Kbb) / (tr(ji,jj,jk,jppoc,Kbb) + rtrn) 
    182                ! 
    183                zgraztotc  = zgrazdc + zgrazz + zgraznc + zgrazm + zgrazpoc + zgrazffep + zgrazffeg 
    184  
    185                !   Compute the proportion of filter feeders 
    186                !   ----------------------------------------   
    187                zproport  = (zgrazffep + zgrazffeg)/(rtrn + zgraztotc) 
    188  
    189                !   Compute fractionation of aggregates. It is assumed that  
    190                !   diatoms based aggregates are more prone to fractionation 
    191                !   since they are more porous (marine snow instead of fecal pellets) 
    192                !   ---------------------------------------------------------------- 
    193                zratio    = tr(ji,jj,jk,jpgsi,Kbb) / ( tr(ji,jj,jk,jpgoc,Kbb) + rtrn ) 
    194                zratio2   = zratio * zratio 
    195                zfracc    = zproport * grazflux  * xstep * wsbio4(ji,jj,jk)      & 
    196                &          * tr(ji,jj,jk,jpgoc,Kbb) * tr(ji,jj,jk,jpmes,Kbb)          & 
    197                &          * ( 0.2 + 3.8 * zratio2 / ( 1.**2 + zratio2 ) ) 
    198                zfracfe   = zfracc * tr(ji,jj,jk,jpbfe,Kbb) / (tr(ji,jj,jk,jpgoc,Kbb) + rtrn) 
    199                zfracn    = zfracc * tr(ji,jj,jk,jpgon,Kbb) / (tr(ji,jj,jk,jpgoc,Kbb) + rtrn) 
    200                zfracp    = zfracc * tr(ji,jj,jk,jpgop,Kbb) / (tr(ji,jj,jk,jpgoc,Kbb) + rtrn) 
    201  
    202                zgrazffep = zproport * zgrazffep   ;   zgrazffeg = zproport * zgrazffeg 
    203                zgrazfffp = zproport * zgrazfffp   ;   zgrazfffg = zproport * zgrazfffg 
    204                zgrazffnp = zproport * zgrazffnp   ;   zgrazffng = zproport * zgrazffng 
    205                zgrazffpp = zproport * zgrazffpp   ;   zgrazffpg = zproport * zgrazffpg 
    206  
    207                zgraztotc  = zgrazdc + zgrazz + zgraznc + zgrazm + zgrazpoc + zgrazffep + zgrazffeg 
    208                zgraztotf  = zgrazdf + zgraznf + ( zgrazz + zgrazm ) * ferat3 + zgrazpof & 
    209                &            + zgrazfffp + zgrazfffg 
    210                zgraztotn  = zgrazdn + (zgrazm + zgrazz) * no3rat3 + zgraznn + zgrazpon  & 
    211                &            + zgrazffnp + zgrazffng 
    212                zgraztotp  = zgrazdp + (zgrazz + zgrazm) * po4rat3 + zgraznp + zgrazpop  & 
    213                &            + zgrazffpp + zgrazffpg 
    214  
    215  
    216                ! Total grazing ( grazing by microzoo is already computed in p5zmicro ) 
    217                zgrazing(ji,jj,jk) = zgraztotc 
    218  
    219                !   Stoichiometruc ratios of the food ingested by zooplanton  
    220                !   -------------------------------------------------------- 
    221                zgrasratf  =  (zgraztotf + rtrn) / ( zgraztotc + rtrn ) 
    222                zgrasratn  =  (zgraztotn + rtrn) / ( zgraztotc + rtrn ) 
    223                zgrasratp  =  (zgraztotp + rtrn) / ( zgraztotc + rtrn ) 
    224  
    225                !   Growth efficiency is made a function of the quality  
    226                !   and the quantity of the preys 
    227                !   --------------------------------------------------- 
    228                zepshert  = MIN( 1., zgrasratn/ no3rat3, zgrasratp/ po4rat3, zgrasratf / ferat3) 
    229                zbeta     = MAX(0., (epsher2 - epsher2min) ) 
    230                zepsherf  = epsher2min + zbeta / ( 1.0 + 0.04E6 * 12. * zfood * zbeta ) 
    231                zepsherv  = zepsherf * zepshert 
    232  
    233                !   Respiration of mesozooplankton 
    234                !   Excess carbon in the food is used preferentially 
    235                !   ----------------  ------------------------------ 
    236                zexcess  = zgraztotc * zepsherf * (1.0 - zepshert) * zmetexcess  
    237                zbasresb = MAX(0., zrespz - zexcess) 
    238                zbasresi = zexcess + MIN(0., zrespz - zexcess) 
    239                zrespirc = srespir2 * zepsherv * zgraztotc + zbasresb 
    240  
    241                !   When excess carbon is used, the other elements in excess 
    242                !   are also used proportionally to their abundance 
    243                !   -------------------------------------------------------- 
    244                zexcess  = ( zgrasratn/ no3rat3 - zepshert ) / ( 1.0 - zepshert + rtrn) 
    245                zbasresn = zbasresi * zexcess * zgrasratn 
    246                zexcess  = ( zgrasratp/ po4rat3 - zepshert ) / ( 1.0 - zepshert + rtrn) 
    247                zbasresp = zbasresi * zexcess * zgrasratp 
    248                zexcess  = ( zgrasratf/ ferat3 - zepshert ) / ( 1.0 - zepshert + rtrn) 
    249                zbasresf = zbasresi * zexcess * zgrasratf 
    250  
    251                !   Voiding of the excessive elements as organic matter 
    252                !   -------------------------------------------------------- 
    253                zgradoct = (1. - unass2c - zepsherv) * zgraztotc - zbasresi 
    254                zgradont = (1. - unass2n) * zgraztotn - zepsherv * no3rat3 * zgraztotc - zbasresn 
    255                zgradopt = (1. - unass2p) * zgraztotp - zepsherv * po4rat3 * zgraztotc - zbasresp 
    256                zgrareft = (1. - unass2c) * zgraztotf - zepsherv * ferat3 * zgraztotc - zbasresf 
    257                ztmp1   = ( 1. - epsher2 - unass2c ) /( 1. - 0.8 * epsher2 ) * ztortz 
    258                zgradoc = (zgradoct + ztmp1) * ssigma2 
    259                zgradon = (zgradont + no3rat3 * ztmp1) * ssigma2 
    260                zgradop = (zgradopt + po4rat3 * ztmp1) * ssigma2 
    261                zgratmp = 0.2 * epsher2 /( 1. - 0.8 * epsher2 ) * ztortz 
    262  
    263                !  Since only semilabile DOM is represented in PISCES 
    264                !  part of DOM is in fact labile and is then released 
    265                !  as dissolved inorganic compounds (ssigma2) 
    266                !  -------------------------------------------------- 
    267                zgrarem = zgratmp + ( zgradoct + ztmp1 ) * (1.0 - ssigma2) 
    268                zgraren = no3rat3 * zgratmp + ( zgradont + no3rat3 * ztmp1 ) * (1.0 - ssigma2) 
    269                zgrarep = po4rat3 * zgratmp + ( zgradopt + po4rat3 * ztmp1 ) * (1.0 - ssigma2) 
    270                zgraref = zgrareft + ferat3 * ( ztmp1 + zgratmp ) 
    271  
    272                !   Defecation as a result of non assimilated products 
    273                !   -------------------------------------------------- 
    274                zgrapoc  = zgraztotc * unass2c + unass2c / ( 1. - 0.8 * epsher2 ) * ztortz 
    275                zgrapon  = zgraztotn * unass2n + no3rat3 * unass2n / ( 1. - 0.8 * epsher2 ) * ztortz 
    276                zgrapop  = zgraztotp * unass2p + po4rat3 * unass2p / ( 1. - 0.8 * epsher2 ) * ztortz 
    277                zgrapof  = zgraztotf * unass2c + ferat3  * unass2c / ( 1. - 0.8 * epsher2 ) * ztortz 
    278  
    279                !  Addition of respiration to the release of inorganic nutrients 
    280                !  ------------------------------------------------------------- 
    281                zgrarem = zgrarem + zbasresi + zrespirc 
    282                zgraren = zgraren + zbasresn + zrespirc * no3rat3 
    283                zgrarep = zgrarep + zbasresp + zrespirc * po4rat3 
    284                zgraref = zgraref + zbasresf + zrespirc * ferat3 
    285  
    286                !   Update the arrays TRA which contain the biological sources and 
    287                !   sinks 
    288                !   -------------------------------------------------------------- 
    289                tr(ji,jj,jk,jppo4,Krhs) = tr(ji,jj,jk,jppo4,Krhs) + zgrarep  
    290                tr(ji,jj,jk,jpnh4,Krhs) = tr(ji,jj,jk,jpnh4,Krhs) + zgraren 
    291                tr(ji,jj,jk,jpdoc,Krhs) = tr(ji,jj,jk,jpdoc,Krhs) + zgradoc 
    292                ! 
    293                IF( ln_ligand ) THEN 
    294                   tr(ji,jj,jk,jplgw,Krhs)  = tr(ji,jj,jk,jplgw,Krhs) + zgradoc * ldocz 
    295                   zz2ligprod(ji,jj,jk) = zgradoc * ldocz 
    296                ENDIF 
    297                ! 
    298                tr(ji,jj,jk,jpdon,Krhs) = tr(ji,jj,jk,jpdon,Krhs) + zgradon 
    299                tr(ji,jj,jk,jpdop,Krhs) = tr(ji,jj,jk,jpdop,Krhs) + zgradop 
    300                tr(ji,jj,jk,jpoxy,Krhs) = tr(ji,jj,jk,jpoxy,Krhs) - o2ut * zgrarem 
    301                tr(ji,jj,jk,jpfer,Krhs) = tr(ji,jj,jk,jpfer,Krhs) + zgraref 
    302                zfezoo2(ji,jj,jk)   = zgraref 
    303                tr(ji,jj,jk,jpdic,Krhs) = tr(ji,jj,jk,jpdic,Krhs) + zgrarem 
    304                tr(ji,jj,jk,jptal,Krhs) = tr(ji,jj,jk,jptal,Krhs) + rno3 * zgraren 
    305                tr(ji,jj,jk,jpmes,Krhs) = tr(ji,jj,jk,jpmes,Krhs) + zepsherv * zgraztotc - zrespirc   & 
    306                &                     - ztortz - zgrazm 
    307                tr(ji,jj,jk,jpdia,Krhs) = tr(ji,jj,jk,jpdia,Krhs) - zgrazdc 
    308                tr(ji,jj,jk,jpndi,Krhs) = tr(ji,jj,jk,jpndi,Krhs) - zgrazdn 
    309                tr(ji,jj,jk,jppdi,Krhs) = tr(ji,jj,jk,jppdi,Krhs) - zgrazdp 
    310                tr(ji,jj,jk,jpdfe,Krhs) = tr(ji,jj,jk,jpdfe,Krhs) - zgrazdf 
    311                tr(ji,jj,jk,jpzoo,Krhs) = tr(ji,jj,jk,jpzoo,Krhs) - zgrazz 
    312                tr(ji,jj,jk,jpphy,Krhs) = tr(ji,jj,jk,jpphy,Krhs) - zgraznc 
    313                tr(ji,jj,jk,jpnph,Krhs) = tr(ji,jj,jk,jpnph,Krhs) - zgraznn 
    314                tr(ji,jj,jk,jppph,Krhs) = tr(ji,jj,jk,jppph,Krhs) - zgraznp 
    315                tr(ji,jj,jk,jpnfe,Krhs) = tr(ji,jj,jk,jpnfe,Krhs) - zgraznf 
    316                tr(ji,jj,jk,jpnch,Krhs) = tr(ji,jj,jk,jpnch,Krhs) - zgraznc * tr(ji,jj,jk,jpnch,Kbb) / ( tr(ji,jj,jk,jpphy,Kbb) + rtrn ) 
    317                tr(ji,jj,jk,jpdch,Krhs) = tr(ji,jj,jk,jpdch,Krhs) - zgrazdc * tr(ji,jj,jk,jpdch,Kbb) / ( tr(ji,jj,jk,jpdia,Kbb) + rtrn ) 
    318                tr(ji,jj,jk,jpdsi,Krhs) = tr(ji,jj,jk,jpdsi,Krhs) - zgrazdc * tr(ji,jj,jk,jpdsi,Kbb) / ( tr(ji,jj,jk,jpdia,Kbb) + rtrn ) 
    319                tr(ji,jj,jk,jpgsi,Krhs) = tr(ji,jj,jk,jpgsi,Krhs) + zgrazdc * tr(ji,jj,jk,jpdsi,Kbb) / ( tr(ji,jj,jk,jpdia,Kbb) + rtrn ) 
    320  
    321                tr(ji,jj,jk,jppoc,Krhs) = tr(ji,jj,jk,jppoc,Krhs) - zgrazpoc - zgrazffep + zfracc 
    322                prodpoc(ji,jj,jk) = prodpoc(ji,jj,jk) + zfracc 
    323                conspoc(ji,jj,jk) = conspoc(ji,jj,jk) - zgrazpoc - zgrazffep 
    324                tr(ji,jj,jk,jppon,Krhs) = tr(ji,jj,jk,jppon,Krhs) - zgrazpon - zgrazffnp + zfracn 
    325                tr(ji,jj,jk,jppop,Krhs) = tr(ji,jj,jk,jppop,Krhs) - zgrazpop - zgrazffpp + zfracp 
    326                tr(ji,jj,jk,jpgoc,Krhs) = tr(ji,jj,jk,jpgoc,Krhs) - zgrazffeg + zgrapoc - zfracc 
    327                prodgoc(ji,jj,jk) = prodgoc(ji,jj,jk) + zgrapoc 
    328                consgoc(ji,jj,jk) = consgoc(ji,jj,jk) - zgrazffeg - zfracc 
    329                tr(ji,jj,jk,jpgon,Krhs) = tr(ji,jj,jk,jpgon,Krhs) - zgrazffng + zgrapon - zfracn 
    330                tr(ji,jj,jk,jpgop,Krhs) = tr(ji,jj,jk,jpgop,Krhs) - zgrazffpg + zgrapop - zfracp 
    331                tr(ji,jj,jk,jpsfe,Krhs) = tr(ji,jj,jk,jpsfe,Krhs) - zgrazpof - zgrazfffp + zfracfe 
    332                tr(ji,jj,jk,jpbfe,Krhs) = tr(ji,jj,jk,jpbfe,Krhs) - zgrazfffg + zgrapof - zfracfe 
    333                zfracal = tr(ji,jj,jk,jpcal,Kbb) / ( tr(ji,jj,jk,jpgoc,Kbb) + rtrn ) 
    334                zgrazcal = zgrazffeg * (1. - part2) * zfracal 
    335  
    336                !  calcite production 
    337                !  ------------------ 
    338                zprcaca = xfracal(ji,jj,jk) * zgraznc 
    339                prodcal(ji,jj,jk) = prodcal(ji,jj,jk) + zprcaca  ! prodcal=prodcal(nanophy)+prodcal(microzoo)+prodcal(mesozoo) 
    340                zprcaca = part2 * zprcaca 
    341                tr(ji,jj,jk,jpdic,Krhs) = tr(ji,jj,jk,jpdic,Krhs) + zgrazcal - zprcaca 
    342                tr(ji,jj,jk,jptal,Krhs) = tr(ji,jj,jk,jptal,Krhs) + 2. * ( zgrazcal - zprcaca ) 
    343                tr(ji,jj,jk,jpcal,Krhs) = tr(ji,jj,jk,jpcal,Krhs) - zgrazcal + zprcaca 
    344             END DO 
    345          END DO 
    346       END DO 
     100      DO_3D_11_11( 1, jpkm1 ) 
     101         zcompam   = MAX( ( tr(ji,jj,jk,jpmes,Kbb) - 1.e-9 ), 0.e0 ) 
     102         zfact     = xstep * tgfunc2(ji,jj,jk) * zcompam 
     103 
     104         !   Michaelis-Menten mortality rates of mesozooplankton 
     105         !   --------------------------------------------------- 
     106         zrespz   = resrat2 * zfact * ( tr(ji,jj,jk,jpmes,Kbb) / ( xkmort + tr(ji,jj,jk,jpmes,Kbb) )  & 
     107         &          + 3. * nitrfac(ji,jj,jk) ) 
     108 
     109         !   Zooplankton mortality. A square function has been selected with 
     110         !   no real reason except that it seems to be more stable and may mimic predation 
     111         !   --------------------------------------------------------------- 
     112         ztortz   = mzrat2 * 1.e6 * zfact * tr(ji,jj,jk,jpmes,Kbb) * (1. - nitrfac(ji,jj,jk)) 
     113 
     114         !   Computation of the abundance of the preys 
     115         !   A threshold can be specified in the namelist 
     116         !   -------------------------------------------- 
     117         zcompadi  = MAX( ( tr(ji,jj,jk,jpdia,Kbb) - xthresh2dia ), 0.e0 ) 
     118         zcompaz   = MAX( ( tr(ji,jj,jk,jpzoo,Kbb) - xthresh2zoo ), 0.e0 ) 
     119         zcompaph  = MAX( ( tr(ji,jj,jk,jpphy,Kbb) - xthresh2phy ), 0.e0 ) 
     120         zcompapoc = MAX( ( tr(ji,jj,jk,jppoc,Kbb) - xthresh2poc ), 0.e0 ) 
     121         zcompames = MAX( ( tr(ji,jj,jk,jpmes,Kbb) - xthresh2mes ), 0.e0 ) 
     122 
     123         !   Mesozooplankton grazing 
     124         !   ------------------------ 
     125         zfood     = xpref2d * zcompadi + xpref2z * zcompaz + xpref2n * zcompaph + xpref2c * zcompapoc   & 
     126         &           + xpref2m * zcompames  
     127         zfoodlim  = MAX( 0., zfood - MIN( 0.5 * zfood, xthresh2 ) ) 
     128         zdenom    = zfoodlim / ( xkgraz2 + zfoodlim ) 
     129         zgraze2   = grazrat2 * xstep * tgfunc2(ji,jj,jk) * tr(ji,jj,jk,jpmes,Kbb) * (1. - nitrfac(ji,jj,jk))  
     130 
     131         !   An active switching parameterization is used here. 
     132         !   We don't use the KTW parameterization proposed by  
     133         !   Vallina et al. because it tends to produce to steady biomass 
     134         !   composition and the variance of Chl is too low as it grazes 
     135         !   too strongly on winning organisms. Thus, instead of a square 
     136         !   a 1.5 power value is used which decreases the pressure on the 
     137         !   most abundant species 
     138         !   ------------------------------------------------------------   
     139         ztmp1 = xpref2n * zcompaph**1.5 
     140         ztmp2 = xpref2m * zcompames**1.5 
     141         ztmp3 = xpref2c * zcompapoc**1.5 
     142         ztmp4 = xpref2d * zcompadi**1.5 
     143         ztmp5 = xpref2z * zcompaz**1.5 
     144         ztmptot = ztmp1 + ztmp2 + ztmp3 + ztmp4 + ztmp5 + rtrn 
     145         ztmp1 = ztmp1 / ztmptot 
     146         ztmp2 = ztmp2 / ztmptot 
     147         ztmp3 = ztmp3 / ztmptot 
     148         ztmp4 = ztmp4 / ztmptot 
     149         ztmp5 = ztmp5 / ztmptot 
     150 
     151         !   Mesozooplankton regular grazing on the different preys 
     152         !   ------------------------------------------------------ 
     153         zgrazdc   = zgraze2 * ztmp4 * zdenom 
     154         zgrazdn   = zgrazdc * tr(ji,jj,jk,jpndi,Kbb) / ( tr(ji,jj,jk,jpdia,Kbb) + rtrn) 
     155         zgrazdp   = zgrazdc * tr(ji,jj,jk,jppdi,Kbb) / ( tr(ji,jj,jk,jpdia,Kbb) + rtrn) 
     156         zgrazdf   = zgrazdc * tr(ji,jj,jk,jpdfe,Kbb) / ( tr(ji,jj,jk,jpdia,Kbb) + rtrn) 
     157         zgrazz    = zgraze2 * ztmp5 * zdenom 
     158         zgrazm    = zgraze2 * ztmp2 * zdenom 
     159         zgraznc   = zgraze2 * ztmp1 * zdenom 
     160         zgraznn   = zgraznc * tr(ji,jj,jk,jpnph,Kbb) / ( tr(ji,jj,jk,jpphy,Kbb) + rtrn) 
     161         zgraznp   = zgraznc * tr(ji,jj,jk,jppph,Kbb) / ( tr(ji,jj,jk,jpphy,Kbb) + rtrn) 
     162         zgraznf   = zgraznc * tr(ji,jj,jk,jpnfe,Kbb) / ( tr(ji,jj,jk,jpphy,Kbb) + rtrn) 
     163         zgrazpoc  = zgraze2 * ztmp3 * zdenom 
     164         zgrazpon  = zgrazpoc * tr(ji,jj,jk,jppon,Kbb) / ( tr(ji,jj,jk,jppoc,Kbb) + rtrn) 
     165         zgrazpop  = zgrazpoc * tr(ji,jj,jk,jppop,Kbb) / ( tr(ji,jj,jk,jppoc,Kbb) + rtrn) 
     166         zgrazpof  = zgrazpoc * tr(ji,jj,jk,jpsfe,Kbb) / ( tr(ji,jj,jk,jppoc,Kbb) + rtrn) 
     167 
     168         !   Mesozooplankton flux feeding on GOC 
     169         !   ---------------------------------- 
     170         zgrazffeg = grazflux  * xstep * wsbio4(ji,jj,jk)      & 
     171         &           * tgfunc2(ji,jj,jk) * tr(ji,jj,jk,jpgoc,Kbb) * tr(ji,jj,jk,jpmes,Kbb)  & 
     172         &           * (1. - nitrfac(ji,jj,jk)) 
     173         zgrazfffg = zgrazffeg * tr(ji,jj,jk,jpbfe,Kbb) / (tr(ji,jj,jk,jpgoc,Kbb) + rtrn) 
     174         zgrazffng = zgrazffeg * tr(ji,jj,jk,jpgon,Kbb) / (tr(ji,jj,jk,jpgoc,Kbb) + rtrn) 
     175         zgrazffpg = zgrazffeg * tr(ji,jj,jk,jpgop,Kbb) / (tr(ji,jj,jk,jpgoc,Kbb) + rtrn) 
     176         zgrazffep = grazflux  * xstep *  wsbio3(ji,jj,jk)     & 
     177         &           * tgfunc2(ji,jj,jk) * tr(ji,jj,jk,jppoc,Kbb) * tr(ji,jj,jk,jpmes,Kbb)   & 
     178         &           * (1. - nitrfac(ji,jj,jk)) 
     179         zgrazfffp = zgrazffep * tr(ji,jj,jk,jpsfe,Kbb) / (tr(ji,jj,jk,jppoc,Kbb) + rtrn) 
     180         zgrazffnp = zgrazffep * tr(ji,jj,jk,jppon,Kbb) / (tr(ji,jj,jk,jppoc,Kbb) + rtrn) 
     181         zgrazffpp = zgrazffep * tr(ji,jj,jk,jppop,Kbb) / (tr(ji,jj,jk,jppoc,Kbb) + rtrn) 
     182         ! 
     183         zgraztotc  = zgrazdc + zgrazz + zgraznc + zgrazm + zgrazpoc + zgrazffep + zgrazffeg 
     184 
     185         !   Compute the proportion of filter feeders 
     186         !   ----------------------------------------   
     187         zproport  = (zgrazffep + zgrazffeg)/(rtrn + zgraztotc) 
     188 
     189         !   Compute fractionation of aggregates. It is assumed that  
     190         !   diatoms based aggregates are more prone to fractionation 
     191         !   since they are more porous (marine snow instead of fecal pellets) 
     192         !   ---------------------------------------------------------------- 
     193         zratio    = tr(ji,jj,jk,jpgsi,Kbb) / ( tr(ji,jj,jk,jpgoc,Kbb) + rtrn ) 
     194         zratio2   = zratio * zratio 
     195         zfracc    = zproport * grazflux  * xstep * wsbio4(ji,jj,jk)      & 
     196         &          * tr(ji,jj,jk,jpgoc,Kbb) * tr(ji,jj,jk,jpmes,Kbb)          & 
     197         &          * ( 0.2 + 3.8 * zratio2 / ( 1.**2 + zratio2 ) ) 
     198         zfracfe   = zfracc * tr(ji,jj,jk,jpbfe,Kbb) / (tr(ji,jj,jk,jpgoc,Kbb) + rtrn) 
     199         zfracn    = zfracc * tr(ji,jj,jk,jpgon,Kbb) / (tr(ji,jj,jk,jpgoc,Kbb) + rtrn) 
     200         zfracp    = zfracc * tr(ji,jj,jk,jpgop,Kbb) / (tr(ji,jj,jk,jpgoc,Kbb) + rtrn) 
     201 
     202         zgrazffep = zproport * zgrazffep   ;   zgrazffeg = zproport * zgrazffeg 
     203         zgrazfffp = zproport * zgrazfffp   ;   zgrazfffg = zproport * zgrazfffg 
     204         zgrazffnp = zproport * zgrazffnp   ;   zgrazffng = zproport * zgrazffng 
     205         zgrazffpp = zproport * zgrazffpp   ;   zgrazffpg = zproport * zgrazffpg 
     206 
     207         zgraztotc  = zgrazdc + zgrazz + zgraznc + zgrazm + zgrazpoc + zgrazffep + zgrazffeg 
     208         zgraztotf  = zgrazdf + zgraznf + ( zgrazz + zgrazm ) * ferat3 + zgrazpof & 
     209         &            + zgrazfffp + zgrazfffg 
     210         zgraztotn  = zgrazdn + (zgrazm + zgrazz) * no3rat3 + zgraznn + zgrazpon  & 
     211         &            + zgrazffnp + zgrazffng 
     212         zgraztotp  = zgrazdp + (zgrazz + zgrazm) * po4rat3 + zgraznp + zgrazpop  & 
     213         &            + zgrazffpp + zgrazffpg 
     214 
     215 
     216         ! Total grazing ( grazing by microzoo is already computed in p5zmicro ) 
     217         zgrazing(ji,jj,jk) = zgraztotc 
     218 
     219         !   Stoichiometruc ratios of the food ingested by zooplanton  
     220         !   -------------------------------------------------------- 
     221         zgrasratf  =  (zgraztotf + rtrn) / ( zgraztotc + rtrn ) 
     222         zgrasratn  =  (zgraztotn + rtrn) / ( zgraztotc + rtrn ) 
     223         zgrasratp  =  (zgraztotp + rtrn) / ( zgraztotc + rtrn ) 
     224 
     225         !   Growth efficiency is made a function of the quality  
     226         !   and the quantity of the preys 
     227         !   --------------------------------------------------- 
     228         zepshert  = MIN( 1., zgrasratn/ no3rat3, zgrasratp/ po4rat3, zgrasratf / ferat3) 
     229         zbeta     = MAX(0., (epsher2 - epsher2min) ) 
     230         zepsherf  = epsher2min + zbeta / ( 1.0 + 0.04E6 * 12. * zfood * zbeta ) 
     231         zepsherv  = zepsherf * zepshert 
     232 
     233         !   Respiration of mesozooplankton 
     234         !   Excess carbon in the food is used preferentially 
     235         !   ----------------  ------------------------------ 
     236         zexcess  = zgraztotc * zepsherf * (1.0 - zepshert) * zmetexcess  
     237         zbasresb = MAX(0., zrespz - zexcess) 
     238         zbasresi = zexcess + MIN(0., zrespz - zexcess) 
     239         zrespirc = srespir2 * zepsherv * zgraztotc + zbasresb 
     240 
     241         !   When excess carbon is used, the other elements in excess 
     242         !   are also used proportionally to their abundance 
     243         !   -------------------------------------------------------- 
     244         zexcess  = ( zgrasratn/ no3rat3 - zepshert ) / ( 1.0 - zepshert + rtrn) 
     245         zbasresn = zbasresi * zexcess * zgrasratn 
     246         zexcess  = ( zgrasratp/ po4rat3 - zepshert ) / ( 1.0 - zepshert + rtrn) 
     247         zbasresp = zbasresi * zexcess * zgrasratp 
     248         zexcess  = ( zgrasratf/ ferat3 - zepshert ) / ( 1.0 - zepshert + rtrn) 
     249         zbasresf = zbasresi * zexcess * zgrasratf 
     250 
     251         !   Voiding of the excessive elements as organic matter 
     252         !   -------------------------------------------------------- 
     253         zgradoct = (1. - unass2c - zepsherv) * zgraztotc - zbasresi 
     254         zgradont = (1. - unass2n) * zgraztotn - zepsherv * no3rat3 * zgraztotc - zbasresn 
     255         zgradopt = (1. - unass2p) * zgraztotp - zepsherv * po4rat3 * zgraztotc - zbasresp 
     256         zgrareft = (1. - unass2c) * zgraztotf - zepsherv * ferat3 * zgraztotc - zbasresf 
     257         ztmp1   = ( 1. - epsher2 - unass2c ) /( 1. - 0.8 * epsher2 ) * ztortz 
     258         zgradoc = (zgradoct + ztmp1) * ssigma2 
     259         zgradon = (zgradont + no3rat3 * ztmp1) * ssigma2 
     260         zgradop = (zgradopt + po4rat3 * ztmp1) * ssigma2 
     261         zgratmp = 0.2 * epsher2 /( 1. - 0.8 * epsher2 ) * ztortz 
     262 
     263         !  Since only semilabile DOM is represented in PISCES 
     264         !  part of DOM is in fact labile and is then released 
     265         !  as dissolved inorganic compounds (ssigma2) 
     266         !  -------------------------------------------------- 
     267         zgrarem = zgratmp + ( zgradoct + ztmp1 ) * (1.0 - ssigma2) 
     268         zgraren = no3rat3 * zgratmp + ( zgradont + no3rat3 * ztmp1 ) * (1.0 - ssigma2) 
     269         zgrarep = po4rat3 * zgratmp + ( zgradopt + po4rat3 * ztmp1 ) * (1.0 - ssigma2) 
     270         zgraref = zgrareft + ferat3 * ( ztmp1 + zgratmp ) 
     271 
     272         !   Defecation as a result of non assimilated products 
     273         !   -------------------------------------------------- 
     274         zgrapoc  = zgraztotc * unass2c + unass2c / ( 1. - 0.8 * epsher2 ) * ztortz 
     275         zgrapon  = zgraztotn * unass2n + no3rat3 * unass2n / ( 1. - 0.8 * epsher2 ) * ztortz 
     276         zgrapop  = zgraztotp * unass2p + po4rat3 * unass2p / ( 1. - 0.8 * epsher2 ) * ztortz 
     277         zgrapof  = zgraztotf * unass2c + ferat3  * unass2c / ( 1. - 0.8 * epsher2 ) * ztortz 
     278 
     279         !  Addition of respiration to the release of inorganic nutrients 
     280         !  ------------------------------------------------------------- 
     281         zgrarem = zgrarem + zbasresi + zrespirc 
     282         zgraren = zgraren + zbasresn + zrespirc * no3rat3 
     283         zgrarep = zgrarep + zbasresp + zrespirc * po4rat3 
     284         zgraref = zgraref + zbasresf + zrespirc * ferat3 
     285 
     286         !   Update the arrays TRA which contain the biological sources and 
     287         !   sinks 
     288         !   -------------------------------------------------------------- 
     289         tr(ji,jj,jk,jppo4,Krhs) = tr(ji,jj,jk,jppo4,Krhs) + zgrarep  
     290         tr(ji,jj,jk,jpnh4,Krhs) = tr(ji,jj,jk,jpnh4,Krhs) + zgraren 
     291         tr(ji,jj,jk,jpdoc,Krhs) = tr(ji,jj,jk,jpdoc,Krhs) + zgradoc 
     292         ! 
     293         IF( ln_ligand ) THEN 
     294            tr(ji,jj,jk,jplgw,Krhs)  = tr(ji,jj,jk,jplgw,Krhs) + zgradoc * ldocz 
     295            zz2ligprod(ji,jj,jk) = zgradoc * ldocz 
     296         ENDIF 
     297         ! 
     298         tr(ji,jj,jk,jpdon,Krhs) = tr(ji,jj,jk,jpdon,Krhs) + zgradon 
     299         tr(ji,jj,jk,jpdop,Krhs) = tr(ji,jj,jk,jpdop,Krhs) + zgradop 
     300         tr(ji,jj,jk,jpoxy,Krhs) = tr(ji,jj,jk,jpoxy,Krhs) - o2ut * zgrarem 
     301         tr(ji,jj,jk,jpfer,Krhs) = tr(ji,jj,jk,jpfer,Krhs) + zgraref 
     302         zfezoo2(ji,jj,jk)   = zgraref 
     303         tr(ji,jj,jk,jpdic,Krhs) = tr(ji,jj,jk,jpdic,Krhs) + zgrarem 
     304         tr(ji,jj,jk,jptal,Krhs) = tr(ji,jj,jk,jptal,Krhs) + rno3 * zgraren 
     305         tr(ji,jj,jk,jpmes,Krhs) = tr(ji,jj,jk,jpmes,Krhs) + zepsherv * zgraztotc - zrespirc   & 
     306         &                     - ztortz - zgrazm 
     307         tr(ji,jj,jk,jpdia,Krhs) = tr(ji,jj,jk,jpdia,Krhs) - zgrazdc 
     308         tr(ji,jj,jk,jpndi,Krhs) = tr(ji,jj,jk,jpndi,Krhs) - zgrazdn 
     309         tr(ji,jj,jk,jppdi,Krhs) = tr(ji,jj,jk,jppdi,Krhs) - zgrazdp 
     310         tr(ji,jj,jk,jpdfe,Krhs) = tr(ji,jj,jk,jpdfe,Krhs) - zgrazdf 
     311         tr(ji,jj,jk,jpzoo,Krhs) = tr(ji,jj,jk,jpzoo,Krhs) - zgrazz 
     312         tr(ji,jj,jk,jpphy,Krhs) = tr(ji,jj,jk,jpphy,Krhs) - zgraznc 
     313         tr(ji,jj,jk,jpnph,Krhs) = tr(ji,jj,jk,jpnph,Krhs) - zgraznn 
     314         tr(ji,jj,jk,jppph,Krhs) = tr(ji,jj,jk,jppph,Krhs) - zgraznp 
     315         tr(ji,jj,jk,jpnfe,Krhs) = tr(ji,jj,jk,jpnfe,Krhs) - zgraznf 
     316         tr(ji,jj,jk,jpnch,Krhs) = tr(ji,jj,jk,jpnch,Krhs) - zgraznc * tr(ji,jj,jk,jpnch,Kbb) / ( tr(ji,jj,jk,jpphy,Kbb) + rtrn ) 
     317         tr(ji,jj,jk,jpdch,Krhs) = tr(ji,jj,jk,jpdch,Krhs) - zgrazdc * tr(ji,jj,jk,jpdch,Kbb) / ( tr(ji,jj,jk,jpdia,Kbb) + rtrn ) 
     318         tr(ji,jj,jk,jpdsi,Krhs) = tr(ji,jj,jk,jpdsi,Krhs) - zgrazdc * tr(ji,jj,jk,jpdsi,Kbb) / ( tr(ji,jj,jk,jpdia,Kbb) + rtrn ) 
     319         tr(ji,jj,jk,jpgsi,Krhs) = tr(ji,jj,jk,jpgsi,Krhs) + zgrazdc * tr(ji,jj,jk,jpdsi,Kbb) / ( tr(ji,jj,jk,jpdia,Kbb) + rtrn ) 
     320 
     321         tr(ji,jj,jk,jppoc,Krhs) = tr(ji,jj,jk,jppoc,Krhs) - zgrazpoc - zgrazffep + zfracc 
     322         prodpoc(ji,jj,jk) = prodpoc(ji,jj,jk) + zfracc 
     323         conspoc(ji,jj,jk) = conspoc(ji,jj,jk) - zgrazpoc - zgrazffep 
     324         tr(ji,jj,jk,jppon,Krhs) = tr(ji,jj,jk,jppon,Krhs) - zgrazpon - zgrazffnp + zfracn 
     325         tr(ji,jj,jk,jppop,Krhs) = tr(ji,jj,jk,jppop,Krhs) - zgrazpop - zgrazffpp + zfracp 
     326         tr(ji,jj,jk,jpgoc,Krhs) = tr(ji,jj,jk,jpgoc,Krhs) - zgrazffeg + zgrapoc - zfracc 
     327         prodgoc(ji,jj,jk) = prodgoc(ji,jj,jk) + zgrapoc 
     328         consgoc(ji,jj,jk) = consgoc(ji,jj,jk) - zgrazffeg - zfracc 
     329         tr(ji,jj,jk,jpgon,Krhs) = tr(ji,jj,jk,jpgon,Krhs) - zgrazffng + zgrapon - zfracn 
     330         tr(ji,jj,jk,jpgop,Krhs) = tr(ji,jj,jk,jpgop,Krhs) - zgrazffpg + zgrapop - zfracp 
     331         tr(ji,jj,jk,jpsfe,Krhs) = tr(ji,jj,jk,jpsfe,Krhs) - zgrazpof - zgrazfffp + zfracfe 
     332         tr(ji,jj,jk,jpbfe,Krhs) = tr(ji,jj,jk,jpbfe,Krhs) - zgrazfffg + zgrapof - zfracfe 
     333         zfracal = tr(ji,jj,jk,jpcal,Kbb) / ( tr(ji,jj,jk,jpgoc,Kbb) + rtrn ) 
     334         zgrazcal = zgrazffeg * (1. - part2) * zfracal 
     335 
     336         !  calcite production 
     337         !  ------------------ 
     338         zprcaca = xfracal(ji,jj,jk) * zgraznc 
     339         prodcal(ji,jj,jk) = prodcal(ji,jj,jk) + zprcaca  ! prodcal=prodcal(nanophy)+prodcal(microzoo)+prodcal(mesozoo) 
     340         zprcaca = part2 * zprcaca 
     341         tr(ji,jj,jk,jpdic,Krhs) = tr(ji,jj,jk,jpdic,Krhs) + zgrazcal - zprcaca 
     342         tr(ji,jj,jk,jptal,Krhs) = tr(ji,jj,jk,jptal,Krhs) + 2. * ( zgrazcal - zprcaca ) 
     343         tr(ji,jj,jk,jpcal,Krhs) = tr(ji,jj,jk,jpcal,Krhs) - zgrazcal + zprcaca 
     344      END_3D 
    347345      ! 
    348346      IF( lk_iomput .AND. knt == nrdttrc ) THEN 
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