Version 18 (modified by cetlod, 5 years ago) (diff)

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Author : Gurvan Madec, Florian Lemarié, George Nurser

ticket : #1593

Branch : 2015/dev_r5721_CNRS9_NOC3_LDF

WP2015 Action : CNRS-9 and NOC-3


Development branch related to CNRS-9 and NOC-3 actions of 2015 work plan :
• simplify and improve the tracer advection and the lateral diffusion and dissipation in NEMO/OPA
• generalization of the use of surface scale factors (e1e2 at T, U, V, F points)

NB: This development consists in merging the current trunk with the last year work on that subject (see ticket #1260, and the associated branch ​​2014/dev_CNRS0_NOC1_LDF​ and wiki page ​​1260_CNRS0_NOC1_LDF.

(1) define bilaplacian operators on dynamics and tracers as re-entrant laplacian ;
(2) change the way the eddy diffusivity and viscosity are specified and controlled by the user ; add a new choice (read the coeff. in a file) ;(3) generalize of the use of surface scale factors and their inverse ;
(4) add a optional read of surface scale factors in coordinate file in case of reduction of the scale factors in some straits (allows to suppress hard coded ORCA staff in domhgr.F90).
(5) suppress some CPP keys

(1) introduce Beckers et al. (2000) compact stencil in the cross-isoneutral direction in triads formalism ;
(2) introduce in both iso-neutral operator the Method of Stabilizing Correction (Lemarié et al. (2012) (it minimizes numerical errors, and allows the implementation of bilaplacian iso-neutral operator) ;

(3) implement bilaplacian iso-neutral operators (Lemarié et al. (2012).


Three steps:

I. Phasing of horizontal scale factors ==⇒>> OK see revision 5737 + minor correction revision 5737 (SETE OK)

(I.1) standardisation of the name of quantities derived from horizontal scale factors (many modules of NEMO)
The chosen names of quantities derived from horizontal scale factors are:
- inverse of scale factors : r1_e1t, r1_e2t, r1_e1u, r1_e2u, r1_e1v, r1_e2v, r1_e1f, r1_e2f ;
- surfaces and their inverse: e1e2t, e1e2u , e1e2v, e1e2f and, r1_e1e2t , r1_e1e2u , r1_e1e2v, r1_e1e2f ;
- ratio (used in traldf…) : e2_e1u , e1_e2v(I.1) generalize of the use of surface scale factors ;
These quantities are defined in memory in dom_oce.F90, and set to their proper value in domhgr.F90

(I.2) add a optional read of surface scale factors at velocity points in coordinate file (domhgr.F90)
The input coordinate file have to include e1e2u and e1e2v in case of reduction of the scale factors in some straits.
When e1u or e2v are reduced in some straits, the surface at u- and v-points remains unchanged.
This allows to suppress the dom_vvl_orca_fix routine from dlmvvl.F90 module.
Note that this change modifies the model results, as it contains a better handling of reduced strait width (i.e. reduced surface between 2 adjacent U or V points, but unchanged U and V points volume).
The implementation performed here is a first step to the full simplification of domhgr.F90. We kept here the hard coded reduction of scale factor in some straits for some given ORCA configuration.
A last step (see IV) will be to suppress the hard coded reduction of some scale factor as it will be always given in the file together with the e1e2u & e1e2v surfaces. ==⇒>> OK see revision 5755

II. Phasing of the advective/diffusive trends on tracers

II.1 — LDF on tracers (both TRA & TRC) - Diffusive trends : ==⇒>> OK see revision 5758 & 5759 &  5760

- laplacian operator: re-entrant laplacian for iso-level, standard iso-neutral, and triad iso-neutral operators ;
- bilaplacian operator: traldf_blp.F90 module: use of the re-entrant laplacian
- both standard and triad iso-neutral operators includes the Method of Stabilizing Correction (Lemarié et al. (2012) which allows bilaplacian along iso-neutral surfaces ;
- triad operator: introduce Beckers et al. (2000) compact stencil in the cross-isoneutral direction ; make the triad operator available in TOP
- change name: traldf_iso_grif.F90 becomes traldf_iso_triad.F90
- suppression of traadv_eiv.F90 ; traldf_bilap.F90 ; traldf_bilapg.F90 ;
- remove the possibility to compute the lateral diffusion from T-S anomalies (key_traldf_ano)

lateral mixing coefficient:
- new user interface (namelist) :

&namtra_ldf    !   lateral diffusion scheme for tracers
   !                       !  Operator type:
   ln_traldf_lap   =  .true.   !    laplacian operator
   ln_traldf_blp   =  .false.  !  bilaplacian operator
   !                       !  Direction of action:
   ln_traldf_lev   =  .false.  !  iso-level
   ln_traldf_hor   =  .false.  !  horizontal (geopotential)
   ln_traldf_iso   =  .true.   !  iso-neutral
   ln_traldf_triad =  .false.  !  iso-neutral using Griffies triads
   !		       	         !  iso-neutral options:        
   ln_traldf_msc   =  .true.   !  Method of Stabilizing Correction (both operators)
   rn_slpmax       =   0.01    !  slope limit                      (both operators)
   ln_triad_iso    =  .false.  !  pure horizontal mixing in ML     (triad only)
   rn_sw_triad     =  1        !  =1 switching triad ; =0 all 4 triads used (triad only)
   ln_botmix_triad =  .false.  !  lateral mixing on bottom         (triad only)
   !                       !  Coefficients:
   nn_aht_ijk_t    = 21        !  space/time variation of eddy coef
   !                                !   =-20 (=-30)    read in ( file
   !                                !   =  0           constant 
   !                                !   = 10 F(k)      =ldf_c1d 
   !                                !   = 20 F(i,j)    =ldf_c2d 
   !                                !   = 21 F(i,j,t)  =Treguier et al. JPO 1997 formulation
   !                                !   = 30 F(i,j,k)  =ldf_c2d + ldf_c1d
   !                                !   = 31 F(i,j,k,t)=F(local velocity)
   rn_aht_0        = 2000.     !  lateral eddy diffusivity   (lap. operator) [m2/s]
   rn_bht_0        = 1.e+12    !  lateral eddy diffusivity (bilap. operator) [m4/s]
&namtra_ldfeiv !   eddy induced velocity param.
   ln_ldfeiv     =.true.   ! use eddy induced velocity parameterization
   ln_ldfeiv_dia =.true.   ! diagnose eiv stream function and velocities
   rn_aeiv_0     = 2000.   ! eddy induced velocity coefficient   [m2/s]
   nn_aei_ijk_t  = 21      ! space/time variation of the eiv coeficient
   !                                !   =-20 (=-30)    read in ( file
   !                                !   =  0           constant 
   !                                !   = 10 F(k)      =ldf_c1d 
   !                                !   = 20 F(i,j)    =ldf_c2d 
   !                                !   = 21 F(i,j,t)  =Treguier et al. JPO 1997 formulation
   !                                !   = 30 F(i,j,k)  =ldf_c2d + ldf_c1d

- ln_traldf_lap=traldf_blp=0 No lateral diffusion applied on tracers
- bi-laplacian eddy coefficient defined as SQRT(bhm)
- ah and bh coefficients defined only at u- and v-points.
- redesign the management of eddy induced velocity and its associated diagnostics. In particular ldfeiv.F90 and ldfeiv_substitute.h90 has been suppressed (ldf_eiv routine is now included in ldftra.F90)
- redesign of space variation of the eddy diffusivity: suppression of: ldftra_substitute.h90 ; ldftra_c1d.h90 , ldftra_c2d.h90 and ldftra_c3d.h90 (replaced by ldfc1d_c2d.F90) ; ldftra_oce.F90 (now included in ldftra.F90)
- remove ldftra_smag.F90 (suppression of smagorinski option) =⇒>> TO BE re-add in the new framework by someone…
- suppression of cpp keys : key_ldfslp ; key_traldf_c1d ; key_traldf_c2d ; key_traldf_c3d ; key_diaeiv ; key_traldf_eiv ; key_traldf_eiv ; key_traldf_ano
- suppression of key_esopa in traldf.F90
- zpshde.F90 correct an issue with position of optional argument in zps_hde_isf routine

passive tracers
- all changes in the management of diffusive coefficients and operator has been taken into account in TOP

  • Pending issues :
    - verify diaptr.F90 : not sure it is OK
    - add the max grid size in the coordinate file and use it to compute grid dependent diffusivity. This will solve an issue with regional and AGRIF configurations
    - test all 6 operators.
    - change default option in the namelist !

II.1 — Advective trends :TRA/traadv….

- traadv_muscl2.F90  removed
- traadv_cen2.F90  replaced by traadv_cen which provides 2nd and 4th order centered scheme on both horizontal and vertical directions.
- name TVD has been changed to the more commonly used FCT (Flux Correction Transport)
- FCT provides now 2nd and 4th order centered scheme on both horizontal and vertical directions.
- NB in case of 4th order in the vertical, both CEN and FCT use a compact 4th order scheme
- key_esopa removed from traadv.F90

Pending issues on TRAADV: 
- QCK: cross terms are missing. alternate direction should be added….

(II.X) ..Miscellaneous :
- Atmospheric pressure forcing: change to a systematic call of sbc_apr in step.F90 (with or without BDY) and remove its call from sbcmod
- remove key_ldftra_smag and associated module (ldftra_smag.F90)
- remove key_vectopt_loop from all the code except in domzgr_substitute.h90 (it is an obsolescent feature only adapted to vector computers)
- remove all "!CDIR " lines = NEC vector compiler instructions

WARNING : Griffies operator is not restartable nor reproducible : check before on 3.6 stable 


III. Phasing of viscous trends

(III.1) LDF on dynamics

  • rotb and rotn arrays suppressed (even from the restart file)
    - hdivn and hdivb removed from restart too
    - divcur.F90 becomes divhor and only computes the horizontal divergence

IV. Solve the pending issues

(IV.1) specification of eddy viscosity/diffusivity coefficients in case of grid-size dependency.
Issue: define the grid-size dependency in such a way that does not require the Equator being inside the domain.
Solution: add a scalar in the coordinate file which is equal to the grid-size at the equator even if Equator is not in the domain
and use this scalar to compute the grid-size dependency of the coefficients. (IV.2) specification of lateral friction at the coast.
Issue: the different values of fmask at the coast have been removed so that this lateral boundary condition doesn't affect the advective term ( double check that !). fmask is still used for laplacian and bilaplacian viscosities. Nevertheless, the magnitude of lateral friction depends on the magnitude of ahm (bhm, reap.). It seems better to define this magnitude
Solution: add a scalar in the coordinate file which is equal to the grid-size at the equator even if Equator is not in the domain
and use this scalar to compute the grid-size dependency of the coefficients.

remaining to do :

  • management of no-slip boundary condition as fmask no more used in dynvor.F90 ….
  • create the 2D ahtu and ahtv file for ORCA_R2 (and also for ORCA_R1)
  • In case of variation of the 2D clef as a function of the grid size, use a reference to a 1 degree grid size for ah on both tracers and momentum
  • suppress Smagorinsky option which does not work any more. Can be re-introduce in a consistent way with the re-design LDF if decided…
  • test with SETE (especially restartability and reproducibility )

V. Finalize the simplification

(V.1) suppression of hard coded reduction of scale factor in some straits for some given ORCA configuration.
add in NEMOGCM/TOOLS a directory a program that read a file apply a reduction of scale factors in some straits, and create the associated extended coordinates file (
create the extended coordinates files form ORCA 2°, 1°, and 0.5°.

To be CHECKED (not necessary associated with this branch

  • check that task_i use ssmask, i.e. that it takes into account the under ice shelf seas.
  • CRS : the new arrays derived from horizontal scale factors MUST be added in CRS.
  • Bug in diawri.F90 when NOT using key_iomput (OK =⇒> see ticket #1596)
  • Idea for finalization of domhgr.F90 :
    add 2 modules (from domhgr.F90), domhgr_read.F90 and domhgr_ana.F90, which contains:
    - domhgr_read.F90: the CASE jphgr_msh=0 of domhgr.F90 (i.e. read the coordinates file)
    - domhgr_ana.F90: the CASE jphgr_msh=5 of domhgr.F90 (i.e. the GYRE analytical definition of the coordinates)
    add in NEMOGCM/TOOLS a directory containing 3 domhgr_ana.F90 modules associated with (1) a geographical mesh on the sphere with regular (in degree) grid-spacing (jphgr_msh=1) ; (2) f- or beta-plane with regular grid-spacing (jphgr_msh=2 or 3)) ; (3) geographical mesh on the sphere, isotropic MERCATOR type (jphgr_msh=4)
    remove from the namelist_ref/namdom all variable related to the horizontal mesh, and add a flag, ln_mesh_read, =T read the file ; =F analytical mesh (by default GYRE mesh).


Testing could consider (where appropriate) other configurations in addition to NVTK].

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If adding new functionality please confirm that the
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and ''works'' when switched on

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'Please add further summary details here'

  • Processor configurations tested
  • etc——

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Does this change preserve answers in your tested standard configurations (to the last bit) ? '''YES/NO '''
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,,''Preserving answers in model runs does not necessarily imply preserved diagnostics. ''

If you answered '''NO''' to any of the above, please provide further details:

  • Which routine(s) are causing the difference?
  • Why the changes are not protected by a logical switch or new section-version
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  • Which diagnostics have you altered and why have they changed?Please add details here……..

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