Changeset 12340 for NEMO/branches/2019/dev_r11943_MERGE_2019/src/TOP/PISCES/P4Z/p4zfechem.F90

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:

• NEMO/branches/2019/dev_r11943_MERGE_2019/src/TOP/PISCES/P4Z/p4zfechem.F90 (modified) (3 diffs)

NEMO/branches/2019/dev_r11943_MERGE_2019/src/TOP/PISCES/P4Z/p4zfechem.F90

@@ -31 +31 @@
    REAL(wp), PUBLIC ::   kfep         !: rate constant for nanoparticle formation
 
+   !! * Substitutions
+#  include "do_loop_substitute.h90"
    !!----------------------------------------------------------------------
    !! NEMO/TOP 4.0 , NEMO Consortium (2018)
@@ -89 +91 @@
       ! Chemistry is supposed to be fast enough to be at equilibrium
       ! ------------------------------------------------------------
-      DO jk = 1, jpkm1
-         DO jj = 1, jpj
-            DO ji = 1, jpi
-               zTL1(ji,jj,jk)  = ztotlig(ji,jj,jk)
-               zkeq            = fekeq(ji,jj,jk)
-               zfesatur        = zTL1(ji,jj,jk) * 1E-9
-               ztfe            = tr(ji,jj,jk,jpfer,Kbb) 
-               ! Fe' is the root of a 2nd order polynom
-               zFe3 (ji,jj,jk) = ( -( 1. + zfesatur * zkeq - zkeq * ztfe )               &
-                  &              + SQRT( ( 1. + zfesatur * zkeq - zkeq * ztfe )**2       &
-                  &              + 4. * ztfe * zkeq) ) / ( 2. * zkeq )
-               zFe3 (ji,jj,jk) = zFe3(ji,jj,jk) * 1E9
-               zFeL1(ji,jj,jk) = MAX( 0., tr(ji,jj,jk,jpfer,Kbb) * 1E9 - zFe3(ji,jj,jk) )
-           END DO
-         END DO
-      END DO
+      DO_3D_11_11( 1, jpkm1 )
+         zTL1(ji,jj,jk)  = ztotlig(ji,jj,jk)
+         zkeq            = fekeq(ji,jj,jk)
+         zfesatur        = zTL1(ji,jj,jk) * 1E-9
+         ztfe            = tr(ji,jj,jk,jpfer,Kbb) 
+         ! Fe' is the root of a 2nd order polynom
+         zFe3 (ji,jj,jk) = ( -( 1. + zfesatur * zkeq - zkeq * ztfe )               &
+            &              + SQRT( ( 1. + zfesatur * zkeq - zkeq * ztfe )**2       &
+            &              + 4. * ztfe * zkeq) ) / ( 2. * zkeq )
+         zFe3 (ji,jj,jk) = zFe3(ji,jj,jk) * 1E9
+         zFeL1(ji,jj,jk) = MAX( 0., tr(ji,jj,jk,jpfer,Kbb) * 1E9 - zFe3(ji,jj,jk) )
+      END_3D
          !
 
       zdust = 0.         ! if no dust available
-      DO jk = 1, jpkm1
-         DO jj = 1, jpj
-            DO ji = 1, jpi
-               ! Scavenging rate of iron. This scavenging rate depends on the load of particles of sea water. 
-               ! This parameterization assumes a simple second order kinetics (k[Particles][Fe]).
-               ! Scavenging onto dust is also included as evidenced from the DUNE experiments.
-               ! --------------------------------------------------------------------------------------
-               zhplus  = max( rtrn, hi(ji,jj,jk) )
-               fe3sol  = fesol(ji,jj,jk,1) * ( zhplus**3 + fesol(ji,jj,jk,2) * zhplus**2  &
-               &         + fesol(ji,jj,jk,3) * zhplus + fesol(ji,jj,jk,4)     &
-               &         + fesol(ji,jj,jk,5) / zhplus )
-               !
-               zfeequi = zFe3(ji,jj,jk) * 1E-9
-               zhplus  = max( rtrn, hi(ji,jj,jk) )
-               fe3sol  = fesol(ji,jj,jk,1) * ( zhplus**3 + fesol(ji,jj,jk,2) * zhplus**2  &
-                  &         + fesol(ji,jj,jk,3) * zhplus + fesol(ji,jj,jk,4)     &
-                  &         + fesol(ji,jj,jk,5) / zhplus )
-               zfecoll = 0.5 * zFeL1(ji,jj,jk) * 1E-9
-               ! precipitation of Fe3+, creation of nanoparticles
-               precip(ji,jj,jk) = MAX( 0., ( zFe3(ji,jj,jk) * 1E-9 - fe3sol ) ) * kfep * xstep
-               !
-               ztrc   = ( tr(ji,jj,jk,jppoc,Kbb) + tr(ji,jj,jk,jpgoc,Kbb) + tr(ji,jj,jk,jpcal,Kbb) + tr(ji,jj,jk,jpgsi,Kbb) ) * 1.e6 
-               IF( ll_dust )  zdust  = dust(ji,jj) / ( wdust / rday ) * tmask(ji,jj,jk) &
-               &  * EXP( -gdept(ji,jj,jk,Kmm) / 540. )
-               IF (ln_ligand) THEN
-                  zxlam  = xlam1 * MAX( 1.E-3, EXP(-2 * etot(ji,jj,jk) / 10. ) * (1. - EXP(-2 * tr(ji,jj,jk,jpoxy,Kbb) / 100.E-6 ) ))
-               ELSE
-                  zxlam  = xlam1 * 1.0
-               ENDIF
-               zlam1b = 3.e-5 + xlamdust * zdust + zxlam * ztrc
-               zscave = zfeequi * zlam1b * xstep
-
-               ! Compute the different ratios for scavenging of iron
-               ! to later allocate scavenged iron to the different organic pools
-               ! ---------------------------------------------------------
-               zdenom1 = zxlam * tr(ji,jj,jk,jppoc,Kbb) / zlam1b
-               zdenom2 = zxlam * tr(ji,jj,jk,jpgoc,Kbb) / zlam1b
-
-               !  Increased scavenging for very high iron concentrations found near the coasts 
-               !  due to increased lithogenic particles and let say it is unknown processes (precipitation, ...)
-               !  -----------------------------------------------------------
-               zlamfac = MAX( 0.e0, ( gphit(ji,jj) + 55.) / 30. )
-               zlamfac = MIN( 1.  , zlamfac )
-               zdep    = MIN( 1., 1000. / gdept(ji,jj,jk,Kmm) )
-               zcoag   = 1E-4 * ( 1. - zlamfac ) * zdep * xstep * tr(ji,jj,jk,jpfer,Kbb)
-
-               !  Compute the coagulation of colloidal iron. This parameterization 
-               !  could be thought as an equivalent of colloidal pumping.
-               !  It requires certainly some more work as it is very poorly constrained.
-               !  ----------------------------------------------------------------
-               zlam1a   = ( 0.369  * 0.3 * tr(ji,jj,jk,jpdoc,Kbb) + 102.4  * tr(ji,jj,jk,jppoc,Kbb) ) * xdiss(ji,jj,jk)    &
-                   &      + ( 114.   * 0.3 * tr(ji,jj,jk,jpdoc,Kbb) )
-               zaggdfea = zlam1a * xstep * zfecoll
-               !
-               zlam1b   = 3.53E3 * tr(ji,jj,jk,jpgoc,Kbb) * xdiss(ji,jj,jk)
-               zaggdfeb = zlam1b * xstep * zfecoll
-               !
-               tr(ji,jj,jk,jpfer,Krhs) = tr(ji,jj,jk,jpfer,Krhs) - zscave - zaggdfea - zaggdfeb &
-               &                     - zcoag - precip(ji,jj,jk)
-               tr(ji,jj,jk,jpsfe,Krhs) = tr(ji,jj,jk,jpsfe,Krhs) + zscave * zdenom1 + zaggdfea
-               tr(ji,jj,jk,jpbfe,Krhs) = tr(ji,jj,jk,jpbfe,Krhs) + zscave * zdenom2 + zaggdfeb
-               zscav3d(ji,jj,jk)   = zscave
-               zcoll3d(ji,jj,jk)   = zaggdfea + zaggdfeb
-               !
-            END DO
-         END DO
-      END DO
+      DO_3D_11_11( 1, jpkm1 )
+         ! Scavenging rate of iron. This scavenging rate depends on the load of particles of sea water. 
+         ! This parameterization assumes a simple second order kinetics (k[Particles][Fe]).
+         ! Scavenging onto dust is also included as evidenced from the DUNE experiments.
+         ! --------------------------------------------------------------------------------------
+         zhplus  = max( rtrn, hi(ji,jj,jk) )
+         fe3sol  = fesol(ji,jj,jk,1) * ( zhplus**3 + fesol(ji,jj,jk,2) * zhplus**2  &
+         &         + fesol(ji,jj,jk,3) * zhplus + fesol(ji,jj,jk,4)     &
+         &         + fesol(ji,jj,jk,5) / zhplus )
+         !
+         zfeequi = zFe3(ji,jj,jk) * 1E-9
+         zhplus  = max( rtrn, hi(ji,jj,jk) )
+         fe3sol  = fesol(ji,jj,jk,1) * ( zhplus**3 + fesol(ji,jj,jk,2) * zhplus**2  &
+            &         + fesol(ji,jj,jk,3) * zhplus + fesol(ji,jj,jk,4)     &
+            &         + fesol(ji,jj,jk,5) / zhplus )
+         zfecoll = 0.5 * zFeL1(ji,jj,jk) * 1E-9
+         ! precipitation of Fe3+, creation of nanoparticles
+         precip(ji,jj,jk) = MAX( 0., ( zFe3(ji,jj,jk) * 1E-9 - fe3sol ) ) * kfep * xstep
+         !
+         ztrc   = ( tr(ji,jj,jk,jppoc,Kbb) + tr(ji,jj,jk,jpgoc,Kbb) + tr(ji,jj,jk,jpcal,Kbb) + tr(ji,jj,jk,jpgsi,Kbb) ) * 1.e6 
+         IF( ll_dust )  zdust  = dust(ji,jj) / ( wdust / rday ) * tmask(ji,jj,jk) &
+         &  * EXP( -gdept(ji,jj,jk,Kmm) / 540. )
+         IF (ln_ligand) THEN
+            zxlam  = xlam1 * MAX( 1.E-3, EXP(-2 * etot(ji,jj,jk) / 10. ) * (1. - EXP(-2 * tr(ji,jj,jk,jpoxy,Kbb) / 100.E-6 ) ))
+         ELSE
+            zxlam  = xlam1 * 1.0
+         ENDIF
+         zlam1b = 3.e-5 + xlamdust * zdust + zxlam * ztrc
+         zscave = zfeequi * zlam1b * xstep
+
+         ! Compute the different ratios for scavenging of iron
+         ! to later allocate scavenged iron to the different organic pools
+         ! ---------------------------------------------------------
+         zdenom1 = zxlam * tr(ji,jj,jk,jppoc,Kbb) / zlam1b
+         zdenom2 = zxlam * tr(ji,jj,jk,jpgoc,Kbb) / zlam1b
+
+         !  Increased scavenging for very high iron concentrations found near the coasts 
+         !  due to increased lithogenic particles and let say it is unknown processes (precipitation, ...)
+         !  -----------------------------------------------------------
+         zlamfac = MAX( 0.e0, ( gphit(ji,jj) + 55.) / 30. )
+         zlamfac = MIN( 1.  , zlamfac )
+         zdep    = MIN( 1., 1000. / gdept(ji,jj,jk,Kmm) )
+         zcoag   = 1E-4 * ( 1. - zlamfac ) * zdep * xstep * tr(ji,jj,jk,jpfer,Kbb)
+
+         !  Compute the coagulation of colloidal iron. This parameterization 
+         !  could be thought as an equivalent of colloidal pumping.
+         !  It requires certainly some more work as it is very poorly constrained.
+         !  ----------------------------------------------------------------
+         zlam1a   = ( 0.369  * 0.3 * tr(ji,jj,jk,jpdoc,Kbb) + 102.4  * tr(ji,jj,jk,jppoc,Kbb) ) * xdiss(ji,jj,jk)    &
+             &      + ( 114.   * 0.3 * tr(ji,jj,jk,jpdoc,Kbb) )
+         zaggdfea = zlam1a * xstep * zfecoll
+         !
+         zlam1b   = 3.53E3 * tr(ji,jj,jk,jpgoc,Kbb) * xdiss(ji,jj,jk)
+         zaggdfeb = zlam1b * xstep * zfecoll
+         !
+         tr(ji,jj,jk,jpfer,Krhs) = tr(ji,jj,jk,jpfer,Krhs) - zscave - zaggdfea - zaggdfeb &
+         &                     - zcoag - precip(ji,jj,jk)
+         tr(ji,jj,jk,jpsfe,Krhs) = tr(ji,jj,jk,jpsfe,Krhs) + zscave * zdenom1 + zaggdfea
+         tr(ji,jj,jk,jpbfe,Krhs) = tr(ji,jj,jk,jpbfe,Krhs) + zscave * zdenom2 + zaggdfeb
+         zscav3d(ji,jj,jk)   = zscave
+         zcoll3d(ji,jj,jk)   = zaggdfea + zaggdfeb
+         !
+      END_3D
       !
       !  Define the bioavailable fraction of iron
@@ -182 +176 @@
       IF( ln_ligand ) THEN
          !
-         DO jk = 1, jpkm1
-            DO jj = 1, jpj
-               DO ji = 1, jpi
-                  zlam1a   = ( 0.369  * 0.3 * tr(ji,jj,jk,jpdoc,Kbb) + 102.4  * tr(ji,jj,jk,jppoc,Kbb) ) * xdiss(ji,jj,jk)    &
-                      &    + ( 114.   * 0.3 * tr(ji,jj,jk,jpdoc,Kbb) )
-                  !
-                  zlam1b   = 3.53E3 *   tr(ji,jj,jk,jpgoc,Kbb) * xdiss(ji,jj,jk)
-                  zligco   = 0.5 * tr(ji,jj,jk,jplgw,Kmm)
-                  zaggliga = zlam1a * xstep * zligco
-                  zaggligb = zlam1b * xstep * zligco
-                  tr(ji,jj,jk,jplgw,Krhs) = tr(ji,jj,jk,jplgw,Krhs) - zaggliga - zaggligb
-                  zlcoll3d(ji,jj,jk)  = zaggliga + zaggligb
-               END DO
-            END DO
-         END DO
+         DO_3D_11_11( 1, jpkm1 )
+            zlam1a   = ( 0.369  * 0.3 * tr(ji,jj,jk,jpdoc,Kbb) + 102.4  * tr(ji,jj,jk,jppoc,Kbb) ) * xdiss(ji,jj,jk)    &
+                &    + ( 114.   * 0.3 * tr(ji,jj,jk,jpdoc,Kbb) )
+            !
+            zlam1b   = 3.53E3 *   tr(ji,jj,jk,jpgoc,Kbb) * xdiss(ji,jj,jk)
+            zligco   = 0.5 * tr(ji,jj,jk,jplgw,Kmm)
+            zaggliga = zlam1a * xstep * zligco
+            zaggligb = zlam1b * xstep * zligco
+            tr(ji,jj,jk,jplgw,Krhs) = tr(ji,jj,jk,jplgw,Krhs) - zaggliga - zaggligb
+            zlcoll3d(ji,jj,jk)  = zaggliga + zaggligb
+         END_3D
          !
          plig(:,:,:) =  MAX( 0., ( ( zFeL1(:,:,:) * 1E-9 ) / ( tr(:,:,:,jpfer,Kbb) +rtrn ) ) )