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2019WP/KERNEL-02_Storkey_Coward_IMMERSE_first_steps – NEMO
wiki:2019WP/KERNEL-02_Storkey_Coward_IMMERSE_first_steps

Version 9 (modified by acc, 5 years ago) (diff)

--

KERNEL-02_DaveStorkey_RK3Preparation

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Summary

Action KERNEL-02_DaveStorkey_RK3Preparation
PI(S) Dave Storkey

Digest

Reorganisation of code to prepare for implementation of RK3 timestepping:

  1. Prognostic fields to be passed to tendency routines as arguments.
  2. Tracers to be consistency updated as extensive (volume-weighted) quantities throughout the code.
Dependencies
Target
Trac Ticket #0000
SVN branch branches/$YEAR/dev_r{REV}_{SCOPE}-{NUM}_{PIS}-{KEYWORDS}
Previewer(s) Gurvan Madec
Reviewer(s) Gurvan Madec
Link ExtractUrl(.)?

Abstract

This section should be completed before starting to develop the code, in order to find agreement on the method beforehand.

Error: Failed to load processor TracForm
No macro or processor named 'TracForm' found

Once the PI has completed this section, he should send a mail to the previewer(s) asking them to preview the work within two weeks.

Preview

Part of the reorganisation for RK3 requires the refactoring of arrays such as un, ub into a single, 4 dimensional array with a time-level dimension. It is expected that much of the work required here can be automated to the extent that it is feasible to re-apply these changes after the annual merge. Below is a working example of how this might be achieved. Perl is used to carry out the pattern matching and substitution because of its ability to match patterns extending over several lines. A random subset of source files are used in this example and serve to illustrate the successes and caveats for the method.

Version 2 -Tweaked refactoring script to handle indirect addressing (i.e. brackets within array indices)

Step 1 Perl is used in a 'edit in place' mode so the original files will be overwritten. Step 1 is therefore to create copies of the test files:

#!/bin/bash
mkdir TEST_FILES
cp FLO/flo_oce.F90 FLO/floats.F90 SBC/sbcfwb.F90 DYN/dynadv_ubs.F90 DYN/dynkeg.F90 DYN/dynvor.F90 DYN/dynadv_cen2.F90 TRA/trabbl.F90 TEST_FILES
cp FLO/flo_oce.F90 FLO/floats.F90 SBC/sbcfwb.F90 DYN/dynadv_ubs.F90 DYN/dynkeg.F90 DYN/dynvor.F90 DYN/dynadv_cen2.F90 TRA/trabbl.F90 TEST_FILES_ORG

The refactoring script

#!/bin/bash
#
 INVARS=( ub  vb  wb  un  vn  wn )
OUTVARS=( uu  vv  ww  uu  vv  ww )
  TLEVS=( Nnn Nnn Nnn Nii Nii Nii )
#
rm patch.list
for f in TEST_FILES/*.F90
do
 echo "{{{#!diff" >> patch.list
 echo "Index: "$f >> patch.list
 echo "==============================" >> patch.list
 n=0
 for n in `seq 0 1 $(( ${#INVARS[*]} - 1 ))`
 do
  perl -0777 -pi -e 's@([+.(,\s\-\/\*\%])'${INVARS[$n]}'(\s*)(\(((?:[^()]++|(?3))*)\))@\1'${OUTVARS[$n]}'\2\(\4,'${TLEVS[$n]}'\)@g'  $f
 done
 diff -u TEST_FILES_ORG/`basename $f` $f >> patch.list
 echo "}}}" >> patch.list
done

The refactoring script explained

# Some bash arrays to list the old names, new names and associated time-level index. 
# The choice of names here is not meant to reflect a desired choice. Note all three arrays 
# must have the same number of entries

   INVARS=( ub  vb  wb  un  vn  wn )
  OUTVARS=( uu  vv  ww  uu  vv  ww )
    TLEVS=( Nnn Nnn Nnn Nii Nii Nii )

#
# Lines referring to patch.list are just generating some output for this Wiki page. 
# They can be ignored for the purposes of explaining the script

# Loop over all files in test directory

  for f in TEST_FILES/*.F90
  do

# Loop over each input variable name

   for n in `seq 0 1 $(( ${#INVARS[*]} - 1 ))`
   do

# The perl command:

# -0777 -pi  are the options that force replace in place operation. 
# Could elect to redirect to new files

# The substitute command matches the INVAR string preceded by any of: +.(,whitespace-/*%
# Any match here goes into the first pattern space (\1)

# The INVAR string can have any amount of whitespace (including none) between it and an 
# opening bracket. This whitespace is preserved in pattern space 2

# Everything following the opening bracket to matching closing bracket 
# is stored in pattern space 3. This requires a recursion and pattern space 4 ends up with
# the interior of the outer brackets

# The RHS of the substitute command rebuilds the line replacing INVARS with OUTVARS and
# adding a ,TLEVS before the closing bracket

   perl -0777 -pi -e 's@([+.(,\s\-\/\*\%])'${INVARS[$n]}'(\s*)(\(((?:[^()]++|(?3))*)\))@\1'${OUTVARS[$n]}'\2\(\4,'${TLEVS[$n]}'\)@g'  $f

# End of variable loop

   done
 
# End of file loop

  done

Some contrived tests:

cat TEST_FILES_ORG/contrived_tests.F90
  un(:,:,:)                    ! The simplest test. Should ==> uu(:,:,:,jtn)
   un ( ji   , jj,   : )        ! Check alternative simple case ==> uu ( ji   , jj,   :,jtn)
   a+ub(:,:,jk)                 ! Check preceeding operators are correctly recognised
   a-vb(:,:,jk)                 ! Check preceeding operators are correctly recognised
   a*vn(:,:,jk)                 ! Check preceeding operators are correctly recognised
   a/wb(:,:,jk)                 ! Check preceeding operators are correctly recognised
   a%wn(:,:,jk)                 ! Check preceeding operators are correctly recognised
 .OR.wn(:,:,jk)                 ! Check preceeding operators are correctly recognised
    (wn(:,:,jk) + wn(:,:,jk-1)) ! Check preceeding brackets are correctly recognised
   un ( ji+1 ,     &            ! Check that entries over
  &     jj, jk - 1 )            !                    multiple lines are handled
   wn( mi0(ii) , mj0(jj ))      ! Brackets within arguments may break [ does this occur?]
  pun(:,:,:)                    ! target preceded by non-whitespace or operator. Should be unchanged
  sbc_fwb(:,:,:)                ! target preceded by non-whitespace or operator. Should be unchanged

Result of the script on the contrived tests:

   uu(:,:,:,Nii)                    ! The simplest test. Should ==> uu(:,:,:,jtn)
   uu ( ji   , jj,   : ,Nii)        ! Check alternative simple case ==> uu ( ji   , jj,   :,jtn)
   a+uu(:,:,jk,Nnn)                 ! Check preceeding operators are correctly recognised
   a-vv(:,:,jk,Nnn)                 ! Check preceeding operators are correctly recognised
   a*vv(:,:,jk,Nii)                 ! Check preceeding operators are correctly recognised
   a/ww(:,:,jk,Nnn)                 ! Check preceeding operators are correctly recognised
   a%ww(:,:,jk,Nii)                 ! Check preceeding operators are correctly recognised
 .OR.ww(:,:,jk,Nii)                 ! Check preceeding operators are correctly recognised
    (ww(:,:,jk,Nii) + ww(:,:,jk-1,Nii)) ! Check preceeding brackets are correctly recognised
   uu ( ji+1 ,     &            ! Check that entries over
  &     jj, jk - 1 ,Nii)            !                    multiple lines are handled
   ww( mi0(ii) , mj0(jj ),Nii)      ! Brackets within arguments may break [ does this occur?]
  pun(:,:,:)                    ! target preceded by non-whitespace or operator. Should be unchanged
  sbc_fwb(:,:,:)                ! target preceded by non-whitespace or operator. Should be unchanged
  • contrived_tests.F90

    ==============================
    old new  
    1    un(:,:,:)                    ! The simplest test. Should ==> uu(:,:,:,jtn) 
    2    un ( ji   , jj,   : )        ! Check alternative simple case ==> uu ( ji   , jj,   :,jtn) 
    3    a+ub(:,:,jk)                 ! Check preceeding operators are correctly recognised 
    4    a-vb(:,:,jk)                 ! Check preceeding operators are correctly recognised 
    5    a*vn(:,:,jk)                 ! Check preceeding operators are correctly recognised 
    6    a/wb(:,:,jk)                 ! Check preceeding operators are correctly recognised 
    7    a%wn(:,:,jk)                 ! Check preceeding operators are correctly recognised 
    8  .OR.wn(:,:,jk)                 ! Check preceeding operators are correctly recognised 
    9     (wn(:,:,jk) + wn(:,:,jk-1)) ! Check preceeding brackets are correctly recognised 
    10    un ( ji+1 ,     &            ! Check that entries over 
    11   &     jj, jk - 1 )            !                    multiple lines are handled 
    12    wn( mi0(ii) , mj0(jj ))      ! Brackets within arguments may break [ does this occur?] 
     1   uu(:,:,:,Nii)                    ! The simplest test. Should ==> uu(:,:,:,jtn) 
     2   uu ( ji   , jj,   : ,Nii)        ! Check alternative simple case ==> uu ( ji   , jj,   :,jtn) 
     3   a+uu(:,:,jk,Nnn)                 ! Check preceeding operators are correctly recognised 
     4   a-vv(:,:,jk,Nnn)                 ! Check preceeding operators are correctly recognised 
     5   a*vv(:,:,jk,Nii)                 ! Check preceeding operators are correctly recognised 
     6   a/ww(:,:,jk,Nnn)                 ! Check preceeding operators are correctly recognised 
     7   a%ww(:,:,jk,Nii)                 ! Check preceeding operators are correctly recognised 
     8 .OR.ww(:,:,jk,Nii)                 ! Check preceeding operators are correctly recognised 
     9    (ww(:,:,jk,Nii) + ww(:,:,jk-1,Nii)) ! Check preceeding brackets are correctly recognised 
     10   uu ( ji+1 ,     &            ! Check that entries over 
     11  &     jj, jk - 1 ,Nii)            !                    multiple lines are handled 
     12   ww( mi0(ii) , mj0(jj ),Nii)      ! Brackets within arguments may break [ does this occur?] 
    1313  pun(:,:,:)                    ! target preceded by non-whitespace or operator. Should be unchanged 
    1414  sbc_fwb(:,:,:)                ! target preceded by non-whitespace or operator. Should be unchanged 

So all changes were made correctly and even those entries which were potential pitfalls (pun and sbc_fwb) were correctly ignored. Time to try a real set:

The results on the sample set of files (patch.list):

  • dynadv_cen2.F90

    ==============================
    old new  
    6666      !                             !==  Horizontal advection  ==! 
    6767      ! 
    6868      DO jk = 1, jpkm1                    ! horizontal transport 
    69          zfu(:,:,jk) = 0.25_wp * e2u(:,:) * e3u_n(:,:,jk) * un(:,:,jk) 
    70          zfv(:,:,jk) = 0.25_wp * e1v(:,:) * e3v_n(:,:,jk) * vn(:,:,jk) 
     69         zfu(:,:,jk) = 0.25_wp * e2u(:,:) * e3u_n(:,:,jk) * uu(:,:,jk,Nii) 
     70         zfv(:,:,jk) = 0.25_wp * e1v(:,:) * e3v_n(:,:,jk) * vv(:,:,jk,Nii) 
    7171         DO jj = 1, jpjm1                 ! horizontal momentum fluxes (at T- and F-point) 
    7272            DO ji = 1, fs_jpim1   ! vector opt. 
    73                zfu_t(ji+1,jj  ,jk) = ( zfu(ji,jj,jk) + zfu(ji+1,jj,jk) ) * ( un(ji,jj,jk) + un(ji+1,jj  ,jk) ) 
    74                zfv_f(ji  ,jj  ,jk) = ( zfv(ji,jj,jk) + zfv(ji+1,jj,jk) ) * ( un(ji,jj,jk) + un(ji  ,jj+1,jk) ) 
    75                zfu_f(ji  ,jj  ,jk) = ( zfu(ji,jj,jk) + zfu(ji,jj+1,jk) ) * ( vn(ji,jj,jk) + vn(ji+1,jj  ,jk) ) 
    76                zfv_t(ji  ,jj+1,jk) = ( zfv(ji,jj,jk) + zfv(ji,jj+1,jk) ) * ( vn(ji,jj,jk) + vn(ji  ,jj+1,jk) ) 
     73               zfu_t(ji+1,jj  ,jk) = ( zfu(ji,jj,jk) + zfu(ji+1,jj,jk) ) * ( uu(ji,jj,jk,Nii) + uu(ji+1,jj  ,jk,Nii) ) 
     74               zfv_f(ji  ,jj  ,jk) = ( zfv(ji,jj,jk) + zfv(ji+1,jj,jk) ) * ( uu(ji,jj,jk,Nii) + uu(ji  ,jj+1,jk,Nii) ) 
     75               zfu_f(ji  ,jj  ,jk) = ( zfu(ji,jj,jk) + zfu(ji,jj+1,jk) ) * ( vv(ji,jj,jk,Nii) + vv(ji+1,jj  ,jk,Nii) ) 
     76               zfv_t(ji  ,jj+1,jk) = ( zfv(ji,jj,jk) + zfv(ji,jj+1,jk) ) * ( vv(ji,jj,jk,Nii) + vv(ji  ,jj+1,jk,Nii) ) 
    7777            END DO 
    7878         END DO 
    7979         DO jj = 2, jpjm1                 ! divergence of horizontal momentum fluxes 
     
    105105      IF( ln_linssh ) THEN                ! linear free surface: advection through the surface 
    106106         DO jj = 2, jpjm1 
    107107            DO ji = fs_2, fs_jpim1 
    108                zfu_uw(ji,jj,1) = 0.5_wp * ( e1e2t(ji,jj) * wn(ji,jj,1) + e1e2t(ji+1,jj) * wn(ji+1,jj,1) ) * un(ji,jj,1) 
    109                zfv_vw(ji,jj,1) = 0.5_wp * ( e1e2t(ji,jj) * wn(ji,jj,1) + e1e2t(ji,jj+1) * wn(ji,jj+1,1) ) * vn(ji,jj,1) 
     108               zfu_uw(ji,jj,1) = 0.5_wp * ( e1e2t(ji,jj) * ww(ji,jj,1,Nii) + e1e2t(ji+1,jj) * ww(ji+1,jj,1,Nii) ) * uu(ji,jj,1,Nii) 
     109               zfv_vw(ji,jj,1) = 0.5_wp * ( e1e2t(ji,jj) * ww(ji,jj,1,Nii) + e1e2t(ji,jj+1) * ww(ji,jj+1,1,Nii) ) * vv(ji,jj,1,Nii) 
    110110            END DO 
    111111         END DO 
    112112      ENDIF 
    113113      DO jk = 2, jpkm1                    ! interior advective fluxes 
    114114         DO jj = 2, jpj                       ! 1/4 * Vertical transport 
    115115            DO ji = 2, jpi 
    116                zfw(ji,jj,jk) = 0.25_wp * e1e2t(ji,jj) * wn(ji,jj,jk) 
     116               zfw(ji,jj,jk) = 0.25_wp * e1e2t(ji,jj) * ww(ji,jj,jk,Nii) 
    117117            END DO 
    118118         END DO 
    119119         DO jj = 2, jpjm1 
    120120            DO ji = fs_2, fs_jpim1   ! vector opt. 
    121                zfu_uw(ji,jj,jk) = ( zfw(ji,jj,jk) + zfw(ji+1,jj  ,jk) ) * ( un(ji,jj,jk) + un(ji,jj,jk-1) ) 
    122                zfv_vw(ji,jj,jk) = ( zfw(ji,jj,jk) + zfw(ji  ,jj+1,jk) ) * ( vn(ji,jj,jk) + vn(ji,jj,jk-1) ) 
     121               zfu_uw(ji,jj,jk) = ( zfw(ji,jj,jk) + zfw(ji+1,jj  ,jk) ) * ( uu(ji,jj,jk,Nii) + uu(ji,jj,jk-1,Nii) ) 
     122               zfv_vw(ji,jj,jk) = ( zfw(ji,jj,jk) + zfw(ji  ,jj+1,jk) ) * ( vv(ji,jj,jk,Nii) + vv(ji,jj,jk-1,Nii) ) 
    123123            END DO 
    124124         END DO 
    125125      END DO 
  • dynadv_ubs.F90

    ==============================
    old new  
    101101      DO jk = 1, jpkm1                       !  Laplacian of the velocity  ! 
    102102         !                                   ! =========================== ! 
    103103         !                                         ! horizontal volume fluxes 
    104          zfu(:,:,jk) = e2u(:,:) * e3u_n(:,:,jk) * un(:,:,jk) 
    105          zfv(:,:,jk) = e1v(:,:) * e3v_n(:,:,jk) * vn(:,:,jk) 
     104         zfu(:,:,jk) = e2u(:,:) * e3u_n(:,:,jk) * uu(:,:,jk,Nii) 
     105         zfv(:,:,jk) = e1v(:,:) * e3v_n(:,:,jk) * vv(:,:,jk,Nii) 
    106106         ! 
    107107         DO jj = 2, jpjm1                          ! laplacian 
    108108            DO ji = fs_2, fs_jpim1   ! vector opt. 
    109                zlu_uu(ji,jj,jk,1) = ( ub (ji+1,jj  ,jk) - 2.*ub (ji,jj,jk) + ub (ji-1,jj  ,jk) ) * umask(ji,jj,jk) 
    110                zlv_vv(ji,jj,jk,1) = ( vb (ji  ,jj+1,jk) - 2.*vb (ji,jj,jk) + vb (ji  ,jj-1,jk) ) * vmask(ji,jj,jk) 
    111                zlu_uv(ji,jj,jk,1) = ( ub (ji  ,jj+1,jk) - ub (ji  ,jj  ,jk) ) * fmask(ji  ,jj  ,jk)   & 
    112                   &               - ( ub (ji  ,jj  ,jk) - ub (ji  ,jj-1,jk) ) * fmask(ji  ,jj-1,jk) 
    113                zlv_vu(ji,jj,jk,1) = ( vb (ji+1,jj  ,jk) - vb (ji  ,jj  ,jk) ) * fmask(ji  ,jj  ,jk)   & 
    114                   &               - ( vb (ji  ,jj  ,jk) - vb (ji-1,jj  ,jk) ) * fmask(ji-1,jj  ,jk) 
     109               zlu_uu(ji,jj,jk,1) = ( uu (ji+1,jj  ,jk,Nnn) - 2.*uu (ji,jj,jk,Nnn) + uu (ji-1,jj  ,jk,Nnn) ) * umask(ji,jj,jk) 
     110               zlv_vv(ji,jj,jk,1) = ( vv (ji  ,jj+1,jk,Nnn) - 2.*vv (ji,jj,jk,Nnn) + vv (ji  ,jj-1,jk,Nnn) ) * vmask(ji,jj,jk) 
     111               zlu_uv(ji,jj,jk,1) = ( uu (ji  ,jj+1,jk,Nnn) - uu (ji  ,jj  ,jk,Nnn) ) * fmask(ji  ,jj  ,jk)   & 
     112                  &               - ( uu (ji  ,jj  ,jk,Nnn) - uu (ji  ,jj-1,jk,Nnn) ) * fmask(ji  ,jj-1,jk) 
     113               zlv_vu(ji,jj,jk,1) = ( vv (ji+1,jj  ,jk,Nnn) - vv (ji  ,jj  ,jk,Nnn) ) * fmask(ji  ,jj  ,jk)   & 
     114                  &               - ( vv (ji  ,jj  ,jk,Nnn) - vv (ji-1,jj  ,jk,Nnn) ) * fmask(ji-1,jj  ,jk) 
    115115               ! 
    116116               zlu_uu(ji,jj,jk,2) = ( zfu(ji+1,jj  ,jk) - 2.*zfu(ji,jj,jk) + zfu(ji-1,jj  ,jk) ) * umask(ji,jj,jk) 
    117117               zlv_vv(ji,jj,jk,2) = ( zfv(ji  ,jj+1,jk) - 2.*zfv(ji,jj,jk) + zfv(ji  ,jj-1,jk) ) * vmask(ji,jj,jk) 
     
    131131      !                                      !  Horizontal advection  ! 
    132132      DO jk = 1, jpkm1                       ! ====================== ! 
    133133         !                                         ! horizontal volume fluxes 
    134          zfu(:,:,jk) = 0.25_wp * e2u(:,:) * e3u_n(:,:,jk) * un(:,:,jk) 
    135          zfv(:,:,jk) = 0.25_wp * e1v(:,:) * e3v_n(:,:,jk) * vn(:,:,jk) 
     134         zfu(:,:,jk) = 0.25_wp * e2u(:,:) * e3u_n(:,:,jk) * uu(:,:,jk,Nii) 
     135         zfv(:,:,jk) = 0.25_wp * e1v(:,:) * e3v_n(:,:,jk) * vv(:,:,jk,Nii) 
    136136         ! 
    137137         DO jj = 1, jpjm1                          ! horizontal momentum fluxes at T- and F-point 
    138138            DO ji = 1, fs_jpim1   ! vector opt. 
    139                zui = ( un(ji,jj,jk) + un(ji+1,jj  ,jk) ) 
    140                zvj = ( vn(ji,jj,jk) + vn(ji  ,jj+1,jk) ) 
     139               zui = ( uu(ji,jj,jk,Nii) + uu(ji+1,jj  ,jk,Nii) ) 
     140               zvj = ( vv(ji,jj,jk,Nii) + vv(ji  ,jj+1,jk,Nii) ) 
    141141               ! 
    142142               IF( zui > 0 ) THEN   ;   zl_u = zlu_uu(ji  ,jj,jk,1) 
    143143               ELSE                 ;   zl_u = zlu_uu(ji+1,jj,jk,1) 
     
    163163               ENDIF 
    164164               ! 
    165165               zfv_f(ji  ,jj  ,jk) = ( zfvi - gamma2 * ( zlv_vu(ji,jj,jk,2) + zlv_vu(ji+1,jj  ,jk,2) )  )   & 
    166                   &                * ( un(ji,jj,jk) + un(ji  ,jj+1,jk) - gamma1 * zl_u ) 
     166                  &                * ( uu(ji,jj,jk,Nii) + uu(ji  ,jj+1,jk,Nii) - gamma1 * zl_u ) 
    167167               zfu_f(ji  ,jj  ,jk) = ( zfuj - gamma2 * ( zlu_uv(ji,jj,jk,2) + zlu_uv(ji  ,jj+1,jk,2) )  )   & 
    168                   &                * ( vn(ji,jj,jk) + vn(ji+1,jj  ,jk) - gamma1 * zl_v ) 
     168                  &                * ( vv(ji,jj,jk,Nii) + vv(ji+1,jj  ,jk,Nii) - gamma1 * zl_v ) 
    169169            END DO 
    170170         END DO 
    171171         DO jj = 2, jpjm1                          ! divergence of horizontal momentum fluxes 
     
    198198      IF( ln_linssh ) THEN                         ! constant volume : advection through the surface 
    199199         DO jj = 2, jpjm1 
    200200            DO ji = fs_2, fs_jpim1 
    201                zfu_uw(ji,jj,1) = 0.5_wp * ( e1e2t(ji,jj) * wn(ji,jj,1) + e1e2t(ji+1,jj) * wn(ji+1,jj,1) ) * un(ji,jj,1) 
    202                zfv_vw(ji,jj,1) = 0.5_wp * ( e1e2t(ji,jj) * wn(ji,jj,1) + e1e2t(ji,jj+1) * wn(ji,jj+1,1) ) * vn(ji,jj,1) 
     201               zfu_uw(ji,jj,1) = 0.5_wp * ( e1e2t(ji,jj) * ww(ji,jj,1,Nii) + e1e2t(ji+1,jj) * ww(ji+1,jj,1,Nii) ) * uu(ji,jj,1,Nii) 
     202               zfv_vw(ji,jj,1) = 0.5_wp * ( e1e2t(ji,jj) * ww(ji,jj,1,Nii) + e1e2t(ji,jj+1) * ww(ji,jj+1,1,Nii) ) * vv(ji,jj,1,Nii) 
    203203            END DO 
    204204         END DO 
    205205      ENDIF 
    206206      DO jk = 2, jpkm1                          ! interior fluxes 
    207207         DO jj = 2, jpj 
    208208            DO ji = 2, jpi 
    209                zfw(ji,jj,jk) = 0.25_wp * e1e2t(ji,jj) * wn(ji,jj,jk) 
     209               zfw(ji,jj,jk) = 0.25_wp * e1e2t(ji,jj) * ww(ji,jj,jk,Nii) 
    210210            END DO 
    211211         END DO 
    212212         DO jj = 2, jpjm1 
    213213            DO ji = fs_2, fs_jpim1   ! vector opt. 
    214                zfu_uw(ji,jj,jk) = ( zfw(ji,jj,jk)+ zfw(ji+1,jj,jk) ) * ( un(ji,jj,jk) + un(ji,jj,jk-1) ) 
    215                zfv_vw(ji,jj,jk) = ( zfw(ji,jj,jk)+ zfw(ji,jj+1,jk) ) * ( vn(ji,jj,jk) + vn(ji,jj,jk-1) ) 
     214               zfu_uw(ji,jj,jk) = ( zfw(ji,jj,jk)+ zfw(ji+1,jj,jk) ) * ( uu(ji,jj,jk,Nii) + uu(ji,jj,jk-1,Nii) ) 
     215               zfv_vw(ji,jj,jk) = ( zfw(ji,jj,jk)+ zfw(ji,jj+1,jk) ) * ( vv(ji,jj,jk,Nii) + vv(ji,jj,jk-1,Nii) ) 
    216216            END DO 
    217217         END DO 
    218218      END DO 
  • dynkeg.F90

    ==============================
    old new  
    5656      !!         zhke = 1/2 [ mi-1( un^2 ) + mj-1( vn^2 ) ] 
    5757      !!              * kscheme = nkeg_HW : Hollingsworth correction following 
    5858      !!      Arakawa (2001). The now horizontal kinetic energy is given by: 
    59       !!         zhke = 1/6 [ mi-1(  2 * un^2 + ((un(j+1)+un(j-1))/2)^2  ) 
    60       !!                    + mj-1(  2 * vn^2 + ((vn(i+1)+vn(i-1))/2)^2  ) ] 
     59      !!         zhke = 1/6 [ mi-1(  2 * un^2 + ((uu(j+1,Nii)+uu(j-1,Nii))/2)^2  ) 
     60      !!                    + mj-1(  2 * vn^2 + ((vv(i+1,Nii)+vv(i-1,Nii))/2)^2  ) ] 
    6161      !! 
    6262      !!      Take its horizontal gradient and add it to the general momentum 
    6363      !!      trend (ua,va). 
     
    108108                     ii   = idx_bdy(ib_bdy)%nbi(jb,igrd) 
    109109                     ij   = idx_bdy(ib_bdy)%nbj(jb,igrd) 
    110110                     ifu   = NINT( idx_bdy(ib_bdy)%flagu(jb,igrd) ) 
    111                      un(ii-ifu,ij,jk) = un(ii,ij,jk) * umask(ii,ij,jk) 
     111                     uu(ii-ifu,ij,jk,Nii) = uu(ii,ij,jk,Nii) * umask(ii,ij,jk) 
    112112                  END DO 
    113113               END DO 
    114114               ! 
     
    118118                     ii   = idx_bdy(ib_bdy)%nbi(jb,igrd) 
    119119                     ij   = idx_bdy(ib_bdy)%nbj(jb,igrd) 
    120120                     ifv   = NINT( idx_bdy(ib_bdy)%flagv(jb,igrd) ) 
    121                      vn(ii,ij-ifv,jk) = vn(ii,ij,jk) * vmask(ii,ij,jk) 
     121                     vv(ii,ij-ifv,jk,Nii) = vv(ii,ij,jk,Nii) * vmask(ii,ij,jk) 
    122122                  END DO 
    123123               END DO 
    124124            ENDIF 
     
    131131         DO jk = 1, jpkm1 
    132132            DO jj = 2, jpj 
    133133               DO ji = fs_2, jpi   ! vector opt. 
    134                   zu =    un(ji-1,jj  ,jk) * un(ji-1,jj  ,jk)   & 
    135                      &  + un(ji  ,jj  ,jk) * un(ji  ,jj  ,jk) 
    136                   zv =    vn(ji  ,jj-1,jk) * vn(ji  ,jj-1,jk)   & 
    137                      &  + vn(ji  ,jj  ,jk) * vn(ji  ,jj  ,jk) 
     134                  zu =    uu(ji-1,jj  ,jk,Nii) * uu(ji-1,jj  ,jk,Nii)   & 
     135                     &  + uu(ji  ,jj  ,jk,Nii) * uu(ji  ,jj  ,jk,Nii) 
     136                  zv =    vv(ji  ,jj-1,jk,Nii) * vv(ji  ,jj-1,jk,Nii)   & 
     137                     &  + vv(ji  ,jj  ,jk,Nii) * vv(ji  ,jj  ,jk,Nii) 
    138138                  zhke(ji,jj,jk) = 0.25_wp * ( zv + zu ) 
    139139               END DO 
    140140            END DO 
     
    144144         DO jk = 1, jpkm1 
    145145            DO jj = 2, jpjm1 
    146146               DO ji = fs_2, jpim1   ! vector opt. 
    147                   zu = 8._wp * ( un(ji-1,jj  ,jk) * un(ji-1,jj  ,jk)    & 
    148                      &         + un(ji  ,jj  ,jk) * un(ji  ,jj  ,jk) )  & 
    149                      &   +     ( un(ji-1,jj-1,jk) + un(ji-1,jj+1,jk) ) * ( un(ji-1,jj-1,jk) + un(ji-1,jj+1,jk) )   & 
    150                      &   +     ( un(ji  ,jj-1,jk) + un(ji  ,jj+1,jk) ) * ( un(ji  ,jj-1,jk) + un(ji  ,jj+1,jk) ) 
     147                  zu = 8._wp * ( uu(ji-1,jj  ,jk,Nii) * uu(ji-1,jj  ,jk,Nii)    & 
     148                     &         + uu(ji  ,jj  ,jk,Nii) * uu(ji  ,jj  ,jk,Nii) )  & 
     149                     &   +     ( uu(ji-1,jj-1,jk,Nii) + uu(ji-1,jj+1,jk,Nii) ) * ( uu(ji-1,jj-1,jk,Nii) + uu(ji-1,jj+1,jk,Nii) )   & 
     150                     &   +     ( uu(ji  ,jj-1,jk,Nii) + uu(ji  ,jj+1,jk,Nii) ) * ( uu(ji  ,jj-1,jk,Nii) + uu(ji  ,jj+1,jk,Nii) ) 
    151151                     ! 
    152                   zv = 8._wp * ( vn(ji  ,jj-1,jk) * vn(ji  ,jj-1,jk)    & 
    153                      &         + vn(ji  ,jj  ,jk) * vn(ji  ,jj  ,jk) )  & 
    154                      &  +      ( vn(ji-1,jj-1,jk) + vn(ji+1,jj-1,jk) ) * ( vn(ji-1,jj-1,jk) + vn(ji+1,jj-1,jk) )   & 
    155                      &  +      ( vn(ji-1,jj  ,jk) + vn(ji+1,jj  ,jk) ) * ( vn(ji-1,jj  ,jk) + vn(ji+1,jj  ,jk) ) 
     152                  zv = 8._wp * ( vv(ji  ,jj-1,jk,Nii) * vv(ji  ,jj-1,jk,Nii)    & 
     153                     &         + vv(ji  ,jj  ,jk,Nii) * vv(ji  ,jj  ,jk,Nii) )  & 
     154                     &  +      ( vv(ji-1,jj-1,jk,Nii) + vv(ji+1,jj-1,jk,Nii) ) * ( vv(ji-1,jj-1,jk,Nii) + vv(ji+1,jj-1,jk,Nii) )   & 
     155                     &  +      ( vv(ji-1,jj  ,jk,Nii) + vv(ji+1,jj  ,jk,Nii) ) * ( vv(ji-1,jj  ,jk,Nii) + vv(ji+1,jj  ,jk,Nii) ) 
    156156                  zhke(ji,jj,jk) = r1_48 * ( zv + zu ) 
    157157               END DO 
    158158            END DO 
     
    163163 
    164164      IF (ln_bdy) THEN 
    165165         ! restore velocity masks at points outside boundary 
    166          un(:,:,:) = un(:,:,:) * umask(:,:,:) 
    167          vn(:,:,:) = vn(:,:,:) * vmask(:,:,:) 
     166         uu(:,:,:,Nii) = uu(:,:,:,Nii) * umask(:,:,:) 
     167         vv(:,:,:,Nii) = vv(:,:,:,Nii) * vmask(:,:,:) 
    168168      ENDIF 
    169169 
    170170      ! 
Index: TEST_FILES/dynvor.F90
==============================
  • flo_oce.F90

    ==============================
    old new  
    5959      !!---------------------------------------------------------------------- 
    6060      !!                 ***  FUNCTION flo_oce_alloc  *** 
    6161      !!---------------------------------------------------------------------- 
    62       ALLOCATE( wb(jpi,jpj,jpk) , nfloat(jpnfl) , nisobfl(jpnfl) , ngrpfl(jpnfl) , & 
     62      ALLOCATE( ww(jpi,jpj,jpk,Nnn) , nfloat(jpnfl) , nisobfl(jpnfl) , ngrpfl(jpnfl) , & 
    6363         &      flxx(jpnfl)     , flyy(jpnfl)   , flzz(jpnfl)    ,                 & 
    6464         &      tpifl(jpnfl)    , tpjfl(jpnfl)  , tpkfl(jpnfl)   , STAT=flo_oce_alloc ) 
    6565      ! 

Ok This was wrong.Nnn is not what should go into the ALLOCATE statement

  • floats.F90

    ==============================
    old new  
    6464      ! 
    6565      CALL flo_rst( kt )      ! trajectories restart 
    6666      ! 
    67       wb(:,:,:) = wn(:,:,:)         ! Save the old vertical velocity field 
     67      ww(:,:,:,Nnn) = ww(:,:,:,Nii)         ! Save the old vertical velocity field 
    6868      ! 
    6969      IF( ln_timing )   CALL timing_stop('flo_stp') 
    7070      ! 
     
    131131      ! 
    132132      CALL flo_dom                  ! compute/read initial position of floats 
    133133      ! 
    134       wb(:,:,:) = wn(:,:,:)         ! set wb for computation of floats trajectories at the first time step 
     134      ww(:,:,:,Nnn) = ww(:,:,:,Nii)         ! set wb for computation of floats trajectories at the first time step 
    135135      ! 
    136136   END SUBROUTINE flo_init 
    137137 
Index: TEST_FILES/sbcfwb.F90
==============================
  • trabbl.F90

    ==============================
    old new  
    347347            zts (ji,jj,jp_sal) = tsb(ji,jj,ik,jp_sal) 
    348348            ! 
    349349            zdep(ji,jj) = gdept_n(ji,jj,ik)              ! bottom T-level reference depth 
    350             zub (ji,jj) = un(ji,jj,mbku(ji,jj))          ! bottom velocity 
    351             zvb (ji,jj) = vn(ji,jj,mbkv(ji,jj)) 
     350            zub (ji,jj) = uu(ji,jj,mbku(ji,jj),Nii)          ! bottom velocity 
     351            zvb (ji,jj) = vv(ji,jj,mbkv(ji,jj),Nii) 
    352352         END DO 
    353353      END DO 
    354354      ! 

Tests

Once the development is done, the PI should complete this section below and ask the reviewers to start their review in the lower section.

Error: Failed to load processor TracForm
No macro or processor named 'TracForm' found

Review

A successful review is needed to schedule the merge of this development into the future NEMO release during next Merge Party (usually in November).

Error: Failed to load processor TracForm
No macro or processor named 'TracForm' found

Once review is successful, the development must be scheduled for merge during next Merge Party Meeting.

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